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StructureInput.py
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StructureInput.py
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from rdkit import Chem
from rdkit.Chem import AllChem
import os
from InchiGen import *
def GenerateMolFromSDF(InputFile):
cwd = os.getcwd()
fullf = os.path.join(cwd, InputFile + '.sdf')
m = Chem.MolFromMolFile(fullf, removeHs=False,sanitize = True)
return m
def GenerateSDFFromTxt(InputFile,inp_type):
Mols = []
cwd = os.getcwd()
InputFile
if os.path.exists(os.path.join(cwd, InputFile)):
fullf = os.path.join(cwd, InputFile)
elif inp_type == 'InChI':
fullf = os.path.join(cwd, InputFile + ".inchi")
elif inp_type == 'Smiles':
fullf = os.path.join(cwd, InputFile + ".smiles")
elif inp_type == 'Smarts':
fullf = os.path.join(cwd, InputFile + ".smarts")
f = open(fullf, "r")
if inp_type == 'InChI':
for line in f.readlines():
if line.strip() == '':
continue
else:
try:
m = Chem.MolFromInchi(line.strip(),sanitize = True)
Mols.append(m)
except:
print(line + " could not be read")
elif inp_type == 'Smiles':
for line in f.readlines():
if line.strip() == '':
continue
else:
try:
m = Chem.MolFromSmiles(line.strip(),sanitize = True)
Mols.append(m)
except:
print(line + " could not be read")
elif inp_type == 'Smarts':
for line in f.readlines():
if line.strip() == '':
continue
else:
try:
m = Chem.MolFromSmarts(line.strip(),sanitize = True)
Mols.append(m)
except:
print(line + " could not be read")
else:
print('unrecognised')
GeneratedFiles = GenerateSDFFromMols(Mols,inp_type )
return GeneratedFiles
def GenerateSDFFromMols(mols,inp_type):
files = []
cwd = os.getcwd()
for ind, m in enumerate(mols):
m = AllChem.AddHs(m, addCoords=True)
AllChem.EmbedMolecule(m)
AllChem.MMFFOptimizeMolecule(m)
Chem.rdmolops.AssignStereochemistryFrom3D(m)
f = inp_type + '_Mol_' + str(ind) +"_.sdf"
files.append(f[:-4])
fullf = os.path.join(cwd, f)
save3d = Chem.SDWriter( fullf)
save3d.write(m)
return files
def CleanUp(InputFiles):
# check input file types
CleanedInputFiles = []
cwd = os.getcwd()
for f in InputFiles:
if f.endswith('.sdf'):
f = f[:-4]
fullf = os.path.join(cwd, f + 'cleaned.sdf')
m = GenerateMolFromSDF(f)
m = AllChem.AddHs(m, addCoords=True)
AllChem.EmbedMolecule(m)
AllChem.MMFFOptimizeMolecule(m)
Chem.rdmolops.AssignStereochemistryFrom3D(m)
save3d = Chem.SDWriter(fullf)
save3d.write(m)
CleanedInputFiles.append( f + 'cleaned')
return CleanedInputFiles
def NumberofStereoCentres(InputFile):
cwd = os.getcwd()
fullf = os.path.join(cwd, InputFile + '.sdf')
m = Chem.MolFromMolFile(fullf, removeHs=False)
m = AllChem.AddHs(m, addCoords=True)
AllChem.EmbedMolecule(m)
AllChem.MMFFOptimizeMolecule(m)
Chem.rdmolops.AssignStereochemistryFrom3D(m)
nStereo = Chem.rdMolDescriptors.CalcNumAtomStereoCenters(m)
return nStereo