How to output a list of ID of compounds forming pairs?
den2882 opened this issue · comments
This is not clear to me. Thanks
Do you mean when doing a prediction, as in the "mmpdb predict" described at https://github.com/rdkit/mmpdb#5-use-mmp-to-make-a-prediction ?
If so, the last paragraph of that section is:
You might try enabling the "--explain" option to see why the algorithm selected a given transformation, or use "--save-details" to save the list of possible rules to the file 'pred_detail_rules.txt' and to save the list of rule pairs to "pred_detail_pairs.txt".
Is that what you are looking for?
I am using MMPs to navigate the SAR, which is a bit different from trying to compute statistics and rules for transformations. I would like to fragment the molecules using only typical synthetic routes (aryl-alkyl cuts and amides, or simply all sp3-sp2 bond cuts). Then retrieve the list of compounds forming pairs to review them manually.
For instance for 10 compounds with ID1,ID2,...,ID10.
It would give me the following information:
ID1 <--> ID3
ID1 <--> ID5
ID2 <--> ID4
etc...
An earlier version of mmpdb supported mmpdb rulecat to dump the rules from the database, but there wasn't a specific need or budget to update that for the public release.
What you can do instead is do mmpb index and specify a CSV file as the output. The mmpdb index --help output mentions "The 'csv' format is a tab-separated table with the columns: SMILES1 SMILES2 id1 id2 V1>>V2 C".
Hi den2882,
does specifying the .csv output solve the issue? If yes, I would like to close it.
Best regards,
Christian
It worked. Thanks!