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zjujdj / MetalProGNet

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issue predict_mt_chembl.py #3

Open CamilaClemente opened 7 months ago

CamilaClemente commented 7 months ago

I have successfully executed the pipeline and I obteined the top1 of MetalProGNet but I would like to clarify some details.

I want to obtain all ranked poses, not just the top one, for each ligand from both PLANTS and MetalProGNet. Is this possible? In which folder can I find it? Thanks!

zjujdj commented 7 months ago

@CamilaClemente sorry for the late reply. sure you can obatin all ranked poses from PLANTS and MetalProGNet after you revised the codes. The concerned codes included https://github.com/zjujdj/MetalProGNet/blob/master/scripts/plants_docking.py (docking_results_collect function) and predict_xxx.py.... all in all, all you need is to revise the codes. best,

CamilaClemente commented 7 months ago

Thanks for your response. The issue is that, as I understand it, the different poses from PLANTS would be located in each ligand folder in ~/docking_running/ligand/ranking.csv file, but it remains empty. Regarding MetalProGNet, I can't find in the code where the ranking of the other poses would be saved, as it only provides the coordinates of the top one. Could you indicate the output of this file with all the poses?

zjujdj commented 7 months ago

@CamilaClemente ,in plants docking, revise the following function can save many poses:

def docking_results_collect(dir, pdb_id, ligand_id):
    score_csv = '%sranking.csv' % dir
    top1_pose = '%s*****_entry_00001_conf_01.mol2' % dir
    if os.path.exists(score_csv) and os.path.exists(top1_pose):
        docking_score = pd.read_csv(score_csv).TOTAL_SCORE.values[0]
        cmdline = 'mv %s %s%s_%s_%.4f.mol2' % (top1_pose, top1_pose_path, pdb_id, ligand_id, docking_score)
        os.system(cmdline)
        cmdline = 'rm -rf %s' % dir
        os.system(cmdline)`

after you get many poses from plants docking, the simplest way if to use for loop in MetalProGNet to make prediction for many poses.

CamilaClemente commented 7 months ago

Problem solved with PLANTS! thank you very much for your help and your time.

My next question is when I have a protein and several ligands for the same protein, in the receptors folder the file XXXX_ligand.mol2 how do I define it? it works for me when I do it for one ligand but not for several.

Thank you again for all your help!

zjujdj commented 7 months ago

@CamilaClemente hi, can you understand the plants_docking.py file totally? if you understand, i think you can easily revise it to to meet your need. The XXXX_ligand.mol2 in receptor folder is just used to define the receptor pocket.