# openforcefield.topology.Topology

class `openforcefield.topology.``Topology`(other=None)

  A Topology is a chemical representation of a system containing one or more molecules appearing in a specified order.

  Warning

  This API is experimental and subject to change.

  Examples

  Import some utilities

      >>> from simtk.openmm import app
      >>> from openforcefield.tests.utils import get_data_filename, get_packmol_pdbfile
      >>> pdb_filepath = get_packmol_pdbfile('cyclohexane_ethanol_0.4_0.6')
      >>> monomer_names = ('cyclohexane', 'ethanol')

  Create a Topology object from a PDB file and sdf files defining the molecular contents

      >>> from openforcefield.topology import Molecule, Topology
      >>> pdbfile = app.PDBFile(pdb_filepath)
      >>> sdf_filepaths = [get_data_filename(f'systems/monomers/{name}.sdf') for name in monomer_names]
      >>> unique_molecules = [Molecule.from_file(sdf_filepath) for sdf_filepath in sdf_filepaths]
      >>> topology = Topology.from_openmm(pdbfile.topology, unique_molecules=unique_molecules)

  Create a Topology object from a PDB file and IUPAC names of the molecular contents

      >>> pdbfile = app.PDBFile(pdb_filepath)
      >>> unique_molecules = [Molecule.from_iupac(name) for name in monomer_names]
      >>> topology = Topology.from_openmm(pdbfile.topology, unique_molecules=unique_molecules)

  Create an empty Topology object and add a few copies of a single benzene molecule

      >>> topology = Topology()
      >>> molecule = Molecule.from_iupac('benzene')
      >>> molecule_topology_indices = [topology.add_molecule(molecule) for index in range(10)]

  Attributes
    `angles`

      Iterable of Tuple[TopologyAtom]: iterator over the angles in this Topology.

    `aromaticity_model`

      Get the aromaticity model applied to all molecules in the topology.

    `box_vectors`

      Return the box vectors of the topology, if specified

    `charge_model`

      Get the partial charge model applied to all molecules in the topology.

    `constrained_atom_pairs`

      Returns the constrained atom pairs of the Topology

    `fractional_bond_order_model`

      Get the fractional bond order model for the Topology.

    `impropers`

      Iterable of Tuple[TopologyAtom]: iterator over the improper torsions in this Topology.

    `n_angles`

      int: number of angles in this Topology.

    `n_impropers`

      int: number of improper torsions in this Topology.

    `n_propers`

      int: number of proper torsions in this Topology.

    `n_reference_molecules`

      Returns the number of reference (unique) molecules in in this Topology.

    `n_topology_atoms`

      Returns the number of topology atoms in in this Topology.

    `n_topology_bonds`

      Returns the number of TopologyBonds in in this Topology.

    `n_topology_molecules`

      Returns the number of topology molecules in in this Topology.

    `n_topology_particles`

      Returns the number of topology particles (TopologyAtoms and TopologyVirtualSites) in in this Topology.

    `n_topology_virtual_sites`

      Returns the number of TopologyVirtualSites in in this Topology.

    `propers`

      Iterable of Tuple[TopologyAtom]: iterator over the proper torsions in this Topology.

    `reference_molecules`

      Get an iterator of reference molecules in this Topology.

    `topology_atoms`

      Returns an iterator over the atoms in this Topology.

    `topology_bonds`

      Returns an iterator over the bonds in this Topology

    `topology_molecules`

      Returns an iterator over all the TopologyMolecules in this Topology

    `topology_particles`

      Returns an iterator over the particles (TopologyAtoms and TopologyVirtualSites) in this Topology.

