Open Force Field Toolkit
0.8.0
Open Force Field Initiative
Open Force Field Toolkit
Installation
Installing via
conda
Required dependencies
Alternative method: Single-file installer
Release History
0.8.0 - Virtual Sites
0.7.2 - Bugfix and minor feature release
0.7.1 - OETK2020 Compatibility and Minor Update
0.7.0 - Charge Increment Model, Proper Torsion interpolation, and new Molecule methods
0.6.0 - Library Charges
0.5.1 - Adding the parameter coverage example notebook
0.5.0 - GBSA support and quality-of-life improvements
0.4.1 - Bugfix Release
0.4.0 - Performance optimizations and support for SMIRNOFF 0.3 specification
0.3.0 - API Improvements
0.2.2 - Bugfix release
0.2.1 - Bugfix release
0.2.0 - Initial RDKit support
0.1.0
The SMIRks Native Open Force Field (SMIRNOFF) specification
Authors and acknowledgments
Representations and encodings
Reference implementation
Support for molecular simulation packages
Basic structure
Units
SMIRNOFF independently applies parameters to each class of potential energy terms
Partial charge and electrostatics models
Parameter sections
Advanced features
The
openforcefield
reference implementation
Version history
Examples using SMIRNOFF with the toolkit
Index of provided examples
Developing for the toolkit
Overview
Setting up a development environment
Development Process
Contributing
How can I become a developer?
Style guide
Frequently asked questions (FAQ)
Input files for applying SMIRNOFF parameters
Can I use an AMBER (or GROMACS) topology/coordinate file as a starting point for applying a SMIRNOFF force field?
What about starting from a PDB file?
What do you recommend as a starting point?
My conda installation of the toolkit doesn’t appear to work. What should I try next?
Molecular topology representations
Primary objects
Secondary objects
Forcefield typing tools
Chemical environments
Forcefield typing engines
Utilities
Toolkit wrappers
Serialization support
Miscellaneous utilities
Page
Index
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A
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B
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C
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D
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E
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F
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G
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H
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I
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K
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L
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M
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N
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O
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P
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R
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S
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T
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U
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V
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X
_
__init__() (openforcefield.topology.Atom method)
(openforcefield.topology.Bond method)
(openforcefield.topology.BondChargeVirtualSite method)
(openforcefield.topology.DivalentLonePairVirtualSite method)
(openforcefield.topology.FrozenMolecule method)
(openforcefield.topology.ImproperDict method)
(openforcefield.topology.Molecule method)
(openforcefield.topology.MonovalentLonePairVirtualSite method)
(openforcefield.topology.Particle method)
(openforcefield.topology.Topology method)
(openforcefield.topology.TopologyAtom method)
(openforcefield.topology.TopologyBond method)
(openforcefield.topology.TopologyMolecule method)
(openforcefield.topology.TopologyVirtualParticle method)
(openforcefield.topology.TopologyVirtualSite method)
(openforcefield.topology.TrivalentLonePairVirtualSite method)
(openforcefield.topology.ValenceDict method)
(openforcefield.topology.VirtualParticle method)
(openforcefield.topology.VirtualSite method)
(openforcefield.typing.chemistry.ChemicalEnvironment method)
(openforcefield.typing.engines.smirnoff.forcefield.ForceField method)
(openforcefield.typing.engines.smirnoff.io.ParameterIOHandler method)
(openforcefield.typing.engines.smirnoff.io.XMLParameterIOHandler method)
(openforcefield.typing.engines.smirnoff.parameters.AngleHandler method)
(openforcefield.typing.engines.smirnoff.parameters.BondHandler method)
(openforcefield.typing.engines.smirnoff.parameters.ElectrostaticsHandler method)
(openforcefield.typing.engines.smirnoff.parameters.GBSAHandler method)
(openforcefield.typing.engines.smirnoff.parameters.ImproperTorsionHandler method)
(openforcefield.typing.engines.smirnoff.parameters.IndexedMappedParameterAttribute method)
(openforcefield.typing.engines.smirnoff.parameters.IndexedParameterAttribute method)
(openforcefield.typing.engines.smirnoff.parameters.LibraryChargeHandler method)
(openforcefield.typing.engines.smirnoff.parameters.MappedParameterAttribute method)
(openforcefield.typing.engines.smirnoff.parameters.ParameterAttribute method)
(openforcefield.typing.engines.smirnoff.parameters.ParameterHandler method)
(openforcefield.typing.engines.smirnoff.parameters.ParameterList method)
(openforcefield.typing.engines.smirnoff.parameters.ParameterType method)
(openforcefield.typing.engines.smirnoff.parameters.ProperTorsionHandler method)
(openforcefield.typing.engines.smirnoff.parameters.ToolkitAM1BCCHandler method)
(openforcefield.typing.engines.smirnoff.parameters.vdWHandler method)
(openforcefield.utils.serialization.Serializable method)
(openforcefield.utils.toolkits.AmberToolsToolkitWrapper method)
(openforcefield.utils.toolkits.OpenEyeToolkitWrapper method)
(openforcefield.utils.toolkits.RDKitToolkitWrapper method)
(openforcefield.utils.toolkits.ToolkitRegistry method)
(openforcefield.utils.toolkits.ToolkitWrapper method)
A
add_atom() (openforcefield.topology.Molecule method)
add_bond() (openforcefield.topology.Atom method)
(openforcefield.topology.Molecule method)
add_bond_charge_virtual_site() (openforcefield.topology.Molecule method)
add_conformer() (openforcefield.topology.Molecule method)
add_constraint() (openforcefield.topology.Topology method)
add_cosmetic_attribute() (openforcefield.typing.engines.smirnoff.parameters.AngleHandler method)
(openforcefield.typing.engines.smirnoff.parameters.AngleHandler.AngleType method)
(openforcefield.typing.engines.smirnoff.parameters.BondHandler method)
(openforcefield.typing.engines.smirnoff.parameters.BondHandler.BondType method)
(openforcefield.typing.engines.smirnoff.parameters.ElectrostaticsHandler method)
(openforcefield.typing.engines.smirnoff.parameters.GBSAHandler method)
(openforcefield.typing.engines.smirnoff.parameters.GBSAHandler.GBSAType method)
(openforcefield.typing.engines.smirnoff.parameters.ImproperTorsionHandler method)
(openforcefield.typing.engines.smirnoff.parameters.ImproperTorsionHandler.ImproperTorsionType method)
(openforcefield.typing.engines.smirnoff.parameters.LibraryChargeHandler method)
(openforcefield.typing.engines.smirnoff.parameters.LibraryChargeHandler.LibraryChargeType method)
(openforcefield.typing.engines.smirnoff.parameters.ParameterHandler method)
(openforcefield.typing.engines.smirnoff.parameters.ParameterType method)
(openforcefield.typing.engines.smirnoff.parameters.ProperTorsionHandler method)
(openforcefield.typing.engines.smirnoff.parameters.ProperTorsionHandler.ProperTorsionType method)
(openforcefield.typing.engines.smirnoff.parameters.ToolkitAM1BCCHandler method)
(openforcefield.typing.engines.smirnoff.parameters.vdWHandler method)
(openforcefield.typing.engines.smirnoff.parameters.vdWHandler.vdWType method)
add_divalent_lone_pair_virtual_site() (openforcefield.topology.Molecule method)
add_molecule() (openforcefield.topology.Topology method)
add_monovalent_lone_pair_virtual_site() (openforcefield.topology.Molecule method)
add_parameter() (openforcefield.typing.engines.smirnoff.parameters.AngleHandler method)
(openforcefield.typing.engines.smirnoff.parameters.BondHandler method)
(openforcefield.typing.engines.smirnoff.parameters.ElectrostaticsHandler method)
(openforcefield.typing.engines.smirnoff.parameters.GBSAHandler method)
(openforcefield.typing.engines.smirnoff.parameters.ImproperTorsionHandler method)
(openforcefield.typing.engines.smirnoff.parameters.LibraryChargeHandler method)
