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116 lines
3.9 KiB
C++
116 lines
3.9 KiB
C++
//
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// Copyright (C) 2018-2021 Greg Landrum and other RDKit contributors
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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 StereoGroup.h
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\brief Defines the class StereoGroup which stores relationships between
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the absolute configurations of atoms within a structure.
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*/
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#include <RDGeneral/export.h>
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#ifndef RD_StereoGroup_092018
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#define RD_StereoGroup_092018
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#include <vector>
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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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// OR means that it is known to be one or the other, but not both
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// AND means that it is known to be a mix.
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enum class StereoGroupType {
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STEREO_ABSOLUTE = 0,
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STEREO_OR = 1,
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STEREO_AND = 2
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};
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//! StereoGroup is a collection of atoms with a known stereochemical
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//! relationship
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/*!
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Used to help represent a sample with unknown stereochemistry, or that is a mix
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of diastereomers.
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*/
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class RDKIT_GRAPHMOL_EXPORT StereoGroup {
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private:
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StereoGroupType d_grouptype{StereoGroupType::STEREO_ABSOLUTE};
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std::vector<Atom *> d_atoms;
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std::vector<Bond *> d_bonds;
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// The group ID for AND/OR groups (it has no meaning in ABS groups).
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// 0 means no group ID is defined.
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unsigned d_readId = 0u;
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unsigned d_writeId = 0u;
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public:
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StereoGroup() {}
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// Takes control of atoms if possible.
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StereoGroup(StereoGroupType grouptype, std::vector<Atom *> &&atoms,
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std::vector<Bond *> &&bonds, unsigned readId = 0);
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StereoGroup(StereoGroupType grouptype, const std::vector<Atom *> &atoms,
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const std::vector<Bond *> &bonds, unsigned readId = 0);
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StereoGroup(const StereoGroup &other) = default;
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StereoGroup &operator=(const StereoGroup &other) = default;
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StereoGroup(StereoGroup &&other) = default;
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StereoGroup &operator=(StereoGroup &&other) = default;
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StereoGroupType getGroupType() const;
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const std::vector<Atom *> &getAtoms() const;
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const std::vector<Bond *> &getBonds() const;
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unsigned getReadId() const { return d_readId; }
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unsigned getWriteId() const { return d_writeId; }
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void setWriteId(unsigned id) { d_writeId = id; }
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// Seems odd to have to define these, but otherwise the SWIG wrappers
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// won't build
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bool operator==(const StereoGroup &other) const {
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return (d_grouptype == other.d_grouptype) && (d_atoms == other.d_atoms) &&
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(d_bonds == other.d_bonds);
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}
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bool operator!=(const StereoGroup &other) const {
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return (d_grouptype != other.d_grouptype) || (d_atoms != other.d_atoms) ||
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(d_bonds != other.d_bonds);
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}
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friend RDKIT_GRAPHMOL_EXPORT void removeAtomFromGroups(
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const Atom *atom, std::vector<StereoGroup> &groups);
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friend RDKIT_GRAPHMOL_EXPORT void removeBondFromGroups(
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const Bond *bond, std::vector<StereoGroup> &groups);
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};
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RDKIT_GRAPHMOL_EXPORT void removeAtomFromGroups(
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const Atom *atom, std::vector<StereoGroup> &groups);
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RDKIT_GRAPHMOL_EXPORT void removeBondFromGroups(
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const Bond *bond, std::vector<StereoGroup> &groups);
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RDKIT_GRAPHMOL_EXPORT void removeGroupsWithAtom(
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const Atom *atom, std::vector<StereoGroup> &groups);
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RDKIT_GRAPHMOL_EXPORT void removeGroupsWithAtoms(
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const std::vector<Atom *> &atoms, std::vector<StereoGroup> &groups);
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//! Assign Group output IDs to all AND and OR StereoGroups in the vector
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//! that don't already have one. The IDs are assigned based on the order
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//! of the groups.
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RDKIT_GRAPHMOL_EXPORT void assignStereoGroupIds(
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std::vector<StereoGroup> &groups);
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//! Copy StereoGroup "read" IDs to "write" IDs so that they will be preserved
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//! when the mol is exported.
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RDKIT_GRAPHMOL_EXPORT void forwardStereoGroupIds(ROMol &mol);
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} // namespace RDKit
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//! allows StereoGroup objects to be dumped to streams
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RDKIT_GRAPHMOL_EXPORT std::ostream &operator<<(std::ostream &target,
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const RDKit::StereoGroup &stg);
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#endif
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