Hi Greg,
when I run the AllChem.RunReactants with rxn'patterns that the reactant have a
plus one charge ,like this :
'''
patterns = [
"[NH+:2]1[C:3][C:4][C:5][C@@H:6]1.[OH2:15].[O:17]=[O:18]>>[NH2+:2][C:3][C:4][C:5][C:6]=[O:17].[OH:18][OH:15]",
"[NH+:2]1[C:3][C:4][C:5][CH:6]1.[OH2:15].[O:17]=[O:18]>>[NH2+:2][C:3][C:4][C:5][C:6]=[O:17].[OH:18][OH:15]",
"[NH+:2]1[C:3][C:4][C:5][C:6]1.[OH2:15].[O:17]=[O:18]>>[NH2+:2][C:3][C:4][C:5][C:6]=[O:17].[OH:18][OH:15]",
"[N+:2]1[C:3][C:4][C:5][C:6]1.[OH2:15].[O:17]=[O:18]>>[N+:2][C:3][C:4][C:5][C:6]=[O:17].[OH:18][OH:15]",
]
rs1 = ['N1CCCC1']
rs2 = ['O']
rs3 = ['O=O']
for idx, pattern in enumerate(patterns, 1):
rxn = ReactionFromSmarts(pattern)
index = 0
for a in rs1:
a_ = MolFromSmiles(a)
for b in rs2:
b_ = MolFromSmiles(b)
for c in rs3:
c_ = MolFromSmiles(c)
ps = [
MolToSmiles(c) for ps in rxn.RunReactants((a_, b_,c_))
for p in ps]
index += 1
print '{idx}.{index} {a}.{b}.{c}>>{ps}'.format(
idx=idx, index=index, a=a, b=b,c=c, ps='.'.join(ps))
'''
why there is no any product output ,and how should I deal with the atom;charge
and stereoisomerism?
also when I remove the charge information(patterns = [
"[N:2]1[C:3][C:4][C:5][C:6]1.[OH2:15].[O:17]=[O:18]>>[N:2][C:3][C:4][C:5][C:6]=[O:17].[OH:18][OH:15]",
]), it occurs an error like below:
File
"/home/qnhu/Project/Database/Rhea_Dedup/AllEcToAllRxn/Chemaxon/predict.py",
line 48, in main3
for p in ps]
Boost.Python.ArgumentError: Python argument types in
rdkit.Chem.rdmolfiles.MolToSmiles(str)
did not match C++ signature:
MolToSmiles(RDKit::ROMol mol, bool isomericSmiles=False, bool
kekuleSmiles=False, int rootedAtAtom=-1, bool canonical=True, bool
allBondsExplicit=False)
how should I do?
best wishes,
wl
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