aiida_gromacs.data package

Submodules

aiida_gromacs.data.editconf module

Data types provided by plugin

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

class aiida_gromacs.data.editconf.EditconfParameters(dict=None, **kwargs)

Bases: Dict

Command line options for diff.

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: EditconfParameters(dict{'ignore-case': True})

Parameters:

• parameters_dict (type) – dictionary with commandline parameters

• parameters_dict – dict

__module__ = 'aiida_gromacs.data.editconf'

__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_gromacs.data.editconf.EditconfParameters (WARNING)>

cmdline_params(input_files)

Synthesize command line parameters.

e.g. [ ‘–ignore-case’, ‘filename1’, ‘filename2’]

Parameters:

• grofile (type) – Name of input gro file

• grofile – str

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'>, 'mead': <class 'str'>, 'w': <class 'str'>, 'ndef': <class 'str'>, 'bt': <class 'str'>, 'box': <class 'str'>, 'angle': <class 'str'>, 'd': <class 'str'>, 'c': <class 'str'>, 'center': <class 'str'>, 'aligncenter': <class 'str'>, 'align': <class 'str'>, 'translate': <class 'str'>, 'rotate': <class 'str'>, 'princ': <class 'str'>, 'scale': <class 'str'>, 'density': <class 'str'>, 'pbc': <class 'str'>, 'resnr': <class 'str'>, 'grasp': <class 'str'>, 'rvdw': <class 'str'>, 'sig56': <class 'str'>, 'vdwread': <class 'str'>, 'atom': <class 'str'>, 'legend': <class 'str'>, 'label': <class 'str'>, 'conect': <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(EditconfParameters).schema.schema

Parameters:

• parameters_dict (type) – dictionary with commandline parameters

• parameters_dict – dict

Returns:

validated dictionary

aiida_gromacs.data.genion module

Data types provided by plugin

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

class aiida_gromacs.data.genion.GenionParameters(dict=None, **kwargs)

Bases: Dict

Command line options for diff.

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

__abstractmethods__ = frozenset({})

__annotations__ = {}

__firstlineno__ = 29

__init__(dict=None, **kwargs)

Constructor for the data class

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

Parameters:

• parameters_dict (type) – dictionary with commandline parameters

• parameters_dict – dict

__module__ = 'aiida_gromacs.data.genion'

__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_gromacs.data.genion.GenionParameters (WARNING)>

cmdline_params(input_files)

Synthesize command line parameters.

e.g. [ ‘–ignore-case’, ‘filename1’, ‘filename2’]

Parameters:

• pdbfile (type) – Name of input pdb file

• pdbfile – str

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'>, 'np': <class 'str'>, 'pname': <class 'str'>, 'pq': <class 'str'>, 'nn': <class 'str'>, 'nname': <class 'str'>, 'nq': <class 'str'>, 'rmin': <class 'str'>, 'seed': <class 'str'>, 'conc': <class 'str'>, 'neutral': <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(GenionParameters).schema.schema

Parameters:

• parameters_dict (type) – dictionary with commandline parameters

• parameters_dict – dict

Returns:

validated dictionary

aiida_gromacs.data.grompp module

Data types provided by plugin

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

class aiida_gromacs.data.grompp.GromppParameters(dict=None, **kwargs)

Bases: Dict

Command line options for diff.

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

__abstractmethods__ = frozenset({})

__annotations__ = {}

__firstlineno__ = 29

__init__(dict=None, **kwargs)

Constructor for the data class

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

Parameters:

• parameters_dict (type) – dictionary with commandline parameters

• parameters_dict – dict

__module__ = 'aiida_gromacs.data.grompp'

__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_gromacs.data.grompp.GromppParameters (WARNING)>

cmdline_params(input_files)

Synthesize command line parameters.

e.g. [ ‘–ignore-case’, ‘filename1’, ‘filename2’]

Parameters:

• pdbfile (type) – Name of input pdb file

• pdbfile – str

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'>, 'po': <class 'str'>, 'pp': <class 'str'>, 'imd': <class 'str'>, 'r': <class 'str'>, 'v': <class 'str'>, 'time': <class 'str'>, 'rmvsbds': <class 'str'>, 'maxwarn': <class 'str'>, 'zero': <class 'str'>, 'renum': <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(GromppParameters).schema.schema

Parameters:

• parameters_dict (type) – dictionary with commandline parameters

• parameters_dict – dict

Returns:

validated dictionary

aiida_gromacs.data.make_ndx module

Data types provided by plugin

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

class aiida_gromacs.data.make_ndx.Make_ndxParameters(dict=None, **kwargs)

Bases: Dict

Command line options for diff.

