aiida_amber.data package

Submodules

aiida_amber.data.antechamber module

Data types provided by plugin

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

class aiida_amber.data.antechamber.AntechamberParameters(dict=None, **kwargs)

Bases: Dict

Command line options for antechamber.

This class represents a python dictionary used to pass command line options to the executable.

__abstractmethods__ = frozenset({})

__annotations__ = {}

__firstlineno__ = 47

__init__(dict=None, **kwargs)

Constructor for the data class

Usage: AntechamberParameters(dict{'ignore-case': True})

Parameters:

• parameters_dict (type) – dictionary with commandline parameters

• parameters_dict – dict

__module__ = 'aiida_amber.data.antechamber'

__parameters__ = ()

__static_attributes__ = ()

__str__()

String representation of node.

Append values of dictionary to usual representation. E.g.:

uuid: b416cbee-24e8-47a8-8c11-6d668770158b (pk: 590)
{'ignore-case': True}

_abc_impl = <_abc._abc_data object>

_logger: Logger | None = <Logger aiida_amber.data.antechamber.AntechamberParameters (WARNING)>

cmdline_params(input_files)

Synthesize command line parameters.

Parameters:

• input_files (type) – list of inputs for antechamber command, containing SinglefileData aiida datatypes used in input nodes.

• input_files – list

fields: QbFields = {'attributes': 'QbDictField(attributes.*) -> Dict[str, Any]',  'ctime': 'QbNumericField(ctime) -> datetime',  'description': 'QbStrField(description) -> str',  'dict': 'QbDictField(dict.*) -> Dict[str, Any]',  'extras': 'QbDictField(extras.*) -> Dict[str, Any]',  'label': 'QbStrField(label) -> str',  'mtime': 'QbNumericField(mtime) -> datetime',  'node_type': 'QbStrField(node_type) -> str',  'pk': 'QbNumericField(pk) -> int',  'repository_metadata': 'QbDictField(repository_metadata) -> Dict[str, Any]',  'source': 'QbDictField(attributes.source.*) -> Optional[dict]',  'user_pk': 'QbNumericField(user_pk) -> int',  'uuid': 'QbStrField(uuid) -> str'}

schema = <Schema({'fi': <class 'str'>, 'o': <class 'str'>, 'fo': <class 'str'>, 'c': <class 'str'>, 'nc': <class 'int'>, 'fa': <class 'str'>, 'ao': <class 'str'>, 'm': <class 'str'>, 'rn': <class 'str'>, 'ek': <class 'str'>, 'gk': <class 'str'>, 'gopt': <class 'str'>, 'gsp': <class 'str'>, 'gm': <class 'str'>, 'gn': <class 'str'>, 'gdsk': <class 'str'>, 'gv': <class 'int'>, 'tor': <class 'str'>, 'df': <class 'int'>, 'at': <class 'str'>, 'du': <class 'str'>, 'bk': <class 'str'>, 'an': <class 'str'>, 'j': <class 'int'>, 's': <class 'int'>, 'eq': <class 'int'>, 'pf': <class 'str'>, 'pl': <class 'str'>, 'seq': <class 'str'>, 'dr': <class 'str'>}, extra=PREVENT_EXTRA, required=False) object>

validate(parameters_dict)

Validate command line options.

Uses the voluptuous package for validation. Find out about allowed keys using:

print(AntechamberParameters).schema.schema

Parameters:

• parameters_dict (type) – dictionary with commandline parameters

• parameters_dict – dict

Returns:

validated dictionary

aiida_amber.data.parmed module

Data types provided by plugin

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

class aiida_amber.data.parmed.ParmedParameters(dict=None, **kwargs)

Bases: Dict

Command line options for parmed.

This class represents a python dictionary used to pass command line options to the executable.

__abstractmethods__ = frozenset({})

__annotations__ = {}

__firstlineno__ = 32

__init__(dict=None, **kwargs)

Constructor for the data class

Usage: ParmedParameters(dict{'ignore-case': True})

Parameters:

• parameters_dict (type) – dictionary with commandline parameters

• parameters_dict – dict

__module__ = 'aiida_amber.data.parmed'

__parameters__ = ()

__static_attributes__ = ()

__str__()

String representation of node.

