def test_eq_overall(self):
ref = pmd.load_file(get_fn('ethane.top'), xyz=get_fn('ethane.gro'))
top1 = from_parmed(ref)
top2 = from_parmed(ref)
assert top1 != top2
def test_from_parmed_member_types(self):
struc = pmd.load_file(get_fn("ethane.top"), xyz=get_fn("ethane.gro"))
top = from_parmed(struc)
for potential_types in [
getattr(top, attr)
for attr in ["bond_types", "angle_types", "dihedral_types"]
]:
for potential in potential_types:
assert potential.member_types
def test_to_parmed_full(self):
struc = pmd.load_file(get_fn('ethane.top'), xyz=get_fn('ethane.gro'))
top = from_parmed(struc)
struc_from_top = to_parmed(top)
assert struc.bond_types == struc_from_top.bond_types
assert struc.angle_types == struc_from_top.angle_types
assert struc.dihedral_types == struc_from_top.dihedral_types
assert struc.rb_torsion_types == struc_from_top.rb_torsion_types
# Detail comparisions
for i in range(len(struc.atoms)):
assert struc_from_top.atoms[i].name == struc.atoms[i].name
assert struc_from_top.atoms[i].atom_type == struc.atoms[
i].atom_type
for i in range(len(struc.bonds)):
assert struc_from_top.bonds[i].atom1.name == struc.bonds[
i].atom1.name
assert struc_from_top.bonds[i].atom2.name == struc.bonds[
i].atom2.name
assert struc_from_top.bonds[i].type == struc.bonds[i].type
for i in range(len(struc.angles)):
assert struc_from_top.angles[i].atom1.name == struc.angles[
i].atom1.name
assert struc_from_top.angles[i].atom2.name == struc.angles[
i].atom2.name
assert struc_from_top.angles[i].atom3.name == struc.angles[
i].atom3.name
assert struc_from_top.angles[i].type == struc.angles[i].type
for i in range(len(struc.dihedrals)):
assert struc_from_top.dihedrals[i].atom1.name == struc.dihedrals[
i].atom1.name
assert struc_from_top.dihedrals[i].atom2.name == struc.dihedrals[
i].atom2.name
assert struc_from_top.dihedrals[i].atom3.name == struc.dihedrals[
i].atom3.name
assert struc_from_top.dihedrals[i].atom4.name == struc.dihedrals[
i].atom4.name
assert struc_from_top.dihedrals[i].type == struc.dihedrals[i].type
for i in range(len(struc.rb_torsions)):
assert struc_from_top.rb_torsions[
i].atom1.name == struc.rb_torsions[i].atom1.name
assert struc_from_top.rb_torsions[
i].atom2.name == struc.rb_torsions[i].atom2.name
assert struc_from_top.rb_torsions[
i].atom3.name == struc.rb_torsions[i].atom3.name
assert struc_from_top.rb_torsions[
i].atom4.name == struc.rb_torsions[i].atom4.name
assert struc_from_top.rb_torsions[i].type == struc.rb_torsions[
i].type
def test_eq_bonds(self):
ref = pmd.load_file(get_fn('ethane.top'), xyz=get_fn('ethane.gro'))
missing_bond = deepcopy(ref)
missing_bond.bonds[0].delete()
assert ref != missing_bond
bad_bond_type = deepcopy(ref)
bad_bond_type.bond_types[0].k = 22
assert ref != bad_bond_type
def test_read_gro(self):
top = read_gro(get_fn('acn.gro'))
assert top.name == 'ACN'
assert top.n_sites == 6
assert_allclose_units(top.box.lengths, 4*np.ones(3)*u.nm, rtol=1e-5, atol=1e-8)
top = read_gro(get_fn('350-waters.gro'))
assert top.name == 'Generic title'
assert top.n_sites == 1050
assert_allclose_units(top.box.lengths, 2.20866*np.ones(3)*u.nm, rtol=1e-5, atol=1e-8)
def test_eq_dihedrals(self):
ref = pmd.load_file(get_fn('ethane.top'), xyz=get_fn('ethane.gro'))
missing_dihedral = deepcopy(ref)
missing_dihedral.rb_torsions[0].delete()
assert ref != missing_dihedral
bad_dihedral_type = deepcopy(ref)
bad_dihedral_type.rb_torsion_types[0].k = 22
assert ref != bad_dihedral_type
def test_eq_angles(self):
ref = pmd.load_file(get_fn('ethane.top'), xyz=get_fn('ethane.gro'))
