Open Force Field Toolkit
0.5.0
Open Force Field Initiative
Open Force Field Toolkit
Installation
Installing via
conda
Required dependencies
Release History
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
Style guide
Contributing
How can I become a developer?
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?
Molecular topology representations
Primary objects
Secondary objects
Forcefield typing tools
Chemical environments
Forcefield typing engines
Utilities
Toolkit wrappers
Serialization support
Miscellaneous utilities
Structure tools
Page
Index
_
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A
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B
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C
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D
|
E
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F
|
G
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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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V
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X
_
__init__() (openforcefield.topology.Atom method)
(openforcefield.topology.Bond method)
(openforcefield.topology.FrozenMolecule method)
(openforcefield.topology.Molecule method)
(openforcefield.topology.Particle method)
(openforcefield.topology.Topology 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.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.IndexedParameterAttribute 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.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)
(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)
,
[1]
(openforcefield.typing.engines.smirnoff.parameters.BondHandler method)
(openforcefield.typing.engines.smirnoff.parameters.BondHandler.BondType method)
,
[1]
(openforcefield.typing.engines.smirnoff.parameters.ElectrostaticsHandler method)
(openforcefield.typing.engines.smirnoff.parameters.GBSAHandler method)
(openforcefield.typing.engines.smirnoff.parameters.GBSAHandler.GBSAType method)
,
[1]
(openforcefield.typing.engines.smirnoff.parameters.ImproperTorsionHandler method)
(openforcefield.typing.engines.smirnoff.parameters.ImproperTorsionHandler.ImproperTorsionType method)
,
[1]
(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)
,
[1]
(openforcefield.typing.engines.smirnoff.parameters.ToolkitAM1BCCHandler method)
(openforcefield.typing.engines.smirnoff.parameters.vdWHandler method)
(openforcefield.typing.engines.smirnoff.parameters.vdWHandler.vdWType method)
,
[1]
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.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)
addANDtype() (openforcefield.typing.chemistry.ChemicalEnvironment.Atom method)
(openforcefield.typing.chemistry.ChemicalEnvironment.Bond method)
addAtom() (openforcefield.typing.chemistry.ChemicalEnvironment method)
addORtype() (openforcefield.typing.chemistry.ChemicalEnvironment.Atom method)
(openforcefield.typing.chemistry.ChemicalEnvironment.Bond 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)
AngleType (class in openforcefield.typing.engines.smirnoff.parameters.AngleHandler)
append() (openforcefield.typing.engines.smirnoff.parameters.ParameterList method)
aromaticity_model() (openforcefield.topology.Topology property)
assert_bonded() (openforcefield.topology.Topology method)
assign_charge_from_molecules() (openforcefield.typing.engines.smirnoff.parameters.ToolkitAM1BCCHandler 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.ParameterHandler method)
(openforcefield.typing.engines.smirnoff.parameters.ProperTorsionHandler method)
(openforcefield.typing.engines.smirnoff.parameters.ToolkitAM1BCCHandler method)
(openforcefield.typing.engines.smirnoff.parameters.vdWHandler method)
asSMARTS() (openforcefield.typing.chemistry.ChemicalEnvironment.Atom method)
(openforcefield.typing.chemistry.ChemicalEnvironment.Bond method)
asSMIRKS() (openforcefield.typing.chemistry.ChemicalEnvironment method)
(openforcefield.typing.chemistry.ChemicalEnvironment.Atom method)
(openforcefield.typing.chemistry.ChemicalEnvironment.Bond method)
Atom (class in openforcefield.topology)
atom() (openforcefield.topology.Topology method)
atomic_number() (openforcefield.topology.Atom property)
atoms() (openforcefield.topology.FrozenMolecule property)
(openforcefield.topology.Molecule property)