    `topology_virtual_sites`

      Get an iterator over the virtual sites in this Topology

  Methods

  `add_constraint`(self, iatom, jatom[, distance]) | Mark a pair of atoms as constrained.
  `add_molecule`(self, molecule[, …]) | Add a Molecule to the Topology.
  `add_particle`(self, particle) | Add a Particle to the Topology.
  `assert_bonded`(self, atom1, atom2) | Raise an exception if the specified atoms are not bonded in the topology.
  `atom`(self, atom_topology_index) | Get the TopologyAtom at a given Topology atom index.
  `bond`(self, bond_topology_index) | Get the TopologyBond at a given Topology bond index.
  `chemical_environment_matches`(self, query[, …]) | Retrieve all matches for a given chemical environment query.
  `from_bson`(serialized) | Instantiate an object from a BSON serialized representation.
  `from_dict`(d) | Static constructor from dictionary representation.
  `from_json`(serialized) | Instantiate an object from a JSON serialized representation.
  `from_mdtraj`(mdtraj_topology[, unique_molecules]) | Construct an openforcefield Topology object from an MDTraj Topology object.
  `from_messagepack`(serialized) | Instantiate an object from a MessagePack serialized representation.
  `from_molecules`(molecules) | Create a new Topology object containing one copy of each of the specified molecule(s).
  `from_openmm`(openmm_topology[, unique_molecules]) | Construct an openforcefield Topology object from an OpenMM Topology object.
  `from_parmed`(parmed_structure[, unique_molecules]) | Warning This functionality will be implemented in a future toolkit release.
  `from_pickle`(serialized) | Instantiate an object from a pickle serialized representation.
  `from_toml`(serialized) | Instantiate an object from a TOML serialized representation.
  `from_xml`(serialized) | Instantiate an object from an XML serialized representation.
  `from_yaml`(serialized) | Instantiate from a YAML serialized representation.
  `get_bond_between`(self, i, j) | Returns the bond between two atoms
  `get_fractional_bond_order`(self, iatom, jatom) | Retrieve the fractional bond order for a bond.
  `is_bonded`(self, i, j) | Returns True if the two atoms are bonded
  `is_constrained`(self, iatom, jatom) | Check if a pair of atoms are marked as constrained.
  `to_bson`(self) | Return a BSON serialized representation.
  `to_dict`(self) | Convert to dictionary representation.
  `to_json`(self[, indent]) | Return a JSON serialized representation.
  `to_messagepack`(self) | Return a MessagePack representation.
  `to_parmed`(self) | Warning This functionality will be implemented in a future toolkit release.
  `to_pickle`(self) | Return a pickle serialized representation.
  `to_toml`(self) | Return a TOML serialized representation.
  `to_xml`(self[, indent]) | Return an XML representation.
  `to_yaml`(self) | Return a YAML serialized representation.
  `virtual_site`(self, vsite_topology_index) | Get the TopologyAtom at a given Topology atom index.

  `__init__`(self, other=None)

    Create a new Topology.

    Parameters
      other optional, default=None

        If specified, attempt to construct a copy of the Topology from the specified object. This might be a Topology object, or a file that can be used to construct a Topology object or serialized Topology object.

  Methods

  `__init__`(self[, other]) | Create a new Topology.
  `add_constraint`(self, iatom, jatom[, distance]) | Mark a pair of atoms as constrained.
  `add_molecule`(self, molecule[, …]) | Add a Molecule to the Topology.
  `add_particle`(self, particle) | Add a Particle to the Topology.
  `assert_bonded`(self, atom1, atom2) | Raise an exception if the specified atoms are not bonded in the topology.
  `atom`(self, atom_topology_index) | Get the TopologyAtom at a given Topology atom index.
  `bond`(self, bond_topology_index) | Get the TopologyBond at a given Topology bond index.
  `chemical_environment_matches`(self, query[, …]) | Retrieve all matches for a given chemical environment query.
  `from_bson`(serialized) | Instantiate an object from a BSON serialized representation.
  `from_dict`(d) | Static constructor from dictionary representation.
  `from_json`(serialized) | Instantiate an object from a JSON serialized representation.
  `from_mdtraj`(mdtraj_topology[, unique_molecules]) | Construct an openforcefield Topology object from an MDTraj Topology object.
  `from_messagepack`(serialized) | Instantiate an object from a MessagePack serialized representation.
  `from_molecules`(molecules) | Create a new Topology object containing one copy of each of the specified molecule(s).
  `from_openmm`(openmm_topology[, unique_molecules]) | Construct an openforcefield Topology object from an OpenMM Topology object.
  `from_parmed`(parmed_structure[, unique_molecules]) | Warning This functionality will be implemented in a future toolkit release.
  `from_pickle`(serialized) | Instantiate an object from a pickle serialized representation.
  `from_toml`(serialized) | Instantiate an object from a TOML serialized representation.
  `from_xml`(serialized) | Instantiate an object from an XML serialized representation.
  `from_yaml`(serialized) | Instantiate from a YAML serialized representation.
  `get_bond_between`(self, i, j) | Returns the bond between two atoms
  `get_fractional_bond_order`(self, iatom, jatom) | Retrieve the fractional bond order for a bond.
  `is_bonded`(self, i, j) | Returns True if the two atoms are bonded
  `is_constrained`(self, iatom, jatom) | Check if a pair of atoms are marked as constrained.
  `to_bson`(self) | Return a BSON serialized representation.
  `to_dict`(self) | Convert to dictionary representation.
  `to_json`(self[, indent]) | Return a JSON serialized representation.
  `to_messagepack`(self) | Return a MessagePack representation.
  `to_parmed`(self) | Warning This functionality will be implemented in a future toolkit release.
  `to_pickle`(self) | Return a pickle serialized representation.
  `to_toml`(self) | Return a TOML serialized representation.
  `to_xml`(self[, indent]) | Return an XML representation.
  `to_yaml`(self) | Return a YAML serialized representation.
  `virtual_site`(self, vsite_topology_index) | Get the TopologyAtom at a given Topology atom index.

