def __init__(self):
"""Returns a CER NS C24 with the head-to-tail vector pointing in +z.
"""
super(UCer2, self).__init__(name='ucer2')
mb.load('ucer2.pdb', compound=self, relative_to_module=self.__module__)
mb.coordinate_transform.z_axis_transform(self,
new_origin=self[2], point_on_z_axis=self[58])
def __init__(self):
"""Returns a CHOL with the head-to-tail vector pointing in +z.
"""
super(Chol, self).__init__(name='chol')
mb.load('chol.pdb', compound=self, relative_to_module=self.__module__)
mb.coordinate_transform.z_axis_transform(self,
new_origin=self[2], point_on_z_axis=self[63])
def __init__(self):
super(CH3, self).__init__()
mb.load('ch3.pdb', compound=self, relative_to_module=self.__module__)
self.translate(-self[0].pos) # Move carbon to origin.
self.add(mb.Port(anchor=self[0]), 'up')
self['up'].translate([0, -0.07, 0])
def __init__(self):
"""Returns a CG CHOL with the head-to-tail vector pointing in -z.
"""
super(Chol, self).__init__()
mb.load('chol.hoomdxml', compound=self, relative_to_module=self.__module__)
xx = list(self.particles())
mb.coordinate_transform.z_axis_transform(self,
new_origin=xx[0], point_on_z_axis=xx[6])
self.rotate(np.pi, [1, 0, 0])
def __init__(self):
"""Returns a CG eCER2 with the head-to-tail vector pointing in -z.
"""
super(ECer2, self).__init__()
mb.load('ecer2.hoomdxml', compound=self, relative_to_module=self.__module__)
self.periodicity = [0, 0, 0]
xx = list(self.particles())
mb.coordinate_transform.z_axis_transform(self,
new_origin=xx[6], point_on_z_axis=xx[11])
self.rotate(np.pi, [1, 0, 0])
def __init__(self):
"""Returns a CG FFA C16 with the head-to-tail vector pointing in -z.
"""
super(FFAC16, self).__init__()
mb.load('ffac16.hoomdxml', compound=self, relative_to_module=self.__module__)
self.periodicity = [0, 0, 0]
xx = list(self.particles())
mb.coordinate_transform.z_axis_transform(self,
new_origin=xx[5], point_on_z_axis=xx[0])
self.spin(np.pi, [1, 0, 0])
def __init__(self):
super(CH2, self).__init__()
mb.load('ch2.pdb', compound=self, relative_to_module=self.__module__)
mb.translate(self, -self[0].pos) # Move carbon to origin.
self.add(mb.Port(anchor=self[0]), 'up')
mb.translate(self['up'], [0, 0.07, 0])
self.add(mb.Port(anchor=self[0]), 'down')
mb.translate(self['down'], [0, -0.07, 0])
def __init__(self):
super(PegMonomer, self).__init__()
mb.load('peg_monomer.pdb', compound=self, relative_to_module=self.__module__)
self.translate(-self[0].pos)
self.add(mb.Port(anchor=self[0]), 'down')
self['down'].translate([0, -0.07, 0])
self.add(mb.Port(anchor=self[6]), 'up')
self['up'].translate([0, 0.073, 0])
def __init__(self):
super(PegMonomer, self).__init__()
mb.load('peg_monomer.pdb', compound=self, relative_to_module=self.__module__)
mb.translate(self, -self.C[0])
self.add(mb.Port(anchor=self.C[0]), 'down')
mb.translate(self.down, [0, -0.07, 0])
self.add(mb.Port(anchor=self.O[0]), 'up')
mb.translate(self.up, [0, 0.364, 0])
def __init__(self):
super(Ester, self).__init__()
mb.load('ester.pdb', compound=self, relative_to_module=self.__module__)
mb.translate(self, -self[0].pos)
self.add(mb.Port(anchor=self[2]), 'up')
mb.rotate_around_z(self['up'], np.pi / 2)
mb.translate_to(self['up'], self[2].pos + np.array([0.07, 0, 0]))
self.add(mb.Port(anchor=self[0]), 'down')
mb.rotate_around_z(self['down'], np.pi / 2)
mb.translate(self['down'], np.array([-0.07, 0, 0]))
def __init__(self):
super(Ester, self).__init__()
mb.load('ester.pdb', compound=self, relative_to_module=self.__module__)
self.translate(-self[0].pos)
self.add(mb.Port(anchor=self[2]), 'up')
self['up'].spin(np.pi / 2, [0, 0, 1])
self['up'].translate_to(np.array([0.07, 0, 0]))
self.add(mb.Port(anchor=self[0]), 'down')
self['down'].spin(np.pi / 2, [0, 0, 1])
self['down'].translate(np.array([-0.07, 0, 0]))
def __init__(self):
super(Carbonyl, self).__init__()
mb.load('carbonyl.pdb',
compound=self,
relative_to_module=self.__module__)
self.translate(-self[0].pos) # Move carbon to origin.
