Hi:
I want to set timeout for the function named RunReactants, because sometimes I
found there needs over 10 minutes when running this function. For example:
>>import rdkit.Chem as Chem
>>from rdkit.Chem import AllChem
>>from rdkit.Chem import MolFromSmiles,MolFromSmarts
>>from rdkit.Chem.Fingerprints import FingerprintMols
>>reactants =
>>['CC(C=CC=C(C)C=CC1=C(C)C(=O)C(OP(=O)(O)O)CC1(C)C)=CC=CC=C(C)C=CC=C(C)C=CC1=C(C)C(=O)C(OP(=O)(O)O)CC1(C)C',
>>
>>'CC(C=CC=C(C)C=CC1=C(C)C(=O)C(OP(=O)(O)O)CC1(C)C)=CC=CC=C(C)C=CC=C(C)C=CC1=C(C)C(=O)C(OP(=O)(O)O)CC1(C)C',
>>
>>'CC(C=CC=C(C)C=CC1=C(C)C(=O)C(OP(=O)(O)O)CC1(C)C)=CC=CC=C(C)C=CC=C(C)C=CC1=C(C)C(=O)C(OP(=O)(O)O)CC1(C)C',
>>
>>'CC(C=CC=C(C)C=CC1=C(C)C(=O)C(OP(=O)(O)O)CC1(C)C)=CC=CC=C(C)C=CC=C(C)C=CC1=C(C)C(=O)C(OP(=O)(O)O)CC1(C)C',
>>
>>'CC(C=CC=C(C)C=CC1=C(C)C(=O)C(OP(=O)(O)O)CC1(C)C)=CC=CC=C(C)C=CC=C(C)C=CC1=C(C)C(=O)C(OP(=O)(O)O)CC1(C)C',
>>
>>'CC(C)=CCCC(C)=CCCC(C)=CCCC(C)=CCCC(C)=CCCC(C)=CCCC(C)=CCCC(C)=CCCC(C)=CCOP(=O)(O)OP(=O)(O)O']
>>rule =
>>'[O:10][P:11](=[O:12])([O:13])[O:14].[O:40][P:41](=[O:42])([O:43])[O:44].[O:30][P:31](=[O:32])([O:33])[O:34].[O:50][P:51](=[O:52])([O:53])[O:54].[O:20][P:21](=[O:22])([O:23])[O:24].[C:1]([CH3:2])=[C:3][C:4][CH2:5][C:6]([CH3:7])=[C:8][C:9][CH2:25][C:26]([CH3:27])=[C:28][C:29][CH2:35][C:36]([CH3:37])=[C:38][C:39][CH2:45][C:46]([CH3:47])=[C:48][C:49][CH2:55][C:56]([CH3:57])=[C:58][C:59][O:0]>>[C:1]([CH3:2])=[C:3][C:4][O:0].[CH2:5]=[C:6]([CH3:7])[C:8][C:9][O:10][P:11](=[O:12])([O:13])[O:14].[CH2:25]=[C:26]([CH3:27])[C:28][C:29][O:20][P:21](=[O:22])([O:23])[O:24].[CH2:45]=[C:46]([CH3:47])[C:48][C:49][O:40][P:41](=[O:42])([O:43])[O:44].[CH2:35]=[C:36]([CH3:37])[C:38][C:39][O:30][P:31](=[O:32])([O:33])[O:34].[CH2:55]=[C:56]([CH3:57])[C:58][C:59][O:50][P:51](=[O:52])([O:53])[O:54]'
>>rxnrs = [Chem.MolFromSmiles(reactant) for reactant in reactants]
>>rxn = AllChem.ReactionFromSmarts(rule)
>>outcomes = rxn.RunReactants(rxnrs)
if this functions cannnot return result within 3s, I will make it return a
empty set.
Could you help me deal with this problems?
Thanks a lot.
Yours
Shaozhen
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