def test_to_file_vsites(self):
"""
Checks that Topology.to_file() doesn't write vsites
"""
from tempfile import NamedTemporaryFile
from openff.toolkit.topology import Molecule, Topology
mol = Molecule.from_pdb_and_smiles(
get_data_file_path("systems/test_systems/1_ethanol.pdb"), "CCO")
carbons = [atom for atom in mol.atoms if atom.atomic_number == 6]
positions = mol.conformers[0]
mol.add_bond_charge_virtual_site(
(carbons[0], carbons[1]),
0.1 * unit.angstrom,
charge_increments=[0.1, 0.05] * unit.elementary_charge,
)
topology = Topology()
topology.add_molecule(mol)
count = 0
# The file should be printed out with 9 atoms and 0 virtualsites, so we check to ensure that thtere are only 9 HETATM entries
with NamedTemporaryFile(suffix=".pdb") as iofile:
topology.to_file(iofile.name, positions)
data = open(iofile.name).readlines()
for line in data:
if line.startswith("HETATM"):
count = count + 1
assert count == 9
def test_to_file_multi_molecule_different_order(self):
"""
Checks for the following if Topology.to_write maintains the order of atoms
for the same molecule with different indexing
"""
from tempfile import NamedTemporaryFile
from openff.toolkit.tests.test_forcefield import (
create_ethanol,
create_reversed_ethanol,
)
from openff.toolkit.topology import Molecule, Topology
topology = Topology()
topology.add_molecule(create_ethanol())
topology.add_molecule(create_reversed_ethanol())
mol = Molecule.from_pdb_and_smiles(
get_data_file_path("systems/test_systems/1_ethanol.pdb"), "CCO")
positions = mol.conformers[0]
# Make up coordinates for the second ethanol by translating the first by 10 angstroms
# (note that this will still be a gibberish conformation, since the atom order in the second molecule is different)
positions = np.concatenate(
[positions, positions + 10.0 * unit.angstrom])
element_order = []
with NamedTemporaryFile(suffix=".pdb") as iofile:
topology.to_file(iofile.name, positions)
data = open(iofile.name).readlines()
for line in data:
if line.startswith("HETATM"):
element_order.append(line.strip()[-1])
assert element_order == [
"C",
"C",
"O",
"H",
"H",
"H",
"H",
"H",
"H",
"H",
"H",
"H",
"H",
"H",
"H",
"O",
"C",
"C",
]
def test_to_file_fileformat_invalid(self):
"""
Checks for invalid file format
"""
from openff.toolkit.topology import Molecule, Topology
topology = Topology()
mol = Molecule.from_pdb_and_smiles(
get_data_file_path("systems/test_systems/1_ethanol.pdb"), "CCO")
topology.add_molecule(mol)
positions = mol.conformers[0]
fname = "ethanol_file.pdb"
with pytest.raises(NotImplementedError):
topology.to_file(fname, positions, file_format="AbC")
def test_to_file_no_molecules(self):
"""
Checks if Topology.to_file() writes a file with no topology and no coordinates
"""
from tempfile import NamedTemporaryFile
from openff.toolkit.topology import Topology
topology = Topology()
lines = []
with NamedTemporaryFile(suffix=".pdb") as iofile:
topology.to_file(iofile.name, [])
data = open(iofile.name).readlines()
for line in data:
lines.append(line.split())
assert lines[1] == ["END"]
def test_to_file_fileformat_lettercase(self):
"""
Checks if fileformat specifier is indpendent of upper/lowercase
"""
from tempfile import NamedTemporaryFile
from openff.toolkit.topology import Molecule, Topology
topology = Topology()
mol = Molecule.from_pdb_and_smiles(
get_data_file_path("systems/test_systems/1_ethanol.pdb"), "CCO")
topology.add_molecule(mol)
positions = mol.conformers[0]
count = 1
with NamedTemporaryFile(suffix=".pdb") as iofile:
topology.to_file(iofile.name, positions, file_format="pDb")
data = open(iofile.name).readlines()
for line in data:
if line.startswith("HETATM") and count == 1:
count = count + 1
coord = line.split()[-6]
assert coord == "10.172"
def test_to_file_units_check(self):
"""
Checks whether writing pdb with unitless positions, Angstrom positions,
nanometer positions, result in the same output
"""
from tempfile import NamedTemporaryFile
from simtk.unit import nanometer
from openff.toolkit.topology import Molecule, Topology
topology = Topology()
mol = Molecule.from_pdb_and_smiles(
get_data_file_path("systems/test_systems/1_ethanol.pdb"), "CCO")
topology.add_molecule(mol)
positions_angstrom = mol.conformers[0]
count = 1
# Write the molecule to PDB and ensure that the X coordinate of the first atom is 10.172
with NamedTemporaryFile(suffix=".pdb") as iofile:
topology.to_file(iofile.name, positions_angstrom)
data = open(iofile.name).readlines()
for line in data:
if line.startswith("HETATM") and count == 1:
count = count + 1
coord = line.split()[-6]
assert coord == "10.172"
# Do the same check, but feed in equivalent positions measured in nanometers and ensure the PDB is still the same
count = 1
coord = None
with NamedTemporaryFile(suffix=".pdb") as iofile:
positions_nanometer = positions_angstrom.in_units_of(nanometer)
topology.to_file(iofile.name, positions_nanometer)
data = open(iofile.name).readlines()
for line in data:
if line.startswith("HETATM") and count == 1:
count = count + 1
coord = line.split()[-6]
assert coord == "10.172"
count = 1
coord = "abc"
with NamedTemporaryFile(suffix=".pdb") as iofile:
positions_unitless = positions_angstrom._value
topology.to_file(iofile.name, positions_unitless)
data = open(iofile.name).readlines()
for line in data:
if line.startswith("HETATM") and count == 1:
count = count + 1
coord = line.split()[-6]
assert coord == "10.172"