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 test_improper_dihedral():
untyped_benzene = pmd.load_file(get_fn('benzene.mol2'), structure=True)
ff_improper = Forcefield(forcefield_files=get_fn('improper_dihedral.xml'))
benzene = ff_improper.apply(untyped_benzene, assert_dihedral_params=False)
assert len(benzene.dihedrals) == 18
assert len([dih for dih in benzene.dihedrals if dih.improper]) == 6
assert len([dih for dih in benzene.dihedrals if not dih.improper]) == 12
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_load_files():
for ff_file in FORCEFIELDS:
ff1 = Forcefield(forcefield_files=ff_file)
assert len(ff1._atomTypes) > 0
ff2 = Forcefield(forcefield_files=ff_file)
assert len(ff1._atomTypes) == len(ff2._atomTypes)
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_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_nbfix(self, ethane):
from foyer import Forcefield
OPLSAA = Forcefield(name="oplsaa")
structure = OPLSAA.apply(ethane)
# Add nbfixes
types = list(set([a.atom_type for a in structure.atoms]))
types[0].add_nbfix(types[1].name, 1.2, 2.1)
types[1].add_nbfix(types[0].name, 1.2, 2.1)
write_lammpsdata(filename="nbfix.lammps", structure=structure)
checked_section = False
with open("nbfix.lammps", "r") as fi:
while not checked_section:
line = fi.readline()
if "PairIJ Coeffs" in line:
fi.readline()
line = fi.readline().partition("#")[0]
assert np.allclose(
np.asarray(line.split(), dtype=float),
[1, 1, 0.066, 3.5],
)
line = fi.readline().partition("#")[0]
assert np.allclose(
np.asarray(line.split(), dtype=float),
[1, 2, 2.1, 1.06907846],
)
line = fi.readline().partition("#")[0]
assert np.allclose(np.asarray(line.split(), dtype=float),
[2, 2, 0.03, 2.5])
line = fi.readline()
checked_section = True
# Break if PairIJ Coeffs is not found
if "Atoms" in line:
break
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_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_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_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 test_preserve_resname():
untyped_ethane = pmd.load_file(get_fn('ethane.mol2'), structure=True)
untyped_resname = untyped_ethane.residues[0].name
oplsaa = Forcefield(name='oplsaa')
typed_ethane = oplsaa.apply(untyped_ethane)
typed_resname = typed_ethane.residues[0].name
assert typed_resname == untyped_resname
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_apply_residues():
import mbuild as mb
from mbuild.examples import Ethane
ethane = Ethane()
opls = Forcefield(name='oplsaa')
typed = opls.apply(ethane, residues='CH3')
assert len([res for res in typed.residues if res.name == 'CH3']) == 2
def test_preserve_resname():
untyped_ethane = pmd.load_file(get_fn('ethane.mol2'), structure=True)
untyped_resname = untyped_ethane.residues[0].name
oplsaa = Forcefield(name='oplsaa')
typed_ethane = oplsaa.apply(untyped_ethane)
typed_resname = typed_ethane.residues[0].name
assert typed_resname == untyped_resname
def test_apply_residues():
import mbuild.recipes
propane = mbuild.recipes.Alkane(n=3)
opls = Forcefield(name='oplsaa')
typed = opls.apply(propane, residues='CH3')
assert len([res for res in typed.residues if res.name == 'CH3']) == 2
def test_improper_dihedral():
untyped_benzene = pmd.load_file(get_fn('benzene.mol2'), structure=True)
ff_improper = Forcefield(forcefield_files=get_fn('improper_dihedral.xml'))
benzene = ff_improper.apply(untyped_benzene, assert_dihedral_params=False)
assert len(benzene.dihedrals) == 18
assert len([dih for dih in benzene.dihedrals if dih.improper]) == 6
assert len([dih for dih in benzene.dihedrals if not dih.improper]) == 12
