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extract_from_reaction error

Open milktea-lab opened this issue 2 years ago • 2 comments

When i extract template from my reaction: single product and single reactant, but i got a template with more than one products and reactants. input: 'reactants': '[N:1]#[C:2][CH2:3][N:4]1[CH2:5][CH2:6]CH:7[CH2:10][CH2:11][O:12][c:13]1[cH:14][cH:15][cH:16][cH:17][c:18]1[F:19]', 'products': '[NH2:1][CH2:2][CH2:3][N:4]1[CH2:5][CH2:6]CH:7[CH2:10][CH2:11][O:12][c:13]1[cH:14][cH:15]c:16[F:19]'

the template i got: [C:1]-[CH2;D2;+0:2]-[NH2;D1;+0:3].[F;H0;D1;+0:4]-c;H0;D3;+0:8:[c:7]:[cH;D2;+0:5]:[c:6]>>[C:1]-[C;H0;D2;+0:2]#[N;H0;D1;+0:3].[F;H0;D1;+0:4]-c;H0;D3;+0:5:[c:7]:[cH;D2;+0:8]:[c:9]

there has "." in both sides of the template.

and when i apply the template on the initial product: [NH2:1][CH2:2][CH2:3][N:4]1[CH2:5][CH2:6]CH:7[CH2:10][CH2:11][O:12][c:13]1[cH:14][cH:15]c:16[F:19] the error i got: ValueError: ChemicalParserException: Number of reactants provided does not match number of reactant templates.

milktea-lab avatar Aug 02 '22 06:08 milktea-lab

Your reactants and products aren't valid SMILES strings, so I'm not sure how to help you debug this.

But, I will say that the templates that RDChiral applies are treated as pseudo-unimolecular regardless of how many fragments appear in the input side. Your template probably has multiple fragments because your presumably-unimolecular reaction has multiple subgraphs that change but are disconnected.

connorcoley avatar Aug 02 '22 19:08 connorcoley

I get it! Thanks for your help!

milktea-lab avatar Aug 03 '22 02:08 milktea-lab