Changes in src/Parser/PdbParser.cpp [4c1230:73916f]

File:

• src/Parser/PdbParser.cpp (modified) (19 diffs)

src/Parser/PdbParser.cpp

@@ -46 +46 @@
 PdbParser::PdbParser() {
   knownTokens["ATOM"] = PdbKey::Atom;
+  knownTokens["HETATM"] = PdbKey::Atom;
   knownTokens["TER"] = PdbKey::Filler;
   knownTokens["END"] = PdbKey::EndOfFile;
@@ -51 +52 @@
   knownTokens["REMARK"] = PdbKey::Remark;
   knownTokens[""] = PdbKey::EndOfFile;
+
+  // argh, why can't just PdbKey::X+(size_t)i
+  PositionEnumMap[0] = PdbKey::X;
+  PositionEnumMap[1] = PdbKey::Y;
+  PositionEnumMap[2] = PdbKey::Z;
 }
 
@@ -99 +105 @@
   size_t linecount  = 0;
   enum PdbKey::KnownTokens token;
+
+  // reset atomIdMap for this file (to correctly parse CONECT entries)
+  atomIdMap.clear();
 
   molecule *newmol = World::getInstance().createMolecule();
@@ -136 +145 @@
 
 /**
- * Saves the World's current state into as a PDB file.
+ * Saves the \a atoms into as a PDB file.
  *
  * \param file where to save the state
- */
-void PdbParser::save(ostream* file) {
+ * \param atoms atoms to store
+ */
+void PdbParser::save(ostream* file, const std::vector<atom *> &AtomList)
+{
   DoLog(0) && (Log() << Verbose(0) << "Saving changes to pdb." << std::endl);
-
   {
     // add initial remark
@@ -157 +167 @@
   }
 
-  // we distribute new atom numbers, hence clear map beforehand
+  // we distribute serials, hence clear map beforehand
   atomIdMap.clear();
   {
-    vector<atom *> AtomList = World::getInstance().getAllAtoms();
-
-    std::vector<int> elementNo(MAX_ELEMENTS,1);
+    std::map<size_t,size_t> MolIdMap;
+    size_t MolNo = 1;  // residue number starts at 1 in pdb
+    for (vector<atom *>::const_iterator atomIt = AtomList.begin(); atomIt != AtomList.end(); atomIt++) {
+      const molecule *mol = (*atomIt)->getMolecule();
+      if ((mol != NULL) && (MolIdMap.find(mol->getId()) == MolIdMap.end())) {
+        MolIdMap[mol->getId()] = MolNo++;
+      }
+    }
+    const size_t MaxMol = MolNo;
+
+    // have a count per element and per molecule (0 is for all homeless atoms)
+    std::vector<int> **elementNo = new std::vector<int>*[MaxMol];
+    for (size_t i = 0; i < MaxMol; ++i)
+      elementNo[i] = new std::vector<int>(MAX_ELEMENTS,1);
     char name[MAXSTRINGSIZE];
+    std::string ResidueName;
 
