Force field typing tools
Chemical environments
Tools for representing and operating on chemical environments
Chemical environment abstract base class used for validating SMIRKS |
Force field typing engines
Engines for applying parameters to chemical systems
The SMIRks-Native Open Force Field (SMIRNOFF)
A reference implementation of the SMIRNOFF specification for parameterizing biomolecular systems
ForceField
The ForceField
class is a primary part of the top-level toolkit API.
ForceField
objects are initialized from SMIRNOFF data sources (e.g. an OFFXML
file).
For a basic example of OpenMM System
creation using a ForceField
, see examples/SMIRNOFF_simulation
.
A factory that assigns SMIRNOFF parameters to a molecular system |
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Get the filenames of all available .offxml force field files. |
Parameter Type
ParameterType
objects are representations of individual SMIRKS-based SMIRNOFF parameters.
These are usually initialized during ForceField
creation, and can be inspected and modified by users via the Python API.
For more information, see examples/forcefield_modification
.
Base class for SMIRNOFF parameter types. |
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A SMIRNOFF constraint type |
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A SMIRNOFF bond type |
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A SMIRNOFF angle type. |
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A SMIRNOFF torsion type for proper torsions. |
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A SMIRNOFF torsion type for improper torsions. |
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A SMIRNOFF vdWForce type. |
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A SMIRNOFF Library Charge type. |
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A SMIRNOFF GBSA type. |
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A SMIRNOFF bond charge correction type. |
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Parameter Handlers
Each ForceField
primarily consists of several ParameterHandler
objects, which each contain the machinery to add one energy component to an OpenMM System
.
During System
creation, each ParameterHandler
registered to a ForceField
has its assign_parameters()
function called.
Parameter list that also supports accessing items by SMARTS string. |
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Base class for parameter handlers. |
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Handle SMIRNOFF |
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Handle SMIRNOFF |
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Handle SMIRNOFF |
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Handle SMIRNOFF |
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Handle SMIRNOFF |
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Handle SMIRNOFF |
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Handles SMIRNOFF |
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Handle SMIRNOFF |
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Handle SMIRNOFF |
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Handle SMIRNOFF |
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Handle SMIRNOFF |
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Handle SMIRNOFF |
Parameter I/O Handlers
ParameterIOHandler
objects handle reading and writing of serialzied SMIRNOFF data sources.
Base class for handling serialization/deserialization of SMIRNOFF ForceField objects |
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Handles serialization/deserialization of SMIRNOFF ForceField objects from OFFXML format. |
Parameter Attributes
ParameterAttribute
and IndexedParameterAttribute
provide a standard backend for ParameterHandler and Parameter attributes, while also enforcing validation of types and units.
A descriptor for |
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The attribute of a parameter with an unspecified number of terms. |
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The attribute of a parameter in which each term is a mapping. |
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The attribute of a parameter with an unspecified number of terms, where each term is a mapping. |