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

__abstractmethods__ = frozenset({})

__annotations__ = {}

__firstlineno__ = 22

__init__(dict=None, **kwargs)

Constructor for the data class

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

Parameters:

• parameters_dict (type) – dictionary with commandline parameters

• parameters_dict – dict

__module__ = 'aiida_gromacs.data.make_ndx'

__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_gromacs.data.make_ndx.Make_ndxParameters (WARNING)>

cmdline_params(input_files)

Synthesize command line parameters.

e.g. [ ‘–ignore-case’, ‘filename1’, ‘filename2’]

Parameters:

• pdbfile (type) – Name of input pdb file

• pdbfile – str

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'>, 'natoms': <class 'str'>, 'notwin': <class 'str'>, 'twin': <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(Make_ndxParameters).schema.schema

Parameters:

• parameters_dict (type) – dictionary with commandline parameters

• parameters_dict – dict

Returns:

validated dictionary

aiida_gromacs.data.mdrun module

Data types provided by plugin

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

class aiida_gromacs.data.mdrun.MdrunParameters(dict=None, **kwargs)

Bases: Dict

Command line options for diff.

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

__abstractmethods__ = frozenset({})

__annotations__ = {}

__firstlineno__ = 74

__init__(dict=None, **kwargs)

Constructor for the data class

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

Parameters:

• parameters_dict (type) – dictionary with commandline parameters

• parameters_dict – dict

__module__ = 'aiida_gromacs.data.mdrun'

__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_gromacs.data.mdrun.MdrunParameters (WARNING)>

cmdline_params(input_files)

Synthesize command line parameters.

e.g. [ ‘–ignore-case’, ‘filename1’, ‘filename2’]

Parameters:

• pdbfile (type) – Name of input pdb file

• pdbfile – str

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({'c': <class 'str'>, 'e': <class 'str'>, 'g': <class 'str'>, 'o': <class 'str'>, 'x': <class 'str'>, 'cpo': <class 'str'>, 'dhdl': <class 'str'>, 'field': <class 'str'>, 'tpi': <class 'str'>, 'tpid': <class 'str'>, 'eo': <class 'str'>, 'px': <class 'str'>, 'pf': <class 'str'>, 'ro': <class 'str'>, 'ra': <class 'str'>, 'rs': <class 'str'>, 'rt': <class 'str'>, 'mtx': <class 'str'>, 'if': <class 'str'>, 'swap': <class 'str'>, 'xvg': <class 'str'>, 'dd': <class 'str'>, 'ddorder': <class 'str'>, 'npme': <class 'str'>, 'nt': <class 'str'>, 'ntmpi': <class 'str'>, 'ntomp': <class 'str'>, 'ntomp_pme': <class 'str'>, 'pin': <class 'str'>, 'pinoffset': <class 'str'>, 'pinstride': <class 'str'>, 'gpu_id': <class 'str'>, 'gputasks': <class 'str'>, 'ddcheck': <class 'str'>, 'rdd': <class 'str'>, 'rcon': <class 'str'>, 'dlb': <class 'str'>, 'dds': <class 'str'>, 'nb': <class 'str'>, 'nstlist': <class 'str'>, 'tunepme': <class 'str'>, 'pme': <class 'str'>, 'pmefft': <class 'str'>, 'bonded': <class 'str'>, 'update': <class 'str'>, 'v': <class 'str'>, 'pforce': <class 'str'>, 'reprod': <class 'str'>, 'cpt': <class 'str'>, 'cpnum': <class 'str'>, 'append': <class 'str'>, 'nsteps': <class 'str'>, 'maxh': <class 'str'>, 'replex': <class 'str'>, 'nex': <class 'str'>, 'reseed': <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(MdrunParameters).schema.schema

Parameters:

• parameters_dict (type) – dictionary with commandline parameters

• parameters_dict – dict

Returns:

validated dictionary

aiida_gromacs.data.pdb2gmx module

Data types provided by plugin

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

class aiida_gromacs.data.pdb2gmx.Pdb2gmxParameters(dict=None, **kwargs)

Bases: Dict

Command line options for diff.

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

__abstractmethods__ = frozenset({})

__annotations__ = {}

__firstlineno__ = 50

__init__(dict=None, **kwargs)

Constructor for the data class

Usage: Pdb2gmxParameters(dict{'ignore-case': True})

Parameters:

• parameters_dict (type) – dictionary with commandline parameters

• parameters_dict – dict

__module__ = 'aiida_gromacs.data.pdb2gmx'

__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_gromacs.data.pdb2gmx.Pdb2gmxParameters (WARNING)>

cmdline_params(pdbfile)

Synthesize command line parameters.

e.g. [ ‘–ignore-case’, ‘filename1’, ‘filename2’]

Parameters:

