molsysmt.form.openmm_Topology package

Submodules

molsysmt.form.openmm_Topology.add module

molsysmt.form.openmm_Topology.add.add(to_item, item, atom_indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.append_structures module

molsysmt.form.openmm_Topology.append_structures.append_structures(item, structure_id=None, time=None, coordinates=None, box=None, skip_digestion=False)

molsysmt.form.openmm_Topology.attributes module

molsysmt.form.openmm_Topology.copy module

molsysmt.form.openmm_Topology.copy.copy(item, skip_digestion=False)

molsysmt.form.openmm_Topology.extract module

molsysmt.form.openmm_Topology.extract.extract(item, atom_indices='all', structure_indices='all', copy_if_all=True, skip_digestion=False)

molsysmt.form.openmm_Topology.get_structural_attributes module

molsysmt.form.openmm_Topology.get_structural_attributes.get_box_from_system(item, structure_indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes module

molsysmt.form.openmm_Topology.get_topological_attributes.get_atom_id_from_atom(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_atom_id_from_chain(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_atom_id_from_component(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_atom_id_from_entity(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_atom_id_from_group(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_atom_id_from_molecule(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_atom_index_from_atom(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_atom_index_from_chain(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_atom_index_from_component(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_atom_index_from_entity(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_atom_index_from_group(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_atom_index_from_molecule(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_atom_name_from_atom(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_atom_name_from_chain(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_atom_name_from_component(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_atom_name_from_entity(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_atom_name_from_group(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_atom_name_from_molecule(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_atom_type_from_atom(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_atom_type_from_chain(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_atom_type_from_component(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_atom_type_from_entity(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_atom_type_from_group(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_atom_type_from_molecule(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_bond_index_from_atom(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_bond_index_from_bond(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_bond_index_from_chain(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_bond_index_from_component(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_bond_index_from_entity(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_bond_index_from_group(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_bond_index_from_molecule(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_bond_index_from_system(item, skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_bond_order_from_atom(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_bond_order_from_bond(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_bond_order_from_chain(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_bond_order_from_component(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_bond_order_from_entity(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_bond_order_from_group(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_bond_order_from_molecule(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_bond_type_from_atom(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_bond_type_from_bond(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_bond_type_from_chain(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_bond_type_from_component(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_bond_type_from_entity(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_bond_type_from_group(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_bond_type_from_molecule(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_bonded_atom_pairs_from_atom(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_bonded_atom_pairs_from_bond(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_bonded_atom_pairs_from_chain(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_bonded_atom_pairs_from_component(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_bonded_atom_pairs_from_entity(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_bonded_atom_pairs_from_group(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_bonded_atom_pairs_from_molecule(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_bonded_atom_pairs_from_system(item, skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_bonded_atoms_from_atom(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_bonded_atoms_from_bond(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_bonded_atoms_from_chain(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_bonded_atoms_from_component(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_bonded_atoms_from_entity(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_bonded_atoms_from_group(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_bonded_atoms_from_molecule(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_bonded_atoms_from_system(item, skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_chain_id_from_atom(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_chain_id_from_chain(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_chain_id_from_component(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_chain_id_from_entity(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_chain_id_from_group(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_chain_id_from_molecule(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_chain_index_from_atom(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_chain_index_from_chain(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_chain_index_from_component(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_chain_index_from_entity(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_chain_index_from_group(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_chain_index_from_molecule(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_chain_name_from_atom(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_chain_name_from_chain(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_chain_name_from_component(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_chain_name_from_entity(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_chain_name_from_group(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_chain_name_from_molecule(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_chain_type_from_atom(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_chain_type_from_chain(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_chain_type_from_component(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_chain_type_from_entity(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_chain_type_from_group(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_chain_type_from_molecule(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_component_id_from_atom(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_component_id_from_chain(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_component_id_from_component(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_component_id_from_entity(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_component_id_from_group(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_component_id_from_molecule(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_component_index_from_atom(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_component_index_from_chain(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_component_index_from_component(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_component_index_from_entity(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_component_index_from_group(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_component_index_from_molecule(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_component_name_from_atom(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_component_name_from_chain(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_component_name_from_component(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_component_name_from_entity(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_component_name_from_group(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_component_name_from_molecule(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_component_type_from_atom(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_component_type_from_chain(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_component_type_from_component(