rev_docking_p.py

#!/usr/bin/env python3

import re, sys, os, subprocess, glob, configparser
from multiprocessing import Pool

cwd = os.getcwd()

#####    config parser    ####
config = configparser.ConfigParser(inline_comment_prefixes="#")
config.optionxform = str
config.read(sys.argv[1])
locals().update(dict(config.items('DOCKING')))

####    call to scripts    ####
pythonsh = MGL_ROOT+'/bin/pythonsh'
u24 = MGL_ROOT+'/MGLToolsPckgs/AutoDockTools/Utilities24/'
def prepare_receptor(inf,outf):
    subprocess.run([pythonsh,u24+'prepare_receptor4.py',
                    '-A "checkhydrogens" -e',
                    '-r',inf,
                    '-o',outf])
def prepare_gpf(receptor, ligand, coord, output):
    os.chdir(out_dir)
    subprocess.run([pythonsh,u24+'prepare_gpf4.py', 
                   '-l',ligand,
                   ' '.join(['-p '+'='.join(i) for i in config.items('GPF')]),
                   '-p gridcenter='+coord,
                   '-r',receptor,
                   '-o',output])
    os.chdir(cwd)
def prepare_dpf(receptor, ligand, output):
    os.chdir(out_dir)
    subprocess.run([pythonsh,u24+'prepare_dpf4.py', 
                   '-l',ligand,
                   ' '.join(['-p '+'='.join(i) for i in config.items('DPF')]),
                   '-r',receptor,
                   '-o',output])
    os.chdir(cwd)
def autogrid(gpf, glg):
    os.chdir(out_dir)
    subprocess.run(['autogrid4',
                    '-p',gpf,
                    '-l',glg])
    os.chdir(cwd)
def autodock(dpf, dlg):
    os.chdir(out_dir)
    subprocess.run(['autodock4',
                    '-p',dpf,
                    '-l',dlg])
    os.chdir(cwd)
    
####   make outdir   ####
i = 1
while os.path.exists(outdir+'_%s' % i):
    i += 1
out_dir = outdir+'_%s' % i+'/'
os.makedirs(out_dir)
if os.path.exists(outdir+'_%s' % i):
    print('writing output in '+out_dir)

####    read coordinates    ####
coordinates = {}
try:
    for line in open(coord_file):
        if '#' in line: #skip comments
            next
        else:
            name, x, y, z = line.split()
            coordinates.setdefault(name, []).append([x,y,z])
    print('Reading '+coord_file+' ...')
except:
    print(coord_file+" doesn't exist")

try:
    os.system('cp '+ligand+' '+out_dir)
    lig_name = os.path.splitext(os.path.basename(ligand))[0]
except:
    print(ligand+" doesn't exist")

####    reverse docking    ####
def reverse_docking(pdb):  
    xyz = coordinates.get(pdb)
    pdb_name = os.path.splitext(pdb)[0]
    for c in xyz:
        
        ####    prepare receptor, gpf and dpf  ####
        i=1
        while os.path.exists(out_dir+pdb_name+'_%s.pdbqt' %i):
            i += 1 # incrementing file number

        print(re.sub('HETATM', '#HETATM', open(receptor_dir+'/'+pdb, 'r').read()), 
              file=open(out_dir+pdb, 'w')) # comment HETATM in pdb file
        prepare_receptor(out_dir+pdb, out_dir+pdb_name+'_%s.pdbqt' %i)
        prepare_gpf(pdb_name+'_%s.pdbqt' %i, 
                    os.path.basename(ligand), 
                    ','.join(map(str,c)), 
                    pdb_name+'_%s.gpf' % i)
        prepare_dpf(pdb_name+'_%s.pdbqt' %i, 
                    os.path.basename(ligand), 
                    pdb_name+'_'+lig_name+'_%s.dpf' % i)

        ## solve bug space in dpf ##
        print(re.sub('#', ' #', open(out_dir+pdb_name+'_'+lig_name+'_%s.dpf' % i).read()), 
              file=open(out_dir+pdb_name+'_'+lig_name+'_%s.dpf' % i, 'w'))

        ####    autogrid    ####
        autogrid(pdb_name+'_%s.gpf' % i, pdb_name+'_%s.glg' % i)

        ####    autodock    ####
        autodock(pdb_name+'_'+lig_name+'_%s.dpf' % i, pdb_name+'_'+lig_name+'_%s.dlg' % i)

####    multiprocessing    ####
Pool(int(processes)).map(reverse_docking,coordinates)