Forcefield typing tools¶
Chemical environments¶
Tools for representing and operating on chemical environments
Warning
This class is largely redundant with the same one in the Chemper package, and will likely be removed.
Chemical environment abstract base class used for validating SMIRKS |
Forcefield 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 system creation using a ForceField
, see examples/SMIRNOFF_simulation
.
A factory that assigns SMIRNOFF parameters to a molecular system |
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 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. |
Parameter Handlers¶
Each ForceField
primarily consists of several ParameterHandler
objects, which each contain the machinery to add one energy component to a 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. |
|
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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Handles 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. |