RDKit::RxnOps Namespace Reference

Enumerations
enum	SanitizeRxnFlags {   SANITIZE_NONE = 0x0 , SANITIZE_RGROUP_NAMES = 0x1 , SANITIZE_ATOM_MAPS = 0x2 , SANITIZE_ADJUST_REACTANTS = 0x4 ,   SANITIZE_MERGEHS = 0x8 , SANITIZE_ADJUST_PRODUCTS = 0x10 , SANITIZE_ALL = 0xFFFFFFFF }

Functions
RDKIT_CHEMREACTIONS_EXPORT void	fixRGroups (ChemicalReaction &rxn)
RDKIT_CHEMREACTIONS_EXPORT void	fixAtomMaps (ChemicalReaction &rxn)
RDKIT_CHEMREACTIONS_EXPORT void	adjustTemplates (const MOL_SPTR_VECT &templates, const MolOps::AdjustQueryParameters &params)
	Adjusts the reactant templates to properly match reagents.
RDKIT_CHEMREACTIONS_EXPORT void	fixHs (ChemicalReaction &rxn)
	merge query Hs if appropriate
const MolOps::AdjustQueryParameters	DefaultRxnAdjustParams ()
const MolOps::AdjustQueryParameters	ChemDrawRxnAdjustParams ()
const MolOps::AdjustQueryParameters	MatchOnlyAtRgroupsAdjustParams ()
RDKIT_CHEMREACTIONS_EXPORT void	sanitizeRxn (ChemicalReaction &rxn, unsigned int &operationsThatFailed, unsigned int sanitizeOps=SANITIZE_ALL, const MolOps::AdjustQueryParameters &params=DefaultRxnAdjustParams())
	carries out a collection of tasks for cleaning up a reaction and ensuring that it makes "chemical sense" in the context of RDKit reacitons
RDKIT_CHEMREACTIONS_EXPORT void	sanitizeRxn (ChemicalReaction &rxn, const MolOps::AdjustQueryParameters &params=DefaultRxnAdjustParams())
	This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
RDKIT_CHEMREACTIONS_EXPORT void	sanitizeRxnAsMols (ChemicalReaction &rxn, unsigned int sanitizeOps=MolOps::SanitizeFlags::SANITIZE_ALL)

Enumeration Type Documentation

SanitizeRxnFlags

enum RDKit::RxnOps::SanitizeRxnFlags

Enumerator
SANITIZE_NONE
SANITIZE_RGROUP_NAMES
SANITIZE_ATOM_MAPS
SANITIZE_ADJUST_REACTANTS
SANITIZE_MERGEHS
SANITIZE_ADJUST_PRODUCTS
SANITIZE_ALL

Definition at line 115 of file SanitizeRxn.h.

Function Documentation

adjustTemplates()

RDKIT_CHEMREACTIONS_EXPORT void RDKit::RxnOps::adjustTemplates	(	const MOL_SPTR_VECT &	templates,
		const MolOps::AdjustQueryParameters &	params )

Adjusts the reactant templates to properly match reagents.

References adjustTemplates().

Referenced by adjustTemplates().

ChemDrawRxnAdjustParams()

const MolOps::AdjustQueryParameters RDKit::RxnOps::ChemDrawRxnAdjustParams ( )

inline

Definition at line 90 of file SanitizeRxn.h.

References RDKit::MolOps::AdjustQueryParameters::adjustDegree, RDKit::MolOps::AdjustQueryParameters::adjustDegreeFlags, RDKit::MolOps::AdjustQueryParameters::adjustRingCount, RDKit::MolOps::AdjustQueryParameters::adjustRingCountFlags, RDKit::MolOps::AdjustQueryParameters::aromatizeIfPossible, BOOST_LOG, ChemDrawRxnAdjustParams(), RDKit::MolOps::AdjustQueryParameters::makeDummiesQueries, and rdWarningLog.

Referenced by ChemDrawRxnAdjustParams().

DefaultRxnAdjustParams()

const MolOps::AdjustQueryParameters RDKit::RxnOps::DefaultRxnAdjustParams ( )

inline

Definition at line 76 of file SanitizeRxn.h.

References RDKit::MolOps::AdjustQueryParameters::adjustDegree, RDKit::MolOps::AdjustQueryParameters::adjustDegreeFlags, RDKit::MolOps::AdjustQueryParameters::adjustRingCount, RDKit::MolOps::AdjustQueryParameters::adjustRingCountFlags, RDKit::MolOps::AdjustQueryParameters::aromatizeIfPossible, DefaultRxnAdjustParams(), and RDKit::MolOps::AdjustQueryParameters::makeDummiesQueries.

