/**
 * \file EMFit \brief
 *
 * Copyright 2007-2013 IMP Inventors. All rights reserved.
 *
 */

#ifndef IMP_EM_FIT_H
#define IMP_EM_FIT_H

#include "FitResult.h"
#include "MapScorer.h"

#include <IMP/em/EnvelopeScore.h>
#include <IMP/em/MapDistanceTransform.h>
#include <IMP/em/DensityMap.h>

#include <IMP/Particle.h>

class EMFit {
public:
  // Constructors
  // for fitting of docking solutions
  EMFit(std::string rec_file_name, std::string lig_file_name,
        std::string map_file_name, float resolution, float dist_thr,
        float volume_scale = 1.5);
  // for fitting of single structure
  EMFit(std::string pdb_file_name, std::string map_file_name,
        float resolution, float dist_thr, float volume_scale = 1.5);

  // docking transformations
  void runPCA(std::string trans_file, bool use_cc_score=false);

  // single structure
  void runPCA();

  void output(std::string out_file_name, std::string out_pdb_file_name="");

private:
  float compute_volume(const IMP::Particles& particles);
  float estimate_density_threshold(float object_volume) const;
  void read_trans_file(const std::string file_name,
                       std::vector<IMP::algebra::Transformation3D>& transforms);

  void read_pdb_atoms(IMP::Model *model, const std::string file_name,
                      IMP::Particles& particles);

  void compute_zscores();

private:
  IMP::OwnerPointer<IMP::Model> model_;
  IMP::Particles rec_particles_, lig_particles_;
  std::string rec_file_name_, lig_file_name_;
  IMP::em::DensityMap *map_;
  IMP::em::MapDistanceTransform *distance_transform_;
  IMP::em::EnvelopeScore *envelope_score_;
  MapScorer *cc_score_;
  float resolution_;
  float dist_thr_;
  float density_threshold_;
  std::vector<FitResult> fit_results_;
};

#endif /* IMP_EM_FIT_H */