def test_missing_overrides():
top = os.path.join(OPLS_TESTFILES_DIR, 'benzene/benzene.top')
gro = os.path.join(OPLS_TESTFILES_DIR, 'benzene/benzene.gro')
structure = pmd.load_file(top, xyz=gro)
forcefield = Forcefield(get_fn('missing_overrides.xml'))
with pytest.raises(FoyerError):
forcefield.apply(structure)
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_load_metadata():
lj_ff = Forcefield(get_fn('lj.xml'))
assert lj_ff.version == '0.4.1'
assert lj_ff.name == 'LJ'
lj_ff = Forcefield(forcefield_files=[get_fn('lj.xml'), get_fn('lj2.xml')])
assert lj_ff.version == ['0.4.1', '4.8.2']
assert lj_ff.name == ['LJ', 'JL']
def test_apply_residues(self):
import mbuild.recipes
propane = mbuild.recipes.Alkane(n=3)
opls = Forcefield(name="oplsaa")
typed = opls.apply(propane, residues="CH3")
assert len([res for res in typed.residues if res.name == "CH3"]) == 2
def test_missing_overrides():
top = os.path.join(OPLS_TESTFILES_DIR, 'benzene/benzene.top')
gro = os.path.join(OPLS_TESTFILES_DIR, 'benzene/benzene.gro')
structure = pmd.load_file(top, xyz=gro)
forcefield = Forcefield(get_fn('bad_ff.xml'))
with pytest.raises(FoyerError):
forcefield.apply(structure)
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 write_lammps(self, filename):
cgff = Forcefield(forcefield_files='mbuild_ONA/ONA.xml')
#apply it to the mbuild structure
test_box_typed = cgff.apply(self, assert_dihedral_params=False)
#Output a LAMMPS data file
mb.formats.lammpsdata.write_lammpsdata(test_box_typed,
filename,
atom_style='full')
def test_load_files():
ff1 = Forcefield(forcefield_files=FORCEFIELDS)
assert len(ff1._atomTypes) > 0
ff2 = Forcefield(forcefield_files=FORCEFIELDS[0])
assert len(ff1._atomTypes) == len(ff2._atomTypes)
ff3 = Forcefield(name='oplsaa')
assert len(ff1._atomTypes) == len(ff3._atomTypes)
def test_load_files():
for ff_file in FORCEFIELDS:
ff1 = Forcefield(forcefield_files=ff_file)
assert len(ff1._atomTypes) > 0
ff2 = Forcefield(forcefield_files=ff_file)
assert len(ff1._atomTypes) == len(ff2._atomTypes)
ff3 = Forcefield(name=os.path.splitext(os.path.basename(ff_file))[0])
assert len(ff1._atomTypes) == len(ff3._atomTypes)
def test_load_xml(self, filename, oplsaa):
mol = pmd.load_file(get_fn(filename), structure=True)
if filename == "ethane.mol2":
ff = Forcefield(get_fn("ethane-multiple.xml"))
else:
ff = oplsaa
typed = ff.apply(mol)
typed.write_foyer(filename="snippet.xml", forcefield=ff, unique=True)
generated_ff = Forcefield("snippet.xml")
def test_load_metadata(self):
lj_ff = Forcefield(get_fn("lj.xml"))
assert lj_ff.version == "0.4.1"
assert lj_ff.name == "LJ"
lj_ff = Forcefield(
forcefield_files=[get_fn("lj.xml"),
get_fn("lj2.xml")])
assert lj_ff.version == ["0.4.1", "4.8.2"]
assert lj_ff.name == ["LJ", "JL"]
def _create_lammps(ethane, tmp):
from foyer import Forcefield
OPLSAA = Forcefield(name="oplsaa")
structure = OPLSAA.apply(ethane)
fn = tmpdir_factory.mktemp("data").join("lj.lammps")
write_lammpsdata(filename=str(fn),
structure=structure,
unit_style="real")
return str(fn)
def convert(correct_structure,
forcefield_files=['foyer_charmm.xml', 'foyer_water.xml']):
""" Convert gmx to lmp structure via foyer
Parameters
---------
correct_structure : str
filename of the correct structure we are pulling xyz from
forcefield_files :
To be passed to foyer
Notes
-----
We are making a 'fake' mbuild compound and then updating the coordinates.
This is done to preserve compound hierarchies and residue names
Note the generation of an extra box according to the correct_structure's
periodicity. This is because update_coordinates doesn't carry over
box/periodicity information.
