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luwei0917 / DynamicBind

repo for DynamicBind: Predicting ligand-specific protein-ligand complex structure with a deep equivariant generative model

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How to import ligand with "name" column in ligand.csv

stan1233 opened this issue · comments

commented

Hi!

Thank you for your selfless open-source contribution, I have two questions.

How to give a name to a compound based on input ligand.csv instead of index+number in results.
If I want to dock multiple proteins, is there a way to change the protein input to CSV?

commented

Multiple Proteins...? Do you mean you have more than one chains? If you want to dock multiple proteins, you could just change the file which generates output files. @stan1233

commented

Multiple Proteins...? Do you mean you have more than one chains? If you want to dock multiple proteins, you could just change the file which generates output files. @stan1233

What I want to express is how to assign a name to each ligand in the input ligand.csv? Also, I noticed that it seems possible in inference.py to submit multiple proteins and ligands for docking in one task. For instance, if I have 20 proteins and want to dock 200 ligands, how should I fill out the input.csv? Could you provide a template for the csv file?

Thank you for your reply, outstanding work!