/**
 * \file em3d_single_score.cpp \brief A program to score a single
 * docking model in PDB file
 *
 * Copyright 2007-2013 IMP Inventors. All rights reserved.
 *
 */
#include "EMFit.h"

#include <boost/program_options.hpp>

#include <stdio.h>
#include <fstream>
#include <iostream>
#include <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;
  std::vector<std::string> pdb_file_names;
  std::string map_file_name;
  std::string out_file_name  = "em_fit.res";
  po::options_description desc("Usage: <pdb1> <pdb2> ... <pdbN> <em_map> ");
   desc.add_options()
     ("help", "Program for filtering of docking solutions with EM density maps")
     ("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)")
     ("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("em_fit.res"),
      "output file name, default name em_fit.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() < 2)
    { std::cout << desc << "\n"; return 0; }

  for(unsigned int i=0; i<files.size()-1; i++)
    pdb_file_names.push_back(files[i]);
  map_file_name = files[files.size()-1];

  for(unsigned int i=0; i<pdb_file_names.size(); i++) {
    EMFit em_fit(pdb_file_names[i], map_file_name,
                 resolution, dist_thr, volume_scale);
    em_fit.runPCA();
    std::string out_file_namei = out_file_name;
    std::string pdb_file_namei = out_file_name;
    if(pdb_file_names.size() > 1) {
      out_file_namei = out_file_name +
        std::string(boost::lexical_cast<std::string>(i)) + ".res";
      pdb_file_namei += std::string(boost::lexical_cast<std::string>(i));
    }
    pdb_file_namei += ".pdb";
    em_fit.output(out_file_namei, pdb_file_namei);
  }
  return 0;
}