The fake mbuild compound is then converted to parmed structure and then atomtyped
It is *necessary* to update how we are making this fakae mbuild compound
It will help to look at the gmx top file to see the order of the molecules
Remember to specify `use_atom_name` to false in order for the ffxml to succesfully
ientify atoms in the mb Compound and pmd Structure
"""
system = mb.Compound()
for i in range(64):
system.add(DSPC.DSPC(use_atom_name=False))
for i in range(1280):
system.add(SOL.SOL(use_atom_name=False))
for i in range(64):
system.add(DSPC.DSPC(use_atom_name=False))
for i in range(1280):
system.add(SOL.SOL(use_atom_name=False))
system.update_coordinates(correct_structure)
system_box = mb.Box(lengths=mb.load(correct_structure).periodicity)
# In order to avoid using smarts, define custom elements in parmed
# by adding underscores to mb particle names
for num, i in enumerate(system.particles()):
i.name = "_{}".format(i.name)
structure = system.to_parmed(
box=system_box,
residues=set([p.parent.name for p in system.particles()]))
ff = Forcefield(forcefield_files=forcefield_files)
structure = ff.apply(structure, assert_dihedral_params=False)
# Because mbuild compounds don't pass charges to parmed structures, need to
# manuallly set the charges AFTER the force field has been applied
for i, j in zip(system.particles(), structure.atoms):
j.charge = i.charge
write_lammpsdata(structure, correct_structure[:-4] + '.lammpsdata')
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 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 test_write_bad_ref(requests_mock):
import mbuild as mb
register_mock_request(mocker=requests_mock,
url='http://api.crossref.org/',
path='works/10.1021/garbage_bad_44444444jjjj/transform/application/x-bibtex',
headers={'accept': 'application/x-bibtex'},
status_code=404)
mol2 = mb.load(get_fn('ethane.mol2'))
oplsaa = Forcefield(forcefield_files=get_fn('refs-bad.xml'))
with pytest.warns(UserWarning):
ethane = oplsaa.apply(mol2, references_file='ethane.bib')
def test_write_refs():
import mbuild as mb
mol2 = mb.load(get_fn('ethane.mol2'))
oplsaa = Forcefield(name='oplsaa')
ethane = oplsaa.apply(mol2, references_file='ethane.bib')
assert os.path.isfile('ethane.bib')
with open(get_fn('ethane.bib')) as file1:
with open('ethane.bib') as file2:
diff = list(
difflib.unified_diff(file1.readlines(), file2.readlines(),
n=0))
assert not diff
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 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 test_pairs(self, benzene):
from foyer import Forcefield
import gsd, gsd.pygsd
benzene.save(filename='benzene.gsd', forcefield_name='oplsaa')
gsd_file = gsd.pygsd.GSDFile(open('benzene.gsd', 'rb'))
frame = gsd.hoomd.HOOMDTrajectory(gsd_file).read_frame(0)
structure = benzene.to_parmed()
forcefield = Forcefield(name='oplsaa')
structure = forcefield.apply(structure)
# Pairs
assert len(frame.pairs.types) == 3
assert frame.pairs.N == 21
def test_assert_bonds():
ff = Forcefield(name='trappe-ua')
derponium = mb.Compound()
at1 = mb.Particle(name='H')
at2 = mb.Particle(name='O')
at3 = mb.Particle(name='_CH4')
derponium.add([at1, at2, at3])
derponium.add_bond((at1, at2))
derponium.add_bond((at2, at3))
with pytest.raises(Exception):
ff.apply(derponium)
thing = ff.apply(derponium, assert_bond_params=False, assert_angle_params=False)
assert any(b.type is None for b in thing.bonds)
def test_residue_map():
ethane = pmd.load_file(get_fn('ethane.mol2'), structure=True)
ethane *= 2
oplsaa = Forcefield(name='oplsaa')
topo, NULL = generate_topology(ethane)
topo_with = oplsaa.run_atomtyping(topo, use_residue_map=True)
topo_without = oplsaa.run_atomtyping(topo, use_residue_map=False)
