schrodinger.application.jaguar.reactiq_validation module

Reactiq keywords input validation and specialized Exceptions

exception schrodinger.application.jaguar.reactiq_validation.AutoTSAtomClassConflict

Bases: schrodinger.application.jaguar.exceptions.JaguarUserFacingException

Runtime Error indicating there is a problem with the atom class definition

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

args
with_traceback()

Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

exception schrodinger.application.jaguar.reactiq_validation.AutoTSInvalidConstraintError

Bases: schrodinger.application.jaguar.exceptions.JaguarUserFacingException

An invalid constraint

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

args
with_traceback()

Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

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 WorkflowKeywordConflictError if conflicting values found.

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

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

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.validate_atom_classes(reactants, products)

Check the input structures to ensure that if atom classes are defined they are defined for an equal number of atoms in each class on each side of the reaction. This is required to be able to compute an atom map.

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 atom classes are valid

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.get_stoich_charge(sts)

Return the stoichiometry and charge of a list of structures or structure as a string

Parameters

sts (list of Structures or Structure instance) – structures to print stoichiometry and charges of

Return type

string

Returns

the stoichiometry and charge of the input structure(s)

schrodinger.application.jaguar.reactiq_validation.validate_jag_keys(jaguar_keywords)

raise an exception if tmpini, press, or pbf_after_pcm are keywords

Parameters

jaguar_keywords (dict) – key: value dict of jaguar keywords

schrodinger.application.jaguar.reactiq_validation.validate_constraints(rinp)

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.

Unless it’s an atomic constraint (frozen atom) in which case it’s the wild west

schrodinger.application.jaguar.reactiq_validation.validate_structures(rinp)

Perform a check to ensure that matter is conserved and that charge/multiplicity are consistent with structures.

A WorkflowConservationError is raised if any test fails.