From 0112f84cc503b2eca05bc3da4c6ff67a6f15022a Mon Sep 17 00:00:00 2001 From: Maximilian Scheurer Date: Mon, 15 May 2023 17:16:39 +0200 Subject: [PATCH 1/2] refactor and remove --- .gitignore | 3 + .travis.yml | 15 - PyContact/core/Biochemistry.py | 59 ++-- PyContact/core/ContactAnalyzer.py | 96 +++---- PyContact/core/ContactFilters.py | 8 +- PyContact/core/Scripting.py | 3 +- PyContact/cy_modules/cy_gridsearch.pyx | 7 +- PyContact/cy_modules/src/gridsearch.C | 24 +- PyContact/cy_modules/src/vmdstream.h | 383 ------------------------- PyContact/db/DbReader.py | 29 -- PyContact/db/__init__.py | 0 PyContact/db/aa.db | Bin 8192 -> 0 bytes PyContact/db/aminoacids.sql | 30 -- PyContact/gui/Canvas.py | 26 -- PyContact/gui/ExportTabWidget.py | 101 ------- PyContact/gui/LabelView.py | 4 +- PyContact/gui/MainQtGui.py | 36 +-- PyContact/gui/MainQtGui.ui | 4 +- PyContact/gui/MainWindow.py | 68 +---- PyContact/gui/SasaWidgets.py | 328 --------------------- PyContact/gui/VMDControlPanel.py | 310 -------------------- PyContact/gui/remote_ctl.tcl | 105 ------- PyContact/gui/sasa.ui | 291 ------------------- PyContact/gui/sasa_gui.py | 166 ----------- setup.cfg | 4 +- setup.py | 4 +- tests/map_animate.py | 94 ------ tests/test_basic.py | 14 +- tests/test_find_contacts.py | 40 +++ 29 files changed, 175 insertions(+), 2077 deletions(-) delete mode 100644 .travis.yml delete mode 100644 PyContact/cy_modules/src/vmdstream.h delete mode 100644 PyContact/db/DbReader.py delete mode 100644 PyContact/db/__init__.py delete mode 100644 PyContact/db/aa.db delete mode 100644 PyContact/db/aminoacids.sql delete mode 100644 PyContact/gui/SasaWidgets.py delete mode 100644 PyContact/gui/VMDControlPanel.py delete mode 100644 PyContact/gui/remote_ctl.tcl delete mode 100644 PyContact/gui/sasa.ui delete mode 100644 PyContact/gui/sasa_gui.py delete mode 100644 tests/map_animate.py create mode 100644 tests/test_find_contacts.py diff --git a/.gitignore b/.gitignore index 2d1b2c4..b1c1341 100644 --- a/.gitignore +++ b/.gitignore @@ -57,3 +57,6 @@ pycontact.egg-info/ #pytest .pytest_cache/ + +*.lock +.vscode/ \ No newline at end of file diff --git a/.travis.yml b/.travis.yml deleted file mode 100644 index b259abd..0000000 --- a/.travis.yml +++ /dev/null @@ -1,15 +0,0 @@ -language: python -jobs: - include: - - os: linux - dist: bionic - - os: osx - osx_image: xcode10.2 -python: - - "3.7" -install: - - pip install cython - - python setup.py build_ext -i - - python setup.py install -script: - - pytest diff --git a/PyContact/core/Biochemistry.py b/PyContact/core/Biochemistry.py index 5d1fedf..c0f8988 100644 --- a/PyContact/core/Biochemistry.py +++ b/PyContact/core/Biochemistry.py @@ -2,8 +2,31 @@ import numpy as np -from ..db.DbReader import read_residue_db - +residue_infos = { + 'gly': {'name': 'gly', 'scpolarity': 'nonpolar', 'hbondtype': 'none'}, + 'ala': {'name': 'ala', 'scpolarity': 'nonpolar', 'hbondtype': 'none'}, + 'leu': {'name': 'leu', 'scpolarity': 'nonpolar', 'hbondtype': 'none'}, + 'ile': {'name': 'ile', 'scpolarity': 'nonpolar', 'hbondtype': 'none'}, + 'val': {'name': 'val', 'scpolarity': 'nonpolar', 'hbondtype': 'none'}, + 'phe': {'name': 'phe', 'scpolarity': 'nonpolar', 'hbondtype': 'none'}, + 'met': {'name': 'met', 'scpolarity': 'nonpolar', 'hbondtype': 'none'}, + 'pro': {'name': 'pro', 'scpolarity': 'nonpolar', 'hbondtype': 'none'}, + 'asp': {'name': 'asp', 'scpolarity': 'negative', 'hbondtype': 'acc'}, + 'glu': {'name': 'glu', 'scpolarity': 'negative', 'hbondtype': 'acc'}, + 'lys': {'name': 'lys', 'scpolarity': 'positive', 'hbondtype': 'don'}, + 'arg': {'name': 'arg', 'scpolarity': 'positive', 'hbondtype': 'don'}, + 'hsp': {'name': 'hsp', 'scpolarity': 'positive', 'hbondtype': 'don'}, + 'asn': {'name': 'asn', 'scpolarity': 'polar', 'hbondtype': 'both'}, + 'gln': {'name': 'gln', 'scpolarity': 'polar', 'hbondtype': 'both'}, + 'his': {'name': 'his', 'scpolarity': 'polar', 'hbondtype': 'both'}, + 'hsd': {'name': 'hsd', 'scpolarity': 'polar', 'hbondtype': 'both'}, + 'hse': {'name': 'hse', 'scpolarity': 'polar', 'hbondtype': 'both'}, + 'cys': {'name': 'cys', 'scpolarity': 'polar', 'hbondtype': 'don'}, + 'ser': {'name': 'ser', 'scpolarity': 'polar', 'hbondtype': 'both'}, + 'thr': {'name': 'thr', 'scpolarity': 'polar', 'hbondtype': 'both'}, + 'tyr': {'name': 'tyr', 'scpolarity': 'nonpolar', 'hbondtype': 'don'}, + 'trp': {'name': 'trp', 'scpolarity': 'nonpolar', 'hbondtype': 'don'}, + } compare = lambda x, y: collections.Counter(x) == collections.Counter(y) @@ -159,10 +182,13 @@ def hbond_percentage(self): def total_time(self, ns_per_frame, threshold): """Returns the total time, the contact score is above the given threshold value.""" - time = 0 - for score in self.scoreArray: - if score > threshold: - time += ns_per_frame + # time = 0 + # for score in self.scoreArray: + # if score > threshold: + # time += ns_per_frame + sa = np.array(self.scoreArray) + time = np.sum(np.where(sa > threshold, ns_per_frame, 0)) + # assert time == time2 self.ttime = time return self.ttime @@ -178,18 +204,13 @@ def median_life_time(self, ns_per_frame, threshold): def mean_score(self): """Returns the mean score of the scoreArray.""" - mean = 0 - for score in self.scoreArray: - mean += score - mean /= len(self.scoreArray) - self.meanScore = mean - return mean + self.meanScore = np.mean(self.scoreArray) + return self.meanScore def median_score(self): """Returns the median score of the scoreArray.""" - med = np.median(self.scoreArray) - self.medianScore = med - return med + self.medianScore = np.median(self.scoreArray) + return self.medianScore def life_time(self, ns_per_frame, threshold): """Computes the life time of a contact in ns, with the given threshold.""" @@ -239,15 +260,15 @@ def determine_ctype(self): # return ContactType.other self.determineBackboneSidechainType() try: - sc1 = str(read_residue_db("scpolarity", "name", r1)[0]["scpolarity"]) + sc1 = residue_infos[r1]["scpolarity"] scpol1 = SideChainPolarity.mapping[sc1] - except IndexError: + except (IndexError, KeyError): scpol1 = SideChainPolarity.other try: - sc2 = str(read_residue_db("scpolarity", "name", r2)[0]["scpolarity"]) + sc2 = residue_infos[r2]["scpolarity"] scpol2 = SideChainPolarity.mapping[sc2] - except IndexError: + except (IndexError, KeyError): scpol2 = SideChainPolarity.other # hydrogen bonds: donor, acceptor, both diff --git a/PyContact/core/ContactAnalyzer.py b/PyContact/core/ContactAnalyzer.py index 36722ba..40e37ae 100644 --- a/PyContact/core/ContactAnalyzer.py +++ b/PyContact/core/ContactAnalyzer.py @@ -2,7 +2,6 @@ import time from .multi_trajectory import run_load_parallel from .LogPool import * -from copy import deepcopy import MDAnalysis import numpy as np @@ -12,9 +11,6 @@ from .Biochemistry import (AccumulatedContact, AtomContact, AccumulationMapIndex, HydrogenBond, TempContactAccumulate, HydrogenBondAtoms) from ..cy_modules.cy_gridsearch import cy_find_contacts -# MDAnalysis.core.flags['use_periodic_selections'] = False -# MDAnalysis.core.flags['use_KDTree_routines'] = True - class Analyzer(QObject): """Performs a contact search and analyzes the results.""" @@ -61,13 +57,13 @@ def runFrameScan(self, nproc): except: raise Exception - def runContactAnalysis(self, map1, map2, nproc): + def runContactAnalysis(self, map1, map2): """Performs a contadt analysis using nproc threads.""" self.finalAccumulatedContacts = self.analyze_contactResultsWithMaps(self.contactResults, map1, map2) self.lastMap1 = map1 self.lastMap2 = map2 - return deepcopy(self.finalAccumulatedContacts) + return self.finalAccumulatedContacts.copy() def setTrajectoryData( self, resname_array, resid_array, name_array, @@ -119,42 +115,21 @@ def makeKeyArraysFromMaps(self, map1, map2, contact): keys2=["none","none","none","22", "ILE, "none"] """ + properties = [ + lambda x: x, + lambda x: self.name_array[x], + lambda x: self.resid_array[x], + lambda x: self.resname_array[x], + lambda x: self.segids[x], + ] idx1 = contact.idx1 idx2 = contact.idx2 - counter = 0 - keys1 = [] - for val in map1: - if val == 1: - if counter == AccumulationMapIndex.index: - keys1.append(idx1) - elif counter == AccumulationMapIndex.name: - keys1.append(self.name_array[idx1]) - elif counter == AccumulationMapIndex.resid: - keys1.append(self.resid_array[idx1]) - elif counter == AccumulationMapIndex.resname: - keys1.append(self.resname_array[idx1]) - elif counter == AccumulationMapIndex.segid: - keys1.append(self.segids[idx1]) - else: - keys1.append("none") - counter += 1 - counter = 0 - keys2 = [] - for val in map2: - if val == 1: - if counter == AccumulationMapIndex.index: - keys2.append(idx2) - elif counter == AccumulationMapIndex.name: - keys2.append(self.name_array[idx2]) - elif counter == AccumulationMapIndex.resid: - keys2.append(self.resid_array[idx2]) - elif counter == AccumulationMapIndex.resname: - keys2.append(self.resname_array[idx2]) - elif counter == AccumulationMapIndex.segid: - keys2.append(self.segids[idx2]) - else: - keys2.append("none") - counter += 1 + keys1 = [ + properties[ii](idx1) if x == 1 else "none" for ii, x in enumerate(map1) + ] + keys2 = [ + properties[ii](idx2) if x == 1 else "none" for ii, x in enumerate(map2) + ] return [keys1, keys2] def makeKeyArraysFromKey(self, key): @@ -345,6 +320,10 @@ def analyze_psf_dcd_grid(self, psf, dcd, cutoff, hbondcutoff, hbondcutangle, sel # individual lists contain atom2 indices nbList1 = cy_find_contacts(xyz1, natoms1, xyz2, natoms2, cutoff) + from scipy.spatial import KDTree + tree = KDTree(sel2.positions) + nbList1 = tree.query_ball_point(sel1.positions, r=cutoff) + # we only need the 1st list # nbList1 = res[:natoms1] # nbList2 = res[natoms1:] @@ -498,7 +477,7 @@ def analyze_psf_dcd_grid(self, psf, dcd, cutoff, hbondcutoff, hbondcutangle, sel stop = time.time() print("grid:",stop-start) return contactResults - + def analyze_contactResultsWithMaps(self, contactResults, map1, map2): """Analyzes contactsResults with the given maps.""" @@ -529,29 +508,18 @@ def analyze_contactResultsWithMaps(self, contactResults, map1, map2): for cont in frame: key1, key2 = self.makeKeyArraysFromMaps(map1, map2, cont) key = self.makeKeyFromKeyArrays(key1, key2) - if key in currentFrameAcc: - currentFrameAcc[key].fscore += cont.weight - currentFrameAcc[key].contributingAtomContacts.append(cont) - if cont.idx1 in self.backbone: - currentFrameAcc[key].bb1score += cont.weight - else: - currentFrameAcc[key].sc1score += cont.weight - if cont.idx2 in self.backbone: - currentFrameAcc[key].bb2score += cont.weight - else: - currentFrameAcc[key].sc2score += cont.weight - else: + if key not in currentFrameAcc: currentFrameAcc[key] = TempContactAccumulate(key1, key2) - currentFrameAcc[key].fscore += cont.weight - currentFrameAcc[key].contributingAtomContacts.append(cont) - if cont.idx1 in self.backbone: - currentFrameAcc[key].bb1score += cont.weight - else: - currentFrameAcc[key].sc1score += cont.weight - if cont.idx2 in self.backbone: - currentFrameAcc[key].bb2score += cont.weight - else: - currentFrameAcc[key].sc2score += cont.weight + currentFrameAcc[key].fscore += cont.weight + currentFrameAcc[key].contributingAtomContacts.append(cont) + if cont.idx1 in self.backbone: + currentFrameAcc[key].bb1score += cont.weight + else: + currentFrameAcc[key].sc1score += cont.weight + if cont.idx2 in self.backbone: + currentFrameAcc[key].bb2score += cont.weight + else: + currentFrameAcc[key].sc2score += cont.weight if key not in allkeys: allkeys.append(key) frame_contacts_accumulated.append(currentFrameAcc) @@ -559,7 +527,7 @@ def analyze_contactResultsWithMaps(self, contactResults, map1, map2): counter += 1 accumulatedContactsDict = {} stop = time.time() - # print(stop - start) + # print("time", stop - start) # accumulatedContactsDict (dict) # ---> key vs. list of TempContactAccumulated # diff --git a/PyContact/core/ContactFilters.py b/PyContact/core/ContactFilters.py index c1cab8c..78b34c3 100644 --- a/PyContact/core/ContactFilters.py +++ b/PyContact/core/ContactFilters.py @@ -107,7 +107,7 @@ def filterByRange(self, contacts, residRangeA, residRangeB, mapindex): bRanges = [] for ran in splitB: r = ran.split(u"-") - print(r) + # print(r) if len(r) == 1: bRanges.append(range(int(r[0]), int(r[0])+1)) else: @@ -148,7 +148,7 @@ def __init__(self, name, operator, value): self.value = value def filterContacts(self, contacts): - pass + raise NotImplementedError class OnlyFilter(object): @@ -193,7 +193,7 @@ def filterContacts(self, contacts): for c in contacts: if op.compare(c.total_time(1, 0), self.value, self.operator): filtered.append(c) - print(unicode(len(filtered))) + # print(unicode(len(filtered))) return filtered @@ -219,7 +219,7 @@ def filterContacts(self, contacts): elif self.ftype == u"HB %": for c in contacts: med = c.hbond_percentage() - print(med) + # print(med) if op.compare(med, self.value, self.operator): filtered.append(c) return filtered diff --git a/PyContact/core/Scripting.py b/PyContact/core/Scripting.py index 763fb11..546e239 100644 --- a/PyContact/core/Scripting.py +++ b/PyContact/core/Scripting.py @@ -27,10 +27,11 @@ def __init__(self, topo, traj, name, configuration): def runJob(self, ncores=1): """Runs contact analysis and accumulation with ncores threads.""" + ncores = 1 print("Running job: " + self.name + " on " + str(ncores) + " cores.") self.analyzer = Analyzer(self.topo,self.traj, self.configuration.cutoff, self.configuration.hbondcutoff, self.configuration.hbondcutangle, self.configuration.sel1, self.configuration.sel2) self.analyzer.runFrameScan(ncores) - self.analyzer.runContactAnalysis(self.configuration.map1, self.configuration.map2, ncores) + self.analyzer.runContactAnalysis(self.configuration.map1, self.configuration.map2) def writeSessionToFile(self, fname=""): """Writes the current analysis session to a file with either self.name + .session or fname as output filename""" diff --git a/PyContact/cy_modules/cy_gridsearch.pyx b/PyContact/cy_modules/cy_gridsearch.pyx index 6ea7395..4c5decd 100644 --- a/PyContact/cy_modules/cy_gridsearch.pyx +++ b/PyContact/cy_modules/cy_gridsearch.pyx @@ -3,7 +3,7 @@ from libcpp.vector cimport vector import numpy as np cdef extern from "src/gridsearch.C": - double sasa_grid(const float *pos,int natoms, float pairdist, int allow_double_counting, int maxpairs, const float *radius,const int npts, double srad, int pointstyle, int restricted, const int* restrictedList) + double sasa_grid(const float *pos,int natoms, float pairdist, int allow_double_counting, int maxpairs, const float *radius,const int npts, double srad, int pointstyle, int restricted, const int* restrictedList, const float* spherepoints) cdef extern from "src/gridsearch.C": int* find_within(const float *xyz, int *flgs, int *others, int num, float r) @@ -13,11 +13,12 @@ cdef extern from "src/gridsearch.C": def cy_sasa(npcoords, natoms, pairdist, allow_double_counting, maxsize, nprad, surfacePoints, probeRadius, pointstyle, - restricted,restrictedList): + restricted,restrictedList, npspherepoints): cdef int [::1] cy_restrictedList = restrictedList cdef float [::1] cy_radius = nprad cdef float [::1] c_coords = npcoords[0] - cdef float sasa = sasa_grid(&c_coords[0], natoms, pairdist, 0, -1, &cy_radius[0] ,surfacePoints, probeRadius, pointstyle, restricted, &cy_restrictedList[0]) + cdef float [::1] c_spherepts = npspherepoints[0] + cdef float sasa = sasa_grid(&c_coords[0], natoms, pairdist, 0, -1, &cy_radius[0] ,surfacePoints, probeRadius, pointstyle, restricted, &cy_restrictedList[0], &c_spherepts[0]) return sasa def cy_find_within(xyz, flgs, others, num, r): diff --git a/PyContact/cy_modules/src/gridsearch.C b/PyContact/cy_modules/src/gridsearch.C index 737e7df..aa3fee0 100644 --- a/PyContact/cy_modules/src/gridsearch.C +++ b/PyContact/cy_modules/src/gridsearch.C @@ -427,7 +427,7 @@ int nAtoms1, int nAtoms2, double cutoff) { } -static double sasa_grid(const float *pos,int natoms, float pairdist, int allow_double_counting, int maxpairs, const float *radius,const int npts, double srad, int pointstyle, int restricted, const int* restrictedList) { +static double sasa_grid(const float *pos,int natoms, float pairdist, int allow_double_counting, int maxpairs, const float *radius,const int npts, double srad, int pointstyle, int restricted, const int* restrictedList, const float* spherepoints) { int on[natoms]; fill_n(on,natoms,1); // printf("natoms %d\n", natoms); @@ -483,8 +483,17 @@ static double sasa_grid(const float *pos,int natoms, float pairdist, int allow_d } } - const float prefac = (float) (4 * M_PI / npts); - float totarea = 0.0f; + if (spherepoints) { + for (int k=0; k &nbrs = pairlist[i]; @@ -518,7 +529,10 @@ static double sasa_grid(const float *pos,int natoms, float pairdist, int allow_d surfpts--; } } - float atomarea = prefac * rad * rad * surfpts; + // printf("left points: %d\n", surfpts); + double atomarea = prefac * rad * rad * surfpts; + // printf("rad: %.15f\n", rad); + printf("atomarea: %.15f\n", atomarea); totarea += atomarea; // } } diff --git a/PyContact/cy_modules/src/vmdstream.h b/PyContact/cy_modules/src/vmdstream.h deleted file mode 100644 index baddfc7..0000000 --- a/PyContact/cy_modules/src/vmdstream.h +++ /dev/null @@ -1,383 +0,0 @@ -/* - Copyright (C) 2012 Aaron S. Keys - - This program is free software: you can redistribute it and/or modify - it under the terms of the GNU General Public License as published by - the Free Software Foundation, either version 3 of the License, or - (at your option) any later version. - - This program is distributed in the hope that it will be useful, - but WITHOUT ANY WARRANTY; without even the implied warranty of - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - GNU General Public License for more details. - - You should have received a copy of the GNU General Public License - along with this program. If not, see . -*/ - -/* *************************** - vmstream.h - A lightweight C++ library to open a TCP connection to VMD - Aaron Keys, June 10, 2009 - - ***************************/ - -/** \mainpage VMD Streams Documentation - -\section intro_sec Introduction -The vmdstreams library provides a simple interface for opening a TCP connection -to VMD from C++. Once the TCP connection is established, the user can remote- -control VMD from a C++ code to automate analysis, control movies, or make custom -animations. All that is required is some knowledge of VMDs Tcl interface (see -http://www.ks.uiuc.edu/Research/vmd/current/ug/node104.html). - -\section examples Examples - -The vmdstream object works the same as an ostream in C++. (That is, it works -the same way as cout, cerr and ofstreams). Here is an example of drawing 20 -spheres on the screen: - -\code - -#include - -using namespace std; - -int main( int argc, char *argv[] ) -{ - //open a TCP connection to VMD - vmdsock_t vmdsock = newvmdsock(); - vmdstream vmd(vmdsock); - - //tell VMD to draw some spheres - cout << "drawing spheres\n"; - - for (int i=0; i<10; i++) { - vmd << "draw sphere {" << i << " 0 0}" << endl; - } - - for (int i=0; i<10; i++) { - vmd << "draw sphere {0 " << i << " 0}" << endl; - } - - //close the tcp connection - cout << "finished" << endl; - closevmdsock(vmdsock); -} - -\endcode - -Notice that the "draw sphere" command is part of the VMD tcl scripting -interface. In fact, we can control almost every aspect of VMD using Tcl -commands. - -\section Installation - -The vmdstreams codes consists of a single header file. - -\section References - -This codes is based on the socket iostream library by David Ryan, released into -public domain in Feb 2004. -*/ - -#ifndef DOXYGEN_SHOULD_SKIP_THIS - -#include -#include -#include -#include -#include - -#include -#include -#include -#include - -#ifndef TIOCINQ -#define TIOCINQ FIONREAD -#endif - -class socket_buf : public std::streambuf -{ -private: - int _socket; - char _inBuffer[1024]; - char _outBuffer[1024]; - -public: - socket_buf( int socket ) - { - _socket = socket; - setg( _inBuffer, _inBuffer, _inBuffer ); - setp( _outBuffer, _outBuffer+1024 ); - } - -protected: - int overflow(int x) - { -#ifdef DEBUG_MODE - std::cout << "socket_buf::overflow()" << x << std::endl; -#endif - return x; - } - - int sync() - { -#ifdef DEBUG_MODE - std::cout << "socket_buf::sync()" << std::endl; -#endif - // if no data availalbe just return. - if ( pbase() == pptr() ) - return 0; - - // try and send the data. - int len = pptr() - pbase(); - int rc = send( _socket, pbase(), len, 0 ); - if ( rc < 0 ) - return rc; - - setp( _outBuffer, _outBuffer+1024 ); - return 0; - } - - int underflow() - { -#ifdef DEBUG_MODE - std::cout << "socket_buf::underflow() " << std::endl; -#endif - if (gptr () < egptr ()) return *(unsigned char*)gptr (); - - int len; - - // find out how much data is available. - if( ioctl( _socket, TIOCINQ, &len) < 0 ) - { - // error - std::cerr << "socket_buf error" << std::endl; - len = 1; - } - - // make sure length is atleast 1. We will block. - if ( len == 0 ) - len = 1; - - // try and read in some data. - int read = recv( _socket, &_inBuffer, len, 0 ); - if ( read > 0 ) - { - setg( _inBuffer, _inBuffer, _inBuffer+read ); - } - else - { - return EOF; - } - - return *(unsigned char*)gptr (); - } - -}; - - -class siostream: public std::iostream -{ -private: - socket_buf _buf; - -public: - siostream( int socket ) - :_buf( socket ), std::iostream( &_buf ) - { - } -}; - -#endif - -typedef siostream vmdstream; - -void writevmdinitscript(int port=5555, std::string extra_commands="") -{ - std::ofstream os("remote_ctl.tcl"); - - os << "#------------------------------------------------------------------" << "\n"; - os << "# $Id: remote_ctl.tcl,v 1.6 2003/02/12 21:33:11 oliver Exp $" << "\n"; - os << "# based on bounce.tcl and vmdcollab.tcl" << "\n"; - os << "# from http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/vmdcollab/" << "\n"; - os << "#" << "\n"; - os << "# start this in VMD and send commands to the listening port to have VMD" << "\n"; - os << "# execute them remotely" << "\n"; - os << "# (also see http://www.tcl.tk/scripting/netserver.html)" << "\n"; - os << "#" << "\n"; - os << "# Usage: vmd -e remote_ctl.tcl" << "\n"; - os << "# or vmd> source remote_ctl.tcl" << "\n"; - os << "#" << "\n"; - os << "# Security: we only allow connections from localhost (see acpt)" << "\n"; - os << "#" << "\n"; - os << "# Bugs:" << "\n"; - os << "# * once a wrong command was sent, the connection appears" << "\n"; - os << "# to 'block' and does not accept correct commands later" << "\n"; - os << "# * does not write result back to socket (one way connection...) so" << "\n"; - os << "# there is no way to inquire objects in vmd" << "\n"; - os << "" << "\n"; - os << "namespace eval remote_ctl {" << "\n"; - os << "variable main" << "\n"; - os << "variable clients" << "\n"; - os << "variable default_vmd_port" << "\n"; - os << "set default_vmd_port 5555" << "\n"; - os << "# I am too dumb to set the default value for port from" << "\n"; - os << "# $default_vmd_port so I put 5555 in there literally" << "\n"; - os << "proc start { {port " << port << "} } {" << "\n"; - os << "variable main" << "\n"; - os << "set main [socket -server remote_ctl::acpt $port]" << "\n"; - os << "putlog \"Listening on port $port\"" << "\n"; - os << "}" << "\n"; - os << "proc acpt { sock addr port } {" << "\n"; - os << "variable clients" << "\n"; - os << "if {[string compare $addr \"127.0.0.1\"] != 0} {" << "\n"; - os << "putlog \"Unauthorized connection attempt from $addr port $port\"" << "\n"; - os << "close $sock" << "\n"; - os << "return" << "\n"; - os << "}" << "\n"; - os << "putlog \"Accept $sock from $addr port $port\"" << "\n"; - os << "set clients($sock) 1" << "\n"; - os << "fconfigure $sock -buffering line" << "\n"; - os << "fileevent $sock readable [list remote_ctl::recv $sock]" << "\n"; - os << "}" << "\n"; - os << "proc recv { sock } {" << "\n"; - os << "variable main" << "\n"; - os << "variable clients" << "\n"; - os << "if { [eof $sock] || [catch {gets $sock line}]} {" << "\n"; - os << "# end of file or abnormal connection drop:" << "\n"; - os << "# shut down this connection" << "\n"; - os << "close $sock" << "\n"; - os << "putlog \"Closing $sock\"" << "\n"; - os << "unset clients($sock)" << "\n"; - os << "} else {" << "\n"; - os << "if {[string compare $line \"quit\"] == 0} {" << "\n"; - os << "# prevent new connections" << "\n"; - os << "# existing connections stay open" << "\n"; - os << "# No -- Bug(?): 'quit' closes VMD..." << "\n"; - os << "putlog \"Disallowing incoming connections by request of $sock\"" << "\n"; - os << "close $main" << "\n"; - os << "}" << "\n"; - os << "# execute the received commands" << "\n"; - os << "# should check for runtime errors which otherwise leave the connection" << "\n"; - os << "# in an unusable state" << "\n"; - os << "# eval $line" << "\n"; - os << "set rc [catch $line result]" << "\n"; - os << "if { $rc } {" << "\n"; - os << "#puts $sock \"Error executing comand '$line': n$result\"" << "\n"; - os << "puts \"Error executing comand '$line': n$result\"" << "\n"; - os << "} else {" << "\n"; - os << "#puts $sock $result" << "\n"; - os << "#puts $result" << "\n"; - os << "}" << "\n"; - os << "}" << "\n"; - os << "}" << "\n"; - os << "###### would like the last line from stdout in line ###########" << "\n"; - os << "# (or any working solution....)" << "\n"; - os << "proc send { sock line} {" << "\n"; - os << "variable clients" << "\n"; - os << "# send reply to connecting client" << "\n"; - os << "putlog \"send '$line' to $sock\"" << "\n"; - os << "puts $sock $line" << "\n"; - os << "}" << "\n"; - os << "" << "\n"; - os << "proc putlog { text } {" << "\n"; - os << "puts $text" << "\n"; - os << "return" << "\n"; - os << "}" << "\n"; - os << "}" << "\n"; - os << "" << "\n"; - os << "remote_ctl::putlog \"Starting remote_ctl server in vmd: connect with something like\"" << "\n"; - os << "remote_ctl::putlog \"telnet localhost " << port << "\"" << "\n"; - os << "remote_ctl::start" << "\n"; - - os << extra_commands; - - os.close(); -} - -typedef int vmdsock_t; - -/** -\brief opens a TCP connection to VMD and returns the socket file descriptor -\param vmd_executable is the name of the vmd program as it is called from - the command line. Typically, if vmd does not live in a global search path - such as /usr/bin or /usr/local/bin, we make a dynamic link to the executable - an place it in the /usr/bin directory. For example, on mac os, the VMD - executable typically lives in an application package, for example: - /Applications/VMD\ 1.8.6.app/Contents/vmd/vmd_MACOSXX86. In this case, - it is easiest to make a dynamic link to the executable using "ln" and place - the link in the /usr/bin folder -\param port is the port to connect over -\param extra_commands is a string containing a list of Tcl commands to parse - on startup -\return the socket file descriptor -*/ -vmdsock_t newvmdsock( - const char* vmd_executable="vmd", - int port=5555, - std::string extra_commands="") -{ - writevmdinitscript(port, extra_commands); - int rv, s; - int count; - - pid_t pid; - pid = fork(); - if (pid == -1) { - std::cerr << "ERROR: failed to fork child process\n"; - exit(1); - } - else if (pid == 0) { //child - std::ostringstream command; - command << vmd_executable <<" -e remote_ctl.tcl"; - int good = system(command.str().c_str()); - if (good != 0) { - std::cerr << "ERROR: vmd executable failed to launch\n"; - std::cerr << "Please check your path: " << vmd_executable << "\n"; - exit(1); - } - std::cout << "VMD killed via quit command\n"; - exit(0); - } - else { - //sleep(2); - std::cout << "test socket" << std::endl; - - struct hostent *he=gethostbyname("localhost"); - struct sockaddr_in sa; - memset(&sa, 0, sizeof(sa)); - sa.sin_family = PF_INET; - sa.sin_addr = *((struct in_addr *)he->h_addr); - sa.sin_port = htons(port); - - - for (count=0, rv=1; rv && count<20; count++) { - s = socket(AF_INET, SOCK_STREAM, 0); - rv = connect( s, (struct sockaddr*) &sa, sizeof(sa) ); - - std::cout << "connect = " << rv << std::endl; - - if (rv) { - std::cerr << "TCP connection to vmd failed\n"; - sleep(2); - close(s); - } - sleep(1); - } - } - - return s; -} - -/** -\brief closes the VMD socket connection -\param socketfd is the file descriptor of the socket to close -*/ -void closevmdsock(vmdsock_t socketfd) -{ - shutdown(socketfd, SHUT_RDWR); - close(socketfd); -} diff --git a/PyContact/db/DbReader.py b/PyContact/db/DbReader.py deleted file mode 100644 index 0282f12..0000000 --- a/PyContact/db/DbReader.py +++ /dev/null @@ -1,29 +0,0 @@ -import sqlite3 -import os - - -def dict_factory(cursor, row): - d = {} - for idx, col in enumerate(cursor.description): - d[col[0]] = row[idx] - return d - - -def read_residue_db(selection, key, value): - connection = sqlite3.connect(os.path.dirname(os.path.abspath(__file__)) + "/aa.db") - connection.row_factory = dict_factory - cursor = connection.cursor() - cursor.execute("SELECT ({sel}) FROM residues WHERE {key}=\'{value}\'".format(sel=selection, key=key, value=value)) - results = cursor.fetchall() - connection.close() - return results - - -def read_residue_db_all(): - connection = sqlite3.connect(os.path.dirname(os.path.abspath(__file__)) + "/aa.db") - connection.row_factory = dict_factory - cursor = connection.cursor() - cursor.execute("SELECT * FROM residues") - results = cursor.fetchall() - connection.close() - return results diff --git a/PyContact/db/__init__.py b/PyContact/db/__init__.py deleted file mode 100644 index e69de29..0000000 diff --git a/PyContact/db/aa.db b/PyContact/db/aa.db deleted file mode 100644 index 1708beca422e7c24df8dcfa89ecf9b5d099028ec..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 8192 zcmeH~Jxatt6vrp)`mHlDaa{`+QYt72)`DN#*{EAs3A4Ln5|~XwW>!h5ohJ~iJb-5q zyn&Smu&}Z90M5%AvH`&Z_#PQ1^W*=9$FG~SljBee?=nsYTzfmjCYD9^JdY5vYF5px zqAc@MFAiph^Ix?}wm#+-P0C`A#C%w201co4G=K)s02)98XaEhM0W^RH(7-PSF0AQh zt7Y9V&AU>hLWTXIP{m$5JZ;JED-bUoq&;dR>QolQ^ml34OI)Y%URx^dLk zSuzT2z}vh@cM1DsZ|sFVv3qvQ2JD<2v2C`-X6P4vr?2#xKG6qyN3W@%Cnk=C2G9T+ zKm%w14WI!ufCkV28bAa8$$-pGB*dzm%~W-9C~@L=gj84Dj8$$jA4x=jSCHC7w$B`fzTB=l_vvH hfs+8QxU9fBz))6`69A 0: - path, file_extension = os.path.splitext(fileName[0]) - if file_extension != ".tcl": - file_extension = ".tcl" - - path += file_extension - - f = open(path, 'w') - f.write('mol new %s \n' % self.psf) - f.write('mol addfile %s \n' % self.dcd) - f.write('mol delrep 0 top \n') - f.write('mol representation NewCartoon \n') - f.write('mol Color ColorID 3 \n') - f.write('mol selection {all} \n') - f.write('mol addrep top \n') - - if self.tab4.splitVisCheckbox.isChecked(): - for cont in self.contacts: - currentSel1 = [] - index = 0 - for item in cont.key1: - if item != "none": - currentSel1.append(AccumulationMapIndex.vmdsel[index] + " " + item) - index += 1 - currentSel1String = " and ".join(currentSel1) - currentSel2 = [] - index = 0 - for item in cont.key2: - if item != "none": - currentSel2.append(AccumulationMapIndex.vmdsel[index] + " " + item) - index += 1 - currentSel2String = " and ".join(currentSel2) - add1 = ("" if self.tab4.additionalText1.text() == "" else (" and " + self.tab4.additionalText1.text())) - add2 = ("" if self.tab4.additionalText2.text() == "" else (" and " + self.tab4.additionalText2.text())) - sel = "("+currentSel1String + add1 + ") or (" + currentSel2String + add2 + ")" - f.write('mol representation Licorice \n') - f.write('mol Color Name \n') - f.write('mol selection {%s} \n' % sel) - f.write('mol addrep top \n') - else: - total = [] - for cont in self.contacts: - currentSel1 = [] - index = 0 - for item in cont.key1: - if item != "none": - currentSel1.append(AccumulationMapIndex.vmdsel[index] + " " + item) - index += 1 - currentSel1String = " and ".join(currentSel1) - currentSel2 = [] - index = 0 - for item in cont.key2: - if item != "none": - currentSel2.append(AccumulationMapIndex.vmdsel[index] + " " + item) - index += 1 - currentSel2String = " and ".join(currentSel2) - add1 = ("" if self.tab4.additionalText1.text() == "" else (" and " + self.tab4.additionalText1.text())) - add2 = ("" if self.tab4.additionalText2.text() == "" else (" and " + self.tab4.additionalText2.text())) - sel = "(" + currentSel1String + add1 + ") or (" + currentSel2String + add2 + ")" - total.append(sel) - seltext = " or ".join(total) - f.write('mol representation Licorice \n') - f.write('mol Color Name \n') - f.write('mol selection {%s} \n' % seltext) - f.write('mol addrep top \n') - f.close() diff --git a/PyContact/gui/LabelView.py b/PyContact/gui/LabelView.py index fa72b2d..7da1e19 100644 --- a/PyContact/gui/LabelView.py +++ b/PyContact/gui/LabelView.py @@ -12,7 +12,7 @@ class LabelView(QWidget): - """Proviedes more detailed statistics of the clicked contact in MainWindow.""" + """Provides more detailed statistics of the clicked contact in MainWindow.""" def __init__(self, contacts): super(QWidget, self).__init__() @@ -49,7 +49,7 @@ def initUI(self): for c in self.contacts: cindex = self.contacts.index(c) self.buttons.append(QPushButton(c.title)) - stylesheet = "border: 0px solid #222222; background-color: " + ContactType.colors[c.determine_ctype()] \ + stylesheet = "color: black; border: 0px solid #222222; background-color: " + ContactType.colors[c.determine_ctype()] \ + " ;" # stylesheet = "border: 0px solid #222222; background-color: " + ContactType.colors[3] + " ;" self.buttons[-1].setStyleSheet(stylesheet) diff --git a/PyContact/gui/MainQtGui.py b/PyContact/gui/MainQtGui.py index 69a73d7..83fb7d3 100644 --- a/PyContact/gui/MainQtGui.py +++ b/PyContact/gui/MainQtGui.py @@ -16,9 +16,9 @@ def setupUi(self, MainWindow): self.centralwidget.setObjectName("centralwidget") self.gridLayout = QtWidgets.QGridLayout(self.centralwidget) self.gridLayout.setObjectName("gridLayout") - self.visModeButton = QtWidgets.QPushButton(self.centralwidget) - self.visModeButton.setObjectName("visModeButton") - self.gridLayout.addWidget(self.visModeButton, 0, 3, 1, 2) + # self.visModeButton = QtWidgets.QPushButton(self.centralwidget) + # self.visModeButton.setObjectName("visModeButton") + # self.gridLayout.addWidget(self.visModeButton, 0, 3, 1, 2) self.infoWidget = QtWidgets.QWidget(self.centralwidget) sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.Preferred, QtWidgets.QSizePolicy.Fixed) sizePolicy.setHorizontalStretch(0) @@ -378,8 +378,8 @@ def setupUi(self, MainWindow): self.actionOpen.setObjectName("actionOpen") self.actionExport = QtWidgets.QAction(MainWindow) self.actionExport.setObjectName("actionExport") - self.actionRun_VMD_contact_search = QtWidgets.QAction(MainWindow) - self.actionRun_VMD_contact_search.setObjectName("actionRun_VMD_contact_search") + # self.actionRun_VMD_contact_search = QtWidgets.QAction(MainWindow) + # self.actionRun_VMD_contact_search.setObjectName("actionRun_VMD_contact_search") self.actionLoad_Data = QtWidgets.QAction(MainWindow) self.actionLoad_Data.setObjectName("actionLoad_Data") self.actionImport_Session = QtWidgets.QAction(MainWindow) @@ -394,12 +394,12 @@ def setupUi(self, MainWindow): self.actionExportData.setCheckable(False) self.actionExportData.setShortcutContext(QtCore.Qt.WindowShortcut) self.actionExportData.setObjectName("actionExportData") - self.actionContact_Area_Calculations = QtWidgets.QAction(MainWindow) - self.actionContact_Area_Calculations.setObjectName("actionContact_Area_Calculations") + # self.actionContact_Area_Calculations = QtWidgets.QAction(MainWindow) + # self.actionContact_Area_Calculations.setObjectName("actionContact_Area_Calculations") self.actionPreferences = QtWidgets.QAction(MainWindow) self.actionPreferences.setObjectName("actionPreferences") - self.actionVMD_Remote_Control = QtWidgets.QAction(MainWindow) - self.actionVMD_Remote_Control.setObjectName("actionVMD_Remote_Control") + # self.actionVMD_Remote_Control = QtWidgets.QAction(MainWindow) + # self.actionVMD_Remote_Control.setObjectName("actionVMD_Remote_Control") self.actionTrack_Molecule = QtWidgets.QAction(MainWindow) self.actionTrack_Molecule.setObjectName("actionTrack_Molecule") self.menuFile.addAction(self.actionLoad_Data) @@ -408,8 +408,8 @@ def setupUi(self, MainWindow): self.menuFile.addAction(self.actionDefault) self.menuAbout.addAction(self.actionShow_Info) self.menuTools.addAction(self.actionExportData) - self.menuTools.addAction(self.actionContact_Area_Calculations) - self.menuTools.addAction(self.actionVMD_Remote_Control) + # self.menuTools.addAction(self.actionContact_Area_Calculations) + # self.menuTools.addAction(self.actionVMD_Remote_Control) self.menuSettings.addAction(self.actionPreferences) self.menubar.addAction(self.menuFile.menuAction()) self.menubar.addAction(self.menuTools.menuAction()) @@ -421,12 +421,12 @@ def setupUi(self, MainWindow): MainWindow.setTabOrder(self.scrollArea, self.lowerRangeField) MainWindow.setTabOrder(self.lowerRangeField, self.upperRangeField) MainWindow.setTabOrder(self.upperRangeField, self.filterRangeCheckbox) - MainWindow.setTabOrder(self.filterRangeCheckbox, self.visModeButton) + # MainWindow.setTabOrder(self.filterRangeCheckbox, self.visModeButton) def retranslateUi(self, MainWindow): _translate = QtCore.QCoreApplication.translate MainWindow.setWindowTitle(_translate("MainWindow", "MainWindow")) - self.visModeButton.setText(_translate("MainWindow", "Vismode")) + # self.visModeButton.setText(_translate("MainWindow", "Vismode")) self.selection1label.setText(_translate("MainWindow", "-")) self.selection1.setText(_translate("MainWindow", "Selection 1:")) self.status.setText(_translate("MainWindow", "Status:")) @@ -498,7 +498,7 @@ def retranslateUi(self, MainWindow): self.actionOpen.setShortcut(_translate("MainWindow", "Ctrl+O")) self.actionExport.setText(_translate("MainWindow", "Export")) self.actionExport.setShortcut(_translate("MainWindow", "Ctrl+E")) - self.actionRun_VMD_contact_search.setText(_translate("MainWindow", "Run VMD contact search")) + # self.actionRun_VMD_contact_search.setText(_translate("MainWindow", "Run VMD contact search")) self.actionLoad_Data.setText(_translate("MainWindow", "Load Trajectory Data")) self.actionLoad_Data.setShortcut(_translate("MainWindow", "Ctrl+I")) self.actionImport_Session.setText(_translate("MainWindow", "Import Session")) @@ -510,12 +510,12 @@ def retranslateUi(self, MainWindow): self.actionShow_Info.setText(_translate("MainWindow", "Developer Info")) self.actionExportData.setText(_translate("MainWindow", "Export Contact Data")) self.actionExportData.setShortcut(_translate("MainWindow", "Ctrl+E")) - self.actionContact_Area_Calculations.setText(_translate("MainWindow", "Contact Area Calculation")) - self.actionContact_Area_Calculations.setShortcut(_translate("MainWindow", "Ctrl+A")) + # self.actionContact_Area_Calculations.setText(_translate("MainWindow", "Contact Area Calculation")) + # self.actionContact_Area_Calculations.setShortcut(_translate("MainWindow", "Ctrl+A")) self.actionPreferences.setText(_translate("MainWindow", "Preferences")) self.actionPreferences.setShortcut(_translate("MainWindow", "Ctrl+,")) - self.actionVMD_Remote_Control.setText(_translate("MainWindow", "VMD Remote Control")) - self.actionVMD_Remote_Control.setShortcut(_translate("MainWindow", "Ctrl+V")) + # self.actionVMD_Remote_Control.setText(_translate("MainWindow", "VMD Remote Control")) + # self.actionVMD_Remote_Control.setShortcut(_translate("MainWindow", "Ctrl+V")) self.actionTrack_Molecule.setText(_translate("MainWindow", "Track Molecule")) self.actionTrack_Molecule.setShortcut(_translate("MainWindow", "Ctrl+T")) diff --git a/PyContact/gui/MainQtGui.ui b/PyContact/gui/MainQtGui.ui index 876412d..ce1de7c 100644 --- a/PyContact/gui/MainQtGui.ui +++ b/PyContact/gui/MainQtGui.ui @@ -15,13 +15,13 @@ - + diff --git a/PyContact/gui/MainWindow.py b/PyContact/gui/MainWindow.py index 53f4816..2e922cd 100644 --- a/PyContact/gui/MainWindow.py +++ b/PyContact/gui/MainWindow.py @@ -13,7 +13,6 @@ import numpy as np from . import MainQtGui -from .SasaWidgets import SasaWidget from .Canvas import Canvas from .Dialogues import FileLoaderDialog, AnalysisDialog from .ExportTabWidget import ExportTabWidget @@ -25,7 +24,6 @@ from ..core.LogPool import * from . import Preferences from ..exampleData.datafiles import DEFAULTSESSION, DEFAULTSESSION_PY3 -from .VMDControlPanel import VMDControlPanel from ..core.DataHandler import DataHandler multiprocessing.log_to_stderr() @@ -77,8 +75,6 @@ def __init__(self, parent=None): # analysis button self.analysisButton.clicked.connect(self.analyzeDataPushed) - # contact area button - self.actionContact_Area_Calculations.triggered.connect(self.showContactAreaView) # preferences self.actionPreferences.triggered.connect(self.openPrefs) @@ -92,21 +88,10 @@ def __init__(self, parent=None): # setup of extra widgets self.exportWidget = ExportTabWidget() - self.sasaView = SasaWidget() self.statisticsView = None self.analysis_state = False - self.vismode = False - self.visModeButton.setCheckable(True) - self.visModeButton.setChecked(False) - self.visModeButton.clicked.connect(self.switchedToVisMode) - - self.vmdpanel = VMDControlPanel() - self.actionVMD_Remote_Control.triggered.connect(self.showVMDControlPanel) - - self.painter.clickedRowSignal.connect(self.updateVMDSelections) - self.painter.clickedColumnSignal.connect(self.updateVMDFrame) self.updateSettings() self.updateFilters() @@ -114,12 +99,6 @@ def __init__(self, parent=None): # self.tableTest.setGeometry(100, 100, 400, 400) # self.tableTest.show() - # from ..db.DbReader import read_residue_db_all - # res = read_residue_db_all() - # residueList = [] # 1st: name, 2nd scpolarity - # for k in res: - # residueList.appen([k["name"], k["scpolarity"]]) - self.actionDefault.setText("Load sample data") def horizontalScrollBarChanged(self): @@ -127,42 +106,6 @@ def horizontalScrollBarChanged(self): y = self.painter.labelView.y() self.painter.labelView.move(x, y) - def showVMDControlPanel(self): - """Shows the VMD control panel, to remotely access VMD from PyContact.""" - self.vmdpanel.show() - - def showContactAreaView(self): - """Shows the SASA computation panel.""" - self.sasaView.nsPerFrame = float(self.settingsView.nsPerFrameField.text()) - self.sasaView.show() - if self.analysis: - self.sasaView.setFilePaths(self.analysis.getFilePaths()) - - def switchedToVisMode(self): - """Switch to vis mode, to show selected contacts directly in VMD.""" - if self.visModeButton.isChecked(): - self.vismode = True - # conversions with clicked frames are not allowed - self.frameStrideField.setText("1") - else: - self.vismode = False - self.painter.switchToVisMode(self.vismode) - self.updateSettings() - self.updateFilters() - - @pyqtSlot() - def updateVMDSelections(self): - """Updates the selected contact in VMD via the vmd panel.""" - if self.vmdpanel.connected: - self.vmdpanel.updateSelections(self.analysis.sel1text, self.analysis.sel2text, - [self.filteredContacts[self.painter.globalClickedRow]]) - - @pyqtSlot() - def updateVMDFrame(self): - """Updates the selected frame in VMD via the vmd panel.""" - if self.vmdpanel.connected: - self.vmdpanel.gotoVMDFrame(self.painter.clickedColumn) - def updateSelectionLabels(self, sel1, sel2): """Updates the current selection in the info labels.""" self.currentSelection1 = sel1 @@ -185,7 +128,6 @@ def importSession(self): self.analysis.contactResults = contactResults self.analysis.setTrajectoryData(*trajArgs) self.analysis.finalAccumulatedContacts = self.contacts - self.sasaView.setFilePaths(*self.analysis.getFilePaths()) self.exportWidget.setFilePaths(*self.analysis.getFilePaths()) self.updateSelectionLabels(arguments[5], arguments[6]) self.updateSettings() @@ -217,7 +159,6 @@ def loadDefault(self): self.analysis.contactResults = contactResults self.analysis.setTrajectoryData(*trajArgs) self.analysis.finalAccumulatedContacts = self.contacts - self.sasaView.setFilePaths(*self.analysis.getFilePaths()) self.exportWidget.setFilePaths(*self.analysis.getFilePaths()) self.updateSelectionLabels(arguments[5], arguments[6]) self.updateSettings() @@ -241,7 +182,6 @@ def loadDataPushed(self): self.loadDataPushed() self.setInfoLabel("%d frames loaded." % len(self.analysis.contactResults)) self.updateSelectionLabels(self.config.sel1text, self.config.sel2text) - self.sasaView.setFilePaths(*self.analysis.getFilePaths()) self.exportWidget.setFilePaths(*self.analysis.getFilePaths()) @pyqtSlot(float) @@ -272,7 +212,7 @@ def analyzeDataPushed(self): map1 = self.maps[0] map2 = self.maps[1] nproc = int(self.settingsView.coreBox.value()) - self.contacts = self.analysis.runContactAnalysis(map1, map2, nproc) + self.contacts = self.analysis.runContactAnalysis(map1, map2) self.progressBar.setValue(0) self.setInfoLabel("Updating timeline...") QApplication.processEvents() @@ -289,12 +229,9 @@ def updateSettings(self): # self.painter.customColor = self.customColor self.painter.repaint() self.painter.update() - self.sasaView.nsPerFrame = float(self.settingsView.nsPerFrameField.text()) def updateFilters(self): """Updates the chosen filters in MainWindow.""" - if self.vismode is True: - self.frameStrideField.setText("1") stride = int(self.frameStrideField.text()) if stride < 1: stride = 1 @@ -415,9 +352,6 @@ def updateFilters(self): if self.maps is not None: self.exportWidget.setMaps(self.maps[0], self.maps[1]) self.exportWidget.setMapLabels(self.analysis.sel1text, self.analysis.sel2text) - self.vmdpanel.sel1 = self.analysis.sel1text - self.vmdpanel.sel2 = self.analysis.sel2text - self.vmdpanel.filteredContactList = self.filteredContacts self.exportWidget.setThresholdAndNsPerFrame(self.painter.threshold, self.painter.nsPerFrame) def openPrefs(self): diff --git a/PyContact/gui/SasaWidgets.py b/PyContact/gui/SasaWidgets.py deleted file mode 100644 index 37fd776..0000000 --- a/PyContact/gui/SasaWidgets.py +++ /dev/null @@ -1,328 +0,0 @@ -import sip -import time -import os - - -from PyQt5.QtWidgets import QWidget, QProgressBar, QApplication, QFileDialog -import MDAnalysis -import numpy as np -# import multiprocessing - -from .Plotters import SimplePlotter -from .sasa_gui import * -from ..core.multi_trajectory import chunks -from ..core.Biochemistry import vdwRadius -from ..core.LogPool import * -from ..cy_modules import cy_gridsearch -from .Dialogues import TopoTrajLoaderDialog -from .ErrorBox import ErrorBox -from .ErrorMessages import ErrorMessages - -# manage processes for SASA -# sasaProgressManager = multiprocessing.Manager() -# sasaProgressDict = sasaProgressManager.dict() -# np.set_printoptions(threshold=np.inf) - - -def calculate_sasa_parallel(input_coords, natoms, pairdist, nprad, - surfacePoints, probeRadius, pointstyle, - restricted, restrictedList, rank): - """Computes the SASA in parallel.""" - - temp_sasa = [] - frames_processed = 0 - # sasaProgressDict[rank] = frames_processed - # print(len(input_coords)) - for c in input_coords: - coords = np.reshape(c, (1, natoms * 3)) - npcoords = np.array(coords, dtype=np.float32) - # print("start C") - # startC = time.time() - asa = cy_gridsearch.cy_sasa(npcoords, natoms, pairdist, 0, -1, nprad, surfacePoints, probeRadius, - pointstyle, restricted, restrictedList) - # stopC = time.time() - # print("time for grid search: ", (stopC - startC)) - # print("asa:", asa) - temp_sasa.append(asa) - frames_processed += 1 - # sasaProgressDict[rank] = frames_processed - return temp_sasa - - -class SasaWidget(QWidget, Ui_SasaWidget): - """Provides a UI for the SASA calculation, including restriction selection and contact area calculation.""" - def __init__(self, parent=None): - super(QtWidgets.QWidget, self).__init__(parent) - self.setupUi(self) - - self.state = True - self.name = None - self.psf, self. dcd = "", "" - self.allSasas = [] - self.totalFramesToProcess = 0 - self.nsPerFrame = 1.0 - - sip.delete(self.sasaProgressBar) - self.sasaProgressBar = PbWidget(total=100) - self.sasaProgressBar.setProperty("value", 0) - self.sasaProgressBar.setTextVisible(True) - self.sasaProgressBar.setInvertedAppearance(False) - self.sasaProgressBar.setObjectName("sasaProgressBar") - self.previewPlot = SimplePlotter(None, width=4, height=2, dpi=70) - self.graphGridLayout.addWidget(self.previewPlot) - self.gridLayout.addWidget(self.sasaProgressBar, 8, 1, 1, 2) - self.calcSasaButton.clicked.connect(self.calculateSasa) - self.loadDataButton.clicked.connect(self.loadData) - self.clearDataButton.clicked.connect(self.clearData) - self.savePlotButton.clicked.connect(self.savePlot) - self.exportDataButton.clicked.connect(self.exportData) - self.topoloader = TopoTrajLoaderDialog() - - def setFilePaths(self, *argv): - """Sets the current trajectory paths from the main view.""" - self.psf = argv[0][0] - self.dcd = argv[0][1] - - def loadData(self): - """Sets the chosen trajectory and topology paths.""" - loadedData = self.topoloader.getConfig() - self.psf = loadedData[0][0] - self.dcd = loadedData[0][1] - - def clearData(self): - """Clears the whole view and sets it to the initial state.""" - self.psf = "" - self.dcd = "" - self.allSasas = [] - self.totalFramesToProcess = 0 - self.sasaProgressBar.setProperty("value", 0) - sip.delete(self.previewPlot) - self.previewPlot = SimplePlotter(None, width=4, height=2, dpi=70) - self.graphGridLayout.addWidget(self.previewPlot) - self.sasaSelection1TextField.setText("") - self.sasaSelection2TextField.setText("") - self.sasaRestrictionTextField.setText("") - - - def savePlot(self): - """Saves the generated SASA plot over all frames.""" - fileName = QFileDialog.getSaveFileName(self, 'Export Path') - if len(fileName[0]) > 0: - path, file_extension = os.path.splitext(fileName[0]) - if file_extension == "": - file_extension = ".png" - file_extension = file_extension[1:] - try: - self.previewPlot.saveFigure(path, file_extension) - except ValueError: - box = ErrorBox("File format " + file_extension + " is not supported.\nPlease choose from eps, pdf, pgf," - " png, ps, raw, rgba, svg, svgz. ") - box.exec_() - - def exportData(self): - """Exports the computed SASA values of each frame to a text file.""" - fileName = QFileDialog.getSaveFileName(self, 'Export Path') - if len(fileName[0]) > 0: - path, file_extension = os.path.splitext(fileName[0]) - if file_extension == "": - file_extension = ".dat" - - f = open(path + file_extension, "w") - for i in range(self.totalFramesToProcess): - f.write(str(i) + "\t" + str(self.allSasas[i]) + "\n") - f.close() - - # TODO: move this somewhere else, e.g., core modules - def calculateSasa(self): - """Computes the SASA of the given selections.""" - self.allSasas = [] - - # load psf and trajectory, make lists with radii and coordinates - if self.psf == "" or self.dcd == "": - e = ErrorBox(ErrorMessages.CHOOSEFILE) - e.exec_() - return - - try: - u = MDAnalysis.Universe(self.psf, self.dcd) - except IOError: - e = ErrorBox(ErrorMessages.FILE_NOT_FOUND) - e.exec_() - return - - probeRadius = 1.4 - - # seltext = "segid UBQ" - # resseltext = "segid UBQ and same residue as around 5.0 (segid RN11)" - seltext = self.sasaSelection1TextField.text() - seltext2 = self.sasaSelection2TextField.text() - resseltext = self.sasaRestrictionTextField.text() - - # 0=spiral, 1=random (VMD) - pointstyle = 1 - # number of points to approximate the sphere - surfacePoints = 50 - # pair distance - pairdist = 2.0 * (2.0 + 1.4) - - if resseltext != "": - restricted = 1 - else: - restricted = 0 - - selection = u.select_atoms(seltext) - - # natoms = len(selection.atoms) - radius = [] - restrictedList = [] - if restricted: - ressel = u.select_atoms(resseltext) - for s in selection.atoms: - if s in ressel.atoms: - restrictedList.append(1) - else: - restrictedList.append(0) - radius.append(vdwRadius(s.name[0])) - else: - restrictedList = [0] - for s in selection.atoms: - radius.append(vdwRadius(s.name[0])) - natoms = len(selection) - nprad = np.array(radius, dtype=np.float32) - restrictedList = np.array(restrictedList, dtype=np.int32) - - # TODO: bug if selection is not static for all frames - # TODO: dynamic allocation of positions in every frame! - input_coords = [] - for ts in u.trajectory: - # ressel = u.select_atoms(resseltext) - # print("restricted: ", len(ressel.atoms)) - input_coords.append(selection.positions) - - nprocs = self.coreBox.value() - input_chunks = chunks(input_coords, nprocs) - pool = LoggingPool(nprocs) - results = [] - rank = 0 - trajLength = len(u.trajectory) - self.totalFramesToProcess = trajLength - for input_coords_chunk in input_chunks: - results.append(pool.apply_async(calculate_sasa_parallel, args=(input_coords_chunk, natoms, pairdist, nprad, - surfacePoints, probeRadius, pointstyle, - restricted, restrictedList, rank))) - rank += 1 - self.state = True - self.sasaEventListener() - pool.close() - pool.join() - - self.state = False - for r in results: - self.allSasas.extend(r.get()) - - del radius - # TODO: one would call the "external" sasa module here again, - # no need to duplicate the code - if self.calculateContactAreaCheckbox.isChecked(): - selection2 = u.select_atoms(seltext2) - - # natoms2 = len(selection2.atoms) - radius2 = [] - restrictedList2 = [] - if restricted: - ressel = u.select_atoms(resseltext) - for s in selection2.atoms: - if s in ressel.atoms: - restrictedList2.append(1) - else: - restrictedList2.append(0) - radius2.append(vdwRadius(s.name[0])) - else: - print("You need a restricted selection for contact areas!") - - natoms2 = len(selection2) - nprad = np.array(radius2, dtype=np.float32) - restrictedList2 = np.array(restrictedList2, dtype=np.int32) - - input_coords2 = [] - for ts in u.trajectory: - input_coords2.append(selection2.positions) - - input_chunks2 = chunks(input_coords2, nprocs) - pool = LoggingPool(nprocs) - results = [] - rank = 0 - trajLength = len(u.trajectory) - self.totalFramesToProcess = trajLength - for input_coords_chunk2 in input_chunks2: - results.append(pool.apply_async(calculate_sasa_parallel, args=(input_coords_chunk2, natoms2, pairdist, - nprad, surfacePoints, probeRadius, - pointstyle, restricted, restrictedList2, - rank))) - rank += 1 - self.state = True - self.sasaEventListener() - pool.close() - pool.join() - - all_sasas2 = [] - for r in results: - all_sasas2.extend(r.get()) - - diff_list = [] - for sasa_value1, sasa_value2 in zip(self.allSasas, all_sasas2): - diff_list.append(sasa_value1 - sasa_value2) - self.allSasas = diff_list - - sip.delete(self.previewPlot) - self.previewPlot = SimplePlotter(None, width=4, height=2, dpi=70) - self.previewPlot.plot(np.arange(0, trajLength, 1) * self.nsPerFrame, self.allSasas) - self.previewPlot.axes.set_xlabel("time [ns]") - if self.calculateContactAreaCheckbox.isChecked(): - self.previewPlot.axes.set_ylabel(r'Contact Area [A$^{\circ}$$^{2}$]') - else: - self.previewPlot.axes.set_ylabel(r'SASA [A$^{\circ}$$^{2}$]') - self.graphGridLayout.addWidget(self.previewPlot) - self.previewPlot.update() - - def sasaEventListener(self): - """Event listener for progress bar updates.""" - while self.state: - QApplication.processEvents() - progress = 0 - # for each in sasaProgressDict.keys(): - # progress += sasaProgressDict[each] - # # sasaProgressDict[each] = 0 - progress = float(progress) / float(self.totalFramesToProcess) * 100 - # if (101 - self.sasaProgressBar.value()) < progress: - # self.sasaProgressBar.update_bar(101 - self.sasaProgressBar.value()) - if progress > 0: - self.sasaProgressBar.setValue(progress) - - if int(progress) == 100: - # for each in sasaProgressDict.keys(): - # sasaProgressDict[each] = 0 - # progress = 0 - self.state = False - - -class PbWidget(QProgressBar): - """Subclassed progressbar for the SASA UI.""" - def __init__(self, total=100): - super(PbWidget, self).