Append values of dictionary to usual representation. E.g.:

uuid: b416cbee-24e8-47a8-8c11-6d668770158b (pk: 590)
{'ignore-case': True}

_abc_impl = <_abc._abc_data object>

_logger: Logger | None = <Logger aiida_amber.data.parmed.ParmedParameters (WARNING)>

cmdline_params(input_files)

Synthesize command line parameters.

Parameters:

• input_files (type) – list of inputs for parmed command, containing SinglefileData aiida datatypes used in input nodes.

• input_files – list

fields: QbFields = {'attributes': 'QbDictField(attributes.*) -> Dict[str, Any]',  'ctime': 'QbNumericField(ctime) -> datetime',  'description': 'QbStrField(description) -> str',  'dict': 'QbDictField(dict.*) -> Dict[str, Any]',  'extras': 'QbDictField(extras.*) -> Dict[str, Any]',  'label': 'QbStrField(label) -> str',  'mtime': 'QbNumericField(mtime) -> datetime',  'node_type': 'QbStrField(node_type) -> str',  'pk': 'QbNumericField(pk) -> int',  'repository_metadata': 'QbDictField(repository_metadata) -> Dict[str, Any]',  'source': 'QbDictField(attributes.source.*) -> Optional[dict]',  'user_pk': 'QbNumericField(user_pk) -> int',  'uuid': 'QbStrField(uuid) -> str'}

schema = <Schema({'parm': <class 'str'>, 'inpcrd': <class 'str'>, 'O': <class 'bool'>, 'overwrite': <class 'bool'>, 'l': <class 'str'>, 'logfile': <class 'str'>, 'prompt': <class 'str'>, 'n': <class 'bool'>, 'no-splash': <class 'bool'>, 'e': <class 'bool'>, 'enable-interpreter': <class 'bool'>, 's': <class 'bool'>, 'strict': <class 'bool'>, 'r': <class 'bool'>, 'relaxed': <class 'bool'>}, extra=PREVENT_EXTRA, required=False) object>

validate(parameters_dict)

Validate command line options.

Uses the voluptuous package for validation. Find out about allowed keys using:

print(ParmedParameters).schema.schema

Parameters:

• parameters_dict (type) – dictionary with commandline parameters

• parameters_dict – dict

Returns:

validated dictionary

aiida_amber.data.parmed_input module

Sub class of Data to handle inputs used and outputs that will be produced from commands in the parmed input file.

class aiida_amber.data.parmed_input.ParmedInputData(file: str | Path | IO, filename: str | Path | None = None, **kwargs: Any)

Bases: SinglefileData

Class to find the inputs used and outputs produced from the commands in the parmed input file

__abstractmethods__ = frozenset({})

__annotations__ = {}

__firstlineno__ = 10

__module__ = 'aiida_amber.data.parmed_input'

__parameters__ = ()

__static_attributes__ = ()

_abc_impl = <_abc._abc_data object>

_logger: Logger | None = <Logger aiida_amber.data.parmed_input.ParmedInputData (WARNING)>

property calculation_inputs_outputs

Return the inputs for the parmed calculation job

fields: QbFields = {'attributes': 'QbDictField(attributes.*) -> Dict[str, Any]',  'ctime': 'QbNumericField(ctime) -> datetime',  'description': 'QbStrField(description) -> str',  'extras': 'QbDictField(extras.*) -> Dict[str, Any]',  'label': 'QbStrField(label) -> str',  'mtime': 'QbNumericField(mtime) -> datetime',  'node_type': 'QbStrField(node_type) -> str',  'pk': 'QbNumericField(pk) -> int',  'repository_metadata': 'QbDictField(repository_metadata) -> Dict[str, Any]',  'source': 'QbDictField(attributes.source.*) -> Optional[dict]',  'user_pk': 'QbNumericField(user_pk) -> int',  'uuid': 'QbStrField(uuid) -> str'}

property inpfile_list

Return the list input files used in the parmed script

property outfile_list

Return the list output files to be produced from the parmed script

set_file(file, filename=None, **kwargs)

Add a file to the node, parse it and set the attributes found.

