def test_to_file_vsites(self):
"""
Checks that Topology.to_file() doesn't write vsites
"""
from tempfile import NamedTemporaryFile
from openforcefield.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 openforcefield.tests.test_forcefield import (
create_ethanol,
create_reversed_ethanol,
)
from openforcefield.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 openforcefield.tests.test_forcefield import create_ethanol
from openforcefield.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 openforcefield.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
"""
import os
from tempfile import NamedTemporaryFile
from openforcefield.tests.test_forcefield import create_ethanol
from openforcefield.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
"""
import filecmp
from tempfile import NamedTemporaryFile
from simtk.unit import nanometer
from openforcefield.tests.test_forcefield import create_ethanol
from openforcefield.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"
