aiida_amber package¶
Subpackages¶
- aiida_amber.calculations package
- Submodules
- aiida_amber.calculations.antechamber module
AntechamberCalculationAntechamberCalculation.__abstractmethods__AntechamberCalculation.__annotations__AntechamberCalculation.__firstlineno__AntechamberCalculation.__module__AntechamberCalculation.__static_attributes__AntechamberCalculation._abc_implAntechamberCalculation.define()AntechamberCalculation.prepare_for_submission()
- aiida_amber.calculations.parmed module
- aiida_amber.calculations.pdb4amber module
- aiida_amber.calculations.sander module
- aiida_amber.calculations.tleap module
- Module contents
- aiida_amber.cli package
- aiida_amber.data package
- Submodules
- aiida_amber.data.antechamber module
AntechamberParametersAntechamberParameters.__abstractmethods__AntechamberParameters.__annotations__AntechamberParameters.__firstlineno__AntechamberParameters.__init__()AntechamberParameters.__module__AntechamberParameters.__parameters__AntechamberParameters.__static_attributes__AntechamberParameters.__str__()AntechamberParameters._abc_implAntechamberParameters._loggerAntechamberParameters.cmdline_params()AntechamberParameters.fieldsAntechamberParameters.schemaAntechamberParameters.validate()
- aiida_amber.data.parmed module
ParmedParametersParmedParameters.__abstractmethods__ParmedParameters.__annotations__ParmedParameters.__firstlineno__ParmedParameters.__init__()ParmedParameters.__module__ParmedParameters.__parameters__ParmedParameters.__static_attributes__ParmedParameters.__str__()ParmedParameters._abc_implParmedParameters._loggerParmedParameters.cmdline_params()ParmedParameters.fieldsParmedParameters.schemaParmedParameters.validate()
- aiida_amber.data.parmed_input module
ParmedInputDataParmedInputData.__abstractmethods__ParmedInputData.__annotations__ParmedInputData.__firstlineno__ParmedInputData.__module__ParmedInputData.__parameters__ParmedInputData.__static_attributes__ParmedInputData._abc_implParmedInputData._loggerParmedInputData.calculation_inputs_outputsParmedInputData.fieldsParmedInputData.inpfile_listParmedInputData.outfile_listParmedInputData.set_file()
add_calculation_inputs()add_calculation_outputs()parse_parmed_input_file()
- aiida_amber.data.pdb4amber module
Pdb4amberParametersPdb4amberParameters.__abstractmethods__Pdb4amberParameters.__annotations__Pdb4amberParameters.__firstlineno__Pdb4amberParameters.__init__()Pdb4amberParameters.__module__Pdb4amberParameters.__parameters__Pdb4amberParameters.__static_attributes__Pdb4amberParameters.__str__()Pdb4amberParameters._abc_implPdb4amberParameters._loggerPdb4amberParameters.cmdline_params()Pdb4amberParameters.fieldsPdb4amberParameters.schemaPdb4amberParameters.validate()
- aiida_amber.data.sander module
SanderParametersSanderParameters.__abstractmethods__SanderParameters.__annotations__SanderParameters.__firstlineno__SanderParameters.__init__()SanderParameters.__module__SanderParameters.__parameters__SanderParameters.__static_attributes__SanderParameters.__str__()SanderParameters._abc_implSanderParameters._loggerSanderParameters.cmdline_params()SanderParameters.fieldsSanderParameters.schemaSanderParameters.validate()
- aiida_amber.data.tleap module
TleapParametersTleapParameters.__abstractmethods__TleapParameters.__annotations__TleapParameters.__firstlineno__TleapParameters.__init__()TleapParameters.__module__TleapParameters.__parameters__TleapParameters.__static_attributes__TleapParameters.__str__()TleapParameters._abc_implTleapParameters._loggerTleapParameters.cmdline_params()TleapParameters.fieldsTleapParameters.schemaTleapParameters.validate()
- aiida_amber.data.tleap_input module
TleapInputDataTleapInputData.__abstractmethods__TleapInputData.__annotations__TleapInputData.__firstlineno__TleapInputData.__module__TleapInputData.__parameters__TleapInputData.__static_attributes__TleapInputData._abc_implTleapInputData._loggerTleapInputData.calculation_inputs_outputsTleapInputData.fieldsTleapInputData.inpfile_listTleapInputData.outfile_listTleapInputData.set_file()
add_calculation_inputs()add_calculation_outputs()parse_tleap_input_file()
- Module contents
- aiida_amber.parsers package
- aiida_amber.utils package
Submodules¶
aiida_amber.helpers module¶
Helper functions for automatically setting up computer & code. Helper functions for setting up
An AiiDA localhost computer
A “sander” code on localhost
Note: Point 2 is made possible by the fact that the sander executable is
available in the PATH on almost any UNIX system.
- aiida_amber.helpers.get_code(entry_point, computer)[source]¶
Get local code. Sets up code for given entry point on given computer.
- Parameters:
entry_point – Entry point of calculation plugin
computer – (local) AiiDA computer
- Returns:
The code node
- Return type:
aiida.orm.nodes.data.code.installed.InstalledCode
- aiida_amber.helpers.get_computer(name='localhost', workdir=None)[source]¶
Get AiiDA computer. Loads computer ‘name’ from the database, if exists. Sets up local computer ‘name’, if it isn’t found in the DB.
- Parameters:
name – Name of computer to load or set up.
workdir – path to work directory Used only when creating a new computer.
- Returns:
The computer node
- Return type:
aiida.orm.computers.Computer
Module contents¶
aiida_amber
A plugin for using Amber with AiiDA for molecular dymanics simulations.