def test_singleterm_charmm(self):
from foyer import Forcefield
from mbuild.formats.lammpsdata import write_lammpsdata
cmpd = mb.load(get_fn("charmm_dihedral.mol2"))
for i in cmpd.particles():
i.name = "_{}".format(i.name)
structure = cmpd.to_parmed(
box=cmpd.get_boundingbox(),
residues=set([p.parent.name for p in cmpd.particles()]),
)
ff = Forcefield(
forcefield_files=[get_fn("charmm_truncated_singleterm.xml")])
structure = ff.apply(structure, assert_dihedral_params=False)
write_lammpsdata(structure, "charmm_dihedral_singleterm.lammps")
out_lammps = open("charmm_dihedral_singleterm.lammps", "r").readlines()
found_dihedrals = False
for i, line in enumerate(out_lammps):
if "Dihedral Coeffs" in line:
assert "# charmm" in line
assert "#k, n, phi, weight" in out_lammps[i + 1]
assert len(out_lammps[i + 2].split("#")[0].split()) == 5
assert float(
out_lammps[i + 2].split("#")[0].split()[4]) == float("1.0")
found_dihedrals = True
else:
pass
assert found_dihedrals
def test_save_charmm(self):
from foyer import Forcefield
cmpd = mb.load(get_fn("charmm_dihedral.mol2"))
for i in cmpd.particles():
i.name = "_{}".format(i.name)
structure = cmpd.to_parmed(
box=cmpd.get_boundingbox(),
residues=set([p.parent.name for p in cmpd.particles()]),
)
ff = Forcefield(forcefield_files=[get_fn("charmm_truncated.xml")])
structure = ff.apply(structure, assert_dihedral_params=False)
write_lammpsdata(structure, "charmm_dihedral.lammps")
out_lammps = open("charmm_dihedral.lammps", "r").readlines()
found_angles = False
found_dihedrals = False
for i, line in enumerate(out_lammps):
if "Angle Coeffs" in line:
assert "# charmm" in line
assert (
"#\tk(kcal/mol/rad^2)\t\ttheteq(deg)\tk(kcal/mol/angstrom^2)\treq(angstrom)\n"
in out_lammps[i + 1])
assert len(out_lammps[i + 2].split("#")[0].split()) == 5
found_angles = True
elif "Dihedral Coeffs" in line:
assert "# charmm" in line
assert "#k, n, phi, weight" in out_lammps[i + 1]
assert len(out_lammps[i + 2].split("#")[0].split()) == 5
found_dihedrals = True
else:
pass
assert found_angles
assert found_dihedrals
def test_save_charmm(self):
cmpd = mb.load(get_fn('charmm_dihedral.mol2'))
for i in cmpd.particles():
i.name = "_{}".format(i.name)
structure = cmpd.to_parmed(box=cmpd.boundingbox,
residues=set([p.parent.name for \
p in cmpd.particles()]))
from foyer import Forcefield
ff = Forcefield(forcefield_files=[get_fn('charmm_truncated.xml')])
structure = ff.apply(structure, assert_dihedral_params=False)
from mbuild.formats.lammpsdata import write_lammpsdata
write_lammpsdata(structure, 'charmm_dihedral.lammps')
out_lammps = open('charmm_dihedral.lammps', 'r').readlines()
for i, line in enumerate(out_lammps):
if 'Angle Coeffs' in line:
assert '# charmm' in line
assert '#\tk(kcal/mol/rad^2)\t\ttheteq(deg)\tk(kcal/mol/angstrom^2)\treq(angstrom)\n' in out_lammps[
i + 1]
assert len(out_lammps[i + 2].split('#')[0].split()) == 5
elif 'Dihedral Coeffs' in line:
assert '# charmm' in line
assert '#k, n, phi, weight' in out_lammps[i + 1]
