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170796a175
* backup, definitely does not work * remove obsolete test (not even really sure anymore that's a bug) * remove code from a false path * at this point the code passes all tests * backup * handle isotopes and h counts properly * remove some compiler warnings * all tests passing * Use InChI minimimum ring size for bonds * Fixes edge-case bug in canonicalization when bond labels are provided * cleanup, no substance here * fixes the last set of problems I've seen * document that this is still experimental * remove obsolete/testing comments * stop considering charge and H count in chirality
128 lines
4.0 KiB
C++
128 lines
4.0 KiB
C++
//
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// Copyright (C) 2008-2020 Greg Landrum
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//
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// @@ All Rights Reserved @@
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// This file is part of the RDKit.
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// The contents are covered by the terms of the BSD license
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// which is included in the file license.txt, found at the root
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// of the RDKit source tree.
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//
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/*! \file Chirality.h
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*/
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#include <RDGeneral/export.h>
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#ifndef RD_CHIRALITY_20AUG2008_H
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#define RD_CHIRALITY_20AUG2008_H
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#include <RDGeneral/types.h>
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#include <GraphMol/Bond.h>
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#include <boost/dynamic_bitset.hpp>
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#include <limits>
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namespace RDKit {
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class Atom;
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class Bond;
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class ROMol;
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namespace Chirality {
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/// @cond
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/*!
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\param mol the molecule to be altered
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\param ranks used to return the set of ranks.
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Should be at least mol.getNumAtoms() long.
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<b>Notes:</b>
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- All atoms gain a property common_properties::_CIPRank with their overall
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CIP ranking.
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*/
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RDKIT_GRAPHMOL_EXPORT void assignAtomCIPRanks(const ROMol &mol,
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UINT_VECT &ranks);
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RDKIT_GRAPHMOL_EXPORT bool hasStereoBondDir(const Bond *bond);
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/**
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* Returns the first neighboring bond that can be found which has a stereo
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* bond direction set. If no such bond can be found, it returns null. No
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* checks are made to ensure there aren't any other conflicting directed bonds.
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*/
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RDKIT_GRAPHMOL_EXPORT const Bond *getNeighboringDirectedBond(const ROMol &mol,
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const Atom *atom);
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/**
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* This just translates the labels, setting/translating StereoAtoms or the
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* label is not the responsibility of this function. If the passed label is not
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* E/Z, it will be returned unchanged.
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*/
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RDKIT_GRAPHMOL_EXPORT Bond::BondStereo translateEZLabelToCisTrans(
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Bond::BondStereo label);
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/// @endcond
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enum class StereoType {
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Unspecified,
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Atom_Tetrahedral,
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Bond_Double, // single double bond and odd-numbered cumulenes
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Bond_Cumulene_Even, // even-numbered cumulenes
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Bond_Atropisomer
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};
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enum class StereoDescriptor { None, Tet_CW, Tet_CCW, Bond_Cis, Bond_Trans };
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enum class StereoSpecified {
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Unspecified, // no information provided
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Specified,
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Unknown // deliberately marked as unknown
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};
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struct RDKIT_GRAPHMOL_EXPORT StereoInfo {
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// REVIEW: absolute stereo data member?
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#ifdef _MSC_VER
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static const unsigned NOATOM =
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std::numeric_limits<unsigned>::max(); // used to mark missing atoms
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#else
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static const unsigned NOATOM; // used to mark missing atoms
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#endif
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StereoType type = StereoType::Unspecified;
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StereoSpecified specified = StereoSpecified::Unspecified;
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unsigned centeredOn = NOATOM;
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StereoDescriptor descriptor = StereoDescriptor::None;
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std::vector<unsigned> controllingAtoms; // all atoms around the atom or bond.
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// Order is important
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bool operator==(const StereoInfo &other) const {
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return type == other.type && specified == other.specified &&
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centeredOn == other.centeredOn && descriptor == other.descriptor &&
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controllingAtoms == other.controllingAtoms;
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}
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};
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//! identifies potential stereoatoms and stereobonds in a molecule
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/*!
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Note that this function is still somewhat experimental and the API
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and results may change in a future release.
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\param mol the molecule to look for stereo in
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\param cleanIt remove chirality/stereo specifications from atoms/bonds that
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cannot be chiral/stereo
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*/
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RDKIT_GRAPHMOL_EXPORT std::vector<StereoInfo> findPotentialStereo(
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ROMol &mol, bool cleanIt, bool flagPossible = true);
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//! overload
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RDKIT_GRAPHMOL_EXPORT std::vector<StereoInfo> findPotentialStereo(
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const ROMol &mol);
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/// @cond
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namespace detail {
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RDKIT_GRAPHMOL_EXPORT bool isAtomPotentialTetrahedralCenter(const Atom *atom);
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RDKIT_GRAPHMOL_EXPORT bool isAtomPotentialStereoAtom(const Atom *atom);
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RDKIT_GRAPHMOL_EXPORT bool isBondPotentialStereoBond(const Bond *bond);
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RDKIT_GRAPHMOL_EXPORT StereoInfo getStereoInfo(const Bond *bond);
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RDKIT_GRAPHMOL_EXPORT StereoInfo getStereoInfo(const Atom *atom);
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} // namespace detail
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/// @endcond
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RDKIT_GRAPHMOL_EXPORT INT_VECT findStereoAtoms(const Bond *bond);
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} // namespace Chirality
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} // namespace RDKit
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#endif
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