/**
 * \file em3d_score.cpp \brief A program to score docking models given a list
 * of transformations for a ligand
 *
 * Copyright 2007-2013 IMP Inventors. All rights reserved.
 *
 */
#include "EMFit.h"

#include <boost/program_options.hpp>

#include <stdio.h>
#include <fstream>
#include <vector>

using std::ifstream;
using std::vector;

namespace po = boost::program_options;

int main(int argc, char **argv) {
  // print program call
  for(int i=0; i<argc; i++) std::cerr << argv[i] << " "; std::cerr << std::endl;
  // parse input options
  float dist_thr = 10.0;
  float resolution = 20.0;
  float volume_scale = 1.5;
  bool cc_score = false;
  std::string rec_file_name, lig_file_name, map_file_name, trans_file_name;
  std::string out_file_name  = "em3d_score.res";
  po::options_description desc("Usage: <pdb1> <pdb2> <trans file> <em map>");
   desc.add_options()
     ("help", "Program for scoring of docking models with EM density map")
     ("input-files", po::value< std::vector<std::string> >(),
     "input PDB, feature points and density map files")
     ("resolution,r", po::value<float>(&resolution)->default_value(20.0),
      "map resolution (default = 20.0)")
     ("score,s", "use envelope score (default = true), \
otherwise use cross correlation")
     ("distance_threshold,d",
       po::value<float>(&dist_thr)->default_value(10.0),
      "distance threshold for map penetration, default value 10A")
     ("volume_scale,v",
       po::value<float>(&volume_scale)->default_value(1.5),
      "volume scale parameter to determine envelope thr, default value 1.5A")
     ("output_file,o",
      po::value<std::string>(&out_file_name)->default_value("em3d_score.res"),
      "output file name, default name em3d_score.res")
     ;
     po::positional_options_description p;
  p.add("input-files", -1);
  po::variables_map vm;
  po::store(
      po::command_line_parser(argc,argv).options(desc).positional(p).run(), vm);
  po::notify(vm);
  // read options
  std::vector<std::string> files;
  if(vm.count("input-files"))
    files = vm["input-files"].as< std::vector<std::string> >();
  if(vm.count("help") || files.size() != 4)
    { std::cout << desc << "\n"; return 0; }
  if(vm.count("score")) cc_score = true;

  rec_file_name = files[0];
  lig_file_name = files[1];
  map_file_name = files[3];
  trans_file_name = files[2];

  //dist_thr = resolution/2.0;
  EMFit em_fit(rec_file_name, lig_file_name, map_file_name,
               resolution, dist_thr, volume_scale);
  em_fit.runPCA(trans_file_name, cc_score);
  em_fit.output(out_file_name);
  return 0;
}