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SynthOn_BBsBulkClassificationAndSynthonization.py
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SynthOn_BBsBulkClassificationAndSynthonization.py
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import os,sys
srcPath = os.path.split(os.path.realpath(__file__))[0]
sys.path.insert(1, srcPath)
from src.SyntOn_Classifier import *
from src.SyntOn_BBs import *
from src.UsefulFunctions import *
from rdkit import Chem
"""from rdkit.Chem.rdMolDescriptors import *
from rdkit.Chem.rdmolops import *"""
from concurrent.futures import ProcessPoolExecutor
"""from rdkit.Chem.Descriptors import *
from rdkit.Chem.rdMolDescriptors import *"""
from functools import partial
def main(inp,keepPG, output=None, Ro2Filtr=False):
if not output:
output=inp
with open(inp) as inp, open(output + "_BBmode.smi", "w") as out, open(output + "_Synthmode.smi", "w") as outS,\
open(output + "_NotProcessed", "w") as notProc, open(output + "_NotClassified", "w") as notClassified:
for line in inp:
sline = line.strip()
if sline:
finalSynthon = {}
classified = False
withoutSynthons = True
allClasses = []
for molSmiles in line.split()[0].split("."):
print(molSmiles)
if "[nH+]" in molSmiles:
molSmiles = molSmiles.replace("[nH+]", "[nH]:", 1)
initMol = readMol(molSmiles)
if initMol == None:
notProc.write(line)
notProc.flush()
continue
Classes = BBClassifier(mol=initMol)
allClasses.extend(Classes)
if Classes:
classified = True
for clas in Classes:
if "MedChemHighlights" not in clas and "DEL" not in clas:
withoutSynthons = False
break
ind2del = []
for ind,Class in enumerate(Classes):
if "MedChemHighlights" in Class or "DEL" in Class:
ind2del.append(ind)
if ind2del:
for ind in ind2del[::-1]:
Classes.pop(ind)
azoles,fSynt = mainSynthonsGenerator( Chem.MolToSmiles(initMol), keepPG, Classes,returnBoolAndDict=True)
for synth1 in fSynt:
if synth1 not in finalSynthon:
finalSynthon[synth1] = fSynt[synth1].copy()
else:
finalSynthon[synth1].update(fSynt[synth1].copy())
if not classified:
notClassified.write(line)
notClassified.flush()
continue
if not finalSynthon and withoutSynthons:
out.write(sline + " " + ",".join(allClasses) + " -\n")
out.flush()
continue
if finalSynthon:
if azoles:
allClasses.append("nHAzoles_nHAzoles")
out.write(sline + " " + ",".join(allClasses) + " " + ".".join(list(finalSynthon)) + " " + str(len(finalSynthon)) + "\n")
for synth2 in finalSynthon:
if Ro2Filtr:
goodSynth, paramsValList = Ro2Filtration(synth2)
if not goodSynth:
continue
else:
outS.write(synth2 + " " + "+".join(finalSynthon[synth2]) + " " + sline + "\n")
else:
outS.write(synth2 + " " + "+".join(finalSynthon[synth2]) + " " + sline + "\n")
elif not withoutSynthons:
out.write(sline + " " + ",".join(Classes) + " NoSynthonsWereGenerated\n")
if __name__ == '__main__':
import argparse
parser = argparse.ArgumentParser(description="BBs classification and Synthons generation for large BBs libraries",
epilog="Code implementation: Yuliana Zabolotna, Alexandre Varnek\n"
" Laboratoire de Chémoinformatique, Université de Strasbourg.\n\n"
"Knowledge base (SMARTS library): Dmitriy M.Volochnyuk, Sergey V.Ryabukhin, Kostiantyn Gavrylenko, Olexandre Oksiuta\n"
" Institute of Organic Chemistry, National Academy of Sciences of Ukraine\n"
" Kyiv National Taras Shevchenko University\n"
"2021 Strasbourg, Kiev",
prog="SyntOn_BBsBulkClassificationAndSynthonization", formatter_class=argparse.RawTextHelpFormatter)
parser.add_argument("-i", "--input", type=str, help="Input file containing 2 columns building blocks smiles and ids.")
