RDKit
Open-source cheminformatics and machine learning.
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MolFileStereochem.h
Go to the documentation of this file.
1//
2// Copyright (C) 2004-2023 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
16namespace RDKit {
17//! deprecated, please use MolOps::assignChiralTypesFromBondDirs instead
19 const Conformer *conf);
20//! deprecated, please use MolOps::detectBondStereoChemistry instead
22 const Conformer *conf);
23
24//! \deprecated use Chirality::wedgeMolBonds instead
26//! \deprecated use Chirality::wedgeBond instead
28 const Conformer *conf);
30 const static unsigned DBL_BOND_NO_STEREO =
31 1000; //!< neighboring double bond without stereo info
32 const static unsigned DBL_BOND_SPECIFIED_STEREO =
33 10000; //!< neighboring double bond with stereo specified
34 const static unsigned CHIRAL_ATOM =
35 100000; //!< atom with specified chirality
36 const static unsigned DIRECTION_SET =
37 1000000; //!< single bond with the direction already set
38};
39//! set wavy bonds around double bonds with STEREOANY stereo
40/*!
41 \param mol molecule to be modified
42 \param clearDoubleBondFlags when this is true flags for unknown double bond
43 stereo will also be removed.
44 \param addWhenImpossible if nonzero a neighboring single bond will be made wavy
45 even if it connects to a chiral center or double bond with specified stereo.
46 one example of this would be the middle double bond in C/C=C/C=C/C=C/C (if
47 that's set to STEREOANY after constructing the molecule) Otherwise, no wavy
48 bond will be set
49*/
51 ROMol &mol, bool clearDoubleBondFlags = true,
53
54//! \deprecated use Chirality::pickBondsToWedge instead
56//! \deprecated, please use MolOps::clearSingleBondDirFlags instead
58//! \deprecated use Chirality::detail::determineBondWedgeState instead
60 const Bond *bond, unsigned int fromAtomIdx, const Conformer *conf);
61//! \deprecated use Chirality::detail::determineBondWedgeState instead
63 const Bond *bond, const INT_MAP_INT &wedgeBonds, const Conformer *conf);
64//! Clears existing bond wedging and forces use of atom wedging from MolBlock.
65/*!
66 \param mol: molecule to have its wedges altered
67 */
69//! Remove MolBlock bond wedging information from molecule.
70/*!
71 \param mol: molecule to modify
72 */
74//! Invert bond wedging information read from a mol block (if present).
75/*!
76 \param mol: molecule to modify
77 */
79
80//! Set double bonds with unspecified stereo to STEREOANY and add wavy bonds to
81/// potential stereocenters with unspecified chirality
83 int confId = -1);
84
85//! generate enhanced stereo groups based on the status of the chiral flag
86/// property
87/*
88 \param mol: molecule to be modified
89 \param zeroFlagGroupType: how to handle non-grouped stereo centers when the
90 chiral flag is set to zero
91
92 If the chiral flag is set to a value of 1 then all specified tetrahedral
93 chiral centers which are not already in StereoGroups will be added to an
94 ABS StereoGroup.
95
96 If the chiral flag is set to a value of 0 then all specified tetrahedral
97 chiral centers will be added to a StereoGroup of the type zeroFlagGroupType
98
99 If there is no chiral flag set (i.e. the property is not present), the
100 molecule will not be modified.
101
102*/
104 ROMol &mol,
106
107} // namespace RDKit
108#endif
pulls in the core RDKit functionality
class for representing a bond
Definition Bond.h:47
BondDir
the bond's direction (for chirality)
Definition Bond.h:83
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:161
Std stuff.
RDKIT_FILEPARSERS_EXPORT void markUnspecifiedStereoAsUnknown(ROMol &mol, int confId=-1)
RDKIT_FILEPARSERS_EXPORT void translateChiralFlagToStereoGroups(ROMol &mol, StereoGroupType zeroFlagGroupType=StereoGroupType::STEREO_AND)
RDKIT_FILEPARSERS_EXPORT void invertMolBlockWedgingInfo(ROMol &mol)
Invert bond wedging information read from a mol block (if present).
RDKIT_FILEPARSERS_EXPORT INT_MAP_INT pickBondsToWedge(const ROMol &mol)
StereoGroupType
Definition StereoGroup.h:29
bool rdvalue_is(const RDValue_cast_t)
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:317
RDKIT_FILEPARSERS_EXPORT void clearMolBlockWedgingInfo(ROMol &mol)
Remove MolBlock bond wedging information from molecule.
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 reapplyMolBlockWedging(ROMol &mol)
Clears existing bond wedging and forces use of atom wedging from MolBlock.
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