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On Tue, Apr 12, 2016 at 6:00 AM, 吴玲 <monicacul...@126.com> wrote:
> Thanks for your help,and the are another two problems.
> 1. according to your advice,I rewrite the patterns as
> *"[NH:2]1[C:3][C:4][C:5][CH,CH2:6]1.[OH2:15].[O:17]=[O:18]>>[NH2:2][C:3][C:4][C:5][*:6]=[O:17].[O:18][O:15]"*,but
> when I test some reactants ,it still does't work, and give the same
> warning ,I can't find what the problem is ,could you help me check it ?
>
> patterns = [
>
> "[NH:2]1[C:3][C:4][C:5][CH,CH2:6]1.[OH2:15].[O:17]=[O:18]>>[NH2:2][C:3][C:4][C:5][*:6]=[O:17].[O:18][O:15]",
> ]
> rs1 = ['N1CCCC1','N1CCCC1C','N1CCCC1c1ccccc1','C[NH+]1CCCC1C',]
> 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]
> *warning:*
> File
> "/home/qnhu/Project/Database/Rhea_Dedup/AllEcToAllRxn/Chemaxon/predict.py",
> line 46, 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)
>
It's a bit cryptic, but the error message does tell you exactly what the
problem is: you are calling MolToSmiles with a string instead of a
molecule. Take a look at the place where you are calling MolToSmiles. It's
useful to be spend a bit of time looking at these error messages and trying
to figure out what they say.
> 2. When I run RunReactants with patterns
> *"[OH:1][CH:2].[c:11]1[c:12][c:13][c:14][n+:15]([C:17])[c:16]1>>[O:1]=[C:2].[C:11]1=[C:16][N:15]([C:17])[C:14]=[C:13][C:12]1*"
> and input reactants1 rs1 = ['CC(C)O','C1CCCC1O','C1CCCCC1O',] , reactants2
> rs2= ['c1ccc[n+](C)c1'],
> the output :
> CC(C)O.c1ccc[n+](C)c1>>CC(C)=O.C*[N+]*1C=CCC=C1
> C1CCCC1O.c1ccc[n+](C)c1>>O=C1CCCC1.C*[N+]*1C=CCC=C1
> C1CCCCC1O.c1ccc[n+](C)c1>>O=C1CCCCC1.C*[N+]*1C=CCC=C1
> do you find that the "N" in the product C*[N+]*1C=CCC=C1 is "N+", the
> "N" in this compound contact three atom , why there be a plus charge in the
> "N"?
>
If you want to specify that the charge goes from +1 to zero, you need to
explicitly provide the +0 charge in the product. Here's a simple example:
In [16]: rxn = AllChem.ReactionFromSmarts('[C:1][N+1:2]>>[C:1].[N+0:2]')
In [17]: [Chem.MolToSmiles(x,True) for x in
rxn.RunReactants((Chem.MolFromSmiles('C[NH3+]'),))[0]]
Out[17]: ['C', 'N']
In [18]: [Chem.MolToSmiles(x,True) for x in
rxn.RunReactants((Chem.MolFromSmiles('C[NH2+]C'),))[0]]
Out[18]: ['C', 'CN']
I hope this helps,
-greg
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