• pdbfile (type) – Name of input pdb file

• pdbfile – str

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'>, 'p': <class 'str'>, 'i': <class 'str'>, 'n': <class 'str'>, 'q': <class 'str'>, 'chainsep': <class 'str'>, 'merge': <class 'str'>, 'ff': <class 'str'>, 'water': <class 'str'>, 'inter': <class 'str'>, 'ss': <class 'str'>, 'ter': <class 'str'>, 'lys': <class 'str'>, 'arg': <class 'str'>, 'asp': <class 'str'>, 'glu': <class 'str'>, 'gln': <class 'str'>, 'his': <class 'str'>, 'angle': <class 'str'>, 'dist': <class 'str'>, 'una': <class 'str'>, 'ignh': <class 'str'>, 'missing': <class 'str'>, 'v': <class 'str'>, 'posrefc': <class 'str'>, 'vsite': <class 'str'>, 'heavyh': <class 'str'>, 'deuterate': <class 'str'>, 'chargegrp': <class 'str'>, 'cmap': <class 'str'>, 'renum': <class 'str'>, 'rtpres': <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(Pdb2gmxParameters).schema.schema

Parameters:

• parameters_dict (type) – dictionary with commandline parameters

• parameters_dict – dict

Returns:

validated dictionary

aiida_gromacs.data.plumed_input module

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

class aiida_gromacs.data.plumed_input.PlumedInputData(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 plumed input file

__abstractmethods__ = frozenset({})

__annotations__ = {}

__firstlineno__ = 40

__module__ = 'aiida_gromacs.data.plumed_input'

__parameters__ = ()

__static_attributes__ = ()

_abc_impl = <_abc._abc_data object>

_logger: Logger | None = <Logger aiida_gromacs.data.plumed_input.PlumedInputData (WARNING)>

property calculation_inputs_outputs

Return the inputs for the plumed 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 plumed script

property outfile_list

Return the list output files to be produced from the plumed 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_gromacs.data.plumed_input.add_calculation_inputs(subdirs, files)

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

Parameters:

• subdirs – list of subdirectories that contain input files

• files – list of input files

aiida_gromacs.data.plumed_input.add_calculation_outputs(files)

Add outputs from plumed script

Parameters:

files – list of output files

aiida_gromacs.data.plumed_input.find_filename_from_string(head, values, filenames)

Find any filenames that are in a line of the plumed input file. Some keyword arguments allow for multiple filenames, which are comma separated. Each argument has an ‘=’ after it.

Parameters:

• head – line of plumed input file that doesn’t start with ‘#’

• values – list of arguments for a plumed keyword that would produce a file

• filenames – list of input/output filenames to append to, that are found in the plumed input

Returns:

list of filenames found in parsed plumed input file

Return type:

list

aiida_gromacs.data.plumed_input.find_plumed_filenames(keywords, i, line, lines)

Find lines that contain a plumed keyword that would require an input/output file

Parameters:

• keywords – dictionary of plumed keywords and their arguments that require an input/output file

• i – the parsed line number

• line – the currently parsed line

• lines – all the lines in the plumed input file

Returns:

list of filenames found in parsed plumed input file

Return type:

list

aiida_gromacs.data.plumed_input.parse_plumed_input_file(lines)

Parse plumed input file and find any instances of reading input files and writing output files. Find the lines that contain the keyword and then find the FILE keyword in the subsequent lines, onces this is found, then stop and carry on with outer loop. If the FILE keyword does not exist, there may be a default filename for some keywords.

Parameters:

lines – parsed lines from the plumed input file

aiida_gromacs.data.plumed_input.populate_plumed_files_to_inputs(inputs, plumed_filename)

Populate the plumed input files and directories into the inputs

Parameters:

• inputs – dictionary of inputs for the calculation

• plumed_filename – name of the plumed input file

aiida_gromacs.data.solvate module

Data types provided by plugin

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

class aiida_gromacs.data.solvate.SolvateParameters(dict=None, **kwargs)

Bases: Dict

Command line options for diff.

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

__abstractmethods__ = frozenset({})

__annotations__ = {}

__firstlineno__ = 26

__init__(dict=None, **kwargs)

Constructor for the data class

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

Parameters:

• parameters_dict (type) – dictionary with commandline parameters

• parameters_dict – dict

__module__ = 'aiida_gromacs.data.solvate'

__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_gromacs.data.solvate.SolvateParameters (WARNING)>

cmdline_params(grofile, topfile)

Synthesize command line parameters.

e.g. [ ‘–ignore-case’, ‘filename1’, ‘filename2’]

Parameters:

• grofile (type) – Name of input gro file

• grofile – str

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({'cs': <class 'str'>, 'o': <class 'str'>, 'box': <class 'str'>, 'radius': <class 'str'>, 'scale': <class 'str'>, 'shell': <class 'str'>, 'maxsol': <class 'str'>, 'vel': <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(SolvateParameters).schema.schema

Parameters:

• parameters_dict (type) – dictionary with commandline parameters

• parameters_dict – dict

Returns:

validated dictionary

Module contents

aiida_gromacs

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