(openforcefield.typing.engines.smirnoff.parameters.ParameterHandler method)
(openforcefield.typing.engines.smirnoff.parameters.ProperTorsionHandler method)
(openforcefield.typing.engines.smirnoff.parameters.ToolkitAM1BCCHandler method)
(openforcefield.typing.engines.smirnoff.parameters.vdWHandler method)
add_particle() (openforcefield.topology.Topology method)
add_toolkit() (openforcefield.utils.toolkits.ToolkitRegistry method)
add_trivalent_lone_pair_virtual_site() (openforcefield.topology.Molecule method)
add_virtual_site() (openforcefield.topology.Atom method)
all_subclasses() (in module openforcefield.utils.utils)
AmberToolsToolkitWrapper (class in openforcefield.utils.toolkits)
AngleHandler (class in openforcefield.typing.engines.smirnoff.parameters)
AngleHandler.AngleType (class in openforcefield.typing.engines.smirnoff.parameters)
angles() (openforcefield.topology.FrozenMolecule property)
(openforcefield.topology.Molecule property)
(openforcefield.topology.Topology property)
(openforcefield.topology.TopologyMolecule property)
append() (openforcefield.typing.engines.smirnoff.parameters.ParameterList method)
are_isomorphic() (openforcefield.topology.FrozenMolecule static method)
(openforcefield.topology.Molecule static method)
aromaticity_model() (openforcefield.topology.Topology property)
(openforcefield.typing.engines.smirnoff.forcefield.ForceField property)
assert_bonded() (openforcefield.topology.Topology method)
assign_charge_from_molecules() (openforcefield.typing.engines.smirnoff.parameters.ElectrostaticsHandler method)
assign_fractional_bond_orders() (openforcefield.topology.FrozenMolecule method)
(openforcefield.topology.Molecule method)
(openforcefield.utils.toolkits.AmberToolsToolkitWrapper method)
(openforcefield.utils.toolkits.OpenEyeToolkitWrapper method)
assign_parameters() (openforcefield.typing.engines.smirnoff.parameters.AngleHandler method)
(openforcefield.typing.engines.smirnoff.parameters.BondHandler method)
(openforcefield.typing.engines.smirnoff.parameters.ElectrostaticsHandler method)
(openforcefield.typing.engines.smirnoff.parameters.GBSAHandler method)
(openforcefield.typing.engines.smirnoff.parameters.ImproperTorsionHandler method)
(openforcefield.typing.engines.smirnoff.parameters.LibraryChargeHandler method)
(openforcefield.typing.engines.smirnoff.parameters.ParameterHandler method)
(openforcefield.typing.engines.smirnoff.parameters.ProperTorsionHandler method)
(openforcefield.typing.engines.smirnoff.parameters.ToolkitAM1BCCHandler method)
(openforcefield.typing.engines.smirnoff.parameters.vdWHandler method)
assign_partial_charges() (openforcefield.topology.FrozenMolecule method)
(openforcefield.topology.Molecule method)
(openforcefield.utils.toolkits.AmberToolsToolkitWrapper method)
(openforcefield.utils.toolkits.OpenEyeToolkitWrapper method)
Atom (class in openforcefield.topology)
atom() (openforcefield.topology.Topology method)
(openforcefield.topology.TopologyAtom property)
(openforcefield.topology.TopologyMolecule method)
(openforcefield.topology.TopologyVirtualParticle method)
(openforcefield.topology.TopologyVirtualSite method)
atom_start_topology_index() (openforcefield.topology.TopologyMolecule property)
atomic_number() (openforcefield.topology.Atom property)
(openforcefield.topology.TopologyAtom property)
atoms() (openforcefield.topology.BondChargeVirtualSite property)
(openforcefield.topology.DivalentLonePairVirtualSite property)
(openforcefield.topology.FrozenMolecule property)
(openforcefield.topology.Molecule property)
(openforcefield.topology.MonovalentLonePairVirtualSite property)
(openforcefield.topology.TopologyBond property)
(openforcefield.topology.TopologyMolecule property)
(openforcefield.topology.TopologyVirtualParticle property)
(openforcefield.topology.TopologyVirtualSite property)
(openforcefield.topology.TrivalentLonePairVirtualSite property)
(openforcefield.topology.VirtualSite property)
attribute_is_cosmetic() (openforcefield.typing.engines.smirnoff.parameters.AngleHandler method)
(openforcefield.typing.engines.smirnoff.parameters.AngleHandler.AngleType method)
(openforcefield.typing.engines.smirnoff.parameters.BondHandler method)
(openforcefield.typing.engines.smirnoff.parameters.BondHandler.BondType method)
(openforcefield.typing.engines.smirnoff.parameters.ElectrostaticsHandler method)
(openforcefield.typing.engines.smirnoff.parameters.GBSAHandler method)
(openforcefield.typing.engines.smirnoff.parameters.GBSAHandler.GBSAType method)
(openforcefield.typing.engines.smirnoff.parameters.ImproperTorsionHandler method)
(openforcefield.typing.engines.smirnoff.parameters.ImproperTorsionHandler.ImproperTorsionType method)
(openforcefield.typing.engines.smirnoff.parameters.LibraryChargeHandler method)
(openforcefield.typing.engines.smirnoff.parameters.LibraryChargeHandler.LibraryChargeType method)
(openforcefield.typing.engines.smirnoff.parameters.ParameterHandler method)
(openforcefield.typing.engines.smirnoff.parameters.ParameterType method)
(openforcefield.typing.engines.smirnoff.parameters.ProperTorsionHandler method)
(openforcefield.typing.engines.smirnoff.parameters.ProperTorsionHandler.ProperTorsionType method)
(openforcefield.typing.engines.smirnoff.parameters.ToolkitAM1BCCHandler method)
(openforcefield.typing.engines.smirnoff.parameters.vdWHandler method)
(openforcefield.typing.engines.smirnoff.parameters.vdWHandler.vdWType method)
author() (openforcefield.typing.engines.smirnoff.forcefield.ForceField property)
B
Bond (class in openforcefield.topology)
bond() (openforcefield.topology.Topology method)
(openforcefield.topology.TopologyBond property)
(openforcefield.topology.TopologyMolecule method)
bond_order() (openforcefield.topology.TopologyBond property)
bond_start_topology_index() (openforcefield.topology.TopologyMolecule property)
BondChargeVirtualSite (class in openforcefield.topology)
bonded_atoms() (openforcefield.topology.Atom property)
BondHandler (class in openforcefield.typing.engines.smirnoff.parameters)
BondHandler.BondType (class in openforcefield.typing.engines.smirnoff.parameters)
bonds() (openforcefield.topology.Atom property)
(openforcefield.topology.FrozenMolecule property)
(openforcefield.topology.Molecule property)
(openforcefield.topology.TopologyMolecule property)
box_vectors() (openforcefield.topology.Topology property)
C
call() (openforcefield.utils.toolkits.ToolkitRegistry method)
canonical_order_atoms() (openforcefield.topology.FrozenMolecule method)
(openforcefield.topology.Molecule method)
(openforcefield.utils.toolkits.OpenEyeToolkitWrapper method)
(openforcefield.utils.toolkits.RDKitToolkitWrapper method)
charge_increments() (openforcefield.topology.BondChargeVirtualSite property)
(openforcefield.topology.DivalentLonePairVirtualSite property)
(openforcefield.topology.MonovalentLonePairVirtualSite property)
(openforcefield.topology.TrivalentLonePairVirtualSite property)
(openforcefield.topology.VirtualSite property)
charge_model() (openforcefield.topology.Topology property)
check_charges_assigned() (openforcefield.typing.engines.smirnoff.parameters.ElectrostaticsHandler static method)
(openforcefield.typing.engines.smirnoff.parameters.LibraryChargeHandler static method)
(openforcefield.typing.engines.smirnoff.parameters.ToolkitAM1BCCHandler static method)
(openforcefield.typing.engines.smirnoff.parameters.vdWHandler static method)
check_handler_compatibility() (openforcefield.typing.engines.smirnoff.parameters.AngleHandler method)
(openforcefield.typing.engines.smirnoff.parameters.BondHandler method)
(openforcefield.typing.engines.smirnoff.parameters.ElectrostaticsHandler method)
(openforcefield.typing.engines.smirnoff.parameters.GBSAHandler method)
(openforcefield.typing.engines.smirnoff.parameters.ImproperTorsionHandler method)
(openforcefield.typing.engines.smirnoff.parameters.LibraryChargeHandler method)
(openforcefield.typing.engines.smirnoff.parameters.ParameterHandler method)
(openforcefield.typing.engines.smirnoff.parameters.ProperTorsionHandler method)
(openforcefield.typing.engines.smirnoff.parameters.ToolkitAM1BCCHandler method)
(openforcefield.typing.engines.smirnoff.parameters.vdWHandler method)
chemical_environment_matches() (openforcefield.topology.FrozenMolecule method)
(openforcefield.topology.Molecule method)
(openforcefield.topology.Topology method)
ChemicalEnvironment (class in openforcefield.typing.chemistry)
clear() (openforcefield.topology.ImproperDict method)
(openforcefield.topology.ValenceDict method)
