openforcefield.topology.TopologyMolecule¶

class openforcefield.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.

Attributes

angles: Iterable of Tuple[TopologyAtom]: iterator over the angles in this Topology.
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 improper torsions in this Topology.
n_angles: int: number of angles in this Topology.
n_atoms: The number of atoms in this topology.
n_bonds: Get the number of bonds in this TopologyMolecule
n_impropers: int: number of proper torsions in this Topology.
n_particles: Get the number of particles in this TopologyMolecule
n_propers: int: number of proper torsions in this Topology.
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 Topology.
reference_molecule: Get the reference molecule for this TopologyMolecule
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

Methods

`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.
`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

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

Create a new TopologyMolecule.

Parameters

reference_moleculean openforcefield.topology.molecule.Molecule: The reference molecule, with details like formal charges, partial charges, bond orders, partial bond orders, and atomic symbols.
topologyan openforcefield.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.
`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

`angles`	Iterable of Tuple[TopologyAtom]: iterator over the angles in this Topology.
`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 improper torsions in this Topology.
`n_angles`	int: number of angles in this Topology.
`n_atoms`	The number of atoms in this topology.
`n_bonds`	Get the number of bonds in this TopologyMolecule
`n_impropers`	int: number of proper torsions in this Topology.
`n_particles`	Get the number of particles in this TopologyMolecule
`n_propers`	int: number of proper torsions in this Topology.
`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 Topology.
`reference_molecule`	Get the reference molecule for this TopologyMolecule
`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 openforcefield.topology.Topology

property reference_molecule¶

Get the reference molecule for this TopologyMolecule

Returns

an openforcefield.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 openforcefield.topology.TopologyAtom

property atoms¶

Return an iterator of all the TopologyAtoms in this TopologyMolecule

Returns

an iterator of openforcefield.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 openforcefield.topology.TopologyBond

property bonds¶

Return an iterator of all the TopologyBonds in this TopologyMolecule

Returns

an iterator of openforcefield.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 openforcefield.topology.TopologyParticle

property particles¶

Return an iterator of all the TopologyParticles in this TopologyMolecules

Returns

an iterator of openforcefield.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 openforcefield.topology.TopologyVirtualSite

property virtual_sites¶

Return an iterator of all the TopologyVirtualSites in this TopologyMolecules

Returns

an iterator of openforcefield.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 Topology.

property n_angles¶: int: number of angles in this Topology.

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

property n_propers¶: int: number of proper torsions in this Topology.

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

property n_impropers¶: int: number of proper torsions in this Topology.

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.