def get_pdb_transform(pdb, center_res, top_res):
"""
Returns a transformation matrix that centers pdb to
center_res on the z-axis and moves top_res above center_res
on the y-axis
"""
soup = pdbatoms.Soup(pdb)
atoms = soup.atoms()
soup_center = pdbatoms.get_center(atoms)
translation = v3.translation(-soup_center)
soup.transform(translation)
result = translation
center_atom = find_ca_of_resname(soup.atoms(), center_res)
view = v3.vector(0, 0, 1)
axis = v3.cross(view, center_atom.pos)
angle = v3.vec_dihedral(view, axis, center_atom.pos)
rotation = v3.rotation(axis, angle)
soup.transform(rotation)
result = v3.combine(rotation, result)
top_atom = find_ca_of_resname(soup.atoms(), top_res)
top_dir = v3.vector(0, 1, 0)
axis = view.copy()
angle = v3.vec_dihedral(top_dir, axis, top_atom.pos)
rotation2 = v3.rotation(axis, angle)
result = v3.combine(rotation2, result)
del soup
return result
def get_pdb_transform(pdb, center_res, top_res): """ Returns a transformation matrix that centers pdb to center_res on the z-axis and moves top_res above center_res on the y-axis """ soup = pdbatoms.Soup(pdb) atoms = soup.atoms() soup_center = pdbatoms.get_center(atoms) translation = v3.translation(-soup_center) soup.transform(translation) result = translation center_atom = find_ca_of_resname(soup.atoms(), center_res) view = v3.vector(0, 0, 1) axis = v3.cross(view, center_atom.pos) angle = v3.vec_dihedral(view, axis, center_atom.pos) rotation = v3.rotation(axis, angle) soup.transform(rotation) result = v3.combine(rotation, result) top_atom = find_ca_of_resname(soup.atoms(), top_res) top_dir = v3.vector(0, 1, 0) axis = view.copy() angle = v3.vec_dihedral(top_dir, axis, top_atom.pos) rotation2 = v3.rotation(axis, angle) result = v3.combine(rotation2, result) del soup return result
def rmsd_of_soups(soup1,
soup2,
segments1=[],
segments2=[],
atom_types=['CA'],
transform_pdb1=None):
"""
Returns the RMSD between two PDB structures and optionally
writes the best transformed structure of pdb1 in transform_pdb.
By default, it chooses the CA atoms in the soup.
Args:
segments1 (list): list of pairs of residue names in pdb1,
such as ['A:1','A:3'], interpreted as the
two ends of a fragment in soup that we want
the atom index of
segments2 (list): same as above but for pdb2
atom_types (list): list of atom_types in the residues that
we want to generate the indices from.
"""
atoms1 = get_superposable_atoms(soup1, segments1, atom_types)
atoms2 = get_superposable_atoms(soup2, segments2, atom_types)
crds1 = [a.pos for a in atoms1]
crds2 = [a.pos for a in atoms2]
center1 = v3.get_center(crds1)
center2 = v3.get_center(crds2)
soup1.transform(v3.translation(-center1))
soup2.transform(v3.translation(-center2))
rmsd, transform_1_to_2 = calc_rmsd_rot(crds1, crds2)
if not transform_pdb1:
return rmsd
soup1.transform(transform_1_to_2)
soup1.transform(v3.translation(center2))
soup2.transform(v3.translation(center2))
soup1.write_pdb(transform_pdb1)
return sum_rmsd(crds1, crds2)
def rmsd_of_soups(
soup1, soup2, segments1=[], segments2=[],
atom_types=['CA'], transform_pdb1=None):
"""
Returns the RMSD between two PDB structures and optionally
writes the best transformed structure of pdb1 in transform_pdb.
By default, it chooses the CA atoms in the soup.
Args:
segments1 (list): list of pairs of residue names in pdb1,
such as ['A:1','A:3'], interpreted as the
two ends of a fragment in soup that we want
the atom index of
segments2 (list): same as above but for pdb2
atom_types (list): list of atom_types in the residues that
we want to generate the indices from.
"""
atoms1 = get_superposable_atoms(soup1, segments1, atom_types)
atoms2 = get_superposable_atoms(soup2, segments2, atom_types)
crds1 = [a.pos for a in atoms1]
crds2 = [a.pos for a in atoms2]
center1 = v3.get_center(crds1)
center2 = v3.get_center(crds2)
soup1.transform(v3.translation(-center1))
soup2.transform(v3.translation(-center2))
rmsd, transform_1_to_2 = calc_rmsd_rot(crds1, crds2)
if not transform_pdb1:
return rmsd
soup1.transform(transform_1_to_2)
soup1.transform(v3.translation(center2))
soup2.transform(v3.translation(center2))
soup1.write_pdb(transform_pdb1)
return sum_rmsd(crds1, crds2)
