def parse_prmtop(self):
self.prmtop_parsed = parse_topology_file(self.prmtopFname)
atoms = self.prmtop_parsed.atoms.nodes()
atoms = sorted(atoms, key=lambda a: a.index)
self.atom_names = [a.element for a in atoms]
self.bonds = [(a1.index, a2.index)
for a1, a2 in self.prmtop_parsed.atoms.edges_iter()]
def parse_prmtop(self):
self.prmtop_parsed = parse_topology_file(self.prmtopFname)
atoms = self.prmtop_parsed.atoms.nodes()
atoms = sorted(atoms, key=lambda a: a.index)
self.atom_names = [a.element for a in atoms]
self.bonds = [(a1.index, a2.index) for a1, a2 in
self.prmtop_parsed.atoms.edges_iter()]
def write_chirality_file(input_filename, output_filename, human_readable_filename):
molecule = ra.parse_topology_file(input_filename)
atoms = molecule.atoms
chiral_cands = chiral_candidates(atoms)
multi_bonds(atoms)
chiral_centres = {}
for i, chiral_atom in enumerate(chiral_cands):
ordered = chiral_order(atoms, chiral_atom)
if len(ordered) == 4:
chiral_centres[chiral_atom] = ordered
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)
with open(human_readable_filename, "w") as human_file:
human_file.write("Atom names given below are in the format: <index (from 0)> <element> <atom name>\n")
human_file.write("e.g.: 12 C CA is the 13th atom, is a carbon and is named \"CA\"\n\n")
output_string = "{0:^16s}{1:^16s}{2:^16s}{3:^16s}{4:^16s}\n".format("central atom", "top ranked", "2nd ranked", "3rd ranked", "lowest ranked")
human_file.write(output_string)
output_string = "{0:^16s}{1:^16s}{2:^16s}{3:^16s}{4:^16s}\n".format("============", "==========", "==========", "==========", "=============")
human_file.write(output_string)
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 - but this time readable for humans.
output_string = "{0:^16s}{1:^16s}{2:^16s}{3:^16s}{4:^16s}\n".format(str(atom), *[str(other_atom) for other_atom in chiral_centres[atom]])
human_file.write(output_string)
def write_cis_trans_file(input_filename, output_filename):
molecule = ra.parse_topology_file(input_filename)
atoms = molecule.atoms
# for atom in atoms:
# print atom.residue
multi_bonds(atoms)
with open(output_filename, "w") as output_file:
for bond in sorted(peptide_bonds(atoms), cmp=lambda x, y: cmp(x[0].index, y[0].index)):
# Write out the list of atoms in peptide bonds (O - C - N - H).
output_string = "{0:>8d}{1:>8d}{2:>8d}{3:>8d}\n".format(*map(lambda x: x.index + 1, bond))
output_file.write(output_string)
def write_chirality_file(input_filename, output_filename,
human_readable_filename):
molecule = ra.parse_topology_file(input_filename)
atoms = molecule.atoms
chiral_cands = chiral_candidates(atoms)
multi_bonds(atoms)
chiral_centres = {}
for i, chiral_atom in enumerate(chiral_cands):
ordered = chiral_order(atoms, chiral_atom)
if len(ordered) == 4:
chiral_centres[chiral_atom] = ordered
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)
with open(human_readable_filename, "w") as human_file:
human_file.write(
"Atom names given below are in the format: <index (from 0)> <element> <atom name>\n"
)
human_file.write(
"e.g.: 12 C CA is the 13th atom, is a carbon and is named \"CA\"\n\n"
)
output_string = "{0:^16s}{1:^16s}{2:^16s}{3:^16s}{4:^16s}\n".format(
"central atom", "top ranked", "2nd ranked", "3rd ranked",
"lowest ranked")
human_file.write(output_string)
output_string = "{0:^16s}{1:^16s}{2:^16s}{3:^16s}{4:^16s}\n".format(
"============", "==========", "==========", "==========",
"=============")
human_file.write(output_string)
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 - but this time readable for humans.
output_string = "{0:^16s}{1:^16s}{2:^16s}{3:^16s}{4:^16s}\n".format(
str(atom),
*[str(other_atom) for other_atom in chiral_centres[atom]])
human_file.write(output_string)
