aiida_amber.parsers package

Submodules

aiida_amber.parsers.antechamber module

Parsers provided by aiida_amber.

This calculation configures the ability to use the ‘antechamber’ executable.

class aiida_amber.parsers.antechamber.AntechamberParser(node)

Bases: Parser

Parser class for parsing output of calculation.

__abstractmethods__ = frozenset({})

__annotations__ = {}

__firstlineno__ = 18

__init__(node)

Initialize Parser instance

Checks that the ProcessNode being passed was produced by a AntechamberCalculation.

Parameters:

• node (type) – ProcessNode of calculation

• node – aiida.orm.nodes.process.process.ProcessNode

__module__ = 'aiida_amber.parsers.antechamber'

__static_attributes__ = ()

_abc_impl = <_abc._abc_data object>

parse(**kwargs)

Parse outputs, store results in database.

Returns:

an exit code, if parsing fails (or nothing if parsing succeeds)

aiida_amber.parsers.parmed module

Parsers provided by aiida_amber.

This calculation configures the ability to use the ‘parmed’ executable.

class aiida_amber.parsers.parmed.ParmedParser(node)

Bases: Parser

Parser class for parsing output of calculation.

__abstractmethods__ = frozenset({})

__annotations__ = {}

__firstlineno__ = 20

__init__(node)

Initialize Parser instance

Checks that the ProcessNode being passed was produced by a ParmedCalculation.

Parameters:

• node (type) – ProcessNode of calculation

• node – aiida.orm.nodes.process.process.ProcessNode

__module__ = 'aiida_amber.parsers.parmed'

__static_attributes__ = ()

_abc_impl = <_abc._abc_data object>

parse(**kwargs)

Parse outputs, store results in database.

Returns:

an exit code, if parsing fails (or nothing if parsing succeeds)

aiida_amber.parsers.pdb4amber module

Parsers provided by aiida_amber.

This calculation configures the ability to use the ‘pdb4amber’ executable.

class aiida_amber.parsers.pdb4amber.Pdb4amberParser(node)

Bases: Parser

Parser class for parsing output of calculation.

__abstractmethods__ = frozenset({})

__annotations__ = {}

__firstlineno__ = 20

__init__(node)

Initialize Parser instance

Checks that the ProcessNode being passed was produced by a Pdb4amberCalculation.

Parameters:

• node (type) – ProcessNode of calculation

• node – aiida.orm.nodes.process.process.ProcessNode

__module__ = 'aiida_amber.parsers.pdb4amber'

__static_attributes__ = ()

_abc_impl = <_abc._abc_data object>

parse(**kwargs)

Parse outputs, store results in database.

Returns:

an exit code, if parsing fails (or nothing if parsing succeeds)

aiida_amber.parsers.sander module

Parsers provided by aiida_amber.

This calculation configures the ability to use the ‘sander’ executable.

class aiida_amber.parsers.sander.SanderParser(node)

Bases: Parser

Parser class for parsing output of calculation.

__abstractmethods__ = frozenset({})

__annotations__ = {}

__firstlineno__ = 18

__init__(node)

Initialize Parser instance

Checks that the ProcessNode being passed was produced by a SanderCalculation.

Parameters:

• node (type) – ProcessNode of calculation

• node – aiida.orm.nodes.process.process.ProcessNode

__module__ = 'aiida_amber.parsers.sander'

__static_attributes__ = ()

_abc_impl = <_abc._abc_data object>

parse(**kwargs)

Parse outputs, store results in database.

Returns:

an exit code, if parsing fails (or nothing if parsing succeeds)

aiida_amber.parsers.tleap module

Parsers provided by aiida_amber.

This calculation configures the ability to use the ‘tleap’ executable.

class aiida_amber.parsers.tleap.TleapParser(node)

Bases: Parser

Parser class for parsing output of calculation.

__abstractmethods__ = frozenset({})

__annotations__ = {}

__firstlineno__ = 20

__init__(node)

Initialize Parser instance

Checks that the ProcessNode being passed was produced by a TleapCalculation.

Parameters:

• node (type) – ProcessNode of calculation

• node – aiida.orm.nodes.process.process.ProcessNode

__module__ = 'aiida_amber.parsers.tleap'

__static_attributes__ = ()

_abc_impl = <_abc._abc_data object>

parse(**kwargs)

Parse outputs, store results in database.

Returns:

an exit code, if parsing fails (or nothing if parsing succeeds)

Module contents

aiida_amber

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