Program written by Aidan Fike, July 2019

NOTE: To successfully run this program, you will need to
load modules for chimera64/1.6.2 and a version of gromacs 5 or 2018.
Alternatively, you can also use gromacs4 (only tested with 4.6.7), 
but to do so, you must include the -gro4 flag when you run the program. 
If you already are following these requirements, ignore this note.

USAGE: To use this program run:

    python main.py isRandom name/proteinLength threshold [-gro4]

    Where isRandom is whether or not you want the sequence you are creating to be
randomly generated. If 'True', you want a random sequence, then the next argument
should be the number of amino acids in your new sequence. Only (G, A, V, F, S, N, R, D)
will be used for random sequences. Instead, if isRandom is given as 'False', the next
argument should be the name of the protein you wish to create. This protein name can 
be make of any of the 21 common amino acids. 
    'threshold' is the minimium backbone-aligned rmsd difference allowed between your
two generated structures. This should be given in units of [nm].
Lastly, you can run this program with gromacs4 rather than the gromacs5/gromacs2018 default.
by adding a -gro4 flag after your other command line options.

A couple examples are:
    For a random 8mer with a minimum rmsd of .19nm created using gromacs4:
        python main.py True 8 .19 -gro4
    For a desired sequence, GNSRVGGGGG, with a minimum rmsd of .3nm using gromacs5/2018 you may want to use:
        python main.py False GNSRVGGGGG .3

PROGRAM DESCRIPTION:
    This program is made to ease the process of running Be-Meta simulations. 
    In these simulations, to confirm convergence, it is necessary to run 2 
    simulations starting with different initial structures. This program automates
    the process of creating these two initial structures. To do so, once a desired 
    sequence is chosen, many potential initial structures are created using chimera. 
    These potential structures have their omega angles measured, and any structures 
    with cis peptide bonds are removed from consideration. With the remaining non-cis structures, a 
    backbone-aligned rmsd is then calculated between each pair of structures. The two structures with
    the largest rmsd are then chosen to be the initial structures.

    This program will begin by creating two random structures and evaluating their rmsd and whether or
    not they have any cis peptide bonds. Then, if one structure has a cis bond or the backbone rmsd 
    between the structures is less than the given threshhold, another
    structure will be created. The process will then repeat, seeing whether the new structure has a
    cis bond and measuring the pairwise rmsd between it and the other initial structures. Then, if none of
    the pairwise rmsd values are greater than the threshold, another structure will be created and the
    process will be repeated. This will occur at most 20 times, at which point the program will
    quit, and the user will have to rerun the program, usually with a lower threshold rmsd value.
    This max-tries variable, default 20, can be manually changed at the top of main.py