SubstanceGroup.h

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//
//
//  Copyright (C) 2018-2020 Greg Landrum and T5 Informatics GmbH
//
//   @@ 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 SubstanceGroup.h
 
  \brief Defines the SubstanceGroup class
 
*/
#include <RDGeneral/export.h>
#ifndef _RD_SGROUP_H
#define _RD_SGROUP_H
 
#include <utility>
#include <unordered_map>
 
#include <Geometry/point.h>
#include <RDGeneral/types.h>
#include <RDGeneral/RDProps.h>
#include <boost/smart_ptr.hpp>
 
namespace RDKit {
class ROMol;
class RWMol;
class Bond;
class Atom;
 
//! used to indicate errors from incorrect sgroup access
class RDKIT_GRAPHMOL_EXPORT SubstanceGroupException
    : public std::runtime_error {
 public:
  //! construct with an error message
  SubstanceGroupException(const char *msg) : std::runtime_error(msg) {}
  //! construct with an error message
  SubstanceGroupException(const std::string &msg) : std::runtime_error(msg) {}
};
 
//! The class for representing SubstanceGroups
/*!
  <b>Notes:</b>
  - These are inspired by the SGroups in the MDL formats
  - Implementation is based on 2010 MDL SD specification:
    http://infochim.u-strasbg.fr/recherche/Download/Fragmentor/MDL_SDF.pdf
  - See SGroups.md for further, more comprehensive notes.
 
*/
 
class RDKIT_GRAPHMOL_EXPORT SubstanceGroup : public RDProps {
 public:
  //! Bond type (see V3000 spec)
  enum class BondType {
    XBOND,  // External/Crossing bond
    CBOND,  // Internal/Contained bond
  };
 
  typedef std::array<RDGeom::Point3D, 3> Bracket;
 
  //! Data structure for SAP lines (see V3000 spec)
  //! lvIdx may not be set; this signaled with value -1
  struct AttachPoint {
    unsigned int aIdx;
    int lvIdx;
    std::string id;
    bool operator==(const AttachPoint &other) const {
      return aIdx == other.aIdx && lvIdx == other.lvIdx && id == other.id;
    }
  };
 
  //! See specification for V3000 CSTATE
  //! vector may or not be considered, depending on TYPE
  struct CState {
    unsigned int bondIdx;
    RDGeom::Point3D vector;
    bool operator==(const CState &other) const {
      // note that we ignore coordinates for this
      return bondIdx == other.bondIdx;
    }
  };
 
//! No default constructor
#ifndef SWIG
  // Unfortunately, SWIG generated wrapper code uses temporary variables that
  // require a default ctor not be deleted.
  SubstanceGroup() = delete;
#endif  // !SWIG
 
  //! Main Constructor. Ownership is only set on this side of the relationship:
  //! mol->addSubstanceGroup(sgroup) still needs to be called to get ownership
  //! on the other side.
  SubstanceGroup(ROMol *owning_mol, const std::string &type);
 
  SubstanceGroup(const SubstanceGroup &other) = default;
  SubstanceGroup &operator=(const SubstanceGroup &other) = default;
 
  SubstanceGroup(SubstanceGroup &&other) noexcept : RDProps(std::move(other)) {
    dp_mol = std::exchange(other.dp_mol, nullptr);
    d_atoms = std::move(other.d_atoms);
    d_patoms = std::move(other.d_patoms);
    d_bonds = std::move(other.d_bonds);
    d_brackets = std::move(other.d_brackets);
    d_cstates = std::move(other.d_cstates);
    d_saps = std::move(other.d_saps);
  }
 
  SubstanceGroup &operator=(SubstanceGroup &&other) noexcept {
    if (this == &other) {
      return *this;
    }
    RDProps::operator=(std::move(other));
    dp_mol = std::exchange(other.dp_mol, nullptr);
    d_atoms = std::move(other.d_atoms);
    d_patoms = std::move(other.d_patoms);
    d_bonds = std::move(other.d_bonds);
    d_brackets = std::move(other.d_brackets);
    d_cstates = std::move(other.d_cstates);
    d_saps = std::move(other.d_saps);
    return *this;
  }
 