(openforcefield.topology.VirtualSite property)
author() (openforcefield.typing.engines.smirnoff.forcefield.ForceField property)
B
Bond (class in openforcefield.topology)
bond() (openforcefield.topology.Topology method)
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)
BondType (class in openforcefield.typing.engines.smirnoff.parameters.BondHandler)
box_vectors() (openforcefield.topology.Topology property)
C
call() (openforcefield.utils.toolkits.ToolkitRegistry method)
charge_increments() (openforcefield.topology.VirtualSite property)
charge_model() (openforcefield.topology.Topology property)
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.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)
ChemicalEnvironment.Atom (class in openforcefield.typing.chemistry)
ChemicalEnvironment.Bond (class in openforcefield.typing.chemistry)
clear() (openforcefield.typing.engines.smirnoff.parameters.ParameterList method)
compute_partial_charges() (openforcefield.topology.FrozenMolecule method)
(openforcefield.topology.Molecule method)
(openforcefield.utils.toolkits.AmberToolsToolkitWrapper method)
(openforcefield.utils.toolkits.OpenEyeToolkitWrapper method)
compute_partial_charges_am1bcc() (openforcefield.topology.FrozenMolecule method)
(openforcefield.topology.Molecule method)
(openforcefield.utils.toolkits.AmberToolsToolkitWrapper method)
(openforcefield.utils.toolkits.OpenEyeToolkitWrapper method)
compute_wiberg_bond_orders() (openforcefield.topology.FrozenMolecule method)
(openforcefield.topology.Molecule 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.IndexedParameterAttribute 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)
,
[1]
(openforcefield.typing.engines.smirnoff.parameters.BondHandler method)
(openforcefield.typing.engines.smirnoff.parameters.BondHandler.BondType method)
,
[1]
(openforcefield.typing.engines.smirnoff.parameters.ElectrostaticsHandler method)
(openforcefield.typing.engines.smirnoff.parameters.GBSAHandler method)
(openforcefield.typing.engines.smirnoff.parameters.GBSAHandler.GBSAType method)
,
[1]
(openforcefield.typing.engines.smirnoff.parameters.ImproperTorsionHandler method)
(openforcefield.typing.engines.smirnoff.parameters.ImproperTorsionHandler.ImproperTorsionType method)
,
[1]
(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)
,
[1]
(openforcefield.typing.engines.smirnoff.parameters.ToolkitAM1BCCHandler method)
(openforcefield.typing.engines.smirnoff.parameters.vdWHandler method)
(openforcefield.typing.engines.smirnoff.parameters.vdWHandler.vdWType method)
,
[1]
E
ElectrostaticsHandler (class in openforcefield.typing.engines.smirnoff.parameters)
element() (openforcefield.topology.Atom property)
epsilon() (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.ParameterHandler method)
(openforcefield.typing.engines.smirnoff.parameters.ProperTorsionHandler method)
(openforcefield.typing.engines.smirnoff.parameters.ToolkitAM1BCCHandler method)
(openforcefield.typing.engines.smirnoff.parameters.vdWHandler 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.FrozenMolecule class method)
(openforcefield.topology.Molecule class method)
(openforcefield.topology.Particle class method)
(openforcefield.topology.Topology 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.FrozenMolecule class method)
(openforcefield.topology.Molecule class method)
(openforcefield.topology.Particle class method)
(openforcefield.topology.Topology 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_iupac() (openforcefield.topology.FrozenMolecule class method)
(openforcefield.topology.Molecule class method)
from_json() (openforcefield.topology.Atom class method)
(openforcefield.topology.Bond class method)
(openforcefield.topology.FrozenMolecule class method)
(openforcefield.topology.Molecule class method)
(openforcefield.topology.Particle class method)
(openforcefield.topology.Topology class method)
(openforcefield.topology.VirtualSite class method)
(openforcefield.utils.serialization.Serializable class method)
from_mdtraj() (openforcefield.topology.Topology static method)
from_messagepack() (openforcefield.topology.Atom class method)
(openforcefield.topology.Bond class method)
(openforcefield.topology.FrozenMolecule class method)
(openforcefield.topology.Molecule class method)
(openforcefield.topology.Particle class method)
