def dlg_nested_loop(inputs, rot, workdir):
'''
Nested loops - DLG file parsing
'''
if os.path.isdir(workdir):
os.chdir(workdir)
else:
raise err.WrongPathError("working directory (DLG parsing)", workdir)
receptors, ligands = fun.prep_loop(inputs)
warnings = 0
for rdir in receptors.keys():
for rec in receptors[rdir]:
for ldir in ligands.keys():
for lig in ligands[ldir]:
print(
">>> DLG parsing for protein '{}' and ligand '{}_{}'.".
format(rec, lig, rot))
path = rdir + "/" + rec + "/" + ldir + "/" + lig + "_" + rot + "/"
radical = rec + "_" + lig + "_" + rot
dlgfile = "dock_{}.dlg".format(radical)
if not os.path.isfile(path + dlgfile):
print("[WARNING] DLG file is missing: '{}'".format(
path + dlgfile))
warnings += 1
continue
os.chdir(path)
#--- Complexe files directory ---#
if not os.path.isdir(CPLXDIR):
os.system("mkdir {}".format(CPLXDIR))
else:
os.system("rm -f {}/*".format(CPLXDIR))
#--- Docked pose files directory ---#
if not os.path.isdir(POSEDIR):
os.system("mkdir {}".format(POSEDIR))
else:
os.system("rm -f {}/*".format(POSEDIR))
#--- DLG file parsing ---#
print(
"> DLG Parsing - DLG file found: '{}'".format(path +
dlgfile))
ranks, subranks, runs = parse_DLG_ranks(dlgfile, warnings)
if not ranks or not subranks or not runs:
print("[WARNING] DLG file parsing failed: '{}'".format(
path + dlgfile))
warnings += 1
continue
write_cplxes(radical, rec, dlgfile, ranks, subranks, runs)
write_poses(lig, rot, dlgfile, ranks, subranks, runs)
os.chdir("../../../../")
print()
print("WARNINGS = {}\n...".format(warnings))
def init_arg(self):
"""
Class initialisation - Arguments parsing and checking
"""
arguments = docopt(ARGS, version=VERSION)
if arguments['--help']:
print(ARGS)
return (0)
if arguments['--version']:
print(VERSION)
return (0)
if arguments['--docking']:
self.option = "docking"
elif arguments['--complex']:
self.option = "complex"
elif arguments['--plip']:
self.option = "plip"
elif arguments['--interact']:
self.option = "interact"
infile = arguments['FILEPATH']
if fun.check_path(infile) == "file" and infile.endswith(".txt"):
self.path_input = infile
self.init_inpaths(infile)
else:
raise err.WrongPathError("parameters file", infile)
if arguments['BONDS_TYPE'] == "free" or arguments[
'BONDS_TYPE'] == "fix":
self.bonds = arguments['BONDS_TYPE']
else:
raise err.WrongBondError(bonds)
outdir = arguments['--outdir']
if outdir is not None:
if fun.check_path(outdir) == "directory":
self.path_output = outdir
else:
raise err.WrongPathError("working directory", outdir)
def adt_nested_loops(inputs, rot, workdir):
'''
Nested loops - Run ADT4
'''
if os.path.isdir(workdir):
os.chdir(workdir)
else:
raise err.WrongPathError("working directory (Docking)", workdir)
receptors, ligands = fun.prep_loop(inputs)
for key, value in inputs.items():
if key == "PROTDIR" and fun.check_path(value[0]) == "directory":
rec_srcdir = value[0] + "/"
elif key == "LIGDIR" and fun.check_path(value[0]) == "directory":
lig_srcdir = value[0] + "/"
warnings = 0
for rdir in receptors.keys():
for rec in receptors[rdir]:
#--- Check GPF reference file ---#
gpf = GPFDIR + "grid_" + rec + "_ref.gpf"
if not os.path.isfile(gpf):
print(
"[WARNING] Grid box reference file not found: '{}'".format(
gpf))
warnings += 1
else:
#os.system("cp {} {}".format(gpf, rdir + "/" + rec + "/"))
print("> GPF reference file copied: '{}'".format(gpf))
for ldir in ligands.keys():
for lig in ligands[ldir]:
path = check_dockpath(rec, rdir, lig, ldir, rot)
warnings += make_docking_dir(path, rec, rdir,
rec_srcdir, lig, ldir,
lig_srcdir, rot)
print("----------------------------------------")
os.chdir(path)
print(">>> Docking in '{}'.".format(path))
warnings += run_docking(rec, rdir, lig, ldir, rot, gpf)
os.chdir("../../../../")
print("----------------------------------------")
print()
print("WARNINGS = {}\n...".format(warnings))
