def from_parmed(structure, refer_type=True):
"""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.
refer_type : bool, optional, default=True
Whether or not to transfer AtomType, BondType, AngleType,
and DihedralType information
Returns
-------
top : gmso.Topology
"""
msg = "Provided argument is not a Parmed Structure"
assert isinstance(structure, pmd.Structure), msg
top = gmso.Topology(name=structure.title)
site_map = dict()
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],
)
# TO DO: come up with a solution to deal with partially parametrized
# Parmed Structure
# Old code:
# simple check if our pmd.Structure is fully parametrized
# is_parametrized = True if (isinstance(structure.atoms[i].atom_type,
# pmd.AtomType) for i in range(len(structure.atoms))) else False
# Consolidate parmed atomtypes and relate topology atomtypes
if refer_type:
pmd_top_atomtypes = _atom_types_from_pmd(structure)
# Consolidate parmed bondtypes and relate to topology bondtypes
bond_types_map = _get_types_map(structure, "bonds")
pmd_top_bondtypes = _bond_types_from_pmd(
structure, bond_types_members_map=bond_types_map
)
# Consolidate parmed angletypes and relate to topology angletypes
angle_types_map = _get_types_map(structure, "angles")
pmd_top_angletypes = _angle_types_from_pmd(
structure, angle_types_member_map=angle_types_map
)
# Consolidate parmed dihedraltypes and relate to topology dihedraltypes
dihedral_types_map = _get_types_map(structure, "dihedrals")
dihedral_types_map.update(_get_types_map(structure, "rb_torsions"))
pmd_top_dihedraltypes = _dihedral_types_from_pmd(
structure, dihedral_types_member_map=dihedral_types_map
)
subtops = list()
for residue in structure.residues:
subtop_name = ("{}[{}]").format(residue.name, residue.idx)
subtops.append(gmso.SubTopology(name=subtop_name, parent=top))
for atom in residue.atoms:
if refer_type and isinstance(atom.atom_type, pmd.AtomType):
site = gmso.Atom(
name=atom.name,
charge=atom.charge * u.elementary_charge,
position=(
[atom.xx, atom.xy, atom.xz] * u.angstrom
).in_units(u.nm),
atom_type=pmd_top_atomtypes[atom.atom_type],
)
else:
site = gmso.Atom(
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
subtops[-1].add_site(site)
top.add_subtopology(subtops[-1])
for bond in structure.bonds:
# Generate bond parameters for BondType that gets passed
# to Bond
if refer_type and isinstance(bond.type, pmd.BondType):
top_connection = gmso.Bond(
connection_members=[site_map[bond.atom1], site_map[bond.atom2]],
bond_type=pmd_top_bondtypes[bond.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]],
bond_type=None,
)
top.add_connection(top_connection, update_types=False)
top.update_topology()
for angle in structure.angles:
# Generate angle parameters for AngleType that gets passed
# to Angle
if refer_type and isinstance(angle.type, pmd.AngleType):
top_connection = gmso.Angle(
connection_members=[
site_map[angle.atom1],
site_map[angle.atom2],
site_map[angle.atom3],
],
angle_type=pmd_top_angletypes[angle.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],
],
angle_type=None,
)
top.add_connection(top_connection, update_types=False)
for dihedral in structure.dihedrals:
# Generate dihedral parameters for DihedralType that gets passed
# to Dihedral
# These all follow periodic torsions functions
# (even if they are improper dihedrals)
# Which are the default expression in top.DihedralType
# These periodic torsion dihedrals get stored in top.dihedrals
if dihedral.improper:
warnings.warn(
"ParmEd improper dihedral {} ".format(dihedral)
+ "following periodic torsion "
+ "expression detected, currently accounted for as "
+ "topology.Dihedral with a periodic torsion expression"
)
if refer_type and isinstance(dihedral.type, pmd.DihedralType):
top_connection = gmso.Dihedral(
connection_members=[
site_map[dihedral.atom1],
site_map[dihedral.atom2],
site_map[dihedral.atom3],
site_map[dihedral.atom4],
],
dihedral_type=pmd_top_dihedraltypes[dihedral.type],
)
# No bond parameters, make Connection with no connection_type
else:
top_connection = gmso.Dihedral(
connection_members=[
site_map[dihedral.atom1],
site_map[dihedral.atom2],
site_map[dihedral.atom3],
site_map[dihedral.atom4],
],
dihedral_type=None,
)
top.add_connection(top_connection, update_types=False)
for rb_torsion in structure.rb_torsions:
# Generate dihedral parameters for DihedralType that gets passed
# to Dihedral
# These all follow RB torsion functions
# These RB torsion dihedrals get stored in top.dihedrals
if rb_torsion.improper:
warnings.warn(
"ParmEd improper dihedral {} ".format(rb_torsion)
+ "following RB torsion "
+ "expression detected, currently accounted for as "
+ "topology.Dihedral with a RB torsion expression"
)
if refer_type and isinstance(rb_torsion.type, pmd.RBTorsionType):
top_connection = gmso.Dihedral(
connection_members=[
site_map[rb_torsion.atom1],
site_map[rb_torsion.atom2],
site_map[rb_torsion.atom3],
site_map[rb_torsion.atom4],
],
dihedral_type=pmd_top_dihedraltypes[rb_torsion.type],
)
# No bond parameters, make Connection with no connection_type
else:
top_connection = gmso.Dihedral(
connection_members=[
site_map[rb_torsion.atom1],
site_map[rb_torsion.atom2],
site_map[rb_torsion.atom3],
site_map[rb_torsion.atom4],
],
dihedral_type=None,
)
top.add_connection(top_connection, update_types=False)
top.update_topology()
top.combining_rule = structure.combining_rule
return top
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