IMP  2.4.0
The Integrative Modeling Platform
rotamer/rotamer_pdb.py

rotamer_pdb.py is a script demonstrating the usage of RotamerCalculator and RotamerLibrary. It reads a PDB file and a rotamer library file, and tries to rotate the atoms based on the most probable chi angles from the rotamer library. Then it saves the rotated atoms to a specified output PDB file.

Usage:

python rotamer_pdb.py -i <input>.pdb -l <rotamer_library>.lib -o <output>.pdb

Example (the result will be saved into transformed_1z5s_A.pdb):

../../../tools/imppy.sh python rotamer_pdb.py -i ../../atom/test/input/1z5s_A.pdb \ -l /path/to/ALL.bbdep.rotamers.lib -o transformed_1z5s_A.pdb

1 ## \example rotamer/rotamer_pdb.py
2 # rotamer_pdb.py is a script demonstrating the usage of RotamerCalculator and RotamerLibrary.
3 # It reads a PDB file and a rotamer library file, and tries to rotate the atoms based on the most
4 # probable chi angles from the rotamer library. Then it saves the rotated atoms to a specified output
5 # PDB file.
6 #
7 # Usage:
8 #
9 # `python rotamer_pdb.py -i <input>.pdb -l <rotamer_library>.lib -o <output>.pdb`
10 #
11 # Example (the result will be saved into transformed_1z5s_A.pdb):
12 #
13 # `../../../tools/imppy.sh python rotamer_pdb.py -i ../../atom/test/input/1z5s_A.pdb \
14 # -l /path/to/ALL.bbdep.rotamers.lib -o transformed_1z5s_A.pdb`
15 #
16 
17 #!/usr/bin/env python
18 
19 from __future__ import print_function
20 import IMP
21 import IMP.base
22 import IMP.core
23 import IMP.atom
24 import IMP.algebra
25 import IMP.rotamer
26 
27 
28 def transform(input_pdb, input_lib, output_pdb):
29  # read the original PDB
30  m = IMP.kernel.Model()
31  orig_h = IMP.atom.read_pdb(input_pdb, m)
32  mh = IMP.atom.get_by_type(orig_h, IMP.atom.RESIDUE_TYPE)
33 
34  # read rotamer library
35  rl = IMP.rotamer.RotamerLibrary()
36  rl.read_library_file(input_lib)
37  rc = IMP.rotamer.RotamerCalculator(rl)
38 
39  # get the most probable rotamers
40  rotamers = list()
41  for h in mh:
42  rd = h.get_as_residue()
43  rr = rc.get_rotamer(rd, 0.01)
44  rotamers.append((rd, rr))
45 
46  # now set the coordinates of all atoms in the residues to the rotated
47  # coordinates
48  for rd, rr in rotamers:
49  for h in IMP.atom.get_by_type(rd, IMP.atom.ATOM_TYPE):
50  at = h.get_as_atom()
51  at_t = at.get_atom_type()
52  if rr.get_atom_exists(at_t):
53  # some atoms might not be rotated
54  idx = min(rr.get_number_of_cases(at_t) - 1, 1)
55  v = rr.get_coordinates(idx, at_t)
56  xyz = IMP.core.XYZ(at)
57  xyz.set_coordinates(v)
58 
59  # save the rotated atoms to output PDB
60  IMP.atom.write_pdb(orig_h, output_pdb)
61 
62 
63 def quick_test():
64  rl = IMP.rotamer.RotamerLibrary()
65  rc = IMP.rotamer.RotamerCalculator(rl)
66  rc.set_was_used(True)
67 
68 
69 if __name__ == '__main__':
70 
71  import sys
72 
73  P = IMP.OptionParser()
74  P.add_option('--input_pdb', '-i', action='store', type='string',
75  help='input PDB file (required)')
76  P.add_option('--input_lib', '-l', action='store', type='string',
77  help='input rotamer library file (required)')
78  P.add_option('--output_pdb', '-o', action='store', type='string',
79  help='output PDB file (required)')
80  P.add_option('--verbose', '-v', action='store_true',
81  help='show more messages')
82  opts, args = P.parse_args()
83  if IMP.base.get_bool_flag('run_quick_test') or \
84  not (opts.input_pdb or opts.input_lib or opts.output_pdb):
85  quick_test()
86  sys.exit(0)
87  if not opts.input_pdb:
88  print('--input_pdb is required')
89  sys.exit(1)
90  if not opts.output_pdb:
91  print('--output_pdb is required')
92  sys.exit(1)
93  if not opts.input_lib:
94  print('--input_lib is required')
95  sys.exit(1)
96  if opts.verbose:
97  IMP.base.set_log_level(IMP.base.VERBOSE)
98  else:
99  IMP.base.set_log_level(IMP.base.SILENT)
100  transform(opts.input_pdb, opts.input_lib, opts.output_pdb)