Changes in src/Parser/PdbParser.cpp [765f16:3bdb6d]

File:

• src/Parser/PdbParser.cpp (modified) (29 diffs)

src/Parser/PdbParser.cpp

@@ -28 +28 @@
 #include "atom.hpp"
 #include "Bond/bond.hpp"
-#include "element.hpp"
+#include "Element/element.hpp"
 #include "molecule.hpp"
-#include "periodentafel.hpp"
+#include "Element/periodentafel.hpp"
 #include "Descriptors/AtomIdDescriptor.hpp"
 #include "Parser/PdbParser.hpp"
@@ -44 +44 @@
 using namespace std;
 
-// declare specialized static variables
-const std::string FormatParserTrait<pdb>::name = "pdb";
-const std::string FormatParserTrait<pdb>::suffix = "pdb";
-const ParserTypes FormatParserTrait<pdb>::type = pdb;
-
 /**
  * Constructor.
  */
-FormatParser< pdb >::FormatParser() :
-  FormatParser_common(NULL)
-{
+PdbParser::PdbParser() {
   knownTokens["ATOM"] = PdbKey::Atom;
   knownTokens["HETATM"] = PdbKey::Atom;
@@ -72 +65 @@
  * Destructor.
  */
-FormatParser< pdb >::~FormatParser() 
-{
+PdbParser::~PdbParser() {
   PdbAtomInfoContainer::clearknownDataKeys();
   additionalAtomData.clear();
@@ -85 +77 @@
  * @return token type
  */
-enum PdbKey::KnownTokens FormatParser< pdb >::getToken(string &line)
+enum PdbKey::KnownTokens PdbParser::getToken(string &line)
 {
   // look for first space
@@ -113 +105 @@
  * \param PDB file
  */
-void FormatParser< pdb >::load(istream* file) {
+void PdbParser::load(istream* file) {
   string line;
   size_t linecount  = 0;
@@ -156 +148 @@
             // TODO: put a throw here
             DoeLog(2) && (eLog() << Verbose(2) << "Unknown token: '" << line << "' for time step " << step << "." << std::endl);
-            //ASSERT(0, "FormatParser< pdb >::load() - Unknown token in line "+toString(linecount)+": "+line+".");
+            //ASSERT(0, "PdbParser::load() - Unknown token in line "+toString(linecount)+": "+line+".");
             break;
         }
@@ -178 +170 @@
  * \param atoms atoms to store
  */
-void FormatParser< pdb >::save(ostream* file, const std::vector<atom *> &AtomList)
+void PdbParser::save(ostream* file, const std::vector<atom *> &AtomList)
 {
   DoLog(0) && (Log() << Verbose(0) << "Saving changes to pdb." << std::endl);
@@ -248 +240 @@
         } else {
           ASSERT(MolIdMap.find(mol->getId()) != MolIdMap.end(),
-              "FormatParser< pdb >::save() - Mol id "+toString(mol->getId())+" not present despite we set it?!");
+              "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()]));
@@ -297 +289 @@
  * @param id of atom
  */
-void FormatParser< pdb >::AtomInserted(atomId_t id)
-{
-  //LOG(3, "FormatParser< pdb >::AtomInserted() - notified of atom " << id << "'s insertion.");
+void PdbParser::AtomInserted(atomId_t id)
+{
+  //LOG(3, "PdbParser::AtomInserted() - notified of atom " << id << "'s insertion.");
   ASSERT(!isPresentadditionalAtomData(id),
-      "FormatParser< pdb >::AtomInserted() - additionalAtomData already present for newly added atom "
+      "PdbParser::AtomInserted() - additionalAtomData already present for newly added atom "
       +toString(id)+".");
   // don't insert here as this is our check whether we are in the first time step
@@ -312 +304 @@
  * @param id of atom
  */
-void FormatParser< pdb >::AtomRemoved(atomId_t id)
-{
-  //LOG(3, "FormatParser< pdb >::AtomRemoved() - notified of atom " << id << "'s removal.");
+void PdbParser::AtomRemoved(atomId_t id)
+{
+  //LOG(3, "PdbParser::AtomRemoved() - notified of atom " << id << "'s removal.");
   std::map<size_t, PdbAtomInfoContainer>::iterator iter = additionalAtomData.find(id);
   // as we do not insert AtomData on AtomInserted, we cannot be assured of its presence
 //  ASSERT(iter != additionalAtomData.end(),
-//      "FormatParser< pdb >::AtomRemoved() - additionalAtomData is not present for atom "
+//      "PdbParser::AtomRemoved() - additionalAtomData is not present for atom "
 //      +toString(id)+" to remove.");
   if (iter != additionalAtomData.end()) {
@@ -333 +325 @@
  * @return true - entry present, false - only for atom's father or no entry
  */
-bool FormatParser< pdb >::isPresentadditionalAtomData(unsigned int _id)
+bool PdbParser::isPresentadditionalAtomData(unsigned int _id)
 {
   return (additionalAtomData.find(_id) != additionalAtomData.end());
@@ -344 +336 @@
  * @return
  */
-PdbAtomInfoContainer& FormatParser< pdb >::getadditionalAtomData(atom *_atom)
+PdbAtomInfoContainer& PdbParser::getadditionalAtomData(atom *_atom)
 {
   if (additionalAtomData.find(_atom->getId()) != additionalAtomData.end()) {
@@ -370 +362 @@
  * \param ResidueNo number of residue
  */
-void FormatParser< pdb >::saveLine(
+void PdbParser::saveLine(
     ostream* file,
     const PdbAtomInfoContainer &atomInfo)
@@ -431 +423 @@
  * \param *currentAtom to the atom of which to take the neighbor information
  */
-void FormatParser< pdb >::writeNeighbors(ostream* file, int MaxnumberOfNeighbors, atom* currentAtom) {
+void PdbParser::writeNeighbors(ostream* file, int MaxnumberOfNeighbors, atom* currentAtom) {
   int MaxNo = MaxnumberOfNeighbors;
   int charsleft = 80;
@@ -460 +452 @@
 }
 
