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Preprocessing

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distmaps
distmaps
 
 
input
input
 
 
input_details
input_details
 
 
processed_features
processed_features
 
 
supporting_scripts
supporting_scripts
 
 
tmp
tmp
 
 
atomic_feature.py
atomic_feature.py
 
 
dssp2aa.py
dssp2aa.py
 
 
extract_dssp_feat.py
extract_dssp_feat.py
 
 
extract_dssp_feat2.py
extract_dssp_feat2.py
 
 
gen_aa_structural_features.py
gen_aa_structural_features.py
 
 
gen_preprocessed_node_features.py
gen_preprocessed_node_features.py
 
 
genpssmto20feat.py
genpssmto20feat.py
 
 
imputed_tetrahedral_geom_feature.py
imputed_tetrahedral_geom_feature.py
 
 
input.list
input.list
 
 
pdb2rr.py
pdb2rr.py
 
 
prepare_25normal_contactcount.py
prepare_25normal_contactcount.py
 
 
prepare_pdb_feature.py
prepare_pdb_feature.py
 
 
prepare_pdb_feature1cd8ss8sa5angle.py
prepare_pdb_feature1cd8ss8sa5angle.py
 
 
prepare_pdb_feature_phi_psi_alpha_sin_cos.py
prepare_pdb_feature_phi_psi_alpha_sin_cos.py
 
 
prepare_pdb_feature_rev_frwd_ca.py
prepare_pdb_feature_rev_frwd_ca.py
 
 
readme.md
readme.md
 
 

readme.md

All input PDB chains, DSSP, FASTA, PSSM, and ESM2 files should be inside input/ directory

All distance maps should be inside distmaps/. An example distance map can be found here

Target list: input.list

  1. Run gen_aa_structural_features.py (feature files will be saved in tmp/ directory)

python gen_aa_structural_features.py -t input.list

  1. Run genpssmto20feat.py (feature files will be saved in tmp/ directory)

python genpssmto20feat.py -i input -o tmp/ -t input.list

  1. Run gen_preprocessed_node_features.py to get combined features generated in processed_features/ directory

python gen_preprocessed_node_features.py -t input.list