parser.add_argument("-o", "--output", type=str, help="Output files suffix name.")
parser.add_argument("--keepPG", action="store_true", help="Write both protected and unprotected "
"synthons to the output (concerns Boc, Bn, Fmoc, Cbz and Esters protections).")
parser.add_argument("--Ro2Filtr", action="store_true", help="Write only synthons satisfying Ro2 (MW <= 200, logP <= 2, H-bond donors count <= 2 and H-bond acceptors count <= 4)")
parser.add_argument("--nCores", default=-1, type=int, help="Number of available cores for parallel calculations. Memory usage is optimized, so maximal number of parallel processes can be launched.")
args = parser.parse_args()
with open(args.input) as f:
colNumb = len(f.readline().strip().split())
if colNumb == 1:
with open(args.input + "_withIDs", "w") as out:
for ind,line in enumerate(open(args.input)):
sline = line.strip()
if sline:
out.write(sline + " BB_" + str(ind+1) + "\n")
inPut = args.input + "_withIDs"
colNumb = 2
else:
inPut = args.input
if args.nCores == -1:
main(inPut, args.keepPG, args.output, args.Ro2Filtr)
else:
wc = countLines(inPut)
linesPerFile = wc // args.nCores
outNamesList = splitFileByLines(inPut, inPut, linesPerFile)
fixed_main = partial(main, keepPG=args.keepPG,
Ro2Filtr=args.Ro2Filtr)
nCores = args.nCores
finalLog = []
with ProcessPoolExecutor(max_workers=nCores) as executor:
for out in executor.map(fixed_main, outNamesList):
finalLog.append(out)
with open(args.output + "_BBmode.smi", "w") as out, open(args.output + "_Synthmode.smi", "w") as outS, \
open(args.output + "_NotProcessed", "w") as notProc, open(args.output + "_NotClassified", "w") as notClassified:
for inp in outNamesList:
for line in open(inp + "_BBmode.smi"):
if line.strip():
out.write(line)
os.remove(inp + "_BBmode.smi")
for line in open( inp + "_Synthmode.smi"):
if line.strip():
outS.write(line)
os.remove(inp + "_Synthmode.smi")
for line in open( inp + "_NotProcessed"):
if line.strip():
notProc.write(line)
os.remove(inp + "_NotProcessed")
for line in open( inp + "_NotClassified"):
if line.strip():
notClassified.write(line)
os.remove(inp + "_NotClassified")
for file in outNamesList:
os.remove(file)
with open(args.output + "_Synthmode.smi") as inpS, open("ttt", "w") as outS:
synthons = {}
for line in inpS:
sline = line.strip()
if sline and len(sline.split()) == colNumb+2:
if sline.split()[0] not in synthons:
synthons[sline.split()[0]] = {"Class": set(sline.split()[1].split(",")),
"BBs": {sline.split()[2]}, "BB_Ids": {sline.split()[3]},
"Count": 1}
else:
synthons[sline.split()[0]]["Class"].update(sline.split()[1].split(","))
synthons[sline.split()[0]]["BBs"].add(sline.split()[2])
synthons[sline.split()[0]]["BB_Ids"].add(sline.split()[3])
synthons[sline.split()[0]]["Count"] += 1
for ind, synth in enumerate(synthons):
outS.write(synth + " " + "+".join(synthons[synth]['BB_Ids']) + " " +
",".join(synthons[synth]['Class']) + " " + ";".join(synthons[synth]['BBs']) + " " + str(
synthons[synth]['Count']) + " " + args.output + "_" + str(ind+1) + "\n")
os.remove(args.output + "_Synthmode.smi")
os.rename("ttt", args.output + "_Synthmode.smi")