schrodinger.application.jaguar.reactiq_input module

Functions and classes for defining the input to a Reactiq workflow.

class schrodinger.application.jaguar.reactiq_input.ReactiqInput(inputfile=None, keywords=None, jaguar_keywords=None, jobname=None)

Bases: object

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 ReactiqKeywordException as e:
print e.allowed_keywords
getDefault(keyword)

Return the default value for Reactiq keyword ‘keyword’. The return type depends on the keyword.

Parameters:keyword (string) – name of keyword

:raise ReactiqKeywordError if no keyword found

getJaguarNonDefault()

Return a dictionary of all non-default Jaguar keys except ‘multip’ and ‘molchg’, which must be retrieved explicitly.

getJaguarValue(key)

Return the value for Jaguar keyword ‘key’. The return type depends on the keyword.

Parameters:key (string) – name of keyword
getNonDefaultJaguarKeys()

Return a dictionary of all non-default-value Jaguar keywords

getNonDefaultKeys()

Return a dictionary of all non-default-value ReactiqKeyword instances indexed by name.

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.
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.
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.
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.
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.
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.
getValue(keyword)

Return the value for Reactiq keyword. The return type depends on the keyword.

Parameters:keyword (string) – name of keyword

:raise ReactiqKeywordError if no keyword found

get_input_files()

Return set of expected input files.

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.
keywords
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 …

&

Parameters:inputfile (str) – Path to a Reactiq 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.

resetAll()

Reset all keywords to their default states.

resetKey(keyword)

Reset keyword to default state.

Parameters:keyword (string) – name of keyword
save(name)

Create a Reactiq 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 Reactiq input file
setConstants()

Set any constants defined by keywords

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
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.
setValue(keyword, value)

Set the Reactiq keyword ‘keyword’ to value ‘value’. Note that there may be type-checking and conversion by the ReactiqKeyword class.

If ‘value’ is None, the keyword will be reset.

Parameters:
  • keyword (string) – name of keyword
  • value (anytype) – value of keyword

:raise ReactiqKeywordError if no keyword found

setValues(keywords)

Set multiple Reactiq keywords.

Parameters:keywords (dict of string/anytype pairs) – keyword/value pairs
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.

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.

validate()

Perform a self-consistency check of all currently set keywords.

:raise ReactiqKeywordConflictError if conflicting values found :raise ReactiqConservationError if matter not conserved

validate_structures()

Perform a check to ensure that matter is conserved and that charge/multiplicity are consistent with structures.

A ReactiqConservationError is raised if any test fails.

values

Support access to ReactiqKeyword values via attribute syntax. e.g.

ri = ReactiqInput() print ri.values.optimize # print ‘optimize’ keyword value
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.