28 namespace MolStandardize {
43 : Name(name), Smarts(smarts), Charge(charge) {}
66 const std::vector<ChargeCorrection> ccs);
70 const std::vector<ChargeCorrection> ccs);
81 std::vector<ChargeCorrection> d_ccs;
83 std::pair<unsigned int, std::vector<unsigned int>> *strongestProtonated(
85 const std::vector<std::pair<ROMOL_SPTR, ROMOL_SPTR>> &abpairs);
86 std::pair<unsigned int, std::vector<unsigned int>> *weakestIonized(
88 const std::vector<std::pair<ROMOL_SPTR, ROMOL_SPTR>> &abpairs);
109 df_canonicalOrdering = canonicalOrdering;
117 bool df_canonicalOrdering =
true;
118 std::shared_ptr<ROMol> pos_h;
119 std::shared_ptr<ROMol> pos_noh;
120 std::shared_ptr<ROMol> neg;
121 std::shared_ptr<ROMol> neg_acid;
A Catalog with a hierarchical structure.
The reionizer class to fix charges and reionize a molecule such that the.
Reionizer(const std::string acidbaseFile, const std::vector< ChargeCorrection > ccs)
construct a Reionizer with a particular acidbaseFile and charge
ROMol * reionize(const ROMol &mol)
Enforce charges on certain atoms, then perform competitive reionization.
Reionizer(std::istream &acidbaseStream, const std::vector< ChargeCorrection > ccs)
construct a Reionizer with a particular acidbaseFile and charge
Reionizer & operator=(Reionizer const &)=delete
Reionizer(const std::string acidbaseFile)
construct a Reionizer with a particular acidbaseFile
Reionizer(const Reionizer &other)=delete
making Reionizer objects non-copyable
The Uncharger class for neutralizing ionized acids and bases.
Uncharger(const Uncharger &other)
ROMol * uncharge(const ROMol &mol)
Uncharger(bool canonicalOrdering)
#define RDKIT_MOLSTANDARDIZE_EXPORT
RDKIT_MOLSTANDARDIZE_EXPORT std::vector< ChargeCorrection > CHARGE_CORRECTIONS
RDKIT_MOLSTANDARDIZE_EXPORT const CleanupParameters defaultCleanupParameters
RDCatalog::HierarchCatalog< AcidBaseCatalogEntry, AcidBaseCatalogParams, int > AcidBaseCatalog
ChargeCorrection(std::string name, std::string smarts, int charge)