assert all([a.id for a in topo_with.atoms()][0])
assert all([a.id for a in topo_without.atoms()][0])
struct_with = pmd.openmm.load_topology(topo_with, oplsaa.createSystem(topo_with))
struct_without = pmd.openmm.load_topology(topo_without, oplsaa.createSystem(topo_without))
for atom_with, atom_without in zip(struct_with.atoms, struct_without.atoms):
assert atom_with.type == atom_without.type
b_with = atom_with.bond_partners
b_without = atom_without.bond_partners
assert [a0.type for a0 in b_with] == [a1.type for a1 in b_without]
assert [a0.idx for a0 in b_with] == [a1.idx for a1 in b_without]
def test_from_parmed():
mol2 = pmd.load_file(get_fn('ethane.mol2'), structure=True)
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)
mol2 = pmd.load_file(get_fn('ethane.mol2'), structure=True)
mol2.box_vectors = [[2, 0, 0], [0, 2, 0], [0, 0, 2]]
oplsaa = Forcefield(name='oplsaa')
ethane = oplsaa.apply(mol2)
assert ethane.box_vectors == mol2.box_vectors
def test_nbfix(self, ethane):
from foyer import Forcefield
OPLSAA = Forcefield(name='oplsaa')
structure = OPLSAA.apply(ethane)
# Add nbfixes
types = list(set([a.atom_type for a in structure.atoms]))
types[0].add_nbfix(types[1].name, 1.2, 2.1)
types[1].add_nbfix(types[0].name, 1.2, 2.1)
write_lammpsdata(filename='nbfix.lammps', structure=structure)
checked_section = False
with open('nbfix.lammps', 'r') as fi:
while not checked_section:
line = fi.readline()
if 'PairIJ Coeffs' in line:
fi.readline()
fi.readline()
fi.readline()
line = fi.readline().partition('#')[0]
assert np.allclose(
np.asarray(line.split(), dtype=float),
[1, 1, 0.066, 3.5])
line = fi.readline().partition('#')[0]
assert np.allclose(
np.asarray(line.split(), dtype=float),
[1, 2, 2.1, 1.06907846])
line = fi.readline().partition('#')[0]
assert np.allclose(
np.asarray(line.split(), dtype=float),
[2, 2, 0.03, 2.5])
line = fi.readline()
checked_section = True
# Break if PairIJ Coeffs is not found
if 'Atoms' in line:
break
def test_overrides_space():
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_missing_type_definitions():
with pytest.raises(FoyerError):
FF = Forcefield()
ethane = pmd.load_file(get_fn('ethane.mol2'), structure=True)
FF.apply(ethane)
import parmed as pmd
from foyer import Forcefield
from foyer.tests.utils import get_fn
mol2_path = get_fn('ethane.mol2')
untyped_ethane = pmd.load_file(mol2_path, structure=True)
oplsaa = Forcefield(name='oplsaa')
ethane = oplsaa.apply(untyped_ethane)
print("Atoms:")
for atom in ethane.atoms:
print('Atom {} is typed as {}'.format(atom, atom.type))
print("Bonds:")
for bond in ethane.bonds:
print('{} '.format(bond))
print("Angles:")
for angle in ethane.angles:
print('{} '.format(angle))
print("Dihedrals:")
for dihedral in ethane.dihedrals:
print('{} '.format(dihedral))
# Save to GROMACS
ethane.save('ethane.gro')
ethane.save('ethane.top')
import parmed as pmd
from foyer import Forcefield
from foyer.tests.utils import get_fn
if __name__ == '__main__':
mol2_path = get_fn('ethane.mol2')
untyped_ethane = pmd.load_file(mol2_path, structure=True)
oplsaa = Forcefield(name='oplsaa')
ethane = oplsaa.apply(untyped_ethane, references_file='ethane.bib')
print("Atoms:")
for atom in ethane.atoms:
print('Atom {} is typed as {}'.format(atom, atom.type))
print("Bonds:")
for bond in ethane.bonds:
print('{} '.format(bond))
print("Angles:")
for angle in ethane.angles:
print('{} '.format(angle))
print("Dihedrals:")
for dihedral in ethane.dihedrals:
print('{} '.format(dihedral))
# Save to GROMACS
ethane.save('ethane.gro')
ethane.save('ethane.top')
# Within the `Forcefield.apply` method, an intermediate OpenMM system is
def test_write_refs():
