py3 for datasets/construct_pdbbind_df.py

Contains methods for generating a pdbbind dataset mapping

  complexes (protein + ligand) to experimental binding measurement.

"""

from __future__ import print_function

import pickle

import os

import pandas as pd

  pdb_directories = [pdb.replace('/', '') for pdb in glob('*/')]

  for pdb_dir in pdb_directories:

    print "About to extract ligand and protein input files"

    print("About to extract ligand and protein input files")

    pdb_id = os.path.basename(pdb_dir)

    ligand_pdb = None

    protein_pdb = None

      elif re.search("_ligand.mol2$", f):

        ligand_mol2 = f

    print "Extracted Input Files:"

    print("Extracted Input Files:")

    print (ligand_pdb, protein_pdb, ligand_mol2)

    if not ligand_pdb or not protein_pdb or not ligand_mol2:

      raise ValueError("Required files not present for %s" % pdb_dir)

    except:

      ligand_mol2_lines = []

    print "About to compute ligand smiles string."

    print("About to compute ligand smiles string.")

    ligand_mol = Chem.MolFromPDBFile(ligand_pdb_path)

    if ligand_mol is None:

      continue