pri-score.py

# Sebastian Raschka 2018
# https://sebastianraschka.com
#
#
# The Protein Recognition Index (PRI)
# measures the similarity between H-bonding
# features in a given complex (predicted or designed)
# and the characteristic H-bond trends from crystallographic complexes.
#
# Source Code Repository: https://github.com/psa-lab/Protein-Recognition-Index
# Documentation: https://psa-lab.github.io/Protein-Recognition-Index
#
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#    Copyright 2018 Michigan State University
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#    The Protein Recognition Index (PRI) software was developed
#    by Sebastian Raschka and Leslie A. Kuhn
#    in the Protein Structure Lab
#    (http://www.kuhnlab.bmb.msu.edu) at Michigan State University.
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import sys


RESIDUE_ATOM = {
 "ALA": {
  "N": {
   "Acceptor": 0,
   "Donor": 18
  },
  "O": {
   "Acceptor": 10,
   "Donor": 0
  }
 },
 "ARG": {
  "N": {
   "Acceptor": 0,
   "Donor": 5
  },
  "NE": {
   "Acceptor": 0,
   "Donor": 28
  },
  "NH1": {
   "Acceptor": 0,
   "Donor": 63
  },
  "NH2": {
   "Acceptor": 0,
   "Donor": 84
  },
  "O": {
   "Acceptor": 8,
   "Donor": 0
  }
 },
 "ASN": {
  "N": {
   "Acceptor": 0,
   "Donor": 10
  },
  "ND2": {
   "Acceptor": 0,
   "Donor": 43
  },
  "O": {
   "Acceptor": 6,
   "Donor": 0
  },
  "OD1": {
   "Acceptor": 13,
   "Donor": 0
  }
 },
 "ASP": {
  "N": {
   "Acceptor": 0,
   "Donor": 4
  },
  "O": {
   "Acceptor": 7,
   "Donor": 0
  },
  "OD1": {
   "Acceptor": 51,
   "Donor": 0
  },
  "OD2": {
   "Acceptor": 57,
   "Donor": 0
  }
 },
 "CYS": {
  "N": {
   "Acceptor": 0,
   "Donor": 5
  },
  "O": {
   "Acceptor": 3,
   "Donor": 0
  }
 },
 "GLN": {
  "N": {
   "Acceptor": 0,
   "Donor": 4
  },
  "NE2": {
   "Acceptor": 0,
   "Donor": 23
  },
  "O": {
   "Acceptor": 5,
   "Donor": 0
  },
  "OE1": {
   "Acceptor": 8,
   "Donor": 0
  }
 },
 "GLU": {
  "N": {
   "Acceptor": 0,
   "Donor": 2
  },
  "O": {
   "Acceptor": 1,
   "Donor": 0
  },
  "OE1": {
   "Acceptor": 27,
   "Donor": 0
  },
  "OE2": {
   "Acceptor": 30,
   "Donor": 0
  }
 },
 "GLY": {
  "N": {
   "Acceptor": 0,
   "Donor": 53
  },
  "O": {
   "Acceptor": 20,
   "Donor": 0
  }
 },
 "HIS": {
  "N": {
   "Acceptor": 0,
   "Donor": 3
  },
  "ND1": {
   "Acceptor": 0,
   "Donor": 7
  },
  "NE2": {
   "Acceptor": 2,
   "Donor": 20
  },
  "O": {
   "Acceptor": 6,
   "Donor": 0
  }
 },
 "ILE": {
  "N": {
   "Acceptor": 0,
   "Donor": 8
  },
  "O": {
   "Acceptor": 6,
   "Donor": 0
  }
 },
 "LEU": {
  "N": {
   "Acceptor": 0,
   "Donor": 6
  },
  "O": {
   "Acceptor": 6,
   "Donor": 0
  }
 },
 "LYS": {
  "N": {
   "Acceptor": 0,
   "Donor": 17
  },
  "NZ": {
   "Acceptor": 0,
   "Donor": 67
  },
  "O": {
   "Acceptor": 2,
   "Donor": 0
  }
 },
 "MET": {
  "N": {
   "Acceptor": 0,
   "Donor": 7
  },
  "O": {
   "Acceptor": 2,
   "Donor": 0
  }
 },
 "PHE": {
  "N": {
   "Acceptor": 0,
   "Donor": 4
  },
  "O": {
   "Acceptor": 4,
   "Donor": 0
  }
 },
 "PRO": {
  "O": {
   "Acceptor": 7,
   "Donor": 0
  }
 },
 "SER": {
  "N": {
   "Acceptor": 0,
   "Donor": 33
  },
  "O": {
   "Acceptor": 10,
   "Donor": 0
  },
  "OG": {
   "Acceptor": 8,
   "Donor": 56
  }
 },
 "THR": {
  "N": {
   "Acceptor": 0,
   "Donor": 22
  },
  "O": {
   "Acceptor": 3,
   "Donor": 0
  },
  "OG1": {
   "Acceptor": 7,
   "Donor": 42
  }
 },
 "TRP": {
  "N": {
   "Acceptor": 0,
   "Donor": 6
  },
  "NE1": {
   "Acceptor": 0,
   "Donor": 10
  },
  "O": {
   "Acceptor": 3,
   "Donor": 0
  }
 },
 "TYR": {
  "N": {
   "Acceptor": 0,
   "Donor": 5
  },
  "O": {
   "Acceptor": 5,
   "Donor": 0
  },
  "OH": {
   "Acceptor": 16,
   "Donor": 37
  }
 },
 "VAL": {
  "N": {
   "Acceptor": 0,
   "Donor": 20
  },
  "O": {
   "Acceptor": 12,
   "Donor": 0
  }
 }
}