Parameters:

• file – absolute path to the file or a filelike object

• filename – specify filename to use (defaults to name of provided file).

aiida_amber.data.parmed_input.add_calculation_inputs(subdirs, files)

If they exist, add input files for parmed and dirs into the calcjob inputs directory

aiida_amber.data.parmed_input.add_calculation_outputs(files)

Add outputs from parmed script

aiida_amber.data.parmed_input.parse_parmed_input_file(lines)

Parse parmed script and find any instances of file inputs or outputs

addPDB, loadCoordinates, loadRestart, = input outparm, outPDB, outCIF, parmout, writeCoordinates, writeFrcmod, writeOFF = outputs

aiida_amber.data.pdb4amber module

Data types provided by plugin

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

class aiida_amber.data.pdb4amber.Pdb4amberParameters(dict=None, **kwargs)

Bases: Dict

Command line options for pdb4amber.

This class represents a python dictionary used to pass command line options to the executable.

__abstractmethods__ = frozenset({})

__annotations__ = {}

__firstlineno__ = 45

__init__(dict=None, **kwargs)

Constructor for the data class

Usage: Pdb4amberParameters(dict{'ignore-case': True})

Parameters:

• parameters_dict (type) – dictionary with commandline parameters

• parameters_dict – dict

__module__ = 'aiida_amber.data.pdb4amber'

__parameters__ = ()

__static_attributes__ = ()

__str__()

String representation of node.

Append values of dictionary to usual representation. E.g.:

uuid: b416cbee-24e8-47a8-8c11-6d668770158b (pk: 590)
{'ignore-case': True}

_abc_impl = <_abc._abc_data object>

_logger: Logger | None = <Logger aiida_amber.data.pdb4amber.Pdb4amberParameters (WARNING)>

cmdline_params(input_files)

Synthesize command line parameters.

Parameters:

• input_files (type) – list of inputs for pdb4amber command, containing SinglefileData aiida datatypes used in input nodes.

• input_files – list

fields: QbFields = {'attributes': 'QbDictField(attributes.*) -> Dict[str, Any]',  'ctime': 'QbNumericField(ctime) -> datetime',  'description': 'QbStrField(description) -> str',  'dict': 'QbDictField(dict.*) -> Dict[str, Any]',  'extras': 'QbDictField(extras.*) -> Dict[str, Any]',  'label': 'QbStrField(label) -> str',  'mtime': 'QbNumericField(mtime) -> datetime',  'node_type': 'QbStrField(node_type) -> str',  'pk': 'QbNumericField(pk) -> int',  'repository_metadata': 'QbDictField(repository_metadata) -> Dict[str, Any]',  'source': 'QbDictField(attributes.source.*) -> Optional[dict]',  'user_pk': 'QbNumericField(user_pk) -> int',  'uuid': 'QbStrField(uuid) -> str'}

schema = <Schema({'out': <class 'str'>, 'y': <class 'bool'>, 'nohyd': <class 'bool'>, 'd': <class 'bool'>, 'dry': <class 'bool'>, 's': <class 'str'>, 'strip': <class 'str'>, 'm': <class 'str'>, 'mutate': <class 'str'>, 'p': <class 'bool'>, 'prot': <class 'bool'>, 'a': <class 'bool'>, 'amber-compatible-residues': <class 'bool'>, 'constantph': <class 'bool'>, 'most-populous': <class 'bool'>, 'keep-altlocs': <class 'bool'>, 'reduce': <class 'bool'>, 'no-reduce-db': <class 'bool'>, 'pdbid': <class 'str'>, 'add-missing-atoms': <class 'bool'>, 'model': <class 'str'>, 'l': <class 'str'>, 'logfile': <class 'str'>, 'v': <class 'bool'>, 'version': <class 'bool'>, 'leap-template': <class 'bool'>, 'no-conect': <class 'str'>, 'noter': <class 'str'>}, extra=PREVENT_EXTRA, required=False) object>

validate(parameters_dict)

Validate command line options.

