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setup.py
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setup.py
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import os.path
from setuptools import setup
from setuptools import find_packages
from setuptools.extension import Extension
import numpy as np
def main():
package_dir = {"": "src"}
packages = find_packages("src")
package_data = {
"qfit": [
os.path.join("data", "*.npy"),
]
}
ext_modules = [
Extension(
"qfit._extensions",
[os.path.join("src", "_extensions.c")],
include_dirs=[np.get_include()],
),
]
setup_requires = [
"setuptools_scm",
]
install_requires = [
"numpy>=1.20,<2",
"scipy>=1.0",
"cvxpy",
"pyscipopt",
"pandas>=1.2",
"pyparsing>=2.2.0",
"tqdm>=4.0.0",
"rdkit",
]
setup(
name="qfit",
use_scm_version=True,
author="Stephanie A. Wankowicz, Blake Riley, Jessica Flowers, Gydo C.P. van Zundert, Saulo H.P. de Oliveira, and Henry van den Bedem",
author_email="[email protected]",
project_urls={"Documentation": "https://github.com/ExcitedStates/qfit-3.0/"},
package_dir=package_dir,
packages=packages,
package_data=package_data,
ext_modules=ext_modules,
setup_requires=setup_requires,
install_requires=install_requires,
zip_safe=False,
python_requires=">=3.9",
entry_points={
"console_scripts": [
"qfit_protein = qfit.qfit_protein:main",
"qfit_residue = qfit.qfit_residue:main",
"qfit_ligand = qfit.qfit_ligand:main",
"qfit_covalent_ligand = qfit.qfit_covalent_ligand:main",
"qfit_prep_map = qfit.qfit_prep_map:main",
"qfit_density = qfit.qfit_density:main",
"qfit_mtz_to_ccp4 = qfit.mtz_to_ccp4:main",
"edia = qfit.edia:main",
"remove_altconfs = qfit.remove_altconfs:main",
"event_map_bdc_scaler = qfit.event_map_bdc_scaler:main",
"side_chain_remover = qfit.side_chain_remover:main",
"redistribute_cull_low_occupancies = qfit.redistribute_cull_low_occupancies:main",
"fix_restraints = qfit.fix_restraints:main",
"add_non_rotamer_atoms = qfit.add_non_rotamer_atoms:main",
"remove_duplicates = qfit.remove_duplicates:main",
"create_rotamer_library = qfit.create_rot_lib:main",
]
},
scripts=[
"scripts/post/qfit_final_refine_xray.sh",
"scripts/post/qfit_final_refine_cryoem.sh",
"scripts/post/qfit_final_refine_ligand.sh",
"scripts/post/find_largest_ligand.py",
"scripts/post/find_altlocs_near_ligand.py",
"scripts/post/get_lig_chain_res.py",
"scripts/post/qfit_RMSF.py",
"scripts/post/find_altlocs_near_ligand.py",
"scripts/post/b_factor.py",
"scripts/post/subset_structure_AH.py",
"scripts/post/alpha_carbon_rmsd.py",
"scripts/post/relabel_chain.py",
"scripts/post/water_stats.py",
"scripts/post/water_clash.py",
"scripts/post/lig_occ.py",
"scripts/post/calc_OP.py",
"scripts/post/make_methyl_df.py",
"scripts/post/find_close_residues.py",
"scripts/post/get_seq.py",
"scripts/post/calc_rscc.py",
"scripts/post/calc_rmsd.py",
"scripts/post/get_smiles.py",
"scripts/post/split_multiconformer_ligand.py",
"scripts/post/compare_rscc_voxel.py",
"scripts/post/create_restraints_file.py",
],
)
if __name__ == "__main__":
main()