  Attributes

  `angles` | Iterable of Tuple[TopologyAtom]: iterator over the angles in this Topology.
  `aromaticity_model` | Get the aromaticity model applied to all molecules in the topology.
  `box_vectors` | Return the box vectors of the topology, if specified Returns ——- box_vectors : simtk.unit.Quantity wrapped numpy array The unit-wrapped box vectors of this topology
  `charge_model` | Get the partial charge model applied to all molecules in the topology.
  `constrained_atom_pairs` | Returns the constrained atom pairs of the Topology
  `fractional_bond_order_model` | Get the fractional bond order model for the Topology.
  `impropers` | Iterable of Tuple[TopologyAtom]: iterator over the improper torsions in this Topology.
  `n_angles` | int: number of angles in this Topology.
  `n_impropers` | int: number of improper torsions in this Topology.
  `n_propers` | int: number of proper torsions in this Topology.
  `n_reference_molecules` | Returns the number of reference (unique) molecules in in this Topology.
  `n_topology_atoms` | Returns the number of topology atoms in in this Topology.
  `n_topology_bonds` | Returns the number of TopologyBonds in in this Topology.
  `n_topology_molecules` | Returns the number of topology molecules in in this Topology.
  `n_topology_particles` | Returns the number of topology particles (TopologyAtoms and TopologyVirtualSites) in in this Topology.
  `n_topology_virtual_sites` | Returns the number of TopologyVirtualSites in in this Topology.
  `propers` | Iterable of Tuple[TopologyAtom]: iterator over the proper torsions in this Topology.
  `reference_molecules` | Get an iterator of reference molecules in this Topology.
  `topology_atoms` | Returns an iterator over the atoms in this Topology.
  `topology_bonds` | Returns an iterator over the bonds in this Topology
  `topology_molecules` | Returns an iterator over all the TopologyMolecules in this Topology
  `topology_particles` | Returns an iterator over the particles (TopologyAtoms and TopologyVirtualSites) in this Topology.
  `topology_virtual_sites` | Get an iterator over the virtual sites in this Topology

  `reference_molecules`

    Get an iterator of reference molecules in this Topology.

    Returns
      iterable of openforcefield.topology.Molecule
  classmethod `from_molecules`(molecules)

    Create a new Topology object containing one copy of each of the specified molecule(s).

    Parameters
      molecules Molecule or iterable of Molecules

        One or more molecules to be added to the Topology

    Returns
      topology Topology

        The Topology created from the specified molecule(s)

  `assert_bonded`(self, atom1, atom2)

    Raise an exception if the specified atoms are not bonded in the topology.

    Parameters
      atom1, atom2 openforcefield.topology.Atom or int

        The atoms or atom topology indices to check to ensure they are bonded

  `aromaticity_model`

    Get the aromaticity model applied to all molecules in the topology.

    Returns
      aromaticity_model str

        Aromaticity model in use.

  `box_vectors`

    Return the box vectors of the topology, if specified Returns ——- box_vectors : simtk.unit.Quantity wrapped numpy array

    > The unit-wrapped box vectors of this topology

  `charge_model`

    Get the partial charge model applied to all molecules in the topology.