assert len(out_lammps[i + 2].split('#')[0].split()) == 5
else:
pass
def test_hoomdsimulation_restart(self):
import gsd.hoomd
import hoomd
from foyer.forcefield import Forcefield
from mbuild.formats.hoomd_simulation import create_hoomd_simulation
box = mb.Compound()
box.add(mb.Compound(name="Ar", pos=[1, 1, 1]))
box.add(mb.Compound(name="Ar", pos=[1, 1, 1]))
ff = Forcefield(forcefield_files=get_fn("lj.xml"))
structure = ff.apply(box)
structure.box = [10, 10, 10, 90, 90, 90]
sim = hoomd.context.SimulationContext()
with sim:
hoomd_obj, ref_vals = create_hoomd_simulation(
structure, 2.5, restart=get_fn("restart.gsd"))
sim_forces = hoomd.context.current.forces
pair_force = import_("hoomd.md.pair")
assert isinstance(sim_forces[0], pair_force.lj)
snap = hoomd_obj[0]
with gsd.hoomd.open(get_fn("restart.gsd")) as f:
rsnap = f[0]
assert np.array_equal(snap.particles.position,
rsnap.particles.position)
def test_save_forcefield_with_file_foyerkwargs(self, methane):
foyerkwargs = {'assert_improper_params': True}
with pytest.raises(Exception):
methane.save('lythem.hoomdxml',
forcefield_files=get_fn('methane_oplssaa.xml'),
overwrite=True, foyerkwargs=foyerkwargs)
methane.save('lythem.hoomdxml',
forcefield_files=get_fn('methane_oplssaa.xml'),
overwrite=True, foyerkwargs={})
def test_save_missing_topo_params(self, ff_filename, foyer_kwargs):
"""Test that the user is notified if not all topology parameters are found."""
from foyer.tests.utils import get_fn
ethane = mb.load(get_fn('ethane.mol2'))
with pytest.raises(Exception):
ethane.save('ethane.mol2', forcefield_files=get_fn(ff_filename))
with pytest.warns(UserWarning):
ethane.save('ethane.mol2',
forcefield_files=get_fn(ff_filename),
overwrite=True,
foyer_kwargs=foyer_kwargs)
def test_save_charmm(self):
cmpd = mb.load(get_fn('charmm_dihedral.mol2'))
for i in cmpd.particles():
i.name = "_{}".format(i.name)
structure = cmpd.to_parmed(box=cmpd.boundingbox,
residues=set([p.parent.name for \
p in cmpd.particles()]))
from foyer import Forcefield
ff = Forcefield(forcefield_files=[get_fn('charmm_truncated.xml')])
structure = ff.apply(structure, assert_dihedral_params=False)
write_par(structure, 'charmm_dihedral.par')
def benzene_from_parts(self):
ch = mb.load(get_fn('ch.mol2'))
ch.name = 'CH'
mb.translate(ch, -ch[0].pos)
ch.add(mb.Port(anchor=ch[0]), 'a')
mb.translate(ch['a'], [0, 0.07, 0])
mb.rotate_around_z(ch['a'], 120.0 * (np.pi / 180.0))
ch.add(mb.Port(anchor=ch[0]), 'b')
mb.translate(ch['b'], [0, 0.07, 0])
mb.rotate_around_z(ch['b'], -120.0 * (np.pi / 180.0))
benzene = mb.Compound(name='Benzene')
benzene.add(ch)
current = ch
for _ in range(5):
ch_new = mb.clone(ch)
mb.force_overlap(move_this=ch_new,
from_positions=ch_new['a'],
to_positions=current['b'])
current = ch_new
benzene.add(ch_new)
carbons = [p for p in benzene.particles_by_name('C')]
benzene.add_bond((carbons[0], carbons[-1]))
return benzene
def test_save_forcefield_with_same_struct(self):
from foyer import Forcefield
from mbuild.formats.lammpsdata import write_lammpsdata
system = mb.load("C1(=CC=CC=C1)F", smiles=True)