(openforcefield.topology.Topology 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_pickle() (openforcefield.topology.Atom class method)
(openforcefield.topology.Bond class method)
(openforcefield.topology.FrozenMolecule class method)
(openforcefield.topology.Molecule class method)
(openforcefield.topology.Particle class method)
(openforcefield.topology.Topology class method)
(openforcefield.topology.VirtualSite class method)
(openforcefield.utils.serialization.Serializable 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.FrozenMolecule class method)
(openforcefield.topology.Molecule class method)
(openforcefield.topology.Particle class method)
(openforcefield.topology.Topology 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.FrozenMolecule class method)
(openforcefield.topology.Molecule class method)
(openforcefield.topology.Particle class method)
(openforcefield.topology.Topology 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.FrozenMolecule class method)
(openforcefield.topology.Molecule class method)
(openforcefield.topology.Particle class method)
(openforcefield.topology.Topology 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)
GBSAType (class in openforcefield.typing.engines.smirnoff.parameters.GBSAHandler)
generate_conformers() (openforcefield.topology.FrozenMolecule method)
(openforcefield.topology.Molecule method)
(openforcefield.utils.toolkits.OpenEyeToolkitWrapper method)
(openforcefield.utils.toolkits.RDKitToolkitWrapper method)
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_fractional_bond_order() (openforcefield.topology.Topology method)
get_fractional_bond_orders() (openforcefield.topology.FrozenMolecule method)
(openforcefield.topology.Molecule method)
get_molecule_parameterIDs() (in module openforcefield.utils.structure)
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.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)
getAlphaAtoms() (openforcefield.typing.chemistry.ChemicalEnvironment method)
getAlphaBonds() (openforcefield.typing.chemistry.ChemicalEnvironment method)
getANDtypes() (openforcefield.typing.chemistry.ChemicalEnvironment.Atom method)
(openforcefield.typing.chemistry.ChemicalEnvironment.Bond method)
getAtoms() (openforcefield.typing.chemistry.ChemicalEnvironment method)
getBetaAtoms() (openforcefield.typing.chemistry.ChemicalEnvironment method)
getBetaBonds() (openforcefield.typing.chemistry.ChemicalEnvironment method)
getBond() (openforcefield.typing.chemistry.ChemicalEnvironment method)
getBondOrder() (openforcefield.typing.chemistry.ChemicalEnvironment method)
getBonds() (openforcefield.typing.chemistry.ChemicalEnvironment method)
getComponentList() (openforcefield.typing.chemistry.ChemicalEnvironment method)
getIndexedAtoms() (openforcefield.typing.chemistry.ChemicalEnvironment method)
getIndexedBonds() (openforcefield.typing.chemistry.ChemicalEnvironment method)
getNeighbors() (openforcefield.typing.chemistry.ChemicalEnvironment method)
getOrder() (openforcefield.typing.chemistry.ChemicalEnvironment.Bond method)
getORtypes() (openforcefield.typing.chemistry.ChemicalEnvironment.Atom method)
(openforcefield.typing.chemistry.ChemicalEnvironment.Bond method)
getType() (openforcefield.typing.chemistry.ChemicalEnvironment method)
getUnindexedAtoms() (openforcefield.typing.chemistry.ChemicalEnvironment method)
getUnindexedBonds() (openforcefield.typing.chemistry.ChemicalEnvironment method)
getValence() (openforcefield.typing.chemistry.ChemicalEnvironment method)
I
impropers() (openforcefield.topology.FrozenMolecule property)
(openforcefield.topology.Molecule property)
(openforcefield.topology.Topology property)
ImproperTorsionHandler (class in openforcefield.typing.engines.smirnoff.parameters)
ImproperTorsionHandler.ImproperTorsionType (class in openforcefield.typing.engines.smirnoff.parameters)
ImproperTorsionType (class in openforcefield.typing.engines.smirnoff.parameters.ImproperTorsionHandler)
index() (openforcefield.typing.engines.smirnoff.parameters.ParameterList method)
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_isomorphic() (openforcefield.topology.FrozenMolecule method)
(openforcefield.topology.Molecule method)
isAlpha() (openforcefield.typing.chemistry.ChemicalEnvironment method)
isBeta() (openforcefield.typing.chemistry.ChemicalEnvironment method)