### Remplacer les cpt des warnings par une liste de str.
### write liste dans log file.
def interacts_nested_loop(inputs, rot, workdir):
'''
Class initialisation: one ligand ~ all proteins
'''
if os.path.isdir(workdir):
os.chdir(workdir)
print(">>> PLIP reports parsing and Interactions inventory <<<")
else:
raise err.WrongPathError("working directory (PLIP tables parsing)",
workdir)
### Outputs destination directory ###
if os.path.isdir(CSVDIR):
print("Directory exists: '{}'".format(CSVDIR))
else:
os.makedirs(CSVDIR)
print("Directory created: '{}'".format(CSVDIR))
receptors, ligands = fun.prep_loop(inputs)
reports = {}
for ldir in ligands.keys():
for lig in ligands[ldir]:
### Ligand Interactions Dataframe ###
key = lig + "_" + rot
reports[key] = pd.DataFrame(columns=COLS)
for rdir in receptors.keys():
for rec in receptors[rdir]:
path = rdir + "/" + rec + "/" + ldir + "/" + lig + "_" + rot
cplxdir = glob.glob(path + "/plip_results/*")
if len(cplxdir) > 0:
print("> PLIP report parsing: '{}--{}'".format(
lig, rec))
for cplx in cplxdir:
reportfile = cplx + "/report.txt"
new_dt = read_report(reportfile, rec, rot)
reports[key] = pd.concat([reports[key], new_dt])
else:
print("[WARNING] Missing PLIP files: '{}'".format(
path + "/plip_results"))
### Write CSV outputs ###
for key in reports.keys():
outfile = CSVDIR + "/" + key + "_binding.csv"
print(">>> Write CSV output for '{}' in '{}'.".format(key, outfile))
reports[key].to_csv(outfile, sep=';', index=False, encoding='utf-8')
def plip_nested_loop(inputs, rot, workdir):
'''
Nested loop - Run PLIP
'''
if os.path.isdir(workdir):
os.chdir(workdir)
else:
raise err.WrongPathError("working directory (PLIP)", workdir)
receptors, ligands = fun.prep_loop(inputs)
warnings = 0
for rdir in receptors.keys():
for rec in receptors[rdir]:
for ldir in ligands.keys():
for lig in ligands[ldir]:
print(
">>> Interactions between protein '{}' and ligand '{}_{}' profiling."
.format(rec, lig, rot))
path = rdir + "/" + rec + "/" + ldir + "/" + lig + "_" + rot + "/"
os.chdir(path)
#--- Complexe files directory ---#
if not os.path.isdir(CPLXDIR):
print("[WARNING] Complexes directory is missing: '{}'".
format(path + CPLXDIR))
warnings += 1
continue
path_cplx = glob.glob(CPLXDIR + "/*.pdb")
if len(path_cplx) != GA_RUN:
print(
"[WARNING] Complex files are missing, {} file.s found: '{}'"
.format(len(path_cplx), path + CPLXDIR))
warnings += 1
continue
#--- PLIP ---#
results = run_plip(path_cplx)
parse_plip(results)
os.chdir("../../../../")
print()
print("WARNINGS = {}\n...".format(warnings))