def _run_atomtyping(self, top, use_residue_map=True, **kwargs):
"""Atomtype the topology.
Parameters
----------
top : gmso.Topology
Molecular Topology to be atomtyped.
use_residue_map : bool, optional, default=True
A speed-up option that utilizes previously atom typed
molecules as a template for future atom typing of
identical molecules, instead of reevaluating them each
individually. To be implemented
"""
if isinstance(top, mb.Compound):
top = from_mbuild(top)
# TO DO in another PR
if use_residue_map:
# Detect duplicates subtopology/residues
# (do matching by name, assert same number
# of atoms)
# Not implemented yet
typemap = find_atomtypes(top, forcefield=self)
else:
typemap = find_atomtypes(top, forcefield=self)
return typemap
def _typed_topology(n_sites=100):
top = from_mbuild(n_ar_system(n_sites=n_sites))
ff = ForceField(get_fn('ar.xml'))
for site in top.sites:
site.atom_type = ff.atom_types['Ar']
top.update_topology()
return top
def water_system(self):
water = mb.load(get_path('tip3p.mol2'))
water.name = 'water'
water[0].name = 'opls_111'
water[1].name = water[2].name = 'opls_112'
packed_system = mb.fill_box(compound=water,
n_compounds=2,
box=mb.Box([2, 2, 2]))
return from_mbuild(packed_system)
def ar_system():
ar = mb.Compound(name='Ar')
packed_system = mb.fill_box(compound=ar,
n_compounds=100,
box=mb.Box([3, 3, 3]))
ff = ForceField(get_fn('ar.xml'))
top = from_mbuild(packed_system)
for site in top.sites:
site.atom_type = ff.atom_types['Ar']
top.update_topology()
return top
def _typed_topology(n_sites=1):
xe = mb.Compound(name="Xe")
packed_system = mb.fill_box(
compound=xe,
n_compounds=n_sites,
box=mb.Box([3, 3, 3]),
)
top = from_mbuild(packed_system)
ff = ForceField(get_path("noble_mie.xml"))
for site in top.sites:
site.atom_type = ff.atom_types["Xe"]
top.update_topology()
return top
def ar_system(self, n_ar_system):
return from_mbuild(n_ar_system())
def ethane(self):
from mbuild.lib.molecules import Ethane
top = from_mbuild(Ethane())
return top
def gmso_topology_graph(self):
import mbuild as mb
from gmso.external import from_mbuild
ethane = mb.load("CC", smiles=True)
return TopologyGraph.from_gmso_topology(from_mbuild(ethane))