ff = Forcefield(forcefield_files=[get_fn("gaff_test.xml")])
struc = ff.apply(
system,
assert_angle_params=False,
assert_dihedral_params=False,
assert_improper_params=False,
)
write_lammpsdata(struc,
"charmm_improper.lammps",
zero_dihedral_weighting_factor=True)
for i in range(3):
xyz = struc.coordinates
xyz = xyz + np.array([1, 1, 1])
struc.coordinates = xyz
write_lammpsdata(
struc,
f"charmm_improper{i}.lammps",
zero_dihedral_weighting_factor=True,
)
def test_save_forcefield_with_file(self, methane):
exts = ['.gsd', '.hoomdxml', '.lammps', '.lmp', '.top', '.gro',
'.mol2', '.pdb', '.xyz']
for ext in exts:
methane.save('lythem' + ext,
forcefield_files=get_fn('methane_oplssaa.xml'),
overwrite=True)
def benzene_from_parts(self):
ch = mb.load(get_fn('ch.mol2'))
ch.name = 'CH'
ch.translate(-ch[0].pos)
ch.add(mb.Port(anchor=ch[0], separation=0.07), 'a')
ch['a'].rotate(120.0 * (np.pi/180.0), around=np.asarray([0, 0, 1]))
ch.add(mb.Port(anchor=ch[0], separation=0.07), 'b')
ch['b'].rotate(-120.0 * (np.pi/180.0), around=np.asarray([0, 0, 1]))
ch_copy = mb.clone(ch)
benzene = mb.Compound(name='Benzene')
benzene.add(ch)
current = ch
for _ in range(5):
ch_new = mb.clone(ch_copy)
mb.force_overlap(move_this=ch_new,
from_positions=ch_new['a'],
to_positions=current['b'])
current = ch_new
benzene.add(ch_new)
carbons = [p for p in benzene.particles_by_name('C')]
benzene.add_bond((carbons[0],carbons[-1]))
return benzene
def test_from_pybel(self):
pybel = import_('pybel')
benzene = list(pybel.readfile('mol2', get_fn('benzene.mol2')))[0]
cmpd = mb.Compound()
cmpd.from_pybel(benzene)
assert benzene.OBMol.NumAtoms() == cmpd.n_particles
assert benzene.OBMol.NumBonds() == cmpd.n_bonds
def benzene_from_parts(self):
ch = mb.load(get_fn('ch.mol2'))
ch.name = 'CH'
mb.translate(ch, -ch[0].pos)
ch.add(mb.Port(anchor=ch[0]), 'a')
mb.translate(ch['a'], [0, 0.07, 0])
mb.rotate_around_z(ch['a'], 120.0 * (np.pi/180.0))
ch.add(mb.Port(anchor=ch[0]), 'b')
mb.translate(ch['b'], [0, 0.07, 0])
mb.rotate_around_z(ch['b'], -120.0 * (np.pi/180.0))
benzene = mb.Compound(name='Benzene')
benzene.add(ch)
current = ch
for _ in range(5):
ch_new = mb.clone(ch)
mb.force_overlap(move_this=ch_new,
from_positions=ch_new['a'],
to_positions=current['b'])
current = ch_new
benzene.add(ch_new)
carbons = [p for p in benzene.particles_by_name('C')]
benzene.add_bond((carbons[0],carbons[-1]))
return benzene
def test_save(self):
methyl = mb.load(get_fn('methyl.pdb'))
extensions = ['.xyz', '.pdb', '.mol2']
for ext in extensions:
outfile = 'methyl_out' + ext
methyl.save(filename=outfile)
assert os.path.exists(outfile)
def test_gmso_backend_lj_site_type(self):
pmd_silica_surface = mb.load(
filename_or_object=get_fn("beta-cristobalite-expanded.mol2"),
backend="parmed",
)
gmso_silica_surface = mb.load(
filename_or_object=get_fn("beta-cristobalite-expanded.mol2"),
backend="gmso",
site_type="lj",
)
assert pmd_silica_surface.n_particles == gmso_silica_surface.n_particles
assert pmd_silica_surface.n_bonds == gmso_silica_surface.n_bonds
