modularized custom pdb functions

pdb_processor.py

@@ -0,0 +1,103 @@
+# -*- coding: utf-8 -*-
+"""
+Created on Mon Jan 13 18:13:15 2020
+
+@author: Saint8312
+
+"""
+
+"""
+dedicated file which contain functions to process custom PDB files
+req : biopandas
+"""
+
+import pandas as pd
+from biopandas.pdb import PandasPdb
+import os
+import itertools
+
+
+def list_files(root_path):
+ return [f for f in os.listdir(root_path) if os.path.isfile(os.path.join(root_path, f))]
+
+def load_custom_pdb(filepath):
+ '''
+ get the 'ATOM' key and set the line index as default index
+ '''
+ ppdb = PandasPdb()
+ ppdb.read_pdb(test_file)
+ df_atoms = ppdb.df["ATOM"].set_index(["line_idx"])
+ return df_atoms
+
+def get_chain_terminals(filepath):
+ """
+ get the terminal indexes in the case of complexes with multiple protein chains
+ """
+ idxes = []
+ idx = 0
+ with open(test_file, 'r') as f:
+ for line in f:
+ if line.startswith('TER'):
+ idxes.append(idx)
+ idx+=1
+ return idxes
+
+def get_sliced_chains(df_atoms, terminal_idxes, zdock=False):
+ '''
+ slice the chains into list based on the "TER" indexes.
+ in case of zdock, atom types need to be added manually
+ '''
+ chains = []
+ split_idxes = []
+ if zdock:
+ #add the atom types to 'element_symbol'
+ df_atoms["element_symbol"] = df_atoms["atom_name"].apply(lambda x:x[0])
+ #get the terminal indexes
+ atom_numbers = df_atoms["atom_number"]
+ length = atom_numbers.shape[0]
+ for i in range(length-1):
+ if atom_numbers[i+1]<atom_numbers[i]:
+ split_idxes.append(i)
+ split_idxes.append(length)
+ else:
+ split_idxes = terminal_idxes
+
+ start_idx = 0
+ for idx in split_idxes:
+ chain=df_atoms.loc[start_idx:idx]
+ chains.append(chain)
+ start_idx = idx+1
+ return chains
+
+
+#####################################
+'''
+specific case/test functions
+'''
+def loader_pdbbind(filepath):
+ df_atoms = load_custom_pdb(filepath)
+ terminal_idxes = get_chain_terminals(filepath)
+ return get_sliced_chains(df_atoms, terminal_idxes)
+
+def loader_zdock(filepath):
+ df_atoms = load_custom_pdb(filepath)
+ terminal_idxes = get_chain_terminals(filepath)
+ return get_sliced_chains(df_atoms, terminal_idxes, zdock=True)
+
+
+if __name__ == '__main__':
+# path = 'C:/Users/beryl/Documents/Computational Science/Kanazawa/Thesis/Dataset/PP'
+ path = 'C:/Users/beryl/Documents/Computational Science/Kanazawa/Thesis/Outputs/PC-PC/top_preds'
+
+ complex_files = [f for f in os.listdir(path) if os.path.isfile(os.path.join(path, f))]
+
+# test_file = path+'/'+complex_files[2]
+# test_file = path+'/1nez.ent.pdb'
+ test_file = path+'/complex.1.pdb'
+
+ df_atoms = load_custom_pdb(test_file)
+ print(df_atoms["residue_name"])
+ terminal_idxes = get_chain_terminals(test_file)
+ chains = get_sliced_chains(df_atoms, terminal_idxes, zdock=True)
+ new_chain = chains[0].set_index(["residue_name"])
+ print(new_chain)