BondStereopermutator.h

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#ifndef INCLUDE_MOLASSEMBLER_BOND_STEREOPERMUTATOR_H
#define INCLUDE_MOLASSEMBLER_BOND_STEREOPERMUTATOR_H

#include "Molassembler/AtomStereopermutator.h"

#include <string>

namespace Scine {
namespace Molassembler {

/* Forward-declarations */
namespace Stereopermutations {
class Composite;
} // namespace Stereopermutations

namespace Random {
class Engine;
} // namespace Random

class AngstromPositions;
class PrivateGraph;
class StereopermutatorList;

namespace DistanceGeometry {
class SpatialModel;
struct ChiralConstraint;
} // namespace DistanceGeometry

class MASM_EXPORT BondStereopermutator {
public:

  enum class Alignment {
    Eclipsed,
    Staggered,
    EclipsedAndStaggered,
    BetweenEclipsedAndStaggered
  };

  enum class FittingMode {
    Thresholded,
    Nearest
  };

  using SitePositions = Eigen::Matrix<double, 3, Eigen::Dynamic>;
  using SitePositionsPair = std::pair<SitePositions, SitePositions>;


  static constexpr double assignmentAcceptanceParameter = 0.1;


  static std::vector<unsigned> notObviouslyInfeasibleStereopermutations(
    const PrivateGraph& graph,
    const AtomStereopermutator& stereopermutatorA,
    const AtomStereopermutator& stereopermutatorB,
    const Stereopermutations::Composite& composite
  );

  BondStereopermutator(BondStereopermutator&& other) noexcept;
  BondStereopermutator& operator = (BondStereopermutator&& other) noexcept;
  BondStereopermutator(const BondStereopermutator& other);
  BondStereopermutator& operator = (const BondStereopermutator& other);
  ~BondStereopermutator();

  BondStereopermutator() = delete;
  BondStereopermutator(
    const AtomStereopermutator& stereopermutatorA,
    const AtomStereopermutator& stereopermutatorB,
    const BondIndex& edge,
    Alignment alignment = Alignment::Eclipsed
  );

  BondStereopermutator(
    const PrivateGraph& graph,
    const StereopermutatorList& stereopermutators,
    const BondIndex& edge,
    Alignment alignment = Alignment::Eclipsed
  );


  void assign(boost::optional<unsigned> assignment);

  void assignRandom(Random::Engine& engine);

  void applyPermutation(const std::vector<AtomIndex>& permutation);

  struct FittingReferences {
    const AtomStereopermutator& stereopermutator;
    const AtomStereopermutator::ShapeMap& shapeMap;
  };

  void fit(
    const SitePositionsPair& sitePositions,
    std::pair<FittingReferences, FittingReferences> fittingReferences,
    FittingMode mode = FittingMode::Thresholded
  );

  void fit(
    const AngstromPositions& angstromWrapper,
    std::pair<FittingReferences, FittingReferences> fittingReferences,
    FittingMode mode = FittingMode::Thresholded
  );

  void propagateGraphChange(
    const AtomStereopermutator::PropagatedState& oldPermutator,
    const AtomStereopermutator& newPermutator,
    const PrivateGraph& inner,
    const StereopermutatorList& permutators
  );

  void propagateVertexRemoval(AtomIndex removedIndex);


  Alignment alignment() const;

  boost::optional<unsigned> assigned() const;

  const Stereopermutations::Composite& composite() const;

  std::pair<AtomIndex, AtomIndex> compositeAlignment() const;

  double dihedral(
    const AtomStereopermutator& stereopermutatorA,
    SiteIndex siteIndexA,
    const AtomStereopermutator& stereopermutatorB,
    SiteIndex siteIndexB
  ) const;

  bool hasSameCompositeOrientation(const BondStereopermutator& other) const;

  boost::optional<unsigned> indexOfPermutation() const;

  unsigned numAssignments() const;

  unsigned numStereopermutations() const;

  std::string info() const;

  std::string rankInfo() const;

  BondIndex placement() const;

  bool operator < (const BondStereopermutator& other) const;
  bool operator == (const BondStereopermutator& other) const;
  bool operator != (const BondStereopermutator& other) const;

private:
  struct Impl;
  std::unique_ptr<Impl> pImpl_;
};

} // namespace Molassembler
} // namespace Scine

#endif