for particle in gmso_silica_surface:
assert particle.element is None
def test_save_forcefield_with_file(self, methane):
exts = ['.gsd', '.hoomdxml', '.lammps', '.lmp', '.top', '.gro',
'.mol2', '.pdb', '.xyz']
for ext in exts:
methane.save('lythem' + ext,
forcefield_files=get_fn('methane_oplssaa.xml'),
overwrite=True)
def test_non_resolved_elements(self):
tip3p_water = mb.load(get_fn("tip3p_water.xyz"))
assert tip3p_water[0].element is None
assert tip3p_water[0].name == "opls_111"
assert tip3p_water[1].element is None
assert tip3p_water[1].name == "opls_112"
assert tip3p_water[2].element is None
assert tip3p_water[2].name == "opls_112"
def test_structure_reproducibility(self, alkane_monolayer):
filename = 'monolayer-tmp.pdb'
alkane_monolayer.save(filename)
with open(get_fn('monolayer.pdb')) as file1:
with open('monolayer-tmp.pdb') as file2:
diff = difflib.ndiff(file1.readlines(), file2.readlines())
changes = [l for l in diff if l.startswith('+ ') or l.startswith('- ')]
assert not changes
def test_structure_reproducibility(self, alkane_monolayer):
filename = 'monolayer-tmp.pdb'
alkane_monolayer.save(filename)
with open(get_fn('monolayer.pdb')) as file1:
with open('monolayer-tmp.pdb') as file2:
diff = difflib.ndiff(file1.readlines(), file2.readlines())
changes = [l for l in diff if l.startswith('+ ') or l.startswith('- ')]
assert not changes
def test_non_resolved_elements(self):
tip3p_water = mb.load(get_fn('tip3p_water.xyz'))
assert tip3p_water[0].element is None
assert tip3p_water[0].name == 'opls_111'
assert tip3p_water[1].element is None
assert tip3p_water[1].name == 'opls_112'
assert tip3p_water[2].element is None
assert tip3p_water[2].name == 'opls_112'
def test_gmso_backend(self):
pmd_silica_surface = mb.load(
filename_or_object=get_fn("beta-cristobalite-expanded.mol2"),
backend="parmed",
)
gmso_silica_surface = mb.load(
filename_or_object=get_fn("beta-cristobalite-expanded.mol2"),
backend="gmso",
)
assert pmd_silica_surface.n_particles == gmso_silica_surface.n_particles
assert pmd_silica_surface.n_bonds == gmso_silica_surface.n_bonds
element_set = set()
for particle in gmso_silica_surface:
element_set.add(particle.element)
assert len(element_set) == 2
def test_from_pybel_monolayer(self):
import pybel
monolayer = list(pybel.readfile('pdb', get_fn('monolayer.pdb')))[0]
# TODO: Actually store the box information
cmpd = mb.Compound()
cmpd.from_pybel(monolayer)
assert monolayer.OBMol.NumAtoms() == cmpd.n_particles
assert monolayer.OBMol.NumBonds() == cmpd.n_bonds
first_atom = monolayer.OBMol.GetAtom(1)
assert np.allclose(cmpd[0].pos, [first_atom.GetX()/10, first_atom.GetY()/10, first_atom.GetZ()/10])
def test_structure_reproducibility(self):
from mbuild.lib.recipes import Alkane
filename = 'decane-tmp.xyz'
decane = Alkane(10)
decane.save(filename)
with open(get_fn('decane.xyz')) as file1:
with open(filename) as file2:
diff = difflib.ndiff(file1.readlines(), file2.readlines())
changes = [l for l in diff if l.startswith('+ ') or l.startswith('- ')]
