Open Force Field Toolkit
0.7.1
Open Force Field Initiative
Open Force Field Toolkit
Installation
Installing via
conda
Required dependencies
Alternative method: Single-file installer
Release History
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?
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
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E
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F
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G
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I
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L
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M
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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.FrozenMolecule method)
(openforcefield.topology.Molecule method)
(openforcefield.topology.Particle method)
(openforcefield.topology.Topology method)
(openforcefield.topology.TopologyAtom method)
(openforcefield.topology.TopologyBond method)
(openforcefield.topology.TopologyMolecule method)
(openforcefield.topology.TopologyVirtualSite 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.IndexedParameterAttribute method)
(openforcefield.typing.engines.smirnoff.parameters.LibraryChargeHandler 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
all_subclasses() (in module openforcefield.utils.utils)
AmberToolsToolkitWrapper (class in openforcefield.utils.toolkits)
AngleHandler (class in openforcefield.typing.engines.smirnoff.parameters)
Atom (class in openforcefield.topology)
attach_units() (in module openforcefield.utils.utils)
B
Bond (class in openforcefield.topology)
BondHandler (class in openforcefield.typing.engines.smirnoff.parameters)
C
check_units_are_compatible() (in module openforcefield.utils.utils)
ChemicalEnvironment (class in openforcefield.typing.chemistry)
convert_0_1_smirnoff_to_0_2() (in module openforcefield.utils.utils)
convert_0_2_smirnoff_to_0_3() (in module openforcefield.utils.utils)
convert_all_quantities_to_string() (in module openforcefield.utils.utils)
convert_all_strings_to_quantity() (in module openforcefield.utils.utils)
D
deserialize_numpy() (in module openforcefield.utils.utils)
detach_units() (in module openforcefield.utils.utils)
E
ElectrostaticsHandler (class in openforcefield.typing.engines.smirnoff.parameters)
extract_serialized_units_from_dict() (in module openforcefield.utils.utils)
F
ForceField (class in openforcefield.typing.engines.smirnoff.forcefield)
FrozenMolecule (class in openforcefield.topology)
G
GBSAHandler (class in openforcefield.typing.engines.smirnoff.parameters)
get_available_force_fields() (in module openforcefield.typing.engines.smirnoff.forcefield)
get_data_file_path() (in module openforcefield.utils.utils)
get_molecule_parameterIDs() (in module openforcefield.utils.structure)
I
ImproperTorsionHandler (class in openforcefield.typing.engines.smirnoff.parameters)
IndexedParameterAttribute (class in openforcefield.typing.engines.smirnoff.parameters)
inherit_docstrings() (in module openforcefield.utils.utils)
L
LibraryChargeHandler (class in openforcefield.typing.engines.smirnoff.parameters)
M
Molecule (class in openforcefield.topology)
O
OpenEyeToolkitWrapper (class in openforcefield.utils.toolkits)
P
ParameterAttribute (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)
ParameterType (class in openforcefield.typing.engines.smirnoff.parameters)
Particle (class in openforcefield.topology)
ProperTorsionHandler (class in openforcefield.typing.engines.smirnoff.parameters)
R
RDKitToolkitWrapper (class in openforcefield.utils.toolkits)
S
Serializable (class in openforcefield.utils.serialization)
serialize_numpy() (in module openforcefield.utils.utils)
string_to_unit() (in module openforcefield.utils.utils)
T
temporary_cd() (in module openforcefield.utils.utils)
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)
TopologyAtom (class in openforcefield.topology)
TopologyBond (class in openforcefield.topology)
TopologyMolecule (class in openforcefield.topology)
TopologyVirtualSite (class in openforcefield.topology)
U
unit_to_string() (in module openforcefield.utils.utils)
V
vdWHandler (class in openforcefield.typing.engines.smirnoff.parameters)
VirtualSite (class in openforcefield.topology)
X
XMLParameterIOHandler (class in openforcefield.typing.engines.smirnoff.io)