schrodinger.application.jaguar.solvation_input module¶
Functions and classes for defining the input to a Solvation workflow.
- class schrodinger.application.jaguar.solvation_input.SolvationInput(inputfile: Optional[str] = None, keywords: Optional[dict] = None, jaguar_keywords: Optional[dict] = None, jobname: Optional[str] = None, add_solvation_jaguar_defaults: bool = False)¶
Bases:
schrodinger.application.jaguar.workflow_input.WorkflowInput
A class to completely specify a Solvation calculation.
Example usage:
input = SolvationInput() # 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 = 'Solvation'¶
- __init__(inputfile: Optional[str] = None, keywords: Optional[dict] = None, jaguar_keywords: Optional[dict] = None, jobname: Optional[str] = None, add_solvation_jaguar_defaults: bool = False)¶
Create a SolvationInput 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 Solvation input file
keywords – Solvation 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.
add_solvation_jaguar_defaults – if True add some custom Jaguar defaults
- static generate_keywords() dict ¶
Initialize dictionary of all possible Solvation keywords
- setJaguarValues(keywords: dict)¶
Set multiple Jaguar &gen section keywords.
- Parameters
keywords – Jaguar &gen section keyword/value pairs
- getInputMolecule() Optional[List[schrodinger.structure._structure.Structure]] ¶
Return list of input molecules. If no file(s) found, return None.
- Returns
reactant Structures
- validate()¶
Perform a self-consistency check of all currently set keywords.
:raise WorkflowKeywordConflictError if conflicting values found :raise WorkflowConservationError if matter not conserved
- read(inputfile: str)¶
Read an existing Solvation input file. Any keywords specified in the input file will override existing values in this SolvationInput instance.
Jaguar &gen section keywords are defined like:
&JaguarKeywords key=val key=val ... &
Constraints can be defined with:
&Constraints st_title atom_index1 atom_index2... value &
- Parameters
inputfile (str) – Path to a Solvation input file