def get_rmsd(pdb1, pdb2, segments1, segments2, atom_types):
polymer1 = polymer.Polymer(pdb1)
atoms1 = get_superposable_atoms(polymer1, segments1, atom_types)
polymer2 = polymer.Polymer(pdb2)
atoms2 = get_superposable_atoms(polymer2, segments2, atom_types)
center1 = molecule.get_center(atoms1)
polymer1.transform(vector3d.Translation(-center1))
polymer2.transform(vector3d.Translation(-molecule.get_center(atoms2)))
crds1 = get_crds(atoms1)
crds2 = get_crds(atoms2)
return rmsd(crds1, crds2)
def get_best_alignment_with_residues(pdb1, pdb2, segments1, segments2,
atom_types):
polymer1 = polymer.Polymer(pdb1)
atoms1 = get_superposable_atoms(polymer1, segments1, atom_types)
polymer2 = polymer.Polymer(pdb2)
atoms2 = get_superposable_atoms(polymer2, segments2, atom_types)
center1 = molecule.get_center(atoms1)
polymer1.transform(vector3d.Translation(-center1))
polymer2.transform(vector3d.Translation(-molecule.get_center(atoms2)))
polymer2.transform(calculate_superposition_matrix(atoms1, atoms2))
residue_rmsd, overall_rmsd = residues_rmsd(atoms1, atoms2)
return residue_rmsd, overall_rmsd
def get_best_alignment(pdb1, pdb2, segments1, segments2, atom_types):
"""Returns rmsd and filename of transformed pdb2."""
polymer1 = polymer.Polymer(pdb1)
atoms1 = get_superposable_atoms(polymer1, segments1, atom_types)
polymer2 = polymer.Polymer(pdb2)
atoms2 = get_superposable_atoms(polymer2, segments2, atom_types)
center1 = molecule.get_center(atoms1)
polymer1.transform(vector3d.Translation(-center1))
polymer2.transform(vector3d.Translation(-molecule.get_center(atoms2)))
polymer2.transform(calculate_superposition_matrix(atoms1, atoms2))
rmsd = sum_rmsd(atoms1, atoms2)
return rmsd
def com_to_zero(self):
self.transform(vector3d.Translation(-self.com()))
def center_box(self):
sys.stderr.write("Centering the box around " +
str(self._box_center.x) + " " +
str(self._box_center.y) + " " +
str(self._box_center.z) + "\n")
self.transform(vector3d.Translation(-self._box_center))