self.add(
mb.Port(anchor=self[0], orientation=[1, 0, 0], separation=0.075),
'right')
self.add(
mb.Port(anchor=self[0], orientation=[-1, 0, 0], separation=0.075),
'left')
def test_save_box(self, ch3):
extensions = ['.mol2', '.pdb', '.hoomdxml', '.gro']
box_attributes = ['mins', 'maxs', 'lengths']
custom_box = mb.Box([.8, .8, .8])
for ext in extensions:
outfile_padded = 'padded_methyl' + ext
outfile_custom = 'custom_methyl' + ext
ch3.save(filename=outfile_padded, box=None, overwrite=True)
ch3.save(filename=outfile_custom, box=custom_box, overwrite=True)
padded_ch3 = mb.load(outfile_padded)
custom_ch3 = mb.load(outfile_custom)
for attr in box_attributes:
pad_attr = getattr(padded_ch3.boundingbox, attr)
custom_attr = getattr(custom_ch3.boundingbox, attr)
assert np.array_equal(pad_attr, custom_attr)
def __init__(self, template, stoichiometry_dict):
# Call the mb.Compound initialisation
super().__init__()
# Load the unit cell
mb.load(os.path.join(PDB_LIBRARY, template), compound=self)
# Replacable atoms in the matrix are assigned as type `X'
# Note: In both Py2 and Py3, subsequent calls to keys() and values()
# with no intervening modifications will directly correspond
# \cite{PyDocumentation}
atom_types, atom_probs, _ = calculate_probabilities(stoichiometry_dict)
for particle in self.particles():
if particle.name == 'X':
# `Randomly' select an atom type based on the biases given in
# stoichiometry_dict
particle.name = np.random.choice(atom_types, p=atom_probs)
def __init__(self, use_atom_name=True):
super(SOL, self).__init__()
if use_atom_name:
mb.load('SOL_new.mol2',
compound=self,
relative_to_module=self.__module__,
infer_hierarchy=False)
else:
mb.load('SOL.mol2',
compound=self,
relative_to_module=self.__module__,
infer_hierarchy=False)
self.children[0].charge = -0.834
self.children[1].charge = 0.417
self.children[2].charge = 0.417
def __init__(self):
super(Betacristobalite, self).__init__()
mb.load('beta-cristobalite-expanded.mol2', compound=self,
relative_to_module=self.__module__)
self.periodicity = np.array([5.3888, 4.6669, 0.0])
count = 0
for particle in self.particles():
if particle.name.startswith('O') and particle.pos[2] > 1.0:
count += 1
port = mb.Port(anchor=particle)
mb.rotate_around_x(port, np.pi/2)
mb.translate(port, particle.pos + np.array([0, 0, .1]))
self.add(port, 'port_{}'.format(count))
def __init__(self):
super(Isopropylbenzene, self).__init__()
mb.load('isopropylbenzene.pdb',
compound=self,
relative_to_module=self.__module__)
# pop off bottom hydrogen on benzene ring
direction = self[18].xyz - self[6].xyz
self.remove(self[18])
# add port anchored to newly hydrogen-less carbon in benzene ring
self.add(
mb.Port(anchor=self[6],
orientation=direction.tolist()[0],
separation=0.07), 'down')
def __init__(self, ):
super(Silane, self).__init__()
mb.load('silane.pdb', compound=self, relative_to_module=self.__module__)