    Returns
      charge_model str

        Charge model used for all molecules in the Topology.

  `constrained_atom_pairs`

    Returns the constrained atom pairs of the Topology

    Returns
      constrained_atom_pairs dict

        dictionary of the form d[(atom1_topology_index, atom2_topology_index)] = distance (float)

  `fractional_bond_order_model`

    Get the fractional bond order model for the Topology.

    Returns
      fractional_bond_order_model str

        Fractional bond order model in use.

  `n_reference_molecules`

    Returns the number of reference (unique) molecules in in this Topology.

    Returns
      n_reference_molecules int
  `n_topology_molecules`

    Returns the number of topology molecules in in this Topology.

    Returns
      n_topology_molecules int
  `topology_molecules`

    Returns an iterator over all the TopologyMolecules in this Topology

    Returns
      topology_molecules Iterable of TopologyMolecule
  `n_topology_atoms`

    Returns the number of topology atoms in in this Topology.

    Returns
      n_topology_atoms int
  `topology_atoms`

    Returns an iterator over the atoms in this Topology. These will be in ascending order of topology index (Note that this is not necessarily the same as the reference molecule index)

    Returns
      topology_atoms Iterable of TopologyAtom
  `n_topology_bonds`

    Returns the number of TopologyBonds in in this Topology.

    Returns
      n_bonds int
  `topology_bonds`

    Returns an iterator over the bonds in this Topology

    Returns
      topology_bonds Iterable of TopologyBond
  `n_topology_particles`

    Returns the number of topology particles (TopologyAtoms and TopologyVirtualSites) in in this Topology.

    Returns
      n_topology_particles int
  `topology_particles`

    Returns an iterator over the particles (TopologyAtoms and TopologyVirtualSites) in this Topology. The TopologyAtoms will be in order of ascending Topology index (Note that this may differ from the order of atoms in the reference molecule index).

    Returns
      topology_particles Iterable of TopologyAtom and TopologyVirtualSite
  `n_topology_virtual_sites`

    Returns the number of TopologyVirtualSites in in this Topology.

    Returns
      n_virtual_sites iterable of TopologyVirtualSites
  `topology_virtual_sites`

    Get an iterator over the virtual sites in this Topology

    Returns
      topology_virtual_sites Iterable of TopologyVirtualSite
  `n_angles`

    int: number of angles in this Topology.

  `angles`

    Iterable of Tuple[TopologyAtom]: iterator over the angles in this Topology.

  `n_propers`

    int: number of proper torsions in this Topology.

  `propers`

    Iterable of Tuple[TopologyAtom]: iterator over the proper torsions in this Topology.

  `n_impropers`

    int: number of improper torsions in this Topology.

  `impropers`

    Iterable of Tuple[TopologyAtom]: iterator over the improper torsions in this Topology.

  `chemical_environment_matches`(self, query, aromaticity_model='MDL', toolkit_registry=<openforcefield.utils.toolkits.ToolkitRegistry object at 0x7fba7ccc7048>)

    Retrieve all matches for a given chemical environment query.

    TODO: * Do we want to generalize this to other kinds of queries too, like mdtraj DSL, pymol selections, atom index slices, etc?

    > We could just call it topology.matches(query)

    Parameters
      query str or ChemicalEnvironment

        SMARTS string (with one or more tagged atoms) or `ChemicalEnvironment` query Query will internally be resolved to SMARTS using `query.as_smarts()` if it has an `.as_smarts` method.

      aromaticity_model str

        Override the default aromaticity model for this topology and use the specified aromaticity model instead. Allowed values: [‘MDL’]

    Returns
      matches list of TopologyAtom tuples

        A list of all matching Atom tuples

  `to_dict`(self)

    Convert to dictionary representation.

  classmethod `from_dict`(d)

    Static constructor from dictionary representation.

  classmethod `from_openmm`(openmm_topology, unique_molecules=None)

    Construct an openforcefield Topology object from an OpenMM Topology object.

