pydft_qmmm.plugins package

Subpackages

• pydft_qmmm.plugins.atom_partition package
  • Submodules
  • pydft_qmmm.plugins.atom_partition.atom_partition module
    • AtomPartition
      • AtomPartition.generate_partition()
      • AtomPartition.modify()
  • Module contents
• pydft_qmmm.plugins.center package
  • Submodules
  • pydft_qmmm.plugins.center.center module
    • CalculatorCenter
      • CalculatorCenter.modify()
    • IntegratorCenter
      • IntegratorCenter.modify()
  • Module contents
• pydft_qmmm.plugins.centroid_partition package
  • Submodules
  • pydft_qmmm.plugins.centroid_partition.centroid_partition module
    • CentroidPartition
      • CentroidPartition.generate_partition()
      • CentroidPartition.modify()
  • Module contents
• pydft_qmmm.plugins.firstatom_partition package
  • Submodules
  • pydft_qmmm.plugins.firstatom_partition.firstatom_partition module
    • FirstAtomPartition
      • FirstAtomPartition.generate_partition()
      • FirstAtomPartition.modify()
  • Module contents
• pydft_qmmm.plugins.plumed package
  • Submodules
  • pydft_qmmm.plugins.plumed.plumed module
    • Plumed
      • Plumed.modify()
  • Module contents
• pydft_qmmm.plugins.pme package
  • Submodules
  • pydft_qmmm.plugins.pme.pme module
    • PME
      • PME.modify()
  • pydft_qmmm.plugins.pme.pme_utils module
    • pme_components()
    • project_to_grid()
  • Module contents
• pydft_qmmm.plugins.rigid package
  • Submodules
  • pydft_qmmm.plugins.rigid.rigid module
    • RigidBody
      • RigidBody.modify()
    • Stationary
      • Stationary.constrain_velocities()
      • Stationary.modify()
  • pydft_qmmm.plugins.rigid.rigid_utils module
  • Module contents
• pydft_qmmm.plugins.settle package
  • Submodules
  • pydft_qmmm.plugins.settle.settle module
    • SETTLE
      • SETTLE.constrain_velocities()
      • SETTLE.modify()
  • pydft_qmmm.plugins.settle.settle_utils module
    • settle_positions()
    • settle_velocities()
  • Module contents
• pydft_qmmm.plugins.wrap package
  • Submodules
  • pydft_qmmm.plugins.wrap.wrap module
    • CalculatorWrap
      • CalculatorWrap.modify()
    • IntegratorWrap
      • IntegratorWrap.modify()
  • Module contents

Submodules

pydft_qmmm.plugins.plugin module

Abstract base classes for plugins.

class pydft_qmmm.plugins.plugin.CalculatorPlugin

Bases: Plugin

The plugin base class for modifying calculator routines.

abstract modify(calculator)

Modify the functionality of a calculator.

Parameters:

calculator (Calculator) – The calculator whose functionality will be modified by the plugin.

Return type:

None

class pydft_qmmm.plugins.plugin.CompositeCalculatorPlugin

Bases: Plugin

The plugin base class for modifying composite calculator routines.

abstract modify(calculator)

Modify the functionality of a calculator.

Parameters:

calculator (CompositeCalculator) – The composite calculator whose functionality will be modified by the plugin.

Return type:

None

class pydft_qmmm.plugins.plugin.IntegratorPlugin

Bases: Plugin

The plugin base class for modifying integrator routines.

abstract modify(integrator)

Modify the functionality of an integrator.

Parameters:

integrator (Integrator) – The integrator whose functionality will be modified by the plugin.

Return type:

None

class pydft_qmmm.plugins.plugin.PartitionPlugin

Bases: CompositeCalculatorPlugin

The plugin base class for modifying partitioning routines.

_query

The VMD-like query representing atoms which will be evaluated with the partitioning scheme.

Type:

str

abstract generate_partition()

Perform the system partitioning.

Return type:

None

class pydft_qmmm.plugins.plugin.Plugin

Bases: ABC

The abstract plugin base class.

_modifieds

A list of names of objects that have been modified by the plugin.

Type:

list[str]

_key

The type of object that the plugin modifies.

Type:

str

pydft_qmmm.plugins.plugin_manager module

Functionality for handling external plugin imports.

pydft_qmmm.plugins.plugin_manager.DISCOVERED_PLUGINS

A list of entry points into the plugin architecture of PyDFT-QMMM within installed package metadata.

pydft_qmmm.plugins.plugin_manager.get_external_plugins()

Get PyDFT-QMMM plugins from externally installed packages.

Returns:

A dictionary of plugin names and loaded classes for the PyDFT-QMMM plugin sub-package.

Return type:

dict[str, Plugin]

Module contents

A sub-package for defining and dynamically loading plugins.