Uses the voluptuous package for validation. Find out about allowed keys using:

print(Pdb4amberParameters).schema.schema

Parameters:

• parameters_dict (type) – dictionary with commandline parameters

• parameters_dict – dict

Returns:

validated dictionary

aiida_amber.data.sander module

Data types provided by plugin

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

class aiida_amber.data.sander.SanderParameters(dict=None, **kwargs)

Bases: Dict

Command line options for sander.

This class represents a python dictionary used to pass command line options to the executable.

__abstractmethods__ = frozenset({})

__annotations__ = {}

__firstlineno__ = 48

__init__(dict=None, **kwargs)

Constructor for the data class

Usage: SanderParameters(dict{'ignore-case': True})

Parameters:

• parameters_dict (type) – dictionary with commandline parameters

• parameters_dict – dict

__module__ = 'aiida_amber.data.sander'

__parameters__ = ()

__static_attributes__ = ()

__str__()

String representation of node.

Append values of dictionary to usual representation. E.g.:

uuid: b416cbee-24e8-47a8-8c11-6d668770158b (pk: 590)
{'ignore-case': True}

_abc_impl = <_abc._abc_data object>

_logger: Logger | None = <Logger aiida_amber.data.sander.SanderParameters (WARNING)>

cmdline_params(input_files)

Synthesize command line parameters.

Parameters:

• input_files (type) – list of inputs for sander command, containing SinglefileData aiida datatypes used in input nodes.

• input_files – list

fields: QbFields = {'attributes': 'QbDictField(attributes.*) -> Dict[str, Any]',  'ctime': 'QbNumericField(ctime) -> datetime',  'description': 'QbStrField(description) -> str',  'dict': 'QbDictField(dict.*) -> Dict[str, Any]',  'extras': 'QbDictField(extras.*) -> Dict[str, Any]',  'label': 'QbStrField(label) -> str',  'mtime': 'QbNumericField(mtime) -> datetime',  'node_type': 'QbStrField(node_type) -> str',  'pk': 'QbNumericField(pk) -> int',  'repository_metadata': 'QbDictField(repository_metadata) -> Dict[str, Any]',  'source': 'QbDictField(attributes.source.*) -> Optional[dict]',  'user_pk': 'QbNumericField(user_pk) -> int',  'uuid': 'QbStrField(uuid) -> str'}

schema = <Schema({'o': <class 'str'>, 'inf': <class 'str'>, 'r': <class 'str'>, 'ref': <class 'str'>, 'mtmd': <class 'str'>, 'x': <class 'str'>, 'y': <class 'str'>, 'v': <class 'str'>, 'frc': <class 'str'>, 'rdip': <class 'str'>, 'mdip': <class 'str'>, 'e': <class 'str'>, 'radii': <class 'str'>, 'cpin': <class 'str'>, 'cpout': <class 'str'>, 'cprestrt': <class 'str'>, 'cein': <class 'str'>, 'ceout': <class 'str'>, 'cerestrt': <class 'str'>, 'evbin': <class 'str'>, 'idip': <class 'str'>, 'amd': <class 'str'>, 'scaledMD': <class 'str'>, 'cph-data': <class 'str'>, 'ce-data': <class 'str'>, 'port': <class 'str'>, 'suffix': <class 'str'>, 'O': <class 'bool'>, 'A': <class 'bool'>}, extra=PREVENT_EXTRA, required=False) object>

validate(parameters_dict)

Validate command line options.

Uses the voluptuous package for validation. Find out about allowed keys using:

print(SanderParameters).schema.schema

Parameters:

• parameters_dict (type) – dictionary with commandline parameters

• parameters_dict – dict

Returns:

validated dictionary

aiida_amber.data.tleap module

Data types provided by plugin

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

class aiida_amber.data.tleap.TleapParameters(dict=None, **kwargs)

Bases: Dict

Command line options for tleap.

This class represents a python dictionary used to pass command line options to the executable.

__abstractmethods__ = frozenset({})

__annotations__ = {}

__firstlineno__ = 19

__init__(dict=None, **kwargs)

Constructor for the data class

Usage: TleapParameters(dict{'ignore-case': True})

Parameters:

• parameters_dict (type) – dictionary with commandline parameters

• parameters_dict – dict

__module__ = 'aiida_amber.data.tleap'

__parameters__ = ()

__static_attributes__ = ()

__str__()

String representation of node.

