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//
// Copyright (C) 2008-2022 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.
//
/*! \file Chirality.h
*/
#include <RDGeneral/export.h>
#ifndef RD_CHIRALITY_20AUG2008_H
#define RD_CHIRALITY_20AUG2008_H
#include <RDGeneral/types.h>
#include <GraphMol/Bond.h>
#include <boost/dynamic_bitset.hpp>
#include <limits>
namespace RDKit {
class Atom;
class Bond;
class ROMol;
namespace Chirality {
//! double bond stereo will be ignored/removed for rings smaller than this:
constexpr unsigned int minRingSizeForDoubleBondStereo = 8;
constexpr auto nonTetrahedralStereoEnvVar = "RDK_ENABLE_NONTETRAHEDRAL_STEREO";
constexpr auto useLegacyStereoEnvVar = "RDK_USE_LEGACY_STEREO_PERCEPTION";
constexpr bool nonTetrahedralStereoDefaultVal =
true; //!< whether or not nontetrahedral stereo is perceived by default
constexpr bool useLegacyStereoDefaultVal =
true; //!< whether or not the legacy stereo perception code is used by
//!< default
RDKIT_GRAPHMOL_EXPORT extern void setAllowNontetrahedralChirality(bool val);
RDKIT_GRAPHMOL_EXPORT extern bool getAllowNontetrahedralChirality();
RDKIT_GRAPHMOL_EXPORT extern void setUseLegacyStereoPerception(bool val);
RDKIT_GRAPHMOL_EXPORT extern bool getUseLegacyStereoPerception();
RDKIT_GRAPHMOL_EXPORT extern bool
useLegacyStereoPerception; //!< Toggle usage of the legacy stereo
//!< perception code
RDKIT_GRAPHMOL_EXPORT extern bool
useLegacyStereoPerception; //!< Toggle usage of the legacy stereo
//!< perception code
/// @cond
/*!
\param mol the molecule to be altered
\param ranks used to return the set of ranks.
Should be at least mol.getNumAtoms() long.
<b>Notes:</b>
- All atoms gain a property common_properties::_CIPRank with their overall
CIP ranking.
*/
RDKIT_GRAPHMOL_EXPORT void assignAtomCIPRanks(const ROMol &mol,
UINT_VECT &ranks);
RDKIT_GRAPHMOL_EXPORT bool hasStereoBondDir(const Bond *bond);
/**
* Returns the first neighboring bond that can be found which has a stereo
* bond direction set. If no such bond can be found, it returns null. No
* checks are made to ensure there aren't any other conflicting directed bonds.
*/
RDKIT_GRAPHMOL_EXPORT const Bond *getNeighboringDirectedBond(const ROMol &mol,
const Atom *atom);
/**
* This just translates the labels, setting/translating StereoAtoms or the
* label is not the responsibility of this function. If the passed label is not
* E/Z, it will be returned unchanged.
*/
RDKIT_GRAPHMOL_EXPORT Bond::BondStereo translateEZLabelToCisTrans(
Bond::BondStereo label);
/// @endcond
enum class StereoType {
Unspecified,
Atom_Tetrahedral,
Atom_SquarePlanar,
Atom_TrigonalBipyramidal,
Atom_Octahedral,
Bond_Double, // single double bond and odd-numbered cumulenes
Bond_Cumulene_Even, // even-numbered cumulenes
Bond_Atropisomer
};
enum class StereoDescriptor { None, Tet_CW, Tet_CCW, Bond_Cis, Bond_Trans };
enum class StereoSpecified {
Unspecified, // no information provided
Specified,
Unknown // deliberately marked as unknown
};
struct RDKIT_GRAPHMOL_EXPORT StereoInfo {
// REVIEW: absolute stereo data member?
#ifdef _MSC_VER
static const unsigned NOATOM =
std::numeric_limits<unsigned>::max(); // used to mark missing atoms
#else
static const unsigned NOATOM; // used to mark missing atoms
#endif
StereoType type = StereoType::Unspecified;
StereoSpecified specified = StereoSpecified::Unspecified;
unsigned centeredOn = NOATOM;
StereoDescriptor descriptor = StereoDescriptor::None;
unsigned permutation = 0; // for the non-tetrahedral stereo cases
std::vector<unsigned> controllingAtoms; // all atoms around the atom or bond.
