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# Copyright (C) 2002, Thomas Hamelryck (thamelry@binf.ku.dk)
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""Superimpose two structures."""
from __future__ import print_function
import numpy
from Bio.SVDSuperimposer import SVDSuperimposer
from Bio.PDB.PDBExceptions import PDBException
class Superimposer(object):
"""
Rotate/translate one set of atoms on top of another,
thereby minimizing the RMSD.
"""
def __init__(self):
self.rotran=None
self.rms=None
def set_atoms(self, fixed, moving):
"""
Put (translate/rotate) the atoms in fixed on the atoms in
moving, in such a way that the RMSD is minimized.
@param fixed: list of (fixed) atoms
@param moving: list of (moving) atoms
@type fixed,moving: [L{Atom}, L{Atom},...]
"""
if not (len(fixed)==len(moving)):
raise PDBException("Fixed and moving atom lists differ in size")
l=len(fixed)
fixed_coord=numpy.zeros((l, 3))
moving_coord=numpy.zeros((l, 3))
for i in range(0, len(fixed)):
fixed_coord[i]=fixed[i].get_coord()
moving_coord[i]=moving[i].get_coord()
sup=SVDSuperimposer()
sup.set(fixed_coord, moving_coord)
sup.run()
self.rms=sup.get_rms()
self.rotran=sup.get_rotran()
def apply(self, atom_list):
"""
Rotate/translate a list of atoms.
"""
if self.rotran is None:
raise PDBException("No transformation has been calculated yet")
rot, tran=self.rotran
rot=rot.astype('f')
tran=tran.astype('f')
for atom in atom_list:
atom.transform(rot, tran)
if __name__=="__main__":
import sys
from Bio.PDB import PDBParser, Selection
p=PDBParser()
s1=p.get_structure("FIXED", sys.argv[1])
fixed=Selection.unfold_entities(s1, "A")
s2=p.get_structure("MOVING", sys.argv[1])
moving=Selection.unfold_entities(s2, "A")
rot=numpy.identity(3).astype('f')
tran=numpy.array((1.0, 2.0, 3.0), 'f')
for atom in moving:
atom.transform(rot, tran)
sup=Superimposer()
sup.set_atoms(fixed, moving)
print(sup.rotran)
print(sup.rms)
sup.apply(moving)
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