(openforcefield.typing.engines.smirnoff.parameters.ParameterList method)
compute_partial_charges_am1bcc() (openforcefield.topology.FrozenMolecule method)
(openforcefield.topology.Molecule method)
(openforcefield.utils.toolkits.AmberToolsToolkitWrapper method)
(openforcefield.utils.toolkits.OpenEyeToolkitWrapper method)
conformers() (openforcefield.topology.FrozenMolecule property)
(openforcefield.topology.Molecule property)
constrained_atom_pairs() (openforcefield.topology.Topology property)
convert_0_1_smirnoff_to_0_2() (in module openforcefield.utils.utils)
convert_0_2_smirnoff_to_0_3() (in module openforcefield.utils.utils)
converter() (openforcefield.typing.engines.smirnoff.parameters.IndexedMappedParameterAttribute method)
(openforcefield.typing.engines.smirnoff.parameters.IndexedParameterAttribute method)
(openforcefield.typing.engines.smirnoff.parameters.MappedParameterAttribute method)
(openforcefield.typing.engines.smirnoff.parameters.ParameterAttribute method)
copy() (openforcefield.typing.engines.smirnoff.parameters.ParameterList method)
count() (openforcefield.typing.engines.smirnoff.parameters.ParameterList method)
create_openmm_system() (openforcefield.typing.engines.smirnoff.forcefield.ForceField method)
create_parmed_structure() (openforcefield.typing.engines.smirnoff.forcefield.ForceField method)
D
date() (openforcefield.typing.engines.smirnoff.forcefield.ForceField property)
delete_cosmetic_attribute() (openforcefield.typing.engines.smirnoff.parameters.AngleHandler method)
(openforcefield.typing.engines.smirnoff.parameters.AngleHandler.AngleType method)
(openforcefield.typing.engines.smirnoff.parameters.BondHandler method)
(openforcefield.typing.engines.smirnoff.parameters.BondHandler.BondType method)
(openforcefield.typing.engines.smirnoff.parameters.ElectrostaticsHandler method)
(openforcefield.typing.engines.smirnoff.parameters.GBSAHandler method)
(openforcefield.typing.engines.smirnoff.parameters.GBSAHandler.GBSAType method)
(openforcefield.typing.engines.smirnoff.parameters.ImproperTorsionHandler method)
(openforcefield.typing.engines.smirnoff.parameters.ImproperTorsionHandler.ImproperTorsionType method)
(openforcefield.typing.engines.smirnoff.parameters.LibraryChargeHandler method)
(openforcefield.typing.engines.smirnoff.parameters.LibraryChargeHandler.LibraryChargeType method)
(openforcefield.typing.engines.smirnoff.parameters.ParameterHandler method)
(openforcefield.typing.engines.smirnoff.parameters.ParameterType method)
(openforcefield.typing.engines.smirnoff.parameters.ProperTorsionHandler method)
(openforcefield.typing.engines.smirnoff.parameters.ProperTorsionHandler.ProperTorsionType method)
(openforcefield.typing.engines.smirnoff.parameters.ToolkitAM1BCCHandler method)
(openforcefield.typing.engines.smirnoff.parameters.vdWHandler method)
(openforcefield.typing.engines.smirnoff.parameters.vdWHandler.vdWType method)
deregister_toolkit() (openforcefield.utils.toolkits.ToolkitRegistry method)
distance() (openforcefield.topology.BondChargeVirtualSite property)
(openforcefield.topology.DivalentLonePairVirtualSite property)
(openforcefield.topology.MonovalentLonePairVirtualSite property)
(openforcefield.topology.TrivalentLonePairVirtualSite property)
DivalentLonePairVirtualSite (class in openforcefield.topology)
E
ElectrostaticsHandler (class in openforcefield.typing.engines.smirnoff.parameters)
element() (openforcefield.topology.Atom property)
enumerate_protomers() (openforcefield.topology.FrozenMolecule method)
(openforcefield.topology.Molecule method)
(openforcefield.utils.toolkits.OpenEyeToolkitWrapper method)
enumerate_stereoisomers() (openforcefield.topology.FrozenMolecule method)
(openforcefield.topology.Molecule method)
(openforcefield.utils.toolkits.OpenEyeToolkitWrapper method)
(openforcefield.utils.toolkits.RDKitToolkitWrapper method)
enumerate_tautomers() (openforcefield.topology.FrozenMolecule method)
(openforcefield.topology.Molecule method)
(openforcefield.utils.toolkits.OpenEyeToolkitWrapper method)
(openforcefield.utils.toolkits.RDKitToolkitWrapper method)
epsilon() (openforcefield.topology.BondChargeVirtualSite property)
(openforcefield.topology.DivalentLonePairVirtualSite property)
(openforcefield.topology.MonovalentLonePairVirtualSite property)
(openforcefield.topology.TrivalentLonePairVirtualSite property)
(openforcefield.topology.VirtualSite property)
extend() (openforcefield.typing.engines.smirnoff.parameters.ParameterList method)
F
find_matches() (openforcefield.typing.engines.smirnoff.parameters.AngleHandler method)
(openforcefield.typing.engines.smirnoff.parameters.BondHandler method)
(openforcefield.typing.engines.smirnoff.parameters.ElectrostaticsHandler method)
(openforcefield.typing.engines.smirnoff.parameters.GBSAHandler method)
(openforcefield.typing.engines.smirnoff.parameters.ImproperTorsionHandler method)
(openforcefield.typing.engines.smirnoff.parameters.LibraryChargeHandler method)
(openforcefield.typing.engines.smirnoff.parameters.ParameterHandler method)
(openforcefield.typing.engines.smirnoff.parameters.ProperTorsionHandler method)
(openforcefield.typing.engines.smirnoff.parameters.ToolkitAM1BCCHandler method)
(openforcefield.typing.engines.smirnoff.parameters.vdWHandler method)
find_rings() (openforcefield.utils.toolkits.RDKitToolkitWrapper method)
find_rotatable_bonds() (openforcefield.topology.FrozenMolecule method)
(openforcefield.topology.Molecule method)
find_smarts_matches() (openforcefield.utils.toolkits.OpenEyeToolkitWrapper method)
(openforcefield.utils.toolkits.RDKitToolkitWrapper method)
ForceField (class in openforcefield.typing.engines.smirnoff.forcefield)
formal_charge() (openforcefield.topology.Atom property)
fractional_bond_order_model() (openforcefield.topology.Topology property)
from_bson() (openforcefield.topology.Atom class method)
(openforcefield.topology.Bond class method)
(openforcefield.topology.BondChargeVirtualSite class method)
(openforcefield.topology.DivalentLonePairVirtualSite class method)
(openforcefield.topology.FrozenMolecule class method)
(openforcefield.topology.Molecule class method)
(openforcefield.topology.MonovalentLonePairVirtualSite class method)
(openforcefield.topology.Particle class method)
(openforcefield.topology.Topology class method)
(openforcefield.topology.TopologyAtom class method)
(openforcefield.topology.TopologyBond class method)
(openforcefield.topology.TopologyVirtualParticle class method)
(openforcefield.topology.TopologyVirtualSite class method)
(openforcefield.topology.TrivalentLonePairVirtualSite class method)
(openforcefield.topology.VirtualParticle class method)
(openforcefield.topology.VirtualSite class method)
(openforcefield.utils.serialization.Serializable class method)
from_dict() (openforcefield.topology.Atom class method)
(openforcefield.topology.Bond class method)
(openforcefield.topology.BondChargeVirtualSite class method)
(openforcefield.topology.DivalentLonePairVirtualSite class method)
(openforcefield.topology.FrozenMolecule class method)
(openforcefield.topology.Molecule class method)
(openforcefield.topology.MonovalentLonePairVirtualSite class method)
(openforcefield.topology.Particle class method)
(openforcefield.topology.Topology class method)
(openforcefield.topology.TopologyAtom class method)
(openforcefield.topology.TopologyBond class method)
(openforcefield.topology.TopologyMolecule class method)
(openforcefield.topology.TopologyVirtualParticle class method)
(openforcefield.topology.TopologyVirtualSite class method)
(openforcefield.topology.TrivalentLonePairVirtualSite class method)
(openforcefield.topology.VirtualParticle class method)
(openforcefield.topology.VirtualSite class method)
from_file() (openforcefield.topology.FrozenMolecule static method)
(openforcefield.topology.Molecule static method)
(openforcefield.utils.toolkits.AmberToolsToolkitWrapper method)
(openforcefield.utils.toolkits.OpenEyeToolkitWrapper method)
(openforcefield.utils.toolkits.RDKitToolkitWrapper method)
(openforcefield.utils.toolkits.ToolkitWrapper method)
from_file_obj() (openforcefield.utils.toolkits.AmberToolsToolkitWrapper method)
(openforcefield.utils.toolkits.OpenEyeToolkitWrapper method)
(openforcefield.utils.toolkits.RDKitToolkitWrapper method)
(openforcefield.utils.toolkits.ToolkitWrapper method)
from_inchi() (openforcefield.topology.FrozenMolecule static method)
(openforcefield.topology.Molecule static method)
(openforcefield.utils.toolkits.OpenEyeToolkitWrapper method)
