aiida_amber.calculations package

Submodules

aiida_amber.calculations.antechamber module

Calculations provided by aiida_amber.

Register calculations via the “aiida.calculations” entry point in setup.json.

class aiida_amber.calculations.antechamber.AntechamberCalculation(*args: Any, **kwargs: Any)

Bases: CalcJob

AiiDA calculation plugin wrapping the antechamber executable.

AiiDA plugin wrapper for the amber ‘antechamber’ command.

__abstractmethods__ = frozenset({})

__annotations__ = {}

__firstlineno__ = 16

__module__ = 'aiida_amber.calculations.antechamber'

__static_attributes__ = ()

_abc_impl = <_abc._abc_data object>

classmethod define(spec)

Define inputs and outputs of the calculation.

prepare_for_submission(folder)

Create input files.

Parameters:

folder – an aiida.common.folders.Folder where the plugin should temporarily place all files needed by the calculation.

Returns:

aiida.common.datastructures.CalcInfo instance

aiida_amber.calculations.parmed module

Calculations provided by aiida_amber.

Register calculations via the “aiida.calculations” entry point in setup.json.

class aiida_amber.calculations.parmed.ParmedCalculation(*args: Any, **kwargs: Any)

Bases: CalcJob

AiiDA calculation plugin wrapping the parmed executable.

AiiDA plugin wrapper for the amber ‘parmed’ command.

__abstractmethods__ = frozenset({})

__annotations__ = {}

__firstlineno__ = 16

__module__ = 'aiida_amber.calculations.parmed'

__static_attributes__ = ()

_abc_impl = <_abc._abc_data object>

classmethod define(spec)

Define inputs and outputs of the calculation.

prepare_for_submission(folder)

Create input files.

Parameters:

folder – an aiida.common.folders.Folder where the plugin should temporarily place all files needed by the calculation.

Returns:

aiida.common.datastructures.CalcInfo instance

aiida_amber.calculations.pdb4amber module

Calculations provided by aiida_amber.

Register calculations via the “aiida.calculations” entry point in setup.json.

class aiida_amber.calculations.pdb4amber.Pdb4amberCalculation(*args: Any, **kwargs: Any)

Bases: CalcJob

AiiDA calculation plugin wrapping the pdb4amber executable.

AiiDA plugin wrapper for the amber ‘pdb4amber’ command.

__abstractmethods__ = frozenset({})

__annotations__ = {}

__firstlineno__ = 16

__module__ = 'aiida_amber.calculations.pdb4amber'

__static_attributes__ = ()

_abc_impl = <_abc._abc_data object>

classmethod define(spec)

Define inputs and outputs of the calculation.

prepare_for_submission(folder)

Create input files.

Parameters:

folder – an aiida.common.folders.Folder where the plugin should temporarily place all files needed by the calculation.

Returns:

aiida.common.datastructures.CalcInfo instance

aiida_amber.calculations.sander module

Calculations provided by aiida_amber.

Register calculations via the “aiida.calculations” entry point in setup.json.

class aiida_amber.calculations.sander.SanderCalculation(*args: Any, **kwargs: Any)

Bases: CalcJob

AiiDA calculation plugin wrapping the sander executable.

AiiDA plugin wrapper for the amber ‘sander’ command.

__abstractmethods__ = frozenset({})

__annotations__ = {}

__firstlineno__ = 16

__module__ = 'aiida_amber.calculations.sander'

__static_attributes__ = ()

_abc_impl = <_abc._abc_data object>

classmethod define(spec)

Define inputs and outputs of the calculation.

prepare_for_submission(folder)

Create input files.

Parameters:

folder – an aiida.common.folders.Folder where the plugin should temporarily place all files needed by the calculation.

Returns:

aiida.common.datastructures.CalcInfo instance

aiida_amber.calculations.tleap module

Calculations provided by aiida_amber.

Register calculations via the “aiida.calculations” entry point in setup.json.

class aiida_amber.calculations.tleap.TleapCalculation(*args: Any, **kwargs: Any)

Bases: CalcJob

AiiDA calculation plugin wrapping the tleap executable.

AiiDA plugin wrapper for the amber ‘tleap’ command.

__abstractmethods__ = frozenset({})

__annotations__ = {}

__firstlineno__ = 16

__module__ = 'aiida_amber.calculations.tleap'

__static_attributes__ = ()

_abc_impl = <_abc._abc_data object>

classmethod define(spec)

Define inputs and outputs of the calculation.

prepare_for_submission(folder)

Create input files.

Parameters:

folder – an aiida.common.folders.Folder where the plugin should temporarily place all files needed by the calculation.

Returns:

aiida.common.datastructures.CalcInfo instance

Module contents

aiida_amber

A plugin for using Amber with AiiDA for molecular dymanics simulations.