chimera_models.py

#!/usr/bin/env python

__doc__ = "Generate complete models from Chimera transformations file."

import sys
import IMP
import IMP.atom
from IMP import OptionParser


def parse_args():
    usage = """%prog [options] <subunit> <symmetry degree>
          <transformations file> <number of models> <output models>

This script, given the structure of a single subunit and the Chimera
transformations file, applies the transformations to generate a number of
complete models.

  <subunit>               subunit PDB, the same given to MultiFit.
  <symmetry degree>       Cn degree.
  <transformations file>  MultiFit output in chimera output format.
  <number of models>      number of models to print.
  <output models>         Solutions are written as output.i.pdb."""
    parser = OptionParser(usage)
    opts, args = parser.parse_args()
    if len(args) != 5:
        parser.error("incorrect number of arguments")
    return args


def get_transformations(sol):
    [ind, dock_rot_s, dock_trans_s, fit_rot_s,
        fit_trans_s, cc_s] = sol.split("|")
    s = dock_rot_s.split(" ")
    s1 = dock_trans_s.split(" ")
    dock_t = IMP.algebra.Transformation3D(
        IMP.algebra.get_rotation_from_matrix(
            float(s[0]), float(s[1]), float(s[2]),
            float(s[3]), float(s[4]), float(s[5]),
            float(s[6]), float(s[7]), float(s[8])),
        IMP.algebra.Vector3D(float(s1[0]), float(s1[1]), float(s1[2])))
    s = fit_rot_s.split(" ")
    s1 = fit_trans_s.split(" ")
    fit_t = IMP.algebra.Transformation3D(
        IMP.algebra.get_rotation_from_matrix(
            float(s[0]), float(s[1]), float(s[2]),
            float(s[3]), float(s[4]), float(s[5]),
            float(s[6]), float(s[7]), float(s[8])),
        IMP.algebra.Vector3D(float(s1[0]), float(s1[1]), float(s1[2])))
    return dock_t, fit_t


def run(subunit_fn, symm_deg, sol_fn, num, output_fn):
    mdl = IMP.Model()
    mhs = []
    for i in range(symm_deg):
        mh = IMP.atom.read_pdb(subunit_fn, mdl)
        mhs.append(mh)
        IMP.atom.setup_as_rigid_body(mh)
    lines = open(sol_fn).readlines()
    for j, sol in enumerate(lines[:num]):
        dock_t, fit_t = get_transformations(sol)
        curr_t = dock_t
        for i in range(symm_deg):
            IMP.core.transform(IMP.core.RigidBody(mhs[i]), curr_t)
            curr_t = dock_t * curr_t
        for i in range(symm_deg):
            IMP.core.transform(IMP.core.RigidBody(mhs[i]), fit_t)
        IMP.atom.write_pdb(mhs, output_fn + ".%03d.pdb" % j)


def main():
    args = parse_args()
    run(args[0], int(args[1]), args[2], int(args[3]), args[4])

if __name__ == "__main__":
    main()