(openforcefield.utils.toolkits.RDKitToolkitWrapper method)
from_iupac() (openforcefield.topology.FrozenMolecule class method)
(openforcefield.topology.Molecule class method)
(openforcefield.utils.toolkits.OpenEyeToolkitWrapper method)
from_json() (openforcefield.topology.Atom class method)
(openforcefield.topology.Bond class method)
(openforcefield.topology.BondChargeVirtualSite class method)
(openforcefield.topology.DivalentLonePairVirtualSite class method)
(openforcefield.topology.FrozenMolecule class method)
(openforcefield.topology.Molecule class method)
(openforcefield.topology.MonovalentLonePairVirtualSite class method)
(openforcefield.topology.Particle class method)
(openforcefield.topology.Topology class method)
(openforcefield.topology.TopologyAtom class method)
(openforcefield.topology.TopologyBond class method)
(openforcefield.topology.TopologyVirtualParticle class method)
(openforcefield.topology.TopologyVirtualSite class method)
(openforcefield.topology.TrivalentLonePairVirtualSite class method)
(openforcefield.topology.VirtualParticle class method)
(openforcefield.topology.VirtualSite class method)
(openforcefield.utils.serialization.Serializable class method)
from_mapped_smiles() (openforcefield.topology.FrozenMolecule class method)
(openforcefield.topology.Molecule class method)
from_mdtraj() (openforcefield.topology.Topology static method)
from_messagepack() (openforcefield.topology.Atom class method)
(openforcefield.topology.Bond class method)
(openforcefield.topology.BondChargeVirtualSite class method)
(openforcefield.topology.DivalentLonePairVirtualSite class method)
(openforcefield.topology.FrozenMolecule class method)
(openforcefield.topology.Molecule class method)
(openforcefield.topology.MonovalentLonePairVirtualSite class method)
(openforcefield.topology.Particle class method)
(openforcefield.topology.Topology class method)
(openforcefield.topology.TopologyAtom class method)
(openforcefield.topology.TopologyBond class method)
(openforcefield.topology.TopologyVirtualParticle class method)
(openforcefield.topology.TopologyVirtualSite class method)
(openforcefield.topology.TrivalentLonePairVirtualSite class method)
(openforcefield.topology.VirtualParticle class method)
(openforcefield.topology.VirtualSite class method)
(openforcefield.utils.serialization.Serializable class method)
from_molecules() (openforcefield.topology.Topology class method)
from_object() (openforcefield.utils.toolkits.OpenEyeToolkitWrapper method)
(openforcefield.utils.toolkits.RDKitToolkitWrapper method)
from_openeye() (openforcefield.topology.FrozenMolecule static method)
(openforcefield.topology.Molecule static method)
(openforcefield.utils.toolkits.OpenEyeToolkitWrapper static method)
from_openmm() (openforcefield.topology.Topology class method)
from_parmed() (openforcefield.topology.Topology static method)
from_pdb_and_smiles() (openforcefield.topology.FrozenMolecule class method)
(openforcefield.topology.Molecule class method)
(openforcefield.utils.toolkits.RDKitToolkitWrapper method)
from_pickle() (openforcefield.topology.Atom class method)
(openforcefield.topology.Bond class method)
(openforcefield.topology.BondChargeVirtualSite class method)
(openforcefield.topology.DivalentLonePairVirtualSite class method)
(openforcefield.topology.FrozenMolecule class method)
(openforcefield.topology.Molecule class method)
(openforcefield.topology.MonovalentLonePairVirtualSite class method)
(openforcefield.topology.Particle class method)
(openforcefield.topology.Topology class method)
(openforcefield.topology.TopologyAtom class method)
(openforcefield.topology.TopologyBond class method)
(openforcefield.topology.TopologyVirtualParticle class method)
(openforcefield.topology.TopologyVirtualSite class method)
(openforcefield.topology.TrivalentLonePairVirtualSite class method)
(openforcefield.topology.VirtualParticle class method)
(openforcefield.topology.VirtualSite class method)
(openforcefield.utils.serialization.Serializable class method)
from_qcschema() (openforcefield.topology.FrozenMolecule class method)
(openforcefield.topology.Molecule class method)
from_rdkit() (openforcefield.topology.FrozenMolecule static method)
(openforcefield.topology.Molecule static method)
(openforcefield.utils.toolkits.RDKitToolkitWrapper method)
from_smiles() (openforcefield.topology.FrozenMolecule static method)
(openforcefield.topology.Molecule static method)
(openforcefield.utils.toolkits.OpenEyeToolkitWrapper method)
(openforcefield.utils.toolkits.RDKitToolkitWrapper method)
from_toml() (openforcefield.topology.Atom class method)
(openforcefield.topology.Bond class method)
(openforcefield.topology.BondChargeVirtualSite class method)
(openforcefield.topology.DivalentLonePairVirtualSite class method)
(openforcefield.topology.FrozenMolecule class method)
(openforcefield.topology.Molecule class method)
(openforcefield.topology.MonovalentLonePairVirtualSite class method)
(openforcefield.topology.Particle class method)
(openforcefield.topology.Topology class method)
(openforcefield.topology.TopologyAtom class method)
(openforcefield.topology.TopologyBond class method)
(openforcefield.topology.TopologyVirtualParticle class method)
(openforcefield.topology.TopologyVirtualSite class method)
(openforcefield.topology.TrivalentLonePairVirtualSite class method)
(openforcefield.topology.VirtualParticle class method)
(openforcefield.topology.VirtualSite class method)
(openforcefield.utils.serialization.Serializable class method)
from_topology() (openforcefield.topology.FrozenMolecule static method)
(openforcefield.topology.Molecule static method)
from_xml() (openforcefield.topology.Atom class method)
(openforcefield.topology.Bond class method)
(openforcefield.topology.BondChargeVirtualSite class method)
(openforcefield.topology.DivalentLonePairVirtualSite class method)
(openforcefield.topology.FrozenMolecule class method)
(openforcefield.topology.Molecule class method)
(openforcefield.topology.MonovalentLonePairVirtualSite class method)
(openforcefield.topology.Particle class method)
(openforcefield.topology.Topology class method)
(openforcefield.topology.TopologyAtom class method)
(openforcefield.topology.TopologyBond class method)
(openforcefield.topology.TopologyVirtualParticle class method)
(openforcefield.topology.TopologyVirtualSite class method)
(openforcefield.topology.TrivalentLonePairVirtualSite class method)
(openforcefield.topology.VirtualParticle class method)
(openforcefield.topology.VirtualSite class method)
(openforcefield.utils.serialization.Serializable class method)
from_yaml() (openforcefield.topology.Atom class method)
(openforcefield.topology.Bond class method)
(openforcefield.topology.BondChargeVirtualSite class method)
(openforcefield.topology.DivalentLonePairVirtualSite class method)
(openforcefield.topology.FrozenMolecule class method)
(openforcefield.topology.Molecule class method)
(openforcefield.topology.MonovalentLonePairVirtualSite class method)
(openforcefield.topology.Particle class method)
(openforcefield.topology.Topology class method)
(openforcefield.topology.TopologyAtom class method)
(openforcefield.topology.TopologyBond class method)
(openforcefield.topology.TopologyVirtualParticle class method)
(openforcefield.topology.TopologyVirtualSite class method)
(openforcefield.topology.TrivalentLonePairVirtualSite class method)
(openforcefield.topology.VirtualParticle class method)
(openforcefield.topology.VirtualSite class method)
(openforcefield.utils.serialization.Serializable class method)
FrozenMolecule (class in openforcefield.topology)
G
GBSAHandler (class in openforcefield.typing.engines.smirnoff.parameters)
GBSAHandler.GBSAType (class in openforcefield.typing.engines.smirnoff.parameters)
generate_conformers() (openforcefield.topology.FrozenMolecule method)
(openforcefield.topology.Molecule method)
(openforcefield.utils.toolkits.OpenEyeToolkitWrapper method)
(openforcefield.utils.toolkits.RDKitToolkitWrapper method)
generate_unique_atom_names() (openforcefield.topology.FrozenMolecule method)
(openforcefield.topology.Molecule method)
get() (openforcefield.topology.ImproperDict method)
(openforcefield.topology.ValenceDict method)
get_available_force_fields() (in module openforcefield.typing.engines.smirnoff.forcefield)
get_bond_between() (openforcefield.topology.FrozenMolecule method)
(openforcefield.topology.Molecule method)
(openforcefield.topology.Topology method)
get_data_file_path() (in module openforcefield.utils.utils)