__init__() - self.setMinimum(0) - self.setMaximum(total) - self._active = False - - def update_bar(self, to_add_number): - while True: - time.sleep(0.01) - value = self.value() + to_add_number - self.setValue(value) - qApp.processEvents() - if not self._active or value >= self.maximum(): - break - self._active = False - - def closeEvent(self, event): - self._active = False diff --git a/PyContact/gui/VMDControlPanel.py b/PyContact/gui/VMDControlPanel.py deleted file mode 100644 index c8a900a..0000000 --- a/PyContact/gui/VMDControlPanel.py +++ /dev/null @@ -1,310 +0,0 @@ -from socket import * -import subprocess -from pkg_resources import resource_filename as res - -from PyQt5.QtWidgets import QWidget, QGridLayout, QLabel, QPushButton, QLineEdit -from PyQt5 import QtCore - -from .Dialogues import TopoTrajLoaderDialog -from ..core.Biochemistry import * - -# from ..cy_modules import wrap_vmd as vmd - - -class VMDCommands: - """Collection of useful commands to remotely control VMD.""" - @staticmethod - def translateSelections(mdanalysis_text): - """Replace segid and around to adopt the VMD syntax.""" - txt = mdanalysis_text.replace("segid", "segname") - txt = txt.replace("-", " to ") - # around x y--> within x of y - lst = txt.split(" ") - idcs = [i for i, j in enumerate(lst) if j == 'around'] - for idx in idcs: - lst.insert(idx + 2, "of") - txt = " ".join(lst) - txt = txt.replace("around", "within") - return txt - - @staticmethod - def gotoFrame(frame): - """Selects and shows the given frame.""" - return "animate goto %s" % str(frame) - - @staticmethod - def styleBackbone(): - """Sets a suitable visualization style for the backbone in VMD.""" - return """ - mol addrep 0 - mol modstyle top 0 NewCartoon 0.300000 10.000000 4.100000 0 - mol modselect top 0 backbone - mol modcolor top 0 Chain - """ - - @staticmethod - def addSelection(sel, representations, colorID): - idx = str(len(representations)) - representations.append(sel) - return [""" - mol addrep top - mol modstyle %s top Licorice - mol modselect %s top (%s) - mol modcolor %s top ColorID %d - """ % (idx, idx, sel, idx, colorID), representations] - - @staticmethod - def addUserFieldSelection(sel, representations): - idx = str(len(representations)) - representations.append(sel) - return [""" - mol addrep top - mol modstyle %s top QuickSurf 0.500000 0.500000 0.500000 1.000000 - mol modselect %s top (%s) - mol modcolor %s top User - mol selupdate %s top 1 - """ % (idx, idx, sel, idx, idx), representations] - - @staticmethod - def removeReps(index): - # delrep rep_number molecule_number - return """ - mol delrep %s top - """ % index - - @staticmethod - def resetView(): - return "display resetview" - - -class VMDTcp: - """Interface to VMD via tcp""" - def __init__(self): - self.commands = VMDCommands() - self.rctl = res(__name__, './remote_ctl.tcl') - self.HOST = 'localhost' - self.PORT = 5050 - self.ADDR = (self.HOST, self.PORT) - self.tcpClientSocket = None - - def attemptConnection(self): - self.tcpClientSocket = socket(AF_INET, SOCK_STREAM) - self.tcpClientSocket.connect(self.ADDR) - - def start(self): - subprocess.Popen(["vmd", "-e", self.rctl]) - try: - self.attemptConnection() - except Exception: - return -1 - - def send_command(self, cmd): - self.tcpClientSocket.send(str(cmd + "\n")) - - def stop(self): - self.send_command("quit") - self.tcpClientSocket.close() - - -class VMDControlPanel(QWidget): - """docstring for VMDControlPanel""" - - def __init__(self): - super(QWidget, self).__init__() - self.grid = QGridLayout() - self.initUI() - self.representations = [] - self.connected = False - - def initUI(self): - self.runningFancy = False - self.fancyPrepared = False - self.setLayout(self.grid) - self.setWindowTitle("VMD Control Panel") - self.resize(640, 444) - self.grid.setGeometry(QtCore.QRect(10, 10, 621, 431)) - - self.startButton = QPushButton("Start VMD") - self.startButton.clicked.connect(self.pushStartVMD) - self.grid.addWidget(self.startButton, 0, 0) - self.startButton.setEnabled(True) - - self.loadTopoTrajButton = QPushButton("Load Molecules into VMD") - self.loadTopoTrajButton.clicked.connect(self.loadTopoTraj) - self.grid.addWidget(self.loadTopoTrajButton, 2, 1) - self.loadTopoTrajButton.setEnabled(False) - - self.connectButton = QPushButton("Connect to VMD") - self.connectButton.clicked.connect(self.pushConnectVMD) - self.grid.addWidget(self.connectButton, 0, 1) - self.connectButton.setEnabled(False) - - self.infoLabel = QLabel("No VMD session running") - self.grid.addWidget(self.infoLabel, 3, 0, 2, 2) - - self.stopButton = QPushButton("Stop VMD") - self.stopButton.clicked.connect(self.pushStopVMD) - self.grid.addWidget(self.stopButton, 0, 2) - self.stopButton.setEnabled(False) - - # self.fancyVisButton = QPushButton("Fancy") - # self.fancyVisButton.clicked.connect(self.fancy_vis) - # self.grid.addWidget(self.fancyVisButton, 2, 2) - # self.fancyVisButton.setEnabled(True) - self.sel1 = "" - self.sel2 = "" - self.filteredContactList = [] - - # just for testing purposes - # self.commandButton = QPushButton("Send command") - # self.commandButton.clicked.connect(self.sendCommand) - # self.grid.addWidget(self.commandButton, 4, 0) - # self.commandButton.setEnabled(False) - - # self.commandField = QLineEdit() - # self.grid.addWidget(self.commandField, 1, 0, 1, 2) - self.vmd = VMDTcp() - - def addRep(self, txt): - self.representations.append(txt) - - def prepareVMDWithTopoTraj(self, top, traj): - self.vmd.send_command("mol new %s" % top) - self.vmd.send_command(self.vmd.commands.removeReps(0)) - self.vmd.send_command("mol addfile %s waitfor all" % traj) - self.vmd.send_command(self.vmd.commands.styleBackbone()) - self.vmd.send_command(self.vmd.commands.resetView()) - self.vmd.send_command(self.vmd.commands.gotoFrame(0)) - self.addRep("initialBB") - - def loadTopoTraj(self): - topoloader = TopoTrajLoaderDialog() - cfg, result = topoloader.getConfig() - if result == 1: - self.prepareVMDWithTopoTraj(cfg[0], cfg[1]) - - def gotoVMDFrame(self, frame): - self.vmd.send_command(self.vmd.commands.gotoFrame(frame)) - - def updateSelections(self, main_sel1, main_sel2, cont_list): - for s in reversed(range(1, len(self.representations) + 1)): - self.vmd.send_command(self.vmd.commands.removeReps(s)) - self.representations = self.representations[:1] - - sel1 = self.vmd.commands.translateSelections(main_sel1) + " and (" - sel2 = self.vmd.commands.translateSelections(main_sel2) + " and (" - for cont in cont_list: - currentSel1 = [] - index = 0 - for item in cont.key1: - if item != "none": - currentSel1.append(AccumulationMapIndex.vmdsel[index] + " " + item) - index += 1 - currentSel1String = " and ".join(currentSel1) - sel1 += currentSel1String + " or " - currentSel2 = [] - index = 0 - for item in cont.key2: - if item != "none": - currentSel2.append(AccumulationMapIndex.vmdsel[index] + " " + item) - index += 1 - currentSel2String = " and ".join(currentSel2) - sel2 += currentSel2String + " or " - sel1 = sel1[:-3] + ")" - sel2 = sel2[:-3] + ")" - - sel1command, self.representations = self.vmd.commands.addSelection(sel1, self.representations, 3) - self.vmd.send_command(sel1command) - sel2command, self.representations = self.vmd.commands.addSelection(sel2, self.representations, 4) - self.vmd.send_command(sel2command) - - def updateInfoLabel(self, txt): - self.infoLabel.setText(txt) - - def fancy_vis(self): - if self.runningFancy and self.fancyPrepared: - self.runningFancy = False - self.vmd.send_command("animate pause") - elif not self.fancyPrepared: - self.runningFancy = True - for s in reversed(range(1, len(self.representations) + 1)): - self.vmd.send_command(self.vmd.commands.removeReps(s)) - self.representations = self.representations[:1] - for c in self.filteredContactList: - sel1 = self.vmd.commands.translateSelections(self.sel1) - sel2 = self.vmd.commands.translateSelections(self.sel2) - currentFrame = 0 - self.vmd.send_command("animate goto 0") - currentSel1 = [] - index = 0 - for item in c.key1: - if item != "none": - currentSel1.append(AccumulationMapIndex.vmdsel[index] + " " + item) - index += 1 - currentSel1String = " and ".join(currentSel1) - sel1 += " and " + currentSel1String - currentSel2 = [] - index = 0 - for item in c.key2: - if item != "none": - currentSel2.append(AccumulationMapIndex.vmdsel[index] + " " + item) - index += 1 - currentSel2String = " and ".join(currentSel2) - sel2 += " and " + currentSel2String - self.vmd.send_command("set ::remote_ctl::sel [atomselect top {(%s) or (%s)}]; $::remote_ctl::sel global" % (sel1, sel2)) - self.vmd.send_command("$::remote_ctl::sel set beta 20") - for e in c.scoreArray: - self.gotoVMDFrame(currentFrame) - self.vmd.send_command("animate goto %d" % currentFrame) - currentFrame += 1 - self.vmd.send_command("set ::remote_ctl::current [$::remote_ctl::sel get user]") - self.vmd.send_command("$::remote_ctl::sel set user [::remote_ctl::addToList [list $::remote_ctl::current] %f]" % e) - # self.vmd.send_command("$::remote_ctl::sel delete") - self.fancyPrepared = True - sel1 = self.vmd.commands.translateSelections(self.sel1) - sel2 = self.vmd.commands.translateSelections(self.sel2) - s = "noh and user > 0 and (("+ sel1 + ") or (" + sel2 + "))" - sel1command, self.representations = self.vmd.commands.addUserFieldSelection(s, self.representations) - self.vmd.send_command(sel1command) - self.vmd.send_command("color scale method BGR") - self.vmd.send_command("animate forward") - else: - pass - - def pushConnectVMD(self): - try: - self.vmd.attemptConnection() - self.updateInfoLabel("Connection established") - self.loadTopoTrajButton.setEnabled(True) - self.connected = True - except Exception: - self.updateInfoLabel("Could not connect to VMD!\nTry to connect using the Connect" - " button\n when VMD is opened.") - - def pushStartVMD(self): - self.startButton.setEnabled(False) - self.stopButton.setEnabled(True) - # self.commandButton.setEnabled(True) - response = self.vmd.start() - if response == -1: - self.connectButton.setEnabled(True) - self.updateInfoLabel("Could not connect to VMD!\nTry to connect using the Connect button\n " - "when VMD is opened.") - else: - self.loadTopoTrajButton.setEnabled(True) - self.connected = True - - def pushStopVMD(self): - self.representations = [] - self.updateInfoLabel("VMD stopped.") - self.connectButton.setEnabled(False) - self.startButton.setEnabled(True) - self.stopButton.setEnabled(False) - # self.commandButton.setEnabled(False) - self.loadTopoTrajButton.setEnabled(False) - self.vmd.stop() - self.connected = False - - def sendCommand(self): - self.vmd.send_command(self.commandField.text()) - self.commandField.setText("") diff --git a/PyContact/gui/remote_ctl.tcl b/PyContact/gui/remote_ctl.tcl deleted file mode 100644 index 0f7aa07..0000000 --- a/PyContact/gui/remote_ctl.tcl +++ /dev/null @@ -1,105 +0,0 @@ -#------------------------------------------------------------------ -# $Id: remote_ctl.tcl,v 1.6 2003/02/12 21:33:11 oliver Exp $ -# based on bounce.tcl and vmdcollab.tcl -# from http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/vmdcollab/ -# -# start this in VMD and send commands to the listening port to have VMD -# execute them remotely -# (also see http://www.tcl.tk/scripting/netserver.html) -# -# Usage: vmd -e remote_ctl.tcl -# or vmd> source remote_ctl.tcl -# -# Security: we only allow connections from localhost (see acpt) -# -# Bugs: -# * once a wrong command was sent, the connection appears -# to 'block' and does not accept correct commands later -# * does not write result back to socket (one way connection...) so -# there is no way to inquire objects in vmd - -namespace eval remote_ctl { - variable main - variable clients - variable default_vmd_port - set default_vmd_port 5555 - # I am too dumb to set the default value for port from - # $default_vmd_port so I put 5555 in there literally - proc start { {port 5050} } { - variable main - set main [socket -server remote_ctl::acpt $port] - putlog "Listening on port $port" - } - proc acpt { sock addr port } { - variable clients - if {[string compare $addr "127.0.0.1"] != 0} { - putlog "Unauthorized connection attempt from $addr port $port" - close $sock - return - } - putlog "Accept $sock from $addr port $port" - set clients($sock) 1 - fconfigure $sock -buffering line - fileevent $sock readable [list remote_ctl::recv $sock] - } - proc recv { sock } { - variable main - variable clients - if { [eof $sock] || [catch {gets $sock line}]} { - # end of file or abnormal connection drop: - # shut down this connection - close $sock - putlog "Closing $sock" - unset clients($sock) - } else { - if {[string compare $line "quit"] == 0} { - # prevent new connections - # existing connections stay open - # No -- Bug(?): 'quit' closes VMD... - putlog "Disallowing incoming connections by request of $sock" - close $main - } - # execute the received commands - # should check for runtime errors which otherwise leave the connection - # in an unusable state - #eval $line - set rc [catch $line result] - if { $rc } { - #puts $sock "Error executing comand '$line': n$result" - puts "Error executing comand '$line': $result" - } else { - #puts $sock $result - puts $result - if {[string first "set" $line] == 0} { - - } - - } - } - } - ###### would like the last line from stdout in line ########### - # (or any working solution....) - proc send { sock line} { - variable clients - # send reply to connecting client - putlog "send '$line' to $sock" - puts $sock $line - } - - proc putlog { text } { - puts $text - return - } - - proc addToList { l numb } { - set result {} - foreach i $numb { - lappend result [expr $i + $numb] - } - return $result - } - } - - remote_ctl::putlog "Starting remote_ctl server in vmd: connect with something like" - remote_ctl::putlog "telnet localhost 5050" - remote_ctl::start diff --git a/PyContact/gui/sasa.ui b/PyContact/gui/sasa.ui deleted file mode 100644 index 8e99bc8..0000000 --- a/PyContact/gui/sasa.ui +++ /dev/null @@ -1,291 +0,0 @@ - - - SasaWidget - - - - 0 - 0 - 712 - 514 - - - - Surface Areas - - - - - - - - - - - - - - - - - - true - - - - 0 - 0 - - - - - 0 - 0 - - - - Qt::StrongFocus - - - - - - - - 0 - 0 - - - - - 75 - true - - - - Restriction: - - - - - - - - - - Qt::Horizontal - - - QSizePolicy::Fixed - - - - 0 - 40 - - - - - - - - Calculate - - - - - - - - - - Load Data - - - - - - - Clear Data - - - - - - - Save Plot - - - - - - - Export Data - - - - - - - Qt::Vertical - - - - 20 - 40 - - - - - - - - Cores: - - - Qt::AlignCenter - - - - - - - 1 - - - 32 - - - 4 - - - - - - - - - - - QLayout::SetNoConstraint - - - - - 0 - - - true - - - false - - - - - - - - - - - 75 - true - - - - Selection: - - - - - - - contact - - - - - - - Qt::StrongFocus - - - - - - - Qt::Horizontal - - - QSizePolicy::Fixed - - - - 40 - 40 - - - - - - - - Qt::Horizontal - - - QSizePolicy::Fixed - - - - 40 - 40 - - - - - - - - - 0 - 0 - - - - - 75 - true - - - - Selection 2: - - - - - - - Qt::Horizontal - - - - - - - - - - sasaSelection1TextField - sasaRestrictionTextField - sasaSelection2TextField - calculateContactAreaCheckbox - coreBox - loadDataButton - savePlotButton - exportDataButton - calcSasaButton - - - - diff --git a/PyContact/gui/sasa_gui.py b/PyContact/gui/sasa_gui.py deleted file mode 100644 index fe21adf..0000000 --- a/PyContact/gui/sasa_gui.py +++ /dev/null @@ -1,166 +0,0 @@ -# -*- coding: utf-8 -*- - -# Form implementation generated from reading ui file 'sasa.ui' -# -# Created by: PyQt5 UI code generator 5.8 -# -# WARNING! All changes made in this file will be lost! - -from PyQt5 import QtCore, QtGui, QtWidgets - -class Ui_SasaWidget(object): - def setupUi(self, SasaWidget): - SasaWidget.setObjectName("SasaWidget") - SasaWidget.resize(712, 514) - self.gridLayout_2 = QtWidgets.QGridLayout(SasaWidget) - self.gridLayout_2.setObjectName("gridLayout_2") - self.gridWidget = QtWidgets.QWidget(SasaWidget) - self.gridWidget.setObjectName("gridWidget") - self.gridLayout = QtWidgets.QGridLayout(self.gridWidget) - self.gridLayout.setContentsMargins(0, 0, 0, 0) - self.gridLayout.setObjectName("gridLayout") - self.gridWidget1 = QtWidgets.QWidget(self.gridWidget) - self.gridWidget1.setObjectName("gridWidget1") - self.gridLayout_3 = QtWidgets.QGridLayout(self.gridWidget1) - self.gridLayout_3.setContentsMargins(0, 0, 0, 0) - self.gridLayout_3.setObjectName("gridLayout_3") - self.graphGridLayout = QtWidgets.QGridLayout() - self.graphGridLayout.setObjectName("graphGridLayout") - self.gridLayout_3.addLayout(self.graphGridLayout, 0, 0, 1, 1) - self.gridLayout.addWidget(self.gridWidget1, 7, 1, 1, 2) - self.sasaSelection2TextField = QtWidgets.QLineEdit(self.gridWidget) - self.sasaSelection2TextField.setEnabled(True) - sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.Expanding, QtWidgets.QSizePolicy.Fixed) - sizePolicy.setHorizontalStretch(0) - sizePolicy.setVerticalStretch(0) - sizePolicy.setHeightForWidth(self.sasaSelection2TextField.sizePolicy().hasHeightForWidth()) - self.sasaSelection2TextField.setSizePolicy(sizePolicy) - self.sasaSelection2TextField.setMinimumSize(QtCore.QSize(0, 0)) - self.sasaSelection2TextField.setFocusPolicy(QtCore.Qt.StrongFocus) - self.sasaSelection2TextField.setObjectName("sasaSelection2TextField") - self.gridLayout.addWidget(self.sasaSelection2TextField, 5, 1, 1, 1) - self.label_2 = QtWidgets.QLabel(self.gridWidget) - sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.Fixed, QtWidgets.QSizePolicy.Preferred) - sizePolicy.setHorizontalStretch(0) - sizePolicy.setVerticalStretch(0) - sizePolicy.setHeightForWidth(self.label_2.sizePolicy().hasHeightForWidth()) - self.label_2.setSizePolicy(sizePolicy) - font = QtGui.QFont() - font.setBold(True) - font.setWeight(75) - self.label_2.setFont(font) - self.label_2.setObjectName("label_2") - self.gridLayout.addWidget(self.label_2, 4, 0, 1, 1) - self.sasaSelection1TextField = QtWidgets.QLineEdit(self.gridWidget) - self.sasaSelection1TextField.setObjectName("sasaSelection1TextField") - self.gridLayout.addWidget(self.sasaSelection1TextField, 3, 1, 1, 1) - spacerItem = QtWidgets.QSpacerItem(0, 40, QtWidgets.QSizePolicy.Fixed, QtWidgets.QSizePolicy.Minimum) - self.gridLayout.addItem(spacerItem, 5, 3, 1, 1) - self.calcSasaButton = QtWidgets.QPushButton(self.gridWidget) - self.calcSasaButton.setObjectName("calcSasaButton") - self.gridLayout.addWidget(self.calcSasaButton, 8, 0, 1, 1) - self.widget = QtWidgets.QWidget(self.gridWidget) - self.widget.setObjectName("widget") - self.verticalLayout = QtWidgets.QVBoxLayout(self.widget) - self.verticalLayout.setContentsMargins(0, 0, 0, 0) - self.verticalLayout.setObjectName("verticalLayout") - self.loadDataButton = QtWidgets.QPushButton(self.widget) - self.loadDataButton.setObjectName("loadDataButton") - self.verticalLayout.addWidget(self.loadDataButton) - self.clearDataButton = QtWidgets.QPushButton(self.widget) - self.clearDataButton.setObjectName("clearDataButton") - self.verticalLayout.addWidget(self.clearDataButton) - self.savePlotButton = QtWidgets.QPushButton(self.widget) - self.savePlotButton.setObjectName("savePlotButton") - self.verticalLayout.addWidget(self.savePlotButton) - self.exportDataButton = QtWidgets.QPushButton(self.widget) - self.exportDataButton.setObjectName("exportDataButton") - self.verticalLayout.addWidget(self.exportDataButton) - spacerItem1 = QtWidgets.QSpacerItem(20, 40, QtWidgets.QSizePolicy.Minimum, QtWidgets.QSizePolicy.Expanding) - self.verticalLayout.addItem(spacerItem1) - self.label_4 = QtWidgets.QLabel(self.widget) - self.label_4.setAlignment(QtCore.Qt.AlignCenter) - self.label_4.setObjectName("label_4") - self.verticalLayout.addWidget(self.label_4) - self.coreBox = QtWidgets.QSpinBox(self.widget) - self.coreBox.setMinimum(1) - self.coreBox.setMaximum(32) - self.coreBox.setProperty("value", 4) - self.coreBox.setObjectName("coreBox") - self.verticalLayout.addWidget(self.coreBox) - self.gridLayout.addWidget(self.widget, 7, 0, 1, 1) - self.horizontalWidget = QtWidgets.QWidget(self.gridWidget) - self.horizontalWidget.setObjectName("horizontalWidget") - self.verticalLayout_2 = QtWidgets.QVBoxLayout(self.horizontalWidget) - self.verticalLayout_2.setSizeConstraint(QtWidgets.QLayout.SetNoConstraint) - self.verticalLayout_2.setContentsMargins(0, 0, 0, 0) - self.verticalLayout_2.setObjectName("verticalLayout_2") - self.sasaProgressBar = QtWidgets.QProgressBar(self.horizontalWidget) - self.sasaProgressBar.setProperty("value", 0) - self.sasaProgressBar.setTextVisible(True) - self.sasaProgressBar.setInvertedAppearance(False) - self.sasaProgressBar.setObjectName("sasaProgressBar") - self.verticalLayout_2.addWidget(self.sasaProgressBar) - self.gridLayout.addWidget(self.horizontalWidget, 8, 1, 1, 2) - self.label = QtWidgets.QLabel(self.gridWidget) - font = QtGui.QFont() - font.setBold(True) - font.setWeight(75) - self.label.setFont(font) - self.label.setObjectName("label") - self.gridLayout.addWidget(self.label, 3, 0, 1, 1) - self.calculateContactAreaCheckbox = QtWidgets.QCheckBox(self.gridWidget) - self.calculateContactAreaCheckbox.setObjectName("calculateContactAreaCheckbox") - self.gridLayout.addWidget(self.calculateContactAreaCheckbox, 5, 2, 1, 1) - self.sasaRestrictionTextField = QtWidgets.QLineEdit(self.gridWidget) - self.sasaRestrictionTextField.setFocusPolicy(QtCore.Qt.StrongFocus) - self.sasaRestrictionTextField.setObjectName("sasaRestrictionTextField") - self.gridLayout.addWidget(self.sasaRestrictionTextField, 4, 1, 1, 1) - spacerItem2 = QtWidgets.QSpacerItem(40, 40, QtWidgets.QSizePolicy.Fixed, QtWidgets.QSizePolicy.Minimum) - self.gridLayout.addItem(spacerItem2, 4, 2, 1, 1) - spacerItem3 = QtWidgets.QSpacerItem(40, 40, QtWidgets.QSizePolicy.Fixed, QtWidgets.QSizePolicy.Minimum) - self.gridLayout.addItem(spacerItem3, 3, 2, 1, 2) - self.label_3 = QtWidgets.QLabel(self.gridWidget) - sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.Minimum, QtWidgets.QSizePolicy.Fixed) - sizePolicy.setHorizontalStretch(0) - sizePolicy.setVerticalStretch(0) - sizePolicy.setHeightForWidth(self.label_3.sizePolicy().hasHeightForWidth()) - self.label_3.setSizePolicy(sizePolicy) - font = QtGui.QFont() - font.setBold(True) - font.setWeight(75) - self.label_3.setFont(font) - self.label_3.setObjectName("label_3") - self.gridLayout.addWidget(self.label_3, 5, 0, 1, 1) - self.line = QtWidgets.QFrame(self.gridWidget) - self.line.setFrameShape(QtWidgets.QFrame.HLine) - self.line.setFrameShadow(QtWidgets.QFrame.Sunken) - self.line.setObjectName("line") - self.gridLayout.addWidget(self.line, 6, 1, 1, 2) - self.gridLayout_2.addWidget(self.gridWidget, 0, 0, 1, 1) - - self.retranslateUi(SasaWidget) - QtCore.QMetaObject.connectSlotsByName(SasaWidget) - SasaWidget.setTabOrder(self.sasaSelection1TextField, self.sasaRestrictionTextField) - SasaWidget.setTabOrder(self.sasaRestrictionTextField, self.sasaSelection2TextField) - SasaWidget.setTabOrder(self.sasaSelection2TextField, self.calculateContactAreaCheckbox) - SasaWidget.setTabOrder(self.calculateContactAreaCheckbox, self.coreBox) - SasaWidget.setTabOrder(self.coreBox, self.loadDataButton) - SasaWidget.setTabOrder(self.loadDataButton, self.savePlotButton) - SasaWidget.setTabOrder(self.savePlotButton, self.exportDataButton) - SasaWidget.setTabOrder(self.exportDataButton, self.calcSasaButton) - - def retranslateUi(self, SasaWidget): - _translate = QtCore.QCoreApplication.translate - SasaWidget.setWindowTitle(_translate("SasaWidget", "Surface Areas")) - self.label_2.setText(_translate("SasaWidget", "Restriction:")) - self.calcSasaButton.setText(_translate("SasaWidget", "Calculate")) - self.loadDataButton.setText(_translate("SasaWidget", "Load Data")) - self.clearDataButton.setText(_translate("SasaWidget", "Clear Data")) - self.savePlotButton.setText(_translate("SasaWidget", "Save Plot")) - self.exportDataButton.setText(_translate("SasaWidget", "Export Data")) - self.label_4.setText(_translate("SasaWidget", "Cores:")) - self.label.setText(_translate("SasaWidget", "Selection:")) - self.calculateContactAreaCheckbox.setText(_translate("SasaWidget", "contact")) - self.label_3.setText(_translate("SasaWidget", "Selection 2:")) - diff --git a/setup.cfg b/setup.cfg index 9d637e9..bcd06ab 100644 --- a/setup.cfg +++ b/setup.cfg @@ -11,5 +11,5 @@ tag = True universal = 0 [metadata] -license_file = LICENSE -description-file = README.md +license_files = LICENSE +description_file = README.md diff --git a/setup.py b/setup.py index 68a3289..48d3492 100644 --- a/setup.py +++ b/setup.py @@ -45,8 +45,8 @@ package_data={'PyContact': ['exampleData/defaultsession', 'exampleData/*.psf', 'exampleData/*.pdb', 'exampleData/*.dcd', 'exampleData/*.tpr', - 'exampleData/*.xtc', 'gui/*.tcl', - 'db/aa.db', 'cy_modules/*.pyx', + 'exampleData/*.xtc', + 'cy_modules/*.pyx', 'cy_modules/src/*']}, entry_points={ 'console_scripts': [ diff --git a/tests/map_animate.py b/tests/map_animate.py deleted file mode 100644 index 9fcc4ef..0000000 --- a/tests/map_animate.py +++ /dev/null @@ -1,94 +0,0 @@ -""" -A simple example of an animated plot -""" -import numpy as np -import matplotlib.pyplot as plt -import matplotlib.animation as animation -import matplotlib -matplotlib.use("qt5agg") - -from PyContact.core.Scripting import PyContactJob, JobConfig -from PyContact.core.Biochemistry import AccumulationMapIndex - -jobAllMD = PyContactJob("./PyContact/exampleData/rpn11_ubq_interface-ionized.psf", - "./PyContact/exampleData/short.dcd", "md_all", JobConfig(5.0, 2.5, 120, [0,0,0,1,1,0], [0,0,0,1,1,0], "segid UBQ", "segid RN11")) - -jobAllMD.runJob(1) -contacts = jobAllMD.analyzer.finalAccumulatedContacts - -map1 = [0,0,0,1,1,0] -map2 = [0,0,0,1,1,0] -label1 = "UBQ" -label2 = "RN11" -attribute = "test" -threshold = 0.0 -nsPerFrame = 1.0 - -minmaxresids1 = [] -minmaxresids2 = [] - -for cont in contacts: - minmaxresids1.append(int(cont.key1[AccumulationMapIndex.resid])) - minmaxresids2.append(int(cont.key2[AccumulationMapIndex.resid])) - -x = np.arange(np.min(minmaxresids1), np.max(minmaxresids1) + 1) -y = np.arange(np.min(minmaxresids2), np.max(minmaxresids2) + 1) - -fig, ax = plt.subplots() - -data = np.ones((len(x), len(y))) -# data = np.random.rand(len(x), len(y)) -print(data.shape) -print(data) - -# cax = ax.matshow(data, cmap=plt.cm.gray) -cax = None -ttl = ax.set_title("test") -plt.draw() -minx = np.min(minmaxresids1) -miny = np.min(minmaxresids2) -rng = np.arange(len(contacts[0].scoreArray)) -# ttl = ax.text(30, -10, ' ') - - -def animate(i): - print(i) - global cax - data = np.zeros((len(x), len(y))) - attribute = "Mean Score" - if attribute == "Mean Score": - for c in contacts: - r1 = int(c.key1[AccumulationMapIndex.resid]) - minx - r2 = int(c.key2[AccumulationMapIndex.resid]) - miny - data[r1, r2] = c.scoreArray[i] - print(data[r1, r2]) - cax.set_data(data) # update the data - ttl.set_text(str(i)) - plt.draw() - return cax, - - -# Init only required for blitting to give a clean slate. -def init(): - global cax - data = np.zeros((len(x), len(y))) - - frame = 0 - print("frame: ", frame) - attribute = "Mean Score" - if attribute == "Mean Score": - for c in contacts: - r1 = int(c.key1[AccumulationMapIndex.resid]) - minx - r2 = int(c.key2[AccumulationMapIndex.resid]) - miny - data[r1, r2] = c.scoreArray[frame] - print(data[r1, r2]) - - # data.fill(10) - # data = np.zeros((len(x), len(y))) - cax = ax.matshow(data, cmap=plt.cm.gray) - ttl.set_text("init") - plt.draw() - return cax, - -ani = animation.FuncAnimation(fig, animate, rng, init_func=init, blit=True, repeat=False) -plt.show() diff --git a/tests/test_basic.py b/tests/test_basic.py index f59b4e3..15b1a20 100644 --- a/tests/test_basic.py +++ b/tests/test_basic.py @@ -35,7 +35,7 @@ def test_singleCore_analysis(self): self.assertEqual(len(analyzer.contactResults), 50) map1 = [0, 0, 1, 1, 0] map2 = [0, 0, 1, 1, 0] - analyzer.runContactAnalysis(map1, map2, 1) + analyzer.runContactAnalysis(map1, map2) self.assertEqual(len(analyzer.finalAccumulatedContacts), 148) hbond_sum = 0 for c in analyzer.finalAccumulatedContacts: @@ -48,7 +48,7 @@ def test_selfInteraction_analysis(self): self.assertEqual(len(analyzer.contactResults), 50) map1 = [0, 0, 1, 1, 0] map2 = [0, 0, 1, 1, 0] - analyzer.runContactAnalysis(map1, map2, 1) + analyzer.runContactAnalysis(map1, map2) def test_zero_atomselection(self): analyzer = Analyzer(self.psffile, self.dcdfile, 5.0, 2.5, 120, "segid A", "resid 100") @@ -68,7 +68,7 @@ def test_selfInteraction_analysis_parallel(self): self.assertEqual(len(analyzer.contactResults), 50) map1 = [0, 0, 1, 1, 0] map2 = [0, 0, 1, 1, 0] - analyzer.runContactAnalysis(map1, map2, 1) + analyzer.runContactAnalysis(map1, map2) def test_multiCore_analysis(self): analyzer = Analyzer(self.psffile, self.dcdfile, 5.0, 2.5, 120, "segid RN11", "segid UBQ") @@ -76,15 +76,9 @@ def test_multiCore_analysis(self): self.assertEqual(len(analyzer.contactResults), 50) map1 = [0, 0, 1, 1, 0] map2 = [0, 0, 1, 1, 0] - analyzer.runContactAnalysis(map1, map2, 2) + analyzer.runContactAnalysis(map1, map2) self.assertEqual(len(analyzer.finalAccumulatedContacts), 148) hbond_sum = 0 for c in analyzer.finalAccumulatedContacts: hbond_sum += c.hbond_percentage() self.assertEqual(hbond_sum, 676.0) - - def test_around_selection_patch(self): - univ = mda.Universe(self.psffile, self.dcdfile) - aroundText = "segid UBQ and around 5 segid RN11" - sel = univ.select_atoms(aroundText) - self.assertEqual(len(sel), 261) diff --git a/tests/test_find_contacts.py b/tests/test_find_contacts.py new file mode 100644 index 0000000..bf7c087 --- /dev/null +++ b/tests/test_find_contacts.py @@ -0,0 +1,40 @@ +import numpy as np +from PyContact.cy_modules.cy_gridsearch import cy_find_contacts +from scipy.spatial import KDTree +from scipy.spatial.distance import cdist + + +def test_find_contacts(): + # pass positions and distance to cython + natoms1 = 1800 + natoms2 = 2100 + box_dimensions = [50, 55, 45] + # generate random positions in a box of size box_dimensions + np.random.seed(42) + pos1 = np.random.rand(natoms1, 3) * box_dimensions + pos2 = np.random.rand(natoms2, 3) * box_dimensions + xyz1 = np.array(np.reshape(pos1, (1, natoms1 * 3)), dtype=np.float32) + xyz2 = np.array(np.reshape(pos2, (1, natoms2 * 3)), dtype=np.float32) + + cutoff = 5.0 + # 2d array with index of atom1 being the index of the first dimension + # individual lists contain atom2 indices + nbList1 = cy_find_contacts(xyz1, natoms1, xyz2, natoms2, cutoff) + + tree = KDTree(pos2) + # Query the KD-Tree to find pairs of points within the cutoff distance + pairs = tree.query_ball_point(pos1, r=cutoff) + + # compute pair list using scipy.spatial distance matrix + dist_mat = cdist(pos1, pos2) + # get indices of atoms that are within cutoff + pair_list = np.where(dist_mat <= cutoff) + assert len(pair_list[0]) > 0 + assert len(pair_list[1]) > 0 + # check if the number of contacts is the same + for (p1, p2) in zip(pair_list[0], pair_list[1]): + assert p2 in nbList1[p1] + assert p2 in pairs[p1] + + for idx, nb_list in enumerate(nbList1[:natoms1]): + assert sorted(nb_list) == sorted(pairs[idx]) \ No newline at end of file From f7078c708d7456fd80989a392e37f94abca2bae4 Mon Sep 17 00:00:00 2001 From: Maximilian Scheurer Date: Mon, 15 May 2023 18:04:56 +0200 Subject: [PATCH 2/2] bye cython --- PyContact/core/ContactAnalyzer.py | 32 +- PyContact/core/multi_trajectory.py | 38 +- PyContact/cy_modules/__init__.py | 0 PyContact/cy_modules/cy_gridsearch.pyx | 36 - PyContact/cy_modules/src/ResizeArray.h | 133 - PyContact/cy_modules/src/gridsearch.C | 1176 -- README.md | 9 +- setup.py | 21 +- testing/BestPractice.txt | 5 - testing/cython/ResizeArray.h | 133 - testing/cython/gridsearch.C | 823 - testing/cython/setup.py | 9 - testing/cython/vmd/a.out | Bin 31688 -> 0 bytes testing/cython/vmd/remote_ctl.tcl | 93 - testing/cython/vmd/setup.py | 9 - testing/cython/vmd/vmd_wrapper.cpp | 34 - testing/cython/vmd/wrap_vmd.c | 1836 --- testing/cython/vmd/wrap_vmd.cpp | 1927 --- testing/cython/vmd/wrap_vmd.pyx | 11 - testing/cython/wrap.c | 1973 --- testing/cython/wrap.cpp | 20119 ----------------------- testing/cython/wrap.pyx | 101 - testing/cython/wrap_cython.py | 15 - testing/cython/wrap_vmd.cpp | 1850 --- testing/tableview.py | 120 - tests/test_basic.py | 13 + tests/test_find_contacts.py | 12 +- 27 files changed, 45 insertions(+), 30483 deletions(-) delete mode 100644 PyContact/cy_modules/__init__.py delete mode 100644 PyContact/cy_modules/cy_gridsearch.pyx delete mode 100644 PyContact/cy_modules/src/ResizeArray.h delete mode 100644 PyContact/cy_modules/src/gridsearch.C delete mode 100644 testing/BestPractice.txt delete mode 100644 testing/cython/ResizeArray.h delete mode 100644 testing/cython/gridsearch.C delete mode 100644 testing/cython/setup.py delete mode 100755 testing/cython/vmd/a.out delete mode 100644 testing/cython/vmd/remote_ctl.tcl delete mode 100644 testing/cython/vmd/setup.py delete mode 100644 testing/cython/vmd/vmd_wrapper.cpp delete mode 100644 testing/cython/vmd/wrap_vmd.c delete mode 100644 testing/cython/vmd/wrap_vmd.cpp delete mode 100644 testing/cython/vmd/wrap_vmd.pyx delete mode 100644 testing/cython/wrap.c delete mode 100644 testing/cython/wrap.cpp delete mode 100644 testing/cython/wrap.pyx delete mode 100644 testing/cython/wrap_cython.py delete mode 100644 testing/cython/wrap_vmd.cpp delete mode 100644 testing/tableview.py diff --git a/PyContact/core/ContactAnalyzer.py b/PyContact/core/ContactAnalyzer.py index 40e37ae..1b15d31 100644 --- a/PyContact/core/ContactAnalyzer.py +++ b/PyContact/core/ContactAnalyzer.py @@ -6,10 +6,9 @@ import MDAnalysis import numpy as np from PyQt5.QtCore import pyqtSignal, QObject +from scipy.spatial import KDTree -# TODO: fix aroundPatch with gridsearch in C code using cython from .Biochemistry import (AccumulatedContact, AtomContact, AccumulationMapIndex, HydrogenBond, TempContactAccumulate, HydrogenBondAtoms) -from ..cy_modules.cy_gridsearch import cy_find_contacts class Analyzer(QObject): @@ -309,26 +308,9 @@ def analyze_psf_dcd_grid(self, psf, dcd, cutoff, hbondcutoff, hbondcutangle, sel frame = ts.frame self.currentFrameNumber = ts.frame - # pass positions and distance to cython - natoms1 = len(sel1.atoms) - natoms2 = len(sel2.atoms) - pos1 = np.array(np.reshape(sel1.positions, (1, natoms1 * 3)), dtype=np.float64) - pos2 = np.array(np.reshape(sel2.positions, (1, natoms2 * 3)), dtype=np.float64) - xyz1 = np.array(pos1, dtype=np.float32) - xyz2 = np.array(pos2, dtype=np.float32) - # 2d array with index of atom1 being the index of the first dimension - # individual lists contain atom2 indices - nbList1 = cy_find_contacts(xyz1, natoms1, xyz2, natoms2, cutoff) - - from scipy.spatial import KDTree tree = KDTree(sel2.positions) nbList1 = tree.query_ball_point(sel1.positions, r=cutoff) - # we only need the 1st list - # nbList1 = res[:natoms1] - # nbList2 = res[natoms1:] - - idx1 = 0 for atom1sNeighbors in nbList1: for idx2 in atom1sNeighbors: @@ -345,7 +327,8 @@ def analyze_psf_dcd_grid(self, psf, dcd, cutoff, hbondcutoff, hbondcutangle, sel continue # distance = distarray[idx1, idx2] # weight = self.weight_function(distance) - dvec = pos1[0][3*idx1:3*idx1+3] - pos2[0][3*idx2:3*idx2+3] + # dvec = pos1[0][3*idx1:3*idx1+3] - pos2[0][3*idx2:3*idx2+3] + dvec = sel1.positions[idx1] - sel2.positions[idx2] distance = np.sqrt(dvec.dot(dvec)) # print(dvec, distance, dvec.dtype) # if (distance - distarray[idx1, idx2]) > 0.001: @@ -415,7 +398,9 @@ def analyze_psf_dcd_grid(self, psf, dcd, cutoff, hbondcutoff, hbondcutangle, sel # if (typeHeavy == AtomHBondType.acc or typeHeavy == AtomHBondType.both) and (distarray[conv_hatom, idx2] <= hbondcutoff): # dist = distarray[conv_hatom, idx2] # dist = np.linalg.norm(sel1.positions[conv_hatom] - sel2.positions[idx2]) - dist = np.linalg.norm(pos1[0][3*conv_hatom:3*conv_hatom+3] - pos2[0][3*idx2:3*idx2+3]) + dist = np.linalg.norm( + sel1.positions[conv_hatom] - sel2.positions[idx2] + ) if (dist <= hbondcutoff): donorPosition = sel1.positions[idx1] hydrogenPosition = np.array(sel1.positions[conv_hatom], dtype=np.float64) @@ -444,7 +429,10 @@ def analyze_psf_dcd_grid(self, psf, dcd, cutoff, hbondcutoff, hbondcutangle, sel # if (distarray[conv_hatom, idx2] <= hbondcutoff): # dist = distarray[idx1, conv_hatom] # dist = np.linalg.norm(sel1.positions[idx1] - sel2.positions[conv_hatom]) - dist = np.linalg.norm(pos1[0][3*idx1:3*idx1+3] - pos2[0][3*conv_hatom:3*conv_hatom+3]) + # dist = np.linalg.norm(pos1[0][3*idx1:3*idx1+3] - pos2[0][3*conv_hatom:3*conv_hatom+3]) + dist = np.linalg.norm( + sel1.positions[idx1] - sel2.positions[conv_hatom] + ) if (dist <= hbondcutoff): donorPosition = sel2.positions[idx2] hydrogenPosition = np.array(sel2.positions[conv_hatom], dtype=np.float64) diff --git a/PyContact/core/multi_trajectory.py b/PyContact/core/multi_trajectory.py index dcb4bbe..39a0a3c 100644 --- a/PyContact/core/multi_trajectory.py +++ b/PyContact/core/multi_trajectory.py @@ -6,10 +6,10 @@ import MDAnalysis from MDAnalysis.analysis import distances import numpy as np +from scipy.spatial import KDTree from .Biochemistry import * from .LogPool import * -from ..cy_modules.cy_gridsearch import cy_find_contacts def weight_function(value): @@ -68,17 +68,8 @@ def loop_trajectory_grid(sel1c, sel2c, indices1, indices2, config, suppl, selfIn for s1, s2 in zip(sel1c, sel2c): frame = 0 currentFrameContacts = [] - natoms1 = len(s1) - natoms2 = len(s2) - pos1 = np.array(np.reshape(s1, (1, natoms1 * 3)), dtype=np.float64) - pos2 = np.array(np.reshape(s2, (1, natoms2 * 3)), dtype=np.float64) - xyz1 = np.array(pos1, dtype=np.float32) - xyz2 = np.array(pos2, dtype=np.float32) - # 2d array with index of atom1 being the index of the first dimension - # individual lists contain atom2 indices - nbList1 = cy_find_contacts(xyz1, natoms1, xyz2, natoms2, cutoff) - # nbList1 = res[:natoms1] - # nbList2 = res[natoms1:] + tree = KDTree(s2) + nbList1 = tree.query_ball_point(s1, r=cutoff, workers=1) idx1 = 0 for atom1sNeighbors in nbList1: for idx2 in atom1sNeighbors: @@ -93,17 +84,10 @@ def loop_trajectory_grid(sel1c, sel2c, indices1, indices2, config, suppl, selfIn if selfInteraction: if (resid_array[convindex1] - resid_array[convindex2]) < 5 and segids[convindex1] == segids[convindex2]: continue - # distance = distarray[idx1, idx2] - # weight = weight_function(distance) - dvec = pos1[0][3*idx1:3*idx1+3] - pos2[0][3*idx2:3*idx2+3] + + dvec = s1[idx1] - s2[idx2] distance = np.sqrt(dvec.dot(dvec)) - # if (distance - distarray[idx1, idx2]) > 0.001: - # print("Error in distance calculations!") - # return - # # print(convindex1, convindex2, distance, distarray[idx1, idx2]) - # if (distance > cutoff): - # print("Distances must be smaller/equal cutoff!") - # return + weight = weight_function(distance) # HydrogenBondAlgorithm @@ -162,7 +146,10 @@ def loop_trajectory_grid(sel1c, sel2c, indices1, indices2, config, suppl, selfIn # if (typeHeavy == AtomHBondType.acc or typeHeavy == AtomHBondType.both) and (distarray[conv_hatom, idx2] <= hbondcutoff): # dist = distarray[conv_hatom, idx2] # dist = np.linalg.norm(sel1.positions[conv_hatom] - sel2.positions[idx2]) - dist = np.linalg.norm(pos1[0][3*conv_hatom:3*conv_hatom+3] - pos2[0][3*idx2:3*idx2+3]) + # dist = np.linalg.norm(pos1[0][3*conv_hatom:3*conv_hatom+3] - pos2[0][3*idx2:3*idx2+3]) + dist = np.linalg.norm( + s1[conv_hatom] - s2[idx2] + ) if (dist <= hbondcutoff): donorPosition = s1[idx1] hydrogenPosition = np.array(s1[conv_hatom], dtype=np.float64) @@ -191,7 +178,10 @@ def loop_trajectory_grid(sel1c, sel2c, indices1, indices2, config, suppl, selfIn # if (distarray[conv_hatom, idx2] <= hbondcutoff): # dist = distarray[idx1, conv_hatom] # dist = np.linalg.norm(sel1.positions[idx1] - sel2.positions[conv_hatom]) - dist = np.linalg.norm(pos1[0][3*idx1:3*idx1+3] - pos2[0][3*conv_hatom:3*conv_hatom+3]) + # dist = np.linalg.norm(pos1[0][3*idx1:3*idx1+3] - pos2[0][3*conv_hatom:3*conv_hatom+3]) + dist = np.linalg.norm( + s1[idx1] - s2[conv_hatom] + ) if (dist <= hbondcutoff): donorPosition = s2[idx2] hydrogenPosition = np.array(s2[conv_hatom], dtype=np.float64) diff --git a/PyContact/cy_modules/__init__.py b/PyContact/cy_modules/__init__.py deleted file mode 100644 index e69de29..0000000 diff --git a/PyContact/cy_modules/cy_gridsearch.pyx b/PyContact/cy_modules/cy_gridsearch.pyx deleted file mode 100644 index 4c5decd..0000000 --- a/PyContact/cy_modules/cy_gridsearch.pyx +++ /dev/null @@ -1,36 +0,0 @@ -from cython.view cimport array as cvarray -from libcpp.vector cimport vector -import numpy as np - -cdef extern from "src/gridsearch.C": - double sasa_grid(const float *pos,int natoms, float pairdist, int allow_double_counting, int maxpairs, const float *radius,const int npts, double srad, int pointstyle, int restricted, const int* restrictedList, const float* spherepoints) - -cdef extern from "src/gridsearch.C": - int* find_within(const float *xyz, int *flgs, int *others, int num, float r) - -cdef extern from "src/gridsearch.C": - vector[vector[int]] find_contacts(const float *pos1, const float *pos2, int nAtoms1, int nAtoms2, double cutoff) - -def cy_sasa(npcoords, natoms, pairdist, allow_double_counting, maxsize, nprad, - surfacePoints, probeRadius, pointstyle, - restricted,restrictedList, npspherepoints): - cdef int [::1] cy_restrictedList = restrictedList - cdef float [::1] cy_radius = nprad - cdef float [::1] c_coords = npcoords[0] - cdef float [::1] c_spherepts = npspherepoints[0] - cdef float sasa = sasa_grid(&c_coords[0], natoms, pairdist, 0, -1, &cy_radius[0] ,surfacePoints, probeRadius, pointstyle, restricted, &cy_restrictedList[0], &c_spherepts[0]) - return sasa - -def cy_find_within(xyz, flgs, others, num, r): - cdef float [::1] cy_pos = xyz[0] - cdef int [::1] cy_flags = flgs - cdef int [::1] cy_others = others - cdef int[::1] result = find_within(&cy_pos[0],&cy_flags[0], &cy_others[0], num, r) - return np.asarray(result) - - -def cy_find_contacts(xyz1, natoms1, xyz2, natoms2, r): - cdef float [::1] cy_pos1 = xyz1[0] - cdef float [::1] cy_pos2 = xyz2[0] - res = find_contacts(&cy_pos1[0], &cy_pos2[0], natoms1, natoms2, r) - return res diff --git a/PyContact/cy_modules/src/ResizeArray.h b/PyContact/cy_modules/src/ResizeArray.h deleted file mode 100644 index 25e3da4..0000000 --- a/PyContact/cy_modules/src/ResizeArray.h +++ /dev/null @@ -1,133 +0,0 @@ -/*************************************************************************** - *cr - *cr (C) Copyright 1995-2011 The Board of Trustees of the - *cr University of Illinois - *cr All Rights Reserved - *cr - ***************************************************************************/ - -/*************************************************************************** - * RCS INFORMATION: - * - * $RCSfile: ResizeArray.h,v $ - * $Author: johns $ $Locker: $ $State: Exp $ - * $Revision: 1.45 $ $Date: 2010/12/16 04:08:38 $ - * - *************************************************************************** - * DESCRIPTION: - * Automatically-adjusting single-dim array template. - * - * LICENSE: - * UIUC Open Source License - * http://www.ks.uiuc.edu/Research/vmd/plugins/pluginlicense.html - * - ***************************************************************************/ -#ifndef RESIZEARRAY_TEMPLATE_H -#define RESIZEARRAY_TEMPLATE_H - -#include - -/// A template class which implements a dynamically-growing, automatically -/// resizing array of data of a given type. Elements in the array may be -/// accessed via the [] operator. When new data is added to the end of an -/// array, the size of the array is automatically increased if necessary. -/// -/// XXX Do not parametrize this class with a datatype which cannot be -/// shallow-copied! This class uses memcpy to resize, and therefore -/// classes which contain dynamically-allocated memory blocks will -/// crash and burn if the ResizeArray ever gets resized. -template -class ResizeArray { -private: - T *allocate(size_t n) { return new T[n]; } - void deallocate(T *p) { delete [] p; } - - T *data; ///< list of items, and pointer to current item. - int sz; ///< max number of items that can be stored in the array - int currSize; ///< largest index used + 1 - -public: - /// Constructor - /// The first argument is the initial internal size of the array, i.e. the - /// initial number of elements for which to allocate memory (although the - /// initial external size of the array will be zero). - ResizeArray(int s = 3) { - currSize = 0; - sz = (s > 0 ? s : 10); - data = allocate(sz); - } - - ~ResizeArray() { - deallocate(data); - } - - int num(void) const { return currSize; } ///< current size of array - T& operator[](int N) { return data[N]; } ///< unchecked accessor, for speed - T const& operator[](int N) const { return data[N]; } ///< a const version of above - - /// add a new element to the end of the array. Return index of new item. - void append(const T& val) { - if (currSize == sz) { // extend size of array if necessary - int newsize = (int)((float)sz * 1.3f); - - // guarantee minimum required size increase, since the scaled value - // may truncate back to the original size value when the initial number - // of elements is very small. - if (newsize == sz) - newsize++; - - // shallow copy the data to a newly allocated block since we can't - // do something better like realloc() - T *newdata = allocate(newsize); - memcpy(newdata, data, currSize * sizeof(T)); - deallocate(data); - - // save new values - data = newdata; - sz = newsize; - } - data[currSize++] = val; - } - - /// remove an item from the array, shifting remaining items down by 1 - void remove(int n) { - if (n < 0 || n >= currSize) return; - for (int i=n; i -#include -#include -#include -#include "ResizeArray.h" -#include - -#define FALSE 0 -#define TRUE 1 -void * find_within_routine( void *v ); - -struct AtomEntry { - float x, y, z; - int index; - AtomEntry() {} - AtomEntry(const float &_x, const float &_y, const float &_z, const int &_i) - : x(_x), y(_y), z(_z), index(_i) {} -}; - -using namespace std; -extern "C" { -struct GridSearchPair { - int ind1, ind2; - GridSearchPair *next; -}; - -GridSearchPair *vmd_gridsearch3(const float *posA, int natomsA, const int *A, - const float *posB, int natomsB, const int *B, - float pairdist, int allow_double_counting, int maxpairs); - -#define VMD_RAND_MAX 2147483647L -long vmd_random(void) { -#ifdef _MSC_VER - return rand(); -#else - return random(); -#endif -} - -void vmd_srandom(unsigned int seed) { -#ifdef _MSC_VER - srand(seed); -#else - srandom(seed); -#endif -} - -float distance2(const float *a, const float *b) { - float delta = a[0] - b[0]; - float r2 = delta*delta; - delta = a[1] - b[1]; - r2 += delta*delta; - delta = a[2] - b[2]; - return r2 + delta*delta; -} - -void vec_sub(float *a, const float *b, const float *c) { - a[0]=b[0]-c[0]; - a[1]=b[1]-c[1]; - a[2]=b[2]-c[2]; -} - -void find_minmax(const float *pos, int n, const int *on, - float *min, float *max, int *oncount) { - float x1, x2, y1, y2, z1, z2; - int i, numon; - - // return immediately if there are no atoms, or no atoms are on. - if (n < 1) return; - - // init on count, i = 0 because all atoms are on - numon = 1; - i = 0; - // find first on atom EDIT: not needed - // for (i=0; i x2) x2 = pos[0]; - if (pos[1] < y1) y1 = pos[1]; - else if (pos[1] > y2) y2 = pos[1]; - if (pos[2] < z1) z1 = pos[2]; - else if (pos[2] > z2) z2 = pos[2]; - numon++; - // } - pos += 3; - } - min[0] = x1; min[1] = y1; min[2] = z1; - max[0] = x2; max[1] = y2; max[2] = z2; - - if (oncount != NULL) - *oncount = numon; -} - - -int find_minmax_selected(int n, const int *flgs, const float *pos, - float &_xmin, float &_ymin, float &_zmin, - float &_xmax, float &_ymax, float &_zmax) { - int i; - float xmin, xmax, ymin, ymax, zmin, zmax; - for (i=0; ixi) xmin=xi; - if (ymin>yi) ymin=yi; - if (zmin>zi) zmin=zi; - if (xmaxnext = (GridSearchPair *) malloc(sizeof(GridSearchPair)); - link->next->ind1 = i; - link->next->ind2 = j; - link->next->next = NULL; -} - -int make_neighborlist(int **nbrlist, int xb, int yb, int zb) { - int xi, yi, zi, aindex, xytotb; - - if (nbrlist == NULL) - return -1; - - xytotb = xb * yb; - aindex = 0; - for (zi=0; zi 0) nbrs[n++] = aindex - xb + 1; - if (xi > 0 && zi < (zb-1)) nbrs[n++] = aindex + xytotb - 1; - if (yi > 0 && zi < (zb-1)) nbrs[n++] = aindex + xytotb - xb; - if (xi < (xb-1) && yi < (yb-1) && zi < (zb-1)) - nbrs[n++] = aindex + xytotb + xb + 1; - if (xi > 0 && yi < (yb-1) && zi < (zb-1)) - nbrs[n++] = aindex + xytotb + xb - 1; - if (xi < (xb-1) && yi > 0 && zi < (zb-1)) - nbrs[n++] = aindex + xytotb - xb + 1; - if (xi > 0 && yi > 0 && zi < (zb-1)) - nbrs[n++] = aindex + xytotb - xb - 1; - nbrs[n++] = -1; // mark end of list - - int *lst = (int *) malloc(n*sizeof(int)); - if (lst == NULL) - return -1; // return on failed allocations - memcpy(lst, nbrs, n*sizeof(int)); - nbrlist[aindex] = lst; - aindex++; - } - } - } - - return 0; -} - -GridSearchPair *vmd_gridsearch1(const float *pos,int natoms, const int *on, - float pairdist, int allow_double_counting, int maxpairs) { - float min[3]={0,0,0}, max[3]={0,0,0}; - float sqdist; - int i, j, xb, yb, zb, xytotb, totb, aindex; - int **boxatom, *numinbox, *maxinbox, **nbrlist; - int numon = 0; - float sidelen[3], volume; - int paircount = 0; - int maxpairsreached = 0; - sqdist = pairdist * pairdist; - // printf("nc: %d \n",natoms); - // find bounding box for selected atoms, and number of atoms in selection. - find_minmax(pos, natoms, on, min, max, &numon); - // printf("minmaxfound: %d,%f, min %f max %f\n",numon,sqdist,min[0],max[0]); - // do sanity checks and complain if we've got bogus atom coordinates, - // we shouldn't ever have density higher than 0.1 atom/A^3, but we'll - // be generous and allow much higher densities. - if (maxpairs != -1) { - vec_sub(sidelen, max, min); - // include estimate for atom radius (1 Angstrom) in volume determination - volume = fabsf((sidelen[0] + 2.0f) * (sidelen[1] + 2.0f) * (sidelen[2] + 2.0f)); - if ((numon / volume) > 1.0) { - // msgWarn << "vmd_gridsearch1: insane atom density" << sendmsg; - } - } - - // I don't want the grid to get too large, otherwise I could run out - // of memory. Octrees would be cool, but I'll just limit the grid size - // and let the performance degrade a little for pathological systems. - // Note that sqdist is what gets used for the actual distance checks; - // from here on out pairdist is only used to set the grid size, so we - // can set it to anything larger than the original pairdist. - const int MAXBOXES = 4000000; - totb = MAXBOXES + 1; - - float newpairdist = pairdist; - float xrange = max[0]-min[0]; - float yrange = max[1]-min[1]; - float zrange = max[2]-min[2]; - do { - // printf("pairdist: %f\n", pairdist); - pairdist = newpairdist; - const float invpairdist = 1.0f / pairdist; - xb = ((int)(xrange*invpairdist))+1; - yb = ((int)(yrange*invpairdist))+1; - zb = ((int)(zrange*invpairdist))+1; - xytotb = yb * xb; - totb = xytotb * zb; - newpairdist = pairdist * 1.26f; // cbrt(2) is about 1.26 - } while (totb > MAXBOXES || totb < 1); // check for integer wraparound too - // printf("boxbuild\n"); - // printf("totb %d\n", totb); - // 2. Sort each atom into appropriate bins - boxatom = (int **) calloc(1, totb*sizeof(int *)); - numinbox = (int *) calloc(1, totb*sizeof(int)); - maxinbox = (int *) calloc(1, totb*sizeof(int)); - if (boxatom == NULL || numinbox == NULL || maxinbox == NULL) { - if (boxatom != NULL) - free(boxatom); - if (numinbox != NULL) - free(numinbox); - if (maxinbox != NULL) - free(maxinbox); - // msgErr << "Gridsearch memory allocation failed, bailing out" << sendmsg; - return NULL; // ran out of memory, bail out! - } - - const float invpairdist = 1.0f / pairdist; - for (i=0; i= xb) axb = xb-1; - if (ayb >= yb) ayb = yb-1; - if (azb >= zb) azb = zb-1; - - aindex = azb * xytotb + ayb * xb + axb; - - // grow box if necessary - if ((num = numinbox[aindex]) == maxinbox[aindex]) { - boxatom[aindex] = (int *) realloc(boxatom[aindex], (num+4)*sizeof(int)); - maxinbox[aindex] += 4; - } - - // store