assert not changes
def test_cif_triclinic_box_properties(self):
lattice_cif = load_cif(file_or_path=get_fn("ETV_triclinic.cif"))
periodic_boxed_molecule = lattice_cif.populate(x=1, y=1, z=1)
periodic_box = periodic_boxed_molecule.box
manual_num_atoms = 42
manual_angles = [105.72, 100.19, 97.02]
manual_lengths = [0.87503, 0.96479, 1.02719]
assert np.all(np.isclose(manual_lengths, list(periodic_box.lengths)))
assert np.all(np.isclose(manual_angles, list(periodic_box.angles)))
assert len(periodic_boxed_molecule.children) == manual_num_atoms
def test_cif_vs_manual_triclinic(self):
spacing = [0.641910000, 0.652305930, 0.704466251]
angles = [91.77954616, 103.97424201, 118.83663410]
points_dict = {
"Re": [
[0.94176500, 0.68947700, 0.50807400],
[0.05823500, 0.31052300, 0.49192600],
[0.51250400, 0.71441700, 0.50209100],
[0.48749600, 0.28558300, 0.49790900],
],
"S": [
[0.74798600, 0.13254800, 0.67588400],
[0.73127300, 0.34781000, 0.26679600],
[0.21989400, 0.10784400, 0.70096800],
[0.25920200, 0.38690600, 0.24012300],
[0.74079800, 0.61309400, 0.75987700],
[0.78010600, 0.89215600, 0.29903200],
[0.25201400, 0.86745200, 0.32411600],
[0.26872700, 0.65219000, 0.73320400],
],
}
lattice_manual = mb.Lattice(
lattice_spacing=spacing, lattice_points=points_dict, angles=angles
)
lattice_cif = load_cif(file_or_path=get_fn("ReS2.cif"))
assert np.all(
np.isclose(
lattice_manual.lattice_spacing, lattice_cif.lattice_spacing
)
)
assert np.all(np.isclose(lattice_manual.angles, lattice_cif.angles))
# sort dicts first (not necessary once we support py 3.7+ only)
# dict sorted by keys
dict_manual = OrderedDict(
sorted(lattice_manual.lattice_points.items(), key=lambda t: t[0])
)
dict_cif = OrderedDict(
sorted(lattice_cif.lattice_points.items(), key=lambda t: t[0])
)
keys_m = dict_manual.keys()
keys_c = dict_cif.keys()
for k_man, k_cif in zip(keys_m, keys_c):
# sort the lists of lists
points_man = dict_manual[k_man]
points_cif = dict_cif[k_cif]
points_man.sort()
points_cif.sort()
points_man = np.asarray(points_man)
points_cif = np.asarray(points_cif)
assert np.all(np.isclose(points_man, points_cif))
def main():
from mbuild.utils.io import get_fn
from mbuild.lib.moieties import H2O
water = H2O()
ecerns = mb.load(get_fn('ecer2.pdb'))
chol = mb.load(get_fn('cg-chol.pdb'))
# Orient along the z-direction.
mb.rotate_around_x(chol, -135.0*np.pi/180)
mb.rotate_around_y(chol, -45.0*np.pi/180)
lipids = [(ecerns, 0.5), (chol, 0.5)]
bilayer = Bilayer(lipids, n_lipids_x=15, n_lipids_y=15, area_per_lipid=1.4,
solvent=water, ref_atoms=[1, 6], spacing_z=0.7,
solvent_per_lipid=20, mirror=False)
bilayer.save(filename='bilayer.pdb')
return bilayer
def rigid_ch(self):
ch = mb.load(get_fn('ch.mol2'))
ch.name = 'CH'
ch.label_rigid_bodies()
mb.translate(ch, -ch[0].pos)
ch.add(mb.Port(anchor=ch[0]), 'a')
mb.translate(ch['a'], [0, 0.07, 0])
mb.rotate_around_z(ch['a'], 120.0 * (np.pi/180.0))
ch.add(mb.Port(anchor=ch[0]), 'b')
mb.translate(ch['b'], [0, 0.07, 0])
mb.rotate_around_z(ch['b'], -120.0 * (np.pi/180.0))
