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.
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
particle_start_topology_index
Get the topology index of the first particle 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_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
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Get the TopologyAtom with a given topology atom index in this TopologyMolecule. |
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Get the TopologyBond with a given reference molecule index in this TopologyMolecule |
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Static constructor from dictionary representation. |
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Get the TopologyParticle with a given reference molecule index in this TopologyMolecule |
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Convert to dictionary representation. |
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Get the TopologyVirtualSite with a given reference molecule index in this TopologyMolecule |
__init__
(self, reference_molecule, topology, local_topology_to_reference_index=None)[source]¶Create a new TopologyMolecule.
The reference molecule, with details like formal charges, partial charges, bond orders, partial bond orders, and atomic symbols.
The topology that this TopologyMolecule belongs to
Dictionary of {TopologyMolecule_atom_index : Molecule_atom_index} for the TopologyMolecule that will be built
Methods
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Create a new TopologyMolecule. |
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Get the TopologyAtom with a given topology atom index in this TopologyMolecule. |
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Get the TopologyBond with a given reference molecule index in this TopologyMolecule |
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Static constructor from dictionary representation. |
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Get the TopologyParticle with a given reference molecule index in this TopologyMolecule |
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Convert to dictionary representation. |
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Get the TopologyVirtualSite with a given reference molecule index in this TopologyMolecule |
Attributes
Iterable of Tuple[TopologyAtom]: iterator over the angles in this Topology. |
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Get the topology index of the first atom in this TopologyMolecule |
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Return an iterator of all the TopologyAtoms in this TopologyMolecule |
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Get the topology index of the first bond in this TopologyMolecule |
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Return an iterator of all the TopologyBonds in this TopologyMolecule |
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Iterable of Tuple[TopologyAtom]: iterator over the improper torsions in this Topology. |
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int: number of angles in this Topology. |
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The number of atoms in this topology. |
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Get the number of bonds in this TopologyMolecule |
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int: number of proper torsions in this Topology. |
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Get the number of particles in this TopologyMolecule |
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int: number of proper torsions in this Topology. |
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Get the number of virtual sites in this TopologyMolecule |
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Get the topology index of the first particle in this TopologyMolecule. |
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Return an iterator of all the TopologyParticles in this TopologyMolecules |
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Iterable of Tuple[TopologyAtom]: iterator over the proper torsions in this Topology. |
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Get the reference molecule for this TopologyMolecule |
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Get the topology that this TopologyMolecule belongs to |
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Get the topology index of the first virtual site in this TopologyMolecule |
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Return an iterator of all the TopologyVirtualSites in this TopologyMolecules |
topology
¶Get the topology that this TopologyMolecule belongs to
reference_molecule
¶Get the reference molecule for this TopologyMolecule
n_atoms
¶The number of atoms in this topology.
atom
(self, index)[source]¶Get the TopologyAtom with a given topology atom index in this TopologyMolecule.
Index of the TopologyAtom within this TopologyMolecule to retrieve
atoms
¶Return an iterator of all the TopologyAtoms in this TopologyMolecule
atom_start_topology_index
¶Get the topology index of the first atom in this TopologyMolecule
bond
(self, index)[source]¶Get the TopologyBond with a given reference molecule index in this TopologyMolecule
Index of the TopologyBond within this TopologyMolecule to retrieve
bonds
¶Return an iterator of all the TopologyBonds in this TopologyMolecule
n_bonds
¶Get the number of bonds in this TopologyMolecule
bond_start_topology_index
¶Get the topology index of the first bond in this TopologyMolecule
particle
(self, index)[source]¶Get the TopologyParticle with a given reference molecule index in this TopologyMolecule
Index of the TopologyParticle within this TopologyMolecule to retrieve
particles
¶Return an iterator of all the TopologyParticles in this TopologyMolecules
n_particles
¶Get the number of particles in this TopologyMolecule
particle_start_topology_index
¶Get the topology index of the first particle in this TopologyMolecule.
virtual_site
(self, index)[source]¶Get the TopologyVirtualSite with a given reference molecule index in this TopologyMolecule
Index of the TopologyVirtualSite within this TopologyMolecule to retrieve
virtual_sites
¶Return an iterator of all the TopologyVirtualSites in this TopologyMolecules
n_virtual_sites
¶Get the number of virtual sites in this TopologyMolecule
angles
¶Iterable of Tuple[TopologyAtom]: iterator over the angles in this Topology.
n_angles
¶int: number of angles in this Topology.
propers
¶Iterable of Tuple[TopologyAtom]: iterator over the proper torsions in this Topology.
n_propers
¶int: number of proper torsions in this Topology.
impropers
¶Iterable of Tuple[TopologyAtom]: iterator over the improper torsions in this Topology.
n_impropers
¶int: number of proper torsions in this Topology.
virtual_site_start_topology_index
¶Get the topology index of the first virtual site in this TopologyMolecule