    Parameters
      openmm_topology simtk.openmm.app.Topology

        An OpenMM Topology object

      unique_molecules iterable of objects that can be used to construct unique Molecule objects

        All unique molecules must be provided, in any order, though multiple copies of each molecule are allowed. The atomic elements and bond connectivity will be used to match the reference molecules to molecule graphs appearing in the OpenMM `Topology`. If bond orders are present in the OpenMM `Topology`, these will be used in matching as well. If all bonds have bond orders assigned in `mdtraj_topology`, these bond orders will be used to attempt to construct the list of unique Molecules if the `unique_molecules` argument is omitted.

    Returns
      topology openforcefield.topology.Topology

        An openforcefield Topology object

  static `from_mdtraj`(mdtraj_topology, unique_molecules=None)

    Construct an openforcefield Topology object from an MDTraj Topology object.

    Parameters
      mdtraj_topology mdtraj.Topology

        An MDTraj Topology object

      unique_molecules iterable of objects that can be used to construct unique Molecule objects

        All unique molecules mult be provided, in any order, though multiple copies of each molecule are allowed. The atomic elements and bond connectivity will be used to match the reference molecules to molecule graphs appearing in the MDTraj `Topology`. If bond orders are present in the MDTraj `Topology`, these will be used in matching as well. If all bonds have bond orders assigned in `mdtraj_topology`, these bond orders will be used to attempt to construct the list of unique Molecules if the `unique_molecules` argument is omitted.

    Returns
      topology openforcefield.Topology

        An openforcefield Topology object

  static `from_parmed`(parmed_structure, unique_molecules=None)

    Warning

    This functionality will be implemented in a future toolkit release.

    Construct an openforcefield Topology object from a ParmEd Structure object.

    Parameters
      parmed_structure parmed.Structure

        A ParmEd structure object

      unique_molecules iterable of objects that can be used to construct unique Molecule objects

        All unique molecules mult be provided, in any order, though multiple copies of each molecule are allowed. The atomic elements and bond connectivity will be used to match the reference molecules to molecule graphs appearing in the structure’s `topology` object. If bond orders are present in the structure’s `topology` object, these will be used in matching as well. If all bonds have bond orders assigned in the structure’s `topology` object, these bond orders will be used to attempt to construct the list of unique Molecules if the `unique_molecules` argument is omitted.

    Returns
      topology openforcefield.Topology

        An openforcefield Topology object

  `to_parmed`(self)

    Warning

    This functionality will be implemented in a future toolkit release.

    Create a ParmEd Structure object.

    Returns
      parmed_structure parmed.Structure

        A ParmEd Structure objecft

  `get_bond_between`(self, i, j)

    Returns the bond between two atoms

    Parameters
      i, j int or TopologyAtom

        Atoms or atom indices to check

    Returns
      bond TopologyBond

        The bond between i and j.

  `is_bonded`(self, i, j)

    Returns True if the two atoms are bonded

    Parameters
      i, j int or TopologyAtom

        Atoms or atom indices to check

    Returns
      is_bonded bool

        True if atoms are bonded, False otherwise.

  `atom`(self, atom_topology_index)

    Get the TopologyAtom at a given Topology atom index.

    Parameters
      atom_topology_index int

        The index of the TopologyAtom in this Topology

    Returns
      An openforcefield.topology.TopologyAtom
  `virtual_site`(self, vsite_topology_index)

    Get the TopologyAtom at a given Topology atom index.

    Parameters
      vsite_topology_index int

        The index of the TopologyVirtualSite in this Topology

    Returns
      An openforcefield.topology.TopologyVirtualSite
  `bond`(self, bond_topology_index)

    Get the TopologyBond at a given Topology bond index.

    Parameters
      bond_topology_index int

        The index of the TopologyBond in this Topology

    Returns
      An openforcefield.topology.TopologyBond
  `add_particle`(self, particle)

    Add a Particle to the Topology.

    Parameters
      particle Particle

        The Particle to be added. The Topology will take ownership of the Particle.

  `add_molecule`(self, molecule, local_topology_to_reference_index=None)

    Add a Molecule to the Topology.

    Parameters
      molecule Molecule

        The Molecule to be added.

      local_topology_to_reference_index: dict, optional, default = None

        Dictionary of {TopologyMolecule_atom_index : Molecule_atom_index} for the TopologyMolecule that will be built

    Returns
      index int

        The index of this molecule in the topology

  classmethod `from_bson`(serialized)

    Instantiate an object from a BSON serialized representation.