     // write ATOMs
     int AtomNo = 1; // serial number starts at 1 in pdb
-    int MolNo = 1;  // residue number starts at 1 in pdb
-    for (vector<atom *>::iterator atomIt = AtomList.begin(); atomIt != AtomList.end(); atomIt++) {
+    for (vector<atom *>::const_iterator atomIt = AtomList.begin(); atomIt != AtomList.end(); atomIt++) {
+      PdbAtomInfoContainer &atomInfo = getadditionalAtomData(*atomIt);
+      // gather info about residue
+      const molecule *mol = (*atomIt)->getMolecule();
+      if (mol == NULL) {
+        MolNo = 0;
+        atomInfo.set(PdbKey::resSeq, "0");
+      } else {
+        ASSERT(MolIdMap.find(mol->getId()) != MolIdMap.end(),
+            "PdbParser::save() - Mol id "+toString(mol->getId())+" not present despite we set it?!");
+        MolNo = MolIdMap[mol->getId()];
+        atomInfo.set(PdbKey::resSeq, toString(MolIdMap[mol->getId()]));
+        if (atomInfo.get<std::string>(PdbKey::resName) == "-")
+          atomInfo.set(PdbKey::resName, mol->getName().substr(0,3));
+      }
+      // get info about atom
       const size_t  Z = (*atomIt)->getType()->getAtomicNumber();
-      sprintf(name, "%2s%02d",(*atomIt)->getType()->getSymbol().c_str(), elementNo[Z]);
-      elementNo[Z] = (elementNo[Z]+1) % 100;   // confine to two digits
-      const molecule *mol = (*atomIt)->getMolecule();
-      if (mol == NULL) {  // for homeless atoms, MolNo = -1 is reserved
-        MolNo = -1;
-      } else {
-        MolNo = mol->getId();
+      if (atomInfo.get<std::string>(PdbKey::name) == "-") {  // if no name set, give it a new name
+        sprintf(name, "%2s%02d",(*atomIt)->getType()->getSymbol().c_str(), (*elementNo[MolNo])[Z]);
+        (*elementNo[MolNo])[Z] = ((*elementNo[MolNo])[Z]+1) % 100;   // confine to two digits
+        atomInfo.set(PdbKey::name, name);
       }
-      saveLine(file, *atomIt, name, AtomNo, MolNo);
-      setAtomId((*atomIt)->getId(), AtomNo);
+      // set position
+      for (size_t i=0; i<NDIM;++i) {
+        stringstream position;
+        position << setw(8) << fixed << setprecision(3) << (*atomIt)->getPosition().at(i);
+        atomInfo.set(PositionEnumMap[i], position.str());
+      }
+      // change element and charge if changed
+      if (atomInfo.get<std::string>(PdbKey::element) != (*atomIt)->getType()->getSymbol())
+        atomInfo.set(PdbKey::element, (*atomIt)->getType()->getSymbol());
+      setSerial((*atomIt)->getId(), AtomNo);
+      atomInfo.set(PdbKey::serial, toString(AtomNo));
+
+      // finally save the line
+      saveLine(file, atomInfo);
       AtomNo++;
     }
+    for (size_t i = 0; i < MaxMol; ++i)
+      delete elementNo[i];
+    delete elementNo;
 
     // write CONECTs
-    for (vector<atom *>::iterator atomIt = AtomList.begin(); atomIt != AtomList.end(); atomIt++) {
+    for (vector<atom *>::const_iterator atomIt = AtomList.begin(); atomIt != AtomList.end(); atomIt++) {
       writeNeighbors(file, 4, *atomIt);
     }
@@ -193 +241 @@
 }
 
