schrodinger.application.jaguar.esol_input module

Functions and classes for defining the input to a Esol workflow

class schrodinger.application.jaguar.esol_input.EsolInput(inputfile: Optional[str] = None, keywords: Optional[dict] = None, jaguar_keywords: Optional[dict] = None, jobname: Optional[str] = None)

Bases: schrodinger.application.jaguar.workflow_input.WorkflowInput

A class to completely specify an Esol calculation.

Example usage:

input = EsolInput()
# 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 '%s' has value %s" % (keyword, 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 = ['input']
workflow_name = 'Esol'
__init__(inputfile: Optional[str] = None, keywords: Optional[dict] = None, jaguar_keywords: Optional[dict] = None, jobname: Optional[str] = None)

Create a EsolInput instance. If a keyword is specified in both ‘inputfile’ and ‘keywords’, then the values in ‘keywords’ will be set preferrentially. This also applies to ‘jaguar_keywords’.

Parameters

  • inputfile – Path to a Esol input file

  • keywords – Esol keyword/value pairs

  • jaguar_keywords – Jaguar &gen section keyword/value pairs

  • jobname – Name of job, if it is not None it will be set to the basename of the input file name.

update_stage_user_keys()

Update self.jaguar_stage_user_keys to include those in self._jaguar_user_keys. Keys in self.jaguar_stage_user_keys take precedence.

generate_keywords() → dict

Initialize dictionary of all possible Esol keywords

getInputMolecules() → Optional[List[schrodinger.structure._structure.Structure]]

Return list of input molecules. If no file(s) found, return None.

Returns

esol Structures

validate()

Perform a self-consistency check of all currently set keywords.

Raises

RuntimeError – If keyword names differ from EsolInput._keywords keys