schrodinger.application.jaguar.macro_pka_input module¶

Functions and classes for defining the input to a Macro-pKa workflow.

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.

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