openff.toolkit.topology.TopologyMolecule

class openff.toolkit.topology.TopologyMolecule(reference_molecule, topology, local_topology_to_reference_index=None)[source]

TopologyMolecules are built to be an efficient way to store large numbers of copies of the same molecule for parameterization and system preparation.

Warning

This API is experimental and subject to change.

__init__(reference_molecule, topology, local_topology_to_reference_index=None)[source]

Create a new TopologyMolecule.

Parameters

reference_moleculean openff.toolkit.topology.molecule.Molecule: The reference molecule, with details like formal charges, partial charges, bond orders, partial bond orders, and atomic symbols.
topologyan openff.toolkit.topology.Topology: The topology that this TopologyMolecule belongs to
local_topology_to_reference_indexdict, optional, default=None: Dictionary of {TopologyMolecule_atom_index : Molecule_atom_index} for the TopologyMolecule that will be built

Methods

`__init__`(reference_molecule, topology[, ...])	Create a new TopologyMolecule.
`atom`(index)	Get the TopologyAtom with a given topology atom index in this TopologyMolecule.
`bond`(index)	Get the TopologyBond with a given reference molecule index in this TopologyMolecule
`from_dict`(d)	Static constructor from dictionary representation.
`nth_degree_neighbors`(n_degrees)	Return canonicalized pairs of atoms whose shortest separation is exactly n bonds. Only pairs with increasing atom indices are returned. Parameters ---------- n: int The number of bonds separating atoms in each pair Returns ------- neighbors: iterator of tuple of TopologyAtom Tuples (len 2) of atom that are separated by `n` bonds. Notes ----- The criteria used here relies on minimum distances; when there are multiple valid paths between atoms, such as atoms in rings, the shortest path is considered. For example, two atoms in "meta" positions with respect to each other in a benzene are separated by two paths, one length 2 bonds and the other length 4 bonds. This function would consider them to be 2 apart and would not include them if `n=4` was passed.
`particle`(index)	Get the TopologyParticle with a given reference molecule index in this TopologyMolecule
`to_dict`()	Convert to dictionary representation.
`virtual_site`(index)	Get the TopologyVirtualSite with a given reference molecule index in this TopologyMolecule

Attributes

`amber_impropers`	Iterate over improper torsions in the molecule, but only those with trivalent centers, reporting the central atom first in each improper.
`angles`	Iterable of Tuple[TopologyAtom]: iterator over the angles in this TopologyMolecule.
`atom_start_topology_index`	Get the topology index of the first atom in this TopologyMolecule
`atoms`	Return an iterator of all the TopologyAtoms in this TopologyMolecule
`bond_start_topology_index`	Get the topology index of the first bond in this TopologyMolecule
`bonds`	Return an iterator of all the TopologyBonds in this TopologyMolecule
`impropers`	Iterable of Tuple[TopologyAtom]: iterator over the possible improper torsions in this TopologyMolecule.
`n_angles`	int: number of angles in this TopologyMolecule.
`n_atoms`	The number of atoms in this topology.
`n_bonds`	Get the number of bonds in this TopologyMolecule
`n_impropers`	int: number of possible improper torsions in this TopologyMolecule.
`n_particles`	Get the number of particles in this TopologyMolecule
`n_propers`	int: number of proper torsions in this TopologyMolecule.
`n_virtual_sites`	Get the number of virtual sites in this TopologyMolecule
`particles`	Return an iterator of all the TopologyParticles in this TopologyMolecules
`propers`	Iterable of Tuple[TopologyAtom]: iterator over the proper torsions in this TopologyMolecule.
`reference_molecule`	Get the reference molecule for this TopologyMolecule
`smirnoff_impropers`	Note that it's possible that a trivalent center will not have an improper assigned.
`topology`	Get the topology that this TopologyMolecule belongs to
`virtual_particle_start_topology_index`	Get the topology index of the first virtual particle in this TopologyMolecule
`virtual_site_start_topology_index`	Get the topology index of the first virtual site in this TopologyMolecule
`virtual_sites`	Return an iterator of all the TopologyVirtualSites in this TopologyMolecules

property topology

Get the topology that this TopologyMolecule belongs to

Returns

an openff.toolkit.topology.Topology

property reference_molecule

Get the reference molecule for this TopologyMolecule

Returns

an openff.toolkit.topology.molecule.Molecule

property n_atoms

The number of atoms in this topology.

Returns

int

atom(index)[source]

Get the TopologyAtom with a given topology atom index in this TopologyMolecule.