Referenced by DefaultRxnAdjustParams(), sanitizeRxn(), and sanitizeRxn().

fixAtomMaps()

RDKIT_CHEMREACTIONS_EXPORT void RDKit::RxnOps::fixAtomMaps

(

ChemicalReaction &

rxn

)

If atom maps are not defined on rgroups, attempt to deduce them from the RGroup labels, or add new ones if possible.

References fixAtomMaps().

Referenced by fixAtomMaps().

fixHs()

RDKIT_CHEMREACTIONS_EXPORT void RDKit::RxnOps::fixHs

(

ChemicalReaction &

rxn

)

merge query Hs if appropriate

References fixHs().

Referenced by fixHs().

fixRGroups()

RDKIT_CHEMREACTIONS_EXPORT void RDKit::RxnOps::fixRGroups

(

ChemicalReaction &

rxn

)

Any dummy atom with a map but no RGroup label, should be an RGroup in RDKit's view of a reaction. See if these atoms can be salvaged into RGroups.

References fixRGroups().

Referenced by fixRGroups().

MatchOnlyAtRgroupsAdjustParams()

const MolOps::AdjustQueryParameters RDKit::RxnOps::MatchOnlyAtRgroupsAdjustParams ( )

inline

Definition at line 104 of file SanitizeRxn.h.

References RDKit::MolOps::AdjustQueryParameters::adjustDegree, RDKit::MolOps::AdjustQueryParameters::adjustDegreeFlags, RDKit::MolOps::AdjustQueryParameters::adjustRingCount, RDKit::MolOps::AdjustQueryParameters::adjustRingCountFlags, RDKit::MolOps::AdjustQueryParameters::aromatizeIfPossible, RDKit::MolOps::AdjustQueryParameters::makeDummiesQueries, and MatchOnlyAtRgroupsAdjustParams().

Referenced by MatchOnlyAtRgroupsAdjustParams().

sanitizeRxn() [1/2]

RDKIT_CHEMREACTIONS_EXPORT void RDKit::RxnOps::sanitizeRxn	(	ChemicalReaction &	rxn,
		const MolOps::AdjustQueryParameters &	params = DefaultRxnAdjustParams() )

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

References DefaultRxnAdjustParams(), and sanitizeRxn().

sanitizeRxn() [2/2]

RDKIT_CHEMREACTIONS_EXPORT void RDKit::RxnOps::sanitizeRxn	(	ChemicalReaction &	rxn,
		unsigned int &	operationsThatFailed,
		unsigned int	sanitizeOps = SANITIZE_ALL,
		const MolOps::AdjustQueryParameters &	params = DefaultRxnAdjustParams() )

carries out a collection of tasks for cleaning up a reaction and ensuring that it makes "chemical sense" in the context of RDKit reacitons

This functions calls the following in sequence

1. RxnOps::fixRGroups()
2. RxnOps::fixupAtomMaps()
3. RxnOps::fixupTemplateAromaticity()
4. RxnOps::mergeHs()

Parameters

rxn	: the ChemicalReaction to be cleaned
operationThatFailed	: the first (if any) sanitization operation that fails is set here. The values are taken from the SanitizeFlags enum. On success, the value is SanitizeFlags::SANITIZE_NONE
sanitizeOps	: the bits here are used to set which sanitization operations are carried out. The elements of the SanitizeFlags enum define the operations.

Notes:

• This attempts to fix known issues with certain reaction drawers. HOWEVER, if any flag is returned in operationsPerformed, the reaction may still be suspect to its validity.
• Aromaticity can be tricky when starting with Kekule structures that have query features, aromaticity works well for non-query rings, however certain structures (substitutions on Kekule rings that should really be aromatic) may not have enough information.

References DefaultRxnAdjustParams(), and sanitizeRxn().

Referenced by sanitizeRxn(), and sanitizeRxn().

sanitizeRxnAsMols()

RDKIT_CHEMREACTIONS_EXPORT void RDKit::RxnOps::sanitizeRxnAsMols	(	ChemicalReaction &	rxn,
		unsigned int	sanitizeOps = MolOps::SanitizeFlags::SANITIZE_ALL )

Does the usual molecular sanitization on each reactant, agent, and product of the reaction

References sanitizeRxnAsMols().

Referenced by sanitizeRxnAsMols().