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, add_autots_jaguar_defaults=False)

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

__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

__iter__()

Provide convenient way to iterate over the keywords.

keywords

values

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

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

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

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

__getitem__(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

__setitem__(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

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 Reactiq keyword ‘keyword’. The return type depends on the keyword.

Parameters:keyword (string) – name of keyword

:raise ReactiqKeywordError if no keyword found

getNonDefaultKeys()

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

getNonDefaultJaguarKeys()

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

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.

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.

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.

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.

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.

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.

setConstraints(constraints)

Set the constraints.

Parameters:constraints (dict) – 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 reactant and product molecules.

validate()

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

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

validate_jaguar_keywords()

Perform a check to ensure that Jaguar keywords are not set that AutoTS cannot handle.

validate_constraints()

Validate any constraints that have been read. This ensures that the constraints can be mapped onto the input reactant/product molecules.

Specifically the properties that are required are:

1. relax_path = True cannot be set if we have constraints
2. The input reactants and products must have unique titles
3. Each constraint must map to some titled molecule or COMPLEX_STRUCTURE_CONSTRAINT if both reactant and product complexes are defined
4. Atom indexes of the constraint must be between 1 and the number of atoms in that molecule.
5. constraints cannot be in rings
6. Atom indexes for complex constraints cannot span multiple molecules.

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.

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

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 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

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.

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.

get_input_files()

Return set of expected input files.

__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.jaguar.reactiq_input', '__doc__': '\n A class to completely specify a Reactiq calculation.\n\n Example usage:\n\n input = ReactiqInput()\n # Set user-defined values\n input.setValue(\'integerKW\', 3)\n input.setValue(\'floatKW\', \'7.0\')\n input.setValue(\'stringKW\', \'foo\')\n\n # Print all keyword/value pairs.\n for keyword in input:\n print "keyword \'%s\' has value %s" % (keyword, input[keyword])\n\n # Handling the case of trying to set an unsupported keyword\n try:\n input[\'mykeyword\'] = \'value\'\n except ReactiqKeywordException as e:\n print e.allowed_keywords\n ', '__init__': <function ReactiqInput.__init__>, '__iter__': <function ReactiqInput.__iter__>, 'keywords': <property object>, 'values': <property object>, 'getValue': <function ReactiqInput.getValue>, 'setValue': <function ReactiqInput.setValue>, '__getitem__': <function ReactiqInput.getValue>, '__setitem__': <function ReactiqInput.setValue>, 'setValues': <function ReactiqInput.setValues>, 'getJaguarValue': <function ReactiqInput.getJaguarValue>, 'setJaguarValue': <function ReactiqInput.setJaguarValue>, 'setJaguarValues': <function ReactiqInput.setJaguarValues>, 'getJaguarNonDefault': <function ReactiqInput.getJaguarNonDefault>, '_addAutoTSJaguarDefaults': <function ReactiqInput._addAutoTSJaguarDefaults>, 'resetKey': <function ReactiqInput.resetKey>, 'resetAll': <function ReactiqInput.resetAll>, 'getDefault': <function ReactiqInput.getDefault>, 'getNonDefaultKeys': <function ReactiqInput.getNonDefaultKeys>, 'getNonDefaultJaguarKeys': <function ReactiqInput.getNonDefaultJaguarKeys>, 'isNonDefault': <function ReactiqInput.isNonDefault>, 'getReactants': <function ReactiqInput.getReactants>, 'getProducts': <function ReactiqInput.getProducts>, 'getReactantComplex': <function ReactiqInput.getReactantComplex>, 'getProductComplex': <function ReactiqInput.getProductComplex>, 'getReferenceReactantComplex': <function ReactiqInput.getReferenceReactantComplex>, 'getReferenceProductComplex': <function ReactiqInput.getReferenceProductComplex>, 'setConstraints': <function ReactiqInput.setConstraints>, 'getConstraints': <function ReactiqInput.getConstraints>, 'validate': <function ReactiqInput.validate>, 'validate_jaguar_keywords': <function ReactiqInput.validate_jaguar_keywords>, 'validate_constraints': <function ReactiqInput.validate_constraints>, 'validate_structures': <function ReactiqInput.validate_structures>, 'save': <function ReactiqInput.save>, 'setConstants': <function ReactiqInput.setConstants>, 'setJobname': <function ReactiqInput.setJobname>, 'read': <function ReactiqInput.read>, 'set_default_template_file': <function ReactiqInput.set_default_template_file>, 'remove_input_file_paths': <function ReactiqInput.remove_input_file_paths>, 'update_input_file_paths': <function ReactiqInput.update_input_file_paths>, 'get_input_files': <function ReactiqInput.get_input_files>, '_parse_keyword_line': <function ReactiqInput._parse_keyword_line>, '_parse_constraint_line': <function ReactiqInput._parse_constraint_line>, '__dict__': <attribute '__dict__' of 'ReactiqInput' objects>, '__weakref__': <attribute '__weakref__' of 'ReactiqInput' objects>})

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.application.jaguar.reactiq_input'

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)

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.