isIndexed() (openforcefield.typing.chemistry.ChemicalEnvironment method)
isUnindexed() (openforcefield.typing.chemistry.ChemicalEnvironment method)
isValid() (openforcefield.typing.chemistry.ChemicalEnvironment method)
K
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.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)
M
mass() (openforcefield.topology.Atom property)
Molecule (class in openforcefield.topology)
molecule() (openforcefield.topology.Atom property)
(openforcefield.topology.Particle 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.Particle property)
(openforcefield.topology.VirtualSite property)
molecule_virtual_site_index() (openforcefield.topology.VirtualSite property)
N
n_angles() (openforcefield.topology.FrozenMolecule property)
(openforcefield.topology.Molecule property)
(openforcefield.topology.Topology property)
n_atoms() (openforcefield.topology.FrozenMolecule property)
(openforcefield.topology.Molecule property)
n_bonds() (openforcefield.topology.FrozenMolecule property)
(openforcefield.topology.Molecule 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)
n_particles() (openforcefield.topology.FrozenMolecule property)
(openforcefield.topology.Molecule property)
n_propers() (openforcefield.topology.FrozenMolecule property)
(openforcefield.topology.Molecule property)
(openforcefield.topology.Topology property)
n_reference_molecules() (openforcefield.topology.Topology 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_sites() (openforcefield.topology.FrozenMolecule property)
(openforcefield.topology.Molecule property)
name() (openforcefield.topology.Atom property)
(openforcefield.topology.FrozenMolecule property)
(openforcefield.topology.Molecule property)
(openforcefield.topology.Particle property)
(openforcefield.topology.VirtualSite property)
O
OpenEyeToolkitWrapper (class in openforcefield.utils.toolkits)
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.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)
particles() (openforcefield.topology.FrozenMolecule property)
(openforcefield.topology.Molecule property)
pop() (openforcefield.typing.engines.smirnoff.parameters.ParameterList 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.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)
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)
ProperTorsionType (class in openforcefield.typing.engines.smirnoff.parameters.ProperTorsionHandler)
R
RDKitToolkitWrapper (class in openforcefield.utils.toolkits)
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_toolkits() (openforcefield.utils.toolkits.ToolkitRegistry property)
remove() (openforcefield.typing.engines.smirnoff.parameters.ParameterList method)
removeAtom() (openforcefield.typing.chemistry.ChemicalEnvironment method)
resolve() (openforcefield.utils.toolkits.ToolkitRegistry method)
reverse() (openforcefield.typing.engines.smirnoff.parameters.ParameterList method)
rmin_half() (openforcefield.topology.VirtualSite property)
S
selectAtom() (openforcefield.typing.chemistry.ChemicalEnvironment method)
selectBond() (openforcefield.typing.chemistry.ChemicalEnvironment method)
Serializable (class in openforcefield.utils.serialization)
setANDtypes() (openforcefield.typing.chemistry.ChemicalEnvironment.Atom method)
(openforcefield.typing.chemistry.ChemicalEnvironment.Bond method)
setORtypes() (openforcefield.typing.chemistry.ChemicalEnvironment.Atom method)
(openforcefield.typing.chemistry.ChemicalEnvironment.Bond method)
sigma() (openforcefield.topology.VirtualSite property)
sort() (openforcefield.typing.engines.smirnoff.parameters.ParameterList method)
stereochemistry() (openforcefield.topology.Atom property)
T
temporary_cd() (in module openforcefield.utils.utils)
temporary_directory() (in module openforcefield.utils.utils)
to_bson() (openforcefield.topology.Atom method)
(openforcefield.topology.Bond method)
(openforcefield.topology.FrozenMolecule method)
(openforcefield.topology.Molecule method)
(openforcefield.topology.Particle method)
(openforcefield.topology.Topology method)
(openforcefield.topology.VirtualSite method)
(openforcefield.utils.serialization.Serializable method)
to_dict() (openforcefield.topology.Atom method)
(openforcefield.topology.Bond method)
(openforcefield.topology.FrozenMolecule method)
(openforcefield.topology.Molecule method)
(openforcefield.topology.Particle method)