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_component_type_from_entity(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_component_type_from_group(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_component_type_from_molecule(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_entity_id_from_atom(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_entity_id_from_chain(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_entity_id_from_component(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_entity_id_from_entity(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_entity_id_from_group(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_entity_id_from_molecule(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_entity_index_from_atom(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_entity_index_from_chain(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_entity_index_from_component(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_entity_index_from_entity(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_entity_index_from_group(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_entity_index_from_molecule(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_entity_name_from_atom(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_entity_name_from_chain(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_entity_name_from_component(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_entity_name_from_entity(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_entity_name_from_group(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_entity_name_from_molecule(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_entity_type_from_atom(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_entity_type_from_chain(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_entity_type_from_component(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_entity_type_from_entity(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_entity_type_from_group(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_entity_type_from_molecule(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_group_id_from_atom(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_group_id_from_chain(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_group_id_from_component(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_group_id_from_entity(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_group_id_from_group(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_group_id_from_molecule(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_group_index_from_atom(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_group_index_from_chain(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_group_index_from_component(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_group_index_from_entity(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_group_index_from_group(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_group_index_from_molecule(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_group_name_from_atom(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_group_name_from_chain(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_group_name_from_component(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_group_name_from_entity(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_group_name_from_group(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_group_name_from_molecule(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_group_type_from_atom(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_group_type_from_chain(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_group_type_from_component(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_group_type_from_entity(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_group_type_from_group(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_group_type_from_molecule(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_inner_bond_index_from_atom(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_inner_bond_index_from_chain(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_inner_bond_index_from_component(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_inner_bond_index_from_entity(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_inner_bond_index_from_group(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_inner_bond_index_from_molecule(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_inner_bond_index_from_system(item, skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_inner_bonded_atom_pairs_from_atom(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_inner_bonded_atom_pairs_from_chain(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_inner_bonded_atom_pairs_from_component(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_inner_bonded_atom_pairs_from_entity(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_inner_bonded_atom_pairs_from_group(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_inner_bonded_atom_pairs_from_molecule(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_inner_bonded_atom_pairs_from_system(item, skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_inner_bonded_atoms_from_atom(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_inner_bonded_atoms_from_chain(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_inner_bonded_atoms_from_component(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_inner_bonded_atoms_from_entity(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_inner_bonded_atoms_from_group(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_inner_bonded_atoms_from_molecule(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_inner_bonded_atoms_from_system(item, skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_molecule_id_from_atom(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_molecule_id_from_chain(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_molecule_id_from_component(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_molecule_id_from_entity(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_molecule_id_from_group(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_molecule_id_from_molecule(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_molecule_index_from_atom(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_molecule_index_from_chain(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_molecule_index_from_component(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_molecule_index_from_entity(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_molecule_index_from_group(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_molecule_index_from_molecule(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_molecule_name_from_atom(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_molecule_name_from_chain(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_molecule_name_from_component(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_molecule_name_from_entity(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_molecule_name_from_group(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_molecule_name_from_molecule(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_molecule_type_from_atom(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_molecule_type_from_chain(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_molecule_type_from_component(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_molecule_type_from_entity(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_molecule_type_from_group(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_molecule_type_from_molecule(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_n_amino_acids_from_atom(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_n_amino_acids_from_chain(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_n_amino_acids_from_component(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_n_amino_acids_from_entity(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_n_amino_acids_from_group(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_n_amino_acids_from_molecule(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_n_amino_acids_from_system(item, skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_n_atoms_from_atom(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_n_atoms_from_chain(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_n_atoms_from_component(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_n_atoms_from_entity(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_n_atoms_from_group(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_n_atoms_from_molecule(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_n_atoms_from_system(item, skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_n_bonds_from_atom(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_n_bonds_from_bond(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_n_bonds_from_chain(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_n_bonds_from_component(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_n_bonds_from_entity(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_n_bonds_from_group(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_n_bonds_from_molecule(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