mol2 = mb.load(get_fn('ethane.mol2'))
oplsaa = Forcefield(name='oplsaa')
ethane = oplsaa.apply(mol2, references_file='ethane.bib')
assert os.path.isfile('ethane.bib')
def test_fullerene():
fullerene = pmd.load_file(get_fn('fullerene.pdb'), structure=True)
forcefield = Forcefield(get_fn('fullerene.xml'))
forcefield.apply(fullerene, assert_dihedral_params=False)
def test_apply_residues():
from mbuild.examples import Ethane
ethane = Ethane()
opls = Forcefield(name='oplsaa')
typed = opls.apply(ethane, residues='CH3')
assert len([res for res in typed.residues if res.name == 'CH3']) == 2
def test_polymer():
peg100 = mb.load(get_fn('peg100.mol2'))
forcefield = Forcefield(name='oplsaa')
forcefield.apply(peg100)
def test_missing_definition():
structure = pmd.load_file(get_fn('silly_chemistry.mol2'), structure=True)
forcefield = Forcefield(get_fn('missing_overrides.xml'))
with pytest.raises(FoyerError):
forcefield.apply(structure)
def test_surface():
surface = mb.load(get_fn('silica.mol2'))
forcefield = Forcefield(get_fn('opls-silica.xml'))
forcefield.apply(surface, assert_bond_params=False)
def test_bonded(self, ethane):
from foyer import Forcefield
import gsd, gsd.pygsd
ethane.save(filename='ethane.gsd', forcefield_name='oplsaa')
gsd_file = gsd.pygsd.GSDFile(open('ethane.gsd', 'rb'))
frame = gsd.hoomd.HOOMDTrajectory(gsd_file).read_frame(0)
structure = ethane.to_parmed()
forcefield = Forcefield(name='oplsaa')
structure = forcefield.apply(structure)
# Bonds
n_bonds = frame.bonds.N
assert n_bonds == len(structure.bonds)
expected_unique_bond_types = ['opls_135-opls_135', 'opls_135-opls_140']
bond_types = frame.bonds.types
assert np.array_equal(bond_types, expected_unique_bond_types)
bond_typeids = frame.bonds.typeid
bond_atoms = frame.bonds.group
expected_bond_atoms = [[bond.atom1.idx, bond.atom2.idx]
for bond in structure.bonds]
assert np.array_equal(bond_atoms, expected_bond_atoms)
bond_type_dict = {('C', 'C') : 0, ('C', 'H') : 1, ('H', 'C') : 1}
expected_bond_typeids = []
for bond in structure.bonds:
expected_bond_typeids.append(bond_type_dict[(bond.atom1.name,
bond.atom2.name)])
assert np.array_equal(bond_typeids, expected_bond_typeids)
# Angles
n_angles = frame.angles.N
assert n_angles == len(structure.angles)
expected_unique_angle_types = ['opls_135-opls_135-opls_140',
'opls_140-opls_135-opls_140']
angle_types = frame.angles.types
assert np.array_equal(angle_types, expected_unique_angle_types)
angle_typeids = frame.angles.typeid
angle_atoms = frame.angles.group
expected_angle_atoms = [[angle.atom1.idx, angle.atom2.idx, angle.atom3.idx]
for angle in structure.angles]
assert np.array_equal(angle_atoms, expected_angle_atoms)
angle_type_dict = {('C', 'C', 'H') : 0, ('H', 'C', 'C') : 0,
('H', 'C', 'H') : 1}
expected_angle_typeids = []
for angle in structure.angles:
expected_angle_typeids.append(angle_type_dict[(angle.atom1.name,
angle.atom2.name,
angle.atom3.name)])
assert np.array_equal(angle_typeids, expected_angle_typeids)
# Dihedrals
n_dihedrals = frame.dihedrals.N
assert n_dihedrals == len(structure.rb_torsions)
expected_unique_dihedral_types = ['opls_140-opls_135-opls_135-opls_140']
dihedral_types = frame.dihedrals.types
assert np.array_equal(dihedral_types, expected_unique_dihedral_types)
dihedral_typeids = frame.dihedrals.typeid
dihedral_atoms = frame.dihedrals.group
expected_dihedral_atoms = []
for dihedral in structure.rb_torsions:
expected_dihedral_atoms.append([dihedral.atom1.idx, dihedral.atom2.idx,
dihedral.atom3.idx, dihedral.atom4.idx])
assert np.array_equal(dihedral_atoms, expected_dihedral_atoms)
assert np.array_equal(dihedral_typeids, np.zeros(n_dihedrals))