source: src/Parser/PdbAtomInfoContainer.cpp@ c88597

/*
 * Project: MoleCuilder
 * Description: creates and alters molecular systems
 * Copyright (C)  2010 University of Bonn. All rights reserved.
 * Please see the LICENSE file or "Copyright notice" in builder.cpp for details.
 */

/*
 * PdbAtomInfoContainer.cpp
 *
 *  Created on: Dec 4, 2010
 *      Author: heber
 */

// include config.h
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif

#include "CodePatterns/MemDebug.hpp"

#include "CodePatterns/Assert.hpp"
//#include "CodePatterns/Log.hpp"
#include "CodePatterns/toString.hpp"
//#include "CodePatterns/Verbose.hpp"
#include "LinearAlgebra/Vector.hpp"
#include "PdbAtomInfoContainer.hpp"

PdbAtomInfoContainer::knownDataKeysMap PdbAtomInfoContainer::knownDataKeys;
bool PdbAtomInfoContainer::knownDataKeys_Filled = false;

PdbAtomInfoContainer::PdbAtomInfoContainer() :
  token("ATOM"),
  serial(0),
  name("-"),
  altLoc('0'),
  resName("-"),
  chainID('0'),
  resSeq(0),
  iCode(' '),
  occupancy(0.),
  tempFactor(0.),
  element(""),
  charge(0)
{
  if (!knownDataKeys_Filled)
    fillknownDataKeys();
}

PdbAtomInfoContainer::~PdbAtomInfoContainer()
{}

void PdbAtomInfoContainer::fillknownDataKeys()
{
  knownDataKeys[PdbKey::token] = "token";
  knownDataKeys[PdbKey::serial] = "serial";
  knownDataKeys[PdbKey::name] = "name";
  knownDataKeys[PdbKey::altLoc] = "altLoc";
  knownDataKeys[PdbKey::resName] = "resName";
  knownDataKeys[PdbKey::chainID] = "chainID";
  knownDataKeys[PdbKey::resSeq] = "resSeq";
  knownDataKeys[PdbKey::iCode] = "iCode";
  knownDataKeys[PdbKey::X] = "X";
  knownDataKeys[PdbKey::Y] = "Y";
  knownDataKeys[PdbKey::Z] = "Z";
  knownDataKeys[PdbKey::occupancy] = "occupancy";
  knownDataKeys[PdbKey::tempFactor] = "tempFactor";
  knownDataKeys[PdbKey::element] = "element";
  knownDataKeys[PdbKey::charge] = "charge";
  knownDataKeys_Filled = true;
}

void PdbAtomInfoContainer::clearknownDataKeys()
{
  knownDataKeys.clear();
  knownDataKeys_Filled = false;
}

void PdbAtomInfoContainer::set(const PdbKey::PdbDataKey key, std::string value)
{
  switch (key) {
    case PdbKey::token :
      ScanKey(token, value);
      break;
    case PdbKey::serial :
      ScanKey(serial, value);
      break;
    case PdbKey::name :
      ScanKey(name, value);
      break;
    case PdbKey::altLoc :
      ScanKey(altLoc, value);
      break;
    case PdbKey::resName :
      ScanKey(resName, value);
      break;
    case PdbKey::chainID :
      ScanKey(chainID, value);
      break;
    case PdbKey::resSeq :
      ScanKey(resSeq, value);
      break;
    case PdbKey::iCode :
      ScanKey(iCode, value);
      break;
    case PdbKey::X :
      ScanKey(XYZ[0], value);
      break;
    case PdbKey::Y :
      ScanKey(XYZ[1], value);
      break;
    case PdbKey::Z :
      ScanKey(XYZ[2], value);
      break;
    case PdbKey::occupancy :
      ScanKey(occupancy, value);
      break;
    case PdbKey::tempFactor :
      ScanKey(tempFactor, value);
      break;
    case PdbKey::element :
      ScanKey(element, value);
      break;
    case PdbKey::charge :
      ScanKey(charge, value);
      break;
    default :
      std::cout << "Unknown key: " << key << ", value: " << value << std::endl;
      break;
  }
}