# Transform the coordinate system such that the silicon atom is at the
# origin and the oxygen atoms are on the x axis.
mb.x_axis_transform(self, new_origin=self[0], point_on_x_axis=self[1])
# Add bottom port.
self.add(mb.Port(anchor=self[0]), 'down')
mb.translate(self['down'], np.array([0, -.07, 0]))
# Add top port.
self.add(mb.Port(anchor=self[0]), 'up')
mb.translate(self['up'], np.array([0, .07, 0]))
def __init__(self, ):
super(Silane, self).__init__()
mb.load('silane.pdb', compound=self, relative_to_module=self.__module__)
# Transform the coordinate system such that the silicon atom is at the
# origin and the oxygen atoms are on the x axis.
mb.x_axis_transform(self, new_origin=self[0], point_on_x_axis=self[1])
# Add bottom port.
self.add(mb.Port(anchor=self[0]), 'down')
self['down'].translate(np.array([0, -.07, 0]))
# Add top port.
self.add(mb.Port(anchor=self[0]), 'up')
self['up'].translate(np.array([0, .07, 0]))
def __init__(self):
"""Returns a CG uCER2 with the head-to-tail vector pointing in -z.
"""
super(Cer2_18, self).__init__()
mb.load('cer2-18.hoomdxml', compound=self, relative_to_module=self.__module__)
self.periodicity = [0, 0, 0]
xx = list(self.particles())
mb.coordinate_transform.z_axis_transform(self,
new_origin=xx[9], point_on_z_axis=xx[14])
self.translate([-self.center[0], -self.center[1], 0]) # center in xy plane
self.masses = [0.403639, 0.584458, 0.584458, 0.584458,
0.584458, 0.584458, 0.597575, 0.556458, 0.556458, 0.584458,
0.584458, 0.584458, 0.598458, 0.236214, 0.236214]
self.mass = np.sum(self.masses)
self.rotate(np.pi, [1, 0, 0])
def test_save_box(self, ch3):
extensions = ['.mol2', '.pdb', '.hoomdxml', '.gro']
box_attributes = ['mins', 'maxs', 'lengths']
custom_box = mb.Box([.8, .8, .8])
for ext in extensions:
outfile_padded = 'padded_methyl' + ext
outfile_custom = 'custom_methyl' + ext
ch3.save(filename=outfile_padded, box=None, overwrite=True)
ch3.save(filename=outfile_custom, box=custom_box, overwrite=True)
padded_ch3 = mb.load(outfile_padded)
custom_ch3 = mb.load(outfile_custom)
for attr in box_attributes:
pad_attr = getattr(padded_ch3.boundingbox, attr)
custom_attr = getattr(custom_ch3.boundingbox, attr)
assert np.array_equal(pad_attr, custom_attr)
def test_non_zero_charge(self):
import mbuild as mb
compound = mb.load("C1=CC=C2C(=C1)C(C3=CC=CC=C3O2)C(=O)O", smiles=True)
oplsaa = Forcefield(name="oplsaa")
with pytest.warns(UserWarning):
oplsaa.apply(compound, assert_dihedral_params=False)
def test_comb_rule(self, mixing_rule):
import mbuild as mb
mol2 = mb.load(get_fn("ethane.mol2"))
oplsaa = Forcefield(name="oplsaa")
ethane = oplsaa.apply(mol2, combining_rule=mixing_rule)
assert ethane.combining_rule == mixing_rule
def get_info(inputfile, frame=-1, show_bonds=False):
"""Get dictionary of information about inputfile.
`info` is a dictionary containing the number of particles, the particle
types in the system, a typeid for each particle, particle positions, the
number of bonds, the particle indices which are bonded, and the box
information. These quantities follow GSD format
Parameters
----------
inputfile: path
Path to file to get info from.
frame: int
If trajectory, frame to get info from.
show_bonds: bool
Whether to show the bonds in the scene.
Returns
-------
dict
"""
name, extension = os.path.splitext(inputfile)
if extension == ".gsd":
# info contains N, types, typeids, positions, N_bonds, bonds, box
info = get_gsd_info(inputfile, frame, show_bonds)
else:
comp = mb.load(inputfile)
# info contains N, types, typeids, positions, N_bonds, bonds, box
info = get_comp_info(comp, show_bonds)
return info
def test_topology_precedence():
"""Test to see if topology precedence is properly adhered to.
