aiida_gromacs.parsers package¶
Submodules¶
aiida_gromacs.parsers.editconf module¶
Parsers provided by aiida_gromacs.
This parser adds the ability to parse the outputs of the ‘gmx editconf’ executable.
- class aiida_gromacs.parsers.editconf.EditconfParser(node)[source]¶
Bases:
Parser
Parser class for parsing output of calculation.
- __abstractmethods__ = frozenset({})¶
- __init__(node)[source]¶
Initialize Parser instance
Checks that the ProcessNode being passed was produced by a EditconfCalculation.
- Parameters:
node (type) – ProcessNode of calculation
- __module__ = 'aiida_gromacs.parsers.editconf'¶
- _abc_impl = <_abc_data object>¶
aiida_gromacs.parsers.genericMD module¶
Parsers provided by aiida_gromacs.
This parser saves outputted files from a generic command.
- class aiida_gromacs.parsers.genericMD.GenericParser(node)[source]¶
Bases:
Parser
Parser class for parsing output of genericMD calculation from which the retrieved outputs files from the calcjob and the nodes of finished calculation can be accessed.
- __abstractmethods__ = frozenset({})¶
- __init__(node)[source]¶
Initialize Parser instance
Checks that the ProcessNode being passed was produced by a GenericCalculation.
- Parameters:
node (type) – ProcessNode of calculation
- __module__ = 'aiida_gromacs.parsers.genericMD'¶
- _abc_impl = <_abc_data object>¶
- _parse_gromacs_top(file_path)[source]¶
Not used yet, test for parsing the gromacs tpr file. :param file_path: The path and name of gtomacs .log file :returns: The required text from the parsed file
- static format_link_label(filename: str) str [source]¶
Modified from: https://github.com/sphuber/aiida-shell/blob/master/src/aiida_shell/parsers/shell.py Format the link label from a given filename with prefix. Valid link labels can only contain alphanumeric characters and underscores, without consecutive underscores. So all characters that are not alphanumeric or an underscore are converted to underscores, where consecutive underscores are merged into one. Additional: Label cannot start with a number or underscore.
- Parameters:
filename – The filename.
- Returns:
The link label.
aiida_gromacs.parsers.genion module¶
Parsers provided by aiida_gromacs.
This parser adds the ability to parse the outputs of the ‘gmx genion’ executable.
- class aiida_gromacs.parsers.genion.GenionParser(node)[source]¶
Bases:
Parser
Parser class for parsing output of calculation.
- __abstractmethods__ = frozenset({})¶
- __init__(node)[source]¶
Initialize Parser instance
Checks that the ProcessNode being passed was produced by a GenionCalculation.
- Parameters:
node (type) – ProcessNode of calculation
- __module__ = 'aiida_gromacs.parsers.genion'¶
- _abc_impl = <_abc_data object>¶
aiida_gromacs.parsers.grompp module¶
Parsers provided by aiida_gromacs.
This parser adds the ability to parse the outputs of the ‘gmx grompp’ executable.
- class aiida_gromacs.parsers.grompp.GromppParser(node)[source]¶
Bases:
Parser
Parser class for parsing output of calculation.
- __abstractmethods__ = frozenset({})¶
- __init__(node)[source]¶
Initialize Parser instance
Checks that the ProcessNode being passed was produced by a GromppCalculation.
- Parameters:
node (type) – ProcessNode of calculation
- __module__ = 'aiida_gromacs.parsers.grompp'¶
- _abc_impl = <_abc_data object>¶
aiida_gromacs.parsers.mdrun module¶
Parsers provided by aiida_gromacs.
This calculation configures the ability to use the ‘gmx mdrun’ executable.
- class aiida_gromacs.parsers.mdrun.MdrunParser(node)[source]¶
Bases:
Parser
Parser class for parsing output of calculation.
- __abstractmethods__ = frozenset({})¶
- __init__(node)[source]¶
Initialize Parser instance
Checks that the ProcessNode being passed was produced by a MdrunCalculation.
- Parameters:
node (type) – ProcessNode of calculation
- __module__ = 'aiida_gromacs.parsers.mdrun'¶
- _abc_impl = <_abc_data object>¶
aiida_gromacs.parsers.pdb2gmx module¶
Parsers provided by aiida_gromacs.
This parser adds the ability to parse the outputs of the ‘gmx pdb2gmx’ executable.
- class aiida_gromacs.parsers.pdb2gmx.Pdb2gmxParser(node)[source]¶
Bases:
Parser
Parser class for parsing output of calculation.
- __abstractmethods__ = frozenset({})¶
- __init__(node)[source]¶
Initialize Parser instance
Checks that the ProcessNode being passed was produced by a Pdb2gmxCalculation.
- Parameters:
node (type) – ProcessNode of calculation
- __module__ = 'aiida_gromacs.parsers.pdb2gmx'¶
- _abc_impl = <_abc_data object>¶
aiida_gromacs.parsers.solvate module¶
Parsers provided by aiida_gromacs.
This parser adds the ability to parse the outputs of the ‘gmx solvate’ executable.
- class aiida_gromacs.parsers.solvate.SolvateParser(node)[source]¶
Bases:
Parser
Parser class for parsing output of calculation.
- __abstractmethods__ = frozenset({})¶
- __init__(node)[source]¶
Initialize Parser instance
Checks that the ProcessNode being passed was produced by a SolvateCalculation.
- Parameters:
node (type) – ProcessNode of calculation
- __module__ = 'aiida_gromacs.parsers.solvate'¶
- _abc_impl = <_abc_data object>¶
Module contents¶
aiida_gromacs
A plugin for using GROMACS with AiiDA for molecular dymanics simulations.