schrodinger.application.jaguar.workflow_validation module

Workflow keywords input validation and specialized Exceptions

exception schrodinger.application.jaguar.workflow_validation.WorkflowKeywordException

Bases: schrodinger.application.jaguar.exceptions.JaguarUserFacingException

Base exception class for all custom Workflow keyword validation errors

exception schrodinger.application.jaguar.workflow_validation.WorkflowConservationError

Bases: schrodinger.application.jaguar.exceptions.JaguarUserFacingException

Runtime error due to a failure to conserve something

exception schrodinger.application.jaguar.workflow_validation.WorkflowKeywordError(keyword: str, allowed_keywords: List)

Bases: schrodinger.application.jaguar.workflow_validation.WorkflowKeywordException

Exception class raised when nonexistent Workflow keyword is requested

__init__(keyword: str, allowed_keywords: List)
Parameters

  • keyword – input keyword

  • allowed_keywords – list of allowed keywords

exception schrodinger.application.jaguar.workflow_validation.WorkflowKeywordValueTypeError(keyword: str, value, valid_type: Type)

Bases: schrodinger.application.jaguar.workflow_validation.WorkflowKeywordException

Exception class raised when Workflow keyword value has wrong type

__init__(keyword: str, value, valid_type: Type)
Parameters

  • keyword – input keyword

  • value – input value

  • valid_type – types as documented in the appropriate *_keywords.py file

exception schrodinger.application.jaguar.workflow_validation.WorkflowKeywordValueError(keyword: str, value, choices: List)

Bases: schrodinger.application.jaguar.workflow_validation.WorkflowKeywordException

Exception class raised when Workflow keyword value is invalid

__init__(keyword: str, value, choices: List)
Parameters

  • keyword – input keyword

  • value – input value

  • choices – valid choices associated with a keyword

exception schrodinger.application.jaguar.workflow_validation.WorkflowKeywordConflictError(mykey: Optional[str] = None, key: Optional[str] = None, value=None, msg: Optional[str] = None)

Bases: schrodinger.application.jaguar.workflow_validation.WorkflowKeywordException

Exception class raised when Workflow keywords have conflicting values

__init__(mykey: Optional[str] = None, key: Optional[str] = None, value=None, msg: Optional[str] = None)
Parameters

  • mykey – keyword name

  • key – required keyword name

  • value – required keyword value

  • msg – generic message to override template

exception schrodinger.application.jaguar.workflow_validation.WorkflowKeywordFormatError(token: str)

Bases: schrodinger.application.jaguar.workflow_validation.WorkflowKeywordException

Exception class raised when a string not in the keyword=value format is found

__init__(token: str)
Parameters

token – The token that violates the keyword=value format

exception schrodinger.application.jaguar.workflow_validation.ConstraintFormatError(token: str)

Bases: schrodinger.application.jaguar.exceptions.JaguarUserFacingException

Exception class raised when a string does not have the correct number of fields for a constraint

__init__(token: str)
Parameters

token – The token that violates the format

exception schrodinger.application.jaguar.workflow_validation.JaguarKeywordConflict

Bases: schrodinger.application.jaguar.workflow_validation.WorkflowKeywordException

Exception class raised when a Jaguar keyword is set that we wish to prevent in this workflow

schrodinger.application.jaguar.workflow_validation.raise_voluptuous_exception(exception: Exception, kwd: schrodinger.application.jaguar.workflow_keywords.WorkflowKeyword)

Re-raise voluptuous Exceptions as WorkflowKeywordException’s

schrodinger.application.jaguar.workflow_validation.estate_is_physical(structures: Union[schrodinger.structure._structure.Structure, Iterable[schrodinger.structure._structure.Structure]], charge: int, mult: int)

Check whether the requested electronic state is plausible. This is done by ensuring the number of electrons is consistent with the requested charge/multiplicity. Raises a WorkflowConservationError

Parameters

  • structures – the reactants or reactant complex

  • charge – overall charge

  • mult – overall spin multiplicity

Raises

WorkflowConservationError –

schrodinger.application.jaguar.workflow_validation.charge_is_consistent(structures: Union[schrodinger.structure._structure.Structure, Iterable[schrodinger.structure._structure.Structure]], charge: int)

Tests that the sum of molecular charges is consistent with the total charge. raises WorkflowConservationError if this criterion is not satisfied.

Parameters

  • structures – reactant or product structure(s) to check

  • charge – overall charge of reaction

schrodinger.application.jaguar.workflow_validation.basis_set_is_valid(structures: Union[schrodinger.structure._structure.Structure, Iterable[schrodinger.structure._structure.Structure]], basis: str)

Checks that the given basis set is defined for all atoms in the structures. A JaguarUnsupportedBasisSet is raised if the basis is not supported.

Parameters

  • structures – structures to check

  • basis – name of basis set

schrodinger.application.jaguar.workflow_validation.valid_smarts(smarts: str)

Checks that the given SMARTS is valid

Parameters

smarts – SMARTS string to check

schrodinger.application.jaguar.workflow_validation.validate_charges(st: schrodinger.structure._structure.Structure, charge: Optional[int] = None, mult: Optional[int] = None) → Tuple[int, int]

Validate the charge and multiplicity for a structure. If charge is not specified, the total charge of the structure is used. If multiplicity is not specified, it is calculated based on the number of electrons and the charge.

Parameters

  • st – structure instance

  • charge – structure total charge

  • mult – specified multiplicity

Raise

WorkflowConservationError if the specification is invalid.