Append values of dictionary to usual representation. E.g.:

uuid: b416cbee-24e8-47a8-8c11-6d668770158b (pk: 590)
{'ignore-case': True}

_abc_impl = <_abc._abc_data object>

_logger: Logger | None = <Logger aiida_amber.data.tleap.TleapParameters (WARNING)>

cmdline_params(input_files)

Synthesize command line parameters.

Parameters:

• input_files (type) – list of inputs for tleap command, containing SinglefileData aiida datatypes used in input nodes.

• input_files – list

fields: QbFields = {'attributes': 'QbDictField(attributes.*) -> Dict[str, Any]',  'ctime': 'QbNumericField(ctime) -> datetime',  'description': 'QbStrField(description) -> str',  'dict': 'QbDictField(dict.*) -> Dict[str, Any]',  'extras': 'QbDictField(extras.*) -> Dict[str, Any]',  'label': 'QbStrField(label) -> str',  'mtime': 'QbNumericField(mtime) -> datetime',  'node_type': 'QbStrField(node_type) -> str',  'pk': 'QbNumericField(pk) -> int',  'repository_metadata': 'QbDictField(repository_metadata) -> Dict[str, Any]',  'source': 'QbDictField(attributes.source.*) -> Optional[dict]',  'user_pk': 'QbNumericField(user_pk) -> int',  'uuid': 'QbStrField(uuid) -> str'}

schema = <Schema({'r': <class 'str'>}, extra=PREVENT_EXTRA, required=False) object>

validate(parameters_dict)

Validate command line options.

Uses the voluptuous package for validation. Find out about allowed keys using:

print(TleapParameters).schema.schema

Parameters:

• parameters_dict (type) – dictionary with commandline parameters

• parameters_dict – dict

Returns:

validated dictionary

aiida_amber.data.tleap_input module

Sub class of Data to handle inputs used and outputs that will be produced from commands in the tleap input file.

class aiida_amber.data.tleap_input.TleapInputData(file: str | Path | IO, filename: str | Path | None = None, **kwargs: Any)

Bases: SinglefileData

Class to find the inputs used and outputs produced from the commands in the tleap input file

__abstractmethods__ = frozenset({})

__annotations__ = {}

__firstlineno__ = 10

__module__ = 'aiida_amber.data.tleap_input'

__parameters__ = ()

__static_attributes__ = ()

_abc_impl = <_abc._abc_data object>

_logger: Logger | None = <Logger aiida_amber.data.tleap_input.TleapInputData (WARNING)>

property calculation_inputs_outputs

Return the inputs for the tleap calculation job

fields: QbFields = {'attributes': 'QbDictField(attributes.*) -> Dict[str, Any]',  'ctime': 'QbNumericField(ctime) -> datetime',  'description': 'QbStrField(description) -> str',  'extras': 'QbDictField(extras.*) -> Dict[str, Any]',  'label': 'QbStrField(label) -> str',  'mtime': 'QbNumericField(mtime) -> datetime',  'node_type': 'QbStrField(node_type) -> str',  'pk': 'QbNumericField(pk) -> int',  'repository_metadata': 'QbDictField(repository_metadata) -> Dict[str, Any]',  'source': 'QbDictField(attributes.source.*) -> Optional[dict]',  'user_pk': 'QbNumericField(user_pk) -> int',  'uuid': 'QbStrField(uuid) -> str'}

property inpfile_list

Return the list input files used in the tleap script

property outfile_list

Return the list output files to be produced from the tleap script

set_file(file, filename=None, **kwargs)

Add a file to the node, parse it and set the attributes found.

Parameters:

• file – absolute path to the file or a filelike object

• filename – specify filename to use (defaults to name of provided file).

aiida_amber.data.tleap_input.add_calculation_inputs(subdirs, files)

If they exist, add input files for tleap and dirs into the calcjob inputs directory

aiida_amber.data.tleap_input.add_calculation_outputs(files)

Add outputs from tleap script

aiida_amber.data.tleap_input.parse_tleap_input_file(lines)

Parse tleap script and find any instances of file loads (inputs) or saves (outputs)

Module contents

aiida_amber

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