CIPMol.h

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//
//
//  Copyright (C) 2020 Schrödinger, LLC
//
//   @@ 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.
//
#pragma once
 
#include <memory>
 
#include <GraphMol/RDKitBase.h>
 
#include "Descriptor.h"
#include "Mancude.h"
 
namespace RDKit {
 
namespace CIPLabeler {
 
template <typename T, typename U>
class CIPMolSpan {
 public:
  class CIPMolIter {
   public:
    CIPMolIter() = delete;
    CIPMolIter(ROMol &mol, U pos) : d_mol{mol}, d_pos{std::move(pos)} {}
 
    T &operator*() {
      d_current = d_mol[*d_pos];
      return d_current;
    }
 
    CIPMolIter &operator++() {
      ++d_pos;
      return *this;
    }
 
    bool operator!=(const CIPMolIter &it) const { return d_pos != it.d_pos; }
 
   private:
    ROMol &d_mol;
    U d_pos;
    T d_current = nullptr;
  };
 
 public:
  CIPMolSpan() = delete;
  CIPMolSpan(ROMol &mol, std::pair<U, U> &&itr)
      : d_mol{mol},
        d_istart{std::move(itr.first)},
        d_iend{std::move(itr.second)} {}
 
  CIPMolIter begin() { return {d_mol, d_istart}; }
  CIPMolIter end() { return {d_mol, d_iend}; }
 
 private:
  ROMol &d_mol;
  const U d_istart;
  const U d_iend;
};
 
class CIPMol {
 public:
  CIPMol() = delete;
 
  explicit CIPMol(ROMol &mol);
 
  // Average atomic number with other atoms that are in an
  // aromatic ring with this one.
  boost::rational<int> getFractionalAtomicNum(Atom *atom) const;
 
  unsigned getNumAtoms() const;
 
  unsigned getNumBonds() const;
 
  Atom *getAtom(int idx) const;
 
  CXXAtomIterator<MolGraph, Atom *> atoms() const;
 
  Bond *getBond(int idx) const;
 
  CIPMolSpan<Bond *, ROMol::OEDGE_ITER> getBonds(Atom *atom) const;
 
  CIPMolSpan<Atom *, ROMol::ADJ_ITER> getNeighbors(Atom *atom) const;
 
  bool isInRing(Bond *bond) const;
 
  // Integer bond order of a kekulized molecule
  // Dative bonds get bond order 0.
  int getBondOrder(Bond *bond) const;
 
 private:
  ROMol &d_mol;
  std::unique_ptr<RWMol> dp_kekulized_mol = nullptr;
 
  std::vector<boost::rational<int>> d_atomnums;
};
 
}  // namespace CIPLabeler
}  // namespace RDKit