atom index in box - boxatom[aindex][num] = i; - numinbox[aindex]++; - // } - } - free(maxinbox); - - nbrlist = (int **) calloc(1, totb*sizeof(int *)); - if (make_neighborlist(nbrlist, xb, yb, zb)) { - if (boxatom != NULL) { - for (i=0; inext = NULL; - cur = head; - // printf("pairlist\n"); - // wkfmsgtimer *msgt = wkf_msg_timer_create(5); - for (aindex = 0; (aindex < totb) && (!maxpairsreached); aindex++) { - // printf("%d\n", aindex); - int *tmpbox, *tmpnbr, *nbr; - tmpbox = boxatom[aindex]; - tmpnbr = nbrlist[aindex]; - - // if (wkf_msg_timer_timeout(msgt)) { - // char tmpbuf[128]; - // sprintf(tmpbuf, "%6.2f", (100.0f * aindex) / (float) totb); - // msgInfo << "vmd_gridsearch1: " << tmpbuf << "% complete" << sendmsg; - // } - - for (nbr = tmpnbr; (*nbr != -1) && (!maxpairsreached); nbr++) { - int *nbrbox = boxatom[*nbr]; - for (i=0; (i sqdist) - continue; - - if (maxpairs > 0) { - if (paircount >= maxpairs) { - maxpairsreached = 1; - continue; - } - } - - add_link(cur, ind1, ind2); - paircount++; - - // XXX double-counting still ignores atoms with same coords... - if (allow_double_counting) { - add_link(cur, ind2, ind1); - paircount++; - } - cur = cur->next; - cur->next = NULL; - // } - } - } - } - } - - for (i=0; inext; - free(head); - - // if (maxpairsreached) { - // printf("maxpairs reached \n"); - // } - - return cur; -} - -std::vector> find_contacts(const float *pos1, const float *pos2, -int nAtoms1, int nAtoms2, double cutoff) { - std::vector> pairlist1(nAtoms1+nAtoms2); - GridSearchPair *p, *tmp; - int allowDouble = 1; - int A[nAtoms1]; - fill_n(A, nAtoms1, 1); - int B[nAtoms2]; - fill_n(B, nAtoms2, 1); - GridSearchPair* pairs = vmd_gridsearch3(pos1, nAtoms1, A, pos2, nAtoms2, B, cutoff, allowDouble, -1); - for (p = pairs; p != NULL; p = tmp) { - int ind1=p->ind1; - int ind2=p->ind2; - pairlist1[ind1].push_back(ind2); - // pairlist1[nAtoms1+ind2].push_back(ind1); - tmp = p->next; - free(p); - } - return pairlist1; -} - - -static double sasa_grid(const float *pos,int natoms, float pairdist, int allow_double_counting, int maxpairs, const float *radius,const int npts, double srad, int pointstyle, int restricted, const int* restrictedList, const float* spherepoints) { - int on[natoms]; - fill_n(on,natoms,1); - // printf("natoms %d\n", natoms); - // printf("pairdist %f\n", pairdist); - // printf("maxpairs %d\n", maxpairs); - GridSearchPair* pairs = vmd_gridsearch1(pos,natoms, on, pairdist, allow_double_counting,maxpairs); - // vector > v(natoms,vector()); - // printf("size: %d\n", v.size()); - ResizeArray *pairlist = new ResizeArray[natoms]; - GridSearchPair *p, *tmp; - for (p = pairs; p != NULL; p = tmp) { - int ind1=p->ind1; - int ind2=p->ind2; - // v[ind1].push_back(ind2); - // v[ind2].push_back(ind1); - pairlist[ind1].append(ind2); - pairlist[ind2].append(ind1); - tmp = p->next; - free(p); - } - - float *spherepts = new float[3*npts]; - - if (pointstyle) { - static const float RAND_MAX_INV = 1.0f/VMD_RAND_MAX; - vmd_srandom(38572111); - - // All the spheres use the same random points. - - for (int i=0; i &nbrs = pairlist[i]; - // printf("neighbors: %d\n", nbrs.num()); - for (int j=0; j > v(natoms,vector()); -// // printf("size: %d\n", v.size()); -// // ResizeArray *pairlist = new ResizeArray[natoms]; -// GridSearchPair *p, *tmp; -// for (p = pairs; p != NULL; p = tmp) { -// int ind1=p->ind1; -// int ind2=p->ind2; -// v[ind1].push_back(ind2); -// v[ind2].push_back(ind1); -// // printf("%f\n", v[ind2]); -// // pairlist[ind1].append(ind2); -// // pairlist[ind2].append(ind1); -// // printf("%d\n", ind1); -// tmp = p->next; -// free(p); -// } -// PyGILState_STATE gstate = PyGILState_Ensure(); -// PyObject* result = PyList_New(0); -// vector< vector >::iterator row; -// vector::iterator col; -// for (row = v.begin(); row != v.end(); row++) { -// // printf("row %d\n", *row); -// PyObject* tempo = PyList_New(0); -// for (col = row->begin(); col != row->end(); col++) { -// // printf("%d \n", *col); -// PyList_Append(tempo, PyInt_FromLong(*col)); -// } -// PyList_Append(result,tempo); -// tempo = NULL; -// } -// PyGILState_Release(gstate); -// return result; -// } - -} - -typedef ResizeArray atomlist; -struct FindWithinData { - int nthreads; - int tid; - int totb; - int xytotb; - int xb; - int yb; - int zb; - float r2; - const float * xyz; - const atomlist * flgatoms; - const atomlist * otheratoms; - int * flgs; - FindWithinData() : flgatoms(0), otheratoms(0), flgs(0) {} - ~FindWithinData() { if (flgs) free(flgs); } -}; - -#define MAXGRIDDIM 31 -static int* find_within(const float *xyz, int *flgs, int *others, int num, float r) { - int i; - float xmin, xmax, ymin, ymax, zmin, zmax; - float oxmin, oymin, ozmin, oxmax, oymax, ozmax; - float xwidth, ywidth, zwidth; - const float *pos; - - int *result = new int[num]; - fill_n(result,num,0); - - // for (size_t i = 0; i < num; i++) { - // pos=xyz+3*i; - // printf("%f %f %f\n", pos[0],pos[1],pos[2]); - // } - - // find min/max bounds of atom coordinates in flgs - if (!find_minmax_selected(num, flgs, xyz, xmin, ymin, zmin, xmax, ymax, zmax) || - !find_minmax_selected(num, others, xyz, oxmin, oymin, ozmin, oxmax, oymax, ozmax)) { - memset(flgs, 0, num*sizeof(int)); - return result; - } - - // Find the set of atoms with the smallest extent; here we use the sum - // of the box dimensions though other choices might be better. - float size = xmax+ymax+zmax - (xmin+ymin+zmin); - float osize = oxmax+oymax+ozmax - (oxmin+oymin+ozmin); - if (osize < size) { - xmin=oxmin; - ymin=oymin; - zmin=ozmin; - xmax=oxmax; - ymax=oymax; - zmax=ozmax; - } - - // Generate a grid of mesh size r based on the computed size of the molecule. - // We limit the size of the grid cell dimensions so that we don't get too - // many grid cells. - xwidth = (xmax-xmin)/(MAXGRIDDIM-1); - if (xwidth < r) xwidth = r; - ywidth = (ymax-ymin)/(MAXGRIDDIM-1); - if (ywidth < r) ywidth = r; - zwidth = (zmax-zmin)/(MAXGRIDDIM-1); - if (zwidth < r) zwidth = r; - - // Adjust the bounds so that we include atoms that are in the outermost - // grid cells. - xmin -= xwidth; - xmax += xwidth; - ymin -= ywidth; - ymax += ywidth; - zmin -= zwidth; - zmax += zwidth; - - // The number of grid cells needed in each dimension is - // (int)((xmax-xmin)/xwidth) + 1 - const int xb = (int)((xmax-xmin)/xwidth) + 1; - const int yb = (int)((ymax-ymin)/ywidth) + 1; - const int zb = (int)((zmax-zmin)/zwidth) + 1; - - int xytotb = yb * xb; - int totb = xytotb * zb; - - atomlist* flgatoms = new atomlist[totb]; - atomlist* otheratoms = new atomlist[totb]; - - float ixwidth = 1.0f/xwidth; - float iywidth = 1.0f/ywidth; - float izwidth = 1.0f/zwidth; - for (i=0; ixmax || yiymax || zizmax) { - continue; - } - AtomEntry entry(xi,yi,zi,i); - int axb = (int)((xi - xmin)*ixwidth); - int ayb = (int)((yi - ymin)*iywidth); - int azb = (int)((zi - zmin)*izwidth); - - // Due to floating point error in the calcuation of bin widths, we - // have to range clamp the computed box indices. - if (axb==xb) axb=xb-1; - if (ayb==yb) ayb=yb-1; - if (azb==zb) azb=zb-1; - - int aindex = azb*xytotb + ayb*xb + axb; - // TODO maybe change so that others does not contain the atoms of flags - if (others[i]) otheratoms[aindex].append(entry); - if ( flgs[i]) flgatoms[aindex].append(entry); - } - - memset(flgs, 0, num*sizeof(int)); - const float r2 = (float) (r*r); - - // set up workspace for multithreaded calculation - int nthreads; -#ifdef VMDTHREADS - nthreads = wkf_thread_numprocessors(); - wkf_thread_t * threads = (wkf_thread_t *)calloc(nthreads, sizeof(wkf_thread_t)); -#else - nthreads = 1; -#endif - FindWithinData *data = new FindWithinData[nthreads]; - for (i=0; inthreads; - const int tid = data->tid; - const int totb = data->totb; - const int xytotb = data->xytotb; - const int xb = data->xb; - const int yb = data->yb; - const int zb = data->zb; - const float r2 = data->r2; - const atomlist * flgatoms = data->flgatoms; - const atomlist * otheratoms = data->otheratoms; - int * flgs = data->flgs; - - // Loop over boxes, checking for flg atoms and other atoms within one - // box of each other. When one is found, mark the flag. - for (int aindex = tid; aindex 0) nbrs[n++] = aindex - xb + 1; - if (xi > 0 && zi < (zb-1)) nbrs[n++] = aindex + xytotb - 1; - if (yi > 0 && zi < (zb-1)) nbrs[n++] = aindex + xytotb - xb; - if (xi < (xb-1) && yi < (yb-1) && zi < (zb-1)) - nbrs[n++] = aindex + xytotb + xb + 1; - if (xi > 0 && yi < (yb-1) && zi < (zb-1)) - nbrs[n++] = aindex + xytotb + xb - 1; - if (xi < (xb-1) && yi > 0 && zi < (zb-1)) - nbrs[n++] = aindex + xytotb - xb + 1; - if (xi > 0 && yi > 0 && zi < (zb-1)) - nbrs[n++] = aindex + xytotb - xb - 1; - - const atomlist& boxflg = flgatoms[aindex]; - // Compare the atoms in boxflg to those in nbrother - int i; - for (i=0; i max[i]) max[i] = maxB[i]; - } - - // do sanity checks and complain if we've got bogus atom coordinates, - // we shouldn't ever have density higher than 0.1 atom/A^3, but we'll - // be generous and allow much higher densities. - if (maxpairs != -1) { - vec_sub(sidelen, max, min); - // include estimate for atom radius (1 Angstrom) in volume determination - volume = fabsf((sidelen[0] + 2.0f) * (sidelen[1] + 2.0f) * (sidelen[2] + 2.0f)); - if (((numonA + numonB) / volume) > 1.0) { - // msgWarn << "vmd_gridsearch3: insane atom density" << sendmsg; - } - } - - // I don't want the grid to get too large, otherwise I could run out - // of memory. Octrees would be cool, but I'll just limit the grid size - // and let the performance degrade a little for pathological systems. - // Note that sqdist is what gets used for the actual distance checks; - // from here on out pairdist is only used to set the grid size, so we - // can set it to anything larger than the original pairdist. - const int MAXBOXES = 4000000; - totb = MAXBOXES + 1; - - float newpairdist = pairdist; - float xrange = max[0]-min[0]; - float yrange = max[1]-min[1]; - float zrange = max[2]-min[2]; - do { - pairdist = newpairdist; - const float invpairdist = 1.0f / pairdist; - xb = ((int)(xrange*invpairdist))+1; - yb = ((int)(yrange*invpairdist))+1; - zb = ((int)(zrange*invpairdist))+1; - xytotb = yb * xb; - totb = xytotb * zb; - newpairdist = pairdist * 1.26f; // cbrt(2) is about 1.26 - } while (totb > MAXBOXES || totb < 1); // check for integer wraparound too - - // 2. Sort each atom into appropriate bins - boxatomA = (int **) calloc(1, totb*sizeof(int *)); - numinboxA = (int *) calloc(1, totb*sizeof(int)); - maxinboxA = (int *) calloc(1, totb*sizeof(int)); - if (boxatomA == NULL || numinboxA == NULL || maxinboxA == NULL) { - if (boxatomA != NULL) - free(boxatomA); - if (numinboxA != NULL) - free(numinboxA); - if (maxinboxA != NULL) - free(maxinboxA); - // msgErr << "Gridsearch memory allocation failed, bailing out" << sendmsg; - return NULL; // ran out of memory, bail out! - } - - const float invpairdist = 1.0f / pairdist; - for (i=0; i= xb) axb = xb-1; - if (ayb >= yb) ayb = yb-1; - if (azb >= zb) azb = zb-1; - - aindex = azb * xytotb + ayb * xb + axb; - - // grow box if necessary - if ((num = numinboxA[aindex]) == maxinboxA[aindex]) { - boxatomA[aindex] = (int *) realloc(boxatomA[aindex], (num+4)*sizeof(int)); - maxinboxA[aindex] += 4; - } - - // store atom index in box - boxatomA[aindex][num] = i; - numinboxA[aindex]++; - } - } - free(maxinboxA); - - boxatomB = (int **) calloc(1, totb*sizeof(int *)); - numinboxB = (int *) calloc(1, totb*sizeof(int)); - maxinboxB = (int *) calloc(1, totb*sizeof(int)); - if (boxatomB == NULL || numinboxB == NULL || maxinboxB == NULL) { - if (boxatomB != NULL) - free(boxatomB); - if (numinboxB != NULL) - free(numinboxB); - if (maxinboxB != NULL) - free(maxinboxB); - // msgErr << "Gridsearch memory allocation failed, bailing out" << sendmsg; - return NULL; // ran out of memory, bail out! - } - - for (i=0; i= xb) axb = xb-1; - if (ayb >= yb) ayb = yb-1; - if (azb >= zb) azb = zb-1; - - aindex = azb * xytotb + ayb * xb + axb; - - // grow box if necessary - if ((num = numinboxB[aindex]) == maxinboxB[aindex]) { - boxatomB[aindex] = (int *) realloc(boxatomB[aindex], (num+4)*sizeof(int)); - maxinboxB[aindex] += 4; - } - - // store atom index in box - boxatomB[aindex][num] = i; - numinboxB[aindex]++; - } - } - free(maxinboxB); - - - // 3. Build pairlists of atoms less than sqrtdist apart - nbrlist = (int **) calloc(1, totb*sizeof(int *)); - if (make_neighborlist_sym(nbrlist, xb, yb, zb)) { - if (boxatomA != NULL) { - for (i=0; inext = NULL; - cur = head; - - for (aindex = 0; aindex < totb; aindex++) { - int *tmpbox, *tmpnbr, *nbr; - tmpbox = boxatomA[aindex]; - tmpnbr = nbrlist[aindex]; - for (nbr = tmpnbr; (*nbr != -1) && (!maxpairsreached); nbr++) { - int *nbrboxB = boxatomB[*nbr]; - for (i=0; (i sqdist) continue; - - if (maxpairs > 0) { - if (paircount >= maxpairs) { - maxpairsreached = 1; - continue; - } - } - - add_link(cur, ind1, ind2); - paircount++; - cur = cur->next; - cur->next = NULL; - } - } - } - } - - for (i=0; inext; - free(head); - - // if (maxpairsreached) - // msgErr << "gridsearch3: exceeded pairlist sanity check, aborted" << sendmsg; - - return cur; -} diff --git a/README.md b/README.md index 9544ee8..b1d80b5 100644 --- a/README.md +++ b/README.md @@ -4,18 +4,15 @@ ## Installation -PyContact requires **at least Python 3.6** installed on your system. +PyContact requires **at least Python 3.7** installed on your system. A recent version can be installed from `pip` via: ```Python -pip install cython -pip install pycontact PyQt5 +pip install pycontact ``` Alternatively, clone the repository and run: ``` -pip install cython PyQt5 -python setup.py build_ext -i -python setup.py install +pip install . ``` ## Citation diff --git a/setup.py b/setup.py index 48d3492..8e1f2a0 100644 --- a/setup.py +++ b/setup.py @@ -2,16 +2,7 @@ by Maximilian Scheurer, Peter Rodenkirch """ from setuptools import setup, find_packages -from setuptools.extension import Extension -from Cython.Distutils import build_ext -from Cython.Build import cythonize - -extensions = [Extension("PyContact.cy_modules.cy_gridsearch", - ["PyContact/cy_modules/cy_gridsearch.pyx"], - language="c++", - include_dirs=[".", "PyContact/cy_modules/src"], - extra_compile_args=["-std=c++0x"]), ] setup( name='pycontact', version='1.0.5', @@ -26,28 +17,24 @@ 'Intended Audience :: Science/Research', 'Topic :: Scientific/Engineering', 'License :: OSI Approved :: GNU General Public License v3 (GPLv3)', - 'Programming Language :: Python :: 3.6', + 'Programming Language :: Python :: 3.7', ], keywords='computational biophysics simulation biology bioinformatics visualization protein biomolecules dna', package_dir={'PyContact': 'PyContact'}, packages=find_packages(), - python_requires=">=3.6", + python_requires=">=3.7", setup_requires=['cython'], install_requires=['numpy >= 1.16', 'matplotlib', - 'mdanalysis >= 0.20.0', - 'cython', + 'mdanalysis >= 2.0.0', 'seaborn', 'scipy', 'PyQt5'], - cmdclass={'build_ext': build_ext}, - ext_modules=cythonize(extensions), package_data={'PyContact': ['exampleData/defaultsession', 'exampleData/*.psf', 'exampleData/*.pdb', 'exampleData/*.dcd', 'exampleData/*.tpr', 'exampleData/*.xtc', - 'cy_modules/*.pyx', - 'cy_modules/src/*']}, + ]}, entry_points={ 'console_scripts': [ 'pycontact=PyContact.pycontact:main', diff --git a/testing/BestPractice.txt b/testing/BestPractice.txt deleted file mode 100644 index 5f4863d..0000000 --- a/testing/BestPractice.txt +++ /dev/null @@ -1,5 +0,0 @@ -Put all imports at the top of the page with three sections, each separated by a blank line, in this order: - -1) System imports -2) Third-party imports -3) Local source tree imports diff --git a/testing/cython/ResizeArray.h b/testing/cython/ResizeArray.h deleted file mode 100644 index 25e3da4..0000000 --- a/testing/cython/ResizeArray.h +++ /dev/null @@ -1,133 +0,0 @@ -/*************************************************************************** - *cr - *cr (C) Copyright 1995-2011 The Board of Trustees of the - *cr University of Illinois - *cr All Rights Reserved - *cr - ***************************************************************************/ - -/*************************************************************************** - * RCS INFORMATION: - * - * $RCSfile: ResizeArray.h,v $ - * $Author: johns $ $Locker: $ $State: Exp $ - * $Revision: 1.45 $ $Date: 2010/12/16 04:08:38 $ - * - *************************************************************************** - * DESCRIPTION: - * Automatically-adjusting single-dim array template. - * - * LICENSE: - * UIUC Open Source License - * http://www.ks.uiuc.edu/Research/vmd/plugins/pluginlicense.html - * - ***************************************************************************/ -#ifndef RESIZEARRAY_TEMPLATE_H -#define RESIZEARRAY_TEMPLATE_H - -#include - -/// A template class which implements a dynamically-growing, automatically -/// resizing array of data of a given type. Elements in the array may be -/// accessed via the [] operator. When new data is added to the end of an -/// array, the size of the array is automatically increased if necessary. -/// -/// XXX Do not parametrize this class with a datatype which cannot be -/// shallow-copied! This class uses memcpy to resize, and therefore -/// classes which contain dynamically-allocated memory blocks will -/// crash and burn if the ResizeArray ever gets resized. -template -class ResizeArray { -private: - T *allocate(size_t n) { return new T[n]; } - void deallocate(T *p) { delete [] p; } - - T *data; ///< list of items, and pointer to current item. - int sz; ///< max number of items that can be stored in the array - int currSize; ///< largest index used + 1 - -public: - /// Constructor - /// The first argument is the initial internal size of the array, i.e. the - /// initial number of elements for which to allocate memory (although the - /// initial external size of the array will be zero). - ResizeArray(int s = 3) { - currSize = 0; - sz = (s > 0 ? s : 10); - data = allocate(sz); - } - - ~ResizeArray() { - deallocate(data); - } - - int num(void) const { return currSize; } ///< current size of array - T& operator[](int N) { return data[N]; } ///< unchecked accessor, for speed - T const& operator[](int N) const { return data[N]; } ///< a const version of above - - /// add a new element to the end of the array. Return index of new item. - void append(const T& val) { - if (currSize == sz) { // extend size of array if necessary - int newsize = (int)((float)sz * 1.3f); - - // guarantee minimum required size increase, since the scaled value - // may truncate back to the original size value when the initial number - // of elements is very small. - if (newsize == sz) - newsize++; - - // shallow copy the data to a newly allocated block since we can't - // do something better like realloc() - T *newdata = allocate(newsize); - memcpy(newdata, data, currSize * sizeof(T)); - deallocate(data); - - // save new values - data = newdata; - sz = newsize; - } - data[currSize++] = val; - } - - /// remove an item from the array, shifting remaining items down by 1 - void remove(int n) { - if (n < 0 || n >= currSize) return; - for (int i=n; i -#include -#include -#include -#include "ResizeArray.h" -#include -// #include "utilities.h" - -#define FALSE 0 -#define TRUE 1 -void * find_within_routine( void *v ); - -struct AtomEntry { - float x, y, z; - int index; - AtomEntry() {} - AtomEntry(const float &_x, const float &_y, const float &_z, const int &_i) - : x(_x), y(_y), z(_z), index(_i) {} -}; - -using namespace std; -extern "C" { -struct GridSearchPair { - int ind1, ind2; - GridSearchPair *next; -}; - -#define VMD_RAND_MAX 2147483647L -long vmd_random(void) { -#ifdef _MSC_VER - return rand(); -#else - return random(); -#endif -} - -void vmd_srandom(unsigned int seed) { -#ifdef _MSC_VER - srand(seed); -#else - srandom(seed); -#endif -} - -float distance2(const float *a, const float *b) { - float delta = a[0] - b[0]; - float r2 = delta*delta; - delta = a[1] - b[1]; - r2 += delta*delta; - delta = a[2] - b[2]; - return r2 + delta*delta; -} - -void vec_sub(float *a, const float *b, const float *c) { - a[0]=b[0]-c[0]; - a[1]=b[1]-c[1]; - a[2]=b[2]-c[2]; -} - -void find_minmax(const float *pos, int n, const int *on, - float *min, float *max, int *oncount) { - float x1, x2, y1, y2, z1, z2; - int i, numon; - - // return immediately if there are no atoms, or no atoms are on. - if (n < 1) return; - - // init on count, i = 0 because all atoms are on - numon = 1; - i = 0; - // find first on atom EDIT: not needed - // for (i=0; i x2) x2 = pos[0]; - if (pos[1] < y1) y1 = pos[1]; - else if (pos[1] > y2) y2 = pos[1]; - if (pos[2] < z1) z1 = pos[2]; - else if (pos[2] > z2) z2 = pos[2]; - numon++; - // } - pos += 3; - } - min[0] = x1; min[1] = y1; min[2] = z1; - max[0] = x2; max[1] = y2; max[2] = z2; - - if (oncount != NULL) - *oncount = numon; -} - - -int find_minmax_selected(int n, const int *flgs, const float *pos, - float &_xmin, float &_ymin, float &_zmin, - float &_xmax, float &_ymax, float &_zmax) { - int i; - float xmin, xmax, ymin, ymax, zmin, zmax; - for (i=0; ixi) xmin=xi; - if (ymin>yi) ymin=yi; - if (zmin>zi) zmin=zi; - if (xmaxnext = (GridSearchPair *) malloc(sizeof(GridSearchPair)); - link->next->ind1 = i; - link->next->ind2 = j; - link->next->next = NULL; -} - -int make_neighborlist(int **nbrlist, int xb, int yb, int zb) { - int xi, yi, zi, aindex, xytotb; - - if (nbrlist == NULL) - return -1; - - xytotb = xb * yb; - aindex = 0; - for (zi=0; zi 0) nbrs[n++] = aindex - xb + 1; - if (xi > 0 && zi < (zb-1)) nbrs[n++] = aindex + xytotb - 1; - if (yi > 0 && zi < (zb-1)) nbrs[n++] = aindex + xytotb - xb; - if (xi < (xb-1) && yi < (yb-1) && zi < (zb-1)) - nbrs[n++] = aindex + xytotb + xb + 1; - if (xi > 0 && yi < (yb-1) && zi < (zb-1)) - nbrs[n++] = aindex + xytotb + xb - 1; - if (xi < (xb-1) && yi > 0 && zi < (zb-1)) - nbrs[n++] = aindex + xytotb - xb + 1; - if (xi > 0 && yi > 0 && zi < (zb-1)) - nbrs[n++] = aindex + xytotb - xb - 1; - nbrs[n++] = -1; // mark end of list - - int *lst = (int *) malloc(n*sizeof(int)); - if (lst == NULL) - return -1; // return on failed allocations - memcpy(lst, nbrs, n*sizeof(int)); - nbrlist[aindex] = lst; - aindex++; - } - } - } - - return 0; -} - -GridSearchPair *vmd_gridsearch1(const float *pos,int natoms, const int *on, - float pairdist, int allow_double_counting, int maxpairs) { - float min[3]={0,0,0}, max[3]={0,0,0}; - float sqdist; - int i, j, xb, yb, zb, xytotb, totb, aindex; - int **boxatom, *numinbox, *maxinbox, **nbrlist; - int numon = 0; - float sidelen[3], volume; - int paircount = 0; - int maxpairsreached = 0; - sqdist = pairdist * pairdist; - printf("nc: %d \n",natoms); - // find bounding box for selected atoms, and number of atoms in selection. - find_minmax(pos, natoms, on, min, max, &numon); - printf("minmaxfound: %d,%f, min %f max %f\n",numon,sqdist,min[0],max[0]); - // do sanity checks and complain if we've got bogus atom coordinates, - // we shouldn't ever have density higher than 0.1 atom/A^3, but we'll - // be generous and allow much higher densities. - if (maxpairs != -1) { - vec_sub(sidelen, max, min); - // include estimate for atom radius (1 Angstrom) in volume determination - volume = fabsf((sidelen[0] + 2.0f) * (sidelen[1] + 2.0f) * (sidelen[2] + 2.0f)); - if ((numon / volume) > 1.0) { - // msgWarn << "vmd_gridsearch1: insane atom density" << sendmsg; - } - } - - // I don't want the grid to get too large, otherwise I could run out - // of memory. Octrees would be cool, but I'll just limit the grid size - // and let the performance degrade a little for pathological systems. - // Note that sqdist is what gets used for the actual distance checks; - // from here on out pairdist is only used to set the grid size, so we - // can set it to anything larger than the original pairdist. - const int MAXBOXES = 4000000; - totb = MAXBOXES + 1; - - float newpairdist = pairdist; - float xrange = max[0]-min[0]; - float yrange = max[1]-min[1]; - float zrange = max[2]-min[2]; - do { - // printf("pairdist: %f\n", pairdist); - pairdist = newpairdist; - const float invpairdist = 1.0f / pairdist; - xb = ((int)(xrange*invpairdist))+1; - yb = ((int)(yrange*invpairdist))+1; - zb = ((int)(zrange*invpairdist))+1; - xytotb = yb * xb; - totb = xytotb * zb; - newpairdist = pairdist * 1.26f; // cbrt(2) is about 1.26 - } while (totb > MAXBOXES || totb < 1); // check for integer wraparound too - printf("boxbuild\n"); - printf("totb %d\n", totb); - // 2. Sort each atom into appropriate bins - boxatom = (int **) calloc(1, totb*sizeof(int *)); - numinbox = (int *) calloc(1, totb*sizeof(int)); - maxinbox = (int *) calloc(1, totb*sizeof(int)); - if (boxatom == NULL || numinbox == NULL || maxinbox == NULL) { - if (boxatom != NULL) - free(boxatom); - if (numinbox != NULL) - free(numinbox); - if (maxinbox != NULL) - free(maxinbox); - // msgErr << "Gridsearch memory allocation failed, bailing out" << sendmsg; - return NULL; // ran out of memory, bail out! - } - - const float invpairdist = 1.0f / pairdist; - for (i=0; i= xb) axb = xb-1; - if (ayb >= yb) ayb = yb-1; - if (azb >= zb) azb = zb-1; - - aindex = azb * xytotb + ayb * xb + axb; - - // grow box if necessary - if ((num = numinbox[aindex]) == maxinbox[aindex]) { - boxatom[aindex] = (int *) realloc(boxatom[aindex], (num+4)*sizeof(int)); - maxinbox[aindex] += 4; - } - - // store atom index in box - boxatom[aindex][num] = i; - numinbox[aindex]++; - // } - } - free(maxinbox); - - nbrlist = (int **) calloc(1, totb*sizeof(int *)); - if (make_neighborlist(nbrlist, xb, yb, zb)) { - if (boxatom != NULL) { - for (i=0; inext = NULL; - cur = head; - printf("pairlist\n"); - // wkfmsgtimer *msgt = wkf_msg_timer_create(5); - for (aindex = 0; (aindex < totb) && (!maxpairsreached); aindex++) { - // printf("%d\n", aindex); - int *tmpbox, *tmpnbr, *nbr; - tmpbox = boxatom[aindex]; - tmpnbr = nbrlist[aindex]; - - // if (wkf_msg_timer_timeout(msgt)) { - // char tmpbuf[128]; - // sprintf(tmpbuf, "%6.2f", (100.0f * aindex) / (float) totb); - // msgInfo << "vmd_gridsearch1: " << tmpbuf << "% complete" << sendmsg; - // } - - for (nbr = tmpnbr; (*nbr != -1) && (!maxpairsreached); nbr++) { - int *nbrbox = boxatom[*nbr]; - for (i=0; (i sqdist) - continue; - - if (maxpairs > 0) { - if (paircount >= maxpairs) { - maxpairsreached = 1; - continue; - } - } - - add_link(cur, ind1, ind2); - paircount++; - - // XXX double-counting still ignores atoms with same coords... - if (allow_double_counting) { - add_link(cur, ind2, ind1); - paircount++; - } - cur = cur->next; - cur->next = NULL; - // } - } - } - } - } - - for (i=0; inext; - free(head); - - // if (maxpairsreached) { - // printf("maxpairs reached \n"); - // } - - return cur; -} - - -static int test_function(int i) { - return i; -} - -static double sasa_grid(const float *pos,int natoms, float pairdist, int allow_double_counting, int maxpairs, const float *radius,const int npts, double srad, int pointstyle, int restricted, const int* restrictedList) { - int on[natoms]; - fill_n(on,natoms,1); - // printf("natoms %d\n", natoms); - // printf("pairdist %f\n", pairdist); - // printf("maxpairs %d\n", maxpairs); - GridSearchPair* pairs = vmd_gridsearch1(pos,natoms, on, pairdist, allow_double_counting,maxpairs); - // vector > v(natoms,vector()); - // printf("size: %d\n", v.size()); - ResizeArray *pairlist = new ResizeArray[natoms]; - GridSearchPair *p, *tmp; - for (p = pairs; p != NULL; p = tmp) { - int ind1=p->ind1; - int ind2=p->ind2; - // v[ind1].push_back(ind2); - // v[ind2].push_back(ind1); - pairlist[ind1].append(ind2); - pairlist[ind2].append(ind1); - tmp = p->next; - free(p); - } - - float *spherepts = new float[3*npts]; - - if (pointstyle) { - static const float RAND_MAX_INV = 1.0f/VMD_RAND_MAX; - vmd_srandom(38572111); - - // All the spheres use the same random points. - - for (int i=0; i &nbrs = pairlist[i]; - // printf("neighbors: %d\n", nbrs.num()); - for (int j=0; j > v(natoms,vector()); -// // printf("size: %d\n", v.size()); -// // ResizeArray *pairlist = new ResizeArray[natoms]; -// GridSearchPair *p, *tmp; -// for (p = pairs; p != NULL; p = tmp) { -// int ind1=p->ind1; -// int ind2=p->ind2; -// v[ind1].push_back(ind2); -// v[ind2].push_back(ind1); -// // printf("%f\n", v[ind2]); -// // pairlist[ind1].append(ind2); -// // pairlist[ind2].append(ind1); -// // printf("%d\n", ind1); -// tmp = p->next; -// free(p); -// } -// PyGILState_STATE gstate = PyGILState_Ensure(); -// PyObject* result = PyList_New(0); -// vector< vector >::iterator row; -// vector::iterator col; -// for (row = v.begin(); row != v.end(); row++) { -// // printf("row %d\n", *row); -// PyObject* tempo = PyList_New(0); -// for (col = row->begin(); col != row->end(); col++) { -// // printf("%d \n", *col); -// PyList_Append(tempo, PyInt_FromLong(*col)); -// } -// PyList_Append(result,tempo); -// tempo = NULL; -// } -// PyGILState_Release(gstate); -// return result; -// } - -} - -typedef ResizeArray atomlist; -struct FindWithinData { - int nthreads; - int tid; - int totb; - int xytotb; - int xb; - int yb; - int zb; - float r2; - const float * xyz; - const atomlist * flgatoms; - const atomlist * otheratoms; - int * flgs; - FindWithinData() : flgatoms(0), otheratoms(0), flgs(0) {} - ~FindWithinData() { if (flgs) free(flgs); } -}; - -#define MAXGRIDDIM 31 -extern "C" int* find_within(const float *xyz, int *flgs, const int *others, int num, float r) { - int i; - float xmin, xmax, ymin, ymax, zmin, zmax; - float oxmin, oymin, ozmin, oxmax, oymax, ozmax; - float xwidth, ywidth, zwidth; - const float *pos; - - int *result = new int[num]; - fill_n(result,num,0); - - // for (size_t i = 0; i < num; i++) { - // pos=xyz+3*i; - // printf("%f %f %f\n", pos[0],pos[1],pos[2]); - // } - - // find min/max bounds of atom coordinates in flgs - if (!find_minmax_selected(num, flgs, xyz, xmin, ymin, zmin, xmax, ymax, zmax) || - !find_minmax_selected(num, others, xyz, oxmin, oymin, ozmin, oxmax, oymax, ozmax)) { - memset(flgs, 0, num*sizeof(int)); - return result; - } - - // Find the set of atoms with the smallest extent; here we use the sum - // of the box dimensions though other choices might be better. - float size = xmax+ymax+zmax - (xmin+ymin+zmin); - float osize = oxmax+oymax+ozmax - (oxmin+oymin+ozmin); - if (osize < size) { - xmin=oxmin; - ymin=oymin; - zmin=ozmin; - xmax=oxmax; - ymax=oymax; - zmax=ozmax; - } - - // Generate a grid of mesh size r based on the computed size of the molecule. - // We limit the size of the grid cell dimensions so that we don't get too - // many grid cells. - xwidth = (xmax-xmin)/(MAXGRIDDIM-1); - if (xwidth < r) xwidth = r; - ywidth = (ymax-ymin)/(MAXGRIDDIM-1); - if (ywidth < r) ywidth = r; - zwidth = (zmax-zmin)/(MAXGRIDDIM-1); - if (zwidth < r) zwidth = r; - - // Adjust the bounds so that we include atoms that are in the outermost - // grid cells. - xmin -= xwidth; - xmax += xwidth; - ymin -= ywidth; - ymax += ywidth; - zmin -= zwidth; - zmax += zwidth; - - // The number of grid cells needed in each dimension is - // (int)((xmax-xmin)/xwidth) + 1 - const int xb = (int)((xmax-xmin)/xwidth) + 1; - const int yb = (int)((ymax-ymin)/ywidth) + 1; - const int zb = (int)((zmax-zmin)/zwidth) + 1; - - int xytotb = yb * xb; - int totb = xytotb * zb; - - atomlist* flgatoms = new atomlist[totb]; - atomlist* otheratoms = new atomlist[totb]; - - float ixwidth = 1.0f/xwidth; - float iywidth = 1.0f/ywidth; - float izwidth = 1.0f/zwidth; - for (i=0; ixmax || yiymax || zizmax) { - continue; - } - AtomEntry entry(xi,yi,zi,i); - int axb = (int)((xi - xmin)*ixwidth); - int ayb = (int)((yi - ymin)*iywidth); - int azb = (int)((zi - zmin)*izwidth); - - // Due to floating point error in the calcuation of bin widths, we - // have to range clamp the computed box indices. - if (axb==xb) axb=xb-1; - if (ayb==yb) ayb=yb-1; - if (azb==zb) azb=zb-1; - - int aindex = azb*xytotb + ayb*xb + axb; - // TODO maybe change so that others does not contain the atoms of flags - if (others[i]) otheratoms[aindex].append(entry); - if ( flgs[i]) flgatoms[aindex].append(entry); - } - - memset(flgs, 0, num*sizeof(int)); - const float r2 = (float) (r*r); - - // set up workspace for multithreaded calculation - int nthreads; -#ifdef VMDTHREADS - nthreads = wkf_thread_numprocessors(); - wkf_thread_t * threads = (wkf_thread_t *)calloc(nthreads, sizeof(wkf_thread_t)); -#else - nthreads = 1; -#endif - FindWithinData *data = new FindWithinData[nthreads]; - for (i=0; inthreads; - const int tid = data->tid; - const int totb = data->totb; - const int xytotb = data->xytotb; - const int xb = data->xb; - const int yb = data->yb; - const int zb = data->zb; - const float r2 = data->r2; - const atomlist * flgatoms = data->flgatoms; - const atomlist * otheratoms = data->otheratoms; - int * flgs = data->flgs; - - // Loop over boxes, checking for flg atoms and other atoms within one - // box of each other. 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* does not write result back to socket (one way connection...) so -# there is no way to inquire objects in vmd - -namespace eval remote_ctl { -variable main -variable clients -variable default_vmd_port -set default_vmd_port 5555 -# I am too dumb to set the default value for port from -# $default_vmd_port so I put 5555 in there literally -proc start { {port 5500} } { -variable main -set main [socket -server remote_ctl::acpt $port] -putlog "Listening on port $port" -} -proc acpt { sock addr port } { -variable clients -if {[string compare $addr "127.0.0.1"] != 0} { -putlog "Unauthorized connection attempt from $addr port $port" -close $sock -return -} -putlog "Accept $sock from $addr port $port" -set clients($sock) 1 -fconfigure $sock -buffering line -fileevent $sock readable [list remote_ctl::recv $sock] -} -proc recv { sock } { -variable main -variable clients -if { [eof $sock] || [catch {gets $sock line}]} { -# end of file or abnormal connection drop: -# shut down this connection -close $sock -putlog "Closing $sock" -unset clients($sock) -} else { -if {[string compare $line "quit"] == 0} { -# prevent new connections -# existing connections stay open -# No -- Bug(?): 'quit' closes VMD... -putlog "Disallowing incoming connections by request of $sock" -close $main -} -# execute the received commands -# should check for runtime errors which otherwise leave the connection -# in an unusable state -# eval $line -set rc [catch $line result] -if { $rc } { -#puts $sock "Error executing comand '$line': n$result" -puts "Error executing comand '$line': n$result" -} else { -#puts $sock $result -#puts $result -} -} -} -###### would like the last line from stdout in line ########### -# (or any working solution....) -proc send { sock line} { -variable clients -# send reply to connecting client -putlog "send '$line' to $sock" -puts $sock $line -} - -proc putlog { text } { -puts $text -return -} -} - -remote_ctl::putlog "Starting remote_ctl server in vmd: connect with something like" -remote_ctl::putlog "telnet localhost 5500" -remote_ctl::start diff --git a/testing/cython/vmd/setup.py b/testing/cython/vmd/setup.py deleted file mode 100644 index a842ee9..0000000 --- a/testing/cython/vmd/setup.py +++ /dev/null @@ -1,9 +0,0 @@ -from distutils.core import setup -from distutils.extension import Extension -from Cython.Distutils import build_ext -setup( - cmdclass = {'build_ext': build_ext}, - ext_modules = [Extension("wrap_vmd",["wrap_vmd.pyx"],language="c++" - ,include_dirs=['/usr/local/include'] -), -]) diff --git a/testing/cython/vmd/vmd_wrapper.cpp b/testing/cython/vmd/vmd_wrapper.cpp deleted file mode 100644 index fecff9a..0000000 --- a/testing/cython/vmd/vmd_wrapper.cpp +++ /dev/null @@ -1,34 +0,0 @@ -#include -#include -#include -#include -#include -#include -#include - -using namespace std; -vmdsock_t vmdsock; - - -static void start_vmd(int pt) { - int port = pt; - vmdsock = newvmdsock("vmd", port); - vmdstream vmdscript(vmdsock); - - //draw a sphere - vmdscript << "draw sphere { 0 0 0 } radius 0.5" << endl; - - //render to a file - // vmdscript << "render snapshot sphere.tga" << endl; - - //quit vmd and exit - // - // - // -} - -static void stop_vmd() { - // vmdscript << "quit" << endl; - // vmdscript.flush(); - closevmdsock(vmdsock); -} diff --git a/testing/cython/vmd/wrap_vmd.c b/testing/cython/vmd/wrap_vmd.c deleted file mode 100644 index 382c53a..0000000 --- a/testing/cython/vmd/wrap_vmd.c +++ /dev/null @@ -1,1836 +0,0 @@ -/* Generated by Cython 0.25.2 */ - -#define PY_SSIZE_T_CLEAN -#include "Python.h" -#ifndef Py_PYTHON_H - #error Python headers needed to compile C extensions, please install development version of Python. -#elif PY_VERSION_HEX < 0x02060000 || (0x03000000 <= PY_VERSION_HEX && PY_VERSION_HEX < 0x03020000) - #error Cython requires Python 2.6+ or Python 3.2+. -#else -#define CYTHON_ABI "0_25_2" -#include -#ifndef offsetof - #define offsetof(type, member) ( (size_t) & ((type*)0) -> member ) -#endif -#if !defined(WIN32) && !defined(MS_WINDOWS) - #ifndef __stdcall - #define __stdcall - #endif - #ifndef __cdecl - #define __cdecl - #endif - #ifndef __fastcall - #define __fastcall - #endif -#endif -#ifndef DL_IMPORT - #define DL_IMPORT(t) t -#endif -#ifndef DL_EXPORT - #define DL_EXPORT(t) t -#endif -#ifndef HAVE_LONG_LONG - #if PY_VERSION_HEX >= 0x03030000 || (PY_MAJOR_VERSION == 2 && PY_VERSION_HEX >= 0x02070000) - #define HAVE_LONG_LONG - #endif -#endif -#ifndef PY_LONG_LONG - #define PY_LONG_LONG LONG_LONG -#endif -#ifndef Py_HUGE_VAL - #define Py_HUGE_VAL HUGE_VAL -#endif -#ifdef PYPY_VERSION - #define CYTHON_COMPILING_IN_PYPY 1 - #define CYTHON_COMPILING_IN_PYSTON 0 - #define CYTHON_COMPILING_IN_CPYTHON 0 - #undef CYTHON_USE_TYPE_SLOTS - #define CYTHON_USE_TYPE_SLOTS 0 - #undef CYTHON_USE_ASYNC_SLOTS - #define CYTHON_USE_ASYNC_SLOTS 0 - #undef CYTHON_USE_PYLIST_INTERNALS - #define CYTHON_USE_PYLIST_INTERNALS 0 - #undef CYTHON_USE_UNICODE_INTERNALS - #define 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__pyx_empty_tuple, /*PyObject *consts,*/ - __pyx_empty_tuple, /*PyObject *names,*/ - __pyx_empty_tuple, /*PyObject *varnames,*/ - __pyx_empty_tuple, /*PyObject *freevars,*/ - __pyx_empty_tuple, /*PyObject *cellvars,*/ - py_srcfile, /*PyObject *filename,*/ - py_funcname, /*PyObject *name,*/ - py_line, - __pyx_empty_bytes /*PyObject *lnotab*/ - ); - Py_DECREF(py_srcfile); - Py_DECREF(py_funcname); - return py_code; -bad: - Py_XDECREF(py_srcfile); - Py_XDECREF(py_funcname); - return NULL; -} -static void __Pyx_AddTraceback(const char *funcname, int c_line, - int py_line, const char *filename) { - PyCodeObject *py_code = 0; - PyFrameObject *py_frame = 0; - py_code = __pyx_find_code_object(c_line ? c_line : py_line); - if (!py_code) { - py_code = __Pyx_CreateCodeObjectForTraceback( - funcname, c_line, py_line, filename); - if (!py_code) goto bad; - __pyx_insert_code_object(c_line ? c_line : py_line, py_code); - } - py_frame = PyFrame_New( - PyThreadState_GET(), /*PyThreadState *tstate,*/ - py_code, /*PyCodeObject *code,*/ - __pyx_d, /*PyObject *globals,*/ - 0 /*PyObject *locals*/ - ); - if (!py_frame) goto bad; - __Pyx_PyFrame_SetLineNumber(py_frame, py_line); - PyTraceBack_Here(py_frame); -bad: - Py_XDECREF(py_code); - Py_XDECREF(py_frame); -} - -/* CIntToPy */ -static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value) { - const long neg_one = (long) -1, const_zero = (long) 0; - const int is_unsigned = neg_one > const_zero; - if (is_unsigned) { - if (sizeof(long) < sizeof(long)) { - return PyInt_FromLong((long) value); - } else if (sizeof(long) <= sizeof(unsigned long)) { - return PyLong_FromUnsignedLong((unsigned long) value); -#ifdef HAVE_LONG_LONG - } else if (sizeof(long) <= sizeof(unsigned PY_LONG_LONG)) { - return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value); -#endif - } - } else { - if (sizeof(long) <= sizeof(long)) { - return PyInt_FromLong((long) value); -#ifdef HAVE_LONG_LONG - } else if (sizeof(long) <= sizeof(PY_LONG_LONG)) { - return PyLong_FromLongLong((PY_LONG_LONG) value); -#endif - } - } - { - int one = 1; int little = (int)*(unsigned char *)&one; - unsigned char *bytes = (unsigned char *)&value; - return _PyLong_FromByteArray(bytes, sizeof(long), - little, !is_unsigned); - } -} - -/* CIntFromPyVerify */ -#define __PYX_VERIFY_RETURN_INT(target_type, func_type, func_value)\ - __PYX__VERIFY_RETURN_INT(target_type, func_type, func_value, 0) -#define __PYX_VERIFY_RETURN_INT_EXC(target_type, func_type, func_value)\ - __PYX__VERIFY_RETURN_INT(target_type, func_type, func_value, 1) -#define __PYX__VERIFY_RETURN_INT(target_type, func_type, func_value, exc)\ - {\ - func_type value = func_value;\ - if (sizeof(target_type) < sizeof(func_type)) {\ - if (unlikely(value != (func_type) (target_type) value)) {\ - func_type zero = 0;\ - if (exc && unlikely(value == (func_type)-1 && PyErr_Occurred()))\ - return (target_type) -1;\ - if (is_unsigned && unlikely(value < zero))\ - goto raise_neg_overflow;\ - else\ - goto raise_overflow;\ - }\ - }\ - return (target_type) value;\ - } - -/* CIntFromPy */ -static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *x) { - const long neg_one = (long) -1, const_zero = (long) 0; - const int is_unsigned = neg_one > const_zero; -#if PY_MAJOR_VERSION < 3 - if (likely(PyInt_Check(x))) { - if (sizeof(long) < sizeof(long)) { - __PYX_VERIFY_RETURN_INT(long, long, PyInt_AS_LONG(x)) - } else { - long val = PyInt_AS_LONG(x); - if (is_unsigned && unlikely(val < 0)) { - goto raise_neg_overflow; - } - return (long) val; - } - } else -#endif - if (likely(PyLong_Check(x))) { - if (is_unsigned) { -#if CYTHON_USE_PYLONG_INTERNALS - const digit* digits = ((PyLongObject*)x)->ob_digit; - switch (Py_SIZE(x)) { - case 0: return (long) 0; - case 1: __PYX_VERIFY_RETURN_INT(long, digit, digits[0]) - case 2: - if (8 * sizeof(long) > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) >= 2 * PyLong_SHIFT) { - return (long) (((((long)digits[1]) << PyLong_SHIFT) | (long)digits[0])); - } - } - break; - case 3: - if (8 * sizeof(long) > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) >= 3 * PyLong_SHIFT) { - return (long) (((((((long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0])); - } - } - break; - case 4: - if (8 * sizeof(long) > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) >= 4 * PyLong_SHIFT) { - return (long) (((((((((long)digits[3]) << PyLong_SHIFT) | (long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0])); - } - } - break; - } -#endif -#if CYTHON_COMPILING_IN_CPYTHON - if (unlikely(Py_SIZE(x) < 0)) { - goto raise_neg_overflow; - } -#else - { - int result = PyObject_RichCompareBool(x, Py_False, Py_LT); - if (unlikely(result < 0)) - return (long) -1; - if (unlikely(result == 1)) - goto raise_neg_overflow; - } -#endif - if (sizeof(long) <= sizeof(unsigned long)) { - __PYX_VERIFY_RETURN_INT_EXC(long, unsigned long, PyLong_AsUnsignedLong(x)) -#ifdef HAVE_LONG_LONG - } else if (sizeof(long) <= sizeof(unsigned PY_LONG_LONG)) { - __PYX_VERIFY_RETURN_INT_EXC(long, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x)) -#endif - } - } else { -#if CYTHON_USE_PYLONG_INTERNALS - const digit* digits = ((PyLongObject*)x)->ob_digit; - switch (Py_SIZE(x)) { - case 0: return (long) 0; - case -1: __PYX_VERIFY_RETURN_INT(long, sdigit, (sdigit) (-(sdigit)digits[0])) - case 1: __PYX_VERIFY_RETURN_INT(long, digit, +digits[0]) - case -2: - if (8 * sizeof(long) - 1 > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { - return (long) (((long)-1)*(((((long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); - } - } - break; - case 2: - if (8 * sizeof(long) > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { - return (long) ((((((long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); - } - } - break; - case -3: - if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { - return (long) (((long)-1)*(((((((long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); - } - } - break; - case 3: - if (8 * sizeof(long) > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { - return (long) ((((((((long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); - } - } - break; - case -4: - if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) { - return (long) (((long)-1)*(((((((((long)digits[3]) << PyLong_SHIFT) | (long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); - } - } - break; - case 4: - if (8 * sizeof(long) > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) { - return (long) ((((((((((long)digits[3]) << PyLong_SHIFT) | (long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); - } - } - break; - } -#endif - if (sizeof(long) <= sizeof(long)) { - __PYX_VERIFY_RETURN_INT_EXC(long, long, PyLong_AsLong(x)) -#ifdef HAVE_LONG_LONG - } else if (sizeof(long) <= sizeof(PY_LONG_LONG)) { - __PYX_VERIFY_RETURN_INT_EXC(long, PY_LONG_LONG, PyLong_AsLongLong(x)) -#endif - } - } - { -#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray) - PyErr_SetString(PyExc_RuntimeError, - "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers"); -#else - long val; - PyObject *v = __Pyx_PyNumber_IntOrLong(x); - #if PY_MAJOR_VERSION < 3 - if (likely(v) && !PyLong_Check(v)) { - PyObject *tmp = v; - v = PyNumber_Long(tmp); - Py_DECREF(tmp); - } - #endif - if (likely(v)) { - int one = 1; int is_little = (int)*(unsigned char *)&one; - unsigned char *bytes = (unsigned char *)&val; - int ret = _PyLong_AsByteArray((PyLongObject *)v, - bytes, sizeof(val), - is_little, !is_unsigned); - Py_DECREF(v); - if (likely(!ret)) - return val; - } -#endif - return (long) -1; - } - } else { - long val; - PyObject *tmp = __Pyx_PyNumber_IntOrLong(x); - if (!tmp) return (long) -1; - val = __Pyx_PyInt_As_long(tmp); - Py_DECREF(tmp); - return val; - } -raise_overflow: - PyErr_SetString(PyExc_OverflowError, - "value too large to convert to long"); - return (long) -1; -raise_neg_overflow: - PyErr_SetString(PyExc_OverflowError, - "can't convert negative value to long"); - return (long) -1; -} - -/* CIntFromPy */ -static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *x) { - const int neg_one = (int) -1, const_zero = (int) 0; - const int is_unsigned = neg_one > const_zero; -#if PY_MAJOR_VERSION < 3 - if (likely(PyInt_Check(x))) { - if (sizeof(int) < sizeof(long)) { - __PYX_VERIFY_RETURN_INT(int, long, PyInt_AS_LONG(x)) - } else { - long val = PyInt_AS_LONG(x); - if (is_unsigned && unlikely(val < 0)) { - goto raise_neg_overflow; - } - return (int) val; - } - } else -#endif - if (likely(PyLong_Check(x))) { - if (is_unsigned) { -#if CYTHON_USE_PYLONG_INTERNALS - const digit* digits = ((PyLongObject*)x)->ob_digit; - switch (Py_SIZE(x)) { - case 0: return (int) 0; - case 1: __PYX_VERIFY_RETURN_INT(int, digit, digits[0]) - case 2: - if (8 * sizeof(int) > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) >= 2 * PyLong_SHIFT) { - return (int) (((((int)digits[1]) << PyLong_SHIFT) | (int)digits[0])); - } - } - break; - case 3: - if (8 * sizeof(int) > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) >= 3 * PyLong_SHIFT) { - return (int) (((((((int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0])); - } - } - break; - case 4: - if (8 * sizeof(int) > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) >= 4 * PyLong_SHIFT) { - return (int) (((((((((int)digits[3]) << PyLong_SHIFT) | (int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0])); - } - } - break; - } -#endif -#if CYTHON_COMPILING_IN_CPYTHON - if (unlikely(Py_SIZE(x) < 0)) { - goto raise_neg_overflow; - } -#else - { - int result = PyObject_RichCompareBool(x, Py_False, Py_LT); - if (unlikely(result < 0)) - return (int) -1; - if (unlikely(result == 1)) - goto raise_neg_overflow; - } -#endif - if (sizeof(int) <= sizeof(unsigned long)) { - __PYX_VERIFY_RETURN_INT_EXC(int, unsigned long, PyLong_AsUnsignedLong(x)) -#ifdef HAVE_LONG_LONG - } else if (sizeof(int) <= sizeof(unsigned PY_LONG_LONG)) { - __PYX_VERIFY_RETURN_INT_EXC(int, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x)) -#endif - } - } else { -#if CYTHON_USE_PYLONG_INTERNALS - const digit* digits = ((PyLongObject*)x)->ob_digit; - switch (Py_SIZE(x)) { - case 0: return (int) 0; - case -1: __PYX_VERIFY_RETURN_INT(int, sdigit, (sdigit) (-(sdigit)digits[0])) - case 1: __PYX_VERIFY_RETURN_INT(int, digit, +digits[0]) - case -2: - if (8 * sizeof(int) - 1 > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) - 1 > 2 * PyLong_SHIFT) { - return (int) (((int)-1)*(((((int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); - } - } - break; - case 2: - if (8 * sizeof(int) > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) - 1 > 2 * PyLong_SHIFT) { - return (int) ((((((int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); - } - } - break; - case -3: - if (8 * sizeof(int) - 1 > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) - 1 > 3 * PyLong_SHIFT) { - return (int) (((int)-1)*(((((((int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); - } - } - break; - case 3: - if (8 * sizeof(int) > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) - 1 > 3 * PyLong_SHIFT) { - return (int) ((((((((int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); - } - } - break; - case -4: - if (8 * sizeof(int) - 1 > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) - 1 > 4 * PyLong_SHIFT) { - return (int) (((int)-1)*(((((((((int)digits[3]) << PyLong_SHIFT) | (int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); - } - } - break; - case 4: - if (8 * sizeof(int) > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) - 1 > 4 * PyLong_SHIFT) { - return (int) ((((((((((int)digits[3]) << PyLong_SHIFT) | (int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); - } - } - break; - } -#endif - if (sizeof(int) <= sizeof(long)) { - __PYX_VERIFY_RETURN_INT_EXC(int, long, PyLong_AsLong(x)) -#ifdef HAVE_LONG_LONG - } else if (sizeof(int) <= sizeof(PY_LONG_LONG)) { - __PYX_VERIFY_RETURN_INT_EXC(int, PY_LONG_LONG, PyLong_AsLongLong(x)) -#endif - } - } - { -#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray) - PyErr_SetString(PyExc_RuntimeError, - "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers"); -#else - int val; - PyObject *v = __Pyx_PyNumber_IntOrLong(x); - #if PY_MAJOR_VERSION < 3 - if (likely(v) && !PyLong_Check(v)) { - PyObject *tmp = v; - v = PyNumber_Long(tmp); - Py_DECREF(tmp); - } - #endif - if (likely(v)) { - int one = 1; int is_little = (int)*(unsigned char *)&one; - unsigned char *bytes = (unsigned char *)&val; - int ret = _PyLong_AsByteArray((PyLongObject *)v, - bytes, sizeof(val), - is_little, !is_unsigned); - Py_DECREF(v); - if (likely(!ret)) - return val; - } -#endif - return (int) -1; - } - } else { - int val; - PyObject *tmp = __Pyx_PyNumber_IntOrLong(x); - if (!tmp) return (int) -1; - val = __Pyx_PyInt_As_int(tmp); - Py_DECREF(tmp); - return val; - } -raise_overflow: - PyErr_SetString(PyExc_OverflowError, - "value too large to convert to int"); - return (int) -1; -raise_neg_overflow: - PyErr_SetString(PyExc_OverflowError, - "can't convert negative value to int"); - return (int) -1; -} - -/* CheckBinaryVersion */ -static int __Pyx_check_binary_version(void) { - char ctversion[4], rtversion[4]; - PyOS_snprintf(ctversion, 4, "%d.%d", PY_MAJOR_VERSION, PY_MINOR_VERSION); - PyOS_snprintf(rtversion, 4, "%s", Py_GetVersion()); - if (ctversion[0] != rtversion[0] || ctversion[2] != rtversion[2]) { - char message[200]; - PyOS_snprintf(message, sizeof(message), - "compiletime version %s of module '%.100s' " - "does not match runtime version %s", - ctversion, __Pyx_MODULE_NAME, rtversion); - return PyErr_WarnEx(NULL, message, 1); - } - return 0; -} - -/* InitStrings */ -static int __Pyx_InitStrings(__Pyx_StringTabEntry *t) { - while (t->p) { - #if PY_MAJOR_VERSION < 3 - if (t->is_unicode) { - *t->p = PyUnicode_DecodeUTF8(t->s, t->n - 1, NULL); - } else if (t->intern) { - *t->p = PyString_InternFromString(t->s); - } else { - *t->p = PyString_FromStringAndSize(t->s, t->n - 1); - } - #else - if (t->is_unicode | t->is_str) { - if (t->intern) { - *t->p = PyUnicode_InternFromString(t->s); - } else if (t->encoding) { - *t->p = PyUnicode_Decode(t->s, t->n - 1, t->encoding, NULL); - } else { - *t->p = PyUnicode_FromStringAndSize(t->s, t->n - 1); - } - } else { - *t->p = PyBytes_FromStringAndSize(t->s, t->n - 1); - } - #endif - if (!