This test uses a force field file where bond, angle, and dihedral
parameters are present with different counts of `type` definitions.
It checks that:
1. The parameters with the higher number of `type` definitions
are assigned (because they are given the highest precedence)
2. That if multiple definitions exist with the same number of
`type` definitions, that the convention from OpenMM is followed
whereby the definitions that occurs earliest in the XML is
assigned.
"""
import mbuild as mb
ethane = mb.load(get_fn('ethane.mol2'))
ff = Forcefield(forcefield_files=get_fn('ethane-topo-precedence.xml'))
typed_ethane = ff.apply(ethane)
assert len([bond for bond in typed_ethane.bonds
if round(bond.type.req, 2) == 1.15]) == 6
assert len([bond for bond in typed_ethane.bonds
if round(bond.type.req, 2) == 1.6]) == 1
assert len([angle for angle in typed_ethane.angles
if round(angle.type.theteq, 3) == 120.321]) == 6
assert len([angle for angle in typed_ethane.angles
if round(angle.type.theteq, 3) == 97.403]) == 6
assert len([rb for rb in typed_ethane.rb_torsions
if round(rb.type.c0, 3) == 0.287]) == 9
def run_nvt(**custom_args):
# Use mBuild to create a methane molecule
methane = mbuild.load("C", smiles=True)
# Create an empty mbuild.Box
box = mbuild.Box(lengths=[3.0, 3.0, 3.0])
# Load force field
oplsaa = foyer.forcefields.load_OPLSAA()
# Use foyer to apply force field to methane
methane_ff = oplsaa.apply(methane)
# Create box and species list
box_list = [box]
species_list = [methane_ff]
# Use Cassandra to insert some initial number of methane molecules
mols_to_add = [[50]]
# Define the System
system = mc.System(box_list, species_list, mols_to_add=mols_to_add)
# Define the MoveSet
moveset = mc.MoveSet("nvt", species_list)
# Run a simulation at 300 K for 10000 MC moves
mc.run(
system=system,
moveset=moveset,
run_type="equilibration",
run_length=10000,
temperature=300.0 * u.K,
**custom_args,
)
def _get_water():
cache_dir = resource_filename('bulk_water', 'lib')
filename = 'water.mol2'
water = mb.load(os.path.join(cache_dir, filename))
water.name = 'SOL'
return water
def test_rb_torsions_vs_foyer(self, ethanol_with_rb_torsions):
# Given that these force constants are copied from Foyer's OPLS-AA file,
# compare to processing through the current MoSDeF pipeline
import foyer
import mbuild
comp = mbuild.load("CC", smiles=True)
comp.xyz = ethanol_with_rb_torsions.positions.m_as(unit.nanometer)
ff = foyer.Forcefield(name="oplsaa")
from_foyer = ff.apply(comp)
from_foyer.box = [40, 40, 40, 90, 90, 90]
from_foyer.save("from_foyer.top")
from_foyer.save("from_foyer.gro")
rb_torsion_energy_from_foyer = _run_gmx_energy(
top_file="from_foyer.top",
gro_file="from_foyer.gro",
mdp_file=_get_mdp_file("default"),
).energies["Torsion"]
# GROMACS vs. OpenMM was already compared, so just use one
omm = get_gromacs_energies(ethanol_with_rb_torsions, decimal=3).energies[
"Torsion"
]
assert (omm - rb_torsion_energy_from_foyer).m_as(kj_mol) < 1e-6
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 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_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_load_with_top(self, ethane):
ethane.save(filename='ethane.xyz')
ethane.save(filename='ethane.mol2')
ethane_in = mb.load('ethane.xyz', top='ethane.mol2')
assert len(ethane_in.children) == 8
assert ethane_in.n_bonds == 7
assert set([child.name for child in ethane_in.children]) == {'C', 'H'}
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_gaff(self, smiles):
import foyer
import mbuild as mb
# These tests are smiles strings
cmpd = mb.load(smiles, smiles=True)
ff = commpare.identify_forcefields()['GAFF']