_n_bonds_from_system(item, skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_n_chains_from_atom(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_n_chains_from_chain(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_n_chains_from_component(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_n_chains_from_entity(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_n_chains_from_group(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_n_chains_from_molecule(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_n_chains_from_system(item, skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_n_components_from_atom(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_n_components_from_chain(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_n_components_from_component(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_n_components_from_entity(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_n_components_from_group(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_n_components_from_molecule(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_n_components_from_system(item, skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_n_dnas_from_atom(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_n_dnas_from_chain(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_n_dnas_from_component(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_n_dnas_from_entity(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_n_dnas_from_group(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_n_dnas_from_molecule(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_n_dnas_from_system(item, skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_n_entities_from_atom(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_n_entities_from_chain(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_n_entities_from_component(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_n_entities_from_entity(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_n_entities_from_group(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_n_entities_from_molecule(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_n_entities_from_system(item, skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_n_groups_from_atom(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_n_groups_from_chain(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_n_groups_from_component(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_n_groups_from_entity(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_n_groups_from_group(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_n_groups_from_molecule(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_n_groups_from_system(item, skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_n_inner_bonds_from_atom(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_n_inner_bonds_from_chain(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_n_inner_bonds_from_component(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_n_inner_bonds_from_entity(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_n_inner_bonds_from_group(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_n_inner_bonds_from_molecule(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_n_ions_from_atom(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_n_ions_from_chain(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_n_ions_from_component(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_n_ions_from_entity(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_n_ions_from_group(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_n_ions_from_molecule(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_n_ions_from_system(item, skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_n_lipids_from_atom(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_n_lipids_from_chain(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_n_lipids_from_component(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_n_lipids_from_entity(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_n_lipids_from_group(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_n_lipids_from_molecule(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_n_lipids_from_system(item, skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_n_molecules_from_atom(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_n_molecules_from_chain(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_n_molecules_from_component(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_n_molecules_from_entity(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_n_molecules_from_group(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_n_molecules_from_molecule(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_n_molecules_from_system(item, skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_n_nucleotides_from_atom(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_n_nucleotides_from_chain(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_n_nucleotides_from_component(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_n_nucleotides_from_entity(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_n_nucleotides_from_group(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_n_nucleotides_from_molecule(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_n_nucleotides_from_system(item, skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_n_peptides_from_atom(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_n_peptides_from_chain(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_n_peptides_from_component(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_n_peptides_from_entity(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_n_peptides_from_group(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_n_peptides_from_molecule(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_n_peptides_from_system(item, skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_n_polysaccharides_from_atom(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_n_polysaccharides_from_chain(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_n_polysaccharides_from_component(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_n_polysaccharides_from_entity(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_n_polysaccharides_from_group(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_n_polysaccharides_from_molecule(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_n_polysaccharides_from_system(item, skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_n_proteins_from_atom(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_n_proteins_from_chain(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_n_proteins_from_component(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_n_proteins_from_entity(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_n_proteins_from_group(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_n_proteins_from_molecule(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_n_proteins_from_system(item, skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_n_rnas_from_atom(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_n_rnas_from_chain(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_n_rnas_from_component(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_n_rnas_from_entity(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_n_rnas_from_group(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_n_rnas_from_molecule(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_n_rnas_from_system(item, skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_n_saccharides_from_atom(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_n_saccharides_from_chain(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_n_saccharides_from_component(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_n_saccharides_from_entity(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_n_saccharides_from_group(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_n_saccharides_from_molecule(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_n_saccharides_from_system(item, skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_n_small_molecules_from_atom(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_n_small_molecules_from_chain(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_n_small_molecules_from_component(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_n_small_molecules_from_entity(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_n_small_molecules_from_group(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_n_small_molecules_from_molecule(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_n_small_molecules_from_system(item, skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_n_waters_from_atom(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_n_waters_from_chain(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_n_waters_from_component(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_n_waters_from_entity(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_n_waters_from_group(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_n_waters_from_molecule(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.get_topological_attributes.get_n_waters_from_system(item, skip_digestion=False)