*t->p) - return -1; - ++t; - } - return 0; -} - -static CYTHON_INLINE PyObject* __Pyx_PyUnicode_FromString(const char* c_str) { - return __Pyx_PyUnicode_FromStringAndSize(c_str, (Py_ssize_t)strlen(c_str)); -} -static CYTHON_INLINE char* __Pyx_PyObject_AsString(PyObject* o) { - Py_ssize_t ignore; - return __Pyx_PyObject_AsStringAndSize(o, &ignore); -} -static CYTHON_INLINE char* __Pyx_PyObject_AsStringAndSize(PyObject* o, Py_ssize_t *length) { -#if CYTHON_COMPILING_IN_CPYTHON && (__PYX_DEFAULT_STRING_ENCODING_IS_ASCII || __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT) - if ( -#if PY_MAJOR_VERSION < 3 && __PYX_DEFAULT_STRING_ENCODING_IS_ASCII - __Pyx_sys_getdefaultencoding_not_ascii && -#endif - PyUnicode_Check(o)) { -#if PY_VERSION_HEX < 0x03030000 - char* defenc_c; - PyObject* defenc = _PyUnicode_AsDefaultEncodedString(o, NULL); - if (!defenc) return NULL; - defenc_c = PyBytes_AS_STRING(defenc); -#if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII - { - char* end = defenc_c + PyBytes_GET_SIZE(defenc); - char* c; - for (c = defenc_c; c < end; c++) { - if ((unsigned char) (*c) >= 128) { - PyUnicode_AsASCIIString(o); - return NULL; - } - } - } -#endif - *length = PyBytes_GET_SIZE(defenc); - return defenc_c; -#else - if (__Pyx_PyUnicode_READY(o) == -1) return NULL; -#if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII - if (PyUnicode_IS_ASCII(o)) { - *length = PyUnicode_GET_LENGTH(o); - return PyUnicode_AsUTF8(o); - } else { - PyUnicode_AsASCIIString(o); - return NULL; - } -#else - return PyUnicode_AsUTF8AndSize(o, length); -#endif -#endif - } else -#endif -#if (!CYTHON_COMPILING_IN_PYPY) || (defined(PyByteArray_AS_STRING) && defined(PyByteArray_GET_SIZE)) - if (PyByteArray_Check(o)) { - *length = PyByteArray_GET_SIZE(o); - return PyByteArray_AS_STRING(o); - } else -#endif - { - char* result; - int r = PyBytes_AsStringAndSize(o, &result, length); - if (unlikely(r < 0)) { - return NULL; - } else { - return result; - } - } -} -static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject* x) { - int is_true = x == Py_True; - if (is_true | (x == Py_False) | (x == Py_None)) return is_true; - else return PyObject_IsTrue(x); -} -static CYTHON_INLINE PyObject* __Pyx_PyNumber_IntOrLong(PyObject* x) { -#if CYTHON_USE_TYPE_SLOTS - PyNumberMethods *m; -#endif - const char *name = NULL; - PyObject *res = NULL; -#if PY_MAJOR_VERSION < 3 - if (PyInt_Check(x) || PyLong_Check(x)) -#else - if (PyLong_Check(x)) -#endif - return __Pyx_NewRef(x); -#if CYTHON_USE_TYPE_SLOTS - m = Py_TYPE(x)->tp_as_number; - #if PY_MAJOR_VERSION < 3 - if (m && m->nb_int) { - name = "int"; - res = PyNumber_Int(x); - } - else if (m && m->nb_long) { - name = "long"; - res = PyNumber_Long(x); - } - #else - if (m && m->nb_int) { - name = "int"; - res = PyNumber_Long(x); - } - #endif -#else - res = PyNumber_Int(x); -#endif - if (res) { -#if PY_MAJOR_VERSION < 3 - if (!PyInt_Check(res) && !PyLong_Check(res)) { -#else - if (!PyLong_Check(res)) { -#endif - PyErr_Format(PyExc_TypeError, - "__%.4s__ returned non-%.4s (type %.200s)", - name, name, Py_TYPE(res)->tp_name); - Py_DECREF(res); - return NULL; - } - } - else if (!PyErr_Occurred()) { - PyErr_SetString(PyExc_TypeError, - "an integer is required"); - } - return res; -} -static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject* b) { - Py_ssize_t ival; - PyObject *x; -#if PY_MAJOR_VERSION < 3 - if (likely(PyInt_CheckExact(b))) { - if (sizeof(Py_ssize_t) >= sizeof(long)) - return PyInt_AS_LONG(b); - else - return PyInt_AsSsize_t(x); - } -#endif - if (likely(PyLong_CheckExact(b))) { - #if CYTHON_USE_PYLONG_INTERNALS - const digit* digits = ((PyLongObject*)b)->ob_digit; - const Py_ssize_t size = Py_SIZE(b); - if (likely(__Pyx_sst_abs(size) <= 1)) { - ival = likely(size) ? digits[0] : 0; - if (size == -1) ival = -ival; - return ival; - } else { - switch (size) { - case 2: - if (8 * sizeof(Py_ssize_t) > 2 * PyLong_SHIFT) { - return (Py_ssize_t) (((((size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); - } - break; - case -2: - if (8 * sizeof(Py_ssize_t) > 2 * PyLong_SHIFT) { - return -(Py_ssize_t) (((((size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); - } - break; - case 3: - if (8 * sizeof(Py_ssize_t) > 3 * PyLong_SHIFT) { - return (Py_ssize_t) (((((((size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); - } - break; - case -3: - if (8 * sizeof(Py_ssize_t) > 3 * PyLong_SHIFT) { - return -(Py_ssize_t) (((((((size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); - } - break; - case 4: - if (8 * sizeof(Py_ssize_t) > 4 * PyLong_SHIFT) { - return (Py_ssize_t) (((((((((size_t)digits[3]) << PyLong_SHIFT) | (size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); - } - break; - case -4: - if (8 * sizeof(Py_ssize_t) > 4 * PyLong_SHIFT) { - return -(Py_ssize_t) (((((((((size_t)digits[3]) << PyLong_SHIFT) | (size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); - } - break; - } - } - #endif - return PyLong_AsSsize_t(b); - } - x = PyNumber_Index(b); - if (!x) return -1; - ival = PyInt_AsSsize_t(x); - Py_DECREF(x); - return ival; -} -static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) { - return PyInt_FromSize_t(ival); -} - - -#endif /* Py_PYTHON_H */ diff --git a/testing/cython/vmd/wrap_vmd.cpp b/testing/cython/vmd/wrap_vmd.cpp deleted file mode 100644 index 206b451..0000000 --- a/testing/cython/vmd/wrap_vmd.cpp +++ /dev/null @@ -1,1927 +0,0 @@ -/* Generated by Cython 0.25.2 */ - -#define PY_SSIZE_T_CLEAN -#include "Python.h" -#ifndef Py_PYTHON_H - #error Python headers needed to compile C extensions, please install development version of Python. -#elif PY_VERSION_HEX < 0x02060000 || (0x03000000 <= PY_VERSION_HEX && PY_VERSION_HEX < 0x03020000) - #error Cython requires Python 2.6+ or Python 3.2+. -#else -#define CYTHON_ABI "0_25_2" -#include -#ifndef offsetof - #define offsetof(type, member) ( (size_t) & ((type*)0) -> member ) -#endif -#if !defined(WIN32) && !defined(MS_WINDOWS) - #ifndef __stdcall - #define __stdcall - #endif - #ifndef __cdecl - #define __cdecl - #endif - #ifndef __fastcall - #define __fastcall - #endif -#endif -#ifndef DL_IMPORT - #define DL_IMPORT(t) t -#endif -#ifndef DL_EXPORT - #define DL_EXPORT(t) t -#endif -#ifndef HAVE_LONG_LONG - #if PY_VERSION_HEX >= 0x03030000 || (PY_MAJOR_VERSION == 2 && PY_VERSION_HEX >= 0x02070000) - #define HAVE_LONG_LONG - #endif -#endif -#ifndef PY_LONG_LONG - #define PY_LONG_LONG LONG_LONG -#endif -#ifndef Py_HUGE_VAL - #define Py_HUGE_VAL HUGE_VAL -#endif -#ifdef PYPY_VERSION - #define CYTHON_COMPILING_IN_PYPY 1 - #define CYTHON_COMPILING_IN_PYSTON 0 - #define CYTHON_COMPILING_IN_CPYTHON 0 - #undef CYTHON_USE_TYPE_SLOTS - #define CYTHON_USE_TYPE_SLOTS 0 - #undef CYTHON_USE_ASYNC_SLOTS - #define CYTHON_USE_ASYNC_SLOTS 0 - #undef CYTHON_USE_PYLIST_INTERNALS - #define CYTHON_USE_PYLIST_INTERNALS 0 - #undef CYTHON_USE_UNICODE_INTERNALS - #define CYTHON_USE_UNICODE_INTERNALS 0 - #undef CYTHON_USE_UNICODE_WRITER - #define CYTHON_USE_UNICODE_WRITER 0 - #undef CYTHON_USE_PYLONG_INTERNALS - #define CYTHON_USE_PYLONG_INTERNALS 0 - #undef CYTHON_AVOID_BORROWED_REFS - #define CYTHON_AVOID_BORROWED_REFS 1 - #undef CYTHON_ASSUME_SAFE_MACROS - #define CYTHON_ASSUME_SAFE_MACROS 0 - #undef CYTHON_UNPACK_METHODS - #define CYTHON_UNPACK_METHODS 0 - #undef CYTHON_FAST_THREAD_STATE - #define CYTHON_FAST_THREAD_STATE 0 - #undef CYTHON_FAST_PYCALL - #define CYTHON_FAST_PYCALL 0 -#elif defined(PYSTON_VERSION) - #define CYTHON_COMPILING_IN_PYPY 0 - #define CYTHON_COMPILING_IN_PYSTON 1 - #define CYTHON_COMPILING_IN_CPYTHON 0 - #ifndef CYTHON_USE_TYPE_SLOTS - #define CYTHON_USE_TYPE_SLOTS 1 - #endif - #undef CYTHON_USE_ASYNC_SLOTS - #define CYTHON_USE_ASYNC_SLOTS 0 - #undef CYTHON_USE_PYLIST_INTERNALS - #define CYTHON_USE_PYLIST_INTERNALS 0 - #ifndef CYTHON_USE_UNICODE_INTERNALS - #define CYTHON_USE_UNICODE_INTERNALS 1 - #endif - #undef CYTHON_USE_UNICODE_WRITER - #define CYTHON_USE_UNICODE_WRITER 0 - #undef CYTHON_USE_PYLONG_INTERNALS - #define CYTHON_USE_PYLONG_INTERNALS 0 - #ifndef CYTHON_AVOID_BORROWED_REFS - #define CYTHON_AVOID_BORROWED_REFS 0 - #endif - #ifndef CYTHON_ASSUME_SAFE_MACROS - #define CYTHON_ASSUME_SAFE_MACROS 1 - #endif - #ifndef CYTHON_UNPACK_METHODS - #define CYTHON_UNPACK_METHODS 1 - #endif - #undef CYTHON_FAST_THREAD_STATE - #define CYTHON_FAST_THREAD_STATE 0 - #undef CYTHON_FAST_PYCALL - #define CYTHON_FAST_PYCALL 0 -#else - #define CYTHON_COMPILING_IN_PYPY 0 - #define CYTHON_COMPILING_IN_PYSTON 0 - #define CYTHON_COMPILING_IN_CPYTHON 1 - #ifndef CYTHON_USE_TYPE_SLOTS - #define CYTHON_USE_TYPE_SLOTS 1 - #endif - #if PY_MAJOR_VERSION < 3 - #undef CYTHON_USE_ASYNC_SLOTS - #define CYTHON_USE_ASYNC_SLOTS 0 - #elif !defined(CYTHON_USE_ASYNC_SLOTS) - #define CYTHON_USE_ASYNC_SLOTS 1 - #endif - #if PY_VERSION_HEX < 0x02070000 - #undef CYTHON_USE_PYLONG_INTERNALS - #define CYTHON_USE_PYLONG_INTERNALS 0 - #elif !defined(CYTHON_USE_PYLONG_INTERNALS) - #define CYTHON_USE_PYLONG_INTERNALS 1 - #endif - #ifndef CYTHON_USE_PYLIST_INTERNALS - #define CYTHON_USE_PYLIST_INTERNALS 1 - #endif - #ifndef CYTHON_USE_UNICODE_INTERNALS - #define CYTHON_USE_UNICODE_INTERNALS 1 - #endif - #if PY_VERSION_HEX < 0x030300F0 - #undef CYTHON_USE_UNICODE_WRITER - #define CYTHON_USE_UNICODE_WRITER 0 - #elif !defined(CYTHON_USE_UNICODE_WRITER) - #define CYTHON_USE_UNICODE_WRITER 1 - #endif - #ifndef CYTHON_AVOID_BORROWED_REFS - #define CYTHON_AVOID_BORROWED_REFS 0 - #endif - #ifndef CYTHON_ASSUME_SAFE_MACROS - #define CYTHON_ASSUME_SAFE_MACROS 1 - #endif - #ifndef CYTHON_UNPACK_METHODS - #define CYTHON_UNPACK_METHODS 1 - #endif - #ifndef CYTHON_FAST_THREAD_STATE - #define CYTHON_FAST_THREAD_STATE 1 - #endif - #ifndef CYTHON_FAST_PYCALL - #define CYTHON_FAST_PYCALL 1 - #endif -#endif -#if !defined(CYTHON_FAST_PYCCALL) -#define CYTHON_FAST_PYCCALL (CYTHON_FAST_PYCALL && PY_VERSION_HEX >= 0x030600B1) -#endif -#if CYTHON_USE_PYLONG_INTERNALS - #include "longintrepr.h" - #undef SHIFT - #undef BASE - #undef MASK -#endif -#if CYTHON_COMPILING_IN_PYPY && PY_VERSION_HEX < 0x02070600 && !defined(Py_OptimizeFlag) - #define Py_OptimizeFlag 0 -#endif -#define __PYX_BUILD_PY_SSIZE_T "n" -#define CYTHON_FORMAT_SSIZE_T "z" -#if PY_MAJOR_VERSION < 3 - #define __Pyx_BUILTIN_MODULE_NAME "__builtin__" - #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)\ - PyCode_New(a+k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) - #define __Pyx_DefaultClassType PyClass_Type -#else - #define __Pyx_BUILTIN_MODULE_NAME "builtins" - #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)\ - PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) - #define __Pyx_DefaultClassType PyType_Type -#endif -#ifndef Py_TPFLAGS_CHECKTYPES - #define Py_TPFLAGS_CHECKTYPES 0 -#endif -#ifndef Py_TPFLAGS_HAVE_INDEX - #define Py_TPFLAGS_HAVE_INDEX 0 -#endif -#ifndef Py_TPFLAGS_HAVE_NEWBUFFER - #define Py_TPFLAGS_HAVE_NEWBUFFER 0 -#endif -#ifndef Py_TPFLAGS_HAVE_FINALIZE - #define Py_TPFLAGS_HAVE_FINALIZE 0 -#endif -#ifndef METH_FASTCALL - #define METH_FASTCALL 0x80 - typedef PyObject *(*__Pyx_PyCFunctionFast) (PyObject *self, PyObject **args, - Py_ssize_t nargs, PyObject *kwnames); -#else - #define __Pyx_PyCFunctionFast _PyCFunctionFast -#endif -#if CYTHON_FAST_PYCCALL -#define __Pyx_PyFastCFunction_Check(func)\ - ((PyCFunction_Check(func) && (METH_FASTCALL == (PyCFunction_GET_FLAGS(func) & ~(METH_CLASS | METH_STATIC | METH_COEXIST))))) -#else -#define __Pyx_PyFastCFunction_Check(func) 0 -#endif -#if PY_VERSION_HEX > 0x03030000 && defined(PyUnicode_KIND) - #define CYTHON_PEP393_ENABLED 1 - #define __Pyx_PyUnicode_READY(op) (likely(PyUnicode_IS_READY(op)) ?\ - 0 : _PyUnicode_Ready((PyObject *)(op))) - #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_LENGTH(u) - #define __Pyx_PyUnicode_READ_CHAR(u, i) PyUnicode_READ_CHAR(u, i) - #define __Pyx_PyUnicode_MAX_CHAR_VALUE(u) PyUnicode_MAX_CHAR_VALUE(u) - #define __Pyx_PyUnicode_KIND(u) PyUnicode_KIND(u) - #define __Pyx_PyUnicode_DATA(u) PyUnicode_DATA(u) - #define __Pyx_PyUnicode_READ(k, d, i) PyUnicode_READ(k, d, i) - 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if (likely(entries)) { - __pyx_code_cache.entries = entries; - __pyx_code_cache.max_count = 64; - __pyx_code_cache.count = 1; - entries[0].code_line = code_line; - entries[0].code_object = code_object; - Py_INCREF(code_object); - } - return; - } - pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line); - if ((pos < __pyx_code_cache.count) && unlikely(__pyx_code_cache.entries[pos].code_line == code_line)) { - PyCodeObject* tmp = entries[pos].code_object; - entries[pos].code_object = code_object; - Py_DECREF(tmp); - return; - } - if (__pyx_code_cache.count == __pyx_code_cache.max_count) { - int new_max = __pyx_code_cache.max_count + 64; - entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Realloc( - __pyx_code_cache.entries, (size_t)new_max*sizeof(__Pyx_CodeObjectCacheEntry)); - if (unlikely(!entries)) { - return; - } - __pyx_code_cache.entries = entries; - __pyx_code_cache.max_count = new_max; - } - for (i=__pyx_code_cache.count; i>pos; i--) { - entries[i] = entries[i-1]; - } - entries[pos].code_line = code_line; - entries[pos].code_object = code_object; - __pyx_code_cache.count++; - Py_INCREF(code_object); -} - -/* AddTraceback */ -#include "compile.h" -#include "frameobject.h" -#include "traceback.h" -static PyCodeObject* __Pyx_CreateCodeObjectForTraceback( - const char *funcname, int c_line, - int py_line, const char *filename) { - PyCodeObject *py_code = 0; - PyObject *py_srcfile = 0; - PyObject *py_funcname = 0; - #if PY_MAJOR_VERSION < 3 - py_srcfile = PyString_FromString(filename); - #else - py_srcfile = PyUnicode_FromString(filename); - #endif - if (!py_srcfile) goto bad; - if (c_line) { - #if PY_MAJOR_VERSION < 3 - py_funcname = PyString_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line); - #else - py_funcname = PyUnicode_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line); - #endif - } - else { - #if PY_MAJOR_VERSION < 3 - py_funcname = PyString_FromString(funcname); - #else - py_funcname = PyUnicode_FromString(funcname); - #endif - } - if (!py_funcname) goto bad; - py_code = __Pyx_PyCode_New( - 0, - 0, - 0, - 0, - 0, - __pyx_empty_bytes, /*PyObject *code,*/ - __pyx_empty_tuple, /*PyObject *consts,*/ - __pyx_empty_tuple, /*PyObject *names,*/ - __pyx_empty_tuple, /*PyObject *varnames,*/ - __pyx_empty_tuple, /*PyObject *freevars,*/ - __pyx_empty_tuple, /*PyObject *cellvars,*/ - py_srcfile, /*PyObject *filename,*/ - py_funcname, /*PyObject *name,*/ - py_line, - __pyx_empty_bytes /*PyObject *lnotab*/ - ); - Py_DECREF(py_srcfile); - Py_DECREF(py_funcname); - return py_code; -bad: - Py_XDECREF(py_srcfile); - Py_XDECREF(py_funcname); - return NULL; -} -static void __Pyx_AddTraceback(const char *funcname, int c_line, - int py_line, const char *filename) { - PyCodeObject *py_code = 0; - PyFrameObject *py_frame = 0; - py_code = __pyx_find_code_object(c_line ? c_line : py_line); - if (!py_code) { - py_code = __Pyx_CreateCodeObjectForTraceback( - funcname, c_line, py_line, filename); - if (!py_code) goto bad; - __pyx_insert_code_object(c_line ? c_line : py_line, py_code); - } - py_frame = PyFrame_New( - PyThreadState_GET(), /*PyThreadState *tstate,*/ - py_code, /*PyCodeObject *code,*/ - __pyx_d, /*PyObject *globals,*/ - 0 /*PyObject *locals*/ - ); - if (!py_frame) goto bad; - __Pyx_PyFrame_SetLineNumber(py_frame, py_line); - PyTraceBack_Here(py_frame); -bad: - Py_XDECREF(py_code); - Py_XDECREF(py_frame); -} - -/* CIntToPy */ -static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value) { - const long neg_one = (long) -1, const_zero = (long) 0; - const int is_unsigned = neg_one > const_zero; - if (is_unsigned) { - if (sizeof(long) < sizeof(long)) { - return PyInt_FromLong((long) value); - } else if (sizeof(long) <= sizeof(unsigned long)) { - return PyLong_FromUnsignedLong((unsigned long) value); -#ifdef HAVE_LONG_LONG - } else if (sizeof(long) <= sizeof(unsigned PY_LONG_LONG)) { - return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value); -#endif - } - } else { - if (sizeof(long) <= sizeof(long)) { - return PyInt_FromLong((long) value); -#ifdef HAVE_LONG_LONG - } else if (sizeof(long) <= sizeof(PY_LONG_LONG)) { - return PyLong_FromLongLong((PY_LONG_LONG) value); -#endif - } - } - { - int one = 1; int little = (int)*(unsigned char *)&one; - unsigned char *bytes = (unsigned char *)&value; - return _PyLong_FromByteArray(bytes, sizeof(long), - little, !is_unsigned); - } -} - -/* CIntFromPyVerify */ -#define __PYX_VERIFY_RETURN_INT(target_type, func_type, func_value)\ - __PYX__VERIFY_RETURN_INT(target_type, func_type, func_value, 0) -#define __PYX_VERIFY_RETURN_INT_EXC(target_type, func_type, func_value)\ - __PYX__VERIFY_RETURN_INT(target_type, func_type, func_value, 1) -#define __PYX__VERIFY_RETURN_INT(target_type, func_type, func_value, exc)\ - {\ - func_type value = func_value;\ - if (sizeof(target_type) < sizeof(func_type)) {\ - if (unlikely(value != (func_type) (target_type) value)) {\ - func_type zero = 0;\ - if (exc && unlikely(value == (func_type)-1 && PyErr_Occurred()))\ - return (target_type) -1;\ - if (is_unsigned && unlikely(value < zero))\ - goto raise_neg_overflow;\ - else\ - goto raise_overflow;\ - }\ - }\ - return (target_type) value;\ - } - -/* CIntFromPy */ -static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *x) { - const long neg_one = (long) -1, const_zero = (long) 0; - const int is_unsigned = neg_one > const_zero; -#if PY_MAJOR_VERSION < 3 - if (likely(PyInt_Check(x))) { - if (sizeof(long) < sizeof(long)) { - __PYX_VERIFY_RETURN_INT(long, long, PyInt_AS_LONG(x)) - } else { - long val = PyInt_AS_LONG(x); - if (is_unsigned && unlikely(val < 0)) { - goto raise_neg_overflow; - } - return (long) val; - } - } else -#endif - if (likely(PyLong_Check(x))) { - if (is_unsigned) { -#if CYTHON_USE_PYLONG_INTERNALS - const digit* digits = ((PyLongObject*)x)->ob_digit; - switch (Py_SIZE(x)) { - case 0: return (long) 0; - case 1: __PYX_VERIFY_RETURN_INT(long, digit, digits[0]) - case 2: - if (8 * sizeof(long) > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) >= 2 * PyLong_SHIFT) { - return (long) (((((long)digits[1]) << PyLong_SHIFT) | (long)digits[0])); - } - } - break; - case 3: - if (8 * sizeof(long) > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) >= 3 * PyLong_SHIFT) { - return (long) (((((((long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0])); - } - } - break; - case 4: - if (8 * sizeof(long) > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) >= 4 * PyLong_SHIFT) { - return (long) (((((((((long)digits[3]) << PyLong_SHIFT) | (long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0])); - } - } - break; - } -#endif -#if CYTHON_COMPILING_IN_CPYTHON - if (unlikely(Py_SIZE(x) < 0)) { - goto raise_neg_overflow; - } -#else - { - int result = PyObject_RichCompareBool(x, Py_False, Py_LT); - if (unlikely(result < 0)) - return (long) -1; - if (unlikely(result == 1)) - goto raise_neg_overflow; - } -#endif - if (sizeof(long) <= sizeof(unsigned long)) { - __PYX_VERIFY_RETURN_INT_EXC(long, unsigned long, PyLong_AsUnsignedLong(x)) -#ifdef HAVE_LONG_LONG - } else if (sizeof(long) <= sizeof(unsigned PY_LONG_LONG)) { - __PYX_VERIFY_RETURN_INT_EXC(long, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x)) -#endif - } - } else { -#if CYTHON_USE_PYLONG_INTERNALS - const digit* digits = ((PyLongObject*)x)->ob_digit; - switch (Py_SIZE(x)) { - case 0: return (long) 0; - case -1: __PYX_VERIFY_RETURN_INT(long, sdigit, (sdigit) (-(sdigit)digits[0])) - case 1: __PYX_VERIFY_RETURN_INT(long, digit, +digits[0]) - case -2: - if (8 * sizeof(long) - 1 > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { - return (long) (((long)-1)*(((((long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); - } - } - break; - case 2: - if (8 * sizeof(long) > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { - return (long) ((((((long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); - } - } - break; - case -3: - if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { - return (long) (((long)-1)*(((((((long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); - } - } - break; - case 3: - if (8 * sizeof(long) > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { - return (long) ((((((((long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); - } - } - break; - case -4: - if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) { - return (long) (((long)-1)*(((((((((long)digits[3]) << PyLong_SHIFT) | (long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); - } - } - break; - case 4: - if (8 * sizeof(long) > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) { - return (long) ((((((((((long)digits[3]) << PyLong_SHIFT) | (long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); - } - } - break; - } -#endif - if (sizeof(long) <= sizeof(long)) { - __PYX_VERIFY_RETURN_INT_EXC(long, long, PyLong_AsLong(x)) -#ifdef HAVE_LONG_LONG - } else if (sizeof(long) <= sizeof(PY_LONG_LONG)) { - __PYX_VERIFY_RETURN_INT_EXC(long, PY_LONG_LONG, PyLong_AsLongLong(x)) -#endif - } - } - { -#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray) - PyErr_SetString(PyExc_RuntimeError, - "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers"); -#else - long val; - PyObject *v = __Pyx_PyNumber_IntOrLong(x); - #if PY_MAJOR_VERSION < 3 - if (likely(v) && !PyLong_Check(v)) { - PyObject *tmp = v; - v = PyNumber_Long(tmp); - Py_DECREF(tmp); - } - #endif - if (likely(v)) { - int one = 1; int is_little = (int)*(unsigned char *)&one; - unsigned char *bytes = (unsigned char *)&val; - int ret = _PyLong_AsByteArray((PyLongObject *)v, - bytes, sizeof(val), - is_little, !is_unsigned); - Py_DECREF(v); - if (likely(!ret)) - return val; - } -#endif - return (long) -1; - } - } else { - long val; - PyObject *tmp = __Pyx_PyNumber_IntOrLong(x); - if (!tmp) return (long) -1; - val = __Pyx_PyInt_As_long(tmp); - Py_DECREF(tmp); - return val; - } -raise_overflow: - PyErr_SetString(PyExc_OverflowError, - "value too large to convert to long"); - return (long) -1; -raise_neg_overflow: - PyErr_SetString(PyExc_OverflowError, - "can't convert negative value to long"); - return (long) -1; -} - -/* CIntFromPy */ -static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *x) { - const int neg_one = (int) -1, const_zero = (int) 0; - const int is_unsigned = neg_one > const_zero; -#if PY_MAJOR_VERSION < 3 - if (likely(PyInt_Check(x))) { - if (sizeof(int) < sizeof(long)) { - __PYX_VERIFY_RETURN_INT(int, long, PyInt_AS_LONG(x)) - } else { - long val = PyInt_AS_LONG(x); - if (is_unsigned && unlikely(val < 0)) { - goto raise_neg_overflow; - } - return (int) val; - } - } else -#endif - if (likely(PyLong_Check(x))) { - if (is_unsigned) { -#if CYTHON_USE_PYLONG_INTERNALS - const digit* digits = ((PyLongObject*)x)->ob_digit; - switch (Py_SIZE(x)) { - case 0: return (int) 0; - case 1: __PYX_VERIFY_RETURN_INT(int, digit, digits[0]) - case 2: - if (8 * sizeof(int) > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) >= 2 * PyLong_SHIFT) { - return (int) (((((int)digits[1]) << PyLong_SHIFT) | (int)digits[0])); - } - } - break; - case 3: - if (8 * sizeof(int) > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) >= 3 * PyLong_SHIFT) { - return (int) (((((((int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0])); - } - } - break; - case 4: - if (8 * sizeof(int) > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) >= 4 * PyLong_SHIFT) { - return (int) (((((((((int)digits[3]) << PyLong_SHIFT) | (int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0])); - } - } - break; - } -#endif -#if CYTHON_COMPILING_IN_CPYTHON - if (unlikely(Py_SIZE(x) < 0)) { - goto raise_neg_overflow; - } -#else - { - int result = PyObject_RichCompareBool(x, Py_False, Py_LT); - if (unlikely(result < 0)) - return (int) -1; - if (unlikely(result == 1)) - goto raise_neg_overflow; - } -#endif - if (sizeof(int) <= sizeof(unsigned long)) { - __PYX_VERIFY_RETURN_INT_EXC(int, unsigned long, PyLong_AsUnsignedLong(x)) -#ifdef HAVE_LONG_LONG - } else if (sizeof(int) <= sizeof(unsigned PY_LONG_LONG)) { - __PYX_VERIFY_RETURN_INT_EXC(int, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x)) -#endif - } - } else { -#if CYTHON_USE_PYLONG_INTERNALS - const digit* digits = ((PyLongObject*)x)->ob_digit; - switch (Py_SIZE(x)) { - case 0: return (int) 0; - case -1: __PYX_VERIFY_RETURN_INT(int, sdigit, (sdigit) (-(sdigit)digits[0])) - case 1: __PYX_VERIFY_RETURN_INT(int, digit, +digits[0]) - case -2: - if (8 * sizeof(int) - 1 > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) - 1 > 2 * PyLong_SHIFT) { - return (int) (((int)-1)*(((((int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); - } - } - break; - case 2: - if (8 * sizeof(int) > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) - 1 > 2 * PyLong_SHIFT) { - return (int) ((((((int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); - } - } - break; - case -3: - if (8 * sizeof(int) - 1 > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) - 1 > 3 * PyLong_SHIFT) { - return (int) (((int)-1)*(((((((int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); - } - } - break; - case 3: - if (8 * sizeof(int) > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) - 1 > 3 * PyLong_SHIFT) { - return (int) ((((((((int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); - } - } - break; - case -4: - if (8 * sizeof(int) - 1 > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) - 1 > 4 * PyLong_SHIFT) { - return (int) (((int)-1)*(((((((((int)digits[3]) << PyLong_SHIFT) | (int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); - } - } - break; - case 4: - if (8 * sizeof(int) > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) - 1 > 4 * PyLong_SHIFT) { - return (int) ((((((((((int)digits[3]) << PyLong_SHIFT) | (int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); - } - } - break; - } -#endif - if (sizeof(int) <= sizeof(long)) { - __PYX_VERIFY_RETURN_INT_EXC(int, long, PyLong_AsLong(x)) -#ifdef HAVE_LONG_LONG - } else if (sizeof(int) <= sizeof(PY_LONG_LONG)) { - __PYX_VERIFY_RETURN_INT_EXC(int, PY_LONG_LONG, PyLong_AsLongLong(x)) -#endif - } - } - { -#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray) - PyErr_SetString(PyExc_RuntimeError, - "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers"); -#else - int val; - PyObject *v = __Pyx_PyNumber_IntOrLong(x); - #if PY_MAJOR_VERSION < 3 - if (likely(v) && !PyLong_Check(v)) { - PyObject *tmp = v; - v = PyNumber_Long(tmp); - Py_DECREF(tmp); - } - #endif - if (likely(v)) { - int one = 1; int is_little = (int)*(unsigned char *)&one; - unsigned char *bytes = (unsigned char *)&val; - int ret = _PyLong_AsByteArray((PyLongObject *)v, - bytes, sizeof(val), - is_little, !is_unsigned); - Py_DECREF(v); - if (likely(!ret)) - return val; - } -#endif - return (int) -1; - } - } else { - int val; - PyObject *tmp = __Pyx_PyNumber_IntOrLong(x); - if (!tmp) return (int) -1; - val = __Pyx_PyInt_As_int(tmp); - Py_DECREF(tmp); - return val; - } -raise_overflow: - PyErr_SetString(PyExc_OverflowError, - "value too large to convert to int"); - return (int) -1; -raise_neg_overflow: - PyErr_SetString(PyExc_OverflowError, - "can't convert negative value to int"); - return (int) -1; -} - -/* CheckBinaryVersion */ -static int __Pyx_check_binary_version(void) { - char ctversion[4], rtversion[4]; - PyOS_snprintf(ctversion, 4, "%d.%d", PY_MAJOR_VERSION, PY_MINOR_VERSION); - PyOS_snprintf(rtversion, 4, "%s", Py_GetVersion()); - if (ctversion[0] != rtversion[0] || ctversion[2] != rtversion[2]) { - char message[200]; - PyOS_snprintf(message, sizeof(message), - "compiletime version %s of module '%.100s' " - "does not match runtime version %s", - ctversion, __Pyx_MODULE_NAME, rtversion); - return PyErr_WarnEx(NULL, message, 1); - } - return 0; -} - -/* InitStrings */ -static int __Pyx_InitStrings(__Pyx_StringTabEntry *t) { - while (t->p) { - #if PY_MAJOR_VERSION < 3 - if (t->is_unicode) { - *t->p = PyUnicode_DecodeUTF8(t->s, t->n - 1, NULL); - } else if (t->intern) { - *t->p = PyString_InternFromString(t->s); - } else { - *t->p = PyString_FromStringAndSize(t->s, t->n - 1); - } - #else - if (t->is_unicode | t->is_str) { - if (t->intern) { - *t->p = PyUnicode_InternFromString(t->s); - } else if (t->encoding) { - *t->p = PyUnicode_Decode(t->s, t->n - 1, t->encoding, NULL); - } else { - *t->p = PyUnicode_FromStringAndSize(t->s, t->n - 1); - } - } else { - *t->p = PyBytes_FromStringAndSize(t->s, t->n - 1); - } - #endif - if (!*t->p) - return -1; - ++t; - } - return 0; -} - -static CYTHON_INLINE PyObject* __Pyx_PyUnicode_FromString(const char* c_str) { - return __Pyx_PyUnicode_FromStringAndSize(c_str, (Py_ssize_t)strlen(c_str)); -} -static CYTHON_INLINE char* __Pyx_PyObject_AsString(PyObject* o) { - Py_ssize_t ignore; - return __Pyx_PyObject_AsStringAndSize(o, &ignore); -} -static CYTHON_INLINE char* __Pyx_PyObject_AsStringAndSize(PyObject* o, Py_ssize_t *length) { -#if CYTHON_COMPILING_IN_CPYTHON && (__PYX_DEFAULT_STRING_ENCODING_IS_ASCII || __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT) - if ( -#if PY_MAJOR_VERSION < 3 && __PYX_DEFAULT_STRING_ENCODING_IS_ASCII - __Pyx_sys_getdefaultencoding_not_ascii && -#endif - PyUnicode_Check(o)) { -#if PY_VERSION_HEX < 0x03030000 - char* defenc_c; - PyObject* defenc = _PyUnicode_AsDefaultEncodedString(o, NULL); - if (!defenc) return NULL; - defenc_c = PyBytes_AS_STRING(defenc); -#if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII - { - char* end = defenc_c + PyBytes_GET_SIZE(defenc); - char* c; - for (c = defenc_c; c < end; c++) { - if ((unsigned char) (*c) >= 128) { - PyUnicode_AsASCIIString(o); - return NULL; - } - } - } -#endif - *length = PyBytes_GET_SIZE(defenc); - return defenc_c; -#else - if (__Pyx_PyUnicode_READY(o) == -1) return NULL; -#if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII - if (PyUnicode_IS_ASCII(o)) { - *length = PyUnicode_GET_LENGTH(o); - return PyUnicode_AsUTF8(o); - } else { - PyUnicode_AsASCIIString(o); - return NULL; - } -#else - return PyUnicode_AsUTF8AndSize(o, length); -#endif -#endif - } else -#endif -#if (!CYTHON_COMPILING_IN_PYPY) || (defined(PyByteArray_AS_STRING) && defined(PyByteArray_GET_SIZE)) - if (PyByteArray_Check(o)) { - *length = PyByteArray_GET_SIZE(o); - return PyByteArray_AS_STRING(o); - } else -#endif - { - char* result; - int r = PyBytes_AsStringAndSize(o, &result, length); - if (unlikely(r < 0)) { - return NULL; - } else { - return result; - } - } -} -static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject* x) { - int is_true = x == Py_True; - if (is_true | (x == Py_False) | (x == Py_None)) return is_true; - else return PyObject_IsTrue(x); -} -static CYTHON_INLINE PyObject* __Pyx_PyNumber_IntOrLong(PyObject* x) { -#if CYTHON_USE_TYPE_SLOTS - PyNumberMethods *m; -#endif - const char *name = NULL; - PyObject *res = NULL; -#if PY_MAJOR_VERSION < 3 - if (PyInt_Check(x) || PyLong_Check(x)) -#else - if (PyLong_Check(x)) -#endif - return __Pyx_NewRef(x); -#if CYTHON_USE_TYPE_SLOTS - m = Py_TYPE(x)->tp_as_number; - #if PY_MAJOR_VERSION < 3 - if (m && m->nb_int) { - name = "int"; - res = PyNumber_Int(x); - } - else if (m && m->nb_long) { - name = "long"; - res = PyNumber_Long(x); - } - #else - if (m && m->nb_int) { - name = "int"; - res = PyNumber_Long(x); - } - #endif -#else - res = PyNumber_Int(x); -#endif - if (res) { -#if PY_MAJOR_VERSION < 3 - if (!PyInt_Check(res) && !PyLong_Check(res)) { -#else - if (!PyLong_Check(res)) { -#endif - PyErr_Format(PyExc_TypeError, - "__%.4s__ returned non-%.4s (type %.200s)", - name, name, Py_TYPE(res)->tp_name); - Py_DECREF(res); - return NULL; - } - } - else if (!PyErr_Occurred()) { - PyErr_SetString(PyExc_TypeError, - "an integer is required"); - } - return res; -} -static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject* b) { - Py_ssize_t ival; - PyObject *x; -#if PY_MAJOR_VERSION < 3 - if (likely(PyInt_CheckExact(b))) { - if (sizeof(Py_ssize_t) >= sizeof(long)) - return PyInt_AS_LONG(b); - else - return PyInt_AsSsize_t(x); - } -#endif - if (likely(PyLong_CheckExact(b))) { - #if CYTHON_USE_PYLONG_INTERNALS - const digit* digits = ((PyLongObject*)b)->ob_digit; - const Py_ssize_t size = Py_SIZE(b); - if (likely(__Pyx_sst_abs(size) <= 1)) { - ival = likely(size) ? digits[0] : 0; - if (size == -1) ival = -ival; - return ival; - } else { - switch (size) { - case 2: - if (8 * sizeof(Py_ssize_t) > 2 * PyLong_SHIFT) { - return (Py_ssize_t) (((((size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); - } - break; - case -2: - if (8 * sizeof(Py_ssize_t) > 2 * PyLong_SHIFT) { - return -(Py_ssize_t) (((((size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); - } - break; - case 3: - if (8 * sizeof(Py_ssize_t) > 3 * PyLong_SHIFT) { - return (Py_ssize_t) (((((((size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); - } - break; - case -3: - if (8 * sizeof(Py_ssize_t) > 3 * PyLong_SHIFT) { - return -(Py_ssize_t) (((((((size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); - } - break; - case 4: - if (8 * sizeof(Py_ssize_t) > 4 * PyLong_SHIFT) { - return (Py_ssize_t) (((((((((size_t)digits[3]) << PyLong_SHIFT) | (size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); - } - break; - case -4: - if (8 * sizeof(Py_ssize_t) > 4 * PyLong_SHIFT) { - return -(Py_ssize_t) (((((((((size_t)digits[3]) << PyLong_SHIFT) | (size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); - } - break; - } - } - #endif - return PyLong_AsSsize_t(b); - } - x = PyNumber_Index(b); - if (!x) return -1; - ival = PyInt_AsSsize_t(x); - Py_DECREF(x); - return ival; -} -static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) { - return PyInt_FromSize_t(ival); -} - - -#endif /* Py_PYTHON_H */ diff --git a/testing/cython/vmd/wrap_vmd.pyx b/testing/cython/vmd/wrap_vmd.pyx deleted file mode 100644 index 5ea14d6..0000000 --- a/testing/cython/vmd/wrap_vmd.pyx +++ /dev/null @@ -1,11 +0,0 @@ -cdef extern from "vmd_wrapper.cpp": - void start_vmd(int pt) - void stop_vmd() - - - -def start(): - start_vmd(5500) - -def stop(): - stop_vmd() diff --git a/testing/cython/wrap.c b/testing/cython/wrap.c deleted file mode 100644 index d90a0cd..0000000 --- a/testing/cython/wrap.c +++ /dev/null @@ -1,1973 +0,0 @@ -/* Generated by Cython 0.25.2 */ - -/* BEGIN: Cython Metadata -{ - "distutils": { - "depends": [ - "gridsearch.C" - ] - }, - "module_name": "wrap" -} -END: Cython Metadata */ - -#define PY_SSIZE_T_CLEAN -#include "Python.h" -#ifndef Py_PYTHON_H - #error Python headers needed to compile C extensions, please install development version of Python. -#elif PY_VERSION_HEX < 0x02060000 || (0x03000000 <= PY_VERSION_HEX && PY_VERSION_HEX < 0x03020000) - #error Cython requires Python 2.6+ or Python 3.2+. -#else -#define CYTHON_ABI "0_25_2" -#include -#ifndef offsetof - #define offsetof(type, member) ( (size_t) & ((type*)0) -> member ) -#endif -#if !defined(WIN32) && !defined(MS_WINDOWS) - #ifndef __stdcall - #define __stdcall - #endif - #ifndef __cdecl - #define __cdecl - #endif - #ifndef __fastcall - #define __fastcall - #endif -#endif -#ifndef DL_IMPORT - #define DL_IMPORT(t) t -#endif -#ifndef DL_EXPORT - #define DL_EXPORT(t) t -#endif -#ifndef HAVE_LONG_LONG - #if PY_VERSION_HEX >= 0x03030000 || (PY_MAJOR_VERSION == 2 && PY_VERSION_HEX >= 0x02070000) - #define HAVE_LONG_LONG - #endif -#endif -#ifndef PY_LONG_LONG - #define PY_LONG_LONG LONG_LONG -#endif -#ifndef Py_HUGE_VAL - #define Py_HUGE_VAL HUGE_VAL -#endif -#ifdef PYPY_VERSION - #define CYTHON_COMPILING_IN_PYPY 1 - #define CYTHON_COMPILING_IN_PYSTON 0 - #define CYTHON_COMPILING_IN_CPYTHON 0 - #undef CYTHON_USE_TYPE_SLOTS - #define CYTHON_USE_TYPE_SLOTS 0 - #undef CYTHON_USE_ASYNC_SLOTS - #define CYTHON_USE_ASYNC_SLOTS 0 - #undef CYTHON_USE_PYLIST_INTERNALS - #define CYTHON_USE_PYLIST_INTERNALS 0 - #undef CYTHON_USE_UNICODE_INTERNALS - #define CYTHON_USE_UNICODE_INTERNALS 0 - #undef CYTHON_USE_UNICODE_WRITER - #define CYTHON_USE_UNICODE_WRITER 0 - #undef CYTHON_USE_PYLONG_INTERNALS - #define CYTHON_USE_PYLONG_INTERNALS 0 - #undef CYTHON_AVOID_BORROWED_REFS - #define CYTHON_AVOID_BORROWED_REFS 1 - #undef CYTHON_ASSUME_SAFE_MACROS - #define CYTHON_ASSUME_SAFE_MACROS 0 - #undef CYTHON_UNPACK_METHODS - #define CYTHON_UNPACK_METHODS 0 - #undef CYTHON_FAST_THREAD_STATE - #define CYTHON_FAST_THREAD_STATE 0 - #undef CYTHON_FAST_PYCALL - #define CYTHON_FAST_PYCALL 0 -#elif defined(PYSTON_VERSION) - #define CYTHON_COMPILING_IN_PYPY 0 - #define CYTHON_COMPILING_IN_PYSTON 1 - #define CYTHON_COMPILING_IN_CPYTHON 0 - #ifndef CYTHON_USE_TYPE_SLOTS - #define CYTHON_USE_TYPE_SLOTS 1 - #endif - #undef CYTHON_USE_ASYNC_SLOTS - #define CYTHON_USE_ASYNC_SLOTS 0 - #undef CYTHON_USE_PYLIST_INTERNALS - #define CYTHON_USE_PYLIST_INTERNALS 0 - #ifndef CYTHON_USE_UNICODE_INTERNALS - #define CYTHON_USE_UNICODE_INTERNALS 1 - #endif - #undef CYTHON_USE_UNICODE_WRITER - #define CYTHON_USE_UNICODE_WRITER 0 - #undef CYTHON_USE_PYLONG_INTERNALS - #define CYTHON_USE_PYLONG_INTERNALS 0 - #ifndef CYTHON_AVOID_BORROWED_REFS - #define CYTHON_AVOID_BORROWED_REFS 0 - #endif - #ifndef CYTHON_ASSUME_SAFE_MACROS - #define CYTHON_ASSUME_SAFE_MACROS 1 - #endif - #ifndef CYTHON_UNPACK_METHODS - #define CYTHON_UNPACK_METHODS 1 - #endif - #undef CYTHON_FAST_THREAD_STATE - #define CYTHON_FAST_THREAD_STATE 0 - #undef CYTHON_FAST_PYCALL - #define CYTHON_FAST_PYCALL 0 -#else - #define CYTHON_COMPILING_IN_PYPY 0 - #define CYTHON_COMPILING_IN_PYSTON 0 - #define CYTHON_COMPILING_IN_CPYTHON 1 - #ifndef CYTHON_USE_TYPE_SLOTS - #define CYTHON_USE_TYPE_SLOTS 1 - #endif - #if PY_MAJOR_VERSION < 3 - #undef CYTHON_USE_ASYNC_SLOTS - #define CYTHON_USE_ASYNC_SLOTS 0 - #elif !defined(CYTHON_USE_ASYNC_SLOTS) - #define CYTHON_USE_ASYNC_SLOTS 1 - #endif - #if PY_VERSION_HEX < 0x02070000 - #undef CYTHON_USE_PYLONG_INTERNALS - #define CYTHON_USE_PYLONG_INTERNALS 0 - #elif !defined(CYTHON_USE_PYLONG_INTERNALS) - #define CYTHON_USE_PYLONG_INTERNALS 1 - #endif - #ifndef CYTHON_USE_PYLIST_INTERNALS - #define CYTHON_USE_PYLIST_INTERNALS 1 - #endif - #ifndef CYTHON_USE_UNICODE_INTERNALS - #define CYTHON_USE_UNICODE_INTERNALS 1 - #endif - #if PY_VERSION_HEX < 0x030300F0 - #undef CYTHON_USE_UNICODE_WRITER - #define CYTHON_USE_UNICODE_WRITER 0 - #elif !defined(CYTHON_USE_UNICODE_WRITER) - #define CYTHON_USE_UNICODE_WRITER 1 - #endif - #ifndef CYTHON_AVOID_BORROWED_REFS - #define CYTHON_AVOID_BORROWED_REFS 0 - #endif - #ifndef CYTHON_ASSUME_SAFE_MACROS - #define CYTHON_ASSUME_SAFE_MACROS 1 - #endif - #ifndef CYTHON_UNPACK_METHODS - #define CYTHON_UNPACK_METHODS 1 - #endif - #ifndef CYTHON_FAST_THREAD_STATE - #define CYTHON_FAST_THREAD_STATE 1 - #endif - #ifndef CYTHON_FAST_PYCALL - #define CYTHON_FAST_PYCALL 1 - #endif -#endif -#if !defined(CYTHON_FAST_PYCCALL) -#define CYTHON_FAST_PYCCALL (CYTHON_FAST_PYCALL && PY_VERSION_HEX >= 0x030600B1) -#endif -#if CYTHON_USE_PYLONG_INTERNALS - #include "longintrepr.h" - #undef SHIFT - #undef BASE - #undef MASK -#endif -#if CYTHON_COMPILING_IN_PYPY && PY_VERSION_HEX < 0x02070600 && !defined(Py_OptimizeFlag) - #define Py_OptimizeFlag 0 -#endif -#define __PYX_BUILD_PY_SSIZE_T "n" -#define CYTHON_FORMAT_SSIZE_T "z" -#if PY_MAJOR_VERSION < 3 - #define __Pyx_BUILTIN_MODULE_NAME "__builtin__" - #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)\ - PyCode_New(a+k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) - #define __Pyx_DefaultClassType PyClass_Type -#else - #define __Pyx_BUILTIN_MODULE_NAME "builtins" - #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)\ - PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) - #define __Pyx_DefaultClassType PyType_Type -#endif -#ifndef Py_TPFLAGS_CHECKTYPES - #define Py_TPFLAGS_CHECKTYPES 0 -#endif -#ifndef Py_TPFLAGS_HAVE_INDEX - #define Py_TPFLAGS_HAVE_INDEX 0 -#endif -#ifndef Py_TPFLAGS_HAVE_NEWBUFFER - #define Py_TPFLAGS_HAVE_NEWBUFFER 0 -#endif -#ifndef Py_TPFLAGS_HAVE_FINALIZE - #define Py_TPFLAGS_HAVE_FINALIZE 0 -#endif -#ifndef METH_FASTCALL - #define METH_FASTCALL 0x80 - typedef PyObject *(*__Pyx_PyCFunctionFast) (PyObject *self, PyObject **args, - Py_ssize_t nargs, PyObject *kwnames); -#else - #define __Pyx_PyCFunctionFast _PyCFunctionFast -#endif -#if CYTHON_FAST_PYCCALL -#define __Pyx_PyFastCFunction_Check(func)\ - ((PyCFunction_Check(func) && (METH_FASTCALL == (PyCFunction_GET_FLAGS(func) & ~(METH_CLASS | METH_STATIC | METH_COEXIST))))) -#else -#define __Pyx_PyFastCFunction_Check(func) 0 -#endif -#if PY_VERSION_HEX > 0x03030000 && defined(PyUnicode_KIND) - #define CYTHON_PEP393_ENABLED 1 - #define __Pyx_PyUnicode_READY(op) (likely(PyUnicode_IS_READY(op)) ?\ - 0 : _PyUnicode_Ready((PyObject *)(op))) - #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_LENGTH(u) - #define __Pyx_PyUnicode_READ_CHAR(u, i) PyUnicode_READ_CHAR(u, i) - #define __Pyx_PyUnicode_MAX_CHAR_VALUE(u) PyUnicode_MAX_CHAR_VALUE(u) - #define __Pyx_PyUnicode_KIND(u) PyUnicode_KIND(u) - #define __Pyx_PyUnicode_DATA(u) PyUnicode_DATA(u) - #define __Pyx_PyUnicode_READ(k, d, i) PyUnicode_READ(k, d, i) - #define __Pyx_PyUnicode_WRITE(k, d, i, ch) PyUnicode_WRITE(k, d, i, ch) - #define __Pyx_PyUnicode_IS_TRUE(u) (0 != (likely(PyUnicode_IS_READY(u)) ? PyUnicode_GET_LENGTH(u) : PyUnicode_GET_SIZE(u))) -#else - #define CYTHON_PEP393_ENABLED 0 - #define PyUnicode_1BYTE_KIND 1 - #define PyUnicode_2BYTE_KIND 2 - #define PyUnicode_4BYTE_KIND 4 - #define __Pyx_PyUnicode_READY(op) (0) - #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_SIZE(u) - #define __Pyx_PyUnicode_READ_CHAR(u, i) ((Py_UCS4)(PyUnicode_AS_UNICODE(u)[i])) - #define __Pyx_PyUnicode_MAX_CHAR_VALUE(u) ((sizeof(Py_UNICODE) == 2) ? 65535 : 1114111) - #define __Pyx_PyUnicode_KIND(u) (sizeof(Py_UNICODE)) - #define __Pyx_PyUnicode_DATA(u) ((void*)PyUnicode_AS_UNICODE(u)) - #define __Pyx_PyUnicode_READ(k, d, i) ((void)(k), (Py_UCS4)(((Py_UNICODE*)d)[i])) - #define __Pyx_PyUnicode_WRITE(k, d, i, ch) (((void)(k)), ((Py_UNICODE*)d)[i] = ch) - #define __Pyx_PyUnicode_IS_TRUE(u) (0 != PyUnicode_GET_SIZE(u)) -#endif -#if CYTHON_COMPILING_IN_PYPY - #define __Pyx_PyUnicode_Concat(a, b) PyNumber_Add(a, b) - #define __Pyx_PyUnicode_ConcatSafe(a, b) PyNumber_Add(a, b) -#else - #define __Pyx_PyUnicode_Concat(a, b) PyUnicode_Concat(a, b) - #define __Pyx_PyUnicode_ConcatSafe(a, b) ((unlikely((a) == Py_None) || unlikely((b) == Py_None)) ?\ - PyNumber_Add(a, b) : __Pyx_PyUnicode_Concat(a, b)) -#endif -#if CYTHON_COMPILING_IN_PYPY && !defined(PyUnicode_Contains) - #define PyUnicode_Contains(u, s) PySequence_Contains(u, s) -#endif -#if CYTHON_COMPILING_IN_PYPY && !defined(PyByteArray_Check) - #define PyByteArray_Check(obj) PyObject_TypeCheck(obj, &PyByteArray_Type) -#endif -#if CYTHON_COMPILING_IN_PYPY && !defined(PyObject_Format) - #define PyObject_Format(obj, fmt) PyObject_CallMethod(obj, "__format__", "O", fmt) -#endif -#if CYTHON_COMPILING_IN_PYPY && !defined(PyObject_Malloc) - #define PyObject_Malloc(s) PyMem_Malloc(s) - #define PyObject_Free(p) PyMem_Free(p) - #define PyObject_Realloc(p) PyMem_Realloc(p) -#endif -#if CYTHON_COMPILING_IN_PYSTON - #define __Pyx_PyCode_HasFreeVars(co) PyCode_HasFreeVars(co) - #define __Pyx_PyFrame_SetLineNumber(frame, lineno) PyFrame_SetLineNumber(frame, lineno) -#else - #define __Pyx_PyCode_HasFreeVars(co) (PyCode_GetNumFree(co) > 0) - #define __Pyx_PyFrame_SetLineNumber(frame, lineno) (frame)->f_lineno = (lineno) -#endif -#define __Pyx_PyString_FormatSafe(a, b) ((unlikely((a) == Py_None)) ? 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Py_XDECREF(py_funcname); - return NULL; -} -static void __Pyx_AddTraceback(const char *funcname, int c_line, - int py_line, const char *filename) { - PyCodeObject *py_code = 0; - PyFrameObject *py_frame = 0; - py_code = __pyx_find_code_object(c_line ? c_line : py_line); - if (!py_code) { - py_code = __Pyx_CreateCodeObjectForTraceback( - funcname, c_line, py_line, filename); - if (!py_code) goto bad; - __pyx_insert_code_object(c_line ? c_line : py_line, py_code); - } - py_frame = PyFrame_New( - PyThreadState_GET(), /*PyThreadState *tstate,*/ - py_code, /*PyCodeObject *code,*/ - __pyx_d, /*PyObject *globals,*/ - 0 /*PyObject *locals*/ - ); - if (!py_frame) goto bad; - __Pyx_PyFrame_SetLineNumber(py_frame, py_line); - PyTraceBack_Here(py_frame); -bad: - Py_XDECREF(py_code); - Py_XDECREF(py_frame); -} - -/* CIntToPy */ -static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int(int value) { - const int neg_one = (int) -1, const_zero = (int) 0; - const int is_unsigned = neg_one > const_zero; - if (is_unsigned) { - 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} - return f; -} -static int __Pyx_Print(PyObject* f, PyObject *arg_tuple, int newline) { - int i; - if (!f) { - if (!(f = __Pyx_GetStdout())) - return -1; - } - Py_INCREF(f); - for (i=0; i < PyTuple_GET_SIZE(arg_tuple); i++) { - PyObject* v; - if (PyFile_SoftSpace(f, 1)) { - if (PyFile_WriteString(" ", f) < 0) - goto error; - } - v = PyTuple_GET_ITEM(arg_tuple, i); - if (PyFile_WriteObject(v, f, Py_PRINT_RAW) < 0) - goto error; - if (PyString_Check(v)) { - char *s = PyString_AsString(v); - Py_ssize_t len = PyString_Size(v); - if (len > 0) { - switch (s[len-1]) { - case ' ': break; - case '\f': case '\r': case '\n': case '\t': case '\v': - PyFile_SoftSpace(f, 0); - break; - default: break; - } - } - } - } - if (newline) { - if (PyFile_WriteString("\n", f) < 0) - goto error; - PyFile_SoftSpace(f, 0); - } - Py_DECREF(f); - return 0; -error: - Py_DECREF(f); - return -1; -} -#else -static int __Pyx_Print(PyObject* stream, PyObject *arg_tuple, int newline) { - PyObject* kwargs = 0; - PyObject* result = 0; - 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if (likely(PyInt_Check(x))) { - if (sizeof(long) < sizeof(long)) { - __PYX_VERIFY_RETURN_INT(long, long, PyInt_AS_LONG(x)) - } else { - long val = PyInt_AS_LONG(x); - if (is_unsigned && unlikely(val < 0)) { - goto raise_neg_overflow; - } - return (long) val; - } - } else -#endif - if (likely(PyLong_Check(x))) { - if (is_unsigned) { -#if CYTHON_USE_PYLONG_INTERNALS - const digit* digits = ((PyLongObject*)x)->ob_digit; - switch (Py_SIZE(x)) { - case 0: return (long) 0; - case 1: __PYX_VERIFY_RETURN_INT(long, digit, digits[0]) - case 2: - if (8 * sizeof(long) > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) >= 2 * PyLong_SHIFT) { - return (long) (((((long)digits[1]) << PyLong_SHIFT) | (long)digits[0])); - } - } - break; - case 3: - if (8 * sizeof(long) > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) >= 3 * PyLong_SHIFT) { - return (long) (((((((long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0])); - } - } - break; - case 4: - if (8 * sizeof(long) > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) >= 4 * PyLong_SHIFT) { - return (long) (((((((((long)digits[3]) << PyLong_SHIFT) | (long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0])); - } - } - break; - } -#endif -#if CYTHON_COMPILING_IN_CPYTHON - if (unlikely(Py_SIZE(x) < 0)) { - goto raise_neg_overflow; - } -#else - { - int result = PyObject_RichCompareBool(x, Py_False, Py_LT); - if (unlikely(result < 0)) - return (long) -1; - if (unlikely(result == 1)) - goto raise_neg_overflow; - } -#endif - if (sizeof(long) <= sizeof(unsigned long)) { - __PYX_VERIFY_RETURN_INT_EXC(long, unsigned long, PyLong_AsUnsignedLong(x)) -#ifdef HAVE_LONG_LONG - } else if (sizeof(long) <= sizeof(unsigned PY_LONG_LONG)) { - __PYX_VERIFY_RETURN_INT_EXC(long, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x)) -#endif - } - } else { -#if CYTHON_USE_PYLONG_INTERNALS - const digit* digits = ((PyLongObject*)x)->ob_digit; - switch (Py_SIZE(x)) { - case 0: return (long) 0; - case -1: __PYX_VERIFY_RETURN_INT(long, sdigit, (sdigit) (-(sdigit)digits[0])) - case 1: __PYX_VERIFY_RETURN_INT(long, digit, +digits[0]) - case -2: - if (8 * sizeof(long) - 1 > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { - return (long) (((long)-1)*(((((long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); - } - } - break; - case 2: - if (8 * sizeof(long) > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { - return (long) ((((((long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); - } - } - break; - case -3: - if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { - return (long) (((long)-1)*(((((((long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); - } - } - break; - case 3: - if (8 * sizeof(long) > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { - return (long) ((((((((long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); - } - } - break; - case -4: - if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) { - return (long) (((long)-1)*(((((((((long)digits[3]) << PyLong_SHIFT) | (long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); - } - } - break; - case 4: - if (8 * sizeof(long) > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) { - return (long) ((((((((((long)digits[3]) << PyLong_SHIFT) | (long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); - } - } - break; - } -#endif - if (sizeof(long) <= sizeof(long)) { - __PYX_VERIFY_RETURN_INT_EXC(long, long, PyLong_AsLong(x)) -#ifdef HAVE_LONG_LONG - } else if (sizeof(long) <= sizeof(PY_LONG_LONG)) { - __PYX_VERIFY_RETURN_INT_EXC(long, PY_LONG_LONG, PyLong_AsLongLong(x)) -#endif - } - } - { -#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray) - PyErr_SetString(PyExc_RuntimeError, - "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers"); -#else - long val; - PyObject *v = __Pyx_PyNumber_IntOrLong(x); - #if PY_MAJOR_VERSION < 3 - if (likely(v) && !PyLong_Check(v)) { - PyObject *tmp = v; - v = PyNumber_Long(tmp); - Py_DECREF(tmp); - } - #endif - if (likely(v)) { - int one = 1; int is_little = (int)*(unsigned char *)&one; - unsigned char *bytes = (unsigned char *)&val; - int ret = _PyLong_AsByteArray((PyLongObject *)v, - bytes, sizeof(val), - is_little, !is_unsigned); - Py_DECREF(v); - if (likely(!ret)) - return val; - } -#endif - return (long) -1; - } - } else { - long val; - PyObject *tmp = __Pyx_PyNumber_IntOrLong(x); - if (!tmp) return (long) -1; - val = __Pyx_PyInt_As_long(tmp); - Py_DECREF(tmp); - return val; - } -raise_overflow: - PyErr_SetString(PyExc_OverflowError, - "value too large to convert to long"); - return (long) -1; -raise_neg_overflow: - PyErr_SetString(PyExc_OverflowError, - "can't convert negative value to long"); - return (long) -1; -} - -/* CIntFromPy */ -static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *x) { - const int neg_one = (int) -1, const_zero = (int) 0; - const int is_unsigned = neg_one > const_zero; -#if PY_MAJOR_VERSION < 3 - if (likely(PyInt_Check(x))) { - if (sizeof(int) < sizeof(long)) { - __PYX_VERIFY_RETURN_INT(int, long, PyInt_AS_LONG(x)) - } else { - long val = PyInt_AS_LONG(x); - if (is_unsigned && unlikely(val < 0)) { - goto raise_neg_overflow; - } - return (int) val; - } - } else -#endif - if (likely(PyLong_Check(x))) { - if (is_unsigned) { -#if CYTHON_USE_PYLONG_INTERNALS - const digit* digits = ((PyLongObject*)x)->ob_digit; - switch (Py_SIZE(x)) { - case 0: return (int) 0; - case 1: __PYX_VERIFY_RETURN_INT(int, digit, digits[0]) - case 2: - if (8 * sizeof(int) > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) >= 2 * PyLong_SHIFT) { - return (int) (((((int)digits[1]) << PyLong_SHIFT) | (int)digits[0])); - } - } - break; - case 3: - if (8 * sizeof(int) > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) >= 3 * PyLong_SHIFT) { - return (int) (((((((int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0])); - } - } - break; - case 4: - if (8 * sizeof(int) > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) >= 4 * PyLong_SHIFT) { - return (int) (((((((((int)digits[3]) << PyLong_SHIFT) | (int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0])); - } - } - break; - } -#endif -#if CYTHON_COMPILING_IN_CPYTHON - if (unlikely(Py_SIZE(x) < 0)) { - goto raise_neg_overflow; - } -#else - { - int result = PyObject_RichCompareBool(x, Py_False, Py_LT); - if (unlikely(result < 0)) - return (int) -1; - if (unlikely(result == 1)) - goto raise_neg_overflow; - } -#endif - if (sizeof(int) <= sizeof(unsigned long)) { - __PYX_VERIFY_RETURN_INT_EXC(int, unsigned long, PyLong_AsUnsignedLong(x)) -#ifdef HAVE_LONG_LONG - } else if (sizeof(int) <= sizeof(unsigned PY_LONG_LONG)) { - __PYX_VERIFY_RETURN_INT_EXC(int, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x)) -#endif - } - } else { -#if CYTHON_USE_PYLONG_INTERNALS - const digit* digits = ((PyLongObject*)x)->ob_digit; - switch (Py_SIZE(x)) { - case 0: return (int) 0; - case -1: __PYX_VERIFY_RETURN_INT(int, sdigit, (sdigit) (-(sdigit)digits[0])) - case 1: __PYX_VERIFY_RETURN_INT(int, digit, +digits[0]) - case -2: - if (8 * sizeof(int) - 1 > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) - 1 > 2 * PyLong_SHIFT) { - return (int) (((int)-1)*(((((int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); - } - } - break; - case 2: - if (8 * sizeof(int) > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) - 1 > 2 * PyLong_SHIFT) { - return (int) ((((((int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); - } - } - break; - case -3: - if (8 * sizeof(int) - 1 > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) - 1 > 3 * PyLong_SHIFT) { - return (int) (((int)-1)*(((((((int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); - } - } - break; - case 3: - if (8 * sizeof(int) > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) - 1 > 3 * PyLong_SHIFT) { - return (int) ((((((((int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); - } - } - break; - case -4: - if (8 * sizeof(int) - 1 > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) - 1 > 4 * PyLong_SHIFT) { - return (int) (((int)-1)*(((((((((int)digits[3]) << PyLong_SHIFT) | (int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); - } - } - break; - case 4: - if (8 * sizeof(int) > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) - 1 > 4 * PyLong_SHIFT) { - return (int) ((((((((((int)digits[3]) << PyLong_SHIFT) | (int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); - } - } - break; - } -#endif - if (sizeof(int) <= sizeof(long)) { - __PYX_VERIFY_RETURN_INT_EXC(int, long, PyLong_AsLong(x)) -#ifdef HAVE_LONG_LONG - } else if (sizeof(int) <= sizeof(PY_LONG_LONG)) { - __PYX_VERIFY_RETURN_INT_EXC(int, PY_LONG_LONG, PyLong_AsLongLong(x)) -#endif - } - } - { -#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray) - PyErr_SetString(PyExc_RuntimeError, - "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers"); -#else - int val; - PyObject *v = __Pyx_PyNumber_IntOrLong(x); - #if PY_MAJOR_VERSION < 3 - if (likely(v) && !PyLong_Check(v)) { - PyObject *tmp = v; - v = PyNumber_Long(tmp); - Py_DECREF(tmp); - } - #endif - if (likely(v)) { - int one = 1; int is_little = (int)*(unsigned char *)&one; - unsigned char *bytes = (unsigned char *)&val; - int ret = _PyLong_AsByteArray((PyLongObject *)v, - bytes, sizeof(val), - is_little, !is_unsigned); - Py_DECREF(v); - if (likely(!ret)) - return val; - } -#endif - return (int) -1; - } - } else { - int val; - PyObject *tmp = __Pyx_PyNumber_IntOrLong(x); - if (!tmp) return (int) -1; - val = __Pyx_PyInt_As_int(tmp); - Py_DECREF(tmp); - return val; - } -raise_overflow: - PyErr_SetString(PyExc_OverflowError, - "value too large to convert to int"); - return (int) -1; -raise_neg_overflow: - PyErr_SetString(PyExc_OverflowError, - "can't convert negative value to int"); - return (int) -1; -} - -/* CheckBinaryVersion */ -static int __Pyx_check_binary_version(void) { - char ctversion[4], rtversion[4]; - PyOS_snprintf(ctversion, 4, "%d.