LIGAND = {
 "Acceptor": 712,
 "Atom": {
  "F": {
   "Acceptor": 2,
   "Donor": 0,
   "Metal": 0
  },
  "N.2": {
   "Acceptor": 14,
   "Donor": 2,
   "Metal": 1
  },
  "N.3": {
   "Acceptor": 0,
   "Donor": 3,
   "Metal": 0
  },
  "N.4": {
   "Acceptor": 0,
   "Donor": 64,
   "Metal": 0
  },
  "N.am": {
   "Acceptor": 4,
   "Donor": 70,
   "Metal": 0
  },
  "N.ar": {
   "Acceptor": 41,
   "Donor": 0,
   "Metal": 1
  },
  "N.pl3": {
   "Acceptor": 0,
   "Donor": 81,
   "Metal": 1
  },
  "O.2": {
   "Acceptor": 221,
   "Donor": 0,
   "Metal": 11
  },
  "O.3": {
   "Acceptor": 268,
   "Donor": 125,
   "Metal": 37
  },
  "O.co2": {
   "Acceptor": 162,
   "Donor": 0,
   "Metal": 9
   }
  }
 }


PROT_MU = 298.139705882
PROT_SIGMA = 213.78356884
LIG_MU = 1323.53676471
LIG_SIGMA = 1022.75276545


def calc_pri(txt):

    pri_lig, pri_prot = 0, 0

    for line in txt.split('\n'):
        if not line.startswith('| hbond'):
            continue
        lig_data, prot_data = line.split('--')
        prot_data = prot_data.split()
        prot_type = prot_data[-1]
        lig_type = prot_data[-3]
        prot_residue = prot_data[0]
        prot_atomtype = prot_data[3]
        lig_atomtype = lig_data.split()[4]

        pri_prot += RESIDUE_ATOM[prot_residue][prot_atomtype][prot_type]
        pri_lig += LIGAND['Atom'][lig_atomtype][lig_type]

    pri = ((pri_lig - LIG_MU)/LIG_SIGMA) + ((pri_prot - PROT_MU)/PROT_SIGMA)

    return pri_prot, pri_lig, pri


if __name__ == '__main__':

    s = """
Protein Recognition Index, version 1.0.0

Documentation: http://psa-lab.github.io/protein-recognition-index
Raschka, Wolf, Bemister-Buffington, Kuhn (2018)
Protein Structure and Analysis Lab, MSU (http://kuhnlab.bmb.msu.edu)
    """
    print(s)

    usage = "\nUSAGE: python code/pri-score.py hbind_table.txt\n"

    if len(sys.argv) < 2:
        print("Argument Error: Missing Hbind table path on the command line")
        print(usage)
        sys.exit()

    in_file = sys.argv[1]

    try:
        with open(in_file, 'r') as f:
            txt = f.read()
    except FileNotFoundError as e:
        print(e)
        print(usage)
        sys.exit()

    pri_prot, pri_lig, pri = calc_pri(txt)

    print('Protein PRI: %d' % pri_prot)
    print('Ligand PRI: %d' % pri_lig)
    print('PRI: %.3f' % pri)