return ch
def test_cif_monoclinic_box_properties(self):
lattice_cif = load_cif(file_or_path=get_fn("ITG_monoclinic.cif"))
periodic_boxed_molecule = lattice_cif.populate(x=1, y=1, z=1)
periodic_box = periodic_boxed_molecule.box
manual_num_atoms = 168
# manual_num_atoms was found using VESTA: https://gist.github.com/ramanishsingh/d712f57b8101eb073cfe010fc3b4edc3
# xyz file used: https://gist.github.com/ramanishsingh/154cf03d12e25f3d608e526500453e2e
# cif file used: https://gist.github.com/ramanishsingh/2db4ff2a266390242a6a05913d31414a
manual_angles = [90.0, 96.29, 90]
manual_lengths = [1.27411, 1.26989, 2.09991]
assert np.all(np.isclose(manual_lengths, list(periodic_box.lengths)))
assert np.all(np.isclose(manual_angles, list(periodic_box.angles)))
assert len(periodic_boxed_molecule.children) == manual_num_atoms
def rigid_ch(self):
ch = mb.load(get_fn('ch.mol2'))
ch.name = 'CH'
ch.label_rigid_bodies()
mb.translate(ch, -ch[0].pos)
ch.add(mb.Port(anchor=ch[0]), 'a')
mb.translate(ch['a'], [0, 0.07, 0])
mb.rotate_around_z(ch['a'], 120.0 * (np.pi / 180.0))
ch.add(mb.Port(anchor=ch[0]), 'b')
mb.translate(ch['b'], [0, 0.07, 0])
mb.rotate_around_z(ch['b'], -120.0 * (np.pi / 180.0))
return ch
def rigid_ch(self):
ch = mb.load(get_fn('ch.mol2'))
ch.name = 'CH'
ch.label_rigid_bodies()
ch.translate(-ch[0].pos)
ch.add(mb.Port(anchor=ch[0]), 'a')
ch['a'].translate([0, 0.07, 0])
ch['a'].rotate(120.0 * (np.pi/180.0), around=np.asarray([0, 0, 1]))
ch.add(mb.Port(anchor=ch[0]), 'b')
ch['b'].translate([0, 0.07, 0])
ch['b'].rotate(-120.0 * (np.pi/180.0), around=np.asarray([0, 0, 1]))
return ch
def test_from_pybel_molecule(self):
pybel = import_('pybel')
chol = list(pybel.readfile('pdb', get_fn('cholesterol.pdb')))[0]
# TODO: Actually store the box information
cmpd = mb.Compound()
cmpd.from_pybel(chol)
assert chol.OBMol.NumAtoms() == cmpd.n_particles
assert chol.OBMol.NumBonds() == cmpd.n_bonds
first_atom = chol.OBMol.GetAtom(1)
assert np.allclose(cmpd[0].pos, [
first_atom.GetX() / 10,
first_atom.GetY() / 10,
first_atom.GetZ() / 10
])
def test_cif_vs_manual(self):
spacing = [0.760296570, 0.760296570, 0.437540800]
points_dict = {
"La": [[1 / 3, 2 / 3, 1 / 4], [2 / 3, 1 / 3, 3 / 4]],
"Cl": [
[0.69490400, 0.08690400, 1 / 4],
[0.60800000, 0.69490400, 3 / 4],
[0.30509600, 0.91309600, 3 / 4],
[0.39200000, 0.30509600, 1 / 4],
[0.91309600, 0.60800000, 1 / 4],
[0.08690400, 0.39200000, 3 / 4],
],
}
lattice_manual = mb.Lattice(
lattice_spacing=spacing,
lattice_points=points_dict,
angles=[90, 90, 120],
)
lattice_cif = load_cif(file_or_path=get_fn("LaCl3.cif"))
assert np.all(
np.isclose(
lattice_manual.lattice_spacing, lattice_cif.lattice_spacing
)
)
assert np.all(np.isclose(lattice_manual.angles, lattice_cif.angles))
# sort dicts first (not necessary once we support py 3.7+ only)
# dict sorted by keys
dict_manual = OrderedDict(
sorted(lattice_manual.lattice_points.items(), key=lambda t: t[0])
)
dict_cif = OrderedDict(
sorted(lattice_cif.lattice_points.items(), key=lambda t: t[0])
)