+/** Either returns reference to present entry or creates new with default values.
+ *
+ * @param _atom atom whose entry we desire
+ * @return
+ */
+PdbAtomInfoContainer& PdbParser::getadditionalAtomData(atom *_atom)
+{
+  if (additionalAtomData.find(_atom->getId()) != additionalAtomData.end()) {
+  } else if (additionalAtomData.find(_atom->father->getId()) != additionalAtomData.end()) {
+    // use info from direct father
+    additionalAtomData[_atom->getId()] = additionalAtomData[_atom->father->getId()];
+  } else if (additionalAtomData.find(_atom->GetTrueFather()->getId()) != additionalAtomData.end()) {
+    // use info from topmost father
+    additionalAtomData[_atom->getId()] = additionalAtomData[_atom->GetTrueFather()->getId()];
+  } else {
+    // create new entry use default values if nothing else is known
+    additionalAtomData[_atom->getId()] = defaultAdditionalData;
+  }
+  return additionalAtomData[_atom->getId()];
+}
+
 /**
  * Writes one line of PDB-formatted data to the provided stream.
@@ -198 +267 @@
  * \param stream where to write the line to
  * \param *currentAtom the atom of which information should be written
+ * \param AtomNo serial number of atom
  * \param *name name of atom, i.e. H01
- * \param AtomNo serial number of atom
+ * \param ResidueName Name of molecule
  * \param ResidueNo number of residue
  */
-void PdbParser::saveLine(ostream* file, const atom* currentAtom, const char *name, const int AtomNo, const int ResidueNo) {
-  *file << "ATOM ";
-  *file << setw(6) << AtomNo; /* atom serial number */
-  *file << setw(1) << " ";
-  *file << setfill(' ') << left << setw(4) << name << right;  /* atom name */
-  *file << setw(1) << " ";
-  *file << setfill(' ') << setw(3) << ((currentAtom->getMolecule() != NULL) ? currentAtom->getMolecule()->getName().substr(0,3) : "-");  /* residue name */
-  *file << setw(1) << " ";
-  *file << setfill(' ') << setw(1) << (char)('a'+(unsigned char)(AtomNo % 26)); /* letter for chain */
-  *file << setw(4) << ResidueNo; /* residue sequence number */
-  *file << setw(4) << "    ";
-  for (int i=0;i<NDIM;i++) {
-    *file << setw(8) << setprecision(3) << showpoint << currentAtom->at(i); /* positional coordinate in Angstroem */
-  }
-  *file << setw(6) << setprecision(2) << showpoint << (double)currentAtom->getType()->getValence(); /* occupancy */
-  *file << setw(6) << setprecision(2) << showpoint << (double)currentAtom->getType()->getNoValenceOrbitals(); /* temperature factor */
-  *file << noshowpoint;
-  *file << setw(6) << "      ";
-  *file << setw(4) << "0";
-  *file << setfill(' ') << setw(2) << currentAtom->getType()->getSymbol();
-  *file << setw(2) << "0";
+void PdbParser::saveLine(
+    ostream* file,
+    const PdbAtomInfoContainer &atomInfo)
+{
+  *file << setfill(' ') << left << setw(6)
+      << atomInfo.get<std::string>(PdbKey::token);
+  *file << setfill(' ') << right << setw(5)
+      << atomInfo.get<int>(PdbKey::serial); /* atom serial number */
+  *file << " "; /* char 12 is empty */
+  *file << setfill(' ') << left << setw(4)
+      << atomInfo.get<std::string>(PdbKey::name);  /* atom name */
+  *file << setfill(' ') << left << setw(1)
+      << atomInfo.get<std::string>(PdbKey::altLoc); /* alternate location/conformation */
+  *file << setfill(' ') << left << setw(3)
+      << atomInfo.get<std::string>(PdbKey::resName);  /* residue name */
+  *file << " "; /* char 21 is empty */
+  *file << setfill(' ') << left << setw(1)
+      << atomInfo.get<std::string>(PdbKey::chainID); /* chain identifier */
+  *file << setfill(' ') << left << setw(4)
+      << atomInfo.get<int>(PdbKey::resSeq); /* residue sequence number */
+  *file << setfill(' ') << left << setw(1)
+      << atomInfo.get<std::string>(PdbKey::iCode); /* iCode */
+  *file << "   "; /* char 28-30 are empty */
+  // have the following operate on stringstreams such that format specifiers
+  // only act on these
+  for (size_t i=0;i<NDIM;++i) {
+    stringstream position;
+    position << fixed << setprecision(3) << showpoint
+        << atomInfo.get<double>(PositionEnumMap[i]);
+    *file << setfill(' ') << right << setw(8) << position.str();
+  }
+  {
+    stringstream occupancy;
+    occupancy << fixed << setprecision(2) << showpoint
+        << atomInfo.get<double>(PdbKey::occupancy); /* occupancy */
+    *file << setfill(' ') << right << setw(6) << occupancy.str();
+  }
+  {
+    stringstream tempFactor;
+    tempFactor << fixed << setprecision(2) << showpoint
+        << atomInfo.get<double>(PdbKey::tempFactor); /* temperature factor */
+    *file << setfill(' ') << right << setw(6) << tempFactor.str();
+  }
+  *file << "          "; /* char 68-76 are empty */
+  *file << setfill(' ') << right << setw(2) << atomInfo.get<std::string>(PdbKey::element); /* element */
+  *file << setfill(' ') << right << setw(2) << atomInfo.get<int>(PdbKey::charge); /* charge */
 
   *file << endl;
@@ -240 +335 @@
       if (MaxNo >= MaxnumberOfNeighbors) {
         *file << "CONECT";
-        *file << setw(5) << getAtomId(currentAtom->getId());
+        *file << setw(5) << getSerial(currentAtom->getId());
         MaxNo = 0;
       }
-      *file << setw(5) << getAtomId((*currentBond)->GetOtherAtom(currentAtom)->getId());
+      *file << setw(5) << getSerial((*currentBond)->GetOtherAtom(currentAtom)->getId());
       MaxNo++;
       if (MaxNo == MaxnumberOfNeighbors)
@@ -253 +348 @@
 }
 
