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