%d", PY_MAJOR_VERSION, PY_MINOR_VERSION); - PyOS_snprintf(rtversion, 4, "%s", Py_GetVersion()); - if (ctversion[0] != rtversion[0] || ctversion[2] != rtversion[2]) { - char message[200]; - PyOS_snprintf(message, sizeof(message), - "compiletime version %s of module '%.100s' " - "does not match runtime version %s", - ctversion, __Pyx_MODULE_NAME, rtversion); - return PyErr_WarnEx(NULL, message, 1); - } - return 0; -} - -/* InitStrings */ -static int __Pyx_InitStrings(__Pyx_StringTabEntry *t) { - while (t->p) { - #if PY_MAJOR_VERSION < 3 - if (t->is_unicode) { - *t->p = PyUnicode_DecodeUTF8(t->s, t->n - 1, NULL); - } else if (t->intern) { - *t->p = PyString_InternFromString(t->s); - } else { - *t->p = PyString_FromStringAndSize(t->s, t->n - 1); - } - #else - if (t->is_unicode | t->is_str) { - if (t->intern) { - *t->p = PyUnicode_InternFromString(t->s); - } else if (t->encoding) { - *t->p = PyUnicode_Decode(t->s, t->n - 1, t->encoding, NULL); - } else { - *t->p = PyUnicode_FromStringAndSize(t->s, t->n - 1); - } - } else { - *t->p = PyBytes_FromStringAndSize(t->s, t->n - 1); - } - #endif - if (!*t->p) - return -1; - ++t; - } - return 0; -} - -static CYTHON_INLINE PyObject* __Pyx_PyUnicode_FromString(const char* c_str) { - return __Pyx_PyUnicode_FromStringAndSize(c_str, (Py_ssize_t)strlen(c_str)); -} -static CYTHON_INLINE char* __Pyx_PyObject_AsString(PyObject* o) { - Py_ssize_t ignore; - return __Pyx_PyObject_AsStringAndSize(o, &ignore); -} -static CYTHON_INLINE char* __Pyx_PyObject_AsStringAndSize(PyObject* o, Py_ssize_t *length) { -#if CYTHON_COMPILING_IN_CPYTHON && (__PYX_DEFAULT_STRING_ENCODING_IS_ASCII || __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT) - if ( -#if PY_MAJOR_VERSION < 3 && __PYX_DEFAULT_STRING_ENCODING_IS_ASCII - __Pyx_sys_getdefaultencoding_not_ascii && -#endif - PyUnicode_Check(o)) { -#if PY_VERSION_HEX < 0x03030000 - char* defenc_c; - PyObject* defenc = _PyUnicode_AsDefaultEncodedString(o, NULL); - if (!defenc) return NULL; - defenc_c = PyBytes_AS_STRING(defenc); -#if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII - { - char* end = defenc_c + PyBytes_GET_SIZE(defenc); - char* c; - for (c = defenc_c; c < end; c++) { - if ((unsigned char) (*c) >= 128) { - PyUnicode_AsASCIIString(o); - return NULL; - } - } - } -#endif - *length = PyBytes_GET_SIZE(defenc); - return defenc_c; -#else - if (__Pyx_PyUnicode_READY(o) == -1) return NULL; -#if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII - if (PyUnicode_IS_ASCII(o)) { - *length = PyUnicode_GET_LENGTH(o); - return PyUnicode_AsUTF8(o); - } else { - PyUnicode_AsASCIIString(o); - return NULL; - } -#else - return PyUnicode_AsUTF8AndSize(o, length); -#endif -#endif - } else -#endif -#if (!CYTHON_COMPILING_IN_PYPY) || (defined(PyByteArray_AS_STRING) && defined(PyByteArray_GET_SIZE)) - if (PyByteArray_Check(o)) { - *length = PyByteArray_GET_SIZE(o); - return PyByteArray_AS_STRING(o); - } else -#endif - { - char* result; - int r = PyBytes_AsStringAndSize(o, &result, length); - if (unlikely(r < 0)) { - return NULL; - } else { - return result; - } - } -} -static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject* x) { - int is_true = x == Py_True; - if (is_true | (x == Py_False) | (x == Py_None)) return is_true; - else return PyObject_IsTrue(x); -} -static CYTHON_INLINE PyObject* __Pyx_PyNumber_IntOrLong(PyObject* x) { -#if CYTHON_USE_TYPE_SLOTS - PyNumberMethods *m; -#endif - const char *name = NULL; - PyObject *res = NULL; -#if PY_MAJOR_VERSION < 3 - if (PyInt_Check(x) || PyLong_Check(x)) -#else - if (PyLong_Check(x)) -#endif - return __Pyx_NewRef(x); -#if CYTHON_USE_TYPE_SLOTS - m = Py_TYPE(x)->tp_as_number; - #if PY_MAJOR_VERSION < 3 - if (m && m->nb_int) { - name = "int"; - res = PyNumber_Int(x); - } - else if (m && m->nb_long) { - name = "long"; - res = PyNumber_Long(x); - } - #else - if (m && m->nb_int) { - name = "int"; - res = PyNumber_Long(x); - } - #endif -#else - res = PyNumber_Int(x); -#endif - if (res) { -#if PY_MAJOR_VERSION < 3 - if (!PyInt_Check(res) && !PyLong_Check(res)) { -#else - if (!PyLong_Check(res)) { -#endif - PyErr_Format(PyExc_TypeError, - "__%.4s__ returned non-%.4s (type %.200s)", - name, name, Py_TYPE(res)->tp_name); - Py_DECREF(res); - return NULL; - } - } - else if (!PyErr_Occurred()) { - PyErr_SetString(PyExc_TypeError, - "an integer is required"); - } - return res; -} -static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject* b) { - Py_ssize_t ival; - PyObject *x; -#if PY_MAJOR_VERSION < 3 - if (likely(PyInt_CheckExact(b))) { - if (sizeof(Py_ssize_t) >= sizeof(long)) - return PyInt_AS_LONG(b); - else - return PyInt_AsSsize_t(x); - } -#endif - if (likely(PyLong_CheckExact(b))) { - #if CYTHON_USE_PYLONG_INTERNALS - const digit* digits = ((PyLongObject*)b)->ob_digit; - const Py_ssize_t size = Py_SIZE(b); - if (likely(__Pyx_sst_abs(size) <= 1)) { - ival = likely(size) ? digits[0] : 0; - if (size == -1) ival = -ival; - return ival; - } else { - switch (size) { - case 2: - if (8 * sizeof(Py_ssize_t) > 2 * PyLong_SHIFT) { - return (Py_ssize_t) (((((size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); - } - break; - case -2: - if (8 * sizeof(Py_ssize_t) > 2 * PyLong_SHIFT) { - return -(Py_ssize_t) (((((size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); - } - break; - case 3: - if (8 * sizeof(Py_ssize_t) > 3 * PyLong_SHIFT) { - return (Py_ssize_t) (((((((size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); - } - break; - case -3: - if (8 * sizeof(Py_ssize_t) > 3 * PyLong_SHIFT) { - return -(Py_ssize_t) (((((((size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); - } - break; - case 4: - if (8 * sizeof(Py_ssize_t) > 4 * PyLong_SHIFT) { - return (Py_ssize_t) (((((((((size_t)digits[3]) << PyLong_SHIFT) | (size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); - } - break; - case -4: - if (8 * sizeof(Py_ssize_t) > 4 * PyLong_SHIFT) { - return -(Py_ssize_t) (((((((((size_t)digits[3]) << PyLong_SHIFT) | (size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); - } - break; - } - } - #endif - return PyLong_AsSsize_t(b); - } - x = PyNumber_Index(b); - if (!x) return -1; - ival = PyInt_AsSsize_t(x); - Py_DECREF(x); - return ival; -} -static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) { - return PyInt_FromSize_t(ival); -} - - -#endif /* Py_PYTHON_H */ diff --git a/testing/cython/wrap.cpp b/testing/cython/wrap.cpp deleted file mode 100644 index 117371e..0000000 --- a/testing/cython/wrap.cpp +++ /dev/null @@ -1,20119 +0,0 @@ -/* Generated by Cython 0.25.2 */ - -#define PY_SSIZE_T_CLEAN -#include "Python.h" -#ifndef Py_PYTHON_H - #error Python headers needed to compile C extensions, please install development version of Python. -#elif PY_VERSION_HEX < 0x02060000 || (0x03000000 <= PY_VERSION_HEX && PY_VERSION_HEX < 0x03020000) - #error Cython requires Python 2.6+ or Python 3.2+. -#else -#define CYTHON_ABI "0_25_2" -#include -#ifndef offsetof - #define offsetof(type, member) ( (size_t) & ((type*)0) -> member ) -#endif -#if !defined(WIN32) && !defined(MS_WINDOWS) - #ifndef __stdcall - #define __stdcall - #endif - #ifndef __cdecl - #define __cdecl - #endif - #ifndef __fastcall - #define __fastcall - #endif -#endif -#ifndef DL_IMPORT - #define DL_IMPORT(t) t -#endif -#ifndef DL_EXPORT - #define DL_EXPORT(t) t -#endif -#ifndef HAVE_LONG_LONG - #if PY_VERSION_HEX >= 0x03030000 || (PY_MAJOR_VERSION == 2 && PY_VERSION_HEX >= 0x02070000) - #define HAVE_LONG_LONG - #endif -#endif -#ifndef PY_LONG_LONG - #define PY_LONG_LONG LONG_LONG -#endif -#ifndef Py_HUGE_VAL - #define Py_HUGE_VAL HUGE_VAL -#endif -#ifdef PYPY_VERSION - #define CYTHON_COMPILING_IN_PYPY 1 - #define CYTHON_COMPILING_IN_PYSTON 0 - #define CYTHON_COMPILING_IN_CPYTHON 0 - #undef CYTHON_USE_TYPE_SLOTS - #define CYTHON_USE_TYPE_SLOTS 0 - #undef CYTHON_USE_ASYNC_SLOTS - #define CYTHON_USE_ASYNC_SLOTS 0 - #undef CYTHON_USE_PYLIST_INTERNALS - #define CYTHON_USE_PYLIST_INTERNALS 0 - #undef CYTHON_USE_UNICODE_INTERNALS - #define CYTHON_USE_UNICODE_INTERNALS 0 - #undef CYTHON_USE_UNICODE_WRITER - #define CYTHON_USE_UNICODE_WRITER 0 - #undef CYTHON_USE_PYLONG_INTERNALS - #define CYTHON_USE_PYLONG_INTERNALS 0 - #undef CYTHON_AVOID_BORROWED_REFS - #define CYTHON_AVOID_BORROWED_REFS 1 - #undef CYTHON_ASSUME_SAFE_MACROS - #define CYTHON_ASSUME_SAFE_MACROS 0 - #undef CYTHON_UNPACK_METHODS - #define CYTHON_UNPACK_METHODS 0 - #undef CYTHON_FAST_THREAD_STATE - #define CYTHON_FAST_THREAD_STATE 0 - #undef CYTHON_FAST_PYCALL - #define CYTHON_FAST_PYCALL 0 -#elif defined(PYSTON_VERSION) - #define CYTHON_COMPILING_IN_PYPY 0 - #define CYTHON_COMPILING_IN_PYSTON 1 - #define CYTHON_COMPILING_IN_CPYTHON 0 - #ifndef CYTHON_USE_TYPE_SLOTS - #define CYTHON_USE_TYPE_SLOTS 1 - #endif - #undef CYTHON_USE_ASYNC_SLOTS - #define CYTHON_USE_ASYNC_SLOTS 0 - #undef CYTHON_USE_PYLIST_INTERNALS - #define CYTHON_USE_PYLIST_INTERNALS 0 - #ifndef CYTHON_USE_UNICODE_INTERNALS - #define CYTHON_USE_UNICODE_INTERNALS 1 - #endif - #undef CYTHON_USE_UNICODE_WRITER - #define CYTHON_USE_UNICODE_WRITER 0 - #undef CYTHON_USE_PYLONG_INTERNALS - #define CYTHON_USE_PYLONG_INTERNALS 0 - #ifndef CYTHON_AVOID_BORROWED_REFS - #define CYTHON_AVOID_BORROWED_REFS 0 - #endif - #ifndef CYTHON_ASSUME_SAFE_MACROS - #define CYTHON_ASSUME_SAFE_MACROS 1 - #endif - #ifndef CYTHON_UNPACK_METHODS - #define CYTHON_UNPACK_METHODS 1 - #endif - #undef CYTHON_FAST_THREAD_STATE - #define CYTHON_FAST_THREAD_STATE 0 - #undef CYTHON_FAST_PYCALL - #define CYTHON_FAST_PYCALL 0 -#else - #define CYTHON_COMPILING_IN_PYPY 0 - #define CYTHON_COMPILING_IN_PYSTON 0 - #define CYTHON_COMPILING_IN_CPYTHON 1 - #ifndef CYTHON_USE_TYPE_SLOTS - #define CYTHON_USE_TYPE_SLOTS 1 - #endif - #if PY_MAJOR_VERSION < 3 - #undef CYTHON_USE_ASYNC_SLOTS - #define CYTHON_USE_ASYNC_SLOTS 0 - #elif !defined(CYTHON_USE_ASYNC_SLOTS) - #define CYTHON_USE_ASYNC_SLOTS 1 - #endif - #if PY_VERSION_HEX < 0x02070000 - #undef CYTHON_USE_PYLONG_INTERNALS - #define CYTHON_USE_PYLONG_INTERNALS 0 - #elif !defined(CYTHON_USE_PYLONG_INTERNALS) - #define CYTHON_USE_PYLONG_INTERNALS 1 - #endif - #ifndef CYTHON_USE_PYLIST_INTERNALS - #define CYTHON_USE_PYLIST_INTERNALS 1 - #endif - #ifndef CYTHON_USE_UNICODE_INTERNALS - #define CYTHON_USE_UNICODE_INTERNALS 1 - #endif - #if PY_VERSION_HEX < 0x030300F0 - #undef CYTHON_USE_UNICODE_WRITER - #define CYTHON_USE_UNICODE_WRITER 0 - #elif !defined(CYTHON_USE_UNICODE_WRITER) - #define CYTHON_USE_UNICODE_WRITER 1 - #endif - #ifndef CYTHON_AVOID_BORROWED_REFS - #define CYTHON_AVOID_BORROWED_REFS 0 - #endif - #ifndef CYTHON_ASSUME_SAFE_MACROS - #define CYTHON_ASSUME_SAFE_MACROS 1 - #endif - #ifndef CYTHON_UNPACK_METHODS - #define CYTHON_UNPACK_METHODS 1 - #endif - #ifndef CYTHON_FAST_THREAD_STATE - #define CYTHON_FAST_THREAD_STATE 1 - #endif - #ifndef CYTHON_FAST_PYCALL - #define CYTHON_FAST_PYCALL 1 - #endif -#endif -#if !defined(CYTHON_FAST_PYCCALL) -#define CYTHON_FAST_PYCCALL (CYTHON_FAST_PYCALL && PY_VERSION_HEX >= 0x030600B1) -#endif -#if CYTHON_USE_PYLONG_INTERNALS - #include "longintrepr.h" - #undef SHIFT - #undef BASE - #undef MASK -#endif -#if CYTHON_COMPILING_IN_PYPY && PY_VERSION_HEX < 0x02070600 && !defined(Py_OptimizeFlag) - #define Py_OptimizeFlag 0 -#endif -#define __PYX_BUILD_PY_SSIZE_T "n" -#define CYTHON_FORMAT_SSIZE_T "z" -#if PY_MAJOR_VERSION < 3 - #define __Pyx_BUILTIN_MODULE_NAME "__builtin__" - #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)\ - PyCode_New(a+k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) - #define __Pyx_DefaultClassType PyClass_Type -#else - #define __Pyx_BUILTIN_MODULE_NAME "builtins" - #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)\ - PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) - #define __Pyx_DefaultClassType PyType_Type -#endif -#ifndef Py_TPFLAGS_CHECKTYPES - #define Py_TPFLAGS_CHECKTYPES 0 -#endif -#ifndef Py_TPFLAGS_HAVE_INDEX - #define Py_TPFLAGS_HAVE_INDEX 0 -#endif -#ifndef Py_TPFLAGS_HAVE_NEWBUFFER - #define Py_TPFLAGS_HAVE_NEWBUFFER 0 -#endif -#ifndef Py_TPFLAGS_HAVE_FINALIZE - #define Py_TPFLAGS_HAVE_FINALIZE 0 -#endif -#ifndef METH_FASTCALL - #define METH_FASTCALL 0x80 - typedef PyObject *(*__Pyx_PyCFunctionFast) (PyObject *self, PyObject **args, - Py_ssize_t nargs, PyObject *kwnames); -#else - #define __Pyx_PyCFunctionFast _PyCFunctionFast -#endif -#if CYTHON_FAST_PYCCALL -#define __Pyx_PyFastCFunction_Check(func)\ - ((PyCFunction_Check(func) && (METH_FASTCALL == (PyCFunction_GET_FLAGS(func) & ~(METH_CLASS | METH_STATIC | METH_COEXIST))))) -#else -#define __Pyx_PyFastCFunction_Check(func) 0 -#endif -#if PY_VERSION_HEX > 0x03030000 && defined(PyUnicode_KIND) - #define CYTHON_PEP393_ENABLED 1 - #define __Pyx_PyUnicode_READY(op) (likely(PyUnicode_IS_READY(op)) ?\ - 0 : _PyUnicode_Ready((PyObject *)(op))) - #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_LENGTH(u) - #define __Pyx_PyUnicode_READ_CHAR(u, i) PyUnicode_READ_CHAR(u, i) - #define __Pyx_PyUnicode_MAX_CHAR_VALUE(u) PyUnicode_MAX_CHAR_VALUE(u) - #define __Pyx_PyUnicode_KIND(u) PyUnicode_KIND(u) - #define __Pyx_PyUnicode_DATA(u) PyUnicode_DATA(u) - #define __Pyx_PyUnicode_READ(k, d, i) PyUnicode_READ(k, d, i) - #define __Pyx_PyUnicode_WRITE(k, d, i, ch) PyUnicode_WRITE(k, d, i, ch) - #define __Pyx_PyUnicode_IS_TRUE(u) (0 != (likely(PyUnicode_IS_READY(u)) ? PyUnicode_GET_LENGTH(u) : PyUnicode_GET_SIZE(u))) -#else - #define CYTHON_PEP393_ENABLED 0 - #define PyUnicode_1BYTE_KIND 1 - #define PyUnicode_2BYTE_KIND 2 - #define PyUnicode_4BYTE_KIND 4 - #define __Pyx_PyUnicode_READY(op) (0) - #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_SIZE(u) - #define __Pyx_PyUnicode_READ_CHAR(u, i) ((Py_UCS4)(PyUnicode_AS_UNICODE(u)[i])) - #define __Pyx_PyUnicode_MAX_CHAR_VALUE(u) ((sizeof(Py_UNICODE) == 2) ? 65535 : 1114111) - #define __Pyx_PyUnicode_KIND(u) (sizeof(Py_UNICODE)) - #define __Pyx_PyUnicode_DATA(u) ((void*)PyUnicode_AS_UNICODE(u)) - #define __Pyx_PyUnicode_READ(k, d, i) ((void)(k), (Py_UCS4)(((Py_UNICODE*)d)[i])) - #define __Pyx_PyUnicode_WRITE(k, d, i, ch) (((void)(k)), ((Py_UNICODE*)d)[i] = ch) - #define __Pyx_PyUnicode_IS_TRUE(u) (0 != PyUnicode_GET_SIZE(u)) -#endif -#if CYTHON_COMPILING_IN_PYPY - #define __Pyx_PyUnicode_Concat(a, b) PyNumber_Add(a, b) - #define __Pyx_PyUnicode_ConcatSafe(a, b) PyNumber_Add(a, b) -#else - #define __Pyx_PyUnicode_Concat(a, b) PyUnicode_Concat(a, b) - #define __Pyx_PyUnicode_ConcatSafe(a, b) ((unlikely((a) == Py_None) || unlikely((b) == Py_None)) ?\ - PyNumber_Add(a, b) : __Pyx_PyUnicode_Concat(a, b)) -#endif -#if CYTHON_COMPILING_IN_PYPY && !defined(PyUnicode_Contains) - #define PyUnicode_Contains(u, s) PySequence_Contains(u, s) -#endif -#if CYTHON_COMPILING_IN_PYPY && !defined(PyByteArray_Check) - #define PyByteArray_Check(obj) PyObject_TypeCheck(obj, &PyByteArray_Type) -#endif -#if CYTHON_COMPILING_IN_PYPY && !defined(PyObject_Format) - #define PyObject_Format(obj, fmt) PyObject_CallMethod(obj, "__format__", "O", fmt) -#endif -#if CYTHON_COMPILING_IN_PYPY && !defined(PyObject_Malloc) - #define PyObject_Malloc(s) PyMem_Malloc(s) - #define PyObject_Free(p) PyMem_Free(p) - #define PyObject_Realloc(p) PyMem_Realloc(p) -#endif -#if CYTHON_COMPILING_IN_PYSTON - #define __Pyx_PyCode_HasFreeVars(co) PyCode_HasFreeVars(co) - #define __Pyx_PyFrame_SetLineNumber(frame, lineno) PyFrame_SetLineNumber(frame, lineno) -#else - #define __Pyx_PyCode_HasFreeVars(co) (PyCode_GetNumFree(co) > 0) - #define __Pyx_PyFrame_SetLineNumber(frame, lineno) (frame)->f_lineno = (lineno) -#endif -#define __Pyx_PyString_FormatSafe(a, b) ((unlikely((a) == Py_None)) ? 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const char *s; const Py_ssize_t n; const char* encoding; - const char is_unicode; const char is_str; const char intern; } __Pyx_StringTabEntry; - -#define __PYX_DEFAULT_STRING_ENCODING_IS_ASCII 0 -#define __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT 0 -#define __PYX_DEFAULT_STRING_ENCODING "" -#define __Pyx_PyObject_FromString __Pyx_PyBytes_FromString -#define __Pyx_PyObject_FromStringAndSize __Pyx_PyBytes_FromStringAndSize -#define __Pyx_uchar_cast(c) ((unsigned char)c) -#define __Pyx_long_cast(x) ((long)x) -#define __Pyx_fits_Py_ssize_t(v, type, is_signed) (\ - (sizeof(type) < sizeof(Py_ssize_t)) ||\ - (sizeof(type) > sizeof(Py_ssize_t) &&\ - likely(v < (type)PY_SSIZE_T_MAX ||\ - v == (type)PY_SSIZE_T_MAX) &&\ - (!is_signed || likely(v > (type)PY_SSIZE_T_MIN ||\ - v == (type)PY_SSIZE_T_MIN))) ||\ - (sizeof(type) == sizeof(Py_ssize_t) &&\ - (is_signed || likely(v < (type)PY_SSIZE_T_MAX ||\ - v == (type)PY_SSIZE_T_MAX))) ) -#if defined (__cplusplus) && __cplusplus >= 201103L - #include - #define __Pyx_sst_abs(value) std::abs(value) -#elif SIZEOF_INT >= SIZEOF_SIZE_T - #define __Pyx_sst_abs(value) abs(value) -#elif SIZEOF_LONG >= SIZEOF_SIZE_T - #define __Pyx_sst_abs(value) labs(value) -#elif defined (_MSC_VER) && defined (_M_X64) - #define __Pyx_sst_abs(value) _abs64(value) -#elif defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L - #define __Pyx_sst_abs(value) llabs(value) -#elif defined (__GNUC__) - #define __Pyx_sst_abs(value) __builtin_llabs(value) -#else - #define __Pyx_sst_abs(value) ((value<0) ? -value : value) -#endif -static CYTHON_INLINE char* __Pyx_PyObject_AsString(PyObject*); 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PyFloat_AS_DOUBLE(x) : PyFloat_AsDouble(x)) -#else -#define __pyx_PyFloat_AsDouble(x) PyFloat_AsDouble(x) -#endif -#define __pyx_PyFloat_AsFloat(x) ((float) __pyx_PyFloat_AsDouble(x)) -#if PY_MAJOR_VERSION >= 3 -#define __Pyx_PyNumber_Int(x) (PyLong_CheckExact(x) ? __Pyx_NewRef(x) : PyNumber_Long(x)) -#else -#define __Pyx_PyNumber_Int(x) (PyInt_CheckExact(x) ? __Pyx_NewRef(x) : PyNumber_Int(x)) -#endif -#define __Pyx_PyNumber_Float(x) (PyFloat_CheckExact(x) ? __Pyx_NewRef(x) : PyNumber_Float(x)) -#if PY_MAJOR_VERSION < 3 && __PYX_DEFAULT_STRING_ENCODING_IS_ASCII -static int __Pyx_sys_getdefaultencoding_not_ascii; -static int __Pyx_init_sys_getdefaultencoding_params(void) { - PyObject* sys; - PyObject* default_encoding = NULL; - PyObject* ascii_chars_u = NULL; - PyObject* ascii_chars_b = NULL; - const char* default_encoding_c; - sys = PyImport_ImportModule("sys"); - if (!sys) goto bad; - default_encoding = PyObject_CallMethod(sys, (char*) "getdefaultencoding", NULL); - Py_DECREF(sys); - if (!default_encoding) goto bad; 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- -/* StrEquals.proto */ -#if PY_MAJOR_VERSION >= 3 -#define __Pyx_PyString_Equals __Pyx_PyUnicode_Equals -#else -#define __Pyx_PyString_Equals __Pyx_PyBytes_Equals -#endif - -/* PyObjectCallMethO.proto */ -#if CYTHON_COMPILING_IN_CPYTHON -static CYTHON_INLINE PyObject* __Pyx_PyObject_CallMethO(PyObject *func, PyObject *arg); -#endif - -/* PyObjectCallOneArg.proto */ -static CYTHON_INLINE PyObject* __Pyx_PyObject_CallOneArg(PyObject *func, PyObject *arg); - -/* PySequenceContains.proto */ -static CYTHON_INLINE int __Pyx_PySequence_ContainsTF(PyObject* item, PyObject* seq, int eq) { - int result = PySequence_Contains(seq, item); - return unlikely(result < 0) ? result : (result == (eq == Py_EQ)); -} - -/* ListAppend.proto */ -#if CYTHON_USE_PYLIST_INTERNALS && CYTHON_ASSUME_SAFE_MACROS -static CYTHON_INLINE int __Pyx_PyList_Append(PyObject* list, PyObject* x) { - PyListObject* L = (PyListObject*) list; - Py_ssize_t len = Py_SIZE(list); - if (likely(L->allocated > len) & likely(len > (L->allocated >> 1))) { - Py_INCREF(x); - PyList_SET_ITEM(list, len, x); - Py_SIZE(list) = len+1; - return 0; - } - return PyList_Append(list, x); -} -#else -#define __Pyx_PyList_Append(L,x) PyList_Append(L,x) -#endif - -/* PyObjectCallMethod1.proto */ -static PyObject* __Pyx_PyObject_CallMethod1(PyObject* obj, PyObject* method_name, PyObject* arg); - -/* append.proto */ -static CYTHON_INLINE int __Pyx_PyObject_Append(PyObject* L, PyObject* x); - -/* GetItemInt.proto */ -#define __Pyx_GetItemInt(o, i, type, is_signed, to_py_func, is_list, wraparound, boundscheck)\ - (__Pyx_fits_Py_ssize_t(i, type, is_signed) ?\ - __Pyx_GetItemInt_Fast(o, (Py_ssize_t)i, is_list, wraparound, boundscheck) :\ - (is_list ? (PyErr_SetString(PyExc_IndexError, "list index out of range"), (PyObject*)NULL) :\ - __Pyx_GetItemInt_Generic(o, to_py_func(i)))) -#define __Pyx_GetItemInt_List(o, i, type, is_signed, to_py_func, is_list, wraparound, boundscheck)\ - (__Pyx_fits_Py_ssize_t(i, type, is_signed) ?\ - __Pyx_GetItemInt_List_Fast(o, (Py_ssize_t)i, wraparound, boundscheck) :\ - (PyErr_SetString(PyExc_IndexError, "list index out of range"), (PyObject*)NULL)) -static CYTHON_INLINE PyObject *__Pyx_GetItemInt_List_Fast(PyObject *o, Py_ssize_t i, - int wraparound, int boundscheck); -#define __Pyx_GetItemInt_Tuple(o, i, type, is_signed, to_py_func, is_list, wraparound, boundscheck)\ - (__Pyx_fits_Py_ssize_t(i, type, is_signed) ?\ - __Pyx_GetItemInt_Tuple_Fast(o, (Py_ssize_t)i, wraparound, boundscheck) :\ - (PyErr_SetString(PyExc_IndexError, "tuple index out of range"), (PyObject*)NULL)) -static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize_t i, - int wraparound, int boundscheck); -static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Generic(PyObject *o, PyObject* j); -static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i, - int is_list, int wraparound, int boundscheck); - -/* BufferFormatCheck.proto */ -static CYTHON_INLINE int __Pyx_GetBufferAndValidate(Py_buffer* buf, PyObject* obj, - __Pyx_TypeInfo* dtype, int flags, int nd, int cast, __Pyx_BufFmt_StackElem* stack); -static CYTHON_INLINE void __Pyx_SafeReleaseBuffer(Py_buffer* info); -static const char* __Pyx_BufFmt_CheckString(__Pyx_BufFmt_Context* ctx, const char* ts); -static void __Pyx_BufFmt_Init(__Pyx_BufFmt_Context* ctx, - __Pyx_BufFmt_StackElem* stack, - __Pyx_TypeInfo* type); // PROTO - -/* MemviewSliceInit.proto */ -#define __Pyx_BUF_MAX_NDIMS %(BUF_MAX_NDIMS)d -#define __Pyx_MEMVIEW_DIRECT 1 -#define __Pyx_MEMVIEW_PTR 2 -#define __Pyx_MEMVIEW_FULL 4 -#define __Pyx_MEMVIEW_CONTIG 8 -#define __Pyx_MEMVIEW_STRIDED 16 -#define __Pyx_MEMVIEW_FOLLOW 32 -#define __Pyx_IS_C_CONTIG 1 -#define __Pyx_IS_F_CONTIG 2 -static int __Pyx_init_memviewslice( - struct __pyx_memoryview_obj *memview, - int ndim, - __Pyx_memviewslice *memviewslice, - int memview_is_new_reference); -static CYTHON_INLINE int __pyx_add_acquisition_count_locked( - __pyx_atomic_int *acquisition_count, PyThread_type_lock lock); -static CYTHON_INLINE int __pyx_sub_acquisition_count_locked( - __pyx_atomic_int *acquisition_count, PyThread_type_lock lock); -#define __pyx_get_slice_count_pointer(memview) (memview->acquisition_count_aligned_p) -#define __pyx_get_slice_count(memview) (*__pyx_get_slice_count_pointer(memview)) -#define __PYX_INC_MEMVIEW(slice, have_gil) __Pyx_INC_MEMVIEW(slice, have_gil, __LINE__) -#define __PYX_XDEC_MEMVIEW(slice, have_gil) __Pyx_XDEC_MEMVIEW(slice, have_gil, __LINE__) -static CYTHON_INLINE void __Pyx_INC_MEMVIEW(__Pyx_memviewslice *, int, int); -static CYTHON_INLINE void __Pyx_XDEC_MEMVIEW(__Pyx_memviewslice *, int, int); - -/* BufferIndexError.proto */ -static void __Pyx_RaiseBufferIndexError(int axis); - -/* RaiseArgTupleInvalid.proto */ -static void __Pyx_RaiseArgtupleInvalid(const char* func_name, int exact, - Py_ssize_t num_min, Py_ssize_t num_max, Py_ssize_t num_found); - -/* RaiseDoubleKeywords.proto */ -static void __Pyx_RaiseDoubleKeywordsError(const char* func_name, PyObject* kw_name); - -/* ParseKeywords.proto */ -static int __Pyx_ParseOptionalKeywords(PyObject *kwds, PyObject **argnames[],\ - PyObject *kwds2, PyObject *values[], Py_ssize_t num_pos_args,\ - const char* function_name); - -/* ArgTypeTest.proto */ -static CYTHON_INLINE int __Pyx_ArgTypeTest(PyObject *obj, PyTypeObject *type, int none_allowed, - const char *name, int exact); - -/* PyThreadStateGet.proto */ -#if CYTHON_FAST_THREAD_STATE -#define __Pyx_PyThreadState_declare PyThreadState *__pyx_tstate; -#define __Pyx_PyThreadState_assign __pyx_tstate = PyThreadState_GET(); -#else -#define __Pyx_PyThreadState_declare -#define __Pyx_PyThreadState_assign -#endif - -/* PyErrFetchRestore.proto */ -#if CYTHON_FAST_THREAD_STATE -#define __Pyx_ErrRestoreWithState(type, value, tb) __Pyx_ErrRestoreInState(PyThreadState_GET(), type, value, tb) -#define __Pyx_ErrFetchWithState(type, value, tb) __Pyx_ErrFetchInState(PyThreadState_GET(), type, value, tb) -#define __Pyx_ErrRestore(type, value, tb) __Pyx_ErrRestoreInState(__pyx_tstate, type, value, tb) -#define __Pyx_ErrFetch(type, value, tb) __Pyx_ErrFetchInState(__pyx_tstate, type, value, tb) -static CYTHON_INLINE void __Pyx_ErrRestoreInState(PyThreadState *tstate, PyObject *type, PyObject *value, PyObject *tb); -static CYTHON_INLINE void __Pyx_ErrFetchInState(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb); -#else -#define __Pyx_ErrRestoreWithState(type, value, tb) PyErr_Restore(type, value, tb) -#define __Pyx_ErrFetchWithState(type, value, tb) PyErr_Fetch(type, value, tb) -#define __Pyx_ErrRestore(type, value, tb) PyErr_Restore(type, value, tb) -#define __Pyx_ErrFetch(type, value, tb) PyErr_Fetch(type, value, tb) -#endif - -/* RaiseException.proto */ -static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause); - -/* None.proto */ -static CYTHON_INLINE Py_ssize_t __Pyx_div_Py_ssize_t(Py_ssize_t, Py_ssize_t); - -/* UnaryNegOverflows.proto */ -#define UNARY_NEG_WOULD_OVERFLOW(x)\ - (((x) < 0) & ((unsigned long)(x) == 0-(unsigned long)(x))) - -static CYTHON_UNUSED int __pyx_array_getbuffer(PyObject *__pyx_v_self, Py_buffer *__pyx_v_info, int __pyx_v_flags); /*proto*/ -static PyObject *__pyx_array_get_memview(struct __pyx_array_obj *); /*proto*/ -/* GetAttr.proto */ -static CYTHON_INLINE PyObject *__Pyx_GetAttr(PyObject *, PyObject *); - -/* decode_c_string.proto */ -static CYTHON_INLINE PyObject* __Pyx_decode_c_string( - const char* cstring, Py_ssize_t start, Py_ssize_t stop, - const char* encoding, const char* errors, - PyObject* (*decode_func)(const char *s, Py_ssize_t size, const char *errors)); - -/* RaiseTooManyValuesToUnpack.proto */ -static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected); - -/* RaiseNeedMoreValuesToUnpack.proto */ -static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index); - -/* RaiseNoneIterError.proto */ -static CYTHON_INLINE void __Pyx_RaiseNoneNotIterableError(void); - -/* ExtTypeTest.proto */ -static CYTHON_INLINE int __Pyx_TypeTest(PyObject *obj, PyTypeObject *type); - -/* SaveResetException.proto */ -#if CYTHON_FAST_THREAD_STATE -#define __Pyx_ExceptionSave(type, value, tb) __Pyx__ExceptionSave(__pyx_tstate, type, value, tb) -static CYTHON_INLINE void __Pyx__ExceptionSave(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb); -#define __Pyx_ExceptionReset(type, value, tb) __Pyx__ExceptionReset(__pyx_tstate, type, value, tb) -static CYTHON_INLINE void __Pyx__ExceptionReset(PyThreadState *tstate, PyObject *type, PyObject *value, PyObject *tb); -#else -#define __Pyx_ExceptionSave(type, value, tb) PyErr_GetExcInfo(type, value, tb) -#define __Pyx_ExceptionReset(type, value, tb) PyErr_SetExcInfo(type, value, tb) -#endif - -/* PyErrExceptionMatches.proto */ -#if CYTHON_FAST_THREAD_STATE -#define __Pyx_PyErr_ExceptionMatches(err) __Pyx_PyErr_ExceptionMatchesInState(__pyx_tstate, err) -static CYTHON_INLINE int __Pyx_PyErr_ExceptionMatchesInState(PyThreadState* tstate, PyObject* err); -#else -#define __Pyx_PyErr_ExceptionMatches(err) PyErr_ExceptionMatches(err) -#endif - -/* GetException.proto */ -#if CYTHON_FAST_THREAD_STATE -#define __Pyx_GetException(type, value, tb) __Pyx__GetException(__pyx_tstate, type, value, tb) -static int __Pyx__GetException(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb); -#else -static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb); -#endif - -/* SwapException.proto */ -#if CYTHON_FAST_THREAD_STATE -#define __Pyx_ExceptionSwap(type, value, tb) __Pyx__ExceptionSwap(__pyx_tstate, type, value, tb) -static CYTHON_INLINE void __Pyx__ExceptionSwap(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb); -#else -static CYTHON_INLINE void __Pyx_ExceptionSwap(PyObject **type, PyObject **value, PyObject **tb); -#endif - -static CYTHON_UNUSED int __pyx_memoryview_getbuffer(PyObject *__pyx_v_self, Py_buffer *__pyx_v_info, int __pyx_v_flags); /*proto*/ -/* ListCompAppend.proto */ -#if CYTHON_USE_PYLIST_INTERNALS && CYTHON_ASSUME_SAFE_MACROS -static CYTHON_INLINE int __Pyx_ListComp_Append(PyObject* list, PyObject* x) { - PyListObject* L = (PyListObject*) list; - Py_ssize_t len = Py_SIZE(list); - if (likely(L->allocated > len)) { - Py_INCREF(x); - PyList_SET_ITEM(list, len, x); - Py_SIZE(list) = len+1; - return 0; - } - return PyList_Append(list, x); -} -#else -#define __Pyx_ListComp_Append(L,x) PyList_Append(L,x) -#endif - -/* PyIntBinop.proto */ -#if !CYTHON_COMPILING_IN_PYPY -static PyObject* __Pyx_PyInt_AddObjC(PyObject *op1, PyObject *op2, long intval, int inplace); -#else -#define __Pyx_PyInt_AddObjC(op1, op2, intval, inplace)\ - (inplace ? PyNumber_InPlaceAdd(op1, op2) : PyNumber_Add(op1, op2)) -#endif - -/* ListExtend.proto */ -static CYTHON_INLINE int __Pyx_PyList_Extend(PyObject* L, PyObject* v) { -#if CYTHON_COMPILING_IN_CPYTHON - PyObject* none = _PyList_Extend((PyListObject*)L, v); - if (unlikely(!none)) - return -1; - Py_DECREF(none); - return 0; -#else - return PyList_SetSlice(L, PY_SSIZE_T_MAX, PY_SSIZE_T_MAX, v); -#endif -} - -/* None.proto */ -static CYTHON_INLINE void __Pyx_RaiseUnboundLocalError(const char *varname); - -/* ForceInitThreads.proto */ -#ifndef __PYX_FORCE_INIT_THREADS - #define __PYX_FORCE_INIT_THREADS 0 -#endif - -/* None.proto */ -static CYTHON_INLINE long __Pyx_div_long(long, long); - -/* WriteUnraisableException.proto */ -static void __Pyx_WriteUnraisable(const char *name, int clineno, - int lineno, const char *filename, - int full_traceback, int nogil); - -/* SetVTable.proto */ -static int __Pyx_SetVtable(PyObject *dict, void *vtable); - -/* CodeObjectCache.proto */ -typedef struct { - PyCodeObject* code_object; - int code_line; -} __Pyx_CodeObjectCacheEntry; -struct __Pyx_CodeObjectCache { - int count; - int max_count; - __Pyx_CodeObjectCacheEntry* entries; -}; -static struct __Pyx_CodeObjectCache __pyx_code_cache = {0,0,NULL}; -static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line); -static PyCodeObject *__pyx_find_code_object(int code_line); -static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object); - -/* AddTraceback.proto */ -static void __Pyx_AddTraceback(const char *funcname, int c_line, - int py_line, const char *filename); - -#if PY_MAJOR_VERSION < 3 - static int __Pyx_GetBuffer(PyObject *obj, Py_buffer *view, int flags); - static void __Pyx_ReleaseBuffer(Py_buffer *view); -#else - #define __Pyx_GetBuffer PyObject_GetBuffer - #define __Pyx_ReleaseBuffer PyBuffer_Release -#endif - - -/* BufferStructDeclare.proto */ -typedef struct { - Py_ssize_t shape, strides, suboffsets; -} __Pyx_Buf_DimInfo; -typedef struct { - size_t refcount; - Py_buffer pybuffer; -} __Pyx_Buffer; -typedef struct { - __Pyx_Buffer *rcbuffer; - char *data; - __Pyx_Buf_DimInfo diminfo[8]; -} __Pyx_LocalBuf_ND; - -/* None.proto */ -static Py_ssize_t __Pyx_zeros[] = {0, 0, 0, 0, 0, 0, 0, 0}; -static Py_ssize_t __Pyx_minusones[] = {-1, -1, -1, -1, -1, -1, -1, -1}; - -/* MemviewSliceIsContig.proto */ -static int __pyx_memviewslice_is_contig(const __Pyx_memviewslice mvs, - char order, int ndim); - -/* OverlappingSlices.proto */ -static int __pyx_slices_overlap(__Pyx_memviewslice *slice1, - __Pyx_memviewslice *slice2, - int ndim, size_t itemsize); - -/* Capsule.proto */ -static CYTHON_INLINE PyObject *__pyx_capsule_create(void *p, const char *sig); - -/* CIntToPy.proto */ -static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int(int value); - -/* CIntToPy.proto */ -static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value); - -/* Print.proto */ -static int __Pyx_Print(PyObject*, PyObject *, int); -#if CYTHON_COMPILING_IN_PYPY || PY_MAJOR_VERSION >= 3 -static PyObject* __pyx_print = 0; -static PyObject* __pyx_print_kwargs = 0; -#endif - -/* MemviewSliceCopyTemplate.proto */ -static __Pyx_memviewslice -__pyx_memoryview_copy_new_contig(const __Pyx_memviewslice *from_mvs, - const char *mode, int ndim, - size_t sizeof_dtype, int contig_flag, - int dtype_is_object); - -/* CIntFromPy.proto */ -static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *); - -/* PrintOne.proto */ -static int __Pyx_PrintOne(PyObject* stream, PyObject *o); - -/* CIntFromPy.proto */ -static CYTHON_INLINE char __Pyx_PyInt_As_char(PyObject *); - -/* CIntFromPy.proto */ -static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *); - -/* TypeInfoCompare.proto */ -static int __pyx_typeinfo_cmp(__Pyx_TypeInfo *a, __Pyx_TypeInfo *b); - -/* MemviewSliceValidateAndInit.proto */ -static int __Pyx_ValidateAndInit_memviewslice( - int *axes_specs, - int c_or_f_flag, - int buf_flags, - int ndim, - __Pyx_TypeInfo *dtype, - __Pyx_BufFmt_StackElem stack[], - __Pyx_memviewslice *memviewslice, - PyObject *original_obj); - -/* ObjectToMemviewSlice.proto */ -static CYTHON_INLINE __Pyx_memviewslice __Pyx_PyObject_to_MemoryviewSlice_dc_int(PyObject *); - -/* ObjectToMemviewSlice.proto */ -static CYTHON_INLINE __Pyx_memviewslice __Pyx_PyObject_to_MemoryviewSlice_dc_float(PyObject *); - -/* CheckBinaryVersion.proto */ -static int __Pyx_check_binary_version(void); - -/* InitStrings.proto */ -static int __Pyx_InitStrings(__Pyx_StringTabEntry *t); - -static PyObject *__pyx_array_get_memview(struct __pyx_array_obj *__pyx_v_self); /* proto*/ -static char *__pyx_memoryview_get_item_pointer(struct __pyx_memoryview_obj *__pyx_v_self, PyObject *__pyx_v_index); /* proto*/ -static PyObject *__pyx_memoryview_is_slice(struct __pyx_memoryview_obj *__pyx_v_self, PyObject *__pyx_v_obj); /* proto*/ -static PyObject *__pyx_memoryview_setitem_slice_assignment(struct __pyx_memoryview_obj *__pyx_v_self, PyObject *__pyx_v_dst, PyObject *__pyx_v_src); /* proto*/ -static PyObject *__pyx_memoryview_setitem_slice_assign_scalar(struct __pyx_memoryview_obj *__pyx_v_self, struct __pyx_memoryview_obj *__pyx_v_dst, PyObject *__pyx_v_value); /* proto*/ -static PyObject *__pyx_memoryview_setitem_indexed(struct __pyx_memoryview_obj *__pyx_v_self, PyObject *__pyx_v_index, PyObject *__pyx_v_value); /* proto*/ -static PyObject *__pyx_memoryview_convert_item_to_object(struct __pyx_memoryview_obj *__pyx_v_self, char *__pyx_v_itemp); /* proto*/ -static PyObject *__pyx_memoryview_assign_item_from_object(struct __pyx_memoryview_obj *__pyx_v_self, char *__pyx_v_itemp, PyObject *__pyx_v_value); /* proto*/ -static PyObject *__pyx_memoryviewslice_convert_item_to_object(struct __pyx_memoryviewslice_obj *__pyx_v_self, char *__pyx_v_itemp); /* proto*/ -static PyObject *__pyx_memoryviewslice_assign_item_from_object(struct __pyx_memoryviewslice_obj *__pyx_v_self, char *__pyx_v_itemp, PyObject *__pyx_v_value); /* proto*/ - -/* Module declarations from 'cython.view' */ - -/* Module declarations from 'wrap_cy' */ -static PyTypeObject *__pyx_array_type = 0; -static PyTypeObject *__pyx_MemviewEnum_type = 0; -static PyTypeObject *__pyx_memoryview_type = 0; -static PyTypeObject *__pyx_memoryviewslice_type = 0; -static PyObject *generic = 0; -static PyObject *strided = 0; -static PyObject *indirect = 0; -static PyObject *contiguous = 0; -static PyObject *indirect_contiguous = 0; -static int __pyx_memoryview_thread_locks_used; -static PyThread_type_lock __pyx_memoryview_thread_locks[8]; -static struct __pyx_array_obj *__pyx_array_new(PyObject *, Py_ssize_t, char *, char *, char *); /*proto*/ -static void *__pyx_align_pointer(void *, size_t); /*proto*/ -static PyObject *__pyx_memoryview_new(PyObject *, int, int, __Pyx_TypeInfo *); /*proto*/ -static CYTHON_INLINE int __pyx_memoryview_check(PyObject *); /*proto*/ -static PyObject *_unellipsify(PyObject *, int); /*proto*/ -static PyObject *assert_direct_dimensions(Py_ssize_t *, int); /*proto*/ -static struct __pyx_memoryview_obj *__pyx_memview_slice(struct __pyx_memoryview_obj *, PyObject *); /*proto*/ -static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *, Py_ssize_t, Py_ssize_t, Py_ssize_t, int, int, int *, Py_ssize_t, Py_ssize_t, Py_ssize_t, int, int, int, int); /*proto*/ -static char *__pyx_pybuffer_index(Py_buffer *, char *, Py_ssize_t, Py_ssize_t); /*proto*/ -static int __pyx_memslice_transpose(__Pyx_memviewslice *); /*proto*/ -static PyObject *__pyx_memoryview_fromslice(__Pyx_memviewslice, int, PyObject *(*)(char *), int (*)(char *, PyObject *), int); /*proto*/ -static __Pyx_memviewslice *__pyx_memoryview_get_slice_from_memoryview(struct __pyx_memoryview_obj *, __Pyx_memviewslice *); /*proto*/ -static void __pyx_memoryview_slice_copy(struct __pyx_memoryview_obj *, __Pyx_memviewslice *); /*proto*/ -static PyObject *__pyx_memoryview_copy_object(struct __pyx_memoryview_obj *); /*proto*/ -static PyObject *__pyx_memoryview_copy_object_from_slice(struct __pyx_memoryview_obj *, __Pyx_memviewslice *); /*proto*/ -static Py_ssize_t abs_py_ssize_t(Py_ssize_t); /*proto*/ -static char __pyx_get_best_slice_order(__Pyx_memviewslice *, int); /*proto*/ -static void _copy_strided_to_strided(char *, Py_ssize_t *, char *, Py_ssize_t *, Py_ssize_t *, Py_ssize_t *, int, size_t); /*proto*/ -static void copy_strided_to_strided(__Pyx_memviewslice *, __Pyx_memviewslice *, int, size_t); /*proto*/ -static Py_ssize_t __pyx_memoryview_slice_get_size(__Pyx_memviewslice *, int); /*proto*/ -static Py_ssize_t __pyx_fill_contig_strides_array(Py_ssize_t *, Py_ssize_t *, Py_ssize_t, int, char); /*proto*/ -static void *__pyx_memoryview_copy_data_to_temp(__Pyx_memviewslice *, __Pyx_memviewslice *, char, int); /*proto*/ -static int __pyx_memoryview_err_extents(int, Py_ssize_t, Py_ssize_t); /*proto*/ -static int __pyx_memoryview_err_dim(PyObject *, char *, int); /*proto*/ -static int __pyx_memoryview_err(PyObject *, char *); /*proto*/ -static int __pyx_memoryview_copy_contents(__Pyx_memviewslice, __Pyx_memviewslice, int, int, int); /*proto*/ -static void __pyx_memoryview_broadcast_leading(__Pyx_memviewslice *, int, int); /*proto*/ -static void __pyx_memoryview_refcount_copying(__Pyx_memviewslice *, int, int, int); /*proto*/ -static void __pyx_memoryview_refcount_objects_in_slice_with_gil(char *, Py_ssize_t *, Py_ssize_t *, int, int); /*proto*/ -static void __pyx_memoryview_refcount_objects_in_slice(char *, Py_ssize_t *, Py_ssize_t *, int, int); /*proto*/ -static void __pyx_memoryview_slice_assign_scalar(__Pyx_memviewslice *, int, size_t, void *, int); /*proto*/ -static void __pyx_memoryview__slice_assign_scalar(char *, Py_ssize_t *, Py_ssize_t *, int, size_t, void *); /*proto*/ -static __Pyx_TypeInfo __Pyx_TypeInfo_int = { "int", NULL, sizeof(int), { 0 }, 0, IS_UNSIGNED(int) ? 'U' : 'I', IS_UNSIGNED(int), 0 }; -static __Pyx_TypeInfo __Pyx_TypeInfo_float = { "float", NULL, sizeof(float), { 0 }, 0, 'R', 0, 0 }; -#define __Pyx_MODULE_NAME "wrap_cy" -int __pyx_module_is_main_wrap_cy = 0; - -/* Implementation of 'wrap_cy' */ -static PyObject *__pyx_builtin_ValueError; -static PyObject *__pyx_builtin_MemoryError; -static PyObject *__pyx_builtin_enumerate; -static PyObject *__pyx_builtin_range; -static PyObject *__pyx_builtin_Ellipsis; -static PyObject *__pyx_builtin_TypeError; -static PyObject *__pyx_builtin_id; -static PyObject *__pyx_builtin_IndexError; -static const char __pyx_k_[] = ""; -static const char __pyx_k_C[] = "C"; -static const char __pyx_k_F[] = "F"; -static const char __pyx_k_H[] = "H"; -static const char __pyx_k_N[] = "N"; -static const char __pyx_k_O[] = "O"; -static const char __pyx_k_P[] = "P"; -static const char __pyx_k_S[] = "S"; -static const char __pyx_k_c[] = "c"; -static const char __pyx_k_i[] = "i"; -static const char __pyx_k_s[] = "s"; -static const char __pyx_k_u[] = "u"; -static const char __pyx_k_Mg[] = "Mg"; -static const char __pyx_k_id[] = "id"; -static const char __pyx_k_np[] = "np"; -static const char __pyx_k_ts[] = "ts"; -static const char __pyx_k_bla[] = "bla"; -static const char __pyx_k_dcd[] = "dcd"; -static const char __pyx_k_end[] = "end"; -static const char __pyx_k_get[] = "get"; -static const char __pyx_k_obj[] = "obj"; -static const char __pyx_k_psf[] = "psf"; -static const char __pyx_k_base[] = "base"; -static const char __pyx_k_file[] = "file"; -static const char __pyx_k_main[] = "__main__"; -static const char __pyx_k_mode[] = "mode"; -static const char __pyx_k_name[] = "name"; -static const char __pyx_k_ndim[] = "ndim"; -static const char __pyx_k_pack[] = "pack"; -static const char __pyx_k_sasa[] = "sasa"; -static const char __pyx_k_segs[] = "segs"; -static const char __pyx_k_size[] = "size"; -static const char __pyx_k_step[] = "step"; -static const char __pyx_k_stop[] = "stop"; -static const char __pyx_k_test[] = "__test__"; -static const char __pyx_k_ASCII[] = "ASCII"; -static const char __pyx_k_array[] = "array"; -static const char __pyx_k_atoms[] = "atoms"; -static const char __pyx_k_class[] = "__class__"; -static const char __pyx_k_dtype[] = "dtype"; -static const char __pyx_k_error[] = "error"; -static const char __pyx_k_flags[] = "flags"; -static const char __pyx_k_int32[] = "int32"; -static const char __pyx_k_nprad[] = "nprad"; -static const char __pyx_k_numpy[] = "numpy"; -static const char __pyx_k_print[] = "print"; -static const char __pyx_k_range[] = "range"; -static const char __pyx_k_shape[] = "shape"; -static const char __pyx_k_start[] = "start"; -static const char __pyx_k_append[] = "append"; -static const char __pyx_k_coords[] = "coords"; -static const char __pyx_k_encode[] = "encode"; -static const char __pyx_k_format[] = "format"; -static const char __pyx_k_import[] = "__import__"; -static const char __pyx_k_name_2[] = "__name__"; -static const char __pyx_k_natoms[] = "natoms"; -static const char __pyx_k_perres[] = "perres"; -static const char __pyx_k_radius[] = "radius"; -static const char __pyx_k_resids[] = "resids"; -static const char __pyx_k_ressel[] = "ressel"; -static const char __pyx_k_result[] = "result"; -static const char __pyx_k_segids[] = "segids"; -static const char __pyx_k_struct[] = "struct"; -static const char __pyx_k_unpack[] = "unpack"; -static const char __pyx_k_float32[] = "float32"; -static const char __pyx_k_fortran[] = "fortran"; -static const char __pyx_k_memview[] = "memview"; -static const char __pyx_k_reshape[] = "reshape"; -static const char __pyx_k_seltext[] = "seltext"; -static const char __pyx_k_wrap_cy[] = "wrap_cy"; -static const char __pyx_k_Ellipsis[] = "Ellipsis"; -static const char __pyx_k_Universe[] = "Universe"; -static const char __pyx_k_atomType[] = "atomType"; -static const char __pyx_k_c_coords[] = "c_coords"; -static const char __pyx_k_itemsize[] = "itemsize"; -static const char __pyx_k_npcoords[] = "npcoords"; -static const char __pyx_k_pairdist[] = "pairdist"; -static const char __pyx_k_seltext2[] = "seltext2"; -static const char __pyx_k_vdwRadii[] = "vdwRadii"; -static const char __pyx_k_TypeError[] = "TypeError"; -static const char __pyx_k_cy_radius[] = "cy_radius"; -static const char __pyx_k_enumerate[] = "enumerate"; -static const char __pyx_k_positions[] = "positions"; -static const char __pyx_k_selection[] = "selection"; -static const char __pyx_k_test_sasa[] = "test_sasa"; -static const char __pyx_k_vdwRadius[] = "vdwRadius"; -static const char __pyx_k_IndexError[] = "IndexError"; -static const char __pyx_k_MDAnalysis[] = "MDAnalysis"; -static const char __pyx_k_ValueError[] = "ValueError"; -static const char __pyx_k_pointstyle[] = "pointstyle"; -static const char __pyx_k_pyx_vtable[] = "__pyx_vtable__"; -static const char __pyx_k_resseltext[] = "resseltext"; -static const char __pyx_k_restricted[] = "restricted"; -static const char __pyx_k_segid_COH3[] = "segid COH3"; -static const char __pyx_k_segid_DOC3[] = "segid DOC3"; -static const char __pyx_k_trajectory[] = "trajectory"; -static const char __pyx_k_MemoryError[] = "MemoryError"; -static const char __pyx_k_probeRadius[] = "probeRadius"; -static const char __pyx_k_input_coords[] = "input_coords"; -static const char __pyx_k_select_atoms[] = "select_atoms"; -static const char __pyx_k_pyx_getbuffer[] = "__pyx_getbuffer"; -static const char __pyx_k_surfacePoints[] = "surfacePoints"; -static const char __pyx_k_restrictedList[] = "restrictedList"; -static const char __pyx_k_allocate_buffer[] = "allocate_buffer"; -static const char __pyx_k_dtype_is_object[] = "dtype_is_object"; -static const char __pyx_k_cy_restrictedList[] = "cy_restrictedList"; -static const char __pyx_k_strided_and_direct[] = ""; -static const char __pyx_k_strided_and_indirect[] = ""; -static const char __pyx_k_contiguous_and_direct[] = ""; -static const char __pyx_k_MemoryView_of_r_object[] = ""; -static const char __pyx_k_MemoryView_of_r_at_0x_x[] = ""; -static const char __pyx_k_contiguous_and_indirect[] = ""; -static const char __pyx_k_Cannot_index_with_type_s[] = "Cannot index with type '%s'"; -static const char __pyx_k_Invalid_shape_in_axis_d_d[] = "Invalid shape in axis %d: %d."; -static const char __pyx_k_itemsize_0_for_cython_array[] = "itemsize <= 0 for cython.array"; -static const char __pyx_k_unable_to_allocate_array_data[] = "unable to allocate array data."; -static const char __pyx_k_strided_and_direct_or_indirect[] = ""; -static const char __pyx_k_home_max_Projects_pycontact_tes[] = "/home/max/Projects/pycontact/testing/cython/wrap.pyx"; -static const char __pyx_k_mnt_workspace_pycontactData_now[] = "/mnt/workspace/pycontactData/nowater.psf"; -static const char __pyx_k_mnt_workspace_pycontactData_tra[] = "/mnt/workspace/pycontactData/trajectory_short.dcd"; -static const char __pyx_k_Buffer_view_does_not_expose_stri[] = "Buffer view does not expose strides"; -static const char __pyx_k_Can_only_create_a_buffer_that_is[] = "Can only create a buffer that is contiguous in memory."; -static const char __pyx_k_Empty_shape_tuple_for_cython_arr[] = "Empty shape tuple for cython.array"; -static const char __pyx_k_Indirect_dimensions_not_supporte[] = "Indirect dimensions not supported"; -static const char __pyx_k_Invalid_mode_expected_c_or_fortr[] = "Invalid mode, expected 'c' or 'fortran', got %s"; -static const char __pyx_k_Out_of_bounds_on_buffer_access_a[] = "Out of bounds on buffer access (axis %d)"; -static const char __pyx_k_Unable_to_convert_item_to_object[] = "Unable to convert item to object"; -static const char __pyx_k_got_differing_extents_in_dimensi[] = "got differing extents in dimension %d (got %d and %d)"; -static const char __pyx_k_segid_COH3_and_around_5_segid_DO[] = "segid COH3 and around 5 segid DOC3"; -static const char __pyx_k_unable_to_allocate_shape_and_str[] = "unable to allocate shape and strides."; -static PyObject *__pyx_kp_s_; -static PyObject *__pyx_n_s_ASCII; -static PyObject *__pyx_kp_s_Buffer_view_does_not_expose_stri; -static PyObject *__pyx_n_s_C; -static PyObject *__pyx_kp_s_Can_only_create_a_buffer_that_is; -static PyObject *__pyx_kp_s_Cannot_index_with_type_s; -static PyObject *__pyx_n_s_Ellipsis; -static PyObject *__pyx_kp_s_Empty_shape_tuple_for_cython_arr; -static PyObject *__pyx_n_s_F; -static PyObject *__pyx_n_s_H; -static PyObject *__pyx_n_s_IndexError; -static PyObject *__pyx_kp_s_Indirect_dimensions_not_supporte; -static PyObject *__pyx_kp_s_Invalid_mode_expected_c_or_fortr; -static PyObject *__pyx_kp_s_Invalid_shape_in_axis_d_d; -static PyObject *__pyx_n_s_MDAnalysis; -static PyObject *__pyx_n_s_MemoryError; -static PyObject *__pyx_kp_s_MemoryView_of_r_at_0x_x; -static PyObject *__pyx_kp_s_MemoryView_of_r_object; -static PyObject *__pyx_n_s_Mg; -static PyObject *__pyx_n_s_N; -static PyObject *__pyx_n_b_O; -static PyObject *__pyx_n_s_O; -static PyObject *__pyx_kp_s_Out_of_bounds_on_buffer_access_a; -static PyObject *__pyx_n_s_P; -static PyObject *__pyx_n_s_S; -static PyObject *__pyx_n_s_TypeError; -static PyObject *__pyx_kp_s_Unable_to_convert_item_to_object; -static PyObject *__pyx_n_s_Universe; -static PyObject *__pyx_n_s_ValueError; -static PyObject *__pyx_n_s_allocate_buffer; -static PyObject *__pyx_n_s_append; -static PyObject *__pyx_n_s_array; -static PyObject *__pyx_n_s_atomType; -static PyObject *__pyx_n_s_atoms; -static PyObject *__pyx_n_s_base; -static PyObject *__pyx_n_s_bla; -static PyObject *__pyx_n_s_c; -static PyObject *__pyx_n_u_c; -static PyObject *__pyx_n_s_c_coords; -static PyObject *__pyx_n_s_class; -static PyObject *__pyx_kp_s_contiguous_and_direct; -static PyObject *__pyx_kp_s_contiguous_and_indirect; -static PyObject *__pyx_n_s_coords; -static PyObject *__pyx_n_s_cy_radius; -static PyObject *__pyx_n_s_cy_restrictedList; -static PyObject *__pyx_n_s_dcd; -static PyObject *__pyx_n_s_dtype; -static PyObject *__pyx_n_s_dtype_is_object; -static PyObject *__pyx_n_s_encode; -static PyObject *__pyx_n_s_end; -static PyObject *__pyx_n_s_enumerate; -static PyObject *__pyx_n_s_error; -static PyObject *__pyx_n_s_file; -static PyObject *__pyx_n_s_flags; -static PyObject *__pyx_n_s_float32; -static PyObject *__pyx_n_s_format; -static PyObject *__pyx_n_s_fortran; -static PyObject *__pyx_n_u_fortran; -static PyObject *__pyx_n_s_get; -static PyObject *__pyx_kp_s_got_differing_extents_in_dimensi; -static PyObject *__pyx_kp_s_home_max_Projects_pycontact_tes; -static PyObject *__pyx_n_s_i; -static PyObject *__pyx_n_s_id; -static PyObject *__pyx_n_s_import; -static PyObject *__pyx_n_s_input_coords; -static PyObject *__pyx_n_s_int32; -static PyObject *__pyx_n_s_itemsize; -static PyObject *__pyx_kp_s_itemsize_0_for_cython_array; -static PyObject *__pyx_n_s_main; -static PyObject *__pyx_n_s_memview; -static PyObject *__pyx_kp_s_mnt_workspace_pycontactData_now; -static PyObject *__pyx_kp_s_mnt_workspace_pycontactData_tra; -static PyObject *__pyx_n_s_mode; -static PyObject *__pyx_n_s_name; -static PyObject *__pyx_n_s_name_2; -static PyObject *__pyx_n_s_natoms; -static PyObject *__pyx_n_s_ndim; -static PyObject *__pyx_n_s_np; -static PyObject *__pyx_n_s_npcoords; -static PyObject *__pyx_n_s_nprad; -static PyObject *__pyx_n_s_numpy; -static PyObject *__pyx_n_s_obj; -static PyObject *__pyx_n_s_pack; -static PyObject *__pyx_n_s_pairdist; -static PyObject *__pyx_n_s_perres; -static PyObject *__pyx_n_s_pointstyle; -static PyObject *__pyx_n_s_positions; -static PyObject *__pyx_n_s_print; -static PyObject *__pyx_n_s_probeRadius; -static PyObject *__pyx_n_s_psf; -static PyObject *__pyx_n_s_pyx_getbuffer; -static PyObject *__pyx_n_s_pyx_vtable; -static PyObject *__pyx_n_s_radius; -static PyObject *__pyx_n_s_range; -static PyObject *__pyx_n_s_reshape; -static PyObject *__pyx_n_s_resids; -static PyObject *__pyx_n_s_ressel; -static PyObject *__pyx_n_s_resseltext; -static PyObject *__pyx_n_s_restricted; -static PyObject *__pyx_n_s_restrictedList; -static PyObject *__pyx_n_s_result; -static PyObject *__pyx_n_s_s; -static PyObject *__pyx_n_s_sasa; -static PyObject *__pyx_kp_s_segid_COH3; -static PyObject *__pyx_kp_s_segid_COH3_and_around_5_segid_DO; -static PyObject *__pyx_kp_s_segid_DOC3; -static PyObject *__pyx_n_s_segids; -static PyObject *__pyx_n_s_segs; -static PyObject *__pyx_n_s_select_atoms; -static PyObject *__pyx_n_s_selection; -static PyObject *__pyx_n_s_seltext; -static PyObject *__pyx_n_s_seltext2; -static PyObject *__pyx_n_s_shape; -static PyObject *__pyx_n_s_size; -static PyObject *__pyx_n_s_start; -static PyObject *__pyx_n_s_step; -static PyObject *__pyx_n_s_stop; -static PyObject *__pyx_kp_s_strided_and_direct; -static PyObject *__pyx_kp_s_strided_and_direct_or_indirect; -static PyObject *__pyx_kp_s_strided_and_indirect; -static PyObject *__pyx_n_s_struct; -static PyObject *__pyx_n_s_surfacePoints; -static PyObject *__pyx_n_s_test; -static PyObject *__pyx_n_s_test_sasa; -static PyObject *__pyx_n_s_trajectory; -static PyObject *__pyx_n_s_ts; -static PyObject *__pyx_n_s_u; -static PyObject *__pyx_kp_s_unable_to_allocate_array_data; -static PyObject *__pyx_kp_s_unable_to_allocate_shape_and_str; -static PyObject *__pyx_n_s_unpack; -static PyObject *__pyx_n_s_vdwRadii; -static PyObject *__pyx_n_s_vdwRadius; -static PyObject *__pyx_n_s_wrap_cy; -static PyObject *__pyx_pf_7wrap_cy_vdwRadius(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_atomType); /* proto */ -static PyObject *__pyx_pf_7wrap_cy_2bla(CYTHON_UNUSED PyObject *__pyx_self, int __pyx_v_i); /* proto */ -static PyObject *__pyx_pf_7wrap_cy_4test_sasa(CYTHON_UNUSED PyObject *__pyx_self); /* proto */ -static int __pyx_array___pyx_pf_15View_dot_MemoryView_5array___cinit__(struct __pyx_array_obj *__pyx_v_self, PyObject *__pyx_v_shape, Py_ssize_t __pyx_v_itemsize, PyObject *__pyx_v_format, PyObject *__pyx_v_mode, int __pyx_v_allocate_buffer); /* proto */ -static int __pyx_array___pyx_pf_15View_dot_MemoryView_5array_2__getbuffer__(struct __pyx_array_obj *__pyx_v_self, Py_buffer *__pyx_v_info, int __pyx_v_flags); /* proto */ -static void __pyx_array___pyx_pf_15View_dot_MemoryView_5array_4__dealloc__(struct __pyx_array_obj *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_15View_dot_MemoryView_5array_7memview___get__(struct __pyx_array_obj *__pyx_v_self); /* proto */ -static PyObject *__pyx_array___pyx_pf_15View_dot_MemoryView_5array_6__getattr__(struct __pyx_array_obj *__pyx_v_self, PyObject *__pyx_v_attr); /* proto */ -static PyObject *__pyx_array___pyx_pf_15View_dot_MemoryView_5array_8__getitem__(struct __pyx_array_obj *__pyx_v_self, PyObject *__pyx_v_item); /* proto */ -static int __pyx_array___pyx_pf_15View_dot_MemoryView_5array_10__setitem__(struct __pyx_array_obj *__pyx_v_self, PyObject *__pyx_v_item, PyObject *__pyx_v_value); /* proto */ -static int __pyx_MemviewEnum___pyx_pf_15View_dot_MemoryView_4Enum___init__(struct __pyx_MemviewEnum_obj *__pyx_v_self, PyObject *__pyx_v_name); /* proto */ -static PyObject *__pyx_MemviewEnum___pyx_pf_15View_dot_MemoryView_4Enum_2__repr__(struct __pyx_MemviewEnum_obj *__pyx_v_self); /* proto */ -static int __pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview___cinit__(struct __pyx_memoryview_obj *__pyx_v_self, PyObject *__pyx_v_obj, int __pyx_v_flags, int __pyx_v_dtype_is_object); /* proto */ -static void __pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_2__dealloc__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ -static PyObject *__pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_4__getitem__(struct __pyx_memoryview_obj *__pyx_v_self, PyObject *__pyx_v_index); /* proto */ -static int __pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_6__setitem__(struct __pyx_memoryview_obj *__pyx_v_self, PyObject *__pyx_v_index, PyObject *__pyx_v_value); /* proto */ -static int 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(__pyx_t_1) { - - /* "View.MemoryView":815 - * if not is_slice: - * - * if start < 0: # <<<<<<<<<<<<<< - * start += shape - * if not 0 <= start < shape: - */ - __pyx_t_1 = ((__pyx_v_start < 0) != 0); - if (__pyx_t_1) { - - /* "View.MemoryView":816 - * - * if start < 0: - * start += shape # <<<<<<<<<<<<<< - * if not 0 <= start < shape: - * _err_dim(IndexError, "Index out of bounds (axis %d)", dim) - */ - __pyx_v_start = (__pyx_v_start + __pyx_v_shape); - - /* "View.MemoryView":815 - * if not is_slice: - * - * if start < 0: # <<<<<<<<<<<<<< - * start += shape - * if not 0 <= start < shape: - */ - } - - /* "View.MemoryView":817 - * if start < 0: - * start += shape - * if not 0 <= start < shape: # <<<<<<<<<<<<<< - * _err_dim(IndexError, "Index out of bounds (axis %d)", dim) - * else: - */ - __pyx_t_1 = (0 <= __pyx_v_start); - if (__pyx_t_1) { - __pyx_t_1 = (__pyx_v_start < __pyx_v_shape); - } - __pyx_t_2 = ((!