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RDKit
Open-source cheminformatics and machine learning.
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Enumerations | |
enum | SanitizeRxnFlags { SANITIZE_NONE = 0x0, SANITIZE_RGROUP_NAMES = 0x1, SANITIZE_ATOM_MAPS = 0x2, SANITIZE_ADJUST_REACTANTS = 0x4, SANITIZE_MERGEHS = 0x8, SANITIZE_ALL = 0xFFFFFFFF } |
Enumerator | |
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SANITIZE_NONE | |
SANITIZE_RGROUP_NAMES | |
SANITIZE_ATOM_MAPS | |
SANITIZE_ADJUST_REACTANTS | |
SANITIZE_MERGEHS | |
SANITIZE_ALL |
Definition at line 113 of file SanitizeRxn.h.
RDKIT_CHEMREACTIONS_EXPORT void RDKit::RxnOps::adjustTemplates | ( | ChemicalReaction & | rxn, |
const MolOps::AdjustQueryParameters & | params | ||
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Adjusts the reactant templates to properly match reagents.
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inline |
Definition at line 88 of file SanitizeRxn.h.
References RDKit::MolOps::ADJUST_IGNOREDUMMIES, RDKit::MolOps::ADJUST_IGNORENONE, RDKit::MolOps::AdjustQueryParameters::adjustDegree, RDKit::MolOps::AdjustQueryParameters::adjustDegreeFlags, RDKit::MolOps::AdjustQueryParameters::adjustRingCount, RDKit::MolOps::AdjustQueryParameters::adjustRingCountFlags, RDKit::MolOps::AdjustQueryParameters::aromatizeIfPossible, BOOST_LOG, RDKit::MolOps::AdjustQueryParameters::makeDummiesQueries, and rdWarningLog.
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inline |
Definition at line 74 of file SanitizeRxn.h.
References RDKit::MolOps::ADJUST_IGNOREALL, RDKit::MolOps::AdjustQueryParameters::adjustDegree, RDKit::MolOps::AdjustQueryParameters::adjustDegreeFlags, RDKit::MolOps::AdjustQueryParameters::adjustRingCount, RDKit::MolOps::AdjustQueryParameters::adjustRingCountFlags, RDKit::MolOps::AdjustQueryParameters::aromatizeIfPossible, and RDKit::MolOps::AdjustQueryParameters::makeDummiesQueries.
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.
RDKIT_CHEMREACTIONS_EXPORT void RDKit::RxnOps::fixHs | ( | ChemicalReaction & | rxn | ) |
merge query Hs if appropriate
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.
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inline |
Definition at line 102 of file SanitizeRxn.h.
References RDKit::MolOps::ADJUST_IGNOREDUMMIES, RDKit::MolOps::ADJUST_IGNORENONE, RDKit::MolOps::AdjustQueryParameters::adjustDegree, RDKit::MolOps::AdjustQueryParameters::adjustDegreeFlags, RDKit::MolOps::AdjustQueryParameters::adjustRingCount, RDKit::MolOps::AdjustQueryParameters::adjustRingCountFlags, RDKit::MolOps::AdjustQueryParameters::aromatizeIfPossible, and RDKit::MolOps::AdjustQueryParameters::makeDummiesQueries.
RDKIT_CHEMREACTIONS_EXPORT void RDKit::RxnOps::sanitizeRxn | ( | ChemicalReaction & | rxn, |
const MolOps::AdjustQueryParameters & | params = DefaultRxnAdjustParams() |
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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 RDKit::RxnOps::sanitizeRxn | ( | ChemicalReaction & | rxn, |
unsigned int & | operationsThatFailed, | ||
unsigned int | sanitizeOps = SANITIZE_ALL , |
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const MolOps::AdjustQueryParameters & | params = DefaultRxnAdjustParams() |
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carries out a collection of tasks for cleaning up a reaction and
that it makes "chemical sense" in the context of RDKit reacitons
This functions calls the following in sequence
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: