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rdkit / mmpdb

A package to identify matched molecular pairs and use them to predict property changes.
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No statistics information in the output when using transform without property argument #28

Closed chengthefang closed 3 years ago

chengthefang commented 3 years ago

Hi all,

I am using the MMP transform without properties information.

For example, python mmpdb transform test_data.mmpdb --smiles 'c1cccnc1O' --no-properties

Output ID SMILES 1 Clc1ccccn1 2 Nc1ccccn1 3 c1ccncc1

In the output, I only got ID and Smiles. But I would like to print other useful information including 'from_smiles,' 'to_smiles', 'radius', 'rule_environment_id', 'count'. Those statistics could give us some confidence for the transform. I think those statistics should be independent of properties. I am curious if there is a way to output those statistics with generated molecules if we work with a MMPDB without property information.

Thanks, Cheng

KramerChristian commented 3 years ago

Hi Cheng,

there is currently no way to output the information that you listed if you call mmpdb transform with the --no-properties flag. It can be added, but that would be a code enhancement project.

A workaround that works with the current version of mmpdb is to use a dummy property that can be calculated for all compounds like e.g. molecular weight during indexing. If you then query for MWt changes, you should get the from_smiles, to_smiles, counts etc. for all results.

Bests, Christian

chengthefang commented 3 years ago

Hi Christian,

Thank you for the kind response. The workaround should work fine.

Best, Cheng