schrodinger.application.jaguar.workflow_input module¶
Functions and classes for defining the input to a Workflow workflow.
Copyright Schrodinger, LLC. All rights reserved.
- class schrodinger.application.jaguar.workflow_input.WorkflowInput(inputfile=None, keywords=None, jaguar_keywords=None, jobname=None)¶
Bases:
abc.ABC
A Base class for specifying parameters in workflow calculations.
- The following functions must be defined in the inheriting class:
validate(self)
generate_keywords(self)
- abstract generate_keywords()¶
Initialize the list of possible keywords
- Return type
dictionary (keys are lowercase string, values are WorkflowKeyword)
- Return param
key, WorkflowKeyword pairs specific to this job’s input file
- abstract validate()¶
Perform a self-consistency check of all currently set keywords.
write for inheriting class
- Return param
Whether or no input passes workflow-specific validation checks
- Return type
bool
- input_file_keys = []¶
- workflow_name = 'Workflow'¶
- __init__(inputfile=None, keywords=None, jaguar_keywords=None, jobname=None)¶
Create a WorkflowInput 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 (str) – Path to a Workflow input file
keywords (dict) – Workflow keyword/value pairs
jaguar_keywords (dict) – Jaguar &gen section keyword/value pairs
jobname (string) – Name of job, if it is not None it will be set to the basename of the input file name.
- property keywords¶
- property values¶
Support access to WorkflowKeyword values via attribute syntax. e.g.:
wi = WorkflowInput() print wi.values.optimize # print 'optimize' keyword value
- getValue(keyword)¶
Return the value for Workflow keyword. The return type depends on the keyword.
- Parameters
keyword (string) – name of keyword
:raise WorkflowKeywordError if no keyword found
- setValue(keyword, value)¶
Set the Workflow keyword ‘keyword’ to value ‘value’. Note that there may be type-checking and conversion by the WorkflowKeyword class.
If ‘value’ is None, the keyword will be reset.
- Parameters
keyword (string) – name of keyword
value (anytype) – value of keyword
- Raises
WorkflowKeywordException – if no keyword found or there is an issue with the keyword or value
- setValues(keywords)¶
Set multiple Workflow keywords.
- Parameters
keywords (dict of string/anytype pairs) – keyword/value pairs
- getJaguarValue(key)¶
Return the value for Jaguar keyword ‘key’. The return type depends on the keyword.
- Parameters
key (string) – name of keyword
- setJaguarValue(key, value)¶
Set the Jaguar &gen section keyword ‘key’ to value ‘value’.
- Parameters
key (string) – name of keyword
value (anytype) – value of keyword
:raise JaguarKeywordException if keyword is invalid
- setJaguarValues(keywords)¶
Set multiple Jaguar &gen section keywords.
- Parameters
keywords (dict of string/anytype pairs) – Jaguar &gen section keyword/value pairs
- getJaguarNonDefault()¶
Return a dictionary of all non-default Jaguar keys except ‘multip’ and ‘molchg’, which must be retrieved explicitly.
- resetKey(keyword)¶
Reset keyword to default state.
- Parameters
keyword (string) – name of keyword
- resetAll()¶
Reset all keywords to their default states.
- getDefault(keyword)¶
Return the default value for Workflow keyword ‘keyword’. The return type depends on the keyword.
- Parameters
keyword (string) – name of keyword
:raise WorkflowKeywordError if no keyword found
- getNonDefaultKeys()¶
Return a dictionary of all non-default-value WorkflowKeyword instances indexed by name.
- isNonDefault(keyword)¶
Has the specified keyword been set to a non-default value?
- Parameters
keyword (str) – The key to check
- Returns
True if the specified keyword is set to a non-default value. False otherwise.
- setConstraints(constraints)¶
Set the constraints.
- Parameters
constraints (dict of str: Coordinate instance) – dictionary relating structure title to a list of Coordinate instances which define the constraints
- getConstraints()¶
Return the constraints defined in the input file
- Returns
a dict relating structure titles to constraints the constraints are given as a list of Coordinate instances and the titles refer to the titles of the input molecules.
- setFrozenAtoms(frozen_atoms)¶
Set the constraints.
- Parameters
frozen_atoms (dict of str: Coordinate instance) – dictionary relating structure title to a list of Coordinate instances which define the frozen atoms
- getFrozenAtoms()¶
Return the frozen atoms defined in the input file
- Returns
a dict relating structure titles to constraints the constraints are given as a list of Coordinate instances and the titles refer to the titles of the input molecules.
- validate_jaguar_keywords(sts)¶
Perform a check to ensure that Jaguar keywords are not set in a way that cannot be handled.
- Parameters
sts (list of Structure objects) – Structures whose basis needs validating
- save(name)¶
Create a Workflow input file called ‘name’ in the current working directory based on this class instance. Only write the non-default keyword values.
- Parameters
name (str) – Path to a Workflow input file
- setJobname(jobname)¶
Set the attribute jobname.
- Parameters
jobname (string) – input name of job. If jobname is None we try to use self._inputfile. If that is also None we assign a unique name.
- read(inputfile)¶
Read an existing Workflow input file.
Any keywords specified in the input file will override existing values in this WorkflowInput 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 Workflow input file
- remove_input_file_paths()¶
Remove full paths from file specifications. A new input file is no longer written, if that is desired the user must call the save method.
- update_input_file_paths()¶
Update full paths for file specifications to reflect the CWD. This is useful if running this job in a subdirectory or on a remote host.
- have_constraints()¶
Do we have internal coordinate constraints
- have_frozen_atoms()¶
Do we have frozen atom constraints
- get_input_files()¶
Return set of expected input files.