keys_m = dict_manual.keys()
keys_c = dict_cif.keys()
for k_man, k_cif in zip(keys_m, keys_c):
# sort the lists of lists
points_man = dict_manual[k_man]
points_cif = dict_cif[k_cif]
points_man.sort()
points_cif.sort()
points_man = np.asarray(points_man)
points_cif = np.asarray(points_cif)
assert np.all(np.isclose(points_man, points_cif))
def rigid_ch(self):
ch = mb.load(get_fn("ch.mol2"))
ch.name = "CH"
ch.label_rigid_bodies()
ch.translate(-ch[0].pos)
ch.add(mb.Port(anchor=ch[0]), "a")
ch["a"].translate([0, 0.07, 0])
ch["a"].rotate(120.0 * (np.pi / 180.0), around=np.asarray([0, 0, 1]))
ch.add(mb.Port(anchor=ch[0]), "b")
ch["b"].translate([0, 0.07, 0])
ch["b"].rotate(-120.0 * (np.pi / 180.0), around=np.asarray([0, 0, 1]))
return ch
def test_lj_to_hoomdsimulation(self):
hoomd = import_("hoomd")
hoomd_simulation = import_("mbuild.formats.hoomd_simulation")
forcefield = import_("foyer.forcefield")
box = mb.Compound()
box.add(mb.Compound(name='Ar', pos=[1, 1, 1]))
box.add(mb.Compound(name='Ar', pos=[1, 1, 1]))
ff = forcefield.Forcefield(forcefield_files=get_fn('lj.xml'))
structure = ff.apply(box)
structure.box = [10, 10, 10, 90, 90, 90]
hoomd_simulation.create_hoomd_simulation(structure)
sim_forces = hoomd.context.current.forces
pair_force = import_("hoomd.md.pair")
assert isinstance(sim_forces[0], pair_force.lj)
def test_lj_to_hoomd_forcefield(self):
import hoomd
from foyer.forcefield import Forcefield
from mbuild.formats.hoomd_forcefield import create_hoomd_forcefield
box = mb.Compound()
box.add(mb.Compound(name="Ar", pos=[1, 1, 1]))
box.add(mb.Compound(name="Ar", pos=[1, 1, 1]))
ff = Forcefield(forcefield_files=get_fn("lj.xml"))
structure = ff.apply(box)
structure.box = [10, 10, 10, 90, 90, 90]
snapshot, forces, ref_values = create_hoomd_forcefield(structure, 2.5)
assert isinstance(forces[0], hoomd.md.pair.LJ)
def test_wrong_n_atoms(self):
with pytest.raises(MBuildError):
mb.load(get_fn('too_few_atoms.xyz'))
with pytest.raises(MBuildError):
mb.load(get_fn('too_many_atoms.xyz'))
def test_smarts_from_file(self):
p3ht = mb.load(get_fn('p3ht.smi'), smiles=True)
assert p3ht.n_bonds == 33
assert p3ht.n_particles == 33
def test_load_mol2_mdtraj(self):
with pytest.raises(KeyError):
mb.load(get_fn('benzene-nonelement.mol2'))
mb.load(get_fn('benzene-nonelement.mol2'), use_parmed=True)
def test_update_from_file(self, ch3):
ch3.update_coordinates(get_fn("methyl.pdb"))
def test_fn(self):
get_fn('benzene.mol2')
with pytest.raises((IOError, OSError)):
get_fn('garbage_file_name.foo')
def rigid_benzene(self):
compound = mb.load(get_fn('benzene.mol2'))
compound.name = 'Benzene'
compound.label_rigid_bodies()
return compound
def benzene(self):
compound = mb.load(get_fn('benzene.mol2'))
compound.name = 'Benzene'
return compound
def test_update_coordinates(self):
methyl = CH3()
methyl.update_coordinates(get_fn('methyl.mol2'))
def test_save(self):
methyl = mb.load(get_fn('methyl.mol2'))
methyl.save(filename='methyl_out.mol2')
def test_load_and_create(self):
mb.load(get_fn('methyl.mol2'))