(__pyx_t_1 != 0)) != 0); - if (__pyx_t_2) { - - /* "View.MemoryView":818 - * start += shape - * if not 0 <= start < shape: - * _err_dim(IndexError, "Index out of bounds (axis %d)", dim) # <<<<<<<<<<<<<< - * else: - * - */ - __pyx_t_3 = __pyx_memoryview_err_dim(__pyx_builtin_IndexError, ((char *)"Index out of bounds (axis %d)"), __pyx_v_dim); if (unlikely(__pyx_t_3 == -1)) __PYX_ERR(1, 818, __pyx_L1_error) - - /* "View.MemoryView":817 - * if start < 0: - * start += shape - * if not 0 <= start < shape: # <<<<<<<<<<<<<< - * _err_dim(IndexError, "Index out of bounds (axis %d)", dim) - * else: - */ - } - - /* "View.MemoryView":813 - * cdef bint negative_step - * - * if not is_slice: # <<<<<<<<<<<<<< - * - * if start < 0: - */ - goto __pyx_L3; - } - - /* "View.MemoryView":821 - * else: - * - * negative_step = have_step != 0 and step < 0 # <<<<<<<<<<<<<< - * - * if have_step and step == 0: - */ - /*else*/ { - __pyx_t_1 = ((__pyx_v_have_step != 0) != 0); - if (__pyx_t_1) { - } else { - __pyx_t_2 = __pyx_t_1; - goto __pyx_L6_bool_binop_done; - } - __pyx_t_1 = ((__pyx_v_step < 0) != 0); - __pyx_t_2 = __pyx_t_1; - __pyx_L6_bool_binop_done:; - __pyx_v_negative_step = __pyx_t_2; - - /* "View.MemoryView":823 - * negative_step = have_step != 0 and step < 0 - * - * if have_step and step == 0: # <<<<<<<<<<<<<< - * _err_dim(ValueError, "Step may not be zero (axis %d)", dim) - * - */ - __pyx_t_1 = (__pyx_v_have_step != 0); - if (__pyx_t_1) { - } else { - __pyx_t_2 = __pyx_t_1; - goto __pyx_L9_bool_binop_done; - } - __pyx_t_1 = ((__pyx_v_step == 0) != 0); - __pyx_t_2 = __pyx_t_1; - __pyx_L9_bool_binop_done:; - if (__pyx_t_2) { - - /* "View.MemoryView":824 - * - * if have_step and step == 0: - * _err_dim(ValueError, "Step may not be zero (axis %d)", dim) # <<<<<<<<<<<<<< - * - * - */ - __pyx_t_3 = __pyx_memoryview_err_dim(__pyx_builtin_ValueError, ((char *)"Step may not be zero (axis %d)"), __pyx_v_dim); if (unlikely(__pyx_t_3 == -1)) __PYX_ERR(1, 824, __pyx_L1_error) - - /* "View.MemoryView":823 - * negative_step = have_step != 0 and step < 0 - * - * if have_step and step == 0: # <<<<<<<<<<<<<< - * _err_dim(ValueError, "Step may not be zero (axis %d)", dim) - * - */ - } - - /* "View.MemoryView":827 - * - * - * if have_start: # <<<<<<<<<<<<<< - * if start < 0: - * start += shape - */ - __pyx_t_2 = (__pyx_v_have_start != 0); - if (__pyx_t_2) { - - /* "View.MemoryView":828 - * - * if have_start: - * if start < 0: # <<<<<<<<<<<<<< - * start += shape - * if start < 0: - */ - __pyx_t_2 = ((__pyx_v_start < 0) != 0); - if (__pyx_t_2) { - - /* "View.MemoryView":829 - * if have_start: - * if start < 0: - * start += shape # <<<<<<<<<<<<<< - * if start < 0: - * start = 0 - */ - __pyx_v_start = (__pyx_v_start + __pyx_v_shape); - - /* "View.MemoryView":830 - * if start < 0: - * start += shape - * if start < 0: # <<<<<<<<<<<<<< - * start = 0 - * elif start >= shape: - */ - __pyx_t_2 = ((__pyx_v_start < 0) != 0); - if (__pyx_t_2) { - - /* "View.MemoryView":831 - * start += shape - * if start < 0: - * start = 0 # <<<<<<<<<<<<<< - * elif start >= shape: - * if negative_step: - */ - __pyx_v_start = 0; - - /* "View.MemoryView":830 - * if start < 0: - * start += shape - * if start < 0: # <<<<<<<<<<<<<< - * start = 0 - * elif start >= shape: - */ - } - - /* "View.MemoryView":828 - * - * if have_start: - * if start < 0: # <<<<<<<<<<<<<< - * start += shape - * if start < 0: - */ - goto __pyx_L12; - } - - /* "View.MemoryView":832 - * if start < 0: - * start = 0 - * elif start >= shape: # <<<<<<<<<<<<<< - * if negative_step: - * start = shape - 1 - */ - __pyx_t_2 = ((__pyx_v_start >= __pyx_v_shape) != 0); - if (__pyx_t_2) { - - /* "View.MemoryView":833 - * start = 0 - * elif start >= shape: - * if negative_step: # <<<<<<<<<<<<<< - * start = shape - 1 - * else: - */ - __pyx_t_2 = (__pyx_v_negative_step != 0); - if (__pyx_t_2) { - - /* "View.MemoryView":834 - * elif start >= shape: - * if negative_step: - * start = shape - 1 # <<<<<<<<<<<<<< - * else: - * start = shape - */ - __pyx_v_start = (__pyx_v_shape - 1); - - /* "View.MemoryView":833 - * start = 0 - * elif start >= shape: - * if negative_step: # <<<<<<<<<<<<<< - * start = shape - 1 - * else: - */ - goto __pyx_L14; - } - - /* "View.MemoryView":836 - * start = shape - 1 - * else: - * start = shape # <<<<<<<<<<<<<< - * else: - * if negative_step: - */ - /*else*/ { - __pyx_v_start = __pyx_v_shape; - } - __pyx_L14:; - - /* "View.MemoryView":832 - * if start < 0: - * start = 0 - * elif start >= shape: # <<<<<<<<<<<<<< - * if negative_step: - * start = shape - 1 - */ - } - __pyx_L12:; - - /* "View.MemoryView":827 - * - * - * if have_start: # <<<<<<<<<<<<<< - * if start < 0: - * start += shape - */ - goto __pyx_L11; - } - - /* "View.MemoryView":838 - * start = shape - * else: - * if negative_step: # <<<<<<<<<<<<<< - * start = shape - 1 - * else: - */ - /*else*/ { - __pyx_t_2 = (__pyx_v_negative_step != 0); - if (__pyx_t_2) { - - /* "View.MemoryView":839 - * else: - * if negative_step: - * start = shape - 1 # <<<<<<<<<<<<<< - * else: - * start = 0 - */ - __pyx_v_start = (__pyx_v_shape - 1); - - /* "View.MemoryView":838 - * start = shape - * else: - * if negative_step: # <<<<<<<<<<<<<< - * start = shape - 1 - * else: - */ - goto __pyx_L15; - } - - /* "View.MemoryView":841 - * start = shape - 1 - * else: - * start = 0 # <<<<<<<<<<<<<< - * - * if have_stop: - */ - /*else*/ { - __pyx_v_start = 0; - } - __pyx_L15:; - } - __pyx_L11:; - - /* "View.MemoryView":843 - * start = 0 - * - * if have_stop: # <<<<<<<<<<<<<< - * if stop < 0: - * stop += shape - */ - __pyx_t_2 = (__pyx_v_have_stop != 0); - if (__pyx_t_2) { - - /* "View.MemoryView":844 - * - * if have_stop: - * if stop < 0: # <<<<<<<<<<<<<< - * stop += shape - * if stop < 0: - */ - __pyx_t_2 = ((__pyx_v_stop < 0) != 0); - if (__pyx_t_2) { - - /* "View.MemoryView":845 - * if have_stop: - * if stop < 0: - * stop += shape # <<<<<<<<<<<<<< - * if stop < 0: - * stop = 0 - */ - __pyx_v_stop = (__pyx_v_stop + __pyx_v_shape); - - /* "View.MemoryView":846 - * if stop < 0: - * stop += shape - * if stop < 0: # <<<<<<<<<<<<<< - * stop = 0 - * elif stop > shape: - */ - __pyx_t_2 = ((__pyx_v_stop < 0) != 0); - if (__pyx_t_2) { - - /* "View.MemoryView":847 - * stop += shape - * if stop < 0: - * stop = 0 # <<<<<<<<<<<<<< - * elif stop > shape: - * stop = shape - */ - __pyx_v_stop = 0; - - /* "View.MemoryView":846 - * if stop < 0: - * stop += shape - * if stop < 0: # <<<<<<<<<<<<<< - * stop = 0 - * elif stop > shape: - */ - } - - /* "View.MemoryView":844 - * - * if have_stop: - * if stop < 0: # <<<<<<<<<<<<<< - * stop += shape - * if stop < 0: - */ - goto __pyx_L17; - } - - /* "View.MemoryView":848 - * if stop < 0: - * stop = 0 - * elif stop > shape: # <<<<<<<<<<<<<< - * stop = shape - * else: - */ - __pyx_t_2 = ((__pyx_v_stop > __pyx_v_shape) != 0); - if (__pyx_t_2) { - - /* "View.MemoryView":849 - * stop = 0 - * elif stop > shape: - * stop = shape # <<<<<<<<<<<<<< - * else: - * if negative_step: - */ - __pyx_v_stop = __pyx_v_shape; - - /* "View.MemoryView":848 - * if stop < 0: - * stop = 0 - * elif stop > shape: # <<<<<<<<<<<<<< - * stop = shape - * else: - */ - } - __pyx_L17:; - - /* "View.MemoryView":843 - * start = 0 - * - * if have_stop: # <<<<<<<<<<<<<< - * if stop < 0: - * stop += shape - */ - goto __pyx_L16; - } - - /* "View.MemoryView":851 - * stop = shape - * else: - * if negative_step: # <<<<<<<<<<<<<< - * stop = -1 - * else: - */ - /*else*/ { - __pyx_t_2 = (__pyx_v_negative_step != 0); - if (__pyx_t_2) { - - /* "View.MemoryView":852 - * else: - * if negative_step: - * stop = -1 # <<<<<<<<<<<<<< - * else: - * stop = shape - */ - __pyx_v_stop = -1L; - - /* "View.MemoryView":851 - * stop = shape - * else: - * if negative_step: # <<<<<<<<<<<<<< - * stop = -1 - * else: - */ - goto __pyx_L19; - } - - /* "View.MemoryView":854 - * stop = -1 - * else: - * stop = shape # <<<<<<<<<<<<<< - * - * if not have_step: - */ - /*else*/ { - __pyx_v_stop = __pyx_v_shape; - } - __pyx_L19:; - } - __pyx_L16:; - - /* "View.MemoryView":856 - * stop = shape - * - * if not 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0: - */ - __pyx_v_new_shape = (__pyx_v_new_shape + 1); - - /* "View.MemoryView":863 - * new_shape = (stop - start) // step - * - * if (stop - start) - step * new_shape: # <<<<<<<<<<<<<< - * new_shape += 1 - * - */ - } - - /* "View.MemoryView":866 - * new_shape += 1 - * - * if new_shape < 0: # <<<<<<<<<<<<<< - * new_shape = 0 - * - */ - __pyx_t_2 = ((__pyx_v_new_shape < 0) != 0); - if (__pyx_t_2) { - - /* "View.MemoryView":867 - * - * if new_shape < 0: - * new_shape = 0 # <<<<<<<<<<<<<< - * - * - */ - __pyx_v_new_shape = 0; - - /* "View.MemoryView":866 - * new_shape += 1 - * - * if new_shape < 0: # <<<<<<<<<<<<<< - * new_shape = 0 - * - */ - } - - /* "View.MemoryView":870 - * - * - * dst.strides[new_ndim] = stride * step # <<<<<<<<<<<<<< - * dst.shape[new_ndim] = new_shape - * dst.suboffsets[new_ndim] = suboffset - */ - (__pyx_v_dst->strides[__pyx_v_new_ndim]) = (__pyx_v_stride * __pyx_v_step); - - /* "View.MemoryView":871 - * - * dst.strides[new_ndim] = stride * step - * dst.shape[new_ndim] = new_shape # <<<<<<<<<<<<<< - * dst.suboffsets[new_ndim] = suboffset - * - */ - (__pyx_v_dst->shape[__pyx_v_new_ndim]) = __pyx_v_new_shape; - - /* "View.MemoryView":872 - * dst.strides[new_ndim] = stride * step - * dst.shape[new_ndim] = new_shape - * dst.suboffsets[new_ndim] = suboffset # <<<<<<<<<<<<<< - * - * - */ - (__pyx_v_dst->suboffsets[__pyx_v_new_ndim]) = __pyx_v_suboffset; - } - __pyx_L3:; - - /* "View.MemoryView":875 - * - * - * if suboffset_dim[0] < 0: # <<<<<<<<<<<<<< - * dst.data += start * stride - * else: - */ - __pyx_t_2 = (((__pyx_v_suboffset_dim[0]) < 0) != 0); - if (__pyx_t_2) { - - /* "View.MemoryView":876 - * - * if suboffset_dim[0] < 0: - * dst.data += start * stride # <<<<<<<<<<<<<< - * else: - * dst.suboffsets[suboffset_dim[0]] += start * stride - */ - __pyx_v_dst->data = (__pyx_v_dst->data + (__pyx_v_start * __pyx_v_stride)); - - /* "View.MemoryView":875 - * - * - * if suboffset_dim[0] < 0: # <<<<<<<<<<<<<< - * dst.data += start * stride - * else: - */ - goto __pyx_L23; - } - - /* "View.MemoryView":878 - * dst.data += start * stride - * else: - * dst.suboffsets[suboffset_dim[0]] += start * stride # <<<<<<<<<<<<<< - * - * if suboffset >= 0: - */ - /*else*/ { - __pyx_t_3 = (__pyx_v_suboffset_dim[0]); - (__pyx_v_dst->suboffsets[__pyx_t_3]) = ((__pyx_v_dst->suboffsets[__pyx_t_3]) + (__pyx_v_start * __pyx_v_stride)); - } - __pyx_L23:; - - /* "View.MemoryView":880 - * dst.suboffsets[suboffset_dim[0]] += start * stride - * - * if suboffset >= 0: # <<<<<<<<<<<<<< - * if not is_slice: - * if new_ndim == 0: - */ - __pyx_t_2 = ((__pyx_v_suboffset >= 0) != 0); - if (__pyx_t_2) { - - /* "View.MemoryView":881 - * - * if suboffset >= 0: - * if not is_slice: # <<<<<<<<<<<<<< - * if new_ndim == 0: - * dst.data = ( dst.data)[0] + suboffset - */ - __pyx_t_2 = ((!(__pyx_v_is_slice != 0)) != 0); - if (__pyx_t_2) { - - /* "View.MemoryView":882 - * if suboffset >= 0: - * if not is_slice: - * if new_ndim == 0: # <<<<<<<<<<<<<< - * dst.data = ( dst.data)[0] + suboffset - * else: - */ - __pyx_t_2 = ((__pyx_v_new_ndim == 0) != 0); - if (__pyx_t_2) { - - /* "View.MemoryView":883 - * if not is_slice: - * if new_ndim == 0: - * dst.data = ( dst.data)[0] + suboffset # <<<<<<<<<<<<<< - * else: - * _err_dim(IndexError, "All dimensions preceding dimension %d " - */ - __pyx_v_dst->data = ((((char **)__pyx_v_dst->data)[0]) + __pyx_v_suboffset); - - /* "View.MemoryView":882 - * if suboffset >= 0: - * if not is_slice: - * if new_ndim == 0: # <<<<<<<<<<<<<< - * dst.data = ( dst.data)[0] + suboffset - * else: - */ - goto __pyx_L26; - } - - /* "View.MemoryView":885 - * dst.data = ( dst.data)[0] + suboffset - * else: - * _err_dim(IndexError, "All dimensions preceding dimension %d " # <<<<<<<<<<<<<< - * "must be indexed and not sliced", dim) - * else: - */ - /*else*/ { - - /* "View.MemoryView":886 - * else: - * _err_dim(IndexError, "All dimensions preceding dimension %d " - * "must be indexed and not sliced", dim) # <<<<<<<<<<<<<< - * else: - * 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src_strides[0] - * cdef Py_ssize_t dst_stride = dst_strides[0] - */ - __pyx_v_dst_extent = (__pyx_v_dst_shape[0]); - - /* "View.MemoryView":1132 - * cdef Py_ssize_t src_extent = src_shape[0] - * cdef Py_ssize_t dst_extent = dst_shape[0] - * cdef Py_ssize_t src_stride = src_strides[0] # <<<<<<<<<<<<<< - * cdef Py_ssize_t dst_stride = dst_strides[0] - * - */ - __pyx_v_src_stride = (__pyx_v_src_strides[0]); - - /* "View.MemoryView":1133 - * cdef Py_ssize_t dst_extent = dst_shape[0] - * cdef Py_ssize_t src_stride = src_strides[0] - * cdef Py_ssize_t dst_stride = dst_strides[0] # <<<<<<<<<<<<<< - * - * if ndim == 1: - */ - __pyx_v_dst_stride = (__pyx_v_dst_strides[0]); - - /* "View.MemoryView":1135 - * cdef Py_ssize_t dst_stride = dst_strides[0] - * - * if ndim == 1: # <<<<<<<<<<<<<< - * if (src_stride > 0 and dst_stride > 0 and - * src_stride == itemsize == dst_stride): - */ - __pyx_t_1 = ((__pyx_v_ndim == 1) != 0); - if (__pyx_t_1) { - - /* "View.MemoryView":1136 - * - * if ndim == 1: - * if (src_stride > 0 and dst_stride > 0 and # <<<<<<<<<<<<<< - * src_stride == itemsize == dst_stride): - * memcpy(dst_data, src_data, itemsize * dst_extent) - */ - __pyx_t_2 = ((__pyx_v_src_stride > 0) != 0); - if (__pyx_t_2) { - } else { - __pyx_t_1 = __pyx_t_2; - goto __pyx_L5_bool_binop_done; - } - __pyx_t_2 = ((__pyx_v_dst_stride > 0) != 0); - if (__pyx_t_2) { - } else { - __pyx_t_1 = __pyx_t_2; - goto __pyx_L5_bool_binop_done; - } - - /* "View.MemoryView":1137 - * if ndim == 1: - * if (src_stride > 0 and dst_stride > 0 and - * src_stride == itemsize == dst_stride): # <<<<<<<<<<<<<< - * memcpy(dst_data, src_data, itemsize * dst_extent) - * else: - */ - __pyx_t_2 = (((size_t)__pyx_v_src_stride) == __pyx_v_itemsize); - if (__pyx_t_2) { - __pyx_t_2 = (__pyx_v_itemsize == ((size_t)__pyx_v_dst_stride)); - } - __pyx_t_3 = (__pyx_t_2 != 0); - __pyx_t_1 = __pyx_t_3; - __pyx_L5_bool_binop_done:; - - /* "View.MemoryView":1136 - * - * if ndim == 1: - * if (src_stride > 0 and dst_stride > 0 and # <<<<<<<<<<<<<< - * src_stride == itemsize == dst_stride): - * memcpy(dst_data, src_data, itemsize * dst_extent) - */ - if (__pyx_t_1) { - - /* "View.MemoryView":1138 - * if (src_stride > 0 and dst_stride > 0 and - * src_stride == itemsize == dst_stride): - * memcpy(dst_data, src_data, itemsize * dst_extent) # <<<<<<<<<<<<<< - * else: - * for i in range(dst_extent): - */ - memcpy(__pyx_v_dst_data, __pyx_v_src_data, (__pyx_v_itemsize * __pyx_v_dst_extent)); - - /* "View.MemoryView":1136 - * - * if ndim == 1: - * if (src_stride > 0 and dst_stride > 0 and # <<<<<<<<<<<<<< - * src_stride == itemsize == dst_stride): - * memcpy(dst_data, src_data, itemsize * dst_extent) - */ - goto __pyx_L4; - } - - /* "View.MemoryView":1140 - * memcpy(dst_data, src_data, itemsize * dst_extent) - * else: - * for i in range(dst_extent): # <<<<<<<<<<<<<< - * memcpy(dst_data, src_data, itemsize) - * src_data += src_stride - */ - /*else*/ { - __pyx_t_4 = __pyx_v_dst_extent; - for (__pyx_t_5 = 0; __pyx_t_5 < __pyx_t_4; __pyx_t_5+=1) { - __pyx_v_i = __pyx_t_5; - - /* "View.MemoryView":1141 - * else: - * for i in range(dst_extent): - * memcpy(dst_data, src_data, itemsize) # <<<<<<<<<<<<<< - * src_data += src_stride - * dst_data += dst_stride - */ - memcpy(__pyx_v_dst_data, __pyx_v_src_data, __pyx_v_itemsize); - - /* "View.MemoryView":1142 - * for i in range(dst_extent): - * memcpy(dst_data, src_data, itemsize) - * src_data += src_stride # <<<<<<<<<<<<<< - * dst_data += dst_stride - * else: - */ - __pyx_v_src_data = (__pyx_v_src_data + __pyx_v_src_stride); - - /* "View.MemoryView":1143 - * memcpy(dst_data, src_data, itemsize) - * src_data += src_stride - * dst_data += dst_stride # <<<<<<<<<<<<<< - * else: - * for i in range(dst_extent): - */ - __pyx_v_dst_data = (__pyx_v_dst_data + __pyx_v_dst_stride); - } - } - __pyx_L4:; - - /* "View.MemoryView":1135 - * cdef Py_ssize_t dst_stride = dst_strides[0] - * - * if ndim == 1: # <<<<<<<<<<<<<< - * if (src_stride > 0 and dst_stride > 0 and - * src_stride == itemsize == dst_stride): - */ - goto __pyx_L3; - } - - /* "View.MemoryView":1145 - * dst_data += dst_stride - * else: - * for i in range(dst_extent): # <<<<<<<<<<<<<< - * _copy_strided_to_strided(src_data, src_strides + 1, - * dst_data, dst_strides + 1, - */ - /*else*/ { - __pyx_t_4 = __pyx_v_dst_extent; - for (__pyx_t_5 = 0; __pyx_t_5 < __pyx_t_4; __pyx_t_5+=1) { - __pyx_v_i = __pyx_t_5; - - /* "View.MemoryView":1146 - * else: - * for i in range(dst_extent): - * _copy_strided_to_strided(src_data, src_strides + 1, # <<<<<<<<<<<<<< - * dst_data, dst_strides + 1, - * src_shape + 1, dst_shape + 1, - */ - _copy_strided_to_strided(__pyx_v_src_data, (__pyx_v_src_strides + 1), __pyx_v_dst_data, (__pyx_v_dst_strides + 1), (__pyx_v_src_shape + 1), (__pyx_v_dst_shape + 1), (__pyx_v_ndim - 1), __pyx_v_itemsize); - - /* "View.MemoryView":1150 - * src_shape + 1, dst_shape + 1, - * ndim - 1, itemsize) - * src_data += src_stride # <<<<<<<<<<<<<< - * dst_data += dst_stride - * - */ - __pyx_v_src_data = (__pyx_v_src_data + __pyx_v_src_stride); - - /* "View.MemoryView":1151 - * ndim - 1, itemsize) - * src_data += src_stride - * dst_data += dst_stride # <<<<<<<<<<<<<< - * - * cdef void copy_strided_to_strided(__Pyx_memviewslice *src, - */ - __pyx_v_dst_data = (__pyx_v_dst_data + __pyx_v_dst_stride); - } - } - __pyx_L3:; - - /* "View.MemoryView":1123 - * - * @cython.cdivision(True) - * cdef void _copy_strided_to_strided(char *src_data, Py_ssize_t *src_strides, # <<<<<<<<<<<<<< - * char *dst_data, Py_ssize_t *dst_strides, - * Py_ssize_t *src_shape, Py_ssize_t *dst_shape, - */ - - /* function exit code */ -} - -/* "View.MemoryView":1153 - * dst_data += dst_stride - * - * cdef void copy_strided_to_strided(__Pyx_memviewslice *src, # <<<<<<<<<<<<<< - * __Pyx_memviewslice *dst, - * int ndim, size_t itemsize) nogil: - */ - -static void copy_strided_to_strided(__Pyx_memviewslice *__pyx_v_src, __Pyx_memviewslice *__pyx_v_dst, int __pyx_v_ndim, size_t __pyx_v_itemsize) { - - /* "View.MemoryView":1156 - * __Pyx_memviewslice *dst, - * int ndim, size_t itemsize) nogil: - * _copy_strided_to_strided(src.data, src.strides, dst.data, dst.strides, # <<<<<<<<<<<<<< - * src.shape, dst.shape, ndim, itemsize) - * - */ - _copy_strided_to_strided(__pyx_v_src->data, __pyx_v_src->strides, __pyx_v_dst->data, __pyx_v_dst->strides, __pyx_v_src->shape, __pyx_v_dst->shape, __pyx_v_ndim, __pyx_v_itemsize); - - /* "View.MemoryView":1153 - * dst_data += dst_stride - * - * cdef void copy_strided_to_strided(__Pyx_memviewslice *src, # <<<<<<<<<<<<<< - * __Pyx_memviewslice *dst, - * int ndim, size_t itemsize) nogil: - */ - - /* function exit code */ -} - -/* "View.MemoryView":1160 - * - * @cname('__pyx_memoryview_slice_get_size') - * cdef Py_ssize_t slice_get_size(__Pyx_memviewslice *src, int ndim) nogil: # <<<<<<<<<<<<<< - * "Return the size of the memory occupied by the slice in number of bytes" - * cdef int i - */ - -static Py_ssize_t __pyx_memoryview_slice_get_size(__Pyx_memviewslice *__pyx_v_src, int __pyx_v_ndim) { - int __pyx_v_i; - Py_ssize_t __pyx_v_size; - Py_ssize_t __pyx_r; - Py_ssize_t __pyx_t_1; - int __pyx_t_2; - int __pyx_t_3; - - /* "View.MemoryView":1163 - * "Return the size of the memory occupied by the slice in number of bytes" - * cdef int i - * cdef Py_ssize_t size = src.memview.view.itemsize # <<<<<<<<<<<<<< - * - * for i in range(ndim): - */ - __pyx_t_1 = __pyx_v_src->memview->view.itemsize; - __pyx_v_size = __pyx_t_1; - - /* "View.MemoryView":1165 - * cdef Py_ssize_t size = src.memview.view.itemsize - * - * for i in range(ndim): # <<<<<<<<<<<<<< - * size *= src.shape[i] - * - */ - __pyx_t_2 = __pyx_v_ndim; - for (__pyx_t_3 = 0; __pyx_t_3 < __pyx_t_2; __pyx_t_3+=1) { - __pyx_v_i = __pyx_t_3; - - /* "View.MemoryView":1166 - * - * for i in range(ndim): - * size *= src.shape[i] # <<<<<<<<<<<<<< - * - * return size - */ - __pyx_v_size = (__pyx_v_size * (__pyx_v_src->shape[__pyx_v_i])); - } - - /* "View.MemoryView":1168 - * size *= src.shape[i] - * - * return size # <<<<<<<<<<<<<< - * - * @cname('__pyx_fill_contig_strides_array') - */ - __pyx_r = __pyx_v_size; - goto __pyx_L0; - - /* "View.MemoryView":1160 - * - * @cname('__pyx_memoryview_slice_get_size') - * cdef Py_ssize_t slice_get_size(__Pyx_memviewslice *src, int ndim) nogil: # <<<<<<<<<<<<<< - * "Return the size of the memory occupied by the slice in number of bytes" - * cdef int i - */ - - /* function exit code */ - __pyx_L0:; - return __pyx_r; -} - -/* "View.MemoryView":1171 - * - * @cname('__pyx_fill_contig_strides_array') - * cdef Py_ssize_t fill_contig_strides_array( # <<<<<<<<<<<<<< - * Py_ssize_t *shape, Py_ssize_t *strides, Py_ssize_t stride, - * int ndim, char order) nogil: - */ - -static Py_ssize_t __pyx_fill_contig_strides_array(Py_ssize_t *__pyx_v_shape, Py_ssize_t *__pyx_v_strides, Py_ssize_t __pyx_v_stride, int __pyx_v_ndim, char __pyx_v_order) { - int __pyx_v_idx; - Py_ssize_t __pyx_r; - int __pyx_t_1; - int __pyx_t_2; - int __pyx_t_3; - - /* "View.MemoryView":1180 - * cdef int idx - * - * if order == 'F': # <<<<<<<<<<<<<< - * for idx in range(ndim): - * strides[idx] = stride - */ - __pyx_t_1 = ((__pyx_v_order == 'F') != 0); - if (__pyx_t_1) { - - /* "View.MemoryView":1181 - * - * if order == 'F': - * for idx in range(ndim): # <<<<<<<<<<<<<< - * strides[idx] = stride - * stride = stride * shape[idx] - */ - __pyx_t_2 = __pyx_v_ndim; - for (__pyx_t_3 = 0; __pyx_t_3 < __pyx_t_2; __pyx_t_3+=1) { - __pyx_v_idx = __pyx_t_3; - - /* "View.MemoryView":1182 - * if order == 'F': - * for idx in range(ndim): - * strides[idx] = stride # <<<<<<<<<<<<<< - * stride = stride * shape[idx] - * else: - */ - (__pyx_v_strides[__pyx_v_idx]) = __pyx_v_stride; - - /* "View.MemoryView":1183 - * for idx in range(ndim): - * strides[idx] = stride - * stride = stride * shape[idx] # <<<<<<<<<<<<<< - * else: - * for idx in range(ndim - 1, -1, -1): - */ - __pyx_v_stride = (__pyx_v_stride * (__pyx_v_shape[__pyx_v_idx])); - } - - /* "View.MemoryView":1180 - * cdef int idx - * - * if order == 'F': # <<<<<<<<<<<<<< - * for idx in range(ndim): - * strides[idx] = stride - */ - goto __pyx_L3; - } - - /* "View.MemoryView":1185 - * stride = stride * shape[idx] - * else: - * for idx in range(ndim - 1, -1, -1): # <<<<<<<<<<<<<< - * strides[idx] = stride - * stride = stride * shape[idx] - */ - /*else*/ { - for (__pyx_t_2 = (__pyx_v_ndim - 1); __pyx_t_2 > -1L; __pyx_t_2-=1) { - __pyx_v_idx = __pyx_t_2; - - /* "View.MemoryView":1186 - * else: - * for idx in range(ndim - 1, -1, -1): - * strides[idx] = stride # <<<<<<<<<<<<<< - * stride = stride * shape[idx] - * - */ - (__pyx_v_strides[__pyx_v_idx]) = __pyx_v_stride; - - /* "View.MemoryView":1187 - * for idx in range(ndim - 1, -1, -1): - * strides[idx] = stride - * stride = stride * shape[idx] # <<<<<<<<<<<<<< - * - * return stride - */ - __pyx_v_stride = (__pyx_v_stride * (__pyx_v_shape[__pyx_v_idx])); - } - } - __pyx_L3:; - - /* "View.MemoryView":1189 - * stride = stride * shape[idx] - * - * return stride # <<<<<<<<<<<<<< - * - * @cname('__pyx_memoryview_copy_data_to_temp') - */ - __pyx_r = __pyx_v_stride; - goto __pyx_L0; - - /* "View.MemoryView":1171 - * - * @cname('__pyx_fill_contig_strides_array') - * cdef Py_ssize_t fill_contig_strides_array( # <<<<<<<<<<<<<< - * Py_ssize_t *shape, Py_ssize_t *strides, Py_ssize_t stride, - * int ndim, char order) nogil: - */ - - /* function exit code */ - __pyx_L0:; - return __pyx_r; -} - -/* "View.MemoryView":1192 - * - * @cname('__pyx_memoryview_copy_data_to_temp') - * cdef void *copy_data_to_temp(__Pyx_memviewslice *src, # <<<<<<<<<<<<<< - * __Pyx_memviewslice *tmpslice, - * char order, - */ - -static void *__pyx_memoryview_copy_data_to_temp(__Pyx_memviewslice *__pyx_v_src, __Pyx_memviewslice *__pyx_v_tmpslice, char __pyx_v_order, int __pyx_v_ndim) { - int __pyx_v_i; - void *__pyx_v_result; - size_t __pyx_v_itemsize; - size_t __pyx_v_size; - void *__pyx_r; - Py_ssize_t __pyx_t_1; - int __pyx_t_2; - int __pyx_t_3; - struct __pyx_memoryview_obj *__pyx_t_4; - int __pyx_t_5; - - /* "View.MemoryView":1203 - * cdef void *result - * - * cdef size_t itemsize = src.memview.view.itemsize # <<<<<<<<<<<<<< - * cdef size_t size = slice_get_size(src, ndim) - * - */ - __pyx_t_1 = __pyx_v_src->memview->view.itemsize; - __pyx_v_itemsize = __pyx_t_1; - - /* "View.MemoryView":1204 - * - * cdef size_t itemsize = src.memview.view.itemsize - * cdef size_t size = slice_get_size(src, ndim) # <<<<<<<<<<<<<< - * - * result = malloc(size) - */ - __pyx_v_size = __pyx_memoryview_slice_get_size(__pyx_v_src, __pyx_v_ndim); - - /* "View.MemoryView":1206 - * cdef size_t size = slice_get_size(src, ndim) - * - * result = malloc(size) # <<<<<<<<<<<<<< - * if not result: - * _err(MemoryError, NULL) - */ - __pyx_v_result = malloc(__pyx_v_size); - - /* "View.MemoryView":1207 - * - * result = malloc(size) - * if not result: # <<<<<<<<<<<<<< - * _err(MemoryError, NULL) - * - */ - __pyx_t_2 = ((!(__pyx_v_result != 0)) != 0); - if (__pyx_t_2) { - - /* "View.MemoryView":1208 - * result = malloc(size) - * if not result: - * _err(MemoryError, NULL) # <<<<<<<<<<<<<< - * - * - */ - __pyx_t_3 = __pyx_memoryview_err(__pyx_builtin_MemoryError, NULL); if (unlikely(__pyx_t_3 == -1)) __PYX_ERR(1, 1208, __pyx_L1_error) - - /* "View.MemoryView":1207 - * - * result = malloc(size) - * if not result: # <<<<<<<<<<<<<< - * _err(MemoryError, NULL) - * - */ - } - - /* "View.MemoryView":1211 - * - * - * tmpslice.data = result # <<<<<<<<<<<<<< - * tmpslice.memview = src.memview - * for i in range(ndim): - */ - __pyx_v_tmpslice->data = ((char *)__pyx_v_result); - - /* "View.MemoryView":1212 - * - * tmpslice.data = result - * tmpslice.memview = src.memview # <<<<<<<<<<<<<< - * for i in range(ndim): - * tmpslice.shape[i] = src.shape[i] - */ - __pyx_t_4 = __pyx_v_src->memview; - __pyx_v_tmpslice->memview = __pyx_t_4; - - /* "View.MemoryView":1213 - * tmpslice.data = result - * tmpslice.memview = src.memview - * for i in range(ndim): 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*/ - __pyx_t_3 = __pyx_v_dst_ndim; - __pyx_t_4 = __pyx_v_src_ndim; - if (((__pyx_t_3 > __pyx_t_4) != 0)) { - __pyx_t_5 = __pyx_t_3; - } else { - __pyx_t_5 = __pyx_t_4; - } - __pyx_v_ndim = __pyx_t_5; - - /* "View.MemoryView":1275 - * cdef int ndim = max(src_ndim, dst_ndim) - * - * for i in range(ndim): # <<<<<<<<<<<<<< - * if src.shape[i] != dst.shape[i]: - * if src.shape[i] == 1: - */ - __pyx_t_5 = __pyx_v_ndim; - for (__pyx_t_3 = 0; __pyx_t_3 < __pyx_t_5; __pyx_t_3+=1) { - __pyx_v_i = __pyx_t_3; - - /* "View.MemoryView":1276 - * - * for i in range(ndim): - * if src.shape[i] != dst.shape[i]: # <<<<<<<<<<<<<< - * if src.shape[i] == 1: - * broadcasting = True - */ - __pyx_t_2 = (((__pyx_v_src.shape[__pyx_v_i]) != (__pyx_v_dst.shape[__pyx_v_i])) != 0); - if (__pyx_t_2) { - - /* "View.MemoryView":1277 - * for i in range(ndim): - * if src.shape[i] != dst.shape[i]: - * if src.shape[i] == 1: # <<<<<<<<<<<<<< - * broadcasting = True - * src.strides[i] = 0 - */ - __pyx_t_2 = (((__pyx_v_src.shape[__pyx_v_i]) == 1) != 0); - if (__pyx_t_2) { - - /* "View.MemoryView":1278 - * if src.shape[i] != dst.shape[i]: - * if src.shape[i] == 1: - * broadcasting = True # <<<<<<<<<<<<<< - * src.strides[i] = 0 - * else: - */ - __pyx_v_broadcasting = 1; - - /* "View.MemoryView":1279 - * if src.shape[i] == 1: - * broadcasting = True - * src.strides[i] = 0 # <<<<<<<<<<<<<< - * else: - * _err_extents(i, dst.shape[i], src.shape[i]) - */ - (__pyx_v_src.strides[__pyx_v_i]) = 0; - - /* "View.MemoryView":1277 - * for i in range(ndim): - * if src.shape[i] != dst.shape[i]: - * if src.shape[i] == 1: # <<<<<<<<<<<<<< - * broadcasting = True - * src.strides[i] = 0 - */ - goto __pyx_L7; - } - - /* "View.MemoryView":1281 - * src.strides[i] = 0 - * else: - * _err_extents(i, dst.shape[i], src.shape[i]) # <<<<<<<<<<<<<< - * - * if src.suboffsets[i] >= 0: - */ - /*else*/ { - __pyx_t_4 = __pyx_memoryview_err_extents(__pyx_v_i, (__pyx_v_dst.shape[__pyx_v_i]), (__pyx_v_src.shape[__pyx_v_i])); if (unlikely(__pyx_t_4 == -1)) __PYX_ERR(1, 1281, __pyx_L1_error) - } - __pyx_L7:; - - /* "View.MemoryView":1276 - * - * for i in range(ndim): - * if src.shape[i] != dst.shape[i]: # <<<<<<<<<<<<<< - * if src.shape[i] == 1: - * broadcasting = True - */ - } - - /* "View.MemoryView":1283 - * _err_extents(i, dst.shape[i], src.shape[i]) - * - * if src.suboffsets[i] >= 0: # <<<<<<<<<<<<<< - * _err_dim(ValueError, "Dimension %d is not direct", i) - * - */ - __pyx_t_2 = (((__pyx_v_src.suboffsets[__pyx_v_i]) >= 0) != 0); - if (__pyx_t_2) { - - /* "View.MemoryView":1284 - * - * if src.suboffsets[i] >= 0: - * _err_dim(ValueError, "Dimension %d is not direct", i) # <<<<<<<<<<<<<< - * - * if slices_overlap(&src, &dst, ndim, itemsize): - */ - __pyx_t_4 = __pyx_memoryview_err_dim(__pyx_builtin_ValueError, ((char *)"Dimension %d is not direct"), __pyx_v_i); if (unlikely(__pyx_t_4 == -1)) __PYX_ERR(1, 1284, __pyx_L1_error) - - /* "View.MemoryView":1283 - * _err_extents(i, dst.shape[i], src.shape[i]) - * - 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__pyx_get_best_slice_order((&__pyx_v_dst), __pyx_v_ndim); - - /* "View.MemoryView":1288 - * if slices_overlap(&src, &dst, ndim, itemsize): - * - * if not slice_is_contig(src, order, ndim): # <<<<<<<<<<<<<< - * order = get_best_order(&dst, ndim) - * - */ - } - - /* "View.MemoryView":1291 - * order = get_best_order(&dst, ndim) - * - * tmpdata = copy_data_to_temp(&src, &tmp, order, ndim) # <<<<<<<<<<<<<< - * src = tmp - * - */ - __pyx_t_6 = __pyx_memoryview_copy_data_to_temp((&__pyx_v_src), (&__pyx_v_tmp), __pyx_v_order, __pyx_v_ndim); if (unlikely(__pyx_t_6 == NULL)) __PYX_ERR(1, 1291, __pyx_L1_error) - __pyx_v_tmpdata = __pyx_t_6; - - /* "View.MemoryView":1292 - * - * tmpdata = copy_data_to_temp(&src, &tmp, order, ndim) - * src = tmp # <<<<<<<<<<<<<< - * - * if not broadcasting: - */ - __pyx_v_src = __pyx_v_tmp; - - /* "View.MemoryView":1286 - * _err_dim(ValueError, "Dimension %d is not direct", i) - * - * if slices_overlap(&src, &dst, ndim, itemsize): # <<<<<<<<<<<<<< - * - * if not slice_is_contig(src, order, ndim): - */ - } - - /* "View.MemoryView":1294 - * src = tmp - * - * if not broadcasting: # <<<<<<<<<<<<<< - * - * - */ - __pyx_t_2 = ((!(__pyx_v_broadcasting != 0)) != 0); - if (__pyx_t_2) { - - /* "View.MemoryView":1297 - * - * - * if slice_is_contig(src, 'C', ndim): # <<<<<<<<<<<<<< - * direct_copy = slice_is_contig(dst, 'C', ndim) - * elif slice_is_contig(src, 'F', ndim): - */ - __pyx_t_2 = (__pyx_memviewslice_is_contig(__pyx_v_src, 'C', __pyx_v_ndim) != 0); - if (__pyx_t_2) { - - /* "View.MemoryView":1298 - * - * if slice_is_contig(src, 'C', ndim): - * direct_copy = slice_is_contig(dst, 'C', ndim) # <<<<<<<<<<<<<< - * elif slice_is_contig(src, 'F', ndim): - * direct_copy = slice_is_contig(dst, 'F', ndim) - */ - __pyx_v_direct_copy = __pyx_memviewslice_is_contig(__pyx_v_dst, 'C', __pyx_v_ndim); - - /* "View.MemoryView":1297 - * - * - * if slice_is_contig(src, 'C', ndim): # <<<<<<<<<<<<<< - * direct_copy = slice_is_contig(dst, 'C', ndim) - * elif slice_is_contig(src, 'F', ndim): - */ - goto __pyx_L12; - } - - /* "View.MemoryView":1299 - * if slice_is_contig(src, 'C', ndim): - * direct_copy = slice_is_contig(dst, 'C', ndim) - * elif slice_is_contig(src, 'F', ndim): # <<<<<<<<<<<<<< - * direct_copy = slice_is_contig(dst, 'F', ndim) - * - */ - __pyx_t_2 = (__pyx_memviewslice_is_contig(__pyx_v_src, 'F', __pyx_v_ndim) != 0); - if (__pyx_t_2) { - - /* "View.MemoryView":1300 - * direct_copy = slice_is_contig(dst, 'C', ndim) - * elif slice_is_contig(src, 'F', ndim): - * direct_copy = slice_is_contig(dst, 'F', ndim) # <<<<<<<<<<<<<< - * - * if direct_copy: - */ - __pyx_v_direct_copy = __pyx_memviewslice_is_contig(__pyx_v_dst, 'F', __pyx_v_ndim); - - /* "View.MemoryView":1299 - * if slice_is_contig(src, 'C', ndim): - * direct_copy = slice_is_contig(dst, 'C', ndim) - * elif slice_is_contig(src, 'F', ndim): # <<<<<<<<<<<<<< - * direct_copy = slice_is_contig(dst, 'F', ndim) - * - */ - } - __pyx_L12:; - - /* "View.MemoryView":1302 - * direct_copy = slice_is_contig(dst, 'F', ndim) - * - * if direct_copy: # <<<<<<<<<<<<<< - * - * refcount_copying(&dst, dtype_is_object, ndim, False) - */ - __pyx_t_2 = (__pyx_v_direct_copy != 0); - if (__pyx_t_2) { - - /* "View.MemoryView":1304 - * if direct_copy: - * - * refcount_copying(&dst, dtype_is_object, ndim, False) # <<<<<<<<<<<<<< - * memcpy(dst.data, src.data, slice_get_size(&src, ndim)) - * refcount_copying(&dst, dtype_is_object, ndim, True) - */ - __pyx_memoryview_refcount_copying((&__pyx_v_dst), __pyx_v_dtype_is_object, __pyx_v_ndim, 0); - - /* "View.MemoryView":1305 - * - * refcount_copying(&dst, dtype_is_object, ndim, False) - * memcpy(dst.data, src.data, slice_get_size(&src, ndim)) # <<<<<<<<<<<<<< - * refcount_copying(&dst, dtype_is_object, ndim, True) - * free(tmpdata) - */ - memcpy(__pyx_v_dst.data, __pyx_v_src.data, __pyx_memoryview_slice_get_size((&__pyx_v_src), __pyx_v_ndim)); - - /* "View.MemoryView":1306 - * refcount_copying(&dst, dtype_is_object, ndim, False) - 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* - */ - } - - /* "View.MemoryView":1310 - * return 0 - * - * if order == 'F' == get_best_order(&dst, ndim): # <<<<<<<<<<<<<< - * - * - */ - __pyx_t_2 = (__pyx_v_order == 'F'); - if (__pyx_t_2) { - __pyx_t_2 = ('F' == __pyx_get_best_slice_order((&__pyx_v_dst), __pyx_v_ndim)); - } - __pyx_t_7 = (__pyx_t_2 != 0); - if (__pyx_t_7) { - - /* "View.MemoryView":1313 - * - * - * transpose_memslice(&src) # <<<<<<<<<<<<<< - * transpose_memslice(&dst) - * - */ - __pyx_t_5 = __pyx_memslice_transpose((&__pyx_v_src)); if (unlikely(__pyx_t_5 == 0)) __PYX_ERR(1, 1313, __pyx_L1_error) - - /* "View.MemoryView":1314 - * - * transpose_memslice(&src) - * transpose_memslice(&dst) # <<<<<<<<<<<<<< - * - * refcount_copying(&dst, dtype_is_object, ndim, False) - */ - __pyx_t_5 = __pyx_memslice_transpose((&__pyx_v_dst)); if (unlikely(__pyx_t_5 == 0)) __PYX_ERR(1, 1314, __pyx_L1_error) - - /* "View.MemoryView":1310 - * return 0 - * - * if order == 'F' == get_best_order(&dst, ndim): # <<<<<<<<<<<<<< - * - * - */ - 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0, /*tp_str*/ - 0, /*tp_getattro*/ - 0, /*tp_setattro*/ - 0, /*tp_as_buffer*/ - Py_TPFLAGS_DEFAULT|Py_TPFLAGS_HAVE_VERSION_TAG|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/ - 0, /*tp_doc*/ - __pyx_tp_traverse_Enum, /*tp_traverse*/ - __pyx_tp_clear_Enum, /*tp_clear*/ - 0, /*tp_richcompare*/ - 0, /*tp_weaklistoffset*/ - 0, /*tp_iter*/ - 0, /*tp_iternext*/ - __pyx_methods_Enum, /*tp_methods*/ - 0, /*tp_members*/ - 0, /*tp_getset*/ - 0, /*tp_base*/ - 0, /*tp_dict*/ - 0, /*tp_descr_get*/ - 0, /*tp_descr_set*/ - 0, /*tp_dictoffset*/ - __pyx_MemviewEnum___init__, /*tp_init*/ - 0, /*tp_alloc*/ - __pyx_tp_new_Enum, /*tp_new*/ - 0, /*tp_free*/ - 0, /*tp_is_gc*/ - 0, /*tp_bases*/ - 0, /*tp_mro*/ - 0, /*tp_cache*/ - 0, /*tp_subclasses*/ - 0, /*tp_weaklist*/ - 0, /*tp_del*/ - 0, /*tp_version_tag*/ - #if PY_VERSION_HEX >= 0x030400a1 - 0, /*tp_finalize*/ - #endif -}; -static struct __pyx_vtabstruct_memoryview __pyx_vtable_memoryview; - -static 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/*tp_hash*/ - 0, /*tp_call*/ - __pyx_memoryview___str__, /*tp_str*/ - 0, /*tp_getattro*/ - 0, /*tp_setattro*/ - &__pyx_tp_as_buffer_memoryview, /*tp_as_buffer*/ - Py_TPFLAGS_DEFAULT|Py_TPFLAGS_HAVE_VERSION_TAG|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/ - 0, /*tp_doc*/ - __pyx_tp_traverse_memoryview, /*tp_traverse*/ - __pyx_tp_clear_memoryview, /*tp_clear*/ - 0, /*tp_richcompare*/ - 0, /*tp_weaklistoffset*/ - 0, /*tp_iter*/ - 0, /*tp_iternext*/ - __pyx_methods_memoryview, /*tp_methods*/ - 0, /*tp_members*/ - __pyx_getsets_memoryview, /*tp_getset*/ - 0, /*tp_base*/ - 0, /*tp_dict*/ - 0, /*tp_descr_get*/ - 0, /*tp_descr_set*/ - 0, /*tp_dictoffset*/ - 0, /*tp_init*/ - 0, /*tp_alloc*/ - __pyx_tp_new_memoryview, /*tp_new*/ - 0, /*tp_free*/ - 0, /*tp_is_gc*/ - 0, /*tp_bases*/ - 0, /*tp_mro*/ - 0, /*tp_cache*/ - 0, /*tp_subclasses*/ - 0, /*tp_weaklist*/ - 0, /*tp_del*/ - 0, /*tp_version_tag*/ - #if PY_VERSION_HEX >= 0x030400a1 - 0, 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- #else - module = PyImport_ImportModuleLevelObject( - name, global_dict, empty_dict, list, 1); - #endif - if (!module) { - if (!PyErr_ExceptionMatches(PyExc_ImportError)) - goto bad; - PyErr_Clear(); - } - } - level = 0; - } - #endif - if (!module) { - #if PY_VERSION_HEX < 0x03030000 - PyObject *py_level = PyInt_FromLong(level); - if (!py_level) - goto bad; - module = PyObject_CallFunctionObjArgs(py_import, - name, global_dict, empty_dict, list, py_level, NULL); - Py_DECREF(py_level); - #else - module = PyImport_ImportModuleLevelObject( - name, global_dict, empty_dict, list, level); - #endif - } - } -bad: - #if PY_VERSION_HEX < 0x03030000 - Py_XDECREF(py_import); - #endif - Py_XDECREF(empty_list); - Py_XDECREF(empty_dict); - return module; -} - -/* BytesEquals */ - static CYTHON_INLINE int __Pyx_PyBytes_Equals(PyObject* s1, PyObject* s2, int equals) { -#if CYTHON_COMPILING_IN_PYPY - return PyObject_RichCompareBool(s1, s2, equals); -#else - if (s1 == s2) { - return (equals == Py_EQ); - } else if (PyBytes_CheckExact(s1) & PyBytes_CheckExact(s2)) { - const char *ps1, *ps2; - Py_ssize_t length = PyBytes_GET_SIZE(s1); - if (length != PyBytes_GET_SIZE(s2)) - return (equals == Py_NE); - ps1 = PyBytes_AS_STRING(s1); - ps2 = PyBytes_AS_STRING(s2); - if (ps1[0] != ps2[0]) { - return (equals == Py_NE); - } else if (length == 1) { - return (equals == Py_EQ); - } else { - int result = memcmp(ps1, ps2, (size_t)length); - return (equals == Py_EQ) ? (result == 0) : (result != 0); - } - } else if ((s1 == Py_None) & PyBytes_CheckExact(s2)) { - return (equals == Py_NE); - } else if ((s2 == Py_None) & PyBytes_CheckExact(s1)) { - return (equals == Py_NE); - } else { - int result; - PyObject* py_result = PyObject_RichCompare(s1, s2, equals); - if (!py_result) - return -1; - result = __Pyx_PyObject_IsTrue(py_result); - Py_DECREF(py_result); - return result; - } -#endif -} - -/* UnicodeEquals */ - static CYTHON_INLINE int __Pyx_PyUnicode_Equals(PyObject* s1, PyObject* s2, int equals) { -#if CYTHON_COMPILING_IN_PYPY - return PyObject_RichCompareBool(s1, s2, equals); -#else -#if PY_MAJOR_VERSION < 3 - PyObject* owned_ref = NULL; -#endif - int s1_is_unicode, s2_is_unicode; - if (s1 == s2) { - goto return_eq; - } - s1_is_unicode = PyUnicode_CheckExact(s1); - s2_is_unicode = PyUnicode_CheckExact(s2); -#if PY_MAJOR_VERSION < 3 - if ((s1_is_unicode & (!s2_is_unicode)) && PyString_CheckExact(s2)) { - owned_ref = PyUnicode_FromObject(s2); - if (unlikely(!owned_ref)) - return -1; - s2 = owned_ref; - s2_is_unicode = 1; - } else if ((s2_is_unicode & (!s1_is_unicode)) && PyString_CheckExact(s1)) { - owned_ref = PyUnicode_FromObject(s1); - if (unlikely(!owned_ref)) - return -1; - s1 = owned_ref; - s1_is_unicode = 1; - } else if (((!s2_is_unicode) & (!s1_is_unicode))) { - return __Pyx_PyBytes_Equals(s1, s2, equals); - } -#endif - if (s1_is_unicode & s2_is_unicode) { - Py_ssize_t length; - int kind; - void *data1, *data2; - if (unlikely(__Pyx_PyUnicode_READY(s1) < 0) || unlikely(__Pyx_PyUnicode_READY(s2) < 0)) - return -1; - length = __Pyx_PyUnicode_GET_LENGTH(s1); - if (length != __Pyx_PyUnicode_GET_LENGTH(s2)) { - goto return_ne; - } - kind = __Pyx_PyUnicode_KIND(s1); - if (kind != __Pyx_PyUnicode_KIND(s2)) { - goto return_ne; - } - data1 = __Pyx_PyUnicode_DATA(s1); - data2 = __Pyx_PyUnicode_DATA(s2); - if (__Pyx_PyUnicode_READ(kind, data1, 0) != __Pyx_PyUnicode_READ(kind, data2, 0)) { - goto return_ne; - } else if (length == 1) { - goto return_eq; - } else { - int result = memcmp(data1, data2, (size_t)(length * kind)); - #if PY_MAJOR_VERSION < 3 - Py_XDECREF(owned_ref); - #endif - return (equals == Py_EQ) ? (result == 0) : (result != 0); - } - } else if ((s1 == Py_None) & s2_is_unicode) { - goto return_ne; - } else if ((s2 == Py_None) & s1_is_unicode) { - goto return_ne; - } else { - int result; - PyObject* py_result = PyObject_RichCompare(s1, s2, equals); - if (!py_result) - return -1; - result = __Pyx_PyObject_IsTrue(py_result); - Py_DECREF(py_result); - return result; - } -return_eq: - #if PY_MAJOR_VERSION < 3 - Py_XDECREF(owned_ref); - #endif - return (equals == Py_EQ); -return_ne: - #if PY_MAJOR_VERSION < 3 - Py_XDECREF(owned_ref); - #endif - return (equals == Py_NE); -#endif -} - -/* PyObjectCallMethO */ - #if CYTHON_COMPILING_IN_CPYTHON -static CYTHON_INLINE PyObject* __Pyx_PyObject_CallMethO(PyObject *func, PyObject *arg) { - PyObject *self, *result; - PyCFunction cfunc; - cfunc = PyCFunction_GET_FUNCTION(func); - self = PyCFunction_GET_SELF(func); - if (unlikely(Py_EnterRecursiveCall((char*)" while calling a Python object"))) - return NULL; - result = cfunc(self, arg); - Py_LeaveRecursiveCall(); - if (unlikely(!result) && unlikely(!PyErr_Occurred())) { - PyErr_SetString( - PyExc_SystemError, - "NULL result without error in PyObject_Call"); - } - return result; -} -#endif - -/* PyObjectCallOneArg */ - #if CYTHON_COMPILING_IN_CPYTHON -static PyObject* __Pyx__PyObject_CallOneArg(PyObject *func, PyObject *arg) { - PyObject *result; - PyObject *args = PyTuple_New(1); - if (unlikely(!args)) return NULL; - Py_INCREF(arg); - PyTuple_SET_ITEM(args, 0, arg); - result = __Pyx_PyObject_Call(func, args, NULL); - Py_DECREF(args); - return result; -} -static CYTHON_INLINE PyObject* __Pyx_PyObject_CallOneArg(PyObject *func, PyObject *arg) { -#if CYTHON_FAST_PYCALL - if (PyFunction_Check(func)) { - return __Pyx_PyFunction_FastCall(func, &arg, 1); - } -#endif -#ifdef __Pyx_CyFunction_USED - if (likely(PyCFunction_Check(func) || PyObject_TypeCheck(func, __pyx_CyFunctionType))) { -#else - if (likely(PyCFunction_Check(func))) { -#endif - if (likely(PyCFunction_GET_FLAGS(func) & METH_O)) { - return __Pyx_PyObject_CallMethO(func, arg); -#if CYTHON_FAST_PYCCALL - } else if (PyCFunction_GET_FLAGS(func) & METH_FASTCALL) { - return __Pyx_PyCFunction_FastCall(func, &arg, 1); -#endif - } - } - return __Pyx__PyObject_CallOneArg(func, arg); -} -#else -static CYTHON_INLINE PyObject* __Pyx_PyObject_CallOneArg(PyObject *func, PyObject *arg) { - PyObject *result; - PyObject *args = PyTuple_Pack(1, arg); - if (unlikely(!args)) return NULL; - result = __Pyx_PyObject_Call(func, args, NULL); - Py_DECREF(args); - return result; -} -#endif - -/* PyObjectCallMethod1 */ - static PyObject* __Pyx_PyObject_CallMethod1(PyObject* obj, PyObject* method_name, PyObject* arg) { - PyObject *method, *result = NULL; - method = __Pyx_PyObject_GetAttrStr(obj, method_name); - if (unlikely(!method)) goto done; -#if CYTHON_UNPACK_METHODS - if (likely(PyMethod_Check(method))) { - PyObject *self = PyMethod_GET_SELF(method); - if (likely(self)) { - PyObject *args; - PyObject *function = PyMethod_GET_FUNCTION(method); - #if CYTHON_FAST_PYCALL - if (PyFunction_Check(function)) { - PyObject *args[2] = {self, arg}; - result = __Pyx_PyFunction_FastCall(function, args, 2); - goto done; - } - #endif - #if CYTHON_FAST_PYCCALL - if (__Pyx_PyFastCFunction_Check(function)) { - PyObject *args[2] = {self, arg}; - result = __Pyx_PyCFunction_FastCall(function, args, 2); - goto done; - } - #endif - args = PyTuple_New(2); - if (unlikely(!args)) goto done; - Py_INCREF(self); - PyTuple_SET_ITEM(args, 0, self); - Py_INCREF(arg); - PyTuple_SET_ITEM(args, 1, arg); - Py_INCREF(function); - Py_DECREF(method); method = NULL; - result = __Pyx_PyObject_Call(function, args, NULL); - Py_DECREF(args); - Py_DECREF(function); - return result; - } - } -#endif - result = __Pyx_PyObject_CallOneArg(method, arg); -done: - Py_XDECREF(method); - return result; -} - -/* append */ - static CYTHON_INLINE int __Pyx_PyObject_Append(PyObject* L, PyObject* x) { - if (likely(PyList_CheckExact(L))) { - if (unlikely(__Pyx_PyList_Append(L, x) < 0)) return -1; - } else { - PyObject* retval = __Pyx_PyObject_CallMethod1(L, __pyx_n_s_append, x); - if (unlikely(!retval)) - return -1; - Py_DECREF(retval); - } - return 0; -} - -/* GetItemInt */ - static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Generic(PyObject *o, PyObject* j) { - PyObject *r; - if (!j) return NULL; - r = PyObject_GetItem(o, j); - Py_DECREF(j); - return r; -} -static CYTHON_INLINE PyObject *__Pyx_GetItemInt_List_Fast(PyObject *o, Py_ssize_t i, - CYTHON_NCP_UNUSED int wraparound, - CYTHON_NCP_UNUSED int boundscheck) { -#if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS - if (wraparound & unlikely(i < 0)) i += PyList_GET_SIZE(o); - if ((!boundscheck) || likely((0 <= i) & (i < PyList_GET_SIZE(o)))) { - PyObject *r = PyList_GET_ITEM(o, i); - Py_INCREF(r); - return r; - } - return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i)); -#else - return PySequence_GetItem(o, i); -#endif -} -static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize_t i, - CYTHON_NCP_UNUSED int wraparound, - CYTHON_NCP_UNUSED int boundscheck) { -#if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS - if (wraparound & unlikely(i < 0)) i += PyTuple_GET_SIZE(o); - if ((!boundscheck) || likely((0 <= i) & (i < PyTuple_GET_SIZE(o)))) { - PyObject *r = PyTuple_GET_ITEM(o, i); - Py_INCREF(r); - return r; - } - return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i)); -#else - return PySequence_GetItem(o, i); -#endif -} -static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i, int is_list, - CYTHON_NCP_UNUSED int wraparound, - CYTHON_NCP_UNUSED int boundscheck) { -#if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS && CYTHON_USE_TYPE_SLOTS - if (is_list || PyList_CheckExact(o)) { - Py_ssize_t n = ((!wraparound) | likely(i >= 0)) ? i : i + PyList_GET_SIZE(o); - if ((!boundscheck) || (likely((n >= 0) & (n < PyList_GET_SIZE(o))))) { - PyObject *r = PyList_GET_ITEM(o, n); - Py_INCREF(r); - return r; - } - } - else if (PyTuple_CheckExact(o)) { - Py_ssize_t n = ((!wraparound) | likely(i >= 0)) ? i : i + PyTuple_GET_SIZE(o); - if ((!boundscheck) || likely((n >= 0) & (n < PyTuple_GET_SIZE(o)))) { - PyObject *r = PyTuple_GET_ITEM(o, n); - Py_INCREF(r); - return r; - } - } else { - PySequenceMethods *m = Py_TYPE(o)->tp_as_sequence; - if (likely(m && m->sq_item)) { - if (wraparound && unlikely(i < 0) && likely(m->sq_length)) { - Py_ssize_t l = m->sq_length(o); - if (likely(l >= 0)) { - i += l; - } else { - if (!PyErr_ExceptionMatches(PyExc_OverflowError)) - return NULL; - PyErr_Clear(); - } - } - return m->sq_item(o, i); - } - } -#else - if (is_list || PySequence_Check(o)) { - return PySequence_GetItem(o, i); - } -#endif - return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i)); -} - -/* BufferFormatCheck */ - static CYTHON_INLINE int __Pyx_IsLittleEndian(void) { - unsigned int n = 1; - return *(unsigned char*)(&n) != 0; -} -static void __Pyx_BufFmt_Init(__Pyx_BufFmt_Context* ctx, - __Pyx_BufFmt_StackElem* stack, - __Pyx_TypeInfo* type) { - stack[0].field = &ctx->root; - stack[0].parent_offset = 0; - ctx->root.type = type; - ctx->root.name = "buffer dtype"; - ctx->root.offset = 0; - ctx->head = stack; - ctx->head->field = &ctx->root; - ctx->fmt_offset = 0; - ctx->head->parent_offset = 0; - ctx->new_packmode = '@'; - ctx->enc_packmode = '@'; - ctx->new_count = 1; - ctx->enc_count = 0; - ctx->enc_type = 0; - ctx->is_complex = 0; - ctx->is_valid_array = 0; - ctx->struct_alignment = 0; - while (type->typegroup == 'S') { - ++ctx->head; - ctx->head->field = type->fields; - ctx->head->parent_offset = 0; - type = type->fields->type; - } -} -static int __Pyx_BufFmt_ParseNumber(const char** ts) { - int count; - const char* t = *ts; - if (*t < '0' || *t > '9') { - return -1; - } else { - count = *t++ - '0'; - while (*t >= '0' && *t < '9') { - count *= 10; - count += *t++ - '0'; - } - } - *ts = t; - return count; -} -static int __Pyx_BufFmt_ExpectNumber(const char **ts) { - int number = __Pyx_BufFmt_ParseNumber(ts); - if (number == -1) - PyErr_Format(PyExc_ValueError,\ - "Does not understand character buffer dtype format string ('%c')", **ts); - return number; -} -static void __Pyx_BufFmt_RaiseUnexpectedChar(char ch) { - PyErr_Format(PyExc_ValueError, - "Unexpected format string character: '%c'", ch); -} -static const char* __Pyx_BufFmt_DescribeTypeChar(char ch, int is_complex) { - switch (ch) { - case 'c': return "'char'"; - case 'b': return "'signed char'"; - case 'B': return "'unsigned char'"; - case 'h': return "'short'"; - case 'H': return "'unsigned short'"; - case 'i': return "'int'"; - case 'I': return "'unsigned int'"; - case 'l': return "'long'"; - case 'L': return "'unsigned long'"; - case 'q': return "'long long'"; - case 'Q': return "'unsigned long long'"; - case 'f': return (is_complex ? "'complex float'" : "'float'"); - case 'd': return (is_complex ? "'complex double'" : "'double'"); - case 'g': return (is_complex ? "'complex long double'" : "'long double'"); - case 'T': return "a struct"; - case 'O': return "Python object"; - case 'P': return "a pointer"; - case 's': case 'p': return "a string"; - case 0: return "end"; - default: return "unparseable format string"; - } -} -static size_t __Pyx_BufFmt_TypeCharToStandardSize(char ch, int is_complex) { - switch (ch) { - case '?': case 'c': case 'b': case 'B': case 's': case 'p': return 1; - case 'h': case 'H': return 2; - case 'i': case 'I': case 'l': case 'L': return 4; - case 'q': case 'Q': return 8; - case 'f': return (is_complex ? 8 : 4); - case 'd': return (is_complex ? 16 : 8); - case 'g': { - PyErr_SetString(PyExc_ValueError, "Python does not define a standard format string size for long double ('g').."); - return 0; - } - case 'O': case 'P': return sizeof(void*); - default: - __Pyx_BufFmt_RaiseUnexpectedChar(ch); - return 0; - } -} -static size_t __Pyx_BufFmt_TypeCharToNativeSize(char ch, int is_complex) { - switch (ch) { - case 'c': case 'b': case 'B': case 's': case 'p': return 1; - case 'h': case 'H': return sizeof(short); - case 'i': case 'I': return sizeof(int); - case 'l': case 'L': return sizeof(long); - #ifdef HAVE_LONG_LONG - case 'q': case 'Q': return sizeof(PY_LONG_LONG); - #endif - case 'f': return sizeof(float) * (is_complex ? 2 : 1); - case 'd': return sizeof(double) * (is_complex ? 2 : 1); - case 'g': return sizeof(long double) * (is_complex ? 