get_molecule_parameterIDs() (in module openforcefield.utils.utils)
get_openmm_virtual_site() (openforcefield.topology.BondChargeVirtualSite method)
(openforcefield.topology.DivalentLonePairVirtualSite method)
(openforcefield.topology.MonovalentLonePairVirtualSite method)
(openforcefield.topology.TrivalentLonePairVirtualSite method)
get_parameter() (openforcefield.typing.engines.smirnoff.parameters.AngleHandler method)
(openforcefield.typing.engines.smirnoff.parameters.BondHandler method)
(openforcefield.typing.engines.smirnoff.parameters.ElectrostaticsHandler method)
(openforcefield.typing.engines.smirnoff.parameters.GBSAHandler method)
(openforcefield.typing.engines.smirnoff.parameters.ImproperTorsionHandler method)
(openforcefield.typing.engines.smirnoff.parameters.LibraryChargeHandler method)
(openforcefield.typing.engines.smirnoff.parameters.ParameterHandler method)
(openforcefield.typing.engines.smirnoff.parameters.ProperTorsionHandler method)
(openforcefield.typing.engines.smirnoff.parameters.ToolkitAM1BCCHandler method)
(openforcefield.typing.engines.smirnoff.parameters.vdWHandler method)
get_parameter_handler() (openforcefield.typing.engines.smirnoff.forcefield.ForceField method)
get_parameter_io_handler() (openforcefield.typing.engines.smirnoff.forcefield.ForceField method)
get_tagged_smarts_connectivity() (openforcefield.utils.toolkits.OpenEyeToolkitWrapper method)
(openforcefield.utils.toolkits.RDKitToolkitWrapper method)
get_type() (openforcefield.typing.chemistry.ChemicalEnvironment method)
H
has_unique_atom_names() (openforcefield.topology.FrozenMolecule property)
(openforcefield.topology.Molecule property)
hill_formula() (openforcefield.topology.FrozenMolecule property)
(openforcefield.topology.Molecule property)
I
ImproperDict (class in openforcefield.topology)
impropers() (openforcefield.topology.FrozenMolecule property)
(openforcefield.topology.Molecule property)
(openforcefield.topology.Topology property)
(openforcefield.topology.TopologyMolecule property)
ImproperTorsionHandler (class in openforcefield.typing.engines.smirnoff.parameters)
ImproperTorsionHandler.ImproperTorsionType (class in openforcefield.typing.engines.smirnoff.parameters)
in_plane_angle() (openforcefield.topology.MonovalentLonePairVirtualSite property)
index() (openforcefield.typing.engines.smirnoff.parameters.ParameterList method)
index_of() (openforcefield.topology.ImproperDict static method)
(openforcefield.topology.ValenceDict static method)
IndexedMappedParameterAttribute (class in openforcefield.typing.engines.smirnoff.parameters)
IndexedMappedParameterAttribute.UNDEFINED (class in openforcefield.typing.engines.smirnoff.parameters)
IndexedParameterAttribute (class in openforcefield.typing.engines.smirnoff.parameters)
IndexedParameterAttribute.UNDEFINED (class in openforcefield.typing.engines.smirnoff.parameters)
inherit_docstrings() (in module openforcefield.utils.utils)
insert() (openforcefield.typing.engines.smirnoff.parameters.ParameterList method)
is_aromatic() (openforcefield.topology.Atom property)
is_available() (openforcefield.utils.toolkits.AmberToolsToolkitWrapper static method)
(openforcefield.utils.toolkits.OpenEyeToolkitWrapper static method)
(openforcefield.utils.toolkits.RDKitToolkitWrapper static method)
(openforcefield.utils.toolkits.ToolkitWrapper static method)
is_bonded() (openforcefield.topology.Topology method)
is_bonded_to() (openforcefield.topology.Atom method)
is_constrained() (openforcefield.topology.Topology method)
is_in_ring() (openforcefield.topology.Atom property)
(openforcefield.topology.Bond property)
is_isomorphic_with() (openforcefield.topology.FrozenMolecule method)
(openforcefield.topology.Molecule method)
items() (openforcefield.topology.ImproperDict method)
(openforcefield.topology.ValenceDict method)
K
key_transform() (openforcefield.topology.ImproperDict static method)
(openforcefield.topology.ValenceDict static method)
keys() (openforcefield.topology.ImproperDict method)
(openforcefield.topology.ValenceDict method)
known_kwargs() (openforcefield.typing.engines.smirnoff.parameters.AngleHandler property)
(openforcefield.typing.engines.smirnoff.parameters.BondHandler property)
(openforcefield.typing.engines.smirnoff.parameters.ElectrostaticsHandler property)
(openforcefield.typing.engines.smirnoff.parameters.GBSAHandler property)
(openforcefield.typing.engines.smirnoff.parameters.ImproperTorsionHandler property)
(openforcefield.typing.engines.smirnoff.parameters.LibraryChargeHandler property)
(openforcefield.typing.engines.smirnoff.parameters.ParameterHandler property)
(openforcefield.typing.engines.smirnoff.parameters.ProperTorsionHandler property)
(openforcefield.typing.engines.smirnoff.parameters.ToolkitAM1BCCHandler property)
(openforcefield.typing.engines.smirnoff.parameters.vdWHandler property)
L
label_molecules() (openforcefield.typing.engines.smirnoff.forcefield.ForceField method)
LibraryChargeHandler (class in openforcefield.typing.engines.smirnoff.parameters)
LibraryChargeHandler.LibraryChargeType (class in openforcefield.typing.engines.smirnoff.parameters)
M
MappedParameterAttribute (class in openforcefield.typing.engines.smirnoff.parameters)
MappedParameterAttribute.UNDEFINED (class in openforcefield.typing.engines.smirnoff.parameters)
mark_charges_assigned() (openforcefield.typing.engines.smirnoff.parameters.ElectrostaticsHandler method)
(openforcefield.typing.engines.smirnoff.parameters.LibraryChargeHandler method)
(openforcefield.typing.engines.smirnoff.parameters.ToolkitAM1BCCHandler method)
(openforcefield.typing.engines.smirnoff.parameters.vdWHandler method)
mass() (openforcefield.topology.Atom property)
Molecule (class in openforcefield.topology)
molecule() (openforcefield.topology.Atom property)
(openforcefield.topology.BondChargeVirtualSite property)
(openforcefield.topology.DivalentLonePairVirtualSite property)
(openforcefield.topology.MonovalentLonePairVirtualSite property)
(openforcefield.topology.Particle property)
(openforcefield.topology.TopologyAtom property)
(openforcefield.topology.TopologyBond property)
(openforcefield.topology.TopologyVirtualParticle property)
(openforcefield.topology.TopologyVirtualSite property)
(openforcefield.topology.TrivalentLonePairVirtualSite property)
(openforcefield.topology.VirtualParticle property)
(openforcefield.topology.VirtualSite property)
molecule_atom_index() (openforcefield.topology.Atom property)
molecule_bond_index() (openforcefield.topology.Bond property)
molecule_particle_index() (openforcefield.topology.Atom property)
(openforcefield.topology.BondChargeVirtualSite property)
(openforcefield.topology.DivalentLonePairVirtualSite property)
(openforcefield.topology.MonovalentLonePairVirtualSite property)
(openforcefield.topology.Particle property)
(openforcefield.topology.TrivalentLonePairVirtualSite property)
(openforcefield.topology.VirtualParticle property)
(openforcefield.topology.VirtualSite property)
molecule_virtual_site_index() (openforcefield.topology.BondChargeVirtualSite property)
(openforcefield.topology.DivalentLonePairVirtualSite property)
(openforcefield.topology.MonovalentLonePairVirtualSite property)
(openforcefield.topology.TrivalentLonePairVirtualSite property)
(openforcefield.topology.VirtualSite property)
MonovalentLonePairVirtualSite (class in openforcefield.topology)
N
n_angles() (openforcefield.topology.FrozenMolecule property)
(openforcefield.topology.Molecule property)
(openforcefield.topology.Topology property)
(openforcefield.topology.TopologyMolecule property)
n_atoms() (openforcefield.topology.FrozenMolecule property)
(openforcefield.topology.Molecule property)
(openforcefield.topology.TopologyMolecule property)
n_bonds() (openforcefield.topology.FrozenMolecule property)
(openforcefield.topology.Molecule property)
(openforcefield.topology.TopologyMolecule property)
n_conformers() (openforcefield.topology.FrozenMolecule property)
(openforcefield.topology.Molecule property)
n_impropers() (openforcefield.topology.FrozenMolecule property)
(openforcefield.topology.Molecule property)
(openforcefield.topology.Topology property)
(openforcefield.topology.TopologyMolecule property)
n_particles() (openforcefield.topology.BondChargeVirtualSite property)
(openforcefield.topology.DivalentLonePairVirtualSite property)
(openforcefield.topology.FrozenMolecule property)
(openforcefield.topology.Molecule property)
(openforcefield.topology.MonovalentLonePairVirtualSite property)
