changeset 3:4a71ada763cd draft

Deleted selected files

--- a/ab_haddock_format.py	Thu May 06 09:01:30 2021 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,192 +0,0 @@
-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-#
-# Copyright 2020:
-#   Francesco Ambrosetti
-#
-
-"""
-Formats the antibody to fit the HADDOCK requirements with the
-specified chain id and returns the list of residues belonging
-to the HV loops defined according to the HADDOCK friendly format.
-
-*** The antibody has to be numbered according to the Chothia scheme ***
-
-Usage:
-    python haddock-format.py <chothia numbered antibody> <output .pdb file> <chain_id>
-
-Example:
-    python 4G6K_ch.pdb 4G6K-HADDOCK.pdb A
-
-Author: {0}
-Email: {1}
-"""
-
-import argparse
-import biopandas.pdb as bp
-import copy as cp
-import os
-import sys
-
-__author__ = "Francesco Ambrosetti"
-__email__ = "[e-mail]"
-USAGE = __doc__.format(__author__, __email__)
-
-
-def check_input():
-    """
-    Check and collect the script inputs
-    Returns:
-        args.pdb (str): path to the pdb-file
-        args.chain (str): chain id to use for the HADDOCK-formatted structure
-    """
-
-    # Parse command line arguments
-    parser = argparse.ArgumentParser(
-        description=USAGE,
-        formatter_class=argparse.RawTextHelpFormatter)
-    parser.add_argument('pdb', help='Path to the Chothia numbered antibody PDB structure', type=str)
-    parser.add_argument('out', help='Path to the output PDB file', type=str)
-    parser.add_argument('chain', help='Chain id to use for the HADDOCK-formatted PDB structure', type=str)
-
-    args = parser.parse_args()
-
-    if not os.path.isfile(args.pdb):
-        emsg = 'ERROR!! File {0} not found or not readable\n'.format(args.pdb)
-        sys.stderr.write(emsg)
-        sys.exit(1)
-
-    if not args.pdb.endswith(".pdb"):
-        emsg = 'ERROR!! File {0} not recognize as a PDB file\n'.format(args.pdb)
-        sys.stderr.write(emsg)
-        sys.exit(1)
-
-    return args.pdb, args.out, args.chain
-
-
-def unique(sequence):
-    seen = set()
-    return [x for x in sequence if not (x in seen or seen.add(x))]
-
-
-class AbHaddockFormat:
-    """Class to renumber a Chothia antibody to make it HADDOCK-ready"""
-
-    # Loops
-    # L chain loops
-    l1 = ['26_L', '27_L', '28_L', '29_L', '30_L', '30A_L', '30B_L', '30C_L', '30D_L', '30E_L', '30F_L', '31_L', '32_L']
-    l2 = ['50_L', '50A_L', '50B_L', '50C_L', '50D_L', '50E_L', '50F_L', '51_L', '52_L']
-    l3 = ['91_L', '92_L', '93_L', '94_L', '95_L', '95A_L', '95B_L', '95C_L', '95D_L', '95E_L', '95F_L', '96_L']
-    loops_l = l1 + l2 + l3
-
-    # H chain loops
-    h1 = ['26_H', '27_H', '28_H', '29_H', '30_H', '31_H', '31A_H', '31B_H', '31C_H', '31D_H', '31E_H', '31F_H', '32_H']
-    h2 = ['52A_H', '52B_H', '52C_H', '52D_H', '52E_H', '52F_H', '53_H', '54_H', '55_H']
-    h3 = ['96_H', '97_H', '98_H', '99_H', '100_H', '100A_H', '100B_H', '100C_H', '100D_H', '100E_H', '100F_H', '100G_H',
-          '100H_H', '100I_H', '100J_H', '100K_H', '101_H']
-    loops_h = h1 + h2 + h3
-
-    def __init__(self, pdbfile, chain):
-        """
-        Constructor for the AbHaddockFormat class
-        Args:
-            pdbfile (str): path to the antibody .pdb file
-            chain (str): chain id to use for the HADDOCK-ready structure
-        """
-        self.file = pdbfile
-        self.pdb = bp.PandasPdb().read_pdb(self.file)
-        self.chain = chain
-
-    def check_chain(self):
-        """
-        Check if the antibody contains the light and heavy chain
-        Returns:
-            0
-        """
-        chain_ids = self.pdb.df['ATOM']['chain_id'].values
-
-        if 'H' not in chain_ids:
-            emsg = 'ERROR!! File {0} does not contain the heavy chain\n'.format(self.file)
-            sys.stderr.write(emsg)
-            sys.exit(1)
-
-        elif 'L' not in chain_ids:
-            emsg = 'ERROR!! File {0} does not contain the light chain\n'.format(self.file)
-            sys.stderr.write(emsg)
-            sys.exit(1)
-
-        return 0
-
-    def ab_format(self):
-        """
-        Renumbers the antibody and extract the HV residues
-
-        Returns:
-            hv_list (list): list of the HV residue numbers
-            new_pdb (biopandas.pdb.pandas_pdb.PandasPdb): HADDOCK-ready pdb
-        """
-
-        # Check antibody chain ids
-        self.check_chain()
-
-        # Modify resno to include insertions and chain id
-        resno = self.pdb.df['ATOM']['residue_number'].values
-        ins = self.pdb.df['ATOM']['insertion'].values
-        chain = self.pdb.df['ATOM']['chain_id'].values
-        ch_resno = ['{0}{1}_{2}'.format(i, j, c) for i, j, c in zip(resno, ins, chain)]
-
-        # Create new resno
-        count = 0
-        prev_resid = None
-        new_resno = []
-
-        # Renumber
-        for r in ch_resno:
-            if r != prev_resid:
-                count += 1
-                new_resno.append(count)
-                prev_resid = r
-            elif r == prev_resid:
-                new_resno.append(count)
-                prev_resid = r
-
-        # Update pdb
-        new_pdb = cp.deepcopy(self.pdb)
-        new_pdb.df['ATOM']['chain_id'] = self.chain
-        new_pdb.df['ATOM']['residue_number'] = new_resno
-        new_pdb.df['ATOM']['insertion'] = ''  # Remove insertions
-
-        # Create dictionary with old and new numbering
-        resno_dict = dict(zip(unique(ch_resno), unique(new_resno)))
-
-        # Collect HV residues with the new numbering
-        hv_list = []
-
-        # Heavy chain
-        for hv_heavy in self.loops_h:
-            if hv_heavy in resno_dict.keys():
-                hv_list.append(resno_dict[hv_heavy])
-         
-        # Light chain
-        for hv_light in self.loops_l:
-            if hv_light in resno_dict.keys():
-                hv_list.append(resno_dict[hv_light])
-
-        hv_list.sort()
-        return hv_list, new_pdb
-
-
-if __name__ == '__main__':
-
-    # Get inputs
-    pdb_file, out_file, chain_id = check_input()
-
-    # Renumber pdb file and get HV residues
-    pdb_format = AbHaddockFormat(pdb_file, chain_id)
-    hv_resno, pdb_ren = pdb_format.ab_format()
-
-    # Write pdb into a file
-    pdb_ren.to_pdb(path=out_file, records=['ATOM'], append_newline=True)
-
-    # Print HV residues
-    print(','.join(map(str, hv_resno)))