openff.interchange package

Subpackages

• openff.interchange.components package
  • Submodules
  • openff.interchange.components.potentials module
  • openff.interchange.components.smirnoff module
  • openff.interchange.components.interchange module
  • Module contents
• openff.interchange.drivers package
  • Submodules
  • openff.interchange.drivers.amber module
  • openff.interchange.drivers.gromacs module
  • openff.interchange.drivers.lammps module
  • openff.interchange.drivers.openmm module
  • openff.interchange.drivers.report module
  • Module contents
• openff.system.interop package
  • Submodules
  • openff.system.interop.external module
  • openff.system.interop.internal module
  • openff.system.interop.openmm module
  • openff.system.interop.parmed module
  • Module contents

Submodules

openff.interchange.exceptions module

Custom exceptions used in Interchange.

exception openff.interchange.exceptions.EnergyError

Bases: BaseException

Base class for energies in reports not matching.

exception openff.interchange.exceptions.GMXGromppError

Bases: openff.interchange.exceptions.GMXRunError

Exception for when gmx grompp fails.

exception openff.interchange.exceptions.GMXMdrunError

Bases: openff.interchange.exceptions.GMXRunError

Exception for when gmx mdrun fails.

exception openff.interchange.exceptions.GMXRunError

Bases: BaseException

Exception for when a GROMACS subprocess fails.

exception openff.interchange.exceptions.InternalInconsistencyError

Bases: BaseException

Fallback exception for bad behavior releating to a self-inconsistent internal state.

These should not be reached but are raised to safeguard against problematic edge cases silently passing.

exception openff.interchange.exceptions.InvalidBoxError

Bases: ValueError

Generic exception for errors reading box data.

exception openff.interchange.exceptions.InvalidExpressionError

Bases: ValueError

Exception for when an expression cannot safely be interpreted.

exception openff.interchange.exceptions.InvalidParameterHandlerError

Bases: ValueError

Generic exception for mismatch between expected and found ParameterHandler types.

exception openff.interchange.exceptions.InvalidTopologyError

Bases: ValueError

Generic exception for errors reading chemical topology data.

exception openff.interchange.exceptions.LAMMPSRunError

Bases: BaseException

Exception for when a LAMMPS subprocess fails.

exception openff.interchange.exceptions.MissingBondOrdersError

Bases: BaseException

Exception for when a parameter handler needs fractional bond orders but they are missing.

exception openff.interchange.exceptions.MissingBoxError

Bases: BaseException

Exception for when box vectors are needed but missing.

exception openff.interchange.exceptions.MissingEnergyError

Bases: BaseException

Exception for when one report has a value for an energy group but the other does not.

exception openff.interchange.exceptions.MissingNonbondedCompatibilityError

Bases: BaseException

Exception for uncovered combination of nonbonded methods.

exception openff.interchange.exceptions.MissingParametersError

Bases: BaseException

Exception for when parameters are needed but missing.

exception openff.interchange.exceptions.MissingPositionsError

Bases: BaseException

Exception for when positions are needed but missing.

exception openff.interchange.exceptions.MissingUnitError

Bases: ValueError

Exception for data missing a unit tag.

exception openff.interchange.exceptions.NonbondedCompatibilityError

Bases: BaseException

Exception for unsupported combination of nonbonded methods.

exception openff.interchange.exceptions.NonbondedEnergyError

Bases: AssertionError

Exception for when non-bonded energies computed from different objects differ.

exception openff.interchange.exceptions.SMIRNOFFHandlersNotImplementedError(*args)

Bases: Exception

Exception for when some parameter handlers in the SMIRNOFF specification are not implemented here.

exception openff.interchange.exceptions.SMIRNOFFParameterAttributeNotImplementedError

Bases: Exception

Exception for when a parameter attribute is supported by the SMIRNOFF specification but not yet implemented.

For example, this was raised when k_bondorder (used in bond order-based interpolation of force constants) before the behavior was supported.

exception openff.interchange.exceptions.SanderError

Bases: BaseException

Exception for when a sander subprocess fails.

exception openff.interchange.exceptions.ToolkitTopologyConformersNotFoundError(*args)

Bases: Exception

Exception for when reference molecules in a toolkit topology lack conformers.

exception openff.interchange.exceptions.UnimplementedCutoffMethodError

Bases: BaseException

Exception for a cutoff method that should be supported but it not yet implemented.

exception openff.interchange.exceptions.UnitValidationError

Bases: ValueError

Exception for bad behavior when validating unit-tagged data.

exception openff.interchange.exceptions.UnsupportedBoxError

Bases: ValueError

Exception for processing an unsupported box, probably non-orthogonal.

exception openff.interchange.exceptions.UnsupportedCutoffMethodError

Bases: BaseException

Exception for a cutoff method that is invalid or not supported by an engine.

exception openff.interchange.exceptions.UnsupportedExportError(*args)

Bases: BaseException

Exception for attempting to write to an unsupported file format.

exception openff.interchange.exceptions.UnsupportedParameterError

Bases: ValueError

Exception for parameters having unsupported values, i.e. non-1.0 idivf.

openff.interchange.models module

openff.interchange.stubs module

openff.interchange.types module

openff.interchange.utils module

Assorted utilities.

openff.interchange.utils.compare_forcefields(ff1, ff2)

Compare dict representations of OpenFF ForceField objects for equality.

openff.interchange.utils.get_nonbonded_force_from_openmm_system(omm_system)

Get a single NonbondedForce object with an OpenMM System.

openff.interchange.utils.get_partial_charges_from_openmm_system(omm_system)

Get partial charges from an OpenMM interchange as a unit.Quantity array.

openff.interchange.utils.get_test_file_path(test_file) → str

Given a filename in the collection of data files, return its full path.

openff.interchange.utils.get_test_files_dir_path(dirname)

Given a directory with a collection of test data files, return its full path.

openff.interchange.utils.pint_to_simtk(quantity)

Convert a pint Quantity to an OpenMM unit.

Module contents

A project (and object) for storing, manipulating, and converting molecular mechanics data.