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