ConformerGeneration.h

Go to the documentation of this file.

#ifndef INCLUDE_MOLASSEMBLER_DISTANCE_GEOMETRY_CONFORMER_GENERATION_H
#define INCLUDE_MOLASSEMBLER_DISTANCE_GEOMETRY_CONFORMER_GENERATION_H

#include "Molassembler/DistanceGeometry/SpatialModel.h"
#include "Molassembler/Log.h"

namespace Scine {
namespace Molassembler {
namespace DistanceGeometry {
namespace Detail {

Eigen::MatrixXd gather(const Eigen::VectorXd& vectorizedPositions);

AngstromPositions convertToAngstromPositions(const Eigen::MatrixXd& positions);

Eigen::MatrixXd fitAndSetFixedPositions(
  const Eigen::MatrixXd& positions,
  const Configuration& configuration
);

Molecule narrow(Molecule molecule, Random::Engine& engine);

} // namespace Detail

struct MoleculeDGInformation {
  struct RotatableGroup {
    AtomIndex side;
    std::vector<AtomIndex> vertices;
  };

  using GroupMapType = std::unordered_map<BondIndex, RotatableGroup, boost::hash<BondIndex>>;

  static GroupMapType make(
    const std::vector<DihedralConstraint>& constraints,
    const Molecule& molecule
  );

  SpatialModel::BoundsMatrix bounds;
  std::vector<ChiralConstraint> chiralConstraints;
  std::vector<DihedralConstraint> dihedralConstraints;
  GroupMapType rotatableGroups;
};

MoleculeDGInformation gatherDGInformation(
  const Molecule& molecule,
  const Configuration& configuration
);

Result<AngstromPositions> refine(
  Eigen::MatrixXd embeddedPositions,
  const DistanceBoundsMatrix& distanceBounds,
  const Configuration& configuration,
  const std::shared_ptr<MoleculeDGInformation>& DgDataPtr
);

// @brief Individual conformer generation routine
Result<AngstromPositions> generateConformer(
  const Molecule& molecule,
  const Configuration& configuration,
  std::shared_ptr<MoleculeDGInformation>& DgDataPtr,
  bool regenerateDGDataEachStep,
  Random::Engine& engine
);

std::vector<
  Result<AngstromPositions>
> run(
  const Molecule& molecule,
  unsigned numConformers,
  const Configuration& configuration,
  boost::optional<unsigned> seedOption
);

} // namespace DistanceGeometry
} // namespace Molassembler
} // namespace Scine

#endif