schrodinger.application.jaguar.autots_input module

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

schrodinger.application.jaguar.autots_input.read_mae_files(fhlist, fileonly, clean_st, reset_bonding=True)

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, cleanup structure file by removing dummy atoms, etc.

• reset_bonding (bool) – if True and clean_st is True, redefine bonding using mmjag.

Returns

Structures or file paths.

class schrodinger.application.jaguar.autots_input.AutoTSInput(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 AutoTS calculation.

Example usage:

input = AutoTSInput()
# 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 = ['reactant', 'product', 'reactant_complex', 'product_complex', 'reference_reactant_complex', 'reference_product_complex', 'template_database_file', 'full_path_file', 'spectators']

workflow_name = 'AutoTS'

__init__(inputfile=None, keywords=None, jaguar_keywords=None, jobname=None, add_autots_jaguar_defaults=False)

Create a AutoTSInput 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 AutoTS input file

• keywords (dict) – AutoTS 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

property reaction_smarts

Reaction smarts identifying input reaction

generate_keywords()

Initialize dictionary of all possible AutoTS keywords

setJaguarValues(keywords)

Set multiple Jaguar &gen section keywords.

Parameters

keywords (dict of string/anytype pairs) – Jaguar &gen section keyword/value pairs

updateJaguarUserKeywords(keywords)

Update the Jaguar &gen section keywords of the user-defined settings only if previous settings exist.

Parameters

keywords (dict of string/anytype pairs) – Jaguar &gen section keyword/value pairs

getReactants(fileonly=False, clean_st=False, reset_bonding=True)

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.

• reset_bonding (bool) – if True and clean_st is True, redefine bonding using mmjag.

Returns

reactant Structures or file paths.

getProducts(fileonly=False, clean_st=False, reset_bonding=True)

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.

• reset_bonding (bool) – if True and clean_st is True, redefine bonding using mmjag.

Returns

product Structures or file paths.

getReactantComplex(fileonly=False, clean_st=False, reset_bonding=True)

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.

• reset_bonding (bool) – if True and clean_st is True, redefine bonding using mmjag.

Returns

Reactant Complex Structures or file path.

getProductComplex(fileonly=False, clean_st=False, reset_bonding=True)

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.

• reset_bonding (bool) – if True and clean_st is True, redefine bonding using mmjag.

Returns

Product Complex Structures or file path.

getReferenceReactantComplex(fileonly=False, clean_st=False, reset_bonding=True)

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.

• reset_bonding (bool) – if True and clean_st is True, redefine bonding using mmjag.

Returns

Reactant Complex Structures or file path.

getReferenceProductComplex(fileonly=False, clean_st=False, reset_bonding=True)

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.

• reset_bonding (bool) – if True and clean_st is True, redefine bonding using mmjag.

Returns

Product Complex Structures or file path.

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.

validate()

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

:raise WorkflowKeywordConflictError if conflicting values found :raise WorkflowConservationError if matter not conserved

validate_jaguar_keywords(strs)

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

setConstants()

Set any constants defined by keywords

read(inputfile)

Read an existing AutoTS input file. Any keywords specified in the input file will override existing values in this AutoTSInput 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 AutoTS 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.

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.

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

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.

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

getNonDefaultKeys()

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

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

get_input_files()

Return set of expected input files.

have_constraints()

Do we have internal coordinate constraints

have_frozen_atoms()

Do we have frozen atom constraints

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.

property keywords

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 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

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

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

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

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 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

setValues(keywords)

Set multiple Workflow keywords.

Parameters

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

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.

property values

Support access to WorkflowKeyword values via attribute syntax. e.g.:

wi = WorkflowInput()
print wi.values.optimize   # print 'optimize' keyword value

schrodinger.application.jaguar.autots_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.