molsysmt.form.openmm_Topology.has_attribute module

molsysmt.form.openmm_Topology.has_attribute.has_attribute(molecular_system, attribute, include_none=False, skip_digestion=False)

molsysmt.form.openmm_Topology.is_form module

molsysmt.form.openmm_Topology.is_form.is_form(item)

molsysmt.form.openmm_Topology.iterators module

class molsysmt.form.openmm_Topology.iterators.TopologyIterator(molecular_system)

Bases: object

molsysmt.form.openmm_Topology.merge module

molsysmt.form.openmm_Topology.merge.merge(items, atom_indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.set module

molsysmt.form.openmm_Topology.set.set_box_to_system(item, structure_indices='all', value=None, skip_digestion=False)

molsysmt.form.openmm_Topology.to_file_pdb module

molsysmt.form.openmm_Topology.to_file_pdb.to_file_pdb(item, atom_indices='all', coordinates=None, output_filename=None, skip_digestion=False)

molsysmt.form.openmm_Topology.to_file_psf module

molsysmt.form.openmm_Topology.to_file_psf.to_file_psf(item, atom_indices='all', output_filename=None, skip_digestion=False)

molsysmt.form.openmm_Topology.to_mdtraj_Topology module

molsysmt.form.openmm_Topology.to_mdtraj_Topology.to_mdtraj_Topology(item, atom_indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.to_molsysmt_MolSys module

molsysmt.form.openmm_Topology.to_molsysmt_MolSys.to_molsysmt_MolSys(item, atom_indices='all', coordinates=None, box=None, skip_digestion=False)

molsysmt.form.openmm_Topology.to_molsysmt_Topology module

molsysmt.form.openmm_Topology.to_molsysmt_Topology.to_molsysmt_Topology(item, atom_indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.to_networkx_Graph module

molsysmt.form.openmm_Topology.to_networkx_Graph.to_networkx_Graph(item, atom_indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.to_nglview_NGLWidget module

molsysmt.form.openmm_Topology.to_nglview_NGLWidget.to_nglview_NGLWidget(item, atom_indices='all', coordinates=None, skip_digestion=False)

molsysmt.form.openmm_Topology.to_openmm_Context module

molsysmt.form.openmm_Topology.to_openmm_Context.to_openmm_Context(item, atom_indices='all', coordinates=None, forcefield='AMBER14', water_model=None, implicit_solvent=None, non_bonded_method='no cutoff', constraints='hbonds', switch_distance=None, dispersion_correction=False, ewald_error_tolerance=0.0005, integrator='Langevin', temperature=None, friction='1.0/picoseconds', time_step='2 femtoseconds', platform='CUDA', skip_digestion=False)

molsysmt.form.openmm_Topology.to_openmm_Modeller module

molsysmt.form.openmm_Topology.to_openmm_Modeller.to_openmm_Modeller(item, atom_indices='all', coordinates=None, box=None, skip_digestion=False)

molsysmt.form.openmm_Topology.to_openmm_PDBFile module

molsysmt.form.openmm_Topology.to_openmm_PDBFile.to_openmm_PDBFile(item, atom_indices='all', coordinates=None, skip_digestion=False)

molsysmt.form.openmm_Topology.to_openmm_Simulation module

molsysmt.form.openmm_Topology.to_openmm_Simulation.to_openmm_Simulation(item, atom_indices='all', coordinates=None, skip_digestion=False)

molsysmt.form.openmm_Topology.to_openmm_System module

molsysmt.form.openmm_Topology.to_openmm_System.to_openmm_System(item, atom_indices='all', forcefield='AMBER14', water_model=None, implicit_solvent=None, non_bonded_method=None, constraints='hbonds', switch_distance=None, dispersion_correction=None, ewald_error_tolerance=None, skip_digestion=False)

molsysmt.form.openmm_Topology.to_openmm_Topology module

molsysmt.form.openmm_Topology.to_openmm_Topology.to_openmm_Topology(item, atom_indices='all', structure_indices='all', copy_if_all=True, skip_digestion=False)

molsysmt.form.openmm_Topology.to_parmed_Structure module

molsysmt.form.openmm_Topology.to_parmed_Structure.to_parmed_Structure(item, atom_indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.to_pdbfixer_PDBFixer module

molsysmt.form.openmm_Topology.to_pdbfixer_PDBFixer.to_pdbfixer_PDBFixer(item, atom_indices='all', coordinates=None, skip_digestion=False)

molsysmt.form.openmm_Topology.to_string_amino_acids_1 module

molsysmt.form.openmm_Topology.to_string_amino_acids_1.to_string_amino_acids_1(item, atom_indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.to_string_amino_acids_3 module

molsysmt.form.openmm_Topology.to_string_amino_acids_3.to_string_amino_acids_3(item, group_indices='all', skip_digestion=False)

molsysmt.form.openmm_Topology.to_string_pdb_text module

molsysmt.form.openmm_Topology.to_string_pdb_text.to_string_pdb_text(item, atom_indices='all', coordinates=None, box=None, skip_digestion=False)

molsysmt.form.openmm_Topology.write_topology_in_h5msm module

molsysmt.form.openmm_Topology.write_topology_in_h5msm.write_topology_in_h5msm(item, file, atom_indices='all', skip_digestion=False)

Module contents