-
 /** Retrieves a value from PdbParser::atomIdMap.
  * \param atomid key
@@ -259 +353 @@
  */
 size_t PdbParser::getSerial(const size_t atomid) const
-{
-  ConvertTo<size_t> toSize_t;
-  ASSERT(additionalAtomData.find(atomid) != additionalAtomData.end(),
-      "PdbParser::getSerial: atomid "+toString(atomid)+" not present in Map.");
-  const PdbAtomInfoContainer &atomInfo = additionalAtomData.at(atomid);
-
-  return toSize_t(atomInfo.get(PdbKey::serial));
-}
-
-/** Retrieves a value from PdbParser::atomIdMap.
- * \param atomid key
- * \return value
- */
-size_t PdbParser::getAtomId(const size_t atomid) const
 {
   ASSERT(atomIdMap.find(atomid) != atomIdMap.end(), "PdbParser::getAtomId: atomid not present in Map.");
@@ -283 +363 @@
  * \return true - key not present, false - value present
  */
-void PdbParser::setAtomId(const size_t localatomid, const size_t atomid)
+void PdbParser::setSerial(const size_t localatomid, const size_t atomid)
 {
   pair<std::map<size_t,size_t>::iterator, bool > inserter;
-  DoLog(1) && (Log() << Verbose(1) << "PdbParser::setAtomId() - Inserting ("
-      << localatomid << " -> " << atomid << ")." << std::endl);
+//  DoLog(1) && (Log() << Verbose(1) << "PdbParser::setAtomId() - Inserting ("
+//      << localatomid << " -> " << atomid << ")." << std::endl);
   inserter = atomIdMap.insert( make_pair(localatomid, atomid) );
   ASSERT(inserter.second, "PdbParser::setAtomId: atomId already present in Map.");
@@ -307 +387 @@
   stringstream lineStream;
   atom* newAtom = World::getInstance().createAtom();
-  additionalAtomData[newAtom->getId()] = *(new PdbAtomInfoContainer);
-  PdbAtomInfoContainer &atomInfo = additionalAtomData[newAtom->getId()];
+  PdbAtomInfoContainer &atomInfo = getadditionalAtomData(newAtom);
   string word;
   ConvertTo<size_t> toSize_t;
@@ -314 +393 @@
 
   lineStream << line;
+  atomInfo.set(PdbKey::token, line.substr(0,6));
   atomInfo.set(PdbKey::serial, line.substr(6,5));
   std::pair< std::set<size_t>::const_iterator, bool> Inserter =
-    SerialSet.insert(toSize_t(atomInfo.get(PdbKey::serial)));
+    SerialSet.insert(toSize_t(atomInfo.get<std::string>(PdbKey::serial)));
   ASSERT(Inserter.second,
       "PdbParser::readAtomDataLine() - ATOM contains entry with serial "
-      +atomInfo.get(PdbKey::serial)+" already present!");
+      +atomInfo.get<std::string>(PdbKey::serial)+" already present!");
   // assign hightest+1 instead, but then beware of CONECT entries! Another map needed!
 //  if (!Inserter.second) {
@@ -326 +406 @@
 //    atomInfo.set(PdbKey::serial, toString(id));
 //    DoeLog(2) && (eLog() << Verbose(2)
-//        << "Serial " << atomInfo.get(PdbKey::serial) << " already present, "
+//        << "Serial " << atomInfo.get<std::string>(PdbKey::serial) << " already present, "
 //        << "assigning " << toString(id) << " instead." << std::endl);
 //  }
@@ -348 +428 @@
 //      << line.substr(78,2) << std::endl);
 
-  setAtomId(toSize_t(atomInfo.get(PdbKey::serial)), newAtom->getId());
+  setSerial(toSize_t(atomInfo.get<std::string>(PdbKey::serial)), newAtom->getId());
   atomInfo.set(PdbKey::name, line.substr(12,4));
-  atomInfo.set(PdbKey::altloc, line.substr(16,1));
+  atomInfo.set(PdbKey::altLoc, line.substr(16,1));
   atomInfo.set(PdbKey::resName, line.substr(17,3));
   atomInfo.set(PdbKey::chainID, line.substr(21,1));
@@ -364 +444 @@
   atomInfo.set(PdbKey::tempFactor, line.substr(60,6));
   atomInfo.set(PdbKey::charge, line.substr(78,2));
-  PdbAtomInfoContainer::ScanKey(word, line.substr(76,2));
-  newAtom->setType(World::getInstance().getPeriode()->FindElement(word));
+  atomInfo.set(PdbKey::element, line.substr(76,2));
+  const element *elem = World::getInstance().getPeriode()
+      ->FindElement(atomInfo.get<std::string>(PdbKey::element));
+  ASSERT(elem != NULL,
+      "PdbParser::readAtomDataLine() - element "+atomInfo.get<std::string>(PdbKey::element)+" is unknown!");
+  newAtom->setType(elem);
 
