1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
|
//
// 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
|
