SmilesMoleculeBuilder.h

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#ifndef INCLUDE_MOLASSEMBLER_IO_SMILES_MOLECULE_BUILDER_H
#define INCLUDE_MOLASSEMBLER_IO_SMILES_MOLECULE_BUILDER_H

#include "Molassembler/Shapes/Data.h"
#include "Molassembler/IO/SmilesParseData.h"
#include "Molassembler/Graph/PrivateGraph.h"
#include "boost/variant.hpp"
#include <stack>

namespace Scine {

namespace Utils {
enum class ElementType : unsigned;
} // namespace Utils


namespace Molassembler {

class Molecule;

namespace IO {

class MoleculeBuilder {
public:
  /* @brief Parsing trigger on encountering an atom
   *
   * Adds an atom with the last set bond information.
   */
  void addAtom(const AtomData& atom);

  void addRingClosure(const BondData& bond);

  inline void branchOpen() {
    vertexStack.push(vertexStack.top());
  }

  inline void branchClose() {
    assert(!vertexStack.empty());
    vertexStack.pop();
  }

  inline void setNextAtomUnbonded() {
    lastBondData = SimpleLastBondData::Unbonded;
  }

  inline void setNextAtomBondInformation(const BondData& bond) {
    lastBondData = bond;
  }

  std::vector<Molecule> interpret();

private:
  static bool isValenceFillElement(Utils::ElementType e);

  static unsigned valenceFillElementImplicitHydrogenCount(
    int valence,
    Utils::ElementType e
  );

  static BondType mutualBondType(
    const boost::optional<BondType>& a,
    const boost::optional<BondType>& b
  );

  static std::vector<Shapes::Vertex> shapeMap(const ChiralData& chiralData);

  void setShapes(
    std::vector<Molecule>& molecules,
    const std::vector<unsigned>& componentMap,
    const std::vector<PrivateGraph::Vertex>& indexInComponentMap
  );

  void setAtomStereo(
    std::vector<Molecule>& molecules,
    const std::vector<unsigned>& componentMap,
    const std::vector<PrivateGraph::Vertex>& indexInComponentMap
  );

  void setBondStereo(
    std::vector<Molecule>& molecules,
    const std::vector<unsigned>& componentMap,
    const std::vector<PrivateGraph::Vertex>& indexInComponentMap
  );

  enum class SimpleLastBondData {
    Unbonded,
    Unspecified
  };

  boost::variant<SimpleLastBondData, BondData> lastBondData = SimpleLastBondData::Unbonded;

  PrivateGraph graph;

  std::stack<PrivateGraph::Vertex> vertexStack;

  using StereoMarkedBondTuple = std::tuple<PrivateGraph::Vertex, PrivateGraph::Vertex, BondData::StereoMarker>;
  std::vector<StereoMarkedBondTuple> stereoMarkedBonds;

  std::unordered_map<
    unsigned,
    std::pair<PrivateGraph::Vertex, boost::optional<BondType>>
  > ringClosures;

  std::vector<AtomData> vertexData;
};

} // namespace IO
} // namespace Molassembler
} // namespace Scine

#endif