Hi,
The reactants that are part of your reaction definition are queries. If
those queries include a charge they won't match molecules that don't have a
charge. If you'd like the reactant patterns to match neutral molecules as
well as charged ones, just remove the charge from the reaction
specification.
The handling of chirality in reactions is explained in the documentation
here:
http://rdkit.org/docs/RDKit_Book.html#chirality
-greg
On Mon, Apr 11, 2016 at 9:21 AM, 吴玲 <monicacul...@126.com> wrote:
> 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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