def _atom_types_from_pmd(structure):
"""Convert ParmEd atomtypes to GMSO AtomType.
This function take in a Parmed Structure, iterate through its
atom's atom_type, create a corresponding GMSO.AtomType, and
finally return a dictionary containing all pairs of pmd.AtomType
and GMSO.AtomType
Parameter
----------
structure: pmd.Structure
Parmed Structure that needed to be converted.
Return
------
pmd_top_atomtypes : dict
A dictionary linking a pmd.AtomType object to its
corresponding GMSO.AtomType object.
"""
unique_atom_types = set()
for atom in structure.atoms:
if isinstance(atom.atom_type, pmd.AtomType):
unique_atom_types.add(atom.atom_type)
unique_atom_types = list(unique_atom_types)
pmd_top_atomtypes = {}
for atom_type in unique_atom_types:
top_atomtype = gmso.AtomType(
name=atom_type.name,
charge=atom_type.charge * u.elementary_charge,
parameters={
"sigma": atom_type.sigma * u.angstrom,
"epsilon": atom_type.epsilon * u.Unit("kcal / mol"),
},
mass=atom_type.mass,
)
pmd_top_atomtypes[atom_type] = top_atomtype
return pmd_top_atomtypes
def from_parmed(structure):
"""Convert a parmed.Structure to a gmso.Topology
Convert a parametrized or un-parametrized parmed.Structure object to a topology.Topology.
Specifically, this method maps Structure to Topology and Atom to Site.
At this point, this method can only convert AtomType, BondType and AngleType.
Conversion of DihedralType will be implement in the near future.
Parameters
----------
structure : parmed.Structure
parmed.Structure instance that need to be converted.
Returns
-------
top : gmso.Topology
"""
msg = ("Provided argument that is not a Parmed Structure")
assert isinstance(structure, pmd.Structure), msg
top = gmso.Topology(name=structure.title)
site_map = dict()
for atom in structure.atoms:
if isinstance(atom.atom_type, pmd.AtomType):
atom_type = gmso.AtomType(
name=atom.atom_type.name,
charge=atom.atom_type.charge * u.elementary_charge,
parameters={
'sigma': (atom.sigma * u.angstrom).in_units(u.nm),
'epsilon': atom.epsilon * u.Unit('kcal / mol')
})
site = gmso.Site(
name=atom.name,
charge=atom.charge * u.elementary_charge,
position=([atom.xx, atom.xy, atom.xz] * u.angstrom).in_units(
u.nm),
atom_type=atom_type)
else:
site = gmso.Site(
name=atom.name,
charge=atom.charge * u.elementary_charge,
position=([atom.xx, atom.xy, atom.xz] * u.angstrom).in_units(
u.nm),
atom_type=None)
site_map[atom] = site
top.add_site(site)
top.update_topology()
if np.all(structure.box):
# This is if we choose for topology to have abox
top.box = gmso.Box(
(structure.box[0:3] * u.angstrom).in_units(u.nm),
angles=u.degree * structure.box[3:6])
for bond in structure.bonds:
# Generate bond parameters for BondType that gets passed
# to Bond
if isinstance(bond.type, pmd.BondType):
bond_params = {
'k': (2 * bond.type.k * u.Unit('kcal / (nm**2 * mol)')),
'r_eq': (bond.type.req * u.angstrom).in_units(u.nm)
}
new_connection_type = gmso.BondType(parameters=bond_params)
top_connection = gmso.Bond(connection_members=[site_map[bond.atom1],
site_map[bond.atom2]],
connection_type=new_connection_type)
# No bond parameters, make Connection with no connection_type
else:
top_connection = gmso.Bond(connection_members=[site_map[bond.atom1],
site_map[bond.atom2]],
connection_type=None)
top.add_connection(top_connection, update_types=False)
top.update_topology()
print(top.n_bonds)
for angle in structure.angles:
# Generate angle parameters for AngleType that gets passed
# to Angle
if isinstance(angle.type, pmd.AngleType):
angle_params = {
'k': (2 * angle.type.k * u.Unit('kcal / (rad**2 * mol)')),
'theta_eq': (angle.type.theteq * u.degree)
}
new_connection_type = gmso.AngleType(parameters=angle_params)
top_connection = gmso.Angle(connection_members=[site_map[angle.atom1],
site_map[angle.atom2], site_map[angle.atom3]],
connection_type=new_connection_type)
# No bond parameters, make Connection with no connection_type
else:
top_connection = gmso.Angle(connection_members=[site_map[angle.atom1],
site_map[angle.atom2], site_map[angle.atom3]],
connection_type=None)
top.add_connection(top_connection, update_types=False)
top.update_topology()
# TODO: Dihedrals
return top