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