(openforcefield.topology.Topology method)
(openforcefield.topology.VirtualSite method)
(openforcefield.typing.engines.smirnoff.parameters.AngleHandler method)
(openforcefield.typing.engines.smirnoff.parameters.AngleHandler.AngleType method)
,
[1]
(openforcefield.typing.engines.smirnoff.parameters.BondHandler method)
(openforcefield.typing.engines.smirnoff.parameters.BondHandler.BondType method)
,
[1]
(openforcefield.typing.engines.smirnoff.parameters.ElectrostaticsHandler method)
(openforcefield.typing.engines.smirnoff.parameters.GBSAHandler method)
(openforcefield.typing.engines.smirnoff.parameters.GBSAHandler.GBSAType method)
,
[1]
(openforcefield.typing.engines.smirnoff.parameters.ImproperTorsionHandler method)
(openforcefield.typing.engines.smirnoff.parameters.ImproperTorsionHandler.ImproperTorsionType method)
,
[1]
(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)
,
[1]
(openforcefield.typing.engines.smirnoff.parameters.ToolkitAM1BCCHandler method)
(openforcefield.typing.engines.smirnoff.parameters.vdWHandler method)
(openforcefield.typing.engines.smirnoff.parameters.vdWHandler.vdWType method)
,
[1]
to_file() (openforcefield.topology.FrozenMolecule method)
(openforcefield.topology.Molecule 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_iupac() (openforcefield.topology.FrozenMolecule method)
(openforcefield.topology.Molecule method)
to_json() (openforcefield.topology.Atom method)
(openforcefield.topology.Bond method)
(openforcefield.topology.FrozenMolecule method)
(openforcefield.topology.Molecule method)
(openforcefield.topology.Particle method)
(openforcefield.topology.Topology 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.FrozenMolecule method)
(openforcefield.topology.Molecule method)
(openforcefield.topology.Particle method)
(openforcefield.topology.Topology 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.FrozenMolecule method)
(openforcefield.topology.Molecule method)
(openforcefield.topology.Particle method)
(openforcefield.topology.Topology method)
(openforcefield.topology.VirtualSite method)
(openforcefield.utils.serialization.Serializable 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 static method)
(openforcefield.utils.toolkits.RDKitToolkitWrapper class 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.FrozenMolecule method)
(openforcefield.topology.Molecule method)
(openforcefield.topology.Particle method)
(openforcefield.topology.Topology 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.FrozenMolecule method)
(openforcefield.topology.Molecule method)
(openforcefield.topology.Particle method)
(openforcefield.topology.Topology method)
(openforcefield.topology.VirtualSite method)
(openforcefield.utils.serialization.Serializable method)
to_yaml() (openforcefield.topology.Atom method)
(openforcefield.topology.Bond method)
(openforcefield.topology.FrozenMolecule method)
(openforcefield.topology.Molecule method)
(openforcefield.topology.Particle method)
(openforcefield.topology.Topology 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)
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_atoms() (openforcefield.topology.Topology property)
topology_bonds() (openforcefield.topology.Topology property)
topology_molecules() (openforcefield.topology.Topology property)
topology_particles() (openforcefield.topology.Topology property)
topology_virtual_sites() (openforcefield.topology.Topology property)
torsions() (openforcefield.topology.FrozenMolecule property)
(openforcefield.topology.Molecule property)
total_charge() (openforcefield.topology.FrozenMolecule property)
(openforcefield.topology.Molecule property)
type() (openforcefield.topology.VirtualSite property)
V
validate() (openforcefield.typing.chemistry.ChemicalEnvironment static method)
vdWHandler (class in openforcefield.typing.engines.smirnoff.parameters)
vdWHandler.vdWType (class in openforcefield.typing.engines.smirnoff.parameters)
vdWType (class in openforcefield.typing.engines.smirnoff.parameters.vdWHandler)
virtual_site() (openforcefield.topology.Topology method)
virtual_sites() (openforcefield.topology.Atom property)
(openforcefield.topology.FrozenMolecule property)
(openforcefield.topology.Molecule property)
VirtualSite (class in openforcefield.topology)
X
XMLParameterIOHandler (class in openforcefield.typing.engines.smirnoff.io)