Parameters

indexint: Index of the TopologyAtom within this TopologyMolecule to retrieve

Returns

an openff.toolkit.topology.TopologyAtom

property atoms

Return an iterator of all the TopologyAtoms in this TopologyMolecule

Returns

an iterator of openff.toolkit.topology.TopologyAtoms

property atom_start_topology_index: Get the topology index of the first atom in this TopologyMolecule

property virtual_particle_start_topology_index: Get the topology index of the first virtual particle in this TopologyMolecule

bond(index)[source]

Get the TopologyBond with a given reference molecule index in this TopologyMolecule

Parameters

indexint: Index of the TopologyBond within this TopologyMolecule to retrieve

Returns

an openff.toolkit.topology.TopologyBond

property bonds

Return an iterator of all the TopologyBonds in this TopologyMolecule

Returns

an iterator of openff.toolkit.topology.TopologyBonds

property n_bonds

Get the number of bonds in this TopologyMolecule

Returns

intnumber of bonds

property bond_start_topology_index: Get the topology index of the first bond in this TopologyMolecule

particle(index)[source]

Get the TopologyParticle with a given reference molecule index in this TopologyMolecule

Parameters

indexint: Index of the TopologyParticle within this TopologyMolecule to retrieve

Returns

an openff.toolkit.topology.TopologyParticle

property particles

Return an iterator of all the TopologyParticles in this TopologyMolecules

Returns

an iterator of openff.toolkit.topology.TopologyParticle

property n_particles

Get the number of particles in this TopologyMolecule

Returns

intThe number of particles

virtual_site(index)[source]

Get the TopologyVirtualSite with a given reference molecule index in this TopologyMolecule

Parameters

indexint: Index of the TopologyVirtualSite within this TopologyMolecule to retrieve

Returns

an openff.toolkit.topology.TopologyVirtualSite

property virtual_sites

Return an iterator of all the TopologyVirtualSites in this TopologyMolecules

Returns

an iterator of openff.toolkit.topology.TopologyVirtualSite

property n_virtual_sites

Get the number of virtual sites in this TopologyMolecule

Returns

int

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

property n_angles: int: number of angles in this TopologyMolecule.

property propers: Iterable of Tuple[TopologyAtom]: iterator over the proper torsions in this TopologyMolecule.

property n_propers: int: number of proper torsions in this TopologyMolecule.

property impropers: Iterable of Tuple[TopologyAtom]: iterator over the possible improper torsions in this TopologyMolecule.

property n_impropers: int: number of possible improper torsions in this TopologyMolecule.

property smirnoff_impropers

Note that it’s possible that a trivalent center will not have an improper assigned. This will depend on the force field that is used.

Also note that this will return 6 possible atom orderings around each improper center. In current SMIRNOFF parameterization, three of these six orderings will be used for the actual assignment of the improper term and measurement of the angles. These three orderings capture the three unique angles that could be calculated around the improper center, therefore the sum of these three terms will always return a consistent energy.

For more details on the use of three-fold (‘trefoil’) impropers, see https://open-forcefield-toolkit.readthedocs.io/en/latest/smirnoff.html#impropertorsions

Returns

impropersset of tuple: An iterator of tuples, each containing the indices of atoms making up a possible improper torsion. The central atom is listed second in each tuple.

property amber_impropers

Iterate over improper torsions in the molecule, but only those with trivalent centers, reporting the central atom first in each improper.

Note that it’s possible that a trivalent center will not have an improper assigned. This will depend on the force field that is used.

Also note that this will return 6 possible atom orderings around each improper center. In current AMBER parameterization, one of these six orderings will be used for the actual assignment of the improper term and measurement of the angle. This method does not encode the logic to determine which of the six orderings AMBER would use.

Returns

impropersset of tuple: An iterator of tuples, each containing the indices of atoms making up a possible improper torsion. The central atom is listed first in each tuple.

nth_degree_neighbors(n_degrees: int)[source]

Return canonicalized pairs of atoms whose shortest separation is exactly n bonds. Only pairs with increasing atom indices are returned. Parameters ———- n: int

The number of bonds separating atoms in each pair

neighbors: iterator of tuple of TopologyAtom: Tuples (len 2) of atom that are separated by n bonds.

The criteria used here relies on minimum distances; when there are multiple valid paths between atoms, such as atoms in rings, the shortest path is considered. For example, two atoms in “meta” positions with respect to each other in a benzene are separated by two paths, one length 2 bonds and the other length 4 bonds. This function would consider them to be 2 apart and would not include them if n=4 was passed.

property virtual_site_start_topology_index: Get the topology index of the first virtual site in this TopologyMolecule

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

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