def save_lammpsdata(self, filename, traj, forcefield, force_overwrite=False, **kwargs):
""" """
from foyer.forcefield import apply_forcefield
import intermol.lammps as lmp
# Create separate file paths for .gro and .top
filepath, filename = os.path.split(filename)
basename = os.path.splitext(filename)[0]
inp_filename = os.path.join(filepath, basename + '.input')
intermol_system = self.to_intermol()
if forcefield:
apply_forcefield(intermol_system, forcefield=forcefield)
lmp.save(inp_filename, intermol_system)
def save_gromacs(self, filename, structure, forcefield, force_overwrite=False, **kwargs):
""" """
from foyer.forcefield import apply_forcefield
# Create separate file paths for .gro and .top
filepath, filename = os.path.split(filename)
basename = os.path.splitext(filename)[0]
top_filename = os.path.join(filepath, basename + '.top')
gro_filename = os.path.join(filepath, basename + '.gro')
if forcefield:
structure = apply_forcefield(structure, forcefield=forcefield)
structure.save(top_filename, 'gromacs', **kwargs)
structure.save(gro_filename, 'gro', **kwargs)
def test_full_parametrization(self):
top = os.path.join(self.resource_dir, 'benzene.top')
gro = os.path.join(self.resource_dir, 'benzene.gro')
ff = os.path.join(self.resource_dir, 'oplsaa.ff/forcefield.itp')
structure = pmd.load_file(top, xyz=gro)
parametrized = apply_forcefield(structure, forcefield=ff, debug=False)
assert sum((1 for at in parametrized.atoms if at.type == 'opls_145')) == 6
assert sum((1 for at in parametrized.atoms if at.type == 'opls_146')) == 6
assert len(parametrized.bonds) == 12
assert all(x.type for x in parametrized.bonds)
assert len(parametrized.angles) == 18
assert all(x.type for x in parametrized.angles)
assert len(parametrized.rb_torsions) == 24
assert all(x.type for x in parametrized.dihedrals)
def save_hoomdxml(self, filename, structure, forcefield, box=None, **kwargs):
""" """
if forcefield:
from foyer.forcefield import apply_forcefield
structure = apply_forcefield(structure, forcefield=forcefield)
if not box:
box = self.boundingbox
for dim, val in enumerate(self.periodicity):
if val:
box.lengths[dim] = val
box.maxs[dim] = val
box.mins[dim] = 0.0
if not val:
box.maxs[dim] += 0.25
box.mins[dim] -= 0.25
box.lengths[dim] += 0.5
write_hoomdxml(structure, filename, forcefield, box, **kwargs)
def test_full_parameterization(self, ethane):
#ethane.save('ethane.gro', forcefield='opls-aa')
intermol_ethane = ethane._to_intermol(molecule_types=[type(ethane)])
apply_forcefield(intermol_ethane, forcefield='opls-aa', debug=False)
mol_name, top_name, list(zip(range(len(generated_opls_types)),
generated_opls_types,
known_opls_types)))
assert all([a == b for a, b in both]), message
print("Passed.\n")
@pytest.mark.skipif(True, reason='Not implemented yet')
def test_full_parameterization(self, ethane):
#ethane.save('ethane.gro', forcefield='opls-aa')
intermol_ethane = ethane._to_intermol(molecule_types=[type(ethane)])
apply_forcefield(intermol_ethane, forcefield='opls-aa', debug=False)
# detect file extension
# save to that MD engine from intermol
if __name__ == "__main__":
# TestOPLS().test_atomtyping('benzene')
# TestOPLS().test_atomtyping()
from mbuild.examples.ethane.ethane import Ethane
import mbuild as mb
ethanes = mb.Compound()
for _ in range(3):
ethanes.add(Ethane())
intermol_ethane = ethanes._to_intermol(molecule_types=[Ethane])
apply_forcefield(intermol_ethane, forcefield='opls-aa', debug=False)
# TestOPLS().test_full_parameterization(ethanes)
import os
import parmed as pmd
from pkg_resources import resource_filename
from foyer.forcefield import apply_forcefield
resource_dir = resource_filename('foyer', '../opls_validation')
top_filename = os.path.join(resource_dir, 'benzene.top')
gro_filename = os.path.join(resource_dir, 'benzene.gro')
ff_filename = os.path.join(resource_dir, 'oplsaa.ff/forcefield.itp')
structure = pmd.load_file(top_filename, xyz=gro_filename)
parametrized = apply_forcefield(structure, forcefield=ff_filename, debug=False)
parametrized.save('benzene.gro', overwrite=True)
parametrized.save('benzene.top', overwrite=True)
def test_full_parameterization(self, ethane):
#ethane.save('ethane.gro', forcefield='opls-aa')
intermol_ethane = ethane._to_intermol(molecule_types=[type(ethane)])
apply_forcefield(intermol_ethane, forcefield='opls-aa', debug=False)
list(
zip(range(len(generated_opls_types)), generated_opls_types,
known_opls_types)))
assert all([a == b for a, b in both]), message
print("Passed.\n")
@pytest.mark.skipif(True, reason='Not implemented yet')
def test_full_parameterization(self, ethane):
#ethane.save('ethane.gro', forcefield='opls-aa')
intermol_ethane = ethane._to_intermol(molecule_types=[type(ethane)])
apply_forcefield(intermol_ethane, forcefield='opls-aa', debug=False)
# detect file extension
# save to that MD engine from intermol
if __name__ == "__main__":
# TestOPLS().test_atomtyping('benzene')
# TestOPLS().test_atomtyping()
from mbuild.examples.ethane.ethane import Ethane
import mbuild as mb
ethanes = mb.Compound()
for _ in range(3):
ethanes.add(Ethane())
intermol_ethane = ethanes._to_intermol(molecule_types=[Ethane])
apply_forcefield(intermol_ethane, forcefield='opls-aa', debug=False)
# TestOPLS().test_full_parameterization(ethanes)