// Order is important
bool operator==(const StereoInfo &other) const {
return type == other.type && specified == other.specified &&
centeredOn == other.centeredOn && descriptor == other.descriptor &&
permutation == other.permutation &&
controllingAtoms == other.controllingAtoms;
}
bool operator!=(const StereoInfo &other) const { return !(*this == other); }
};
//! identifies potential stereoatoms and stereobonds in a molecule
/*!
Note that this function is still somewhat experimental and the API
and results may change in a future release.
\param mol the molecule to look for stereo in
\param cleanIt remove chirality/stereo specifications from atoms/bonds that
cannot be chiral/stereo
*/
RDKIT_GRAPHMOL_EXPORT std::vector<StereoInfo> findPotentialStereo(
ROMol &mol, bool cleanIt, bool flagPossible = true);
//! overload
RDKIT_GRAPHMOL_EXPORT std::vector<StereoInfo> findPotentialStereo(
const ROMol &mol);
//! removes atoms without specified chirality from stereo groups
RDKIT_GRAPHMOL_EXPORT void cleanupStereoGroups(ROMol &mol);
//! calls the approximate legacy code for assigning CIP labels
RDKIT_GRAPHMOL_EXPORT void assignLegacyCIPLabels(
ROMol &mol, bool flagPossibleStereoCenters = false);
/// @cond
namespace detail {
RDKIT_GRAPHMOL_EXPORT bool isAtomPotentialNontetrahedralCenter(
const Atom *atom);
RDKIT_GRAPHMOL_EXPORT bool isAtomPotentialTetrahedralCenter(const Atom *atom);
RDKIT_GRAPHMOL_EXPORT bool isAtomPotentialStereoAtom(const Atom *atom);
RDKIT_GRAPHMOL_EXPORT bool isBondPotentialStereoBond(const Bond *bond);
RDKIT_GRAPHMOL_EXPORT StereoInfo getStereoInfo(const Bond *bond);
RDKIT_GRAPHMOL_EXPORT StereoInfo getStereoInfo(const Atom *atom);
RDKIT_GRAPHMOL_EXPORT bool bondAffectsAtomChirality(const Bond *bond,
const Atom *atom);
RDKIT_GRAPHMOL_EXPORT unsigned int getAtomNonzeroDegree(const Atom *atom);
} // namespace detail
/// @endcond
RDKIT_GRAPHMOL_EXPORT INT_VECT findStereoAtoms(const Bond *bond);
//! \name Non-tetrahedral stereochemistry
//! @{
RDKIT_GRAPHMOL_EXPORT bool hasNonTetrahedralStereo(const Atom *center);
RDKIT_GRAPHMOL_EXPORT Bond *getChiralAcrossBond(const Atom *center,
const Bond *qry);
RDKIT_GRAPHMOL_EXPORT Bond *getChiralAcrossBond(const Atom *center,
const Atom *qry);
RDKIT_GRAPHMOL_EXPORT Atom *getChiralAcrossAtom(const Atom *center,
const Bond *qry);
RDKIT_GRAPHMOL_EXPORT Atom *getChiralAcrossAtom(const Atom *center,
const Atom *qry);
//! \param which: if this is -1 then the second axial bond will be returned,
//! otherwise the first
RDKIT_GRAPHMOL_EXPORT Bond *getTrigonalBipyramidalAxialBond(const Atom *center,
int which = 0);
RDKIT_GRAPHMOL_EXPORT Atom *getTrigonalBipyramidalAxialAtom(const Atom *center,
int which = 0);
//! \returns 1 if it's the first axial atom, -1 if it's the second
RDKIT_GRAPHMOL_EXPORT int isTrigonalBipyramidalAxialBond(const Atom *center,
const Bond *qry);
RDKIT_GRAPHMOL_EXPORT int isTrigonalBipyramidalAxialAtom(const Atom *center,
const Atom *qry);
RDKIT_GRAPHMOL_EXPORT double getIdealAngleBetweenLigands(const Atom *center,
const Atom *lig1,
const Atom *lig2);
RDKIT_GRAPHMOL_EXPORT unsigned int getChiralPermutation(const Atom *center,
const INT_LIST &probe);
//! @}
RDKIT_GRAPHMOL_EXPORT std::ostream &operator<<(std::ostream &oss,
const StereoSpecified &s);
RDKIT_GRAPHMOL_EXPORT std::ostream &operator<<(std::ostream &oss,
const StereoType &s);
} // namespace Chirality
} // namespace RDKit
#endif
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