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_to_parmed_loop(self, parmed_methylnitroaniline,
parmed_chloroethanol, parmed_ethane):
for struc in [parmed_methylnitroaniline, parmed_chloroethanol]:
top_from_struc = from_parmed(struc)
struc_from_top = to_parmed(top_from_struc)
assert set(struc.bond_types) == set(struc_from_top.bond_types)
assert set(struc.angle_types) == set(struc_from_top.angle_types)
assert set(struc.dihedral_types) == set(
struc_from_top.dihedral_types)
assert set(struc.rb_torsion_types) == set(
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_box_info(self, parmed_hexane_box):
struc = parmed_hexane_box
top_from_struc = from_parmed(struc)
assert_allclose_units(top_from_struc.box.lengths.to("nm").value, [6., 6., 6.], rtol=1e-5, atol=1e-8)
assert_allclose_units(top_from_struc.box.angles.to("degree").value, [90., 90., 90.], rtol=1e-5, atol=1e-8)
struc_from_top = to_parmed(top_from_struc)
assert_allclose_units(struc_from_top.box, [60, 60, 60, 90, 90, 90], rtol=1e-5, atol=1e-8)
def test_box_info(self, parmed_hexane_box):
struc = parmed_hexane_box
top_from_struc = from_parmed(struc)
assert np.allclose(top_from_struc.box.lengths.to("nm").value, [6., 6., 6.])
assert np.allclose(top_from_struc.box.angles.to("degree").value, [90., 90., 90.])
struc_from_top = to_parmed(top_from_struc)
assert np.allclose(struc_from_top.box, [60, 60, 60, 90, 90, 90])
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_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_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 test_residues_info(self, parmed_hexane_box):
struc = parmed_hexane_box
top_from_struc = from_parmed(struc)
assert len(top_from_struc.subtops) == len(struc.residues)
for i in range(len(top_from_struc.subtops)):
assert len(top_from_struc.subtops[i].sites) == 20
assert top_from_struc.subtops[i].name == "HEX[{}]".format(i)
struc_from_top = to_parmed(top_from_struc)
assert len(struc_from_top.residues) == len(struc.residues)
for i in range(len(top_from_struc.subtops)):
assert len(struc_from_top.residues[i].atoms) == 20
assert struc_from_top.residues[i].name == "HEX"
assert struc_from_top.residues[i].idx == i
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 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 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 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_write_gsd(self):
top = from_parmed(
pmd.load_file(get_fn('ethane.top'), xyz=get_fn('ethane.gro')))
write_gsd(top, 'out.gsd')
def test_write_gsd_non_orthogonal(self):
top = from_parmed(
pmd.load_file(get_fn('ethane.top'), xyz=get_fn('ethane.gro')))
top.box.angles = u.degree * [90, 90, 120]
write_gsd(top, 'out.gsd')
def test_write_gsd(self):
top = from_parmed(
pmd.load_file(get_fn("ethane.top"), xyz=get_fn("ethane.gro")))
write_gsd(top, "out.gsd")