2 : 1); - case 'O': case 'P': return sizeof(void*); - default: { - __Pyx_BufFmt_RaiseUnexpectedChar(ch); - return 0; - } - } -} -typedef struct { char c; short x; } __Pyx_st_short; -typedef struct { char c; int x; } __Pyx_st_int; -typedef struct { char c; long x; } __Pyx_st_long; -typedef struct { char c; float x; } __Pyx_st_float; -typedef struct { char c; double x; } __Pyx_st_double; -typedef struct { char c; long double x; } __Pyx_st_longdouble; -typedef struct { char c; void *x; } __Pyx_st_void_p; -#ifdef HAVE_LONG_LONG -typedef struct { char c; PY_LONG_LONG x; } __Pyx_st_longlong; -#endif -static size_t __Pyx_BufFmt_TypeCharToAlignment(char ch, CYTHON_UNUSED int is_complex) { - switch (ch) { - case '?': case 'c': case 'b': case 'B': case 's': case 'p': return 1; - case 'h': case 'H': return sizeof(__Pyx_st_short) - sizeof(short); - case 'i': case 'I': return sizeof(__Pyx_st_int) - sizeof(int); - case 'l': case 'L': return sizeof(__Pyx_st_long) - sizeof(long); -#ifdef HAVE_LONG_LONG - case 'q': case 'Q': return sizeof(__Pyx_st_longlong) - sizeof(PY_LONG_LONG); -#endif - case 'f': return sizeof(__Pyx_st_float) - sizeof(float); - case 'd': return sizeof(__Pyx_st_double) - sizeof(double); - case 'g': return sizeof(__Pyx_st_longdouble) - sizeof(long double); - case 'P': case 'O': return sizeof(__Pyx_st_void_p) - sizeof(void*); - default: - __Pyx_BufFmt_RaiseUnexpectedChar(ch); - return 0; - } -} -/* These are for computing the padding at the end of the struct to align - on the first member of the struct. This will probably the same as above, - but we don't have any guarantees. - */ -typedef struct { short x; char c; } __Pyx_pad_short; -typedef struct { int x; char c; } __Pyx_pad_int; -typedef struct { long x; char c; } __Pyx_pad_long; -typedef struct { float x; char c; } __Pyx_pad_float; -typedef struct { double x; char c; } __Pyx_pad_double; -typedef struct { long double x; char c; } __Pyx_pad_longdouble; -typedef struct { void *x; char c; } __Pyx_pad_void_p; -#ifdef HAVE_LONG_LONG -typedef struct { PY_LONG_LONG x; char c; } __Pyx_pad_longlong; -#endif -static size_t __Pyx_BufFmt_TypeCharToPadding(char ch, CYTHON_UNUSED int is_complex) { - switch (ch) { - case '?': case 'c': case 'b': case 'B': case 's': case 'p': return 1; - case 'h': case 'H': return sizeof(__Pyx_pad_short) - sizeof(short); - case 'i': case 'I': return sizeof(__Pyx_pad_int) - sizeof(int); - case 'l': case 'L': return sizeof(__Pyx_pad_long) - sizeof(long); -#ifdef HAVE_LONG_LONG - case 'q': case 'Q': return sizeof(__Pyx_pad_longlong) - sizeof(PY_LONG_LONG); -#endif - case 'f': return sizeof(__Pyx_pad_float) - sizeof(float); - case 'd': return sizeof(__Pyx_pad_double) - sizeof(double); - case 'g': return sizeof(__Pyx_pad_longdouble) - sizeof(long double); - case 'P': case 'O': return sizeof(__Pyx_pad_void_p) - sizeof(void*); - default: - __Pyx_BufFmt_RaiseUnexpectedChar(ch); - return 0; - } -} -static char __Pyx_BufFmt_TypeCharToGroup(char ch, int is_complex) { - switch (ch) { - case 'c': - return 'H'; - case 'b': case 'h': case 'i': - case 'l': case 'q': case 's': case 'p': - return 'I'; - case 'B': case 'H': case 'I': case 'L': case 'Q': - return 'U'; - case 'f': case 'd': case 'g': - return (is_complex ? 'C' : 'R'); - case 'O': - return 'O'; - case 'P': - return 'P'; - default: { - __Pyx_BufFmt_RaiseUnexpectedChar(ch); - return 0; - } - } -} -static void __Pyx_BufFmt_RaiseExpected(__Pyx_BufFmt_Context* ctx) { - if (ctx->head == NULL || ctx->head->field == &ctx->root) { - const char* expected; - const char* quote; - if (ctx->head == NULL) { - expected = "end"; - quote = ""; - } else { - expected = ctx->head->field->type->name; - quote = "'"; - } - PyErr_Format(PyExc_ValueError, - "Buffer dtype mismatch, expected %s%s%s but got %s", - quote, expected, quote, - __Pyx_BufFmt_DescribeTypeChar(ctx->enc_type, ctx->is_complex)); - } else { - __Pyx_StructField* field = ctx->head->field; - __Pyx_StructField* parent = (ctx->head - 1)->field; - PyErr_Format(PyExc_ValueError, - "Buffer dtype mismatch, expected '%s' but got %s in '%s.%s'", - field->type->name, __Pyx_BufFmt_DescribeTypeChar(ctx->enc_type, ctx->is_complex), - parent->type->name, field->name); - } -} -static int __Pyx_BufFmt_ProcessTypeChunk(__Pyx_BufFmt_Context* ctx) { - char group; - size_t size, offset, arraysize = 1; - if (ctx->enc_type == 0) return 0; - if (ctx->head->field->type->arraysize[0]) { - int i, ndim = 0; - if (ctx->enc_type == 's' || ctx->enc_type == 'p') { - ctx->is_valid_array = ctx->head->field->type->ndim == 1; - ndim = 1; - if (ctx->enc_count != ctx->head->field->type->arraysize[0]) { - PyErr_Format(PyExc_ValueError, - "Expected a dimension of size %zu, got %zu", - ctx->head->field->type->arraysize[0], ctx->enc_count); - return -1; - } - } - if (!ctx->is_valid_array) { - PyErr_Format(PyExc_ValueError, "Expected %d dimensions, got %d", - ctx->head->field->type->ndim, ndim); - return -1; - } - for (i = 0; i < ctx->head->field->type->ndim; i++) { - arraysize *= ctx->head->field->type->arraysize[i]; - } - ctx->is_valid_array = 0; - ctx->enc_count = 1; - } - group = __Pyx_BufFmt_TypeCharToGroup(ctx->enc_type, ctx->is_complex); - do { - __Pyx_StructField* field = ctx->head->field; - __Pyx_TypeInfo* type = field->type; - if (ctx->enc_packmode == '@' || ctx->enc_packmode == '^') { - size = __Pyx_BufFmt_TypeCharToNativeSize(ctx->enc_type, ctx->is_complex); - } else { - size = __Pyx_BufFmt_TypeCharToStandardSize(ctx->enc_type, ctx->is_complex); - } - if (ctx->enc_packmode == '@') { - size_t align_at = __Pyx_BufFmt_TypeCharToAlignment(ctx->enc_type, ctx->is_complex); - size_t align_mod_offset; - if (align_at == 0) return -1; - align_mod_offset = ctx->fmt_offset % align_at; - if (align_mod_offset > 0) ctx->fmt_offset += align_at - align_mod_offset; - if (ctx->struct_alignment == 0) - ctx->struct_alignment = __Pyx_BufFmt_TypeCharToPadding(ctx->enc_type, - ctx->is_complex); - } - if (type->size != size || type->typegroup != group) { - if (type->typegroup == 'C' && type->fields != NULL) { - size_t parent_offset = ctx->head->parent_offset + field->offset; - ++ctx->head; - ctx->head->field = type->fields; - ctx->head->parent_offset = parent_offset; - continue; - } - if ((type->typegroup == 'H' || group == 'H') && type->size == size) { - } else { - __Pyx_BufFmt_RaiseExpected(ctx); - return -1; - } - } - offset = ctx->head->parent_offset + field->offset; - if (ctx->fmt_offset != offset) { - PyErr_Format(PyExc_ValueError, - "Buffer dtype mismatch; next field is at offset %" CYTHON_FORMAT_SSIZE_T "d but %" CYTHON_FORMAT_SSIZE_T "d expected", - (Py_ssize_t)ctx->fmt_offset, (Py_ssize_t)offset); - return -1; - } - ctx->fmt_offset += size; - if (arraysize) - ctx->fmt_offset += (arraysize - 1) * size; - --ctx->enc_count; - while (1) { - if (field == &ctx->root) { - ctx->head = NULL; - if (ctx->enc_count != 0) { - __Pyx_BufFmt_RaiseExpected(ctx); - return -1; - } - break; - } - ctx->head->field = ++field; - if (field->type == NULL) { - --ctx->head; - field = ctx->head->field; - continue; - } else if (field->type->typegroup == 'S') { - size_t parent_offset = ctx->head->parent_offset + field->offset; - if (field->type->fields->type == NULL) continue; - field = field->type->fields; - ++ctx->head; - ctx->head->field = field; - ctx->head->parent_offset = parent_offset; - break; - } else { - break; - } - } - } while (ctx->enc_count); - ctx->enc_type = 0; - ctx->is_complex = 0; - return 0; -} -static CYTHON_INLINE PyObject * -__pyx_buffmt_parse_array(__Pyx_BufFmt_Context* ctx, const char** tsp) -{ - const char *ts = *tsp; - int i = 0, number; - int ndim = ctx->head->field->type->ndim; -; - ++ts; - if (ctx->new_count != 1) { - PyErr_SetString(PyExc_ValueError, - "Cannot handle repeated arrays in format string"); - return NULL; - } - if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; - while (*ts && *ts != ')') { - switch (*ts) { - case ' ': case '\f': case '\r': case '\n': case '\t': case '\v': continue; - default: break; - } - number = __Pyx_BufFmt_ExpectNumber(&ts); - if (number == -1) return NULL; - if (i < ndim && (size_t) number != ctx->head->field->type->arraysize[i]) - return PyErr_Format(PyExc_ValueError, - "Expected a dimension of size %zu, got %d", - ctx->head->field->type->arraysize[i], number); - if (*ts != ',' && *ts != ')') - return PyErr_Format(PyExc_ValueError, - "Expected a comma in format string, got '%c'", *ts); - if (*ts == ',') ts++; - i++; - } - if (i != ndim) - return PyErr_Format(PyExc_ValueError, "Expected %d dimension(s), got %d", - ctx->head->field->type->ndim, i); - if (!*ts) { - PyErr_SetString(PyExc_ValueError, - "Unexpected end of format string, expected ')'"); - return NULL; - } - ctx->is_valid_array = 1; - ctx->new_count = 1; - *tsp = ++ts; - return Py_None; -} -static const char* __Pyx_BufFmt_CheckString(__Pyx_BufFmt_Context* ctx, const char* ts) { - int got_Z = 0; - while (1) { - switch(*ts) { - case 0: - if (ctx->enc_type != 0 && ctx->head == NULL) { - __Pyx_BufFmt_RaiseExpected(ctx); - return NULL; - } - if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; - if (ctx->head != NULL) { - __Pyx_BufFmt_RaiseExpected(ctx); - return NULL; - } - return ts; - case ' ': - case '\r': - case '\n': - ++ts; - break; - case '<': - if (!__Pyx_IsLittleEndian()) { - PyErr_SetString(PyExc_ValueError, "Little-endian buffer not supported on big-endian compiler"); - return NULL; - } - ctx->new_packmode = '='; - ++ts; - break; - case '>': - case '!': - if (__Pyx_IsLittleEndian()) { - PyErr_SetString(PyExc_ValueError, "Big-endian buffer not supported on little-endian compiler"); - return NULL; - } - ctx->new_packmode = '='; - ++ts; - break; - case '=': - case '@': - case '^': - ctx->new_packmode = *ts++; - break; - case 'T': - { - const char* ts_after_sub; - size_t i, struct_count = ctx->new_count; - size_t struct_alignment = ctx->struct_alignment; - ctx->new_count = 1; - ++ts; - if (*ts != '{') { - PyErr_SetString(PyExc_ValueError, "Buffer acquisition: Expected '{' after 'T'"); - return NULL; - } - if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; - ctx->enc_type = 0; - ctx->enc_count = 0; - ctx->struct_alignment = 0; - ++ts; - ts_after_sub = ts; - for (i = 0; i != struct_count; ++i) { - ts_after_sub = __Pyx_BufFmt_CheckString(ctx, ts); - if (!ts_after_sub) return NULL; - } - ts = ts_after_sub; - if (struct_alignment) ctx->struct_alignment = struct_alignment; - } - break; - case '}': - { - size_t alignment = ctx->struct_alignment; - ++ts; - if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; - ctx->enc_type = 0; - if (alignment && ctx->fmt_offset % alignment) { - ctx->fmt_offset += alignment - (ctx->fmt_offset % alignment); - } - } - return ts; - case 'x': - if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; - ctx->fmt_offset += ctx->new_count; - ctx->new_count = 1; - ctx->enc_count = 0; - ctx->enc_type = 0; - ctx->enc_packmode = ctx->new_packmode; - ++ts; - break; - case 'Z': - got_Z = 1; - ++ts; - if (*ts != 'f' && *ts != 'd' && *ts != 'g') { - __Pyx_BufFmt_RaiseUnexpectedChar('Z'); - return NULL; - } - case 'c': case 'b': case 'B': case 'h': case 'H': case 'i': case 'I': - case 'l': case 'L': case 'q': case 'Q': - case 'f': case 'd': case 'g': - case 'O': case 'p': - if (ctx->enc_type == *ts && got_Z == ctx->is_complex && - ctx->enc_packmode == ctx->new_packmode) { - ctx->enc_count += ctx->new_count; - ctx->new_count = 1; - got_Z = 0; - ++ts; - break; - } - case 's': - if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; - ctx->enc_count = ctx->new_count; - ctx->enc_packmode = ctx->new_packmode; - ctx->enc_type = *ts; - ctx->is_complex = got_Z; - ++ts; - ctx->new_count = 1; - got_Z = 0; - break; - case ':': - ++ts; - while(*ts != ':') ++ts; - ++ts; - break; - case '(': - if (!__pyx_buffmt_parse_array(ctx, &ts)) return NULL; - break; - default: - { - int number = __Pyx_BufFmt_ExpectNumber(&ts); - if (number == -1) return NULL; - ctx->new_count = (size_t)number; - } - } - } -} -static CYTHON_INLINE void __Pyx_ZeroBuffer(Py_buffer* buf) { - buf->buf = NULL; - buf->obj = NULL; - buf->strides = __Pyx_zeros; - buf->shape = __Pyx_zeros; - buf->suboffsets = __Pyx_minusones; -} -static CYTHON_INLINE int __Pyx_GetBufferAndValidate( - Py_buffer* buf, PyObject* obj, __Pyx_TypeInfo* dtype, int flags, - int nd, int cast, __Pyx_BufFmt_StackElem* stack) -{ - if (obj == Py_None || obj == NULL) { - __Pyx_ZeroBuffer(buf); - return 0; - } - buf->buf = NULL; - if (__Pyx_GetBuffer(obj, buf, flags) == -1) goto fail; - if (buf->ndim != nd) { - PyErr_Format(PyExc_ValueError, - "Buffer has wrong number of dimensions (expected %d, got %d)", - nd, buf->ndim); - goto fail; - } - if (!cast) { - __Pyx_BufFmt_Context ctx; - __Pyx_BufFmt_Init(&ctx, stack, dtype); - if (!__Pyx_BufFmt_CheckString(&ctx, buf->format)) goto fail; - } - if ((unsigned)buf->itemsize != dtype->size) { - PyErr_Format(PyExc_ValueError, - "Item size of buffer (%" CYTHON_FORMAT_SSIZE_T "d byte%s) does not match size of '%s' (%" CYTHON_FORMAT_SSIZE_T "d byte%s)", - buf->itemsize, (buf->itemsize > 1) ? "s" : "", - dtype->name, (Py_ssize_t)dtype->size, (dtype->size > 1) ? "s" : ""); - goto fail; - } - if (buf->suboffsets == NULL) buf->suboffsets = __Pyx_minusones; - return 0; -fail:; - __Pyx_ZeroBuffer(buf); - return -1; -} -static CYTHON_INLINE void __Pyx_SafeReleaseBuffer(Py_buffer* info) { - if (info->buf == NULL) return; - if (info->suboffsets == __Pyx_minusones) info->suboffsets = NULL; - __Pyx_ReleaseBuffer(info); -} - -/* MemviewSliceInit */ - static int -__Pyx_init_memviewslice(struct __pyx_memoryview_obj *memview, - int ndim, - __Pyx_memviewslice *memviewslice, - int memview_is_new_reference) -{ - __Pyx_RefNannyDeclarations - int i, retval=-1; - Py_buffer *buf = &memview->view; - __Pyx_RefNannySetupContext("init_memviewslice", 0); - if (!buf) { - PyErr_SetString(PyExc_ValueError, - "buf is NULL."); - goto fail; - } else if (memviewslice->memview || memviewslice->data) { - PyErr_SetString(PyExc_ValueError, - "memviewslice is already initialized!"); - goto fail; - } - if (buf->strides) { - for (i = 0; i < ndim; i++) { - memviewslice->strides[i] = buf->strides[i]; - } - } else { - Py_ssize_t stride = buf->itemsize; - for (i = ndim - 1; i >= 0; i--) { - memviewslice->strides[i] = stride; - stride *= buf->shape[i]; - } - } - for (i = 0; i < ndim; i++) { - memviewslice->shape[i] = buf->shape[i]; - if (buf->suboffsets) { - memviewslice->suboffsets[i] = buf->suboffsets[i]; - } else { - memviewslice->suboffsets[i] = -1; - } - } - memviewslice->memview = memview; - memviewslice->data = (char *)buf->buf; - if (__pyx_add_acquisition_count(memview) == 0 && !memview_is_new_reference) { - Py_INCREF(memview); - } - retval = 0; - goto no_fail; -fail: - memviewslice->memview = 0; - memviewslice->data = 0; - retval = -1; -no_fail: - __Pyx_RefNannyFinishContext(); - return retval; -} -static CYTHON_INLINE void __pyx_fatalerror(const char *fmt, ...) { - va_list vargs; - char msg[200]; -#ifdef HAVE_STDARG_PROTOTYPES - va_start(vargs, fmt); -#else - va_start(vargs); -#endif - vsnprintf(msg, 200, fmt, vargs); - Py_FatalError(msg); - va_end(vargs); -} -static CYTHON_INLINE int -__pyx_add_acquisition_count_locked(__pyx_atomic_int *acquisition_count, - PyThread_type_lock lock) -{ - int result; - PyThread_acquire_lock(lock, 1); - result = (*acquisition_count)++; - PyThread_release_lock(lock); - return result; -} -static CYTHON_INLINE int -__pyx_sub_acquisition_count_locked(__pyx_atomic_int *acquisition_count, - PyThread_type_lock lock) -{ - int result; - PyThread_acquire_lock(lock, 1); - result = (*acquisition_count)--; - PyThread_release_lock(lock); - return result; -} -static CYTHON_INLINE void -__Pyx_INC_MEMVIEW(__Pyx_memviewslice *memslice, int have_gil, int lineno) -{ - int first_time; - struct __pyx_memoryview_obj *memview = memslice->memview; - if (!memview || (PyObject *) memview == Py_None) - return; - if (__pyx_get_slice_count(memview) < 0) - __pyx_fatalerror("Acquisition count is %d (line %d)", - __pyx_get_slice_count(memview), lineno); - first_time = __pyx_add_acquisition_count(memview) == 0; - if (first_time) { - if (have_gil) { - Py_INCREF((PyObject *) memview); - } else { - PyGILState_STATE _gilstate = PyGILState_Ensure(); - Py_INCREF((PyObject *) memview); - PyGILState_Release(_gilstate); - } - } -} -static CYTHON_INLINE void __Pyx_XDEC_MEMVIEW(__Pyx_memviewslice *memslice, - int have_gil, int lineno) { - int last_time; - struct __pyx_memoryview_obj *memview = memslice->memview; - if (!memview ) { - return; - } else if ((PyObject *) memview == Py_None) { - memslice->memview = NULL; - return; - } - if (__pyx_get_slice_count(memview) <= 0) - __pyx_fatalerror("Acquisition count is %d (line %d)", - __pyx_get_slice_count(memview), lineno); - last_time = __pyx_sub_acquisition_count(memview) == 1; - memslice->data = NULL; - if (last_time) { - if (have_gil) { - Py_CLEAR(memslice->memview); - } else { - PyGILState_STATE _gilstate = PyGILState_Ensure(); - Py_CLEAR(memslice->memview); - PyGILState_Release(_gilstate); - } - } else { - memslice->memview = NULL; - } -} - -/* BufferIndexError */ - static void __Pyx_RaiseBufferIndexError(int axis) { - PyErr_Format(PyExc_IndexError, - "Out of bounds on buffer access (axis %d)", axis); -} - -/* RaiseArgTupleInvalid */ - static void __Pyx_RaiseArgtupleInvalid( - const char* func_name, - int exact, - Py_ssize_t num_min, - Py_ssize_t num_max, - Py_ssize_t num_found) -{ - Py_ssize_t num_expected; - const char *more_or_less; - if (num_found < num_min) { - num_expected = num_min; - more_or_less = "at least"; - } else { - num_expected = num_max; - more_or_less = "at most"; - } - if (exact) { - more_or_less = "exactly"; - } - PyErr_Format(PyExc_TypeError, - "%.200s() takes %.8s %" CYTHON_FORMAT_SSIZE_T "d positional argument%.1s (%" CYTHON_FORMAT_SSIZE_T "d given)", - func_name, more_or_less, num_expected, - (num_expected == 1) ? "" : "s", num_found); -} - -/* RaiseDoubleKeywords */ - static void __Pyx_RaiseDoubleKeywordsError( - const char* func_name, - PyObject* kw_name) -{ - PyErr_Format(PyExc_TypeError, - #if PY_MAJOR_VERSION >= 3 - "%s() got multiple values for keyword argument '%U'", func_name, kw_name); - #else - "%s() got multiple values for keyword argument '%s'", func_name, - PyString_AsString(kw_name)); - #endif -} - -/* ParseKeywords */ - static int __Pyx_ParseOptionalKeywords( - PyObject *kwds, - PyObject **argnames[], - PyObject *kwds2, - PyObject *values[], - Py_ssize_t num_pos_args, - const char* function_name) -{ - PyObject *key = 0, *value = 0; - Py_ssize_t pos = 0; - PyObject*** name; - PyObject*** first_kw_arg = argnames + num_pos_args; - while (PyDict_Next(kwds, &pos, &key, &value)) { - name = first_kw_arg; - while (*name && (**name != key)) name++; - if (*name) { - values[name-argnames] = value; - continue; - } - name = first_kw_arg; - #if PY_MAJOR_VERSION < 3 - if (likely(PyString_CheckExact(key)) || likely(PyString_Check(key))) { - while (*name) { - if ((CYTHON_COMPILING_IN_PYPY || PyString_GET_SIZE(**name) == PyString_GET_SIZE(key)) - && _PyString_Eq(**name, key)) { - values[name-argnames] = value; - break; - } - name++; - } - if (*name) continue; - else { - PyObject*** argname = argnames; - while (argname != first_kw_arg) { - if ((**argname == key) || ( - (CYTHON_COMPILING_IN_PYPY || PyString_GET_SIZE(**argname) == PyString_GET_SIZE(key)) - && _PyString_Eq(**argname, key))) { - goto arg_passed_twice; - } - argname++; - } - } - } else - #endif - if (likely(PyUnicode_Check(key))) { - while (*name) { - int cmp = (**name == key) ? 0 : - #if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION >= 3 - (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : - #endif - PyUnicode_Compare(**name, key); - if (cmp < 0 && unlikely(PyErr_Occurred())) goto bad; - if (cmp == 0) { - values[name-argnames] = value; - break; - } - name++; - } - if (*name) continue; - else { - PyObject*** argname = argnames; - while (argname != first_kw_arg) { - int cmp = (**argname == key) ? 0 : - #if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION >= 3 - (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : - #endif - PyUnicode_Compare(**argname, key); - if (cmp < 0 && unlikely(PyErr_Occurred())) goto bad; - if (cmp == 0) goto arg_passed_twice; - argname++; - } - } - } else - goto invalid_keyword_type; - if (kwds2) { - if (unlikely(PyDict_SetItem(kwds2, key, value))) goto bad; - } else { - goto invalid_keyword; - } - } - return 0; -arg_passed_twice: - __Pyx_RaiseDoubleKeywordsError(function_name, key); - goto bad; -invalid_keyword_type: - PyErr_Format(PyExc_TypeError, - "%.200s() keywords must be strings", function_name); - goto bad; -invalid_keyword: - PyErr_Format(PyExc_TypeError, - #if PY_MAJOR_VERSION < 3 - "%.200s() got an unexpected keyword argument '%.200s'", - function_name, PyString_AsString(key)); - #else - "%s() got an unexpected keyword argument '%U'", - function_name, key); - #endif -bad: - return -1; -} - -/* ArgTypeTest */ - static void __Pyx_RaiseArgumentTypeInvalid(const char* name, PyObject *obj, PyTypeObject *type) { - PyErr_Format(PyExc_TypeError, - "Argument '%.200s' has incorrect type (expected %.200s, got %.200s)", - name, type->tp_name, Py_TYPE(obj)->tp_name); -} -static CYTHON_INLINE int __Pyx_ArgTypeTest(PyObject *obj, PyTypeObject *type, int none_allowed, - const char *name, int exact) -{ - if (unlikely(!type)) { - PyErr_SetString(PyExc_SystemError, "Missing type object"); - return 0; - } - if (none_allowed && obj == Py_None) return 1; - else if (exact) { - if (likely(Py_TYPE(obj) == type)) return 1; - #if PY_MAJOR_VERSION == 2 - else if ((type == &PyBaseString_Type) && likely(__Pyx_PyBaseString_CheckExact(obj))) return 1; - #endif - } - else { - if (likely(PyObject_TypeCheck(obj, type))) return 1; - } - __Pyx_RaiseArgumentTypeInvalid(name, obj, type); - return 0; -} - -/* PyErrFetchRestore */ - #if CYTHON_FAST_THREAD_STATE -static CYTHON_INLINE void __Pyx_ErrRestoreInState(PyThreadState *tstate, PyObject *type, PyObject *value, PyObject *tb) { - PyObject *tmp_type, *tmp_value, *tmp_tb; - tmp_type = tstate->curexc_type; - tmp_value = tstate->curexc_value; - tmp_tb = tstate->curexc_traceback; - tstate->curexc_type = type; - tstate->curexc_value = value; - tstate->curexc_traceback = tb; - Py_XDECREF(tmp_type); - Py_XDECREF(tmp_value); - Py_XDECREF(tmp_tb); -} -static CYTHON_INLINE void __Pyx_ErrFetchInState(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb) { - *type = tstate->curexc_type; - *value = tstate->curexc_value; - *tb = tstate->curexc_traceback; - tstate->curexc_type = 0; - tstate->curexc_value = 0; - tstate->curexc_traceback = 0; -} -#endif - -/* RaiseException */ - #if PY_MAJOR_VERSION < 3 -static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, - CYTHON_UNUSED PyObject *cause) { - __Pyx_PyThreadState_declare - Py_XINCREF(type); - if (!value || value == Py_None) - value = NULL; - else - Py_INCREF(value); - if (!tb || tb == Py_None) - tb = NULL; - else { - Py_INCREF(tb); - if (!PyTraceBack_Check(tb)) { - PyErr_SetString(PyExc_TypeError, - "raise: arg 3 must be a traceback or None"); - goto raise_error; - } - } - if (PyType_Check(type)) { -#if CYTHON_COMPILING_IN_PYPY - if (!value) { - Py_INCREF(Py_None); - value = Py_None; - } -#endif - PyErr_NormalizeException(&type, &value, &tb); - } else { - if (value) { - PyErr_SetString(PyExc_TypeError, - "instance exception may not have a separate value"); - goto raise_error; - } - value = type; - type = (PyObject*) Py_TYPE(type); - Py_INCREF(type); - if (!PyType_IsSubtype((PyTypeObject *)type, (PyTypeObject *)PyExc_BaseException)) { - PyErr_SetString(PyExc_TypeError, - "raise: exception class must be a subclass of BaseException"); - goto raise_error; - } - } - __Pyx_PyThreadState_assign - __Pyx_ErrRestore(type, value, tb); - return; -raise_error: - Py_XDECREF(value); - Py_XDECREF(type); - Py_XDECREF(tb); - return; -} -#else -static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause) { - PyObject* owned_instance = NULL; - if (tb == Py_None) { - tb = 0; - } else if (tb && !PyTraceBack_Check(tb)) { - PyErr_SetString(PyExc_TypeError, - "raise: arg 3 must be a traceback or None"); - goto bad; - } - if (value == Py_None) - value = 0; - if (PyExceptionInstance_Check(type)) { - if (value) { - PyErr_SetString(PyExc_TypeError, - "instance exception may not have a separate value"); - goto bad; - } - value = type; - type = (PyObject*) Py_TYPE(value); - } else if (PyExceptionClass_Check(type)) { - PyObject *instance_class = NULL; - if (value && PyExceptionInstance_Check(value)) { - instance_class = (PyObject*) Py_TYPE(value); - if (instance_class != type) { - int is_subclass = PyObject_IsSubclass(instance_class, type); - if (!is_subclass) { - instance_class = NULL; - } else if (unlikely(is_subclass == -1)) { - goto bad; - } else { - type = instance_class; - } - } - } - if (!instance_class) { - PyObject *args; - if (!value) - args = PyTuple_New(0); - else if (PyTuple_Check(value)) { - Py_INCREF(value); - args = value; - } else - args = PyTuple_Pack(1, value); - if (!args) - goto bad; - owned_instance = PyObject_Call(type, args, NULL); - Py_DECREF(args); - if (!owned_instance) - goto bad; - value = owned_instance; - if (!PyExceptionInstance_Check(value)) { - PyErr_Format(PyExc_TypeError, - "calling %R should have returned an instance of " - "BaseException, not %R", - type, Py_TYPE(value)); - goto bad; - } - } - } else { - PyErr_SetString(PyExc_TypeError, - "raise: exception class must be a subclass of BaseException"); - goto bad; - } -#if PY_VERSION_HEX >= 0x03030000 - if (cause) { -#else - if (cause && cause != Py_None) { -#endif - PyObject *fixed_cause; - if (cause == Py_None) { - fixed_cause = NULL; - } else if (PyExceptionClass_Check(cause)) { - fixed_cause = PyObject_CallObject(cause, NULL); - if (fixed_cause == NULL) - goto bad; - } else if (PyExceptionInstance_Check(cause)) { - fixed_cause = cause; - Py_INCREF(fixed_cause); - } else { - PyErr_SetString(PyExc_TypeError, - "exception causes must derive from " - "BaseException"); - goto bad; - } - PyException_SetCause(value, fixed_cause); - } - PyErr_SetObject(type, value); - if (tb) { -#if CYTHON_COMPILING_IN_PYPY - PyObject *tmp_type, *tmp_value, *tmp_tb; - PyErr_Fetch(&tmp_type, &tmp_value, &tmp_tb); - Py_INCREF(tb); - PyErr_Restore(tmp_type, tmp_value, tb); - Py_XDECREF(tmp_tb); -#else - PyThreadState *tstate = PyThreadState_GET(); - PyObject* tmp_tb = tstate->curexc_traceback; - if (tb != tmp_tb) { - Py_INCREF(tb); - tstate->curexc_traceback = tb; - Py_XDECREF(tmp_tb); - } -#endif - } -bad: - Py_XDECREF(owned_instance); - return; -} -#endif - -/* None */ - static CYTHON_INLINE Py_ssize_t __Pyx_div_Py_ssize_t(Py_ssize_t a, Py_ssize_t b) { - Py_ssize_t q = a / b; - Py_ssize_t r = a - q*b; - q -= ((r != 0) & ((r ^ b) < 0)); - return q; -} - -/* GetAttr */ - static CYTHON_INLINE PyObject *__Pyx_GetAttr(PyObject *o, PyObject *n) { -#if CYTHON_COMPILING_IN_CPYTHON -#if PY_MAJOR_VERSION >= 3 - if (likely(PyUnicode_Check(n))) -#else - if (likely(PyString_Check(n))) -#endif - return __Pyx_PyObject_GetAttrStr(o, n); -#endif - return PyObject_GetAttr(o, n); -} - -/* decode_c_string */ - static CYTHON_INLINE PyObject* __Pyx_decode_c_string( - const char* cstring, Py_ssize_t start, Py_ssize_t stop, - const char* encoding, const char* errors, - PyObject* (*decode_func)(const char *s, Py_ssize_t size, const char *errors)) { - Py_ssize_t length; - if (unlikely((start < 0) | (stop < 0))) { - size_t slen = strlen(cstring); - if (unlikely(slen > (size_t) PY_SSIZE_T_MAX)) { - PyErr_SetString(PyExc_OverflowError, - "c-string too long to convert to Python"); - return NULL; - } - length = (Py_ssize_t) slen; - if (start < 0) { - start += length; - if (start < 0) - start = 0; - } - if (stop < 0) - stop += length; - } - length = stop - start; - if (unlikely(length <= 0)) - return PyUnicode_FromUnicode(NULL, 0); - cstring += start; - if (decode_func) { - return decode_func(cstring, length, errors); - } else { - return PyUnicode_Decode(cstring, length, encoding, errors); - } -} - -/* RaiseTooManyValuesToUnpack */ - static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected) { - PyErr_Format(PyExc_ValueError, - "too many values to unpack (expected %" CYTHON_FORMAT_SSIZE_T "d)", expected); -} - -/* RaiseNeedMoreValuesToUnpack */ - static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index) { - PyErr_Format(PyExc_ValueError, - "need more than %" CYTHON_FORMAT_SSIZE_T "d value%.1s to unpack", - index, (index == 1) ? "" : "s"); -} - -/* RaiseNoneIterError */ - static CYTHON_INLINE void __Pyx_RaiseNoneNotIterableError(void) { - PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable"); -} - -/* ExtTypeTest */ - static CYTHON_INLINE int __Pyx_TypeTest(PyObject *obj, PyTypeObject *type) { - if (unlikely(!type)) { - PyErr_SetString(PyExc_SystemError, "Missing type object"); - return 0; - } - if (likely(PyObject_TypeCheck(obj, type))) - return 1; - PyErr_Format(PyExc_TypeError, "Cannot convert %.200s to %.200s", - Py_TYPE(obj)->tp_name, type->tp_name); - return 0; -} - -/* SaveResetException */ - #if CYTHON_FAST_THREAD_STATE -static CYTHON_INLINE void __Pyx__ExceptionSave(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb) { - *type = tstate->exc_type; - *value = tstate->exc_value; - *tb = tstate->exc_traceback; - Py_XINCREF(*type); - Py_XINCREF(*value); - Py_XINCREF(*tb); -} -static CYTHON_INLINE void __Pyx__ExceptionReset(PyThreadState *tstate, PyObject *type, PyObject *value, PyObject *tb) { - PyObject *tmp_type, *tmp_value, *tmp_tb; - tmp_type = tstate->exc_type; - tmp_value = tstate->exc_value; - tmp_tb = tstate->exc_traceback; - tstate->exc_type = type; - tstate->exc_value = value; - tstate->exc_traceback = tb; - Py_XDECREF(tmp_type); - Py_XDECREF(tmp_value); - Py_XDECREF(tmp_tb); -} -#endif - -/* PyErrExceptionMatches */ - #if CYTHON_FAST_THREAD_STATE -static CYTHON_INLINE int __Pyx_PyErr_ExceptionMatchesInState(PyThreadState* tstate, PyObject* err) { - PyObject *exc_type = tstate->curexc_type; - if (exc_type == err) return 1; - if (unlikely(!exc_type)) return 0; - return PyErr_GivenExceptionMatches(exc_type, err); -} -#endif - -/* GetException */ - #if CYTHON_FAST_THREAD_STATE -static int __Pyx__GetException(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb) { -#else -static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb) { -#endif - PyObject *local_type, *local_value, *local_tb; -#if CYTHON_FAST_THREAD_STATE - PyObject *tmp_type, *tmp_value, *tmp_tb; - local_type = tstate->curexc_type; - local_value = tstate->curexc_value; - local_tb = tstate->curexc_traceback; - tstate->curexc_type = 0; - tstate->curexc_value = 0; - tstate->curexc_traceback = 0; -#else - PyErr_Fetch(&local_type, &local_value, &local_tb); -#endif - PyErr_NormalizeException(&local_type, &local_value, &local_tb); -#if CYTHON_FAST_THREAD_STATE - if (unlikely(tstate->curexc_type)) -#else - if (unlikely(PyErr_Occurred())) -#endif - goto bad; - #if PY_MAJOR_VERSION >= 3 - if (local_tb) { - if (unlikely(PyException_SetTraceback(local_value, local_tb) < 0)) - goto bad; - } - #endif - Py_XINCREF(local_tb); - Py_XINCREF(local_type); - Py_XINCREF(local_value); - *type = local_type; - *value = local_value; - *tb = local_tb; -#if CYTHON_FAST_THREAD_STATE - tmp_type = tstate->exc_type; - tmp_value = tstate->exc_value; - tmp_tb = tstate->exc_traceback; - tstate->exc_type = local_type; - tstate->exc_value = local_value; - tstate->exc_traceback = local_tb; - Py_XDECREF(tmp_type); - Py_XDECREF(tmp_value); - Py_XDECREF(tmp_tb); -#else - PyErr_SetExcInfo(local_type, local_value, local_tb); -#endif - return 0; -bad: - *type = 0; - *value = 0; - *tb = 0; - Py_XDECREF(local_type); - Py_XDECREF(local_value); - Py_XDECREF(local_tb); - return -1; -} - -/* SwapException */ - #if CYTHON_FAST_THREAD_STATE -static CYTHON_INLINE void __Pyx__ExceptionSwap(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb) { - PyObject *tmp_type, *tmp_value, *tmp_tb; - tmp_type = tstate->exc_type; - tmp_value = tstate->exc_value; - tmp_tb = tstate->exc_traceback; - tstate->exc_type = *type; - tstate->exc_value = *value; - tstate->exc_traceback = *tb; - *type = tmp_type; - *value = tmp_value; - *tb = tmp_tb; -} -#else -static CYTHON_INLINE void __Pyx_ExceptionSwap(PyObject **type, PyObject **value, PyObject **tb) { - PyObject *tmp_type, *tmp_value, *tmp_tb; - PyErr_GetExcInfo(&tmp_type, &tmp_value, &tmp_tb); - PyErr_SetExcInfo(*type, *value, *tb); - *type = tmp_type; - *value = tmp_value; - *tb = tmp_tb; -} -#endif - -/* PyIntBinop */ - #if !CYTHON_COMPILING_IN_PYPY -static PyObject* __Pyx_PyInt_AddObjC(PyObject *op1, PyObject *op2, CYTHON_UNUSED long intval, CYTHON_UNUSED int inplace) { - #if PY_MAJOR_VERSION < 3 - if (likely(PyInt_CheckExact(op1))) { - const long b = intval; - long x; - long a = PyInt_AS_LONG(op1); - x = (long)((unsigned long)a + b); - if (likely((x^a) >= 0 || (x^b) >= 0)) - return PyInt_FromLong(x); - return PyLong_Type.tp_as_number->nb_add(op1, op2); - } - #endif - #if CYTHON_USE_PYLONG_INTERNALS - if (likely(PyLong_CheckExact(op1))) { - const long b = intval; - long a, x; -#ifdef HAVE_LONG_LONG - const PY_LONG_LONG llb = intval; - PY_LONG_LONG lla, llx; -#endif - const digit* digits = ((PyLongObject*)op1)->ob_digit; - const Py_ssize_t size = Py_SIZE(op1); - if (likely(__Pyx_sst_abs(size) <= 1)) { - a = likely(size) ? digits[0] : 0; - if (size == -1) a = -a; - } else { - switch (size) { - case -2: - if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { - a = -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); - break; -#ifdef HAVE_LONG_LONG - } else if (8 * sizeof(PY_LONG_LONG) - 1 > 2 * PyLong_SHIFT) { - lla = -(PY_LONG_LONG) (((((unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0])); - goto long_long; -#endif - } - case 2: - if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { - a = (long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); - break; -#ifdef HAVE_LONG_LONG - } else if (8 * sizeof(PY_LONG_LONG) - 1 > 2 * PyLong_SHIFT) { - lla = (PY_LONG_LONG) (((((unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0])); - goto long_long; -#endif - } - case -3: - if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { - a = -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); - break; -#ifdef HAVE_LONG_LONG - } else if (8 * sizeof(PY_LONG_LONG) - 1 > 3 * PyLong_SHIFT) { - lla = -(PY_LONG_LONG) (((((((unsigned PY_LONG_LONG)digits[2]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0])); - goto long_long; -#endif - } - case 3: - if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { - a = (long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); - break; -#ifdef HAVE_LONG_LONG - } else if (8 * sizeof(PY_LONG_LONG) - 1 > 3 * PyLong_SHIFT) { - lla = (PY_LONG_LONG) (((((((unsigned PY_LONG_LONG)digits[2]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0])); - goto long_long; -#endif - } - case -4: - if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) { - a = -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); - break; -#ifdef HAVE_LONG_LONG - } else if (8 * sizeof(PY_LONG_LONG) - 1 > 4 * PyLong_SHIFT) { - lla = -(PY_LONG_LONG) (((((((((unsigned PY_LONG_LONG)digits[3]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[2]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0])); - goto long_long; -#endif - } - case 4: - if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) { - a = (long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); - break; -#ifdef HAVE_LONG_LONG - } else if (8 * sizeof(PY_LONG_LONG) - 1 > 4 * PyLong_SHIFT) { - lla = (PY_LONG_LONG) (((((((((unsigned PY_LONG_LONG)digits[3]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[2]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0])); - goto long_long; -#endif - } - default: return PyLong_Type.tp_as_number->nb_add(op1, op2); - } - } - x = a + b; - return PyLong_FromLong(x); -#ifdef HAVE_LONG_LONG - long_long: - llx = lla + llb; - return PyLong_FromLongLong(llx); -#endif - - - } - #endif - if (PyFloat_CheckExact(op1)) { - const long b = intval; - double a = PyFloat_AS_DOUBLE(op1); - double result; - PyFPE_START_PROTECT("add", return NULL) - result = ((double)a) + (double)b; - PyFPE_END_PROTECT(result) - return PyFloat_FromDouble(result); - } - return (inplace ? PyNumber_InPlaceAdd : PyNumber_Add)(op1, op2); -} -#endif - -/* None */ - static CYTHON_INLINE void __Pyx_RaiseUnboundLocalError(const char *varname) { - PyErr_Format(PyExc_UnboundLocalError, "local variable '%s' referenced before assignment", varname); -} - -/* None */ - static CYTHON_INLINE long __Pyx_div_long(long a, long b) { - long q = a / b; - long r = a - q*b; - q -= ((r != 0) & ((r ^ b) < 0)); - return q; -} - -/* WriteUnraisableException */ - static void __Pyx_WriteUnraisable(const char *name, CYTHON_UNUSED int clineno, - CYTHON_UNUSED int lineno, CYTHON_UNUSED const char *filename, - int full_traceback, CYTHON_UNUSED int nogil) { - PyObject *old_exc, *old_val, *old_tb; - PyObject *ctx; - __Pyx_PyThreadState_declare -#ifdef WITH_THREAD - PyGILState_STATE state; - if (nogil) - state = PyGILState_Ensure(); -#ifdef _MSC_VER - else state = (PyGILState_STATE)-1; -#endif -#endif - __Pyx_PyThreadState_assign - __Pyx_ErrFetch(&old_exc, &old_val, &old_tb); - if (full_traceback) { - Py_XINCREF(old_exc); - Py_XINCREF(old_val); - Py_XINCREF(old_tb); - __Pyx_ErrRestore(old_exc, old_val, old_tb); - PyErr_PrintEx(1); - } - #if PY_MAJOR_VERSION < 3 - ctx = PyString_FromString(name); - #else - ctx = PyUnicode_FromString(name); - #endif - __Pyx_ErrRestore(old_exc, old_val, old_tb); - if (!ctx) { - PyErr_WriteUnraisable(Py_None); - } else { - PyErr_WriteUnraisable(ctx); - Py_DECREF(ctx); - } -#ifdef WITH_THREAD - if (nogil) - PyGILState_Release(state); -#endif -} - -/* SetVTable */ - static int __Pyx_SetVtable(PyObject *dict, void *vtable) { -#if PY_VERSION_HEX >= 0x02070000 - PyObject *ob = PyCapsule_New(vtable, 0, 0); -#else - PyObject *ob = PyCObject_FromVoidPtr(vtable, 0); -#endif - if (!ob) - goto bad; - if (PyDict_SetItem(dict, __pyx_n_s_pyx_vtable, ob) < 0) - goto bad; - Py_DECREF(ob); - return 0; -bad: - Py_XDECREF(ob); - return -1; -} - -/* CodeObjectCache */ - static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line) { - int start = 0, mid = 0, end = count - 1; - if (end >= 0 && code_line > entries[end].code_line) { - return count; - } - while (start < end) { - mid = start + (end - start) / 2; - if (code_line < entries[mid].code_line) { - end = mid; - } else if (code_line > entries[mid].code_line) { - start = mid + 1; - } else { - return mid; - } - } - if (code_line <= entries[mid].code_line) { - return mid; - } else { - return mid + 1; - } -} -static PyCodeObject *__pyx_find_code_object(int code_line) { - PyCodeObject* code_object; - int pos; - if (unlikely(!code_line) || unlikely(!__pyx_code_cache.entries)) { - return NULL; - } - pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line); - if (unlikely(pos >= __pyx_code_cache.count) || unlikely(__pyx_code_cache.entries[pos].code_line != code_line)) { - return NULL; - } - code_object = __pyx_code_cache.entries[pos].code_object; - Py_INCREF(code_object); - return code_object; -} -static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object) { - int pos, i; - __Pyx_CodeObjectCacheEntry* entries = __pyx_code_cache.entries; - if (unlikely(!code_line)) { - return; - } - if (unlikely(!entries)) { - entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Malloc(64*sizeof(__Pyx_CodeObjectCacheEntry)); - if (likely(entries)) { - __pyx_code_cache.entries = entries; - __pyx_code_cache.max_count = 64; - __pyx_code_cache.count = 1; - entries[0].code_line = code_line; - entries[0].code_object = code_object; - Py_INCREF(code_object); - } - return; - } - pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line); - if ((pos < __pyx_code_cache.count) && unlikely(__pyx_code_cache.entries[pos].code_line == code_line)) { - PyCodeObject* tmp = entries[pos].code_object; - entries[pos].code_object = code_object; - Py_DECREF(tmp); - return; - } - if (__pyx_code_cache.count == __pyx_code_cache.max_count) { - int new_max = __pyx_code_cache.max_count + 64; - entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Realloc( - __pyx_code_cache.entries, (size_t)new_max*sizeof(__Pyx_CodeObjectCacheEntry)); - if (unlikely(!entries)) { - return; - } - __pyx_code_cache.entries = entries; - __pyx_code_cache.max_count = new_max; - } - for (i=__pyx_code_cache.count; i>pos; i--) { - entries[i] = entries[i-1]; - } - entries[pos].code_line = code_line; - entries[pos].code_object = code_object; - __pyx_code_cache.count++; - Py_INCREF(code_object); -} - -/* AddTraceback */ - #include "compile.h" -#include "frameobject.h" -#include "traceback.h" -static PyCodeObject* __Pyx_CreateCodeObjectForTraceback( - const char *funcname, int c_line, - int py_line, const char *filename) { - PyCodeObject *py_code = 0; - PyObject *py_srcfile = 0; - PyObject *py_funcname = 0; - #if PY_MAJOR_VERSION < 3 - py_srcfile = PyString_FromString(filename); - #else - py_srcfile = PyUnicode_FromString(filename); - #endif - if (!py_srcfile) goto bad; - if (c_line) { - #if PY_MAJOR_VERSION < 3 - py_funcname = PyString_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line); - #else - py_funcname = PyUnicode_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line); - #endif - } - else { - #if PY_MAJOR_VERSION < 3 - py_funcname = PyString_FromString(funcname); - #else - py_funcname = PyUnicode_FromString(funcname); - #endif - } - if (!py_funcname) goto bad; - py_code = __Pyx_PyCode_New( - 0, - 0, - 0, - 0, - 0, - __pyx_empty_bytes, /*PyObject *code,*/ - __pyx_empty_tuple, /*PyObject *consts,*/ - __pyx_empty_tuple, /*PyObject *names,*/ - __pyx_empty_tuple, /*PyObject *varnames,*/ - __pyx_empty_tuple, /*PyObject *freevars,*/ - __pyx_empty_tuple, /*PyObject *cellvars,*/ - py_srcfile, /*PyObject *filename,*/ - py_funcname, /*PyObject *name,*/ - py_line, - __pyx_empty_bytes /*PyObject *lnotab*/ - ); - Py_DECREF(py_srcfile); - Py_DECREF(py_funcname); - return py_code; -bad: - Py_XDECREF(py_srcfile); - Py_XDECREF(py_funcname); - return NULL; -} -static void __Pyx_AddTraceback(const char *funcname, int c_line, - int py_line, const char *filename) { - PyCodeObject *py_code = 0; - PyFrameObject *py_frame = 0; - py_code = __pyx_find_code_object(c_line ? c_line : py_line); - if (!py_code) { - py_code = __Pyx_CreateCodeObjectForTraceback( - funcname, c_line, py_line, filename); - if (!py_code) goto bad; - __pyx_insert_code_object(c_line ? c_line : py_line, py_code); - } - py_frame = PyFrame_New( - PyThreadState_GET(), /*PyThreadState *tstate,*/ - py_code, /*PyCodeObject *code,*/ - __pyx_d, /*PyObject *globals,*/ - 0 /*PyObject *locals*/ - ); - if (!py_frame) goto bad; - __Pyx_PyFrame_SetLineNumber(py_frame, py_line); - PyTraceBack_Here(py_frame); -bad: - Py_XDECREF(py_code); - Py_XDECREF(py_frame); -} - -#if PY_MAJOR_VERSION < 3 -static int __Pyx_GetBuffer(PyObject *obj, Py_buffer *view, int flags) { - if (PyObject_CheckBuffer(obj)) return PyObject_GetBuffer(obj, view, flags); - if (PyObject_TypeCheck(obj, __pyx_array_type)) return __pyx_array_getbuffer(obj, view, flags); - if (PyObject_TypeCheck(obj, __pyx_memoryview_type)) return __pyx_memoryview_getbuffer(obj, view, flags); - PyErr_Format(PyExc_TypeError, "'%.200s' does not have the buffer interface", Py_TYPE(obj)->tp_name); - return -1; -} -static void __Pyx_ReleaseBuffer(Py_buffer *view) { - PyObject *obj = view->obj; - if (!obj) return; - if (PyObject_CheckBuffer(obj)) { - PyBuffer_Release(view); - return; - } - Py_DECREF(obj); - view->obj = NULL; -} -#endif - - - /* MemviewSliceIsContig */ - static int -__pyx_memviewslice_is_contig(const __Pyx_memviewslice mvs, - char order, int ndim) -{ - int i, index, step, start; - Py_ssize_t itemsize = mvs.memview->view.itemsize; - if (order == 'F') { - step = 1; - start = 0; - } else { - step = -1; - start = ndim - 1; - } - for (i = 0; i < ndim; i++) { - index = start + step * i; - if (mvs.suboffsets[index] >= 0 || mvs.strides[index] != itemsize) - return 0; - itemsize *= mvs.shape[index]; - } - return 1; -} - -/* OverlappingSlices */ - static void -__pyx_get_array_memory_extents(__Pyx_memviewslice *slice, - void **out_start, void **out_end, - int ndim, size_t itemsize) -{ - char *start, *end; - int i; - start = end = slice->data; - for (i = 0; i < ndim; i++) { - Py_ssize_t stride = slice->strides[i]; - Py_ssize_t extent = slice->shape[i]; - if (extent == 0) { - *out_start = *out_end = start; - return; - } else { - if (stride > 0) - end += stride * (extent - 1); - else - start += stride * (extent - 1); - } - } - *out_start = start; - *out_end = end + itemsize; -} -static int -__pyx_slices_overlap(__Pyx_memviewslice *slice1, - __Pyx_memviewslice *slice2, - int ndim, size_t itemsize) -{ - void *start1, *end1, *start2, *end2; - __pyx_get_array_memory_extents(slice1, &start1, &end1, ndim, itemsize); - __pyx_get_array_memory_extents(slice2, &start2, &end2, ndim, itemsize); - return (start1 < end2) && (start2 < end1); -} - -/* Capsule */ - static CYTHON_INLINE PyObject * -__pyx_capsule_create(void *p, CYTHON_UNUSED const char *sig) -{ - PyObject *cobj; -#if PY_VERSION_HEX >= 0x02070000 - cobj = PyCapsule_New(p, sig, NULL); -#else - cobj = PyCObject_FromVoidPtr(p, NULL); -#endif - return cobj; -} - -/* CIntFromPyVerify */ - #define __PYX_VERIFY_RETURN_INT(target_type, func_type, func_value)\ - __PYX__VERIFY_RETURN_INT(target_type, func_type, func_value, 0) -#define __PYX_VERIFY_RETURN_INT_EXC(target_type, func_type, func_value)\ - __PYX__VERIFY_RETURN_INT(target_type, func_type, func_value, 1) -#define __PYX__VERIFY_RETURN_INT(target_type, func_type, func_value, exc)\ - {\ - func_type value = func_value;\ - if (sizeof(target_type) < sizeof(func_type)) {\ - if (unlikely(value != (func_type) (target_type) value)) {\ - func_type zero = 0;\ - if (exc && unlikely(value == (func_type)-1 && PyErr_Occurred()))\ - return (target_type) -1;\ - if (is_unsigned && unlikely(value < zero))\ - goto raise_neg_overflow;\ - else\ - goto raise_overflow;\ - }\ - }\ - return (target_type) value;\ - } - -/* CIntToPy */ - static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int(int value) { - const int neg_one = (int) -1, const_zero = (int) 0; - const int is_unsigned = neg_one > const_zero; - if (is_unsigned) { - if (sizeof(int) < sizeof(long)) { - return PyInt_FromLong((long) value); - } else if (sizeof(int) <= sizeof(unsigned long)) { - return PyLong_FromUnsignedLong((unsigned long) value); -#ifdef HAVE_LONG_LONG - } else if (sizeof(int) <= sizeof(unsigned PY_LONG_LONG)) { - return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value); -#endif - } - } else { - if (sizeof(int) <= sizeof(long)) { - return PyInt_FromLong((long) value); -#ifdef HAVE_LONG_LONG - } else if (sizeof(int) <= sizeof(PY_LONG_LONG)) { - return PyLong_FromLongLong((PY_LONG_LONG) value); -#endif - } - } - { - int one = 1; int little = (int)*(unsigned char *)&one; - unsigned char *bytes = (unsigned char *)&value; - return _PyLong_FromByteArray(bytes, sizeof(int), - little, !is_unsigned); - } -} - -/* CIntToPy */ - static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value) { - const long neg_one = (long) -1, const_zero = (long) 0; - const int is_unsigned = neg_one > const_zero; - if (is_unsigned) { - if (sizeof(long) < sizeof(long)) { - return PyInt_FromLong((long) value); - } else if (sizeof(long) <= sizeof(unsigned long)) { - return PyLong_FromUnsignedLong((unsigned long) value); -#ifdef HAVE_LONG_LONG - } else if (sizeof(long) <= sizeof(unsigned PY_LONG_LONG)) { - return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value); -#endif - } - } else { - if (sizeof(long) <= sizeof(long)) { - return PyInt_FromLong((long) value); -#ifdef HAVE_LONG_LONG - } else if (sizeof(long) <= sizeof(PY_LONG_LONG)) { - return PyLong_FromLongLong((PY_LONG_LONG) value); -#endif - } - } - { - int one = 1; int little = (int)*(unsigned char *)&one; - unsigned char *bytes = (unsigned char *)&value; - return _PyLong_FromByteArray(bytes, sizeof(long), - little, !is_unsigned); - } -} - -/* Print */ - #if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION < 3 -static PyObject *__Pyx_GetStdout(void) { - PyObject *f = PySys_GetObject((char *)"stdout"); - if (!f) { - PyErr_SetString(PyExc_RuntimeError, "lost sys.stdout"); - } - return f; -} -static int __Pyx_Print(PyObject* f, PyObject *arg_tuple, int newline) { - int i; - if (!f) { - if (!(f = __Pyx_GetStdout())) - return -1; - } - Py_INCREF(f); - for (i=0; i < PyTuple_GET_SIZE(arg_tuple); i++) { - PyObject* v; - if (PyFile_SoftSpace(f, 1)) { - if (PyFile_WriteString(" ", f) < 0) - goto error; - } - v = PyTuple_GET_ITEM(arg_tuple, i); - if (PyFile_WriteObject(v, f, Py_PRINT_RAW) < 0) - goto error; - if (PyString_Check(v)) { - char *s = PyString_AsString(v); - Py_ssize_t len = PyString_Size(v); - if (len > 0) { - switch (s[len-1]) { - case ' ': break; - case '\f': case '\r': case '\n': case '\t': case '\v': - PyFile_SoftSpace(f, 0); - break; - default: break; - } - } - } - } - if (newline) { - if (PyFile_WriteString("\n", f) < 0) - goto error; - PyFile_SoftSpace(f, 0); - } - Py_DECREF(f); - return 0; -error: - Py_DECREF(f); - return -1; -} -#else -static int __Pyx_Print(PyObject* stream, PyObject *arg_tuple, int newline) { - PyObject* kwargs = 0; - PyObject* result = 0; - PyObject* end_string; - if (unlikely(!__pyx_print)) { - __pyx_print = PyObject_GetAttr(__pyx_b, __pyx_n_s_print); - if (!__pyx_print) - return -1; - } - if (stream) { - kwargs = PyDict_New(); - if (unlikely(!kwargs)) - return -1; - if (unlikely(PyDict_SetItem(kwargs, __pyx_n_s_file, stream) < 0)) - goto bad; - if (!newline) { - end_string = PyUnicode_FromStringAndSize(" ", 1); - if (unlikely(!end_string)) - goto bad; - if (PyDict_SetItem(kwargs, __pyx_n_s_end, end_string) < 0) { - Py_DECREF(end_string); - goto bad; - } - Py_DECREF(end_string); - } - } else if (!newline) { - if (unlikely(!__pyx_print_kwargs)) { - __pyx_print_kwargs = PyDict_New(); - if (unlikely(!__pyx_print_kwargs)) - return -1; - end_string = PyUnicode_FromStringAndSize(" ", 1); - if (unlikely(!end_string)) - return -1; - if (PyDict_SetItem(__pyx_print_kwargs, __pyx_n_s_end, end_string) < 0) { - Py_DECREF(end_string); - return -1; - } - Py_DECREF(end_string); - } - kwargs = __pyx_print_kwargs; - } - result = PyObject_Call(__pyx_print, arg_tuple, kwargs); - if (unlikely(kwargs) && (kwargs != __pyx_print_kwargs)) - Py_DECREF(kwargs); - if (!result) - return -1; - Py_DECREF(result); - return 0; -bad: - if (kwargs != __pyx_print_kwargs) - Py_XDECREF(kwargs); - return -1; -} -#endif - -/* MemviewSliceCopyTemplate */ - static __Pyx_memviewslice -__pyx_memoryview_copy_new_contig(const __Pyx_memviewslice *from_mvs, - const char *mode, int ndim, - size_t sizeof_dtype, int contig_flag, - int dtype_is_object) -{ - __Pyx_RefNannyDeclarations - int i; - __Pyx_memviewslice new_mvs = { 0, 0, { 0 }, { 0 }, { 0 } }; - struct __pyx_memoryview_obj *from_memview = from_mvs->memview; - Py_buffer *buf = &from_memview->view; - PyObject *shape_tuple = NULL; - PyObject *temp_int = NULL; - struct __pyx_array_obj *array_obj = NULL; - struct __pyx_memoryview_obj *memview_obj = NULL; - __Pyx_RefNannySetupContext("__pyx_memoryview_copy_new_contig", 0); - for (i = 0; i < ndim; i++) { - if (from_mvs->suboffsets[i] >= 0) { - PyErr_Format(PyExc_ValueError, "Cannot copy memoryview slice with " - "indirect dimensions (axis %d)", i); - goto fail; - } - } - shape_tuple = PyTuple_New(ndim); - if (unlikely(!shape_tuple)) { - goto fail; - } - __Pyx_GOTREF(shape_tuple); - for(i = 0; i < ndim; i++) { - temp_int = PyInt_FromSsize_t(from_mvs->shape[i]); - if(unlikely(!temp_int)) { - goto fail; - } else { - PyTuple_SET_ITEM(shape_tuple, i, temp_int); - temp_int = NULL; - } - } - array_obj = __pyx_array_new(shape_tuple, sizeof_dtype, buf->format, (char *) mode, NULL); - if (unlikely(!array_obj)) { - goto fail; - } - __Pyx_GOTREF(array_obj); - memview_obj = (struct __pyx_memoryview_obj *) __pyx_memoryview_new( - (PyObject *) array_obj, contig_flag, - dtype_is_object, - from_mvs->memview->typeinfo); - if (unlikely(!memview_obj)) - goto fail; - if (unlikely(__Pyx_init_memviewslice(memview_obj, ndim, &new_mvs, 1) < 0)) - goto fail; - if (unlikely(__pyx_memoryview_copy_contents(*from_mvs, new_mvs, ndim, ndim, - dtype_is_object) < 0)) - goto fail; - goto no_fail; -fail: - __Pyx_XDECREF(new_mvs.memview); - new_mvs.memview = NULL; - new_mvs.data = NULL; -no_fail: - __Pyx_XDECREF(shape_tuple); - __Pyx_XDECREF(temp_int); - __Pyx_XDECREF(array_obj); - __Pyx_RefNannyFinishContext(); - return new_mvs; -} - -/* CIntFromPy */ - static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *x) { - const int neg_one = (int) -1, const_zero = (int) 0; - const int is_unsigned = neg_one > const_zero; -#if PY_MAJOR_VERSION < 3 - if (likely(PyInt_Check(x))) { - if (sizeof(int) < sizeof(long)) { - __PYX_VERIFY_RETURN_INT(int, long, PyInt_AS_LONG(x)) - } else { - long val = PyInt_AS_LONG(x); - if (is_unsigned && unlikely(val < 0)) { - goto raise_neg_overflow; - } - return (int) val; - } - } else -#endif - if (likely(PyLong_Check(x))) { - if (is_unsigned) { -#if CYTHON_USE_PYLONG_INTERNALS - const digit* digits = ((PyLongObject*)x)->ob_digit; - switch (Py_SIZE(x)) { - case 0: return (int) 0; - case 1: __PYX_VERIFY_RETURN_INT(int, digit, digits[0]) - case 2: - if (8 * sizeof(int) > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) >= 2 * PyLong_SHIFT) { - return (int) (((((int)digits[1]) << PyLong_SHIFT) | (int)digits[0])); - } - } - break; - case 3: - if (8 * sizeof(int) > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) >= 3 * PyLong_SHIFT) { - return (int) (((((((int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0])); - } - } - break; - case 4: - if (8 * sizeof(int) > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) >= 4 * PyLong_SHIFT) { - return (int) (((((((((int)digits[3]) << PyLong_SHIFT) | (int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0])); - } - } - break; - } -#endif -#if CYTHON_COMPILING_IN_CPYTHON - if (unlikely(Py_SIZE(x) < 0)) { - goto raise_neg_overflow; - } -#else - { - int result = PyObject_RichCompareBool(x, Py_False, Py_LT); - if (unlikely(result < 0)) - return (int) -1; - if (unlikely(result == 1)) - goto raise_neg_overflow; - } -#endif - if (sizeof(int) <= sizeof(unsigned long)) { - __PYX_VERIFY_RETURN_INT_EXC(int, unsigned long, PyLong_AsUnsignedLong(x)) -#ifdef HAVE_LONG_LONG - } else if (sizeof(int) <= sizeof(unsigned PY_LONG_LONG)) { - __PYX_VERIFY_RETURN_INT_EXC(int, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x)) -#endif - } - } else { -#if CYTHON_USE_PYLONG_INTERNALS - const digit* digits = ((PyLongObject*)x)->ob_digit; - switch (Py_SIZE(x)) { - case 0: return (int) 0; - case -1: __PYX_VERIFY_RETURN_INT(int, sdigit, (sdigit) (-(sdigit)digits[0])) - case 1: __PYX_VERIFY_RETURN_INT(int, digit, +digits[0]) - case -2: - if (8 * sizeof(int) - 1 > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) - 1 > 2 * PyLong_SHIFT) { - return (int) (((int)-1)*(((((int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); - } - } - break; - case 2: - if (8 * sizeof(int) > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) - 1 > 2 * PyLong_SHIFT) { - return (int) ((((((int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); - } - } - break; - case -3: - if (8 * sizeof(int) - 1 > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) - 1 > 3 * PyLong_SHIFT) { - return (int) (((int)-1)*(((((((int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); - } - } - break; - case 3: - if (8 * sizeof(int) > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) - 1 > 3 * PyLong_SHIFT) { - return (int) ((((((((int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); - } - } - break; - case -4: - if (8 * sizeof(int) - 1 > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) - 1 > 4 * PyLong_SHIFT) { - return (int) (((int)-1)*(((((((((int)digits[3]) << PyLong_SHIFT) | (int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); - } - } - break; - case 4: - if (8 * sizeof(int) > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) - 1 > 4 * PyLong_SHIFT) { - return (int) ((((((((((int)digits[3]) << PyLong_SHIFT) | (int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); - } - } - break; - } -#endif - if (sizeof(int) <= sizeof(long)) { - __PYX_VERIFY_RETURN_INT_EXC(int, long, PyLong_AsLong(x)) -#ifdef HAVE_LONG_LONG - } else if (sizeof(int) <= sizeof(PY_LONG_LONG)) { - __PYX_VERIFY_RETURN_INT_EXC(int, PY_LONG_LONG, PyLong_AsLongLong(x)) -#endif - } - } - { -#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray) - PyErr_SetString(PyExc_RuntimeError, - "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers"); -#else - int val; - PyObject *v = __Pyx_PyNumber_IntOrLong(x); - #if PY_MAJOR_VERSION < 3 - if (likely(v) && !PyLong_Check(v)) { - PyObject *tmp = v; - v = PyNumber_Long(tmp); - Py_DECREF(tmp); - } - #endif - if (likely(v)) { - int one = 1; int is_little = (int)*(unsigned char *)&one; - unsigned char *bytes = (unsigned char *)&val; - int ret = _PyLong_AsByteArray((PyLongObject *)v, - bytes, sizeof(val), - is_little, !is_unsigned); - Py_DECREF(v); - if (likely(!ret)) - return val; - } -#endif - return (int) -1; - } - } else { - int val; - PyObject *tmp = __Pyx_PyNumber_IntOrLong(x); - if (!tmp) return (int) -1; - val = __Pyx_PyInt_As_int(tmp); - Py_DECREF(tmp); - return val; - } -raise_overflow: - PyErr_SetString(PyExc_OverflowError, - "value too large to convert to int"); - return (int) -1; -raise_neg_overflow: - PyErr_SetString(PyExc_OverflowError, - "can't convert negative value to int"); - return (int) -1; -} - -/* PrintOne */ - #if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION < 3 -static int __Pyx_PrintOne(PyObject* f, PyObject *o) { - if (!f) { - if (!