schrodinger.application.jaguar.macro_pka_input module¶
Functions and classes for defining the input to a Macro-pKa workflow.
Copyright Schrodinger, LLC. All rights reserved.
- class schrodinger.application.jaguar.macro_pka_input.MacroKaInput(inputfile: Optional[str] = None, keywords: Optional[dict] = None, jobname: Optional[str] = None)¶
Bases:
schrodinger.application.jaguar.workflow_input.WorkflowInput
A class to completely specify a Macro-pKa calculation.
Example usage:
input = MacroKaInput() # Set user-defined values input.setValue('integerKW', 3) input.setValue('floatKW', '7.0') input.setValue('stringKW', 'foo') # Print all keyword/value pairs. for keyword in input: print(keyword {keyword} has value {input[keyword]}) # Handling the case of trying to set an unsupported keyword try: input['mykeyword'] = 'value' except WorkflowKeywordException as e: print(e.allowed_keywords)
- input_file_keys = ['infile', 'autoconf_config', 'conformer_files']¶
- workflow_name = 'macro_pka'¶
- __init__(inputfile: Optional[str] = None, keywords: Optional[dict] = None, jobname: Optional[str] = None)¶
Create a MacroKaInput instance. If a keyword is specified in both ‘inputfile’ and ‘keywords’, then the values in ‘keywords’ will be set preferrentially.
- Parameters
inputfile – Path to a Macro-pKa input file
keywords – Macro-pKa keyword/value pairs
jobname – Name of job, if it is not None it will be set to the basename of the input file name.
- static generate_keywords() dict ¶
Initialize dictionary of all possible Macro-pKa keywords
- getInputMolecule() schrodinger.structure._structure.Structure ¶
Return input molecule.
- Returns
input structure
- Raise
IOError if no input file found
- validate(validate_structs: bool = True)¶
Perform a self-consistency check of all currently set keywords.
- Parameters
validate_structs – Whether to validate input structures
:raise WorkflowKeywordConflictError if conflicting values found :raise WorkflowConservationError if charge/multiplicity unphysical