    Specification: http://bsonspec.org/

    Parameters
      serialized bytes

        A BSON serialized representation of the object

    Returns
      instance cls

        An instantiated object

  classmethod `from_json`(serialized)

    Instantiate an object from a JSON serialized representation.

    Specification: https://www.json.org/

    Parameters
      serialized str

        A JSON serialized representation of the object

    Returns
      instance cls

        An instantiated object

  classmethod `from_messagepack`(serialized)

    Instantiate an object from a MessagePack serialized representation.

    Specification: https://msgpack.org/index.html

    Parameters
      serialized bytes

        A MessagePack-encoded bytes serialized representation

    Returns
      instance cls

        Instantiated object.

  classmethod `from_pickle`(serialized)

    Instantiate an object from a pickle serialized representation.

    Warning

    This is not recommended for safe, stable storage since the pickle specification may change between Python versions.

    Parameters
      serialized str

        A pickled representation of the object

    Returns
      instance cls

        An instantiated object

  classmethod `from_toml`(serialized)

    Instantiate an object from a TOML serialized representation.

    Specification: https://github.com/toml-lang/toml

    Parameters
      serlialized str

        A TOML serialized representation of the object

    Returns
      instance cls

        An instantiated object

  classmethod `from_xml`(serialized)

    Instantiate an object from an XML serialized representation.

    Specification: https://www.w3.org/XML/

    Parameters
      serialized bytes

        An XML serialized representation

    Returns
      instance cls

        Instantiated object.

  classmethod `from_yaml`(serialized)

    Instantiate from a YAML serialized representation.

    Specification: http://yaml.org/

    Parameters
      serialized str

        A YAML serialized representation of the object

    Returns
      instance cls

        Instantiated object

  `to_bson`(self)

    Return a BSON serialized representation.

    Specification: http://bsonspec.org/

    Returns
      serialized bytes

        A BSON serialized representation of the objecft

  `to_json`(self, indent=None)

    Return a JSON serialized representation.

    Specification: https://www.json.org/

    Parameters
      indent int, optional, default=None

        If not None, will pretty-print with specified number of spaces for indentation

    Returns
      serialized str

        A JSON serialized representation of the object

  `to_messagepack`(self)

    Return a MessagePack representation.

    Specification: https://msgpack.org/index.html

    Returns
      serialized bytes

        A MessagePack-encoded bytes serialized representation of the object

  `to_pickle`(self)

    Return a pickle serialized representation.

    Warning

    This is not recommended for safe, stable storage since the pickle specification may change between Python versions.

    Returns
      serialized str

        A pickled representation of the object

  `to_toml`(self)

    Return a TOML serialized representation.

    Specification: https://github.com/toml-lang/toml

    Returns
      serialized str

        A TOML serialized representation of the object

  `to_xml`(self, indent=2)

    Return an XML representation.

    Specification: https://www.w3.org/XML/

    Parameters
      indent int, optional, default=2

        If not None, will pretty-print with specified number of spaces for indentation

    Returns
      serialized bytes

        A MessagePack-encoded bytes serialized representation.

  `to_yaml`(self)

    Return a YAML serialized representation.

    Specification: http://yaml.org/

    Returns
      serialized str

        A YAML serialized representation of the object

  `add_constraint`(self, iatom, jatom, distance=True)

    Mark a pair of atoms as constrained.

    Constraints between atoms that are not bonded (e.g., rigid waters) are permissible.

    Parameters
      iatom, jatom Atom

        Atoms to mark as constrained These atoms may be bonded or not in the Topology

      distance simtk.unit.Quantity, optional, default=True

        Constraint distance `True` if distance has yet to be determined `False` if constraint is to be removed

  `is_constrained`(self, iatom, jatom)

    Check if a pair of atoms are marked as constrained.

    Parameters
      iatom, jatom int

        Indices of atoms to mark as constrained.

    Returns
      distance simtk.unit.Quantity or bool

        True if constrained but constraints have not yet been applied Distance if constraint has already been added to System

  `get_fractional_bond_order`(self, iatom, jatom)

    Retrieve the fractional bond order for a bond.

    An Exception is raised if it cannot be determined.

    Parameters
      iatom, jatom Atom

        Atoms for which a fractional bond order is to be retrieved.

    Returns
      order float

        Fractional bond order between the two specified atoms.