structure = ff.apply(cmpd)
# Enlarge box to avoid cutoff issues
bbox = cmpd.boundingbox
bbox.lengths *= 10
if any(bbox.lengths < 10):
bbox.lengths = [100, 100, 100]
structure.box = [
bbox.lengths[0], bbox.lengths[1], bbox.lengths[2], 90, 90, 90
]
energies = commpare.spawn_engine_simulations(structure,
hoomd_kwargs={
'ref_distance': 10,
'ref_energy':
1 / 4.184
})
print(smiles)
print(energies)
print('=' * 20)
def run_gcmc_restricted():
# Use mbuild to create molecules
methane = mbuild.load("C", smiles=True)
# Create an empty mbuild.Box
box = mbuild.Box(lengths=[5.0, 5.0, 5.0])
# Load forcefields
oplsaa = foyer.forcefields.load_OPLSAA()
# Use foyer to apply forcefields
methane_ff = oplsaa.apply(methane)
# Create box and species list
box_list = [box]
species_list = [methane_ff]
mols_to_add = [[10]]
system = mc.System(box_list, species_list, mols_to_add=mols_to_add)
moves = mc.Moves("gcmc", species_list)
# Specify restricted insertions
moves.add_restricted_insertions(species_list, [["sphere"]], [[20]])
mc.run(
system=system,
moves=moves,
run_type="equilibration",
run_length=100,
temperature=300.0,
chemical_potentials=[-35.0],
prop_freq=10,
)
def test_allow_empty_def(self):
import mbuild as mb
ethane = mb.load(get_fn("ethane.mol2"))
with pytest.warns(ValidationWarning):
ff = Forcefield(forcefield_files=get_fn("empty_def.xml"))
ff.apply(ethane)
def test_write_refs_multiple(self, requests_mock):
import mbuild as mb
register_mock_request(
mocker=requests_mock,
url="http://api.crossref.org/",
path="works/10.1021/ja9621760/transform/application/x-bibtex",
headers={"accept": "application/x-bibtex"},
text=RESPONSE_BIB_ETHANE_JA962170,
)
register_mock_request(
mocker=requests_mock,
url="http://api.crossref.org/",
path="works/10.1021/jp0484579/transform/application/x-bibtex",
headers={"accept": "application/x-bibtex"},
text=RESPONSE_BIB_ETHANE_JP0484579,
)
mol2 = mb.load(get_fn("ethane.mol2"))
oplsaa = Forcefield(forcefield_files=get_fn("refs-multi.xml"))
ethane = oplsaa.apply(mol2, references_file="ethane-multi.bib")
assert os.path.isfile("ethane-multi.bib")
with open(get_fn("ethane-multi.bib")) as file1:
with open("ethane-multi.bib") as file2:
diff = list(
difflib.unified_diff(file1.readlines(),
file2.readlines(),
n=0))
assert not diff
def test_overrides_space(self):
import mbuild as mb
ethane = mb.load(get_fn("ethane.mol2"))
ff = Forcefield(forcefield_files=get_fn("overrides-space.xml"))
typed_ethane = ff.apply(ethane)
assert typed_ethane.atoms[0].type == "CT3"
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 __init__(self):
super(PegMonomer, self).__init__()
mb.load(
"peg_monomer.pdb",
compound=self,
relative_to_module=self.__module__,
infer_hierarchy=False,
)
self.translate(-self[0].pos)
self.add(mb.Port(anchor=self[0]), "down")
self["down"].translate([0, -0.07, 0])
self.add(mb.Port(anchor=self[6]), "up")
self["up"].translate([0, 0.073, 0])
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_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_reload(self):
# Create a compound and write it to file.
p3ht1 = mb.load('CCCCCCC1=C(SC(=C1)C)C', smiles=True)
p3ht1.save("p3ht1.pdb")
# Create another compound, rotate it and write it to file.
p3ht2 = mb.load('CCCCCCC1=C(SC(=C1)C)C', smiles=True)
mb.rotate(p3ht2, np.pi / 2, [0, 0, 1])
p3ht2.save("p3ht2.pdb")
# Load p3ht2.pdb into p3ht1, modifying the atom positions of p3ht1.
p3ht1.update_coordinates("p3ht2.pdb")
p3ht1.save("modified_p3ht1.pdb")
assert p3ht1.n_particles == 33
assert p3ht1.n_bonds == 33
def test_topology_precedence():
"""Test to see if topology precedence is properly adhered to.