   if (newmol != NULL)
@@ -381 +465 @@
 
   DoLog(1) && (Log() << Verbose(1) << "We know about atom " << newAtom->getId() << ":" << std::endl);
-  DoLog(1) && (Log() << Verbose(1) << "\tserial is " << atomInfo.get(PdbKey::serial) << std::endl);
-  DoLog(1) && (Log() << Verbose(1) << "\tname is " << atomInfo.get(PdbKey::name) << std::endl);
-  DoLog(1) && (Log() << Verbose(1) << "\taltloc is " << atomInfo.get(PdbKey::altloc) << std::endl);
-  DoLog(1) && (Log() << Verbose(1) << "\tresName is " << atomInfo.get(PdbKey::resName) << std::endl);
-  DoLog(1) && (Log() << Verbose(1) << "\tchainID is " << atomInfo.get(PdbKey::chainID) << std::endl);
-  DoLog(1) && (Log() << Verbose(1) << "\tresSeq is " << atomInfo.get(PdbKey::resSeq) << std::endl);
-  DoLog(1) && (Log() << Verbose(1) << "\tiCode is " << atomInfo.get(PdbKey::iCode) << std::endl);
-  DoLog(1) && (Log() << Verbose(1) << "\tx is " << newAtom->getPosition() << std::endl);
-  DoLog(1) && (Log() << Verbose(1) << "\toccupancy is " << atomInfo.get(PdbKey::occupancy) << std::endl);
-  DoLog(1) && (Log() << Verbose(1) << "\ttempFactor is " << atomInfo.get(PdbKey::tempFactor) << std::endl);
+  DoLog(1) && (Log() << Verbose(1) << "\ttoken is " << atomInfo.get<std::string>(PdbKey::token) << std::endl);
+  DoLog(1) && (Log() << Verbose(1) << "\tserial is " << atomInfo.get<int>(PdbKey::serial) << std::endl);
+  DoLog(1) && (Log() << Verbose(1) << "\tname is " << atomInfo.get<std::string>(PdbKey::name) << std::endl);
+  DoLog(1) && (Log() << Verbose(1) << "\taltLoc is " << atomInfo.get<std::string>(PdbKey::altLoc) << std::endl);
+  DoLog(1) && (Log() << Verbose(1) << "\tresName is " << atomInfo.get<std::string>(PdbKey::resName) << std::endl);
+  DoLog(1) && (Log() << Verbose(1) << "\tchainID is " << atomInfo.get<std::string>(PdbKey::chainID) << std::endl);
+  DoLog(1) && (Log() << Verbose(1) << "\tresSeq is " << atomInfo.get<int>(PdbKey::resSeq) << std::endl);
+  DoLog(1) && (Log() << Verbose(1) << "\tiCode is " << atomInfo.get<std::string>(PdbKey::iCode) << std::endl);
+  DoLog(1) && (Log() << Verbose(1) << "\tX is " << atomInfo.get<double>(PdbKey::X) << std::endl);
+  DoLog(1) && (Log() << Verbose(1) << "\tY is " << atomInfo.get<double>(PdbKey::Y) << std::endl);
+  DoLog(1) && (Log() << Verbose(1) << "\tZ is " << atomInfo.get<double>(PdbKey::Z) << std::endl);
+  DoLog(1) && (Log() << Verbose(1) << "\toccupancy is " << atomInfo.get<double>(PdbKey::occupancy) << std::endl);
+  DoLog(1) && (Log() << Verbose(1) << "\ttempFactor is " << atomInfo.get<double>(PdbKey::tempFactor) << std::endl);
   DoLog(1) && (Log() << Verbose(1) << "\telement is '" << *(newAtom->getType()) << "'" << std::endl);
-  DoLog(1) && (Log() << Verbose(1) << "\tcharge is " << atomInfo.get(PdbKey::charge) << std::endl);
+  DoLog(1) && (Log() << Verbose(1) << "\tcharge is " << atomInfo.get<int>(PdbKey::charge) << std::endl);
 }
 
@@ -426 +513 @@
 
   // add neighbours
-  atom *_atom = World::getInstance().getAtom(AtomById(getAtomId(id)));
+  atom *_atom = World::getInstance().getAtom(AtomById(getSerial(id)));
   for (std::list<size_t>::const_iterator iter = ListOfNeighbors.begin();
       iter != ListOfNeighbors.end();
       ++iter) {
 //    DoLog(1) && (Log() << Verbose(1) << "Adding Bond (" << getAtomId(id) << "," << getAtomId(*iter) << ")" << std::endl);
-    atom * const _Otheratom = World::getInstance().getAtom(AtomById(getAtomId(*iter)));
+    atom * const _Otheratom = World::getInstance().getAtom(AtomById(getSerial(*iter)));
     _atom->addBond(_Otheratom);
   }
@@ -478 +565 @@
       const PdbAtomInfoContainer &OtheratomInfo = b.additionalAtomData.at((*iter)->getId());
 
