source: molecuilder/src/Parser/TremoloParser.cpp@ 0f7883

/*
 * TremoloParser.cpp
 *
 *  Created on: Mar 2, 2010
 *      Author: metzler
 */

#include "TremoloParser.hpp"
#include "World.hpp"
#include "atom.hpp"
#include "element.hpp"
#include "periodentafel.hpp"
#include <map>
#include <vector>

using namespace std;

/**
 * Constructor.
 */
TremoloParser::TremoloParser() {
  knownKeys[" "] = noKey; // so we can detect invalid keys
  knownKeys["x"] = x;
  knownKeys["u"] = u;
  knownKeys["F"] = F;
  knownKeys["stress"] = stress;
  knownKeys["Id"] = Id;
  knownKeys["neighbors"] = neighbors;
  knownKeys["imprData"] = imprData;
  knownKeys["GroupMeasureTypeNo"] = GroupMeasureTypeNo;
  knownKeys["Type"] = Type;
  knownKeys["extType"] = extType;
  knownKeys["name"] = name;
  knownKeys["resName"] = resName;
  knownKeys["chainID"] = chainID;
  knownKeys["resSeq"] = resSeq;
  knownKeys["occupancy"] = occupancy;
  knownKeys["tempFactor"] = tempFactor;
  knownKeys["segID"] = segID;
  knownKeys["Charge"] = Charge;
  knownKeys["charge"] = charge;
  knownKeys["GrpTypeNo"] = GrpTypeNo;
}

/**
 * Destructor.
 */
TremoloParser::~TremoloParser() {
}

/**
 * Stores keys from the ATOMDATA line.
 *
 * \param line to parse the keys from
 * \param with which offset the keys begin within the line
 */
void TremoloParser::parseAtomDataKeysLine(string line, int offset) {
  string keyword;
  stringstream lineStream;

  lineStream << line.substr(offset);
  while (lineStream.good()) {
    lineStream >> keyword;
    if (knownKeys[keyword.substr(0, keyword.find("="))] == noKey) {
      // throw exception about unknown key
      cout << "Unknown key: " << keyword << " is not part of the tremolo format specification." << endl;
      break;
    }
    usedFields.push_back(keyword);
  }
}

/**
 * Reads one data line of a tremolo file and interprets it according to the keys
 * obtained from the ATOMDATA line.
 *
 * \param line to parse as an atom
 */
void TremoloParser::readAtomDataLine(string line) {
  vector<string>::iterator it;
  stringstream lineStream;
  atom* newAtom = World::getInstance().createAtom();
  TremoloAtomInfoContainer atomInfo = *(new TremoloAtomInfoContainer());
  atomDataKey currentField;
  string word;

  lineStream << line;
  for (it=usedFields.begin(); it < usedFields.end(); it++) {
    cout << *it << " -- " << it->substr(0, it->find("=")) << " -- " << knownKeys[it->substr(0, it->find("="))] << endl;
    currentField = knownKeys[it->substr(0, it->find("="))];
    switch (currentField) {
      case x :
        // for the moment, assume there are always three dimensions
        lineStream >> newAtom->x.x[0];
        lineStream >> newAtom->x.x[1];
        lineStream >> newAtom->x.x[2];
        break;
      case u :
        // for the moment, assume there are always three dimensions
        lineStream >> newAtom->v.x[0];
        lineStream >> newAtom->v.x[1];
        lineStream >> newAtom->v.x[2];
        break;
      case F :
        lineStream >> word;
        atomInfo.F = word;
        break;
      case stress :
        lineStream >> word;
        atomInfo.F = word;
       break;
      case Id :
        // this ID is not used
        break;
      case neighbors :
        // TODO neighbor information
        lineStream >> word;
        break;
      case imprData :
        lineStream >> word;
        atomInfo.imprData = word;
        break;
      case GroupMeasureTypeNo :
        lineStream >> word;
        atomInfo.GroupMeasureTypeNo = word;
        break;
      case Type :
        char type[3];
        lineStream >> type;
        newAtom->setType(World::getInstance().getPeriode()->FindElement(type));
        break;
      case extType :
        lineStream >> word;
        atomInfo.extType = word;
        break;
      case name :
        lineStream >> word;
        atomInfo.name = word;
        break;
      case resName :
        lineStream >> word;
        atomInfo.resName = word;
        break;
      case chainID :
        lineStream >> word;
        atomInfo.chainID = word;
        break;
      case resSeq :
        lineStream >> word;
        atomInfo.resSeq = word;
        break;
      case occupancy :
        lineStream >> word;
        atomInfo.occupancy = word;
        break;
      case tempFactor :
        lineStream >> word;
        atomInfo.segID = word;
        break;
      case segID :
        lineStream >> word;
        atomInfo.F = word;
        break;
      case Charge :
        lineStream >> word;
        atomInfo.Charge = word;
        break;
      case charge :
        lineStream >> word;
        atomInfo.charge = word;
        break;
      case GrpTypeNo :
        lineStream >> word;
        atomInfo.GrpTypeNo = word;
        break;
      default :
        lineStream >> word;
        cout << "Unknown key: " << *it << ", word: " << word << endl;
        break;
    }
  }
  moreData[newAtom->getId()] = atomInfo;
}


/**
 * Loads atoms from a tremolo-formatted file.
 *
 * \param tremolo file
 */
void TremoloParser::load(istream* file) {
  string line;
  string::size_type location;

  usedFields.clear();
  while (file->good()) {
    std::getline(*file, line, '\n');
    if (usedFields.empty()) {
      location = line.find("ATOMDATA", 0);
      if (location != string::npos) {
       parseAtomDataKeysLine(line, location + 8);
      }
    }
    if (line.length() > 0 && line.at(0) != '#') {
      readAtomDataLine(line);
    }
  }
}

/**
 * Saves the World's current state into as a tremolo file.
 *
 * \param file where to save the state
 */
void TremoloParser::save(ostream* file) {
/*
write header
for (each atom in world) {
  write coordinates and additional data
}
*/
}

TremoloAtomInfoContainer::TremoloAtomInfoContainer() {
  name = "none";
  /* Add suitable default values.
  std::string F;
  std::string stress;
  std::string imprData;
  std::string GroupMeasureTypeNo;
  std::string extType;
  std::string name;
  std::string resName;
  std::string chainID;
  std::string resSeq;
  std::string occupancy;
  std::string tempFactor;
  std::string segID;
  std::string Charge;
  std::string charge;
  std::string GrpTypeNo;
*/
};