(f = __Pyx_GetStdout())) - return -1; - } - Py_INCREF(f); - if (PyFile_SoftSpace(f, 0)) { - if (PyFile_WriteString(" ", f) < 0) - goto error; - } - if (PyFile_WriteObject(o, f, Py_PRINT_RAW) < 0) - goto error; - if (PyFile_WriteString("\n", f) < 0) - goto error; - Py_DECREF(f); - return 0; -error: - Py_DECREF(f); - return -1; - /* the line below is just to avoid C compiler - * warnings about unused functions */ - return __Pyx_Print(f, NULL, 0); -} -#else -static int __Pyx_PrintOne(PyObject* stream, PyObject *o) { - int res; - PyObject* arg_tuple = PyTuple_Pack(1, o); - if (unlikely(!arg_tuple)) - return -1; - res = __Pyx_Print(stream, arg_tuple, 1); - Py_DECREF(arg_tuple); - return res; -} -#endif - -/* CIntFromPy */ - static CYTHON_INLINE char __Pyx_PyInt_As_char(PyObject *x) { - const char neg_one = (char) -1, const_zero = (char) 0; - const int is_unsigned = neg_one > const_zero; -#if PY_MAJOR_VERSION < 3 - if (likely(PyInt_Check(x))) { - if (sizeof(char) < sizeof(long)) { - __PYX_VERIFY_RETURN_INT(char, long, PyInt_AS_LONG(x)) - } else { - long val = PyInt_AS_LONG(x); - if (is_unsigned && unlikely(val < 0)) { - goto raise_neg_overflow; - } - return (char) val; - } - } else -#endif - if (likely(PyLong_Check(x))) { - if (is_unsigned) { -#if CYTHON_USE_PYLONG_INTERNALS - const digit* digits = ((PyLongObject*)x)->ob_digit; - switch (Py_SIZE(x)) { - case 0: return (char) 0; - case 1: __PYX_VERIFY_RETURN_INT(char, digit, digits[0]) - case 2: - if (8 * sizeof(char) > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(char, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(char) >= 2 * PyLong_SHIFT) { - return (char) (((((char)digits[1]) << PyLong_SHIFT) | (char)digits[0])); - } - } - break; - case 3: - if (8 * sizeof(char) > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(char, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(char) >= 3 * PyLong_SHIFT) { - return (char) (((((((char)digits[2]) << PyLong_SHIFT) | (char)digits[1]) << PyLong_SHIFT) | (char)digits[0])); - } - } - break; - case 4: - if (8 * sizeof(char) > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(char, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(char) >= 4 * PyLong_SHIFT) { - return (char) (((((((((char)digits[3]) << PyLong_SHIFT) | (char)digits[2]) << PyLong_SHIFT) | (char)digits[1]) << PyLong_SHIFT) | (char)digits[0])); - } - } - break; - } -#endif -#if CYTHON_COMPILING_IN_CPYTHON - if (unlikely(Py_SIZE(x) < 0)) { - goto raise_neg_overflow; - } -#else - { - int result = PyObject_RichCompareBool(x, Py_False, Py_LT); - if (unlikely(result < 0)) - return (char) -1; - if (unlikely(result == 1)) - goto raise_neg_overflow; - } -#endif - if (sizeof(char) <= sizeof(unsigned long)) { - __PYX_VERIFY_RETURN_INT_EXC(char, unsigned long, PyLong_AsUnsignedLong(x)) -#ifdef HAVE_LONG_LONG - } else if (sizeof(char) <= sizeof(unsigned PY_LONG_LONG)) { - __PYX_VERIFY_RETURN_INT_EXC(char, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x)) -#endif - } - } else { -#if CYTHON_USE_PYLONG_INTERNALS - const digit* digits = ((PyLongObject*)x)->ob_digit; - switch (Py_SIZE(x)) { - case 0: return (char) 0; - case -1: __PYX_VERIFY_RETURN_INT(char, sdigit, (sdigit) (-(sdigit)digits[0])) - case 1: __PYX_VERIFY_RETURN_INT(char, digit, +digits[0]) - case -2: - if (8 * sizeof(char) - 1 > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(char, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(char) - 1 > 2 * PyLong_SHIFT) { - return (char) (((char)-1)*(((((char)digits[1]) << PyLong_SHIFT) | (char)digits[0]))); - } - } - break; - case 2: - if (8 * sizeof(char) > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(char, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(char) - 1 > 2 * PyLong_SHIFT) { - return (char) ((((((char)digits[1]) << PyLong_SHIFT) | (char)digits[0]))); - } - } - break; - case -3: - if (8 * sizeof(char) - 1 > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(char, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(char) - 1 > 3 * PyLong_SHIFT) { - return (char) (((char)-1)*(((((((char)digits[2]) << PyLong_SHIFT) | (char)digits[1]) << PyLong_SHIFT) | (char)digits[0]))); - } - } - break; - case 3: - if (8 * sizeof(char) > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(char, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(char) - 1 > 3 * PyLong_SHIFT) { - return (char) ((((((((char)digits[2]) << PyLong_SHIFT) | (char)digits[1]) << PyLong_SHIFT) | (char)digits[0]))); - } - } - break; - case -4: - if (8 * sizeof(char) - 1 > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(char, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(char) - 1 > 4 * PyLong_SHIFT) { - return (char) (((char)-1)*(((((((((char)digits[3]) << PyLong_SHIFT) | (char)digits[2]) << PyLong_SHIFT) | (char)digits[1]) << PyLong_SHIFT) | (char)digits[0]))); - } - } - break; - case 4: - if (8 * sizeof(char) > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(char, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(char) - 1 > 4 * PyLong_SHIFT) { - return (char) ((((((((((char)digits[3]) << PyLong_SHIFT) | (char)digits[2]) << PyLong_SHIFT) | (char)digits[1]) << PyLong_SHIFT) | (char)digits[0]))); - } - } - break; - } -#endif - if (sizeof(char) <= sizeof(long)) { - __PYX_VERIFY_RETURN_INT_EXC(char, long, PyLong_AsLong(x)) -#ifdef HAVE_LONG_LONG - } else if (sizeof(char) <= sizeof(PY_LONG_LONG)) { - __PYX_VERIFY_RETURN_INT_EXC(char, PY_LONG_LONG, PyLong_AsLongLong(x)) -#endif - } - } - { -#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray) - PyErr_SetString(PyExc_RuntimeError, - "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers"); -#else - char val; - PyObject *v = __Pyx_PyNumber_IntOrLong(x); - #if PY_MAJOR_VERSION < 3 - if (likely(v) && !PyLong_Check(v)) { - PyObject *tmp = v; - v = PyNumber_Long(tmp); - Py_DECREF(tmp); - } - #endif - if (likely(v)) { - int one = 1; int is_little = (int)*(unsigned char *)&one; - unsigned char *bytes = (unsigned char *)&val; - int ret = _PyLong_AsByteArray((PyLongObject *)v, - bytes, sizeof(val), - is_little, !is_unsigned); - Py_DECREF(v); - if (likely(!ret)) - return val; - } -#endif - return (char) -1; - } - } else { - char val; - PyObject *tmp = __Pyx_PyNumber_IntOrLong(x); - if (!tmp) return (char) -1; - val = __Pyx_PyInt_As_char(tmp); - Py_DECREF(tmp); - return val; - } -raise_overflow: - PyErr_SetString(PyExc_OverflowError, - "value too large to convert to char"); - return (char) -1; -raise_neg_overflow: - PyErr_SetString(PyExc_OverflowError, - "can't convert negative value to char"); - return (char) -1; -} - -/* CIntFromPy */ - static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *x) { - const long neg_one = (long) -1, const_zero = (long) 0; - const int is_unsigned = neg_one > const_zero; -#if PY_MAJOR_VERSION < 3 - if (likely(PyInt_Check(x))) { - if (sizeof(long) < sizeof(long)) { - __PYX_VERIFY_RETURN_INT(long, long, PyInt_AS_LONG(x)) - } else { - long val = PyInt_AS_LONG(x); - if (is_unsigned && unlikely(val < 0)) { - goto raise_neg_overflow; - } - return (long) val; - } - } else -#endif - if (likely(PyLong_Check(x))) { - if (is_unsigned) { -#if CYTHON_USE_PYLONG_INTERNALS - const digit* digits = ((PyLongObject*)x)->ob_digit; - switch (Py_SIZE(x)) { - case 0: return (long) 0; - case 1: __PYX_VERIFY_RETURN_INT(long, digit, digits[0]) - case 2: - if (8 * sizeof(long) > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) >= 2 * PyLong_SHIFT) { - return (long) (((((long)digits[1]) << PyLong_SHIFT) | (long)digits[0])); - } - } - break; - case 3: - if (8 * sizeof(long) > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) >= 3 * PyLong_SHIFT) { - return (long) (((((((long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0])); - } - } - break; - case 4: - if (8 * sizeof(long) > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) >= 4 * PyLong_SHIFT) { - return (long) (((((((((long)digits[3]) << PyLong_SHIFT) | (long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0])); - } - } - break; - } -#endif -#if CYTHON_COMPILING_IN_CPYTHON - if (unlikely(Py_SIZE(x) < 0)) { - goto raise_neg_overflow; - } -#else - { - int result = PyObject_RichCompareBool(x, Py_False, Py_LT); - if (unlikely(result < 0)) - return (long) -1; - if (unlikely(result == 1)) - goto raise_neg_overflow; - } -#endif - if (sizeof(long) <= sizeof(unsigned long)) { - __PYX_VERIFY_RETURN_INT_EXC(long, unsigned long, PyLong_AsUnsignedLong(x)) -#ifdef HAVE_LONG_LONG - } else if (sizeof(long) <= sizeof(unsigned PY_LONG_LONG)) { - __PYX_VERIFY_RETURN_INT_EXC(long, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x)) -#endif - } - } else { -#if CYTHON_USE_PYLONG_INTERNALS - const digit* digits = ((PyLongObject*)x)->ob_digit; - switch (Py_SIZE(x)) { - case 0: return (long) 0; - case -1: __PYX_VERIFY_RETURN_INT(long, sdigit, (sdigit) (-(sdigit)digits[0])) - case 1: __PYX_VERIFY_RETURN_INT(long, digit, +digits[0]) - case -2: - if (8 * sizeof(long) - 1 > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { - return (long) (((long)-1)*(((((long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); - } - } - break; - case 2: - if (8 * sizeof(long) > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { - return (long) ((((((long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); - } - } - break; - case -3: - if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { - return (long) (((long)-1)*(((((((long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); - } - } - break; - case 3: - if (8 * sizeof(long) > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { - return (long) ((((((((long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); - } - } - break; - case -4: - if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) { - return (long) (((long)-1)*(((((((((long)digits[3]) << PyLong_SHIFT) | (long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); - } - } - break; - case 4: - if (8 * sizeof(long) > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) { - return (long) ((((((((((long)digits[3]) << PyLong_SHIFT) | (long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); - } - } - break; - } -#endif - if (sizeof(long) <= sizeof(long)) { - __PYX_VERIFY_RETURN_INT_EXC(long, long, PyLong_AsLong(x)) -#ifdef HAVE_LONG_LONG - } else if (sizeof(long) <= sizeof(PY_LONG_LONG)) { - __PYX_VERIFY_RETURN_INT_EXC(long, PY_LONG_LONG, PyLong_AsLongLong(x)) -#endif - } - } - { -#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray) - PyErr_SetString(PyExc_RuntimeError, - "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers"); -#else - long val; - PyObject *v = __Pyx_PyNumber_IntOrLong(x); - #if PY_MAJOR_VERSION < 3 - if (likely(v) && !PyLong_Check(v)) { - PyObject *tmp = v; - v = PyNumber_Long(tmp); - Py_DECREF(tmp); - } - #endif - if (likely(v)) { - int one = 1; int is_little = (int)*(unsigned char *)&one; - unsigned char *bytes = (unsigned char *)&val; - int ret = _PyLong_AsByteArray((PyLongObject *)v, - bytes, sizeof(val), - is_little, !is_unsigned); - Py_DECREF(v); - if (likely(!ret)) - return val; - } -#endif - return (long) -1; - } - } else { - long val; - PyObject *tmp = __Pyx_PyNumber_IntOrLong(x); - if (!tmp) return (long) -1; - val = __Pyx_PyInt_As_long(tmp); - Py_DECREF(tmp); - return val; - } -raise_overflow: - PyErr_SetString(PyExc_OverflowError, - "value too large to convert to long"); - return (long) -1; -raise_neg_overflow: - PyErr_SetString(PyExc_OverflowError, - "can't convert negative value to long"); - return (long) -1; -} - -/* TypeInfoCompare */ - static int -__pyx_typeinfo_cmp(__Pyx_TypeInfo *a, __Pyx_TypeInfo *b) -{ - int i; - if (!a || !b) - return 0; - if (a == b) - return 1; - if (a->size != b->size || a->typegroup != b->typegroup || - a->is_unsigned != b->is_unsigned || a->ndim != b->ndim) { - if (a->typegroup == 'H' || b->typegroup == 'H') { - return a->size == b->size; - } else { - return 0; - } - } - if (a->ndim) { - for (i = 0; i < a->ndim; i++) - if (a->arraysize[i] != b->arraysize[i]) - return 0; - } - if (a->typegroup == 'S') { - if (a->flags != b->flags) - return 0; - if (a->fields || b->fields) { - if (!(a->fields && b->fields)) - return 0; - for (i = 0; a->fields[i].type && b->fields[i].type; i++) { - __Pyx_StructField *field_a = a->fields + i; - __Pyx_StructField *field_b = b->fields + i; - if (field_a->offset != field_b->offset || - !__pyx_typeinfo_cmp(field_a->type, field_b->type)) - return 0; - } - return !a->fields[i].type && !b->fields[i].type; - } - } - return 1; -} - -/* MemviewSliceValidateAndInit */ - static int -__pyx_check_strides(Py_buffer *buf, int dim, int ndim, int spec) -{ - if (buf->shape[dim] <= 1) - return 1; - if (buf->strides) { - if (spec & __Pyx_MEMVIEW_CONTIG) { - if (spec & (__Pyx_MEMVIEW_PTR|__Pyx_MEMVIEW_FULL)) { - if (buf->strides[dim] != sizeof(void *)) { - PyErr_Format(PyExc_ValueError, - "Buffer is not indirectly contiguous " - "in dimension %d.", dim); - goto fail; - } - } else if (buf->strides[dim] != buf->itemsize) { - PyErr_SetString(PyExc_ValueError, - "Buffer and memoryview are not contiguous " - "in the same dimension."); - goto fail; - } - } - if (spec & __Pyx_MEMVIEW_FOLLOW) { - Py_ssize_t stride = buf->strides[dim]; - if (stride < 0) - stride = -stride; - if (stride < buf->itemsize) { - PyErr_SetString(PyExc_ValueError, - "Buffer and memoryview are not contiguous " - "in the same dimension."); - goto fail; - } - } - } else { - if (spec & __Pyx_MEMVIEW_CONTIG && dim != ndim - 1) { - PyErr_Format(PyExc_ValueError, - "C-contiguous buffer is not contiguous in " - "dimension %d", dim); - goto fail; - } else if (spec & (__Pyx_MEMVIEW_PTR)) { - PyErr_Format(PyExc_ValueError, - "C-contiguous buffer is not indirect in " - "dimension %d", dim); - goto fail; - } else if (buf->suboffsets) { - PyErr_SetString(PyExc_ValueError, - "Buffer exposes suboffsets but no strides"); - goto fail; - } - } - return 1; -fail: - return 0; -} -static int -__pyx_check_suboffsets(Py_buffer *buf, int dim, CYTHON_UNUSED int ndim, int spec) -{ - if (spec & __Pyx_MEMVIEW_DIRECT) { - if (buf->suboffsets && buf->suboffsets[dim] >= 0) { - PyErr_Format(PyExc_ValueError, - "Buffer not compatible with direct access " - "in dimension %d.", dim); - goto fail; - } - } - if (spec & __Pyx_MEMVIEW_PTR) { - if (!buf->suboffsets || (buf->suboffsets && buf->suboffsets[dim] < 0)) { - PyErr_Format(PyExc_ValueError, - "Buffer is not indirectly accessible " - "in dimension %d.", dim); - goto fail; - } - } - return 1; -fail: - return 0; -} -static int -__pyx_verify_contig(Py_buffer *buf, int ndim, int c_or_f_flag) -{ - int i; - if (c_or_f_flag & __Pyx_IS_F_CONTIG) { - Py_ssize_t stride = 1; - for (i = 0; i < ndim; i++) { - if (stride * buf->itemsize != buf->strides[i] && - buf->shape[i] > 1) - { - PyErr_SetString(PyExc_ValueError, - "Buffer not fortran contiguous."); - goto fail; - } - stride = stride * buf->shape[i]; - } - } else if (c_or_f_flag & __Pyx_IS_C_CONTIG) { - Py_ssize_t stride = 1; - for (i = ndim - 1; i >- 1; i--) { - if (stride * buf->itemsize != buf->strides[i] && - buf->shape[i] > 1) { - PyErr_SetString(PyExc_ValueError, - "Buffer not C contiguous."); - goto fail; - } - stride = stride * buf->shape[i]; - } - } - return 1; -fail: - return 0; -} -static int __Pyx_ValidateAndInit_memviewslice( - int *axes_specs, - int c_or_f_flag, - int buf_flags, - int ndim, - __Pyx_TypeInfo *dtype, - __Pyx_BufFmt_StackElem stack[], - __Pyx_memviewslice *memviewslice, - PyObject *original_obj) -{ - struct __pyx_memoryview_obj *memview, *new_memview; - __Pyx_RefNannyDeclarations - Py_buffer *buf; - int i, spec = 0, retval = -1; - __Pyx_BufFmt_Context ctx; - int from_memoryview = __pyx_memoryview_check(original_obj); - __Pyx_RefNannySetupContext("ValidateAndInit_memviewslice", 0); - if (from_memoryview && __pyx_typeinfo_cmp(dtype, ((struct __pyx_memoryview_obj *) - original_obj)->typeinfo)) { - memview = (struct __pyx_memoryview_obj *) original_obj; - new_memview = NULL; - } else { - memview = (struct __pyx_memoryview_obj *) __pyx_memoryview_new( - original_obj, buf_flags, 0, dtype); - new_memview = memview; - if (unlikely(!memview)) - goto fail; - } - buf = &memview->view; - if (buf->ndim != ndim) { - PyErr_Format(PyExc_ValueError, - "Buffer has wrong number of dimensions (expected %d, got %d)", - ndim, buf->ndim); - goto fail; - } - if (new_memview) { - __Pyx_BufFmt_Init(&ctx, stack, dtype); - if (!__Pyx_BufFmt_CheckString(&ctx, buf->format)) goto fail; - } - if ((unsigned) buf->itemsize != dtype->size) { - PyErr_Format(PyExc_ValueError, - "Item size of buffer (%" CYTHON_FORMAT_SSIZE_T "u byte%s) " - "does not match size of '%s' (%" CYTHON_FORMAT_SSIZE_T "u byte%s)", - buf->itemsize, - (buf->itemsize > 1) ? "s" : "", - dtype->name, - dtype->size, - (dtype->size > 1) ? "s" : ""); - goto fail; - } - for (i = 0; i < ndim; i++) { - spec = axes_specs[i]; - if (!__pyx_check_strides(buf, i, ndim, spec)) - goto fail; - if (!__pyx_check_suboffsets(buf, i, ndim, spec)) - goto fail; - } - if (buf->strides && !__pyx_verify_contig(buf, ndim, c_or_f_flag)) - goto fail; - if (unlikely(__Pyx_init_memviewslice(memview, ndim, memviewslice, - new_memview != NULL) == -1)) { - goto fail; - } - retval = 0; - goto no_fail; -fail: - Py_XDECREF(new_memview); - retval = -1; -no_fail: - __Pyx_RefNannyFinishContext(); - return retval; -} - -/* ObjectToMemviewSlice */ - static CYTHON_INLINE __Pyx_memviewslice __Pyx_PyObject_to_MemoryviewSlice_dc_int(PyObject *obj) { - __Pyx_memviewslice result = { 0, 0, { 0 }, { 0 }, { 0 } }; - __Pyx_BufFmt_StackElem stack[1]; - int axes_specs[] = { (__Pyx_MEMVIEW_DIRECT | __Pyx_MEMVIEW_CONTIG) }; - int retcode; - if (obj == Py_None) { - result.memview = (struct __pyx_memoryview_obj *) Py_None; - return result; - } - retcode = __Pyx_ValidateAndInit_memviewslice(axes_specs, __Pyx_IS_C_CONTIG, - (PyBUF_C_CONTIGUOUS | PyBUF_FORMAT | PyBUF_WRITABLE), 1, - &__Pyx_TypeInfo_int, stack, - &result, obj); - if (unlikely(retcode == -1)) - goto __pyx_fail; - return result; -__pyx_fail: - result.memview = NULL; - result.data = NULL; - return result; -} - -/* ObjectToMemviewSlice */ - static CYTHON_INLINE __Pyx_memviewslice __Pyx_PyObject_to_MemoryviewSlice_dc_float(PyObject *obj) { - __Pyx_memviewslice result = { 0, 0, { 0 }, { 0 }, { 0 } }; - __Pyx_BufFmt_StackElem stack[1]; - int axes_specs[] = { (__Pyx_MEMVIEW_DIRECT | __Pyx_MEMVIEW_CONTIG) }; - int retcode; - if (obj == Py_None) { - result.memview = (struct __pyx_memoryview_obj *) Py_None; - return result; - } - retcode = __Pyx_ValidateAndInit_memviewslice(axes_specs, __Pyx_IS_C_CONTIG, - (PyBUF_C_CONTIGUOUS | PyBUF_FORMAT | PyBUF_WRITABLE), 1, - &__Pyx_TypeInfo_float, stack, - &result, obj); - if (unlikely(retcode == -1)) - goto __pyx_fail; - return result; -__pyx_fail: - result.memview = NULL; - result.data = NULL; - return result; -} - 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} else if (t->encoding) { - *t->p = PyUnicode_Decode(t->s, t->n - 1, t->encoding, NULL); - } else { - *t->p = PyUnicode_FromStringAndSize(t->s, t->n - 1); - } - } else { - *t->p = PyBytes_FromStringAndSize(t->s, t->n - 1); - } - #endif - if (!*t->p) - return -1; - ++t; - } - return 0; -} - -static CYTHON_INLINE PyObject* __Pyx_PyUnicode_FromString(const char* c_str) { - return __Pyx_PyUnicode_FromStringAndSize(c_str, (Py_ssize_t)strlen(c_str)); -} -static CYTHON_INLINE char* __Pyx_PyObject_AsString(PyObject* o) { - Py_ssize_t ignore; - return __Pyx_PyObject_AsStringAndSize(o, &ignore); -} -static CYTHON_INLINE char* __Pyx_PyObject_AsStringAndSize(PyObject* o, Py_ssize_t *length) { -#if CYTHON_COMPILING_IN_CPYTHON && (__PYX_DEFAULT_STRING_ENCODING_IS_ASCII || __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT) - if ( -#if PY_MAJOR_VERSION < 3 && __PYX_DEFAULT_STRING_ENCODING_IS_ASCII - __Pyx_sys_getdefaultencoding_not_ascii && -#endif - PyUnicode_Check(o)) { -#if PY_VERSION_HEX < 0x03030000 - char* defenc_c; - 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if (res) { -#if PY_MAJOR_VERSION < 3 - if (!PyInt_Check(res) && !PyLong_Check(res)) { -#else - if (!PyLong_Check(res)) { -#endif - PyErr_Format(PyExc_TypeError, - "__%.4s__ returned non-%.4s (type %.200s)", - name, name, Py_TYPE(res)->tp_name); - Py_DECREF(res); - return NULL; - } - } - else if (!PyErr_Occurred()) { - PyErr_SetString(PyExc_TypeError, - "an integer is required"); - } - return res; -} -static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject* b) { - Py_ssize_t ival; - PyObject *x; -#if PY_MAJOR_VERSION < 3 - if (likely(PyInt_CheckExact(b))) { - if (sizeof(Py_ssize_t) >= sizeof(long)) - return PyInt_AS_LONG(b); - else - return PyInt_AsSsize_t(x); - } -#endif - if (likely(PyLong_CheckExact(b))) { - #if CYTHON_USE_PYLONG_INTERNALS - const digit* digits = ((PyLongObject*)b)->ob_digit; - const Py_ssize_t size = Py_SIZE(b); - if (likely(__Pyx_sst_abs(size) <= 1)) { - ival = likely(size) ? digits[0] : 0; - if (size == -1) ival = -ival; - return ival; - } else { - switch (size) { - case 2: - if (8 * sizeof(Py_ssize_t) > 2 * PyLong_SHIFT) { - return (Py_ssize_t) (((((size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); - } - break; - case -2: - if (8 * sizeof(Py_ssize_t) > 2 * PyLong_SHIFT) { - return -(Py_ssize_t) (((((size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); - } - break; - case 3: - if (8 * sizeof(Py_ssize_t) > 3 * PyLong_SHIFT) { - return (Py_ssize_t) (((((((size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); - } - break; - case -3: - if (8 * sizeof(Py_ssize_t) > 3 * PyLong_SHIFT) { - return -(Py_ssize_t) (((((((size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); - } - break; - case 4: - if (8 * sizeof(Py_ssize_t) > 4 * PyLong_SHIFT) { - return (Py_ssize_t) (((((((((size_t)digits[3]) << PyLong_SHIFT) | (size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); - } - break; - case -4: - if (8 * sizeof(Py_ssize_t) > 4 * PyLong_SHIFT) { - return -(Py_ssize_t) (((((((((size_t)digits[3]) << PyLong_SHIFT) | (size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); - } - break; - } - } - #endif - return PyLong_AsSsize_t(b); - } - x = PyNumber_Index(b); - if (!x) return -1; - ival = PyInt_AsSsize_t(x); - Py_DECREF(x); - return ival; -} -static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) { - return PyInt_FromSize_t(ival); -} - - -#endif /* Py_PYTHON_H */ diff --git a/testing/cython/wrap.pyx b/testing/cython/wrap.pyx deleted file mode 100644 index f712ff7..0000000 --- a/testing/cython/wrap.pyx +++ /dev/null @@ -1,101 +0,0 @@ -from cython.view cimport array as cvarray - - -vdwRadii = {"H": 1.0, - "C": 1.5, - "N": 1.399999976158142, - "O": 1.2999999523162842, - "F": 1.47, - "Mg": 1.73, - "P": 1.8, - "S": 1.899999976158142} - -def vdwRadius(atomType): - return vdwRadii.get(atomType, 1.5) - - -cdef extern from "gridsearch.C": - int test_function(int i) - - -cdef extern from "gridsearch.C": - double sasa_grid(const float *pos,int natoms, float pairdist, int allow_double_counting, int maxpairs, const float *radius,const int npts, double srad, int pointstyle, int restricted, const int* restrictedList) - -def bla(int i): - return test_function(i) - - -def test_sasa(): - import MDAnalysis - import numpy as np - psf = "/mnt/workspace/pycontactData/nowater.psf" - dcd = "/mnt/workspace/pycontactData/trajectory_short.dcd" - - # load psf and trajectory, make lists with radii and coordinates - u = MDAnalysis.Universe(psf, dcd) - - probeRadius = 1.4 - - # seltext = "segid UBQ" - # resseltext = "segid UBQ and same residue as around 5.0 (segid RN11)" - seltext = "segid COH3" - seltext2 = "segid DOC3" - resseltext = "segid COH3 and around 5 segid DOC3" - perres = 0 - - # 0=spiral, 1=random (VMD) - pointstyle = 1 - # number of points to approximate the sphere - surfacePoints = 50 - # pair distance - pairdist = 2 * (2.0 + 1.4) - - if resseltext != "": - restricted = 1 - else: - restricted = 0 - - selection = u.select_atoms(seltext) - - if perres: - resids = sorted(set(selection.resids)) - segs = sorted(set(selection.segids)) - else: - pass - - natoms = len(selection.atoms) - radius = [] - restrictedList = [] - if restricted: - ressel = u.select_atoms(resseltext) - for s in selection.atoms: - if s in ressel.atoms: - restrictedList.append(1) - else: - restrictedList.append(0) - radius.append(vdwRadius(s.name[0])) - else: - for s in selection.atoms: - radius.append(vdwRadius(s.name[0])) - natoms = len(selection) - nprad = np.array(radius, dtype=np.float32) - restrictedList = np.array(restrictedList, dtype=np.int32) - cdef int [::1] cy_restrictedList = restrictedList - cdef float [::1] cy_radius = nprad - - input_coords = [] - ressel = u.select_atoms(resseltext) - for ts in u.trajectory: - # print("restricted: ", len(ressel.atoms)) - input_coords.append(selection.positions) - - cdef float [::1] c_coords; - result = [] - for c in input_coords: - coords = np.reshape(c, (1, natoms * 3)) - npcoords = np.array(coords, dtype=np.float32) - print(npcoords[0]) - c_coords = npcoords[0] - sasa = sasa_grid(&c_coords[0], natoms, pairdist, 0, -1, &cy_radius[0] ,surfacePoints, probeRadius, pointstyle, restricted, &cy_restrictedList[0]) - result.append(sasa) - return result diff --git a/testing/cython/wrap_cython.py b/testing/cython/wrap_cython.py deleted file mode 100644 index 74e2156..0000000 --- a/testing/cython/wrap_cython.py +++ /dev/null @@ -1,15 +0,0 @@ -# testing wrapper - -import matplotlib.pyplot as plt -from wrap_cy import bla, test_sasa - -a = bla(2) -print(a) - -import time -start = time.time() -r = test_sasa() -stop = time.time() -print(stop-start) -plt.plot(r) -plt.show() diff --git a/testing/cython/wrap_vmd.cpp b/testing/cython/wrap_vmd.cpp deleted file mode 100644 index d486122..0000000 --- a/testing/cython/wrap_vmd.cpp +++ /dev/null @@ -1,1850 +0,0 @@ -/* Generated by Cython 0.25.2 */ - -#define PY_SSIZE_T_CLEAN -#include "Python.h" -#ifndef Py_PYTHON_H - #error Python headers needed to compile C extensions, please install development version of Python. -#elif PY_VERSION_HEX < 0x02060000 || (0x03000000 <= PY_VERSION_HEX && PY_VERSION_HEX < 0x03020000) - 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Py_XDECREF(py_frame); -} - -/* CIntToPy */ -static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value) { - const long neg_one = (long) -1, const_zero = (long) 0; - const int is_unsigned = neg_one > const_zero; - if (is_unsigned) { - if (sizeof(long) < sizeof(long)) { - return PyInt_FromLong((long) value); - } else if (sizeof(long) <= sizeof(unsigned long)) { - return PyLong_FromUnsignedLong((unsigned long) value); -#ifdef HAVE_LONG_LONG - } else if (sizeof(long) <= sizeof(unsigned PY_LONG_LONG)) { - return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value); -#endif - } - } else { - if (sizeof(long) <= sizeof(long)) { - return PyInt_FromLong((long) value); -#ifdef HAVE_LONG_LONG - } else if (sizeof(long) <= sizeof(PY_LONG_LONG)) { - return PyLong_FromLongLong((PY_LONG_LONG) value); -#endif - } - } - { - int one = 1; int little = (int)*(unsigned char *)&one; - unsigned char *bytes = (unsigned char *)&value; - return _PyLong_FromByteArray(bytes, sizeof(long), - little, !is_unsigned); - } -} - -/* CIntFromPyVerify */ -#define __PYX_VERIFY_RETURN_INT(target_type, func_type, func_value)\ - __PYX__VERIFY_RETURN_INT(target_type, func_type, func_value, 0) -#define __PYX_VERIFY_RETURN_INT_EXC(target_type, func_type, func_value)\ - __PYX__VERIFY_RETURN_INT(target_type, func_type, func_value, 1) -#define __PYX__VERIFY_RETURN_INT(target_type, func_type, func_value, exc)\ - {\ - func_type value = func_value;\ - if (sizeof(target_type) < sizeof(func_type)) {\ - if (unlikely(value != (func_type) (target_type) value)) {\ - func_type zero = 0;\ - if (exc && unlikely(value == (func_type)-1 && PyErr_Occurred()))\ - return (target_type) -1;\ - if (is_unsigned && unlikely(value < zero))\ - goto raise_neg_overflow;\ - else\ - goto raise_overflow;\ - }\ - }\ - return (target_type) value;\ - } - -/* CIntFromPy */ -static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *x) { - const long neg_one = (long) -1, const_zero = (long) 0; - const int is_unsigned = neg_one > const_zero; -#if PY_MAJOR_VERSION < 3 - if (likely(PyInt_Check(x))) { - if (sizeof(long) < sizeof(long)) { - __PYX_VERIFY_RETURN_INT(long, long, PyInt_AS_LONG(x)) - } else { - long val = PyInt_AS_LONG(x); - if (is_unsigned && unlikely(val < 0)) { - goto raise_neg_overflow; - } - return (long) val; - } - } else -#endif - if (likely(PyLong_Check(x))) { - if (is_unsigned) { -#if CYTHON_USE_PYLONG_INTERNALS - const digit* digits = ((PyLongObject*)x)->ob_digit; - switch (Py_SIZE(x)) { - case 0: return (long) 0; - case 1: __PYX_VERIFY_RETURN_INT(long, digit, digits[0]) - case 2: - if (8 * sizeof(long) > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) >= 2 * PyLong_SHIFT) { - return (long) (((((long)digits[1]) << PyLong_SHIFT) | (long)digits[0])); - } - } - break; - case 3: - if (8 * sizeof(long) > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) >= 3 * PyLong_SHIFT) { - return (long) (((((((long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0])); - } - } - break; - case 4: - if (8 * sizeof(long) > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) >= 4 * PyLong_SHIFT) { - return (long) (((((((((long)digits[3]) << PyLong_SHIFT) | (long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0])); - } - } - break; - } -#endif -#if CYTHON_COMPILING_IN_CPYTHON - if (unlikely(Py_SIZE(x) < 0)) { - goto raise_neg_overflow; - } -#else - { - int result = PyObject_RichCompareBool(x, Py_False, Py_LT); - if (unlikely(result < 0)) - return (long) -1; - if (unlikely(result == 1)) - goto raise_neg_overflow; - } -#endif - if (sizeof(long) <= sizeof(unsigned long)) { - __PYX_VERIFY_RETURN_INT_EXC(long, unsigned long, PyLong_AsUnsignedLong(x)) -#ifdef HAVE_LONG_LONG - } else if (sizeof(long) <= sizeof(unsigned PY_LONG_LONG)) { - __PYX_VERIFY_RETURN_INT_EXC(long, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x)) -#endif - } - } else { -#if CYTHON_USE_PYLONG_INTERNALS - const digit* digits = ((PyLongObject*)x)->ob_digit; - switch (Py_SIZE(x)) { - case 0: return (long) 0; - case -1: __PYX_VERIFY_RETURN_INT(long, sdigit, (sdigit) (-(sdigit)digits[0])) - case 1: __PYX_VERIFY_RETURN_INT(long, digit, +digits[0]) - case -2: - if (8 * sizeof(long) - 1 > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { - return (long) (((long)-1)*(((((long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); - } - } - break; - case 2: - if (8 * sizeof(long) > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { - return (long) ((((((long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); - } - } - break; - case -3: - if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { - return (long) (((long)-1)*(((((((long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); - } - } - break; - case 3: - if (8 * sizeof(long) > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { - return (long) ((((((((long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); - } - } - break; - case -4: - if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) { - return (long) (((long)-1)*(((((((((long)digits[3]) << PyLong_SHIFT) | (long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); - } - } - break; - case 4: - if (8 * sizeof(long) > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) { - return (long) ((((((((((long)digits[3]) << PyLong_SHIFT) | (long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); - } - } - break; - } -#endif - if (sizeof(long) <= sizeof(long)) { - __PYX_VERIFY_RETURN_INT_EXC(long, long, PyLong_AsLong(x)) -#ifdef HAVE_LONG_LONG - } else if (sizeof(long) <= sizeof(PY_LONG_LONG)) { - __PYX_VERIFY_RETURN_INT_EXC(long, PY_LONG_LONG, PyLong_AsLongLong(x)) -#endif - } - } - { -#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray) - PyErr_SetString(PyExc_RuntimeError, - "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers"); -#else - long val; - PyObject *v = __Pyx_PyNumber_IntOrLong(x); - #if PY_MAJOR_VERSION < 3 - if (likely(v) && !PyLong_Check(v)) { - PyObject *tmp = v; - v = PyNumber_Long(tmp); - Py_DECREF(tmp); - } - #endif - if (likely(v)) { - int one = 1; int is_little = (int)*(unsigned char *)&one; - unsigned char *bytes = (unsigned char *)&val; - int ret = _PyLong_AsByteArray((PyLongObject *)v, - bytes, sizeof(val), - is_little, !is_unsigned); - Py_DECREF(v); - if (likely(!ret)) - return val; - } -#endif - return (long) -1; - } - } else { - long val; - PyObject *tmp = __Pyx_PyNumber_IntOrLong(x); - if (!tmp) return (long) -1; - val = __Pyx_PyInt_As_long(tmp); - Py_DECREF(tmp); - return val; - } -raise_overflow: - PyErr_SetString(PyExc_OverflowError, - "value too large to convert to long"); - return (long) -1; -raise_neg_overflow: - PyErr_SetString(PyExc_OverflowError, - "can't convert negative value to long"); - return (long) -1; -} - -/* CIntFromPy */ -static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *x) { - const int neg_one = (int) -1, const_zero = (int) 0; - const int is_unsigned = neg_one > const_zero; -#if PY_MAJOR_VERSION < 3 - if (likely(PyInt_Check(x))) { - if (sizeof(int) < sizeof(long)) { - __PYX_VERIFY_RETURN_INT(int, long, PyInt_AS_LONG(x)) - } else { - long val = PyInt_AS_LONG(x); - if (is_unsigned && unlikely(val < 0)) { - goto raise_neg_overflow; - } - return (int) val; - } - } else -#endif - if (likely(PyLong_Check(x))) { - if (is_unsigned) { -#if CYTHON_USE_PYLONG_INTERNALS - const digit* digits = ((PyLongObject*)x)->ob_digit; - switch (Py_SIZE(x)) { - case 0: return (int) 0; - case 1: __PYX_VERIFY_RETURN_INT(int, digit, digits[0]) - case 2: - if (8 * sizeof(int) > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) >= 2 * PyLong_SHIFT) { - return (int) (((((int)digits[1]) << PyLong_SHIFT) | (int)digits[0])); - } - } - break; - case 3: - if (8 * sizeof(int) > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) >= 3 * PyLong_SHIFT) { - return (int) (((((((int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0])); - } - } - break; - case 4: - if (8 * sizeof(int) > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) >= 4 * PyLong_SHIFT) { - return (int) (((((((((int)digits[3]) << PyLong_SHIFT) | (int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0])); - } - } - break; - } -#endif -#if CYTHON_COMPILING_IN_CPYTHON - if (unlikely(Py_SIZE(x) < 0)) { - goto raise_neg_overflow; - } -#else - { - int result = PyObject_RichCompareBool(x, Py_False, Py_LT); - if (unlikely(result < 0)) - return (int) -1; - if (unlikely(result == 1)) - goto raise_neg_overflow; - } -#endif - if (sizeof(int) <= sizeof(unsigned long)) { - __PYX_VERIFY_RETURN_INT_EXC(int, unsigned long, PyLong_AsUnsignedLong(x)) -#ifdef HAVE_LONG_LONG - } else if (sizeof(int) <= sizeof(unsigned PY_LONG_LONG)) { - __PYX_VERIFY_RETURN_INT_EXC(int, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x)) -#endif - } - } else { -#if CYTHON_USE_PYLONG_INTERNALS - const digit* digits = ((PyLongObject*)x)->ob_digit; - switch (Py_SIZE(x)) { - case 0: return (int) 0; - case -1: __PYX_VERIFY_RETURN_INT(int, sdigit, (sdigit) (-(sdigit)digits[0])) - case 1: __PYX_VERIFY_RETURN_INT(int, digit, +digits[0]) - case -2: - if (8 * sizeof(int) - 1 > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) - 1 > 2 * PyLong_SHIFT) { - return (int) (((int)-1)*(((((int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); - } - } - break; - case 2: - if (8 * sizeof(int) > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) - 1 > 2 * PyLong_SHIFT) { - return (int) ((((((int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); - } - } - break; - case -3: - if (8 * sizeof(int) - 1 > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) - 1 > 3 * PyLong_SHIFT) { - return (int) (((int)-1)*(((((((int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); - } - } - break; - case 3: - if (8 * sizeof(int) > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) - 1 > 3 * PyLong_SHIFT) { - return (int) ((((((((int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); - } - } - break; - case -4: - if (8 * sizeof(int) - 1 > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) - 1 > 4 * PyLong_SHIFT) { - return (int) (((int)-1)*(((((((((int)digits[3]) << PyLong_SHIFT) | (int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); - } - } - break; - case 4: - if (8 * sizeof(int) > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) - 1 > 4 * PyLong_SHIFT) { - return (int) ((((((((((int)digits[3]) << PyLong_SHIFT) | (int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); - } - } - break; - } -#endif - if (sizeof(int) <= sizeof(long)) { - __PYX_VERIFY_RETURN_INT_EXC(int, long, PyLong_AsLong(x)) -#ifdef HAVE_LONG_LONG - } else if (sizeof(int) <= sizeof(PY_LONG_LONG)) { - __PYX_VERIFY_RETURN_INT_EXC(int, PY_LONG_LONG, PyLong_AsLongLong(x)) -#endif - } - } - { -#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray) - PyErr_SetString(PyExc_RuntimeError, - "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers"); -#else - int val; - PyObject *v = __Pyx_PyNumber_IntOrLong(x); - #if PY_MAJOR_VERSION < 3 - if (likely(v) && !PyLong_Check(v)) { - PyObject *tmp = v; - v = PyNumber_Long(tmp); - Py_DECREF(tmp); - } - #endif - if (likely(v)) { - int one = 1; int is_little = (int)*(unsigned char *)&one; - unsigned char *bytes = (unsigned char *)&val; - int ret = _PyLong_AsByteArray((PyLongObject *)v, - bytes, sizeof(val), - is_little, !is_unsigned); - Py_DECREF(v); - if (likely(!ret)) - return val; - } -#endif - return (int) -1; - } - } else { - int val; - PyObject *tmp = __Pyx_PyNumber_IntOrLong(x); - if (!tmp) return (int) -1; - val = __Pyx_PyInt_As_int(tmp); - Py_DECREF(tmp); - return val; - } -raise_overflow: - PyErr_SetString(PyExc_OverflowError, - "value too large to convert to int"); - return (int) -1; -raise_neg_overflow: - PyErr_SetString(PyExc_OverflowError, - "can't convert negative value to int"); - return (int) -1; -} - -/* CheckBinaryVersion */ -static int __Pyx_check_binary_version(void) { - char ctversion[4], rtversion[4]; - PyOS_snprintf(ctversion, 4, "%d.%d", PY_MAJOR_VERSION, PY_MINOR_VERSION); - PyOS_snprintf(rtversion, 4, "%s", Py_GetVersion()); - if (ctversion[0] != rtversion[0] || ctversion[2] != rtversion[2]) { - char message[200]; - PyOS_snprintf(message, sizeof(message), - "compiletime version %s of module '%.100s' " - "does not match runtime version %s", - ctversion, __Pyx_MODULE_NAME, rtversion); - return PyErr_WarnEx(NULL, message, 1); - } - return 0; -} - -/* InitStrings */ -static int __Pyx_InitStrings(__Pyx_StringTabEntry *t) { - while (t->p) { - #if PY_MAJOR_VERSION < 3 - if (t->is_unicode) { - *t->p = PyUnicode_DecodeUTF8(t->s, t->n - 1, NULL); - } else if (t->intern) { - *t->p = PyString_InternFromString(t->s); - } else { - *t->p = PyString_FromStringAndSize(t->s, t->n - 1); - } - #else - if (t->is_unicode | t->is_str) { - if (t->intern) { - *t->p = PyUnicode_InternFromString(t->s); - } else if (t->encoding) { - *t->p = PyUnicode_Decode(t->s, t->n - 1, t->encoding, NULL); - } else { - *t->p = PyUnicode_FromStringAndSize(t->s, t->n - 1); - } - } else { - *t->p = PyBytes_FromStringAndSize(t->s, t->n - 1); - } - #endif - if (!*t->p) - return -1; - ++t; - } - return 0; -} - -static CYTHON_INLINE PyObject* __Pyx_PyUnicode_FromString(const char* c_str) { - return __Pyx_PyUnicode_FromStringAndSize(c_str, (Py_ssize_t)strlen(c_str)); -} -static CYTHON_INLINE char* __Pyx_PyObject_AsString(PyObject* o) { - Py_ssize_t ignore; - return __Pyx_PyObject_AsStringAndSize(o, &ignore); -} -static CYTHON_INLINE char* __Pyx_PyObject_AsStringAndSize(PyObject* o, Py_ssize_t *length) { -#if CYTHON_COMPILING_IN_CPYTHON && (__PYX_DEFAULT_STRING_ENCODING_IS_ASCII || __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT) - if ( -#if PY_MAJOR_VERSION < 3 && __PYX_DEFAULT_STRING_ENCODING_IS_ASCII - __Pyx_sys_getdefaultencoding_not_ascii && -#endif - PyUnicode_Check(o)) { -#if PY_VERSION_HEX < 0x03030000 - char* defenc_c; - PyObject* defenc = _PyUnicode_AsDefaultEncodedString(o, NULL); - if (!defenc) return NULL; - defenc_c = PyBytes_AS_STRING(defenc); -#if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII - { - char* end = defenc_c + PyBytes_GET_SIZE(defenc); - char* c; - for (c = defenc_c; c < end; c++) { - if ((unsigned char) (*c) >= 128) { - PyUnicode_AsASCIIString(o); - return NULL; - } - } - } -#endif - *length = PyBytes_GET_SIZE(defenc); - return defenc_c; -#else - if (__Pyx_PyUnicode_READY(o) == -1) return NULL; -#if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII - if (PyUnicode_IS_ASCII(o)) { - *length = PyUnicode_GET_LENGTH(o); - return PyUnicode_AsUTF8(o); - } else { - PyUnicode_AsASCIIString(o); - return NULL; - } -#else - return PyUnicode_AsUTF8AndSize(o, length); -#endif -#endif - } else -#endif -#if (!CYTHON_COMPILING_IN_PYPY) || (defined(PyByteArray_AS_STRING) && defined(PyByteArray_GET_SIZE)) - if (PyByteArray_Check(o)) { - *length = PyByteArray_GET_SIZE(o); - return PyByteArray_AS_STRING(o); - } else -#endif - { - char* result; - int r = PyBytes_AsStringAndSize(o, &result, length); - if (unlikely(r < 0)) { - return NULL; - } else { - return result; - } - } -} -static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject* x) { - int is_true = x == Py_True; - if (is_true | (x == Py_False) | (x == Py_None)) return is_true; - else return PyObject_IsTrue(x); -} -static CYTHON_INLINE PyObject* __Pyx_PyNumber_IntOrLong(PyObject* x) { -#if CYTHON_USE_TYPE_SLOTS - PyNumberMethods *m; -#endif - const char *name = NULL; - PyObject *res = NULL; -#if PY_MAJOR_VERSION < 3 - if (PyInt_Check(x) || PyLong_Check(x)) -#else - if (PyLong_Check(x)) -#endif - return __Pyx_NewRef(x); -#if CYTHON_USE_TYPE_SLOTS - m = Py_TYPE(x)->tp_as_number; - #if PY_MAJOR_VERSION < 3 - if (m && m->nb_int) { - name = "int"; - res = PyNumber_Int(x); - } - else if (m && m->nb_long) { - name = "long"; - res = PyNumber_Long(x); - } - #else - if (m && m->nb_int) { - name = "int"; - res = PyNumber_Long(x); - } - #endif -#else - res = PyNumber_Int(x); -#endif - if (res) { -#if PY_MAJOR_VERSION < 3 - if (!PyInt_Check(res) && !PyLong_Check(res)) { -#else - if (!PyLong_Check(res)) { -#endif - PyErr_Format(PyExc_TypeError, - "__%.4s__ returned non-%.4s (type %.200s)", - name, name, Py_TYPE(res)->tp_name); - Py_DECREF(res); - return NULL; - } - } - else if (!PyErr_Occurred()) { - PyErr_SetString(PyExc_TypeError, - "an integer is required"); - } - return res; -} -static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject* b) { - Py_ssize_t ival; - PyObject *x; -#if PY_MAJOR_VERSION < 3 - if (likely(PyInt_CheckExact(b))) { - if (sizeof(Py_ssize_t) >= sizeof(long)) - return PyInt_AS_LONG(b); - else - return PyInt_AsSsize_t(x); - } -#endif - if (likely(PyLong_CheckExact(b))) { - #if CYTHON_USE_PYLONG_INTERNALS - const digit* digits = ((PyLongObject*)b)->ob_digit; - const Py_ssize_t size = Py_SIZE(b); - if (likely(__Pyx_sst_abs(size) <= 1)) { - ival = likely(size) ? digits[0] : 0; - if (size == -1) ival = -ival; - return ival; - } else { - switch (size) { - case 2: - if (8 * sizeof(Py_ssize_t) > 2 * PyLong_SHIFT) { - return (Py_ssize_t) (((((size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); - } - break; - case -2: - if (8 * sizeof(Py_ssize_t) > 2 * PyLong_SHIFT) { - return -(Py_ssize_t) (((((size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); - } - break; - case 3: - if (8 * sizeof(Py_ssize_t) > 3 * PyLong_SHIFT) { - return (Py_ssize_t) (((((((size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); - } - break; - case -3: - if (8 * sizeof(Py_ssize_t) > 3 * PyLong_SHIFT) { - return -(Py_ssize_t) (((((((size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); - } - break; - case 4: - if (8 * sizeof(Py_ssize_t) > 4 * PyLong_SHIFT) { - return (Py_ssize_t) (((((((((size_t)digits[3]) << PyLong_SHIFT) | (size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); - } - break; - case -4: - if (8 * sizeof(Py_ssize_t) > 4 * PyLong_SHIFT) { - return -(Py_ssize_t) (((((((((size_t)digits[3]) << PyLong_SHIFT) | (size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); - } - break; - } - } - #endif - return PyLong_AsSsize_t(b); - } - x = PyNumber_Index(b); - if (!x) return -1; - ival = PyInt_AsSsize_t(x); - Py_DECREF(x); - return ival; -} -static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) { - return PyInt_FromSize_t(ival); -} - - -#endif /* Py_PYTHON_H */ diff --git a/testing/tableview.py b/testing/tableview.py deleted file mode 100644 index 9236b4b..0000000 --- a/testing/tableview.py +++ /dev/null @@ -1,120 +0,0 @@ -import operator -from PyQt5.QtCore import QAbstractTableModel,Qt,pyqtSlot -from PyQt5.QtGui import * -from PyQt5.QtWidgets import * -class MyWindow(QWidget): - def __init__(self, data_list, header, *args): - QWidget.__init__(self, *args) - # setGeometry(x_pos, y_pos, width, height) - self.setGeometry(300, 200, 570, 450) - self.setWindowTitle("Click on column title to sort") - table_model = MyTableModel(self, data_list, header) - table_view = QTableView() - table_view.setModel(table_model) - # set font - font = QFont("Courier New", 14) - table_view.setFont(font) - # set column width to fit contents (set font first!) - table_view.resizeColumnsToContents() - # enable sorting - table_view.setSortingEnabled(True) - layout = QVBoxLayout(self) - layout.addWidget(table_view) - self.setLayout(layout) -class MyTableModel(QAbstractTableModel): - def __init__(self, parent, mylist, header, *args): - QAbstractTableModel.__init__(self, parent, *args) - self.mylist = mylist - self.header = header - def rowCount(self, parent): - return len(self.mylist) - def columnCount(self, parent): - return len(self.mylist[0]) - def data(self, index, role): - if not index.isValid(): - return None - elif role != Qt.DisplayRole: - return None - return self.mylist[index.row()][index.column()] - def headerData(self, col, orientation, role): - if orientation == Qt.Horizontal and role == Qt.DisplayRole: - return self.header[col] - return None - - @pyqtSlot() - def sort(self, col, order): - """sort table by given column number col""" - # self.emit(SIGNAL("layoutAboutToBeChanged()")) - self.layoutAboutToBeChanged() - self.mylist = sorted(self.mylist, - key=operator.itemgetter(col)) - if order == Qt.DescendingOrder: - self.mylist.reverse() - # self.emit(SIGNAL("layoutChanged()")) - self.layoutChanged() -# the solvent data ... -header = ['Solvent Name', ' BP (deg C)', ' MP (deg C)', ' Density (g/ml)'] -# use numbers for numeric data to sort properly -data_list = [ -('ACETIC ACID', 117.9, 16.7, 1.049), -('ACETIC ANHYDRIDE', 140.1, -73.1, 1.087), -('ACETONE', 56.3, -94.7, 0.791), -('ACETONITRILE', 81.6, -43.8, 0.786), -('ANISOLE', 154.2, -37.0, 0.995), -('BENZYL ALCOHOL', 205.4, -15.3, 1.045), -('BENZYL BENZOATE', 323.5, 19.4, 1.112), -('BUTYL ALCOHOL NORMAL', 117.7, -88.6, 0.81), -('BUTYL ALCOHOL SEC', 99.6, -114.7, 0.805), -('BUTYL ALCOHOL TERTIARY', 82.2, 25.5, 0.786), -('CHLOROBENZENE', 131.7, -45.6, 1.111), -('CYCLOHEXANE', 80.7, 6.6, 0.779), -('CYCLOHEXANOL', 161.1, 25.1, 0.971), -('CYCLOHEXANONE', 155.2, -47.0, 0.947), -('DICHLOROETHANE 1 2', 83.5, -35.7, 1.246), -('DICHLOROMETHANE', 39.8, -95.1, 1.325), -('DIETHYL ETHER', 34.5, -116.2, 0.715), -('DIMETHYLACETAMIDE', 166.1, -20.0, 0.937), -('DIMETHYLFORMAMIDE', 153.3, -60.4, 0.944), -('DIMETHYLSULFOXIDE', 189.4, 18.5, 1.102), -('DIOXANE 1 4', 101.3, 11.8, 1.034), -('DIPHENYL ETHER', 258.3, 26.9, 1.066), -('ETHYL ACETATE', 77.1, -83.9, 0.902), -('ETHYL ALCOHOL', 78.3, -114.1, 0.789), -('ETHYL DIGLYME', 188.2, -45.0, 0.906), -('ETHYLENE CARBONATE', 248.3, 36.4, 1.321), -('ETHYLENE GLYCOL', 197.3, -13.2, 1.114), -('FORMIC ACID', 100.6, 8.3, 1.22), -('HEPTANE', 98.4, -90.6, 0.684), -('HEXAMETHYL PHOSPHORAMIDE', 233.2, 7.2, 1.027), -('HEXANE', 68.7, -95.3, 0.659), -('ISO OCTANE', 99.2, -107.4, 0.692), -('ISOPROPYL ACETATE', 88.6, -73.4, 0.872), -('ISOPROPYL ALCOHOL', 82.3, -88.0, 0.785), -('METHYL ALCOHOL', 64.7, -97.7, 0.791), -('METHYL ETHYLKETONE', 79.6, -86.7, 0.805), -('METHYL ISOBUTYL KETONE', 116.5, -84.0, 0.798), -('METHYL T-BUTYL ETHER', 55.5, -10.0, 0.74), -('METHYLPYRROLIDINONE N', 203.2, -23.5, 1.027), -('MORPHOLINE', 128.9, -3.1, 1.0), -('NITROBENZENE', 210.8, 5.7, 1.208), -('NITROMETHANE', 101.2, -28.5, 1.131), -('PENTANE', 36.1, ' -129.7', 0.626), -('PHENOL', 181.8, 40.9, 1.066), -('PROPANENITRILE', 97.1, -92.8, 0.782), -('PROPIONIC ACID', 141.1, -20.7, 0.993), -('PROPIONITRILE', 97.4, -92.8, 0.782), -('PROPYLENE GLYCOL', 187.6, -60.1, 1.04), -('PYRIDINE', 115.4, -41.6, 0.978), -('SULFOLANE', 287.3, 28.5, 1.262), -('TETRAHYDROFURAN', 66.2, -108.5, 0.887), -('TOLUENE', 110.6, -94.9, 0.867), -('TRIETHYL PHOSPHATE', 215.4, -56.4, 1.072), -('TRIETHYLAMINE', 89.5, -114.7, 0.726), -('TRIFLUOROACETIC ACID', 71.8, -15.3, 1.489), -('WATER', 100.0, 0.0, 1.0), -('XYLENES', 139.1, -47.8, 0.86) -] -app = QApplication([]) -win = MyWindow(data_list, header) -win.show() -app.exec_() diff --git a/tests/test_basic.py b/tests/test_basic.py index 15b1a20..d51f37c 100644 --- a/tests/test_basic.py +++ b/tests/test_basic.py @@ -42,6 +42,19 @@ def test_singleCore_analysis(self): hbond_sum += c.hbond_percentage() self.assertEqual(hbond_sum, 676.0) + def test_multiCore_analysis(self): + analyzer = Analyzer(self.psffile, self.dcdfile, 5.0, 2.5, 120, "segid RN11", "segid UBQ") + analyzer.runFrameScan(2) + self.assertEqual(len(analyzer.contactResults), 50) + map1 = [0, 0, 1, 1, 0] + map2 = [0, 0, 1, 1, 0] + analyzer.runContactAnalysis(map1, map2) + self.assertEqual(len(analyzer.finalAccumulatedContacts), 148) + hbond_sum = 0 + for c in analyzer.finalAccumulatedContacts: + hbond_sum += c.hbond_percentage() + self.assertEqual(hbond_sum, 676.0) + def test_selfInteraction_analysis(self): analyzer = Analyzer(self.psffile, self.dcdfile, 5.0, 2.5, 120, "segid RN11", "self") analyzer.runFrameScan(1) diff --git a/tests/test_find_contacts.py b/tests/test_find_contacts.py index bf7c087..86b5f0b 100644 --- a/tests/test_find_contacts.py +++ b/tests/test_find_contacts.py @@ -1,11 +1,9 @@ import numpy as np -from PyContact.cy_modules.cy_gridsearch import cy_find_contacts from scipy.spatial import KDTree from scipy.spatial.distance import cdist def test_find_contacts(): - # pass positions and distance to cython natoms1 = 1800 natoms2 = 2100 box_dimensions = [50, 55, 45] @@ -13,13 +11,9 @@ def test_find_contacts(): np.random.seed(42) pos1 = np.random.rand(natoms1, 3) * box_dimensions pos2 = np.random.rand(natoms2, 3) * box_dimensions - xyz1 = np.array(np.reshape(pos1, (1, natoms1 * 3)), dtype=np.float32) - xyz2 = np.array(np.reshape(pos2, (1, natoms2 * 3)), dtype=np.float32) - cutoff = 5.0 # 2d array with index of atom1 being the index of the first dimension # individual lists contain atom2 indices - nbList1 = cy_find_contacts(xyz1, natoms1, xyz2, natoms2, cutoff) tree = KDTree(pos2) # Query the KD-Tree to find pairs of points within the cutoff distance @@ -33,8 +27,4 @@ def test_find_contacts(): assert len(pair_list[1]) > 0 # check if the number of contacts is the same for (p1, p2) in zip(pair_list[0], pair_list[1]): - assert p2 in nbList1[p1] - assert p2 in pairs[p1] - - for idx, nb_list in enumerate(nbList1[:natoms1]): - assert sorted(nb_list) == sorted(pairs[idx]) \ No newline at end of file + assert p2 in pairs[p1] \ No newline at end of file