Conformers.h

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#ifndef INCLUDE_MOLASSEMBLER_CONFORMER_GENERATION_H
#define INCLUDE_MOLASSEMBLER_CONFORMER_GENERATION_H

#include "Molassembler/Types.h"
#include "Utils/Typenames.h"
#include "Molassembler/Detail/Outcome.h"
#include <vector>

namespace Scine {
namespace Molassembler {

// Forward-declarations
class Molecule;

namespace DistanceGeometry {

enum class MASM_EXPORT Partiality {
  FourAtom,
  TenPercent,
  All
};

struct MASM_EXPORT Configuration {
  Partiality partiality {Partiality::FourAtom};

  unsigned refinementStepLimit {10'000};

  double refinementGradientTarget {1e-5};

  double spatialModelLoosening {1.0};

  std::vector<
    std::pair<AtomIndex, Utils::Position>
  > fixedPositions;
};

} // namespace DistanceGeometry

MASM_EXPORT std::vector<
  Result<Utils::PositionCollection>
> generateRandomEnsemble(
  const Molecule& molecule,
  unsigned numStructures,
  const DistanceGeometry::Configuration& configuration = DistanceGeometry::Configuration {}
);

MASM_EXPORT std::vector<
  Result<Utils::PositionCollection>
> generateEnsemble(
  const Molecule& molecule,
  unsigned numStructures,
  unsigned seed,
  const DistanceGeometry::Configuration& configuration = DistanceGeometry::Configuration {}
);

MASM_EXPORT Result<Utils::PositionCollection> generateRandomConformation(
  const Molecule& molecule,
  const DistanceGeometry::Configuration& configuration = DistanceGeometry::Configuration {}
);

MASM_EXPORT Result<Utils::PositionCollection> generateConformation(
  const Molecule& molecule,
  unsigned seed,
  const DistanceGeometry::Configuration& configuration = DistanceGeometry::Configuration {}
);

} // namespace Molassembler
} // namespace Scine

#endif