schrodinger.application.jaguar.reactiq_input module¶
Functions and classes for defining the input to a Reactiq workflow.
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schrodinger.application.jaguar.reactiq_input.
read_mae_files
(fhlist, fileonly, clean_st)¶ Process a list of mae files and return extant file paths or associated Structure instances if requested.
Parameters: - fhlist (list of strings) – list of filehandles
- fileonly (bool) – if True, return only file paths, else Structures.
- clean_st (bool) – if True redefine bonding using mmlewis.
Returns: Structures or file paths.
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class
schrodinger.application.jaguar.reactiq_input.
ReactiqInput
(inputfile=None, keywords=None, jaguar_keywords=None, jobname=None, add_autots_jaguar_defaults=False)¶ Bases:
schrodinger.application.jaguar.workflow_input.WorkflowInput
A class to completely specify a Reactiq calculation.
Example usage:
input = ReactiqInput() # 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
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__init__
(inputfile=None, keywords=None, jaguar_keywords=None, jobname=None, add_autots_jaguar_defaults=False)¶ Create a ReactiqInput 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 Reactiq input file
- keywords (dict) – Reactiq 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.
- add_autots_jaguar_defaults (boolean) – if True add some custom Jaguar defaults
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reaction_smarts
¶ Reaction smarts identifying input reaction
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generate_keywords
()¶ Initialize dictionary of all possible AutoTS keywords
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setJaguarValues
(keywords)¶ Set multiple Jaguar &gen section keywords.
Parameters: keywords (dict of string/anytype pairs) – Jaguar &gen section keyword/value pairs
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getReactants
(fileonly=False, clean_st=False)¶ Return list of reactants. If no file(s) found, return empty list.
Parameters: - fileonly (bool) – if True, return only file paths, else Structures.
- clean_st (bool) – if True redefine bonding using mmlewis.
Returns: reactant Structures or file paths.
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getProducts
(fileonly=False, clean_st=False)¶ Return list of products. If no file(s) found, return empty list.
Parameters: - fileonly (bool) – if True, return only file paths, else Structures.
- clean_st (bool) – if True redefine bonding using mmlewis.
Returns: product Structures or file paths.
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getReactantComplex
(fileonly=False, clean_st=False)¶ Return Reactant Complex. If no file found, return NoneType.
Parameters: - fileonly (bool) – if True, return only file paths, else Structures.
- clean_st (bool) – if True redefine bonding using mmlewis.
Returns: Reactant Complex Structures or file path.
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getProductComplex
(fileonly=False, clean_st=False)¶ Return Product Complex. If no file found, return NoneType.
Parameters: - fileonly (bool) – if True, return only file paths, else Structures.
- clean_st (bool) – if True redefine bonding using mmlewis.
Returns: Product Complex Structures or file path.
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getReferenceReactantComplex
(fileonly=False, clean_st=False)¶ Return Reference Reactant Complex. If no file found, return NoneType.
Parameters: - fileonly (bool) – if True, return only file paths, else Structures.
- clean_st (bool) – if True redefine bonding using mmlewis.
Returns: Reactant Complex Structures or file path.
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getReferenceProductComplex
(fileonly=False, clean_st=False)¶ Return Reference Product Complex. If no file found, return NoneType.
Parameters: - fileonly (bool) – if True, return only file paths, else Structures.
- clean_st (bool) – if True redefine bonding using mmlewis.
Returns: Product Complex Structures or file path.
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getSpectators
(fileonly=False, clean_st=False)¶ Return spectator. If no file found, return NoneType.
Parameters: - fileonly (bool) – if True, return only file paths, else Structures.
- clean_st (bool) – if True redefine bonding using mmlewis.
Returns: Reactant Complex Structures or file path.
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setConstraints
(constraints)¶ Set the constraints.
Parameters: constraints (dict) – dictionary relating structure title to a list of Coordinate instances which define the constraints
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validate
()¶ Perform a self-consistency check of all currently set keywords.
:raise WorkflowKeywordConflictError if conflicting values found :raise WorkflowConservationError if matter not conserved
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validate_jaguar_keywords
(strs)¶ Perform a check to ensure that Jaguar keywords are not set that AutoTS cannot handle.
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setConstants
()¶ Set any constants defined by keywords
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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.
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read
(inputfile)¶ Read an existing Reactiq input file. Any keywords specified in the input file will override existing values in this ReactiqInput 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 Reactiq input file
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set_default_template_file
()¶ If the default template file is not set and the keyword use_default_templates is True and that file exists, set the template file to the default one.
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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.
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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.
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get_input_files
()¶ Return set of expected input files.
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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.
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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
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getJaguarNonDefault
()¶ Return a dictionary of all non-default Jaguar keys except ‘multip’ and ‘molchg’, which must be retrieved explicitly.
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getJaguarValue
(key)¶ Return the value for Jaguar keyword ‘key’. The return type depends on the keyword.
Parameters: key (string) – name of keyword
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getNonDefaultKeys
()¶ Return a dictionary of all non-default-value WorkflowKeyword instances indexed by name.
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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
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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.
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keywords
¶
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resetAll
()¶ Reset all keywords to their default states.
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resetKey
(keyword)¶ Reset keyword to default state.
Parameters: keyword (string) – name of keyword
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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
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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
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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
:raise WorkflowKeywordError if no keyword found
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setValues
(keywords)¶ Set multiple Workflow keywords.
Parameters: keywords (dict of string/anytype pairs) – keyword/value pairs
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values
¶ Support access to WorkflowKeyword values via attribute syntax. e.g.
wi = WorkflowInput() print wi.values.optimize # print ‘optimize’ keyword value
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schrodinger.application.jaguar.reactiq_input.
users_default_template_filename
()¶ Returns the name of the users template file that should be found in .schrodinger/autots_templates. The file may or may not exist.