MolFileStereochem.h

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//
//  Copyright (C) 2004-2023 Greg Landrum and other RDKit contributors
//
//   @@ All Rights Reserved @@
//  This file is part of the RDKit.
//  The contents are covered by the terms of the BSD license
//  which is included in the file license.txt, found at the root
//  of the RDKit source tree.
//
#include <RDGeneral/export.h>
#ifndef RD_MOL_FILE_STEREOCHEM_H
#define RD_MOL_FILE_STEREOCHEM_H
 
#include <GraphMol/RDKitBase.h>
#include <GraphMol/Chirality.h>
 
namespace RDKit {
//! deprecated, please use MolOps::assignChiralTypesFromBondDirs instead
RDKIT_FILEPARSERS_EXPORT void DetectAtomStereoChemistry(RWMol &mol,
                                                        const Conformer *conf);
//! deprecated, please use MolOps::detectBondStereoChemistry instead
RDKIT_FILEPARSERS_EXPORT void DetectBondStereoChemistry(ROMol &mol,
                                                        const Conformer *conf);
 
//! \deprecated use Chirality::wedgeMolBonds instead
RDKIT_FILEPARSERS_EXPORT void WedgeMolBonds(ROMol &mol, const Conformer *conf);
//! \deprecated use Chirality::wedgeBond instead
RDKIT_FILEPARSERS_EXPORT void WedgeBond(Bond *bond, unsigned int fromAtomIdx,
                                        const Conformer *conf);
 
struct RDKIT_FILEPARSERS_EXPORT StereoBondThresholds {
  const static unsigned DBL_BOND_NO_STEREO =
      1000;  //!< neighboring double bond without stereo info
  const static unsigned DBL_BOND_SPECIFIED_STEREO =
      10000;  //!< neighboring double bond with stereo specified
  const static unsigned CHIRAL_ATOM =
      100000;  //!< atom with specified chirality
  const static unsigned DIRECTION_SET =
      1000000;  //!< single bond with the direction already set
};
//! set wavy bonds around double bonds with STEREOANY stereo
/*!
 \param mol molecule to be modified
 \param clearDoubleBondFlags when this is true flags for unknown double bond
   stereo will also be removed.
 \param addWhenImpossible if nonzero a neighboring single bond will be made
 wavy even if it connects to a chiral center or double bond with specified
 stereo. one example of this would be the middle double bond in
 C/C=C/C=C/C=C/C (if that's set to STEREOANY after constructing the molecule)
 Otherwise, no wavy bond will be set
*/
RDKIT_FILEPARSERS_EXPORT void addWavyBondsForStereoAny(
    ROMol &mol, bool clearDoubleBondFlags = true,
    unsigned addWhenImpossible = StereoBondThresholds::DBL_BOND_NO_STEREO);
 
//! \deprecated, please use MolOps::clearSingleBondDirFlags instead
RDKIT_FILEPARSERS_EXPORT void ClearSingleBondDirFlags(ROMol &mol);
//! \deprecated use Chirality::detail::determineBondWedgeState instead
RDKIT_FILEPARSERS_EXPORT Bond::BondDir DetermineBondWedgeState(
    const Bond *bond, unsigned int fromAtomIdx, const Conformer *conf);
//! \deprecated use Chirality::detail::determineBondWedgeState instead
RDKIT_FILEPARSERS_EXPORT Bond::BondDir DetermineBondWedgeState(
    const Bond *bond,
    const std::map<int, std::unique_ptr<RDKit::Chirality::WedgeInfoBase>>
        &wedgeBonds,
    const Conformer *conf);
 
//! \deprecated use Chirality::reapplyMolBlockWedging instead
RDKIT_FILEPARSERS_EXPORT void reapplyMolBlockWedging(ROMol &mol);
//! \deprecated use Chirality::clearMolBlockWedgingInfo instead
RDKIT_FILEPARSERS_EXPORT void clearMolBlockWedgingInfo(ROMol &mol);
//! \deprecated use Chirality::invertMolBlockWedgingInfo instead
RDKIT_FILEPARSERS_EXPORT void invertMolBlockWedgingInfo(ROMol &mol);
 
//! Set double bonds with unspecified stereo to STEREOANY and add wavy bonds
//! to
///  potential stereocenters with unspecified chirality
RDKIT_FILEPARSERS_EXPORT void markUnspecifiedStereoAsUnknown(ROMol &mol,
                                                             int confId = -1);
 
//! generate enhanced stereo groups based on the status of the chiral flag
/// property
/*
 \param mol: molecule to be modified
 \param zeroFlagGroupType: how to handle non-grouped stereo centers when the
        chiral flag is set to zero
 
  If the chiral flag is set to a value of 1 then all specified tetrahedral
  chiral centers which are not already in StereoGroups will be added to an
  ABS StereoGroup.
 
  If the chiral flag is set to a value of 0 then all specified tetrahedral
  chiral centers will be added to a StereoGroup of the type zeroFlagGroupType
 
  If there is no chiral flag set (i.e. the property is not present), the
  molecule will not be modified.
 
*/
RDKIT_FILEPARSERS_EXPORT void translateChiralFlagToStereoGroups(
    ROMol &mol,
    StereoGroupType zeroFlagGroupType = StereoGroupType::STEREO_AND);
 
}  // namespace RDKit
#endif