  //! Destructor
  ~SubstanceGroup() = default;
 
  //! returns whether or not this belongs to a molecule
  bool hasOwningMol() const { return dp_mol != nullptr; }
 
  //! Get the molecule that owns this instance
  ROMol &getOwningMol() const {
    PRECONDITION(dp_mol, "no owner");
    return *dp_mol;
  }
 
  //! returns whether or not this group is valid; invalid groups must be
  //! ignored.
  bool getIsValid() const { return d_isValid; }
 
  //! set whether or not this group is valid; invalid groups must be ignored.
  void setIsValid(bool isValid) { d_isValid = isValid; }
 
  //! get the index of this sgroup in dp_mol's sgroups vector
  //! (do not mistake this by the ID!)
  unsigned int getIndexInMol() const;
 
  /* Atom and Bond methods */
  void addAtomWithIdx(unsigned int idx);
  void addParentAtomWithIdx(unsigned int idx);
  void addBondWithIdx(unsigned int idx);
  void addAtomWithBookmark(int mark);
  void addParentAtomWithBookmark(int mark);
  void addBondWithBookmark(int mark);
 
  // These methods should be handled with care, since they can leave
  // Attachment points and CStates in an invalid state!
  void removeAtomWithIdx(unsigned int idx);
  void removeParentAtomWithIdx(unsigned int idx);
  void removeBondWithIdx(unsigned int idx);
 
  void addBracket(const Bracket &bracket);
  void addCState(unsigned int bondIdx, const RDGeom::Point3D &vector);
  void addAttachPoint(unsigned int aIdx, int lvIdx, const std::string &idStr);
 
  BondType getBondType(unsigned int bondIdx) const;
 
  const std::vector<unsigned int> &getAtoms() const { return d_atoms; }
  const std::vector<unsigned int> &getParentAtoms() const { return d_patoms; }
  const std::vector<unsigned int> &getBonds() const { return d_bonds; }
 
  void setAtoms(std::vector<unsigned int> atoms);
  void setParentAtoms(std::vector<unsigned int> patoms);
  void setBonds(std::vector<unsigned int> bonds);
 
  const std::vector<Bracket> &getBrackets() const { return d_brackets; }
  const std::vector<CState> &getCStates() const { return d_cstates; }
  const std::vector<AttachPoint> &getAttachPoints() const { return d_saps; }
 
  std::vector<Bracket> &getBrackets() { return d_brackets; }
  std::vector<CState> &getCStates() { return d_cstates; }
  std::vector<AttachPoint> &getAttachPoints() { return d_saps; }
 
  void clearBrackets() { d_brackets.clear(); }
  void clearCStates() { d_cstates.clear(); }
  void clearAttachPoints() { d_saps.clear(); }
 
  //! adjusts our atom IDs to reflect that an atom has been removed from the
  //! parent molecule
  //!   decrements all atom IDs that are higher than \c atomIdx
  //!   raises a \c SubstanceGroupException if \c atomIdx is actually part of
  //!   this substance group
  //! \returns whether or not anything was changed
  bool adjustToRemovedAtom(unsigned int atomIdx);
 
  //! \returns whether or not anything the specified atom is part of the
  //! definition of this substance group
  bool includesAtom(unsigned int atomIdx) const;
 
  //! adjusts our bond IDs to reflect that a bond has been removed from the
  //! parent molecule
  //!   decrements all bond IDs that are higher than \c bondIdx
  //!   raises a \c SubstanceGroupException if \c bondIdx is actually part of
  //!   this substance group
  //! \returns whether or not anything was changed
  bool adjustToRemovedBond(unsigned int bondIdx);
 
  //! \returns whether or not anything the specified bond is part of the
  //! definition of this substance group
  bool includesBond(unsigned int bondIdx) const;
 