(openforcefield.topology.TopologyMolecule property)
(openforcefield.topology.TopologyVirtualParticle property)
(openforcefield.topology.TopologyVirtualSite property)
(openforcefield.topology.TrivalentLonePairVirtualSite property)
(openforcefield.topology.VirtualSite property)
n_propers() (openforcefield.topology.FrozenMolecule property)
(openforcefield.topology.Molecule property)
(openforcefield.topology.Topology property)
(openforcefield.topology.TopologyMolecule property)
n_reference_molecules() (openforcefield.topology.Topology property)
n_rings() (openforcefield.topology.FrozenMolecule property)
(openforcefield.topology.Molecule property)
n_topology_atoms() (openforcefield.topology.Topology property)
n_topology_bonds() (openforcefield.topology.Topology property)
n_topology_molecules() (openforcefield.topology.Topology property)
n_topology_particles() (openforcefield.topology.Topology property)
n_topology_virtual_sites() (openforcefield.topology.Topology property)
n_virtual_particles() (openforcefield.topology.FrozenMolecule property)
(openforcefield.topology.Molecule property)
n_virtual_sites() (openforcefield.topology.FrozenMolecule property)
(openforcefield.topology.Molecule property)
(openforcefield.topology.TopologyMolecule property)
name() (openforcefield.topology.Atom property)
(openforcefield.topology.BondChargeVirtualSite property)
(openforcefield.topology.DivalentLonePairVirtualSite property)
(openforcefield.topology.FrozenMolecule property)
(openforcefield.topology.Molecule property)
(openforcefield.topology.MonovalentLonePairVirtualSite property)
(openforcefield.topology.Particle property)
(openforcefield.topology.TrivalentLonePairVirtualSite property)
(openforcefield.topology.VirtualParticle property)
(openforcefield.topology.VirtualSite property)
O
OpenEyeToolkitWrapper (class in openforcefield.utils.toolkits)
out_of_plane_angle() (openforcefield.topology.DivalentLonePairVirtualSite property)
(openforcefield.topology.MonovalentLonePairVirtualSite property)
P
ParameterAttribute (class in openforcefield.typing.engines.smirnoff.parameters)
ParameterAttribute.UNDEFINED (class in openforcefield.typing.engines.smirnoff.parameters)
ParameterHandler (class in openforcefield.typing.engines.smirnoff.parameters)
ParameterIOHandler (class in openforcefield.typing.engines.smirnoff.io)
ParameterList (class in openforcefield.typing.engines.smirnoff.parameters)
parameters() (openforcefield.typing.engines.smirnoff.parameters.AngleHandler property)
(openforcefield.typing.engines.smirnoff.parameters.BondHandler property)
(openforcefield.typing.engines.smirnoff.parameters.ElectrostaticsHandler property)
(openforcefield.typing.engines.smirnoff.parameters.GBSAHandler property)
(openforcefield.typing.engines.smirnoff.parameters.ImproperTorsionHandler property)
(openforcefield.typing.engines.smirnoff.parameters.LibraryChargeHandler property)
(openforcefield.typing.engines.smirnoff.parameters.ParameterHandler property)
(openforcefield.typing.engines.smirnoff.parameters.ProperTorsionHandler property)
(openforcefield.typing.engines.smirnoff.parameters.ToolkitAM1BCCHandler property)
(openforcefield.typing.engines.smirnoff.parameters.vdWHandler property)
ParameterType (class in openforcefield.typing.engines.smirnoff.parameters)
parse_file() (openforcefield.typing.engines.smirnoff.io.ParameterIOHandler method)
(openforcefield.typing.engines.smirnoff.io.XMLParameterIOHandler method)
parse_smirnoff_from_source() (openforcefield.typing.engines.smirnoff.forcefield.ForceField method)
parse_sources() (openforcefield.typing.engines.smirnoff.forcefield.ForceField method)
parse_string() (openforcefield.typing.engines.smirnoff.io.ParameterIOHandler method)
(openforcefield.typing.engines.smirnoff.io.XMLParameterIOHandler method)
partial_charge() (openforcefield.topology.Atom property)
partial_charges() (openforcefield.topology.FrozenMolecule property)
(openforcefield.topology.Molecule property)
Particle (class in openforcefield.topology)
particle() (openforcefield.topology.TopologyMolecule method)
particles() (openforcefield.topology.BondChargeVirtualSite property)
(openforcefield.topology.DivalentLonePairVirtualSite property)
(openforcefield.topology.FrozenMolecule property)
(openforcefield.topology.Molecule property)
(openforcefield.topology.MonovalentLonePairVirtualSite property)
(openforcefield.topology.TopologyMolecule property)
(openforcefield.topology.TopologyVirtualParticle property)
(openforcefield.topology.TopologyVirtualSite property)
(openforcefield.topology.TrivalentLonePairVirtualSite property)
(openforcefield.topology.VirtualSite property)
pop() (openforcefield.topology.ImproperDict method)
(openforcefield.topology.ValenceDict method)
(openforcefield.typing.engines.smirnoff.parameters.ParameterList method)
popitem() (openforcefield.topology.ImproperDict method)
(openforcefield.topology.ValenceDict method)
postprocess_system() (openforcefield.typing.engines.smirnoff.parameters.AngleHandler method)
(openforcefield.typing.engines.smirnoff.parameters.BondHandler method)
(openforcefield.typing.engines.smirnoff.parameters.ElectrostaticsHandler method)
(openforcefield.typing.engines.smirnoff.parameters.GBSAHandler method)
(openforcefield.typing.engines.smirnoff.parameters.ImproperTorsionHandler method)
(openforcefield.typing.engines.smirnoff.parameters.LibraryChargeHandler method)
(openforcefield.typing.engines.smirnoff.parameters.ParameterHandler method)
(openforcefield.typing.engines.smirnoff.parameters.ProperTorsionHandler method)
(openforcefield.typing.engines.smirnoff.parameters.ToolkitAM1BCCHandler method)
(openforcefield.typing.engines.smirnoff.parameters.vdWHandler method)
propers() (openforcefield.topology.FrozenMolecule property)
(openforcefield.topology.Molecule property)
(openforcefield.topology.Topology property)
(openforcefield.topology.TopologyMolecule property)
properties() (openforcefield.topology.FrozenMolecule property)
(openforcefield.topology.Molecule property)
ProperTorsionHandler (class in openforcefield.typing.engines.smirnoff.parameters)
ProperTorsionHandler.ProperTorsionType (class in openforcefield.typing.engines.smirnoff.parameters)
R
RDKitToolkitWrapper (class in openforcefield.utils.toolkits)
reference_molecule() (openforcefield.topology.TopologyMolecule property)
reference_molecules() (openforcefield.topology.Topology property)
register_parameter_handler() (openforcefield.typing.engines.smirnoff.forcefield.ForceField method)
register_parameter_io_handler() (openforcefield.typing.engines.smirnoff.forcefield.ForceField method)
register_toolkit() (openforcefield.utils.toolkits.ToolkitRegistry method)
registered_parameter_handlers() (openforcefield.typing.engines.smirnoff.forcefield.ForceField property)
registered_toolkit_versions() (openforcefield.utils.toolkits.ToolkitRegistry property)
registered_toolkits() (openforcefield.utils.toolkits.ToolkitRegistry property)
remap() (openforcefield.topology.FrozenMolecule method)
(openforcefield.topology.Molecule method)
remove() (openforcefield.typing.engines.smirnoff.parameters.ParameterList method)
resolve() (openforcefield.utils.toolkits.ToolkitRegistry method)
reverse() (openforcefield.typing.engines.smirnoff.parameters.ParameterList method)
rings() (openforcefield.topology.FrozenMolecule property)
(openforcefield.topology.Molecule property)
rmin_half() (openforcefield.topology.BondChargeVirtualSite property)
(openforcefield.topology.DivalentLonePairVirtualSite property)
(openforcefield.topology.MonovalentLonePairVirtualSite property)
(openforcefield.topology.TrivalentLonePairVirtualSite property)
(openforcefield.topology.VirtualSite property)
S
Serializable (class in openforcefield.utils.serialization)
setdefault() (openforcefield.topology.ImproperDict method)
(openforcefield.topology.ValenceDict method)
sigma() (openforcefield.topology.BondChargeVirtualSite property)
(openforcefield.topology.DivalentLonePairVirtualSite property)
(openforcefield.topology.MonovalentLonePairVirtualSite property)
(openforcefield.topology.TrivalentLonePairVirtualSite property)
(openforcefield.topology.VirtualSite property)
sort() (openforcefield.typing.engines.smirnoff.parameters.ParameterList method)
stereochemistry() (openforcefield.topology.Atom property)
strip_atom_stereochemistry() (openforcefield.topology.FrozenMolecule method)
(openforcefield.topology.Molecule method)
T
TAGNAME() (openforcefield.typing.engines.smirnoff.parameters.AngleHandler property)
