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: str | None = None, keywords: dict | None = None, jaguar_keywords: dict | None = None, jobname: str | None = None, add_solvation_jaguar_defaults: bool = False)¶

Bases: 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']¶

keyword_source = {}¶

static keyword_generator()¶

Function to generate the keyword source dictionary. This is used to initialize the keyword_source property.

Returns:: None

workflow_name = 'Solvation'¶

__init__(inputfile: str | None = None, keywords: dict | None = None, jaguar_keywords: dict | None = None, jobname: str | None = 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

setJaguarValues(keywords: dict)¶

Set multiple Jaguar &gen section keywords.

Parameters:: keywords – Jaguar &gen section keyword/value pairs

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