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Laboratoire-de-Chemoinformatique / Synt-On

Open-source tool for synthons-based library design.
BSD 3-Clause "New" or "Revised" License
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General question on fragments generated by BRoad Collection #10

Open agiani99 opened 1 year ago

agiani99 commented 1 year ago

Hi all, I am trying to fragment a collection of compounds from Broad Repurposing Library, a famous repurposing collection with FDA approved drugs in it. After RDKit preprocessing, where some compounds are lost, I run "SynthOn_BBsBulkClassificationAndSynthonization.py" to generate fragments. While BBMode.smi file is generated, the relative Synthmode.smi is empty. This lack implies I cannot run SyntOn_BulkFragmentationEnumerationAndAnaloguesDesign, correct? Any tip for me? Best regards Andrea

agiani99 commented 1 year ago

HI all, I think you can close the issue as I found that input format is essential to correctly generate Synthmode.smi. I would encourage to add a csv/smi file format examples in README.md for clarity. I noticed that csv file with only smiles are perfectly fine (for mapping an undocumented .csv_withID file is generated, which is good), while when CSV containing ID in second position (e.g. c1ccccnc1, "Mol1"): a) any split() must be explicitedly modified to all .py scripts (not a problem for SyntOn/src/SyntOn_Classifier.py) but b) SynthOn_BBsBulkClassificationAndSynthonization.py does not generate Synthmode.smi .... Best regards