missing_angle = deepcopy(ref)
missing_angle.angles[0].delete()
assert ref != missing_angle
bad_angle_type = deepcopy(ref)
bad_angle_type.angle_types[0].k = 22
assert ref != bad_angle_type
def test_to_parmed_simple(self):
struc = pmd.load_file(get_fn('ethane.top'), xyz=get_fn('ethane.gro'))
struc.title = "Ethane"
top = from_parmed(struc)
assert top.name == "Ethane"
struc_from_top = to_parmed(top, refer_type=False)
assert struc_from_top.title == "Ethane"
assert len(struc.atoms) == len(struc_from_top.atoms)
assert len(struc.bonds) == len(struc_from_top.bonds)
assert len(struc.angles) == len(struc_from_top.angles)
assert len(struc.dihedrals) == len(struc_from_top.dihedrals)
assert len(struc.rb_torsions) == len(struc_from_top.rb_torsions)
def test_read_xyz(self):
top = read_xyz(get_fn("ethane.xyz"))
assert top.n_sites == 8
assert top.n_connections == 0
assert set([type(site.position)
for site in top.sites]) == {u.unyt_array}
assert set([site.position.units for site in top.sites]) == {u.nm}
top = read_xyz(get_fn("cu_block.xyz"))
assert top.n_sites == 108
assert top.n_connections == 0
assert set([type(site.position)
for site in top.sites]) == {u.unyt_array}
assert set([site.position.units for site in top.sites]) == {u.nm}
def foyer_periodic(self):
if has_foyer:
import foyer
from foyer.tests.utils import get_fn
from_foyer_xml(get_fn("oplsaa-periodic.xml"), overwrite=True)
gmso_ff = ForceField("oplsaa-periodic_gmso.xml")
return gmso_ff
def foyer_fullerene(self):
if has_foyer:
import foyer
from foyer.tests.utils import get_fn
from_foyer_xml(get_fn("fullerene.xml"), overwrite=True)
gmso_ff = ForceField("fullerene_gmso.xml")
return gmso_ff
def foyer_urey_bradley(self):
if has_foyer:
import foyer
from foyer.tests.utils import get_fn
from_foyer_xml(get_fn("charmm36_cooh.xml"), overwrite=True)
gmso_ff = ForceField("charmm36_cooh_gmso.xml")
return gmso_ff
def test_full_io(self):
original_top = read_xyz(get_fn('ethane.xyz'))
write_xyz(original_top, 'full_conversion.xyz')
new_top = read_xyz('full_conversion.xyz')
assert original_top.n_sites == new_top.n_sites
assert original_top.n_connections == new_top.n_connections
assert allclose(original_top.positions, new_top.positions)
def test_to_parmed_incompatible_expression(self):
struc = pmd.load_file(get_fn('ethane.top'), xyz=get_fn('ethane.gro'))
top = from_parmed(struc)
with pytest.raises(Exception):
top.atom_types[0] = "sigma + epsilon"
struc_from_top = to_parmed(top)
with pytest.raises(Exception):
top.bond_types[0] = "k * r_eq"
struc_from_top = to_parmed(top)
with pytest.raises(Exception):
top.angle_types[0] = "k - theta_eq"
struc_from_top = to_parmed(top)
with pytest.raises(Exception):
top.dihedral_types[0] = "c0 - c1 + c2 - c3 + c4 - c5"
struc_from_top = to_parmed(top)
def foyer_rb_torsion(self):
if has_foyer:
import foyer
from foyer.tests.utils import get_fn
from_foyer_xml(get_fn("refs-multi.xml"),
overwrite=True,
validate_foyer=True)
gmso_ff = ForceField("refs-multi_gmso.xml")
return gmso_ff
def test_from_parmed_parametrized_structure(self, angles):
struc = pmd.load_file(get_fn('ethane.top'), xyz=get_fn('ethane.gro'))
top = from_parmed(struc)
assert top.n_sites == 8
assert top.n_bonds == 7
assert top.n_angles == 12
assert top.n_connections == 19
for site in top.sites:
assert site.atom_type is not None
assert site.charge is not None
for connection in top.connections:
assert connection.connection_type is not None
assert top.box is not None
lengths = u.nm * [0.714, 0.7938, 0.6646]
assert allclose(top.box.lengths, lengths)
assert allclose(top.box.angles, angles)
