/**
 *  \file ligand_score.cpp   \brief A class for reading mol2 files
 *
 *  Copyright 2007-2013 IMP Inventors. All rights reserved.
 *
 */

#include <IMP/atom/protein_ligand_score.h>
#include <IMP/atom/pdb.h>
#include <IMP/atom/mol2.h>
#include <IMP/core/GridClosePairsFinder.h>
#include <IMP/particle_index.h>
#include <IMP/Model.h>

int main(int argc, char *argv[]) {
  IMP::set_log_level(IMP::SILENT);
  std::string mol2name, pdbname;
  for (int i=1; i < argc; ++i) {
    std::string nm(argv[i]);
    if (nm.rfind(".mol2") == nm.size()-5) {
      mol2name= nm;
    } else if (nm.rfind(".pdb") == nm.size()-4) {
      pdbname= nm;
    } else {
      break;
    }
  }
  if (mol2name.empty() || pdbname.empty()) {
    std::cerr << "Usage: " << argv[0]
              << " file.mol2 file.pdb [libfile]" << std::endl;
    return EXIT_FAILURE;
  }
  IMP::base::TextInput lib;
  if (argc==4) {
    lib= IMP::base::TextInput(argv[3]);
  }

  IMP_NEW(IMP::Model, m, ());
  IMP::atom::Hierarchy p, l;
  {
    IMP::SetLogState ss(IMP::SILENT);
    p= IMP::atom::read_pdb(pdbname, m, new IMP::atom::ATOMPDBSelector());
    IMP::atom::add_protein_ligand_score_data(p);
    l= IMP::atom::read_mol2(mol2name, m);
    IMP::atom::add_protein_ligand_score_data(l);
  }
  IMP::atom::Hierarchies mols
    = IMP::atom::get_by_type(l, IMP::atom::RESIDUE_TYPE);
  IMP::Pointer<IMP::atom::ProteinLigandAtomPairScore> ps;
  if (lib) {
    ps = new IMP::atom::ProteinLigandAtomPairScore(100000, lib);
  } else {
    ps= new IMP::atom::ProteinLigandAtomPairScore();
  }
  double d= ps->get_maximum_distance();
  IMP_NEW(IMP::core::GridClosePairsFinder, gcpf, ());
  gcpf->set_distance(d);

  IMP::ParticlesTemp patoms= IMP::atom::get_leaves(p);
  IMP::ParticleIndexes ipatoms= IMP::get_indexes(patoms);
  for (unsigned int i=0; i< mols.size(); ++i) {
    //IMP::SetLogState ss(i==0? TERSE: IMP::SILENT);
    IMP::ParticlesTemp latoms= IMP::atom::get_leaves(mols[i]);
    IMP::ParticleIndexes ilatoms= IMP::get_indexes(latoms);
    IMP::ParticleIndexPairs ppt= gcpf->get_close_pairs(m, ipatoms, ilatoms);
    double score=ps->evaluate_indexes(m, ppt, NULL, 0, ppt.size());
    std::cout << "Score for " << mols[i]->get_name() << " is "
              << score << std::endl;
  }
  ps->set_was_used(true);
  return EXIT_SUCCESS;
}