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__ = {'_CLS_COLLECTION': 'Type[CollectionType]', '__plugin_type_string': 'ClassVar[str]', '__query_type_string': 'ClassVar[str]', '_export_format_replacements': 'Dict[str, str]', '_hash_ignored_attributes': 'Tuple[str, ...]', '_logger': 'Optional[Logger]', '_updatable_attributes': 'Tuple[str, ...]'}

__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__ = ()

__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

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__ = {'_CLS_COLLECTION': 'Type[CollectionType]', '__plugin_type_string': 'ClassVar[str]', '__query_type_string': 'ClassVar[str]', '_export_format_replacements': 'Dict[str, str]', '_hash_ignored_attributes': 'Tuple[str, ...]', '_logger': 'Optional[Logger]', '_updatable_attributes': 'Tuple[str, ...]'}

__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__ = ()

__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

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__ = {'_CLS_COLLECTION': 'Type[CollectionType]', '__plugin_type_string': 'ClassVar[str]', '__query_type_string': 'ClassVar[str]', '_export_format_replacements': 'Dict[str, str]', '_hash_ignored_attributes': 'Tuple[str, ...]', '_logger': 'Optional[Logger]', '_updatable_attributes': 'Tuple[str, ...]'}

__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__ = ()

__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

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__ = {'_CLS_COLLECTION': 'Type[CollectionType]', '__plugin_type_string': 'ClassVar[str]', '__query_type_string': 'ClassVar[str]', '_export_format_replacements': 'Dict[str, str]', '_hash_ignored_attributes': 'Tuple[str, ...]', '_logger': 'Optional[Logger]', '_updatable_attributes': 'Tuple[str, ...]'}

__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__ = ()

__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

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__ = {'_CLS_COLLECTION': 'Type[CollectionType]', '__plugin_type_string': 'ClassVar[str]', '__query_type_string': 'ClassVar[str]', '_export_format_replacements': 'Dict[str, str]', '_hash_ignored_attributes': 'Tuple[str, ...]', '_logger': 'Optional[Logger]', '_updatable_attributes': 'Tuple[str, ...]'}

__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__ = ()

__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

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__ = {'_CLS_COLLECTION': 'Type[CollectionType]', '__plugin_type_string': 'ClassVar[str]', '__query_type_string': 'ClassVar[str]', '_export_format_replacements': 'Dict[str, str]', '_hash_ignored_attributes': 'Tuple[str, ...]', '_logger': 'Optional[Logger]', '_updatable_attributes': 'Tuple[str, ...]'}

__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__ = ()

__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

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.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__ = {'_CLS_COLLECTION': 'Type[CollectionType]', '__plugin_type_string': 'ClassVar[str]', '__query_type_string': 'ClassVar[str]', '_export_format_replacements': 'Dict[str, str]', '_hash_ignored_attributes': 'Tuple[str, ...]', '_logger': 'Optional[Logger]', '_updatable_attributes': 'Tuple[str, ...]'}

__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__ = ()

__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

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.