def _bond_types_from_pmd(structure, bond_types_members_map=None):
""" Helper function to convert GMSO BondType
This function take in a Parmed Structure, iterate through its
bond_types, create a corresponding GMSO.BondType, and finally
return a dictionary containing all pairs of pmd.BondType
and GMSO.BondType
Parameters
----------
structure: pmd.Structure
Parmed Structure that needed to be converted.
bond_types_members_map: optional, dict, default=None
The member types (atomtype string) for each atom associated with the bond_types the structure
Returns
-------
pmd_top_bondtypes : dict
A dictionary linking a pmd.BondType object to its
corresponding GMSO.BondType object.
"""
pmd_top_bondtypes = dict()
bond_types_members_map = _assert_dict(bond_types_members_map,
'bond_types_members_map')
for btype in structure.bond_types:
bond_params = {
'k': (2 * btype.k * u.Unit('kcal / (angstrom**2 * mol)')),
'r_eq': btype.req * u.angstrom
}
member_types = bond_types_members_map.get(id(btype))
top_bondtype = gmso.BondType(parameters=bond_params,
member_types=member_types)
pmd_top_bondtypes[btype] = top_bondtype
return pmd_top_bondtypes
def _bond_types_from_pmd(structure):
""" Helper function to convert GMSO BondType
This function take in a Parmed Structure, iterate through its
bond_types, create a corresponding GMSO.BondType, and finally
return a dictionary containing all pairs of pmd.BondType
and GMSO.BondType
Parameter
----------
structure: pmd.Structure
Parmed Structure that needed to be converted.
Return
------
pmd_top_bondtypes : dict
A dictionary linking a pmd.BondType object to its
corresponding GMSO.BondType object.
"""
pmd_top_bondtypes = dict()
for btype in structure.bond_types:
bond_params = {
'k': (2 * btype.k * u.Unit('kcal / (angstrom**2 * mol)')),
'r_eq': btype.req * u.angstrom
}
top_bondtype = gmso.BondType(parameters=bond_params)
pmd_top_bondtypes[btype] = top_bondtype
return pmd_top_bondtypes
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