def write_chirality_file(input_filename, output_filename):
molecule = ra.parse_topology_file(input_filename)
atoms = molecule.atoms
chiral_centres = get_chiral_sets(atoms)
with open(output_filename, "w") as output_file:
for atom in sorted(chiral_centres.keys(), cmp=lambda x, y: cmp(x.index, y.index)):
# Write out the list of chiral atoms and their CIP-ranked neighbours.
output_string = "{0:>8d}{1:>8d}{2:>8d}{3:>8d}{4:>8d}\n".format(atom.index + 1,
*[other_atom.index + 1 for other_atom in
chiral_centres[atom]])
output_file.write(output_string)
def write_chirality_file(input_filename, output_filename):
molecule = ra.parse_topology_file(input_filename)
atoms = molecule.atoms
chiral_centres = get_chiral_sets(atoms)
with open(output_filename, "w") as output_file:
for atom in sorted(chiral_centres.keys(),
cmp=lambda x, y: cmp(x.index, y.index)):
# Write out the list of chiral atoms and their CIP-ranked neighbours.
output_string = "{0:>8d}{1:>8d}{2:>8d}{3:>8d}{4:>8d}\n".format(
atom.index + 1,
*[other_atom.index + 1 for other_atom in chiral_centres[atom]])
output_file.write(output_string)
angles = []
# For centre atom C and atoms ordered I, J, K and L
# Calculate dihedral of I-C-L-J
for atom_list in chiral_centres:
b1 = coords[atom_list[0]] - coords[atom_list[1]]
b2 = coords[atom_list[4]] - coords[atom_list[0]]
b3 = coords[atom_list[2]] - coords[atom_list[4]]
b1xb2 = np.cross(b1, b2)
b2xb3 = np.cross(b2, b3)
b1xb2_x_b2xb3 = np.cross(b1xb2, b2xb3)
b2_norm = b2 / np.linalg.norm(b2)
angles.append(
np.arctan2(np.dot(b1xb2_x_b2xb3, b2_norm), np.dot(b1xb2, b2xb3)))
return angles
if __name__ == "__main__":
import rotamer.io.gmin
molecule = ra.parse_topology_file("../library/coords.prmtop")
atoms = molecule.atoms
chiral_centres = get_chiral_sets(atoms)
chiral_centres_list = [[k.index] + [val.index for val in v]
for k, v in chiral_centres.items()]
# Starting coords
coords = rotamer.io.amber.read_amber_restart("../library/coords.inpcrd")
print calculate_chirality(coords.reshape((-1, 3)), chiral_centres_list)
# Lowest file
coords = rotamer.io.gmin.read_lowest("../library/lowest")[0]["coords"]
print calculate_chirality(coords.reshape((-1, 3)), chiral_centres_list)
def calculate_chirality(coords, chiral_centres):
import numpy as np
angles = []
# For centre atom C and atoms ordered I, J, K and L
# Calculate dihedral of I-C-L-J
for atom_list in chiral_centres:
b1 = coords[atom_list[0]] - coords[atom_list[1]]
b2 = coords[atom_list[4]] - coords[atom_list[0]]
b3 = coords[atom_list[2]] - coords[atom_list[4]]
b1xb2 = np.cross(b1, b2)
b2xb3 = np.cross(b2, b3)
b1xb2_x_b2xb3 = np.cross(b1xb2, b2xb3)
b2_norm = b2 / np.linalg.norm(b2)
angles.append(np.arctan2(np.dot(b1xb2_x_b2xb3, b2_norm), np.dot(b1xb2, b2xb3)))
return angles
if __name__ == "__main__":
import rotamer.io.gmin
molecule = ra.parse_topology_file("../library/coords.prmtop")
atoms = molecule.atoms
chiral_centres = get_chiral_sets(atoms)
chiral_centres_list = [[k.index] + [val.index for val in v] for k, v in chiral_centres.items()]
# Starting coords
coords = rotamer.io.amber.read_amber_restart("../library/coords.inpcrd")
print calculate_chirality(coords.reshape((-1, 3)), chiral_centres_list)
# Lowest file
coords = rotamer.io.gmin.read_lowest("../library/lowest")[0]["coords"]
print calculate_chirality(coords.reshape((-1, 3)), chiral_centres_list)