(openforcefield.typing.engines.smirnoff.parameters.BondHandler property)
(openforcefield.typing.engines.smirnoff.parameters.ElectrostaticsHandler property)
(openforcefield.typing.engines.smirnoff.parameters.GBSAHandler property)
(openforcefield.typing.engines.smirnoff.parameters.ImproperTorsionHandler property)
(openforcefield.typing.engines.smirnoff.parameters.LibraryChargeHandler property)
(openforcefield.typing.engines.smirnoff.parameters.ParameterHandler property)
(openforcefield.typing.engines.smirnoff.parameters.ProperTorsionHandler property)
(openforcefield.typing.engines.smirnoff.parameters.ToolkitAM1BCCHandler property)
(openforcefield.typing.engines.smirnoff.parameters.vdWHandler property)
temporary_cd() (in module openforcefield.utils.utils)
to_bson() (openforcefield.topology.Atom method)
(openforcefield.topology.Bond method)
(openforcefield.topology.BondChargeVirtualSite method)
(openforcefield.topology.DivalentLonePairVirtualSite method)
(openforcefield.topology.FrozenMolecule method)
(openforcefield.topology.Molecule method)
(openforcefield.topology.MonovalentLonePairVirtualSite method)
(openforcefield.topology.Particle method)
(openforcefield.topology.Topology method)
(openforcefield.topology.TopologyAtom method)
(openforcefield.topology.TopologyBond method)
(openforcefield.topology.TopologyVirtualParticle method)
(openforcefield.topology.TopologyVirtualSite method)
(openforcefield.topology.TrivalentLonePairVirtualSite method)
(openforcefield.topology.VirtualParticle method)
(openforcefield.topology.VirtualSite method)
(openforcefield.utils.serialization.Serializable method)
to_dict() (openforcefield.topology.Atom method)
(openforcefield.topology.Bond method)
(openforcefield.topology.BondChargeVirtualSite method)
(openforcefield.topology.DivalentLonePairVirtualSite method)
(openforcefield.topology.FrozenMolecule method)
(openforcefield.topology.Molecule method)
(openforcefield.topology.MonovalentLonePairVirtualSite method)
(openforcefield.topology.Particle method)
(openforcefield.topology.Topology method)
(openforcefield.topology.TopologyAtom method)
(openforcefield.topology.TopologyBond method)
(openforcefield.topology.TopologyMolecule method)
(openforcefield.topology.TopologyVirtualParticle method)
(openforcefield.topology.TopologyVirtualSite method)
(openforcefield.topology.TrivalentLonePairVirtualSite method)
(openforcefield.topology.VirtualParticle method)
(openforcefield.topology.VirtualSite method)
(openforcefield.typing.engines.smirnoff.parameters.AngleHandler method)
(openforcefield.typing.engines.smirnoff.parameters.AngleHandler.AngleType method)
(openforcefield.typing.engines.smirnoff.parameters.BondHandler method)
(openforcefield.typing.engines.smirnoff.parameters.BondHandler.BondType method)
(openforcefield.typing.engines.smirnoff.parameters.ElectrostaticsHandler method)
(openforcefield.typing.engines.smirnoff.parameters.GBSAHandler method)
(openforcefield.typing.engines.smirnoff.parameters.GBSAHandler.GBSAType method)
(openforcefield.typing.engines.smirnoff.parameters.ImproperTorsionHandler method)
(openforcefield.typing.engines.smirnoff.parameters.ImproperTorsionHandler.ImproperTorsionType method)
(openforcefield.typing.engines.smirnoff.parameters.LibraryChargeHandler method)
(openforcefield.typing.engines.smirnoff.parameters.LibraryChargeHandler.LibraryChargeType method)
(openforcefield.typing.engines.smirnoff.parameters.ParameterHandler method)
(openforcefield.typing.engines.smirnoff.parameters.ParameterType method)
(openforcefield.typing.engines.smirnoff.parameters.ProperTorsionHandler method)
(openforcefield.typing.engines.smirnoff.parameters.ProperTorsionHandler.ProperTorsionType method)
(openforcefield.typing.engines.smirnoff.parameters.ToolkitAM1BCCHandler method)
(openforcefield.typing.engines.smirnoff.parameters.vdWHandler method)
(openforcefield.typing.engines.smirnoff.parameters.vdWHandler.vdWType method)
to_file() (openforcefield.topology.FrozenMolecule method)
(openforcefield.topology.Molecule method)
(openforcefield.topology.Topology method)
(openforcefield.typing.engines.smirnoff.forcefield.ForceField method)
(openforcefield.typing.engines.smirnoff.io.ParameterIOHandler method)
(openforcefield.typing.engines.smirnoff.io.XMLParameterIOHandler method)
(openforcefield.utils.toolkits.OpenEyeToolkitWrapper method)
(openforcefield.utils.toolkits.RDKitToolkitWrapper method)
to_file_obj() (openforcefield.utils.toolkits.OpenEyeToolkitWrapper method)
(openforcefield.utils.toolkits.RDKitToolkitWrapper method)
to_hill_formula() (openforcefield.topology.FrozenMolecule static method)
(openforcefield.topology.Molecule static method)
to_inchi() (openforcefield.topology.FrozenMolecule method)
(openforcefield.topology.Molecule method)
(openforcefield.utils.toolkits.OpenEyeToolkitWrapper method)
(openforcefield.utils.toolkits.RDKitToolkitWrapper method)
to_inchikey() (openforcefield.topology.FrozenMolecule method)
(openforcefield.topology.Molecule method)
(openforcefield.utils.toolkits.OpenEyeToolkitWrapper method)
(openforcefield.utils.toolkits.RDKitToolkitWrapper method)
to_iupac() (openforcefield.topology.FrozenMolecule method)
(openforcefield.topology.Molecule method)
(openforcefield.utils.toolkits.OpenEyeToolkitWrapper method)
to_json() (openforcefield.topology.Atom method)
(openforcefield.topology.Bond method)
(openforcefield.topology.BondChargeVirtualSite method)
(openforcefield.topology.DivalentLonePairVirtualSite method)
(openforcefield.topology.FrozenMolecule method)
(openforcefield.topology.Molecule method)
(openforcefield.topology.MonovalentLonePairVirtualSite method)
(openforcefield.topology.Particle method)
(openforcefield.topology.Topology method)
(openforcefield.topology.TopologyAtom method)
(openforcefield.topology.TopologyBond method)
(openforcefield.topology.TopologyVirtualParticle method)
(openforcefield.topology.TopologyVirtualSite method)
(openforcefield.topology.TrivalentLonePairVirtualSite method)
(openforcefield.topology.VirtualParticle method)
(openforcefield.topology.VirtualSite method)
(openforcefield.utils.serialization.Serializable method)
to_list() (openforcefield.typing.engines.smirnoff.parameters.ParameterList method)
to_messagepack() (openforcefield.topology.Atom method)
(openforcefield.topology.Bond method)
(openforcefield.topology.BondChargeVirtualSite method)
(openforcefield.topology.DivalentLonePairVirtualSite method)
(openforcefield.topology.FrozenMolecule method)
(openforcefield.topology.Molecule method)
(openforcefield.topology.MonovalentLonePairVirtualSite method)
(openforcefield.topology.Particle method)
(openforcefield.topology.Topology method)
(openforcefield.topology.TopologyAtom method)
(openforcefield.topology.TopologyBond method)
(openforcefield.topology.TopologyVirtualParticle method)
(openforcefield.topology.TopologyVirtualSite method)
(openforcefield.topology.TrivalentLonePairVirtualSite method)
(openforcefield.topology.VirtualParticle method)
(openforcefield.topology.VirtualSite method)
(openforcefield.utils.serialization.Serializable method)
to_networkx() (openforcefield.topology.FrozenMolecule method)
(openforcefield.topology.Molecule method)
to_openeye() (openforcefield.topology.FrozenMolecule method)
(openforcefield.topology.Molecule method)
(openforcefield.utils.toolkits.OpenEyeToolkitWrapper static method)
to_openmm() (openforcefield.topology.Topology method)
to_parmed() (openforcefield.topology.Topology method)
to_pickle() (openforcefield.topology.Atom method)
(openforcefield.topology.Bond method)
(openforcefield.topology.BondChargeVirtualSite method)
(openforcefield.topology.DivalentLonePairVirtualSite method)
(openforcefield.topology.FrozenMolecule method)
(openforcefield.topology.Molecule method)
(openforcefield.topology.MonovalentLonePairVirtualSite method)
(openforcefield.topology.Particle method)
(openforcefield.topology.Topology method)
(openforcefield.topology.TopologyAtom method)
(openforcefield.topology.TopologyBond method)
(openforcefield.topology.TopologyVirtualParticle method)
(openforcefield.topology.TopologyVirtualSite method)
(openforcefield.topology.TrivalentLonePairVirtualSite method)
(openforcefield.topology.VirtualParticle method)
(openforcefield.topology.VirtualSite method)
(openforcefield.utils.serialization.Serializable method)
to_qcschema() (openforcefield.topology.FrozenMolecule method)
(openforcefield.topology.Molecule method)
to_rdkit() (openforcefield.topology.FrozenMolecule method)
