RDKit
Open-source cheminformatics and machine learning.
MolFileStereochem.h
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1 //
2 // Copyright (C) 2004-2021 Greg Landrum and other RDKit contributors
3 //
4 // @@ All Rights Reserved @@
5 // This file is part of the RDKit.
6 // The contents are covered by the terms of the BSD license
7 // which is included in the file license.txt, found at the root
8 // of the RDKit source tree.
9 //
10 #include <RDGeneral/export.h>
11 #ifndef RD_MOL_FILE_STEREOCHEM_H
12 #define RD_MOL_FILE_STEREOCHEM_H
13 
14 #include <GraphMol/RDKitBase.h>
15 
16 namespace RDKit {
17 //! deprecated, please use MolOps::assignChiralTypesFromBondDirs instead
19  const Conformer *conf);
20 //! deprecated, please use MolOps::detectBondStereoChemistry instead
22  const Conformer *conf);
24 RDKIT_FILEPARSERS_EXPORT void WedgeBond(Bond *bond, unsigned int fromAtomIdx,
25  const Conformer *conf);
27  const static unsigned DBL_BOND_NO_STEREO =
28  1000; //!< neighboring double bond without stereo info
29  const static unsigned DBL_BOND_SPECIFIED_STEREO =
30  10000; //!< neighboring double bond with stereo specified
31  const static unsigned CHIRAL_ATOM =
32  100000; //!< atom with specified chirality
33  const static unsigned DIRECTION_SET =
34  1000000; //!< single bond with the direction already set
35 };
36 //! set wavy bonds around double bonds with STEREOANY stereo
37 /*!
38  \param mol molecule to be modified
39  \param clearDoubleBondFlags when this is true flags for unknown double bond
40  stereo will also be removed.
41  \param addWhenImpossible if nonzero a neighboring single bond will be made wavy
42  even if it connects to a chiral center or double bond with specified stereo.
43  one example of this would be the middle double bond in C/C=C/C=C/C=C/C (if
44  that's set to STEREOANY after constructing the molecule) Otherwise, no wavy
45  bond will be set
46 */
48  ROMol &mol, bool clearDoubleBondFlags = true,
49  unsigned addWhenImpossible = StereoBondThresholds::DBL_BOND_NO_STEREO);
50 
51 //! picks the bonds which should be wedged
52 /// \returns a map from bond idx -> controlling atom idx
56  const Bond *bond, unsigned int fromAtomIdx, const Conformer *conf);
58  const Bond *bond, const INT_MAP_INT &wedgeBonds, const Conformer *conf);
59 } // namespace RDKit
60 #endif
pulls in the core RDKit functionality
class for representing a bond
Definition: Bond.h:46
BondDir
the bond's direction (for chirality)
Definition: Bond.h:82
The class for representing 2D or 3D conformation of a molecule.
Definition: Conformer.h:45
RWMol is a molecule class that is intended to be edited.
Definition: RWMol.h:32
#define RDKIT_FILEPARSERS_EXPORT
Definition: export.h:153
Std stuff.
Definition: Abbreviations.h:18
RDKIT_FILEPARSERS_EXPORT INT_MAP_INT pickBondsToWedge(const ROMol &mol)
RDKIT_FILEPARSERS_EXPORT void DetectBondStereoChemistry(ROMol &mol, const Conformer *conf)
deprecated, please use MolOps::detectBondStereoChemistry instead
std::map< int, int > INT_MAP_INT
Definition: types.h:312
RDKIT_FILEPARSERS_EXPORT void WedgeMolBonds(ROMol &mol, const Conformer *conf)
RDKIT_FILEPARSERS_EXPORT Bond::BondDir DetermineBondWedgeState(const Bond *bond, unsigned int fromAtomIdx, const Conformer *conf)
RDKIT_FILEPARSERS_EXPORT void ClearSingleBondDirFlags(ROMol &mol)
RDKIT_FILEPARSERS_EXPORT void WedgeBond(Bond *bond, unsigned int fromAtomIdx, const Conformer *conf)
RDKIT_FILEPARSERS_EXPORT void DetectAtomStereoChemistry(RWMol &mol, const Conformer *conf)
deprecated, please use MolOps::assignChiralTypesFromBondDirs instead
RDKIT_FILEPARSERS_EXPORT void addWavyBondsForStereoAny(ROMol &mol, bool clearDoubleBondFlags=true, unsigned addWhenImpossible=StereoBondThresholds::DBL_BOND_NO_STEREO)
set wavy bonds around double bonds with STEREOANY stereo
static const unsigned DBL_BOND_NO_STEREO
neighboring double bond without stereo info