Properties.h

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#ifndef INCLUDE_SHAPE_PROPERTIES_H
#define INCLUDE_SHAPE_PROPERTIES_H

#include "Molassembler/Shapes/Data.h"

#include <set>

namespace Scine {
namespace Molassembler {
namespace Shapes {

namespace Properties {

constexpr double floatingPointEqualityThreshold [[gnu::unused]] = 1e-4;

MASM_EXPORT Permutation applyPermutation(
  const Permutation& occupation,
  const Permutation& permutation
);

MASM_EXPORT std::vector<Vertex> applyRotation(
  const Permutation& occupation,
  Shape shape,
  unsigned rotationFunctionIndex
);

MASM_EXPORT unsigned rotationPeriodicity(
  Shape shape,
  const Permutation& rotation
);

PURITY_WEAK MASM_EXPORT std::vector<std::vector<Vertex>> positionGroups(Shape shape);

MASM_EXPORT std::vector<char> positionGroupCharacters(Shape shape);

MASM_EXPORT Permutation inverseRotation(const Permutation& rotation);

MASM_EXPORT Eigen::Vector3d getCoordinates(
  Shape shape,
  const boost::optional<Vertex>& vertexOption
);

MASM_EXPORT double getTetrahedronVolume(
  const Eigen::Vector3d& i,
  const Eigen::Vector3d& j,
  const Eigen::Vector3d& k,
  const Eigen::Vector3d& l
);

MASM_EXPORT double calculateAngleDistortion(
  Shape from,
  Shape to,
  const std::vector<Vertex>& indexMapping
);

MASM_EXPORT boost::optional<Vertex> propagateIndexOptionalThroughMapping(
  const boost::optional<Vertex>& indexOptional,
  const std::vector<Vertex>& indexMapping
);

MASM_EXPORT double calculateChiralDistortion(
  Shape from,
  Shape to,
  const std::vector<Vertex>& indexMapping
);

MASM_EXPORT
std::set<
  std::vector<Vertex>
> generateAllRotations(
  Shape shape,
  const std::vector<Vertex>& indices
);

MASM_EXPORT std::vector<Vertex> applyIndexMapping(
  Shape to,
  const std::vector<Vertex>& mapping
);

struct MASM_EXPORT DistortionInfo {
  std::vector<Vertex> indexMapping;
  double angularDistortion;
  double chiralDistortion;

  DistortionInfo(
    std::vector<Vertex> passIndexMapping,
    double passAngularDistortion,
    double passChiralDistortion
  );
};

MASM_EXPORT std::vector<DistortionInfo> shapeTransitionMappings(
  Shape from,
  Shape to
);

MASM_EXPORT std::vector<DistortionInfo> ligandLossTransitionMappings(
  Shape from,
  Shape to,
  Vertex positionInSourceShape
);

struct MASM_EXPORT ShapeTransitionGroup {
  std::vector<
    std::vector<Vertex>
  > indexMappings;
  double angularDistortion;
  double chiralDistortion;

  ShapeTransitionGroup(
    std::vector<
      std::vector<Vertex>
    > passIndexMappings,
    double passAngleDistortion,
    double passChiralDistortion
  );

  ShapeTransitionGroup() = default;
};

MASM_EXPORT ShapeTransitionGroup selectBestTransitionMappings(
  const std::vector<DistortionInfo>& distortions
);

PURITY_WEAK MASM_EXPORT unsigned numUnlinkedStereopermutations(
  Shape shape,
  unsigned nIdenticalLigands
);

PURITY_WEAK MASM_EXPORT bool hasMultipleUnlinkedStereopermutations(
  Shape shape,
  unsigned nIdenticalLigands
);

PURITY_WEAK MASM_EXPORT Shape mostSymmetric(std::vector<Shape> selection);

PURITY_WEAK MASM_EXPORT Shape mostSymmetric(unsigned shapeSize);

} // namespace Properties
} // namespace Shapes
} // namespace Molassembler
} // namespace Scine

#endif