16 #ifndef __RD_CHARGE_H__ 17 #define __RD_CHARGE_H__ 28 namespace MolStandardize {
43 : Name(name), Smarts(smarts), Charge(charge) {}
62 Reionizer(
const std::string acidbaseFile);
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_quat;
120 std::shared_ptr<ROMol> neg;
121 std::shared_ptr<ROMol> neg_acid;
RDKIT_MOLSTANDARDIZE_EXPORT const CleanupParameters defaultCleanupParameters
A Catalog with a hierarchical structure.
The reionizer class to fix charges and reionize a molecule such that the.
RDKIT_MOLSTANDARDIZE_EXPORT std::vector< ChargeCorrection > CHARGE_CORRECTIONS
RDKIT_MOLSTANDARDIZE_EXPORT RWMol * reionize(const RWMol *mol, const CleanupParameters ¶ms=defaultCleanupParameters)
Works the same as Reionizer().reionize(mol)
RDCatalog::HierarchCatalog< AcidBaseCatalogEntry, AcidBaseCatalogParams, int > AcidBaseCatalog
The Uncharger class for neutralizing ionized acids and bases.
Defines the CleanupParameters and some convenience functions.
Uncharger(bool canonicalOrdering)
#define RDKIT_MOLSTANDARDIZE_EXPORT
ChargeCorrection(std::string name, std::string smarts, int charge)