// $Id$
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//  Copyright (c) 2013, Novartis Institutes for BioMedical Research Inc.
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#include <Geometry/point.h>
#include <GraphMol/RDKitBase.h>
#include <GraphMol/SmilesParse/SmilesParse.h>
#include <RDGeneral/BadFileException.h>
#include <boost/foreach.hpp>
#include "ConformerParser.h"

#include <fstream>


namespace RDKit{
  namespace ConformerParser {

    INT_VECT addConformersFromList(ROMol &mol, const std::vector<std::vector<double> > &coords,
                               int numConf){
      unsigned int numAtomsPerConf = mol.getNumAtoms();
      unsigned int numCoordPerConf = 3 * numAtomsPerConf;
      PRECONDITION(numConf <= int(coords.size()), "numConf greater than number of conformations");
      if (numConf < 0) {
        numConf = coords.size();
      }
      // loop over the conformers
      INT_VECT confIds;
      for (unsigned int i = 0; i < numConf; ++i) {
        if (coords[i].size() != numCoordPerConf) {
          throw ValueErrorException("Wrong number of coordinates");
        }
        RDKit::Conformer *conf = new RDKit::Conformer(numAtomsPerConf);
        // loop over atoms
        for (unsigned int atom = 0; atom < numAtomsPerConf; ++atom) {
          //RDGeom::Point3D p(coords[i][3*atom], coords[i][3*atom+1], coords[i][3*atom+2]);
          (*conf).setAtomPos(atom, RDGeom::Point3D(coords[i][3*atom], coords[i][3*atom+1], coords[i][3*atom+2]));
        }
        int confId = mol.addConformer(conf, true);
        confIds.push_back(confId);
      }
      return confIds;
    }

    void readAmberTrajectory(std::string fName, std::vector<std::vector<double> > &coords,
                             unsigned int numAtoms) {
      std::ifstream inStream(fName.c_str());
      if (!inStream || (inStream.bad()) ) {
        std::ostringstream errout;
        errout << "Bad input file " << fName;
        throw BadFileException(errout.str());
      }
      std::string tempStr;
      // title
      std::getline(inStream, tempStr);
      // read coordinates
      std::vector<double> tmpCoords;
      while (true) {
        double c;
        if (!(inStream >> c)) {
          if (!inStream.eof()) {
            throw ValueErrorException("Error while reading file");
          }
          break;
        }
        tmpCoords.push_back(c);
      }
      // convert to conformers
      unsigned int numCoordsPerConf = 3 * numAtoms;
      if (tmpCoords.size() % numCoordsPerConf != 0) {
        throw ValueErrorException("Wrong number of coordinates");
      }
      unsigned int numConfs = tmpCoords.size() / numCoordsPerConf;
      unsigned int c = 0;
      for (unsigned int i = 0; i < numConfs; ++i) {
        std::vector<double> coordConf(numCoordsPerConf);
        for (unsigned int atom = 0; atom < numCoordsPerConf; ++atom, ++c) {
          coordConf[atom] = tmpCoords[c];
        }
        coords.push_back(coordConf);
      }
    }


  } // end namespace ConformerParser
} // end namespace RDKit