  //! Set owning molecule
  //! This only updates atoms and bonds; parent sgroup has to be updated
  //! independently, since parent might not exist at the time this is
  //! called.
  void setOwningMol(ROMol *mol);
 
  bool operator==(const SubstanceGroup &other) const {
    // we ignore brackets and cstates, which involve coordinates
    return dp_mol == other.dp_mol && d_atoms == other.d_atoms &&
           d_patoms == other.d_patoms && d_bonds == other.d_bonds &&
           d_saps == other.d_saps;
  }
 
 private:
  ROMol *dp_mol = nullptr;  // owning molecule
 
  bool d_isValid = true;
 
  std::vector<unsigned int> d_atoms;
  std::vector<unsigned int> d_patoms;
  std::vector<unsigned int> d_bonds;
 
  std::vector<Bracket> d_brackets;
  std::vector<CState> d_cstates;
  std::vector<AttachPoint> d_saps;
};  // namespace RDKit
 
namespace SubstanceGroupChecks {
 
const std::vector<std::string> sGroupTypes = {
    // polymer sgroups:
    "SRU", "MON", "COP", "CRO", "GRA", "MOD", "MER", "ANY",
    // formulations/mixtures:
    "COM", "MIX", "FOR",
    // other
    "SUP", "MUL", "DAT", "GEN"};
 
const std::vector<std::string> sGroupSubtypes = {"ALT", "RAN", "BLO"};
const std::vector<std::string> sGroupConnectTypes = {"HH", "HT", "EU"};
const std::vector<std::string> sGroupClasses = {
    "AA",        "dAA",    "DNA",     "RNA",      "SUGAR",    "BASE",
    "PHOSPHATE", "LINKER", "CHEM",    "LGRP",     "MODAA",    "MODdAA",
    "MODDNA",    "MODRNA", "XLINKAA", "XLINKdAA", "XLINKDNA", "XLINKRNA",
};
 
RDKIT_GRAPHMOL_EXPORT bool isValidType(const std::string &type);
 
RDKIT_GRAPHMOL_EXPORT bool isValidSubType(const std::string &type);
 
RDKIT_GRAPHMOL_EXPORT bool isValidConnectType(const std::string &type);
 
RDKIT_GRAPHMOL_EXPORT bool isValidClass(const std::string &sgroupClass);
 
RDKIT_GRAPHMOL_EXPORT bool isSubstanceGroupIdFree(const ROMol &mol,
                                                  unsigned int id);
 
}  // namespace SubstanceGroupChecks
 
//! \name SubstanceGroups and molecules
//! @{
 
RDKIT_GRAPHMOL_EXPORT std::vector<SubstanceGroup> &getSubstanceGroups(
    ROMol &mol);
RDKIT_GRAPHMOL_EXPORT const std::vector<SubstanceGroup> &getSubstanceGroups(
    const ROMol &mol);
 
//! Add a new SubstanceGroup. A copy is added, so we can be sure that no other
//! references to the SubstanceGroup exist.
/*!
  \param sgroup - SubstanceGroup to be added to the molecule.
*/
RDKIT_GRAPHMOL_EXPORT unsigned int addSubstanceGroup(ROMol &mol,
                                                     SubstanceGroup sgroup);
 
//! Removes SubstanceGroups which reference a particular atom index
/*!
  \param mol - molecule to be edited.
  \param idx - atom index
*/
RDKIT_GRAPHMOL_EXPORT void removeSubstanceGroupsReferencingAtom(
    RWMol &mol, unsigned int idx);
//! Removes SubstanceGroups which reference a particular bond index
/*!
  \param mol - molecule to be edited.
  \param idx - bond index
*/
RDKIT_GRAPHMOL_EXPORT void removeSubstanceGroupsReferencingBond(
    RWMol &mol, unsigned int idx);
//! @}
 
}  // namespace RDKit
 
//! allows SubstanceGroup objects to be dumped to streams
RDKIT_GRAPHMOL_EXPORT std::ostream &operator<<(std::ostream &target,
                                               const RDKit::SubstanceGroup &sg);
#endif