openforcefield.topology.Topology¶

class openforcefield.topology.Topology(other=None)[source]¶

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:

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

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`(iatom, jatom[, distance])	Mark a pair of atoms as constrained.
`add_molecule`(molecule[, …])	Add a Molecule to the Topology.
`add_particle`(particle)	Add a Particle to the Topology.
`assert_bonded`(atom1, atom2)	Raise an exception if the specified atoms are not bonded in the topology.
`atom`(atom_topology_index)	Get the TopologyAtom at a given Topology atom index.
`bond`(bond_topology_index)	Get the TopologyBond at a given Topology bond index.
`chemical_environment_matches`(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`(i, j)	Returns the bond between two atoms
`get_fractional_bond_order`(iatom, jatom)	Retrieve the fractional bond order for a bond.
`is_bonded`(i, j)	Returns True if the two atoms are bonded
`is_constrained`(iatom, jatom)	Check if a pair of atoms are marked as constrained.
`to_bson`()	Return a BSON serialized representation.
`to_dict`()	Convert to dictionary representation.
`to_json`([indent])	Return a JSON serialized representation.
`to_messagepack`()	Return a MessagePack representation.
`to_parmed`()	Warning This functionality will be implemented in a future toolkit release.
`to_pickle`()	Return a pickle serialized representation.
`to_toml`()	Return a TOML serialized representation.
`to_xml`([indent])	Return an XML representation.
`to_yaml`()	Return a YAML serialized representation.
`virtual_site`(vsite_topology_index)	Get the TopologyAtom at a given Topology atom index.

__init__(other=None)[source]¶

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__`([other])	Create a new Topology.
`add_constraint`(iatom, jatom[, distance])	Mark a pair of atoms as constrained.
`add_molecule`(molecule[, …])	Add a Molecule to the Topology.
`add_particle`(particle)	Add a Particle to the Topology.
`assert_bonded`(atom1, atom2)	Raise an exception if the specified atoms are not bonded in the topology.
`atom`(atom_topology_index)	Get the TopologyAtom at a given Topology atom index.
`bond`(bond_topology_index)	Get the TopologyBond at a given Topology bond index.
`chemical_environment_matches`(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`(i, j)	Returns the bond between two atoms
`get_fractional_bond_order`(iatom, jatom)	Retrieve the fractional bond order for a bond.
`is_bonded`(i, j)	Returns True if the two atoms are bonded
`is_constrained`(iatom, jatom)	Check if a pair of atoms are marked as constrained.
`to_bson`()	Return a BSON serialized representation.
`to_dict`()	Convert to dictionary representation.
`to_json`([indent])	Return a JSON serialized representation.
`to_messagepack`()	Return a MessagePack representation.
`to_parmed`()	Warning This functionality will be implemented in a future toolkit release.
`to_pickle`()	Return a pickle serialized representation.
`to_toml`()	Return a TOML serialized representation.
`to_xml`([indent])	Return an XML representation.
`to_yaml`()	Return a YAML serialized representation.
`virtual_site`(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)[source]¶

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(atom1, atom2)[source]¶

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(query, aromaticity_model='MDL', toolkit_registry=<openforcefield.utils.toolkits.ToolkitRegistry object>)[source]¶

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()[source]¶: Convert to dictionary representation.

classmethod from_dict(d)[source]¶: Static constructor from dictionary representation.

classmethod from_openmm(openmm_topology, unique_molecules=None)[source]¶

Construct an openforcefield Topology object from an OpenMM Topology object.

Parameters:

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

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)[source]¶

Construct an openforcefield Topology object from an MDTraj Topology object.

Parameters:

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

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)[source]¶

Warning

This functionality will be implemented in a future toolkit release.

Construct an openforcefield Topology object from a ParmEd Structure object.

Parameters:

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

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()[source]¶

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(i, j)[source]¶

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(i, j)[source]¶

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(atom_topology_index)[source]¶

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(vsite_topology_index)[source]¶

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(bond_topology_index)[source]¶

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(particle)[source]¶

Add a Particle to the Topology.

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

add_molecule(molecule, local_topology_to_reference_index=None)[source]¶

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()¶

Return a BSON serialized representation.

Specification: http://bsonspec.org/

Returns:	serialized : bytes A BSON serialized representation of the objecft

to_json(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()¶

Return a MessagePack representation.

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

Returns:	serialized : bytes A MessagePack-encoded bytes serialized representation of the object

to_pickle()¶

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()¶

Return a TOML serialized representation.

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

Returns:	serialized : str A TOML serialized representation of the object

to_xml(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()¶

Return a YAML serialized representation.

Specification: http://yaml.org/

Returns:	serialized : str A YAML serialized representation of the object

add_constraint(iatom, jatom, distance=True)[source]¶

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(iatom, jatom)[source]¶

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(iatom, jatom)[source]¶

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.