def to_openmm_PDBFile(item,
molecular_system,
atom_indices='all',
structure_indices='all'):
from molsysmt.form.openmm_Topology import to_openmm_PDBFile as openmm_Topology_to_openmm_PDBFile
from molsysmt.basic import get
coordinates = get(molecular_system,
atom_indices=atom_indices,
structure_indices=structure_indices,
coordinates=True)
tmp_item = openmm_Topology_to_openmm_PDBFile(item,
atom_indices=atom_indices,
coordinates=coordinates,
check=False)
return tmp_item
def to_nglview_NGLWidget(item,
molecular_system=None,
atom_indices='all',
structure_indices='all'):
from molsysmt.form.openmm_Topology import to_nglview_NGLWidget as openmm_Topology_to_nglview_NGLWidget
from molsysmt.basic import get
coordinates = get(molecular_system,
atom_indices=atom_indices,
structure_indices=structure_indices,
coordinates=True)
tmp_item = openmm_Topology_to_nglview_NGLWidget(item,
atom_indices=atom_indices,
coordinates=coordinates,
check=False)
return tmp_item
def to_file_pdb(item,
molecular_system,
atom_indices='all',
structure_indices='all',
output_filename=None):
from molsysmt.form.openmm_Topology import to_file_pdb as openmm_Topology_to_file_pdb
from molsysmt.basic import get
coordinates = get(molecular_system,
atom_indices=atom_indices,
structure_indices=structure_indices,
coordinates=True)
tmp_item = openmm_Topology_to_file_pdb(item,
atom_indices=atom_indices,
coordinates=coordinates,
check=False)
return tmp_item
def to_molsysmt_MolSys(item,
molecular_system,
atom_indices='all',
structure_indices='all'):
from molsysmt.form.openmm_Topology import to_molsysmt_MolSys as openmm_Topology_to_molsysmt_MolSys
from molsysmt.basic import get
coordinates, box = get(molecular_system,
atom_indices=atom_indices,
structure_indices=structure_indices,
coordinates=True,
box=True)
tmp_item = openmm_Topology_to_molsysmt_MolSys(item,
atom_indices=atom_indices,
coordinates=coordinates,
box=box,
check=False)
return tmp_item