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