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Fix mass type in convert_parmed #754

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merged 3 commits into from
Aug 7, 2023
Merged

Fix mass type in convert_parmed #754

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1c05525
fix atype_mass type in _atom_types_from_gmso
marjanalbooyeh Aug 7, 2023
86477c7
add unit test.
marjanalbooyeh Aug 7, 2023
054e544
add to and from parmed unit test with dihedral.
marjanalbooyeh Aug 7, 2023
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7 changes: 4 additions & 3 deletions gmso/external/convert_parmed.py
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Original file line number Diff line number Diff line change
Expand Up @@ -568,15 +568,16 @@
atype_charge = float(atom_type.charge.to("Coulomb").value) / (
1.6 * 10 ** (-19)
)
atype_mass = float(atom_type.mass.to("amu"))
atype_sigma = float(atom_type.parameters["sigma"].to("angstrom").value)
atype_epsilon = float(
atom_type.parameters["epsilon"].to("kcal/mol").value
)
if atom_type.mass:
atype_mass = atom_type.mass.to("amu").value
atype_mass = float(atom_type.mass.to("amu").value)
else:
atype_mass = element_by_symbol(atom_type.name).mass.to("amu").value
atype_mass = float(

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element_by_symbol(atom_type.name).mass.to("amu").value
)
atype_atomic_number = getattr(
element_by_symbol(atom_type.name), "atomic_number", None
)
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10 changes: 10 additions & 0 deletions gmso/tests/test_convert_parmed.py
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Expand Up @@ -716,3 +716,13 @@ def test_pmd_complex_ureybradleys(self, parmed_methylnitroaniline):
for t in dihedrals_list
)
)

def test_to_and_from_parmed_with_topology(self, typed_ethane):
top = typed_ethane
struc = to_parmed(top)
top_from_struc = from_parmed(struc)
assert top.n_sites == top_from_struc.n_sites
assert top.n_bonds == top_from_struc.n_bonds
assert top.n_angles == top_from_struc.n_angles
assert top.n_dihedrals == top_from_struc.n_dihedrals
assert len(top.atom_types) == len(top_from_struc.atom_types)
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