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
19 from __future__
import print_function
27 def transform(input_pdb, input_lib, output_pdb):
31 mh = IMP.atom.get_by_type(orig_h, IMP.atom.RESIDUE_TYPE)
35 rl.read_library_file(input_lib)
42 rr = rc.get_rotamer(rd, 0.01)
43 rotamers.append((rd, rr))
47 for rd, rr
in rotamers:
48 for h
in IMP.atom.get_by_type(rd, IMP.atom.ATOM_TYPE):
50 at_t = at.get_atom_type()
51 if rr.get_atom_exists(at_t):
53 idx = min(rr.get_number_of_cases(at_t) - 1, 1)
54 v = rr.get_coordinates(idx, at_t)
56 xyz.set_coordinates(v)
68 if __name__ ==
'__main__':
73 P.add_option(
'--input_pdb',
'-i', action=
'store', type=
'string',
74 help=
'input PDB file (required)')
75 P.add_option(
'--input_lib',
'-l', action=
'store', type=
'string',
76 help=
'input rotamer library file (required)')
77 P.add_option(
'--output_pdb',
'-o', action=
'store', type=
'string',
78 help=
'output PDB file (required)')
79 P.add_option(
'--verbose',
'-v', action=
'store_true',
80 help=
'show more messages')
81 opts, args = P.parse_args()
83 not (opts.input_pdb
or opts.input_lib
or opts.output_pdb):
86 if not opts.input_pdb:
87 print(
'--input_pdb is required')
89 if not opts.output_pdb:
90 print(
'--output_pdb is required')
92 if not opts.input_lib:
93 print(
'--input_lib is required')
99 transform(opts.input_pdb, opts.input_lib, opts.output_pdb)