def _typed_topology(n_sites=100):
top = from_mbuild(n_ar_system(n_sites=n_sites))
ff = ForceField(get_fn('ar.xml'))
for site in top.sites:
site.atom_type = ff.atom_types['Ar']
top.update_topology()
return top
def test_from_parmed_parametrized_structure(self, angles):
struc = pmd.load_file(get_fn("ethane.top"), xyz=get_fn("ethane.gro"))
top = from_parmed(struc)
assert top.n_sites == 8
assert top.n_bonds == 7
assert top.n_angles == 12
assert top.n_dihedrals == 9
assert top.n_connections == 28
for site in top.sites:
assert site.atom_type is not None
assert site.charge is not None
for connection in top.connections:
assert connection.connection_type is not None
assert top.box is not None
lengths = u.nm * [0.714, 0.7938, 0.6646]
assert_allclose_units(top.box.lengths, lengths, rtol=1e-5, atol=1e-8)
assert_allclose_units(top.box.angles, angles, rtol=1e-5, atol=1e-8)
def typed_ar_system(self, ar_system):
top = ar_system
ff = ForceField(get_fn('ar.xml'))
for site in top.sites:
site.atom_type = ff.atom_types['Ar']
top.update_topology()
return top
def test_full_io(self):
original_top = read_xyz(get_fn("ethane.xyz"))
write_xyz(original_top, "full_conversion.xyz")
new_top = read_xyz("full_conversion.xyz")
assert original_top.n_sites == new_top.n_sites
assert original_top.n_connections == new_top.n_connections
assert_allclose_units(original_top.positions,
new_top.positions,
rtol=1e-5,
atol=1e-8)
def test_from_parmed_basic(self, angles):
struc = pmd.load_file(get_fn('ethane.mol2'), structure=True)
top = from_parmed(struc, refer_type=False)
for site in top.sites:
assert site.atom_type is None
for connection in top.connections:
assert connection.connection_type is None
assert top.n_sites == 8
assert top.n_bonds == 7
assert top.box is not None
lengths = u.nm * [0.714, 0.7938, 0.6646]
assert_allclose_units(top.box.lengths, lengths, rtol=1e-5, atol=1e-8)
assert_allclose_units(top.box.angles, angles, rtol=1e-5, atol=1e-8)
def ar_system():
ar = mb.Compound(name='Ar')
packed_system = mb.fill_box(compound=ar,
n_compounds=100,
box=mb.Box([3, 3, 3]))
ff = ForceField(get_fn('ar.xml'))
top = from_mbuild(packed_system)
for site in top.sites:
site.atom_type = ff.atom_types['Ar']
top.update_topology()
return top
def test_modified_potentials(self, ar_system):
top = ar_system
ff = gmso.ForceField(get_fn('ar.xml'))
for site in top.sites:
site.atom_type = ff.atom_types['Ar']
top.update_topology()
top.atom_types[0].set_expression('sigma + epsilon*r')
with pytest.raises(EngineIncompatibilityError):
write_top(top, 'out.top')
alternate_lj = '4*epsilon*sigma**12/r**12 - 4*epsilon*sigma**6/r**6'
top.atom_types[0].set_expression(alternate_lj)
write_top(top, 'ar.top')
def test_write_gro_non_orthogonal(self):
top = from_parmed(pmd.load_file(get_fn('ethane.gro'), structure=True))
top.box.angles = u.degree * [90, 90, 120]
write_gro(top, 'out.gro')
def test_write_gro(self):
top = from_parmed(pmd.load_file(get_fn('ethane.gro'), structure=True))
write_gro(top, 'out.gro')
def test_wrong_n_atoms(self):
with pytest.raises(ValueError):
read_gro(get_fn('too_few_atoms.gro'))
with pytest.raises(ValueError):
read_gro(get_fn('too_many_atoms.gro'))
def test_wrong_n_atoms(self):
with pytest.raises(ValueError):
read_xyz(get_fn("too_few_atoms.xyz"))
with pytest.raises(ValueError):
read_xyz(get_fn("too_many_atoms.xyz"))
def test_write_xyz(self):
top = read_xyz(get_fn("ethane.xyz"))
write_xyz(top, "tmp.xyz")
def mb_ethane(self):
return mb.load(get_fn("ethane.mol2"))
def ethane(self):
return mb.load(get_fn('ethane.mol2'))