Interpret.h

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#ifndef INCLUDE_MOLASSEMBLER_INTERPRET_H
#define INCLUDE_MOLASSEMBLER_INTERPRET_H

#include "Molassembler/Export.h"
#include "Molassembler/PeriodicBoundaries.h"
#include "boost/optional.hpp"

namespace Scine {
namespace Utils {

// External forward-declarations
enum class ElementType : unsigned;
class AtomCollection;
class BondOrderCollection;
using ElementTypeCollection = std::vector<ElementType>;
} // namespace Utils

namespace Molassembler {

// Forward-declarations
class Molecule;
class AngstromPositions;

namespace Interpret {

enum class MASM_EXPORT BondDiscretizationOption {
  Binary,
  RoundToNearest
};

struct MASM_EXPORT ComponentMap {
  struct ComponentIndexPair {
    unsigned component;
    unsigned long atomIndex;
  };

  ComponentIndexPair apply(unsigned index) const;
  unsigned invert(const ComponentIndexPair& pair) const;


  std::vector<
    std::vector<unsigned>
  > invert() const;

  std::vector<Utils::AtomCollection> apply(const Utils::AtomCollection& atomCollection) const;

  MASM_NO_EXPORT std::vector<AngstromPositions> apply(const AngstromPositions& positions) const;

  MASM_NO_EXPORT std::vector<PeriodicBoundaryDuplicates> apply(
    const std::unordered_set<unsigned>& uninterestingAtoms,
    const std::unordered_map<unsigned, unsigned>& ghostAtomMap
  ) const;

  inline unsigned size() const { return map.size(); }

  unsigned countComponents() const;

  using Iterator = std::vector<unsigned>::iterator;
  using ConstIterator = std::vector<unsigned>::const_iterator;
  inline Iterator begin() { return std::begin(map); }
  inline Iterator end() { return std::end(map); }
  inline ConstIterator begin() const { return std::begin(map); }
  inline ConstIterator end() const { return std::end(map); }

  std::vector<unsigned> map;
};

struct MASM_EXPORT MoleculesResult {
  std::vector<Molecule> molecules;
  ComponentMap componentMap;
};

MASM_EXPORT MoleculesResult molecules(
  const Utils::ElementTypeCollection& elements,
  const AngstromPositions& angstromWrapper,
  const Utils::BondOrderCollection& bondOrders,
  BondDiscretizationOption discretization = BondDiscretizationOption::Binary,
  const boost::optional<double>& stereopermutatorThreshold = 1.4
);

MASM_EXPORT MoleculesResult molecules(
  const Utils::ElementTypeCollection& elements,
  const AngstromPositions& angstromWrapper,
  BondDiscretizationOption discretization = BondDiscretizationOption::Binary,
  const boost::optional<double>& stereopermutatorThreshold = 1.4
);

MASM_EXPORT MoleculesResult molecules(
  const Utils::AtomCollection& atomCollection,
  const Utils::BondOrderCollection& bondOrders,
  BondDiscretizationOption discretization = BondDiscretizationOption::Binary,
  const boost::optional<double>& stereopermutatorThreshold = 1.4
);

MASM_EXPORT MoleculesResult molecules(
  const Utils::AtomCollection& atoms,
  const Utils::BondOrderCollection& periodicBonds,
  const std::unordered_set<unsigned>& uninterestingAtoms,
  const std::unordered_map<unsigned, unsigned>& ghostAtomMap,
  BondDiscretizationOption discretization = BondDiscretizationOption::Binary,
  const boost::optional<double>& stereopermutatorThreshold = 1.4
);

MASM_EXPORT MoleculesResult molecules(
  const Utils::AtomCollection& atomCollection,
  BondDiscretizationOption discretization = BondDiscretizationOption::Binary,
  const boost::optional<double>& stereopermutatorThreshold = 1.4
);

struct MASM_EXPORT GraphsResult {
  std::vector<Graph> graphs;
  ComponentMap componentMap;
};

MASM_EXPORT GraphsResult graphs(
  const Utils::ElementTypeCollection& elements,
  const AngstromPositions& angstromWrapper,
  const Utils::BondOrderCollection& bondOrders,
  BondDiscretizationOption discretization = BondDiscretizationOption::Binary
);

MASM_EXPORT GraphsResult graphs(
  const Utils::AtomCollection& atomCollection,
  const Utils::BondOrderCollection& bondOrders,
  BondDiscretizationOption discretization = BondDiscretizationOption::Binary
);

struct FalsePositive {
  unsigned i;
  unsigned j;
  double probability;

  inline bool operator < (const FalsePositive& other) const {
    return probability < other.probability;
  }
};

MASM_EXPORT std::vector<FalsePositive> uncertainBonds(
  const Utils::AtomCollection& atomCollection,
  const Utils::BondOrderCollection& bondOrders
);

MASM_EXPORT std::vector<FalsePositive> badHapticLigandBonds(
  const Utils::AtomCollection& atomCollection,
  const Utils::BondOrderCollection& bondOrders
);

MASM_EXPORT Utils::BondOrderCollection removeFalsePositives(
  const Utils::AtomCollection& atoms,
  Utils::BondOrderCollection bonds
);

} // namespace Interpret
} // namespace Molassembler
} // namespace Scine

#endif