template <>
std::string PdbAtomInfoContainer::get<std::string>(const PdbKey::PdbDataKey key) const
{
  switch (key) {
    case PdbKey::token :
      return toString(token);
    case PdbKey::serial :
      return toString(serial);
    case PdbKey::name :
      return toString(name);
    case PdbKey::altLoc :
      return toString(altLoc);
    case PdbKey::resName :
      return toString(resName);
    case PdbKey::chainID :
      return toString(chainID);
    case PdbKey::resSeq :
      return toString(resSeq);
    case PdbKey::iCode :
      return toString(iCode);
    case PdbKey::X :
      return toString(XYZ[0]);
    case PdbKey::Y :
      return toString(XYZ[1]);
    case PdbKey::Z :
      return toString(XYZ[2]);
    case PdbKey::occupancy :
      return toString(occupancy);
    case PdbKey::tempFactor :
      return toString(tempFactor);
    case PdbKey::element :
      return toString(element);
    case PdbKey::charge :
      return toString(charge);
    default :
      std::cout << "Unknown key: " << key << std::endl;
      return "";
  }
}

template <>
int PdbAtomInfoContainer::get<int>(const PdbKey::PdbDataKey key) const
{
  switch (key) {
    case PdbKey::serial :
      return serial;
    case PdbKey::resSeq :
      return resSeq;
    case PdbKey::charge :
      return charge;
    default :
      std::cout << "Unknown key or not presentable as int: " << key << std::endl;
      return 0;
  }
}

template <>
double PdbAtomInfoContainer::get<double>(const PdbKey::PdbDataKey key) const
{
  switch (key) {
    case PdbKey::X :
      return XYZ[0];
    case PdbKey::Y :
      return XYZ[1];
    case PdbKey::Z :
      return XYZ[2];
    case PdbKey::occupancy :
      return occupancy;
    case PdbKey::tempFactor :
      return tempFactor;
    default :
      std::cout << "Unknown key or not presentable as double: " << key << std::endl;
      return 0.;
  }
}

const std::string& PdbAtomInfoContainer::getDataKey(PdbKey::PdbDataKey key) const
{
  knownDataKeysMap::const_iterator iter;
  iter = knownDataKeys.find(key);
  ASSERT(iter != knownDataKeys.end(),
      "PdbAtomInfoContainer::getDataKey() - unknown key "
      +toString(key)+" request, did someone add a key to PdbKey?");
  return iter->second;
}

std::ostream& operator<<(std::ostream &ost, const PdbAtomInfoContainer& m)
{
  ost << m.getDataKey(PdbKey::token) << "(" << m.get<std::string>(PdbKey::token) <<") ";
  ost << m.getDataKey(PdbKey::serial) << "(" << m.get<std::string>(PdbKey::serial) <<") ";
  ost << m.getDataKey(PdbKey::name) << "(" << m.get<std::string>(PdbKey::name) <<") ";
  ost << m.getDataKey(PdbKey::altLoc) << "(" << m.get<std::string>(PdbKey::altLoc) <<") ";
  ost << m.getDataKey(PdbKey::resName) << "(" << m.get<std::string>(PdbKey::resName) <<") ";
  ost << m.getDataKey(PdbKey::chainID) << "(" << m.get<std::string>(PdbKey::chainID) <<") ";
  ost << m.getDataKey(PdbKey::resSeq) << "(" << m.get<std::string>(PdbKey::resSeq) <<") ";
  ost << m.getDataKey(PdbKey::iCode) << "(" << m.get<std::string>(PdbKey::iCode) <<") ";
  ost << m.getDataKey(PdbKey::X) << "(" << m.get<std::string>(PdbKey::X) <<") ";
  ost << m.getDataKey(PdbKey::Y) << "(" << m.get<std::string>(PdbKey::Y) <<") ";
  ost << m.getDataKey(PdbKey::Z) << "(" << m.get<std::string>(PdbKey::Z) <<") ";
  ost << m.getDataKey(PdbKey::occupancy) << "(" << m.get<std::string>(PdbKey::occupancy) <<") ";
  ost << m.getDataKey(PdbKey::tempFactor) << "(" << m.get<std::string>(PdbKey::tempFactor) <<") ";
  ost << m.getDataKey(PdbKey::element) << "(" << m.get<std::string>(PdbKey::element) <<") ";
  ost << m.getDataKey(PdbKey::charge) << "(" << m.get<std::string>(PdbKey::charge) <<") ";
  return ost;
}