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1 #!/usr/bin/env python
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2 # -*- coding: utf-8 -*-
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3 #
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4 # Copyright 2020:
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5 # Francesco Ambrosetti
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6 #
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7
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8 """
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9 Formats the antibody to fit the HADDOCK requirements with the
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10 specified chain id and returns the list of residues belonging
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11 to the HV loops defined according to the HADDOCK friendly format.
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12
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13 *** The antibody has to be numbered according to the Chothia scheme ***
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14
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15 Usage:
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16 python haddock-format.py <chothia numbered antibody> <output .pdb file> <chain_id>
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17
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18 Example:
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19 python 4G6K_ch.pdb 4G6K-HADDOCK.pdb A
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20
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21 Author: {0}
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22 Email: {1}
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23 """
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24
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25 import argparse
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26 import biopandas.pdb as bp
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27 import copy as cp
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28 import os
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29 import sys
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30
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31 __author__ = "Francesco Ambrosetti"
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32 __email__ = "ambrosetti.francesco@gmail.com"
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33 USAGE = __doc__.format(__author__, __email__)
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34
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35
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36 def check_input():
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37 """
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38 Check and collect the script inputs
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39 Returns:
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40 args.pdb (str): path to the pdb-file
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41 args.chain (str): chain id to use for the HADDOCK-formatted structure
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42 """
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43
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44 # Parse command line arguments
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45 parser = argparse.ArgumentParser(
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46 description=USAGE,
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47 formatter_class=argparse.RawTextHelpFormatter)
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48 parser.add_argument('pdb', help='Path to the Chothia numbered antibody PDB structure', type=str)
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49 parser.add_argument('out', help='Path to the output PDB file', type=str)
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50 parser.add_argument('chain', help='Chain id to use for the HADDOCK-formatted PDB structure', type=str)
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51
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52 args = parser.parse_args()
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53
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54 if not os.path.isfile(args.pdb):
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55 emsg = 'ERROR!! File {0} not found or not readable\n'.format(args.pdb)
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56 sys.stderr.write(emsg)
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57 sys.exit(1)
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58
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59 if not args.pdb.endswith(".pdb"):
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60 emsg = 'ERROR!! File {0} not recognize as a PDB file\n'.format(args.pdb)
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61 sys.stderr.write(emsg)
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62 sys.exit(1)
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63
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64 return args.pdb, args.out, args.chain
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65
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66
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67 def unique(sequence):
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68 seen = set()
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69 return [x for x in sequence if not (x in seen or seen.add(x))]
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70
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71
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72 class AbHaddockFormat:
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73 """Class to renumber a Chothia antibody to make it HADDOCK-ready"""
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74
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75 # Loops
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76 # L chain loops
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77 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']
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78 l2 = ['50_L', '50A_L', '50B_L', '50C_L', '50D_L', '50E_L', '50F_L', '51_L', '52_L']
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79 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']
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80 loops_l = l1 + l2 + l3
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81
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82 # H chain loops
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83 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']
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84 h2 = ['52A_H', '52B_H', '52C_H', '52D_H', '52E_H', '52F_H', '53_H', '54_H', '55_H']
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85 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',
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86 '100H_H', '100I_H', '100J_H', '100K_H', '101_H']
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87 loops_h = h1 + h2 + h3
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88
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89 def __init__(self, pdbfile, chain):
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90 """
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91 Constructor for the AbHaddockFormat class
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92 Args:
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93 pdbfile (str): path to the antibody .pdb file
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94 chain (str): chain id to use for the HADDOCK-ready structure
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95 """
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96 self.file = pdbfile
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97 self.pdb = bp.PandasPdb().read_pdb(self.file)
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98 self.chain = chain
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99
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100 def check_chain(self):
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101 """
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102 Check if the antibody contains the light and heavy chain
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103 Returns:
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104 0
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105 """
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106 chain_ids = self.pdb.df['ATOM']['chain_id'].values
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107
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108 if 'H' not in chain_ids:
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109 emsg = 'ERROR!! File {0} does not contain the heavy chain\n'.format(self.file)
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110 sys.stderr.write(emsg)
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111 sys.exit(1)
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112
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113 elif 'L' not in chain_ids:
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114 emsg = 'ERROR!! File {0} does not contain the light chain\n'.format(self.file)
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115 sys.stderr.write(emsg)
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116 sys.exit(1)
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117
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118 return 0
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119
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120 def ab_format(self):
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121 """
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122 Renumbers the antibody and extract the HV residues
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123
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124 Returns:
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125 hv_list (list): list of the HV residue numbers
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126 new_pdb (biopandas.pdb.pandas_pdb.PandasPdb): HADDOCK-ready pdb
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127 """
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128
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129 # Check antibody chain ids
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130 self.check_chain()
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131
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132 # Modify resno to include insertions and chain id
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133 resno = self.pdb.df['ATOM']['residue_number'].values
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134 ins = self.pdb.df['ATOM']['insertion'].values
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135 chain = self.pdb.df['ATOM']['chain_id'].values
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136 ch_resno = ['{0}{1}_{2}'.format(i, j, c) for i, j, c in zip(resno, ins, chain)]
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137
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138 # Create new resno
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139 count = 0
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140 prev_resid = None
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141 new_resno = []
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142
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143 # Renumber
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144 for r in ch_resno:
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145 if r != prev_resid:
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146 count += 1
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147 new_resno.append(count)
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148 prev_resid = r
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149 elif r == prev_resid:
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150 new_resno.append(count)
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151 prev_resid = r
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152
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153 # Update pdb
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154 new_pdb = cp.deepcopy(self.pdb)
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155 new_pdb.df['ATOM']['chain_id'] = self.chain
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156 new_pdb.df['ATOM']['residue_number'] = new_resno
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157 new_pdb.df['ATOM']['insertion'] = '' # Remove insertions
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158
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159 # Create dictionary with old and new numbering
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160 resno_dict = dict(zip(unique(ch_resno), unique(new_resno)))
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161
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162 # Collect HV residues with the new numbering
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163 hv_list = []
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164
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165 # Heavy chain
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166 for hv_heavy in self.loops_h:
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167 if hv_heavy in resno_dict.keys():
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168 hv_list.append(resno_dict[hv_heavy])
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169
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170 # Light chain
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171 for hv_light in self.loops_l:
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172 if hv_light in resno_dict.keys():
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173 hv_list.append(resno_dict[hv_light])
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174
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175 hv_list.sort()
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176 return hv_list, new_pdb
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177
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178
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179 if __name__ == '__main__':
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180
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181 # Get inputs
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182 pdb_file, out_file, chain_id = check_input()
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183
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184 # Renumber pdb file and get HV residues
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185 pdb_format = AbHaddockFormat(pdb_file, chain_id)
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186 hv_resno, pdb_ren = pdb_format.ab_format()
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187
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188 # Write pdb into a file
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189 pdb_ren.to_pdb(path=out_file, records=['ATOM'], append_newline=True)
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190
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191 # Print HV residues
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192 print(','.join(map(str, hv_resno)))
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