This test uses a force field file where bond, angle, and dihedral
parameters are present with different counts of `type` definitions.
It checks that:
1. The parameters with the higher number of `type` definitions
are assigned (because they are given the highest precedence)
2. That if multiple definitions exist with the same number of
`type` definitions, that the convention from OpenMM is followed
whereby the definitions that occurs earliest in the XML is
assigned.
"""
ethane = mb.load(get_fn('ethane.mol2'))
ff = Forcefield(forcefield_files=get_fn('ethane-topo-precedence.xml'))
typed_ethane = ff.apply(ethane)
assert len([bond for bond in typed_ethane.bonds
if round(bond.type.req, 2) == 1.15]) == 6
assert len([bond for bond in typed_ethane.bonds
if round(bond.type.req, 2) == 1.6]) == 1
assert len([angle for angle in typed_ethane.angles
if round(angle.type.theteq, 3) == 120.321]) == 6
assert len([angle for angle in typed_ethane.angles
if round(angle.type.theteq, 3) == 97.403]) == 6
assert len([rb for rb in typed_ethane.rb_torsions
if round(rb.type.c0, 3) == 0.287]) == 9
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 Compare_Standard_Mol(test_molecule_path,test_forcefield_path):
molecule=mb.load(test_molecule_path)
parmed_structure = molecule.to_parmed()
opls = foyer.Forcefield(forcefield_files=[test_forcefield_path])
typed_molecule = opls.apply(parmed_structure)
filepath=os.path.join("./test_molecules/test_molecule_comp.top")
typed_molecule.save(filepath,overwrite=True)
originalfilepath=os.path.join(test_molecule_path[:-4]+'top')
count=0
total=0
halt=0
with open(filepath,'r') as openfile:
with open(originalfilepath,'r') as compfile:
comp_lines=compfile.readlines()[17:]
lines=openfile.readlines()[17:]
#print(len(comp_lines),len(lines))
for i,line in enumerate(lines):
#print(line)
if line == '[ bonds ]\n':
halt = 1
if line == '[ pairs ]\n':
halt = 0
if not(halt):
total+=1
if line == comp_lines[i]:
count+=1
if count/total==1.0:
print(test_molecule_path[:-5] +' Passed')
else:
print(test_molecule_path[:-5] +' Failed')
def __init__(self):
super(Betacristobalite, self).__init__()
mb.load('beta-cristobalite-expanded.mol2', compound=self,
relative_to_module=self.__module__)
self.periodicity = np.array([5.3888, 4.6669, 0.0])
count = 0
for particle in self.particles():
if particle.name.startswith('O') and particle.pos[2] > 1.0:
count += 1
port = mb.Port(anchor=particle, orientation=[0, 0, 1],
separation=0.1)
self.add(port, 'port_{}'.format(count))
particle.name = 'O' # Strip numbers required in .mol2 files.
elif particle.name.startswith('Si'):
particle.name = 'Si'
def test_missing_topo_params(ff_filename, kwargs):
"""Test that the user is notified if not all topology parameters are found."""
ethane = mb.load(get_fn('ethane.mol2'))
oplsaa_with_typo = Forcefield(forcefield_files=get_fn(ff_filename))
with pytest.raises(Exception):
ethane = oplsaa_with_typo.apply(ethane)
with pytest.warns(UserWarning):
ethane = oplsaa_with_typo.apply(ethane, **kwargs)
def test_box_dimensions(self, benzene):
n_benzenes = 10
filled = mb.fill_box(benzene,
n_compounds=n_benzenes,
box=[0, 0, 0, 4, 4, 4])
filled.save(filename='benzene.hoomdxml')
for atom in mb.load('benzene.hoomdxml'):
assert atom.pos.max() < 20
assert atom.pos.min() > -20
def __init__(self):
super(Initiator, self).__init__()
# Look for data file in same directory as this python module.
mb.load('initiator.pdb', compound=self, relative_to_module=self.__module__)
