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TencentAI4S / tfold

open source code for Tencent tFold
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icf.files.ppi #8

Closed chiarinival closed 2 months ago

chiarinival commented 6 months ago

Hi!!!

Congratulation for the amazing work!! I would like to ask about the following line:

generate inter-chain feature (ppi)

python projects/tfold_ag/gen_icf_feat.py --pid_fpath=examples/prot_ids.abag.txt --fas_dpath=examples/fasta.files --pdb_dpath=examples/pdb.files.native --icf_dpath=examples/icf.files.ppi --icf_type=ppi

if it was possible to have a look a the "icf.files.ppi" which seems to be missing in the repository. Given that I assume it to be the output, does it calculate it directly from the input structures? Should the user input the ppi from some experimental evidence in the prediction script:

antibody-antigen complex prediction with inter-chain feature

python projects/tfold_ag/predict.py --pid_fpath=examples/prot_ids.abag.txt --fas_dpath=examples/fasta.files --msa_fpath=examples/msa.files/8df5_R.a3m --pdb_dpath=examples/pdb.files.abag --icf_dpath=examples/icf.files.ppi --model_ver=ppi

Could you provide some examples? All the rest (fasta.files/prot_ids.abag.txt etc) seems pretty clear.

Thanks a lot!!!

Valerio

Cloud-Rambler commented 6 months ago

Hi!!!

Congratulation for the amazing work!! I would like to ask about the following line:

generate inter-chain feature (ppi)

python projects/tfold_ag/gen_icf_feat.py --pid_fpath=examples/prot_ids.abag.txt --fas_dpath=examples/fasta.files --pdb_dpath=examples/pdb.files.native --icf_dpath=examples/icf.files.ppi --icf_type=ppi

if it was possible to have a look a the "icf.files.ppi" which seems to be missing in the repository. Given that I assume it to be the output, does it calculate it directly from the input structures? Should the user input the ppi from some experimental evidence in the prediction script:

antibody-antigen complex prediction with inter-chain feature

python projects/tfold_ag/predict.py --pid_fpath=examples/prot_ids.abag.txt --fas_dpath=examples/fasta.files --msa_fpath=examples/msa.files/8df5_R.a3m --pdb_dpath=examples/pdb.files.abag --icf_dpath=examples/icf.files.ppi --model_ver=ppi

Could you provide some examples? All the rest (fasta.files/prot_ids.abag.txt etc) seems pretty clear.

Thanks a lot!!!

Valerio

Thank you for your interest in our work. I've put the files on ppi in the examples/icf.files.ppi directory. You can check this using pytorch. The contents of one of these files are shown below. 1 represents contact and 0 is no contact.

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