def get_coords(self, row, parser, chain, length=9):
backbone_atoms = self.params['backbone_atoms']
cb = self.params['cb']
stored_atoms = self.params['stored_atoms']
modelid = row['modelid']
structure = parser.get_structure(modelid, shared.strip_h(row['path']))
chainstruc = structure[0][chain]
# Don't enforce length check if length is None
if length is not None:
if len(chainstruc) != length:
raise LoadModelScoresError("%s has %s residues, expected %s" %
(modelid, len(chainstruc), length))
coordinates = list()
for x, residue in enumerate(chainstruc):
het, resi, icode = residue.id
resname = residue.resname
if het.strip(): continue
if icode.strip():
raise LoadModelScoresError("Can't handle PDB insertion code")
residue_coordinates = list()
# Load atoms
atom_coords = {
name: residue[name].coord
for name in backbone_atoms
}
if resname == "GLY":
# Generate virtual CB for GLY
vectors = {
name: residue[name].get_vector()
for name in backbone_atoms
}
# Center
n = vectors['N'] - vectors['CA']
c = vectors['C'] - vectors['CA']
# Find rotation axis around N for CA-C vector
rot = PDB.rotaxis(-np.pi * 120.0 / 180.0, c)
# Apply rotation to CA-N vector
cb_at_origin = n.left_multiply(rot)
# Put on top of CA atom
CB = cb_at_origin + vectors['CA']
atom_coords[cb] = CB.get_array()
else:
atom_coords[cb] = residue[cb].coord
for name in stored_atoms:
coords = [float(c) for c in atom_coords[name]]
residue_coordinates.append(coords)
assert len(residue_coordinates) == len(stored_atoms)
coordinates.extend(residue_coordinates)
if not coordinates:
raise LoadModelScoresError("No coordinates")
coordinates = json.dumps(coordinates)
row = dict(modelid=modelid, di=row['di'], coordinates=coordinates)
return pd.Series(row)
def generate_Cb(residue):
'''
creates phantom Cb atom
'''
n = residue['N'].get_vector()
c = residue['C'].get_vector()
ca = residue['CA'].get_vector()
n = n - ca
c = c - ca
rot = bp.rotaxis(-np.pi * 120.0 / 180.0, c)
cb_at_origin = n.left_multiply(rot)
return np.array(list(cb_at_origin + ca))
def rotate_throught_bond(bond, angle, rotated_atoms, atoms_fixed):
# Obtain the axis that we want to use as reference for the rotation
vector = bond.getCoords()[0] - bond.getCoords()[1]
vector = bio.Vector(vector)
# Obtain the rotation matrix for the vector (axis) and the angle (theta)
rot_mat = bio.rotaxis(angle, vector)
new_coords = []
for coords in rotated_atoms.getCoords():
new_coord = np.dot(coords, rot_mat)
new_coords.append(new_coord)
rotated_atoms.setCoords(new_coords)
structure_result = atoms_fixed + rotated_atoms
return structure_result
def rotation_thought_axis(bond, theta, core_bond, list_of_atoms, fragment_bond,
core_structure, fragment_structure, pdb_complex,
pdb_fragment, chain_complex, chain_fragment):
"""
Given a core molecule and a fragment, this function rotates the fragment atoms a certain theta angle around an axis
(set by the bond).
:param bond: Bio.PDB.Atom list composed by two elements: [heavy atom of the core, heavy atom of the fragment]
:param theta: Rotation angle in rads.
:param core_bond: Bio.PDB.Atom list with two elements: [heavy atom, hydrogen atom]. These two atoms have to be the
ones participating in the bond of the core that we would like to use as linking point between core and fragment.
:param list_of_atoms: list_of_atoms: Bio.PDB.Atom list with all the atoms of the fragment. These atoms have to contain
coordinates.
:param fragment_bond: Bio.PDB.Atom list with two elements: [hydrogen atom, heavy atom]. These two atoms have to be the
ones participating in the bond of the fragment that we would like to use as linking point between fragment and core.
:param core_structure: ProDy molecule that contain only the core ligand.
:param fragment_structure: ProDy molecule that contain only the fragment ligand.
:return: ProDy molecule with the core_structure and the fragment_structure rotated around the axis of the bond.
"""
# Obtain the axis that we want to use as reference for the rotation
vector = bond[1].get_vector() - bond[0].get_vector()
# Obtain the rotation matrix for the vector (axis) and the angle (theta)
rot_mat = bio.rotaxis(theta, vector)
for atom in list_of_atoms:
# Multiply the matrix of coordinates for the transpose of the rotation matrix to get the coordinates rotated
atom.transform(rot_mat, (0, 0, 0))
transform_coords_from_bio2prody(fragment_structure, list_of_atoms)
rotated_structure, core_original_atom, fragment_original_atom = join_structures(
core_bond,
fragment_bond,
core_structure,
fragment_structure,
pdb_complex=pdb_complex,
pdb_fragment=pdb_fragment,
chain_complex=chain_complex,
chain_fragment=chain_fragment)
return rotated_structure