-      status = status && (atomInfo.get(PdbKey::serial) == OtheratomInfo.get(PdbKey::serial));
+      status = status && (atomInfo.get<std::string>(PdbKey::serial) == OtheratomInfo.get<std::string>(PdbKey::serial));
       if (!status) DoeLog(1) && (eLog() << Verbose(1) << "Mismatch in serials!" << std::endl);
-      status = status && (atomInfo.get(PdbKey::name) == OtheratomInfo.get(PdbKey::name));
+      status = status && (atomInfo.get<std::string>(PdbKey::name) == OtheratomInfo.get<std::string>(PdbKey::name));
       if (!status) DoeLog(1) && (eLog() << Verbose(1) << "Mismatch in names!" << std::endl);
-      status = status && (atomInfo.get(PdbKey::altloc) == OtheratomInfo.get(PdbKey::altloc));
-      if (!status) DoeLog(1) && (eLog() << Verbose(1) << "Mismatch in altlocs!" << std::endl);
-      status = status && (atomInfo.get(PdbKey::resName) == OtheratomInfo.get(PdbKey::resName));
+      status = status && (atomInfo.get<std::string>(PdbKey::altLoc) == OtheratomInfo.get<std::string>(PdbKey::altLoc));
+      if (!status) DoeLog(1) && (eLog() << Verbose(1) << "Mismatch in altLocs!" << std::endl);
+      status = status && (atomInfo.get<std::string>(PdbKey::resName) == OtheratomInfo.get<std::string>(PdbKey::resName));
       if (!status) DoeLog(1) && (eLog() << Verbose(1) << "Mismatch in resNames!" << std::endl);
-      status = status && (atomInfo.get(PdbKey::chainID) == OtheratomInfo.get(PdbKey::chainID));
+      status = status && (atomInfo.get<std::string>(PdbKey::chainID) == OtheratomInfo.get<std::string>(PdbKey::chainID));
       if (!status) DoeLog(1) && (eLog() << Verbose(1) << "Mismatch in chainIDs!" << std::endl);
-      status = status && (atomInfo.get(PdbKey::resSeq) == OtheratomInfo.get(PdbKey::resSeq));
+      status = status && (atomInfo.get<std::string>(PdbKey::resSeq) == OtheratomInfo.get<std::string>(PdbKey::resSeq));
       if (!status) DoeLog(1) && (eLog() << Verbose(1) << "Mismatch in resSeqs!" << std::endl);
-      status = status && (atomInfo.get(PdbKey::iCode) == OtheratomInfo.get(PdbKey::iCode));
+      status = status && (atomInfo.get<std::string>(PdbKey::iCode) == OtheratomInfo.get<std::string>(PdbKey::iCode));
       if (!status) DoeLog(1) && (eLog() << Verbose(1) << "Mismatch in iCodes!" << std::endl);
-      status = status && (atomInfo.get(PdbKey::occupancy) == OtheratomInfo.get(PdbKey::occupancy));
+      status = status && (atomInfo.get<std::string>(PdbKey::occupancy) == OtheratomInfo.get<std::string>(PdbKey::occupancy));
       if (!status) DoeLog(1) && (eLog() << Verbose(1) << "Mismatch in occupancies!" << std::endl);
-      status = status && (atomInfo.get(PdbKey::tempFactor) == OtheratomInfo.get(PdbKey::tempFactor));
+      status = status && (atomInfo.get<std::string>(PdbKey::tempFactor) == OtheratomInfo.get<std::string>(PdbKey::tempFactor));
       if (!status) DoeLog(1) && (eLog() << Verbose(1) << "Mismatch in tempFactors!" << std::endl);
-      status = status && (atomInfo.get(PdbKey::charge) == OtheratomInfo.get(PdbKey::charge));
+      status = status && (atomInfo.get<std::string>(PdbKey::charge) == OtheratomInfo.get<std::string>(PdbKey::charge));
       if (!status) DoeLog(1) && (eLog() << Verbose(1) << "Mismatch in charges!" << std::endl);
     }