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_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_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_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