(openforcefield.topology.Molecule method)
(openforcefield.utils.toolkits.RDKitToolkitWrapper class method)
to_smiles() (openforcefield.topology.FrozenMolecule method)
(openforcefield.topology.Molecule method)
(openforcefield.utils.toolkits.OpenEyeToolkitWrapper method)
(openforcefield.utils.toolkits.RDKitToolkitWrapper method)
to_string() (openforcefield.typing.engines.smirnoff.forcefield.ForceField method)
(openforcefield.typing.engines.smirnoff.io.ParameterIOHandler method)
(openforcefield.typing.engines.smirnoff.io.XMLParameterIOHandler method)
to_toml() (openforcefield.topology.Atom method)
(openforcefield.topology.Bond method)
(openforcefield.topology.BondChargeVirtualSite method)
(openforcefield.topology.DivalentLonePairVirtualSite method)
(openforcefield.topology.FrozenMolecule method)
(openforcefield.topology.Molecule method)
(openforcefield.topology.MonovalentLonePairVirtualSite method)
(openforcefield.topology.Particle method)
(openforcefield.topology.Topology method)
(openforcefield.topology.TopologyAtom method)
(openforcefield.topology.TopologyBond method)
(openforcefield.topology.TopologyVirtualParticle method)
(openforcefield.topology.TopologyVirtualSite method)
(openforcefield.topology.TrivalentLonePairVirtualSite method)
(openforcefield.topology.VirtualParticle method)
(openforcefield.topology.VirtualSite method)
(openforcefield.utils.serialization.Serializable method)
to_topology() (openforcefield.topology.FrozenMolecule method)
(openforcefield.topology.Molecule method)
to_xml() (openforcefield.topology.Atom method)
(openforcefield.topology.Bond method)
(openforcefield.topology.BondChargeVirtualSite method)
(openforcefield.topology.DivalentLonePairVirtualSite method)
(openforcefield.topology.FrozenMolecule method)
(openforcefield.topology.Molecule method)
(openforcefield.topology.MonovalentLonePairVirtualSite method)
(openforcefield.topology.Particle method)
(openforcefield.topology.Topology method)
(openforcefield.topology.TopologyAtom method)
(openforcefield.topology.TopologyBond method)
(openforcefield.topology.TopologyVirtualParticle method)
(openforcefield.topology.TopologyVirtualSite method)
(openforcefield.topology.TrivalentLonePairVirtualSite method)
(openforcefield.topology.VirtualParticle method)
(openforcefield.topology.VirtualSite method)
(openforcefield.utils.serialization.Serializable method)
to_yaml() (openforcefield.topology.Atom method)
(openforcefield.topology.Bond method)
(openforcefield.topology.BondChargeVirtualSite method)
(openforcefield.topology.DivalentLonePairVirtualSite method)
(openforcefield.topology.FrozenMolecule method)
(openforcefield.topology.Molecule method)
(openforcefield.topology.MonovalentLonePairVirtualSite method)
(openforcefield.topology.Particle method)
(openforcefield.topology.Topology method)
(openforcefield.topology.TopologyAtom method)
(openforcefield.topology.TopologyBond method)
(openforcefield.topology.TopologyVirtualParticle method)
(openforcefield.topology.TopologyVirtualSite method)
(openforcefield.topology.TrivalentLonePairVirtualSite method)
(openforcefield.topology.VirtualParticle method)
(openforcefield.topology.VirtualSite method)
(openforcefield.utils.serialization.Serializable method)
toolkit_file_read_formats() (openforcefield.utils.toolkits.AmberToolsToolkitWrapper property)
(openforcefield.utils.toolkits.OpenEyeToolkitWrapper property)
(openforcefield.utils.toolkits.RDKitToolkitWrapper property)
(openforcefield.utils.toolkits.ToolkitWrapper property)
toolkit_file_write_formats() (openforcefield.utils.toolkits.AmberToolsToolkitWrapper property)
(openforcefield.utils.toolkits.OpenEyeToolkitWrapper property)
(openforcefield.utils.toolkits.RDKitToolkitWrapper property)
(openforcefield.utils.toolkits.ToolkitWrapper property)
toolkit_installation_instructions() (openforcefield.utils.toolkits.AmberToolsToolkitWrapper property)
(openforcefield.utils.toolkits.OpenEyeToolkitWrapper property)
(openforcefield.utils.toolkits.RDKitToolkitWrapper property)
(openforcefield.utils.toolkits.ToolkitWrapper property)
toolkit_name() (openforcefield.utils.toolkits.AmberToolsToolkitWrapper property)
(openforcefield.utils.toolkits.OpenEyeToolkitWrapper property)
(openforcefield.utils.toolkits.RDKitToolkitWrapper property)
(openforcefield.utils.toolkits.ToolkitWrapper property)
toolkit_version() (openforcefield.utils.toolkits.AmberToolsToolkitWrapper property)
(openforcefield.utils.toolkits.OpenEyeToolkitWrapper property)
(openforcefield.utils.toolkits.RDKitToolkitWrapper property)
(openforcefield.utils.toolkits.ToolkitWrapper property)
ToolkitAM1BCCHandler (class in openforcefield.typing.engines.smirnoff.parameters)
ToolkitRegistry (class in openforcefield.utils.toolkits)
ToolkitWrapper (class in openforcefield.utils.toolkits)
Topology (class in openforcefield.topology)
topology() (openforcefield.topology.TopologyMolecule property)
topology_atom_index() (openforcefield.topology.TopologyAtom property)
topology_atoms() (openforcefield.topology.Topology property)
topology_bond_index() (openforcefield.topology.TopologyBond property)
topology_bonds() (openforcefield.topology.Topology property)
(openforcefield.topology.TopologyAtom property)
topology_molecule() (openforcefield.topology.TopologyAtom property)
(openforcefield.topology.TopologyBond property)
(openforcefield.topology.TopologyVirtualParticle property)
(openforcefield.topology.TopologyVirtualSite property)
topology_molecules() (openforcefield.topology.Topology property)
topology_particle_index() (openforcefield.topology.TopologyAtom property)
(openforcefield.topology.TopologyVirtualParticle property)
topology_particles() (openforcefield.topology.Topology property)
topology_virtual_particle_start_index() (openforcefield.topology.TopologyVirtualParticle property)
(openforcefield.topology.TopologyVirtualSite property)
topology_virtual_site_index() (openforcefield.topology.TopologyVirtualParticle property)
(openforcefield.topology.TopologyVirtualSite property)
topology_virtual_sites() (openforcefield.topology.Topology property)
TopologyAtom (class in openforcefield.topology)
TopologyBond (class in openforcefield.topology)
TopologyMolecule (class in openforcefield.topology)
TopologyVirtualParticle (class in openforcefield.topology)
TopologyVirtualSite (class in openforcefield.topology)
torsions() (openforcefield.topology.FrozenMolecule property)
(openforcefield.topology.Molecule property)
total_charge() (openforcefield.topology.FrozenMolecule property)
(openforcefield.topology.Molecule property)
TrivalentLonePairVirtualSite (class in openforcefield.topology)
type() (openforcefield.topology.BondChargeVirtualSite property)
(openforcefield.topology.DivalentLonePairVirtualSite property)
(openforcefield.topology.MonovalentLonePairVirtualSite property)
(openforcefield.topology.TopologyVirtualParticle property)
(openforcefield.topology.TopologyVirtualSite property)
(openforcefield.topology.TrivalentLonePairVirtualSite property)
(openforcefield.topology.VirtualSite property)
U
update() (openforcefield.topology.ImproperDict method)
(openforcefield.topology.ValenceDict method)
V
ValenceDict (class in openforcefield.topology)
validate() (openforcefield.typing.chemistry.ChemicalEnvironment method)
validate_smirks() (openforcefield.typing.chemistry.ChemicalEnvironment class method)
values() (openforcefield.topology.ImproperDict method)
(openforcefield.topology.ValenceDict method)
vdWHandler (class in openforcefield.typing.engines.smirnoff.parameters)
vdWHandler.vdWType (class in openforcefield.typing.engines.smirnoff.parameters)
virtual_particle_start_topology_index() (openforcefield.topology.TopologyMolecule property)
virtual_site() (openforcefield.topology.Topology method)
(openforcefield.topology.TopologyMolecule method)
(openforcefield.topology.TopologyVirtualParticle property)
(openforcefield.topology.TopologyVirtualSite property)
virtual_site_particle_index() (openforcefield.topology.VirtualParticle property)
virtual_site_start_topology_index() (openforcefield.topology.TopologyMolecule property)
virtual_sites() (openforcefield.topology.Atom property)
(openforcefield.topology.FrozenMolecule property)
(openforcefield.topology.Molecule property)
(openforcefield.topology.TopologyMolecule property)
VirtualParticle (class in openforcefield.topology)
VirtualSite (class in openforcefield.topology)
visualize() (openforcefield.topology.Molecule method)
X
XMLParameterIOHandler (class in openforcefield.typing.engines.smirnoff.io)