schrodinger.application.jaguar.hydrokinetic_input module

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

class schrodinger.application.jaguar.hydrokinetic_input.HydrokineticInput(inputfile=None, keywords=None, jaguar_keywords=None, jobname=None, add_hydrokinetic_jaguar_defaults=False)

Bases: schrodinger.application.jaguar.workflow_input.WorkflowInput

A class to completely specify a Hydrokinetic calculation.

Example usage:

input = HydrokineticInput() input.setValue(‘integerKW’, 3) input.setValue(‘floatKW’, ‘7.0’) input.setValue(‘stringKW’, ‘foo’)

for keyword in input:

print “keyword ‘%s’ has value %s” % (keyword, input[keyword])

try:

input[‘mykeyword’] = ‘value’

except WorkflowKeywordException as e:

print e.allowed_keywords

input_file_keys = ['input']

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

Create a HydrokineticInput 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 Hydrokinetic input file

• keywords (dict) – Hydrokinetic 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_hydrokinetic_jaguar_defaults (boolean) – if True add some custom Jaguar defaults

generate_keywords()

Initialize dictionary of all possible Hydrokinetic keywords

setJaguarValues(keywords)

Set multiple Jaguar &gen section keywords.

Parameters

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

getInputMolecule(clean_st: bool = False) → schrodinger.structure._structure.Structure

Return list of input molecules. If no file(s) found, return empty list.

Parameters

clean_st (bool) – if True redefine bonding using mmlewis.

Returns

reactant Structures or file paths.

validate()

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

:raise WorkflowKeywordConflictError if conflicting values found :raise WorkflowConservationError if matter not conserved :raise JaguarUnsupportedBasisSet: if basis is not supported

validate_jaguar_keywords(strs)

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

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 Hydrokinetic input file. Any keywords specified in the input file will override existing values in this HydrokineticInput 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 Hydrokinetic 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.

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: str)

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

Parameters

keyword – name of keyword

:raise WorkflowKeywordError if no keyword found

getFrozenAtoms() → Dict[str, List[schrodinger.application.jaguar.autots_bonding.Coordinate]]

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() → Dict[str, Any]

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

getJaguarValue(key: str) → Any

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

Parameters

key – name of keyword

getNonDefaultKeys()

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

getValue(keyword: str)

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

Parameters

keyword – name of keyword

:raise WorkflowKeywordError if no keyword found

get_input_files() → Set[str]

Return set of expected input files.

have_constraints() → bool

Do we have internal coordinate constraints

have_frozen_atoms() → bool

Do we have frozen atom constraints

isNonDefault(keyword: str) → bool

Has the specified keyword been set to a non-default value?

Parameters

keyword – The key to check

Returns

True if the specified keyword is set to a non-default value. False otherwise.

property keywords

resetAll()

Reset all keywords to their default states.

resetKey(keyword: str)

Reset keyword to default state.

Parameters

keyword – name of keyword

save(name: str)

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 – Path to a Workflow input file

setConstraints(constraints: Dict[str, List[schrodinger.application.jaguar.autots_bonding.Coordinate]])

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: Dict[str, List[schrodinger.application.jaguar.autots_bonding.Coordinate]])

Set the constraints.

Parameters

frozen_atoms – dictionary relating structure title to a list of Coordinate instances which define the frozen atoms

setJaguarValue(key: str, value: Any)

Set the Jaguar &gen section keyword ‘key’ to value ‘value’.

Parameters

• key – name of keyword

• value – value of keyword

:raise JaguarKeywordException if keyword is invalid

setValue(keyword: str, value: Any)

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

Parameters

• keyword – name of keyword

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

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

property values

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

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

workflow_name = 'Workflow'

schrodinger.application.jaguar.hydrokinetic_input.users_default_template_filename()

Returns the name of the users template file that should be found in .schrodinger/hydrokinetic_templates. The file may or may not exist.

schrodinger.application.jaguar.hydrokinetic_input.create_autots_template_file(hinp, autots_kwds, fname='hydrokinetic_template.in')

Create AutoTS template file for use in Hydrokinetic from HydrokineticInput.

Parameters

• hinp (HydrokineticInput) – HydrokineticInput instance containing keywords for AutoTS

• autots_kwds (dict) – AutoTS workflow keywords to use

• fname (str) – filename to use for AutoTS template file