schrodinger.application.jaguar.reactiq_validation module

Reactiq keywords input validation and specialized Exceptions

exception schrodinger.application.jaguar.reactiq_validation.ReactiqConservationError

Bases: schrodinger.application.jaguar.exceptions.JaguarUserFacingException

Runtime error due to a failure to conserve matter

exception schrodinger.application.jaguar.reactiq_validation.ReactiqKeywordConflictError(mykey, key, value)

Bases: schrodinger.application.jaguar.reactiq_validation.ReactiqKeywordException

Exception class raised when Reactiq keywords have conflicting values

exception schrodinger.application.jaguar.reactiq_validation.ReactiqKeywordError(keyword, allowed_keywords)

Bases: schrodinger.application.jaguar.reactiq_validation.ReactiqKeywordException

Exception class raised when nonexistant Reactiq keyword is requested

exception schrodinger.application.jaguar.reactiq_validation.ReactiqKeywordException

Bases: schrodinger.application.jaguar.exceptions.JaguarUserFacingException

Base exception class for all custom Reactiq keyword validation errors

exception schrodinger.application.jaguar.reactiq_validation.ReactiqKeywordFormatError(token)

Bases: schrodinger.application.jaguar.reactiq_validation.ReactiqKeywordException

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

exception schrodinger.application.jaguar.reactiq_validation.ReactiqKeywordValueError(keyword, value, choices)

Bases: schrodinger.application.jaguar.reactiq_validation.ReactiqKeywordException

Exception class raised when Reactiq keyword value is invalid

exception schrodinger.application.jaguar.reactiq_validation.ReactiqKeywordValueTypeError(keyword, value, valid_type)

Bases: schrodinger.application.jaguar.reactiq_validation.ReactiqKeywordException

Exception class raised when Reactiq keyword value has wrong type

schrodinger.application.jaguar.reactiq_validation.charge_is_conserved(reactants, products)

Check the input structures to ensure that charge is conserved. If charge is not conserved a ReactiqConservationError is raised.

Parameters:
  • reactants (Structure object or iterable of Structure objects) – the reactants or reactant complex
  • products (Structure object or iterable of Structure objects) – the reactants or reactant complex
Return type:

bool
Returns:

whether or not matter is conserved
schrodinger.application.jaguar.reactiq_validation.charge_is_consistent(strs, charge)

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

Parameters:
  • strs (Structure or iterable of Structure objects) – reactant or product structure(s) to check
  • charge (int) – overall charge of reaction
schrodinger.application.jaguar.reactiq_validation.check_conflicts(kwd, all_keywords)

Raise Exception if keyword value is inconsistent with the other keywords. This is done in an adhoc case-by-case way.

Parameters:
  • kwd (ReactiqKeyword) – reference Reactiq keyword
  • all_keywords (dict of ReactiqKeyword instances indexed by name) – all the other Reactiq keywords set

:raise ReactiqKeywordConflictError if conflicting values found.

schrodinger.application.jaguar.reactiq_validation.estate_is_physical(strs, charge, mult)

Check whether or not the requested electronic state is plausible. This is done by ensuring the number of electrons is consistent with the requested charge/multiplicity. Raises a ReactiqConservationError

Parameters:
  • strs (Structure object or iterable of Structure objects) – the reactants or reactant complex
  • charge (int) – overall charge
schrodinger.application.jaguar.reactiq_validation.matter_is_conserved(reactants, products)

Check the input structures to ensure that matter is conserved. If matter is not conserved a ReactiqConservationError is raised.

Parameters:
  • reactants (Structure object or iterable of Structure objects) – the reactants or reactant complex
  • products (Structure object or iterable of Structure objects) – the reactants or reactant complex
Return type:

bool
Returns:

whether or not matter is conserved
schrodinger.application.jaguar.reactiq_validation.raise_voluptuous_exception(exception, kwd)

Re-raise voluptuous Exceptions as ReactiqKeywordException’s

schrodinger.application.jaguar.reactiq_validation.reaction_is_supported(reactants, products)

Check that the input reaction is supported, if not raise an UnsupportedReaction.