def _angle_types_from_pmd(structure):
""" Helper function to convert GMSO AngleType
This function take in a Parmed Structure, iterate through its
angle_types, create a corresponding GMSO.AngleType, and finally
return a dictionary containing all pairs of pmd.AngleType
and GMSO.AngleType
Parameter
----------
structure: pmd.Structure
Parmed Structure that needed to be converted.
Return
------
pmd_top_angletypes : dict
A dictionary linking a pmd.AngleType object to its
corresponding GMSO.AngleType object.
"""
pmd_top_angletypes = dict()
for angletype in structure.angle_types:
angle_params = {
'k': (2 * angletype.k * u.Unit('kcal / (rad**2 * mol)')),
'theta_eq': (angletype.theteq * u.degree)
}
# Do we need to worry about Urey Bradley terms
# For Urey Bradley:
# k in (kcal/(angstrom**2 * mol))
# r_eq in angstrom
top_angletype = gmso.AngleType(parameters=angle_params)
pmd_top_angletypes[angletype] = top_angletype
return pmd_top_angletypes
def _angle_types_from_pmd(structure, angle_types_member_map=None):
"""Convert ParmEd angle types to GMSO AngleType.
This function takes in a Parmed Structure, iterates through its
angle_types, create a corresponding GMSO.AngleType, and finally
return a dictionary containing all pairs of pmd.AngleType
and GMSO.AngleType
Parameters
----------
structure: pmd.Structure
Parmed Structure that needed to be converted.
angle_types_member_map: optional, dict, default=None
The member types (atomtype string) for each atom associated with the angle_types the structure
Returns
-------
pmd_top_angletypes : dict
A dictionary linking a pmd.AngleType object to its
corresponding GMSO.AngleType object.
"""
pmd_top_angletypes = dict()
angle_types_member_map = _assert_dict(
angle_types_member_map, "angle_types_member_map"
)
for angletype in structure.angle_types:
angle_params = {
"k": (2 * angletype.k * u.Unit("kcal / (rad**2 * mol)")),
"theta_eq": (angletype.theteq * u.degree),
}
# Do we need to worry about Urey Bradley terms
# For Urey Bradley:
# k in (kcal/(angstrom**2 * mol))
# r_eq in angstrom
member_types = angle_types_member_map.get(id(angletype))
top_angletype = gmso.AngleType(
parameters=angle_params, member_types=member_types
)
pmd_top_angletypes[angletype] = top_angletype
return pmd_top_angletypes
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