def _lookup_element_symbol(atom_type):
"""Look up an atomic_number based on atom type information, 0 if non-element type."""
try:
element = element_by_atom_type(atom_type)
return element.symbol
except GMSOError:
return "X"
def _lookup_atomic_number(atom_type):
"""Attempt to look up an atomic_number based on atom type information, 0 if non-element type"""
try:
element = element_by_atom_type(atom_type)
return element.atomic_number
except GMSOError:
return 0
def test_element_by_atom_type(self):
carbon_type = AtomType(mass=12.011, definition="C", name="C")
mass_only = AtomType(mass=12.011)
def_only = AtomType(definition="C")
name_only = AtomType(name="C")
for atom_type in [carbon_type, mass_only, def_only, name_only]:
carbon = element.element_by_atom_type(atom_type)
assert carbon.name == element.Carbon.name
assert carbon.symbol == element.Carbon.symbol
assert carbon.mass == element.Carbon.mass
def _atom_types_from_gmso(top, structure, atom_map):
"""Convert gmso.Topology AtomType to parmed.Structure AtomType.
This function will first check the AtomType expression of Topology and make sure it match with the one default in Parmed.
After that, it would start atomtyping and parametrizing this part of the structure.
Parameters
----------
top : topology.Topology
The topology that need to be converted
structure: parmed.Structure
The destination parmed Structure
"""
# Maps
atype_map = dict()
for atom_type in top.atom_types:
msg = "Atom type {} expression does not match Parmed AtomType default expression".format(
atom_type.name
)
assert atom_type.expression == parse_expr(
"4*epsilon*(-sigma**6/r**6 + sigma**12/r**12)"
), msg
# Extract Topology atom type information
atype_name = atom_type.name
# Convert charge to elementary_charge
atype_charge = float(atom_type.charge.to("Coulomb").value) / (
1.6 * 10 ** (-19)
)
atype_sigma = float(atom_type.parameters["sigma"].to("angstrom").value)
atype_epsilon = float(
atom_type.parameters["epsilon"].to("kcal/mol").value
)
atype_element = element_by_atom_type(atom_type)
atype_rmin = atype_sigma * 2 ** (1 / 6) / 2 # to rmin/2
# Create unique Parmed AtomType object
atype = pmd.AtomType(
atype_name,
None,
atype_element.mass,
atype_element.atomic_number,
atype_charge,
)
atype.set_lj_params(atype_epsilon, atype_rmin)
# Type map to match AtomType to its name
atype_map[atype_name] = atype
for site in top.sites:
# Assign atom_type to atom
pmd_atom = atom_map[site]
pmd_atom.type = site.atom_type.name
pmd_atom.atom_type = atype_map[site.atom_type.name]