# Transform the coordinate system such that the two carbon atoms
# that are part of the backbone are on the y axis, C_1 at the origin.
mb.y_axis_transform(self, new_origin=self[0], point_on_y_axis=self[21])
# Add bottom port
self.add(mb.Port(anchor=self[0]), 'down')
# Place the port.
mb.translate(self['down'], self[0].pos + np.array([0.0, -0.07, 0.0]))
# Add top port.
self.add(mb.Port(anchor=self[21]), 'up')
# Place the port.
mb.translate(self['up'], self[21].pos + np.array([0.0, 0.07, 0.0]))
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 test_write_refs_multiple():
mol2 = mb.load(get_fn('ethane.mol2'))
oplsaa = Forcefield(forcefield_files=get_fn('refs-multi.xml'))
ethane = oplsaa.apply(mol2, references_file='ethane-multi.bib')
assert os.path.isfile('ethane-multi.bib')
with open(get_fn('ethane-multi.bib')) as file1:
with open('ethane-multi.bib') as file2:
diff = list(difflib.unified_diff(file1.readlines(),
file2.readlines(),
n=0))
assert not diff
def __init__(self, surface_roughness=1.0):
super(AmorphousSilica, self).__init__()
if surface_roughness == 1.0:
# TODO: description of how this surface was generated/citation
mb.load('amorphous_silica_sr1.0.pdb', compound=self,
relative_to_module=self.__module__)
self.periodicity = np.array([5.4366, 4.7082, 0.0])
else:
raise ValueError('Amorphous silica input file with surface '
'roughness of {0:.1f} does not exist. If you have '
'this structure, please submit a pull request to'
'add it! '.format(surface_roughness))
count = 0
for particle in self.particles():
if particle.name == 'OB':
count += 1
port = mb.Port(anchor=particle, orientation=[0, 0, 1],
separation=0.1)
self.add(port, 'port_{}'.format(count))
def test_from_mbuild():
mol2 = mb.load(get_fn('ethane.mol2'))
oplsaa = Forcefield(name='oplsaa')
ethane = oplsaa.apply(mol2)
assert sum((1 for at in ethane.atoms if at.type == 'opls_135')) == 2
assert sum((1 for at in ethane.atoms if at.type == 'opls_140')) == 6
assert len(ethane.bonds) == 7
assert all(x.type for x in ethane.bonds)
assert len(ethane.angles) == 12
assert all(x.type for x in ethane.angles)
assert len(ethane.rb_torsions) == 9
assert all(x.type for x in ethane.dihedrals)
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_from_mbuild_customtype():
mol2 = mb.load(get_fn('ethane_customtype.pdb'))
customtype_ff = Forcefield(forcefield_files=get_fn('validate_customtypes.xml'))
ethane = customtype_ff.apply(mol2)
assert sum((1 for at in ethane.atoms if at.type == 'C3')) == 2
assert sum((1 for at in ethane.atoms if at.type == 'Hb')) == 6
assert len(ethane.bonds) == 7
assert all(x.type for x in ethane.bonds)
assert len(ethane.angles) == 12
assert all(x.type for x in ethane.angles)
assert len(ethane.rb_torsions) == 9
assert all(x.type for x in ethane.dihedrals)
def __init__(self, alpha=0):
super(MPC, self).__init__()
# Look for data file in same directory as this python module.
mb.load('mpc.pdb', compound=self, relative_to_module=self.__module__)
# Transform the coordinate system of mpc such that the two carbon atoms
# that are part of the backbone are on the y axis, c_backbone at the origin.
C_top = self[37]
# this can be achieved with the following alternative syntax:
# C_top = self.labels["atom[37]"]
# C_top = self.labels["atom"][37]
C_bottom = self[1]
mb.y_axis_transform(self, new_origin=C_top, point_on_y_axis=C_bottom)
# Add top port.
self.add(mb.Port(anchor=C_top), label='up')
mb.translate(self['up'], C_top.pos - (C_top.pos - C_bottom.pos)*1.50)
# Add bottom port
self.add(mb.Port(anchor=C_bottom), 'down')
mb.rotate_around_y(self['down'], alpha)
mb.translate(self['down'], C_bottom.pos - (C_bottom.pos - C_top.pos)*1.50)
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'))