-/** Retrieves a value from  FormatParser< pdb >::atomIdMap.
+/** Retrieves a value from PdbParser::atomIdMap.
  * \param atomid key
  * \return value
  */
-size_t FormatParser< pdb >::getSerial(const size_t atomid) const
-{
-  ASSERT(atomIdMap.find(atomid) != atomIdMap.end(), 
-      "FormatParser< pdb >::getAtomId: atomid "+toString(atomid)+" not present in Map.");
+size_t PdbParser::getSerial(const size_t atomid) const
+{
+  ASSERT(atomIdMap.find(atomid) != atomIdMap.end(),
+      "PdbParser::getSerial() - atomid "+toString(atomid)+" not present in Map.");
   return (atomIdMap.find(atomid)->second);
 }
 
-/** Sets an entry in  FormatParser< pdb >::atomIdMap.
+/** Sets an entry in PdbParser::atomIdMap.
  * \param localatomid key
  * \param atomid value
  * \return true - key not present, false - value present
  */
-void FormatParser< pdb >::setSerial(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) << "FormatParser< pdb >::setAtomId() - Inserting ("
+//  DoLog(1) && (Log() << Verbose(1) << "PdbParser::setAtomId() - Inserting ("
 //      << localatomid << " -> " << atomid << ")." << std::endl);
   inserter = atomIdMap.insert( make_pair(localatomid, atomid) );
-  ASSERT(inserter.second, "FormatParser< pdb >::setAtomId: atomId already present in Map.");
+  ASSERT(inserter.second, "PdbParser::setAtomId: atomId already present in Map.");
 }
 
@@ -490 +482 @@
  * @return
  */
-atom* FormatParser< pdb >::getAtomToParse(std::string id_string) const
+atom* PdbParser::getAtomToParse(std::string id_string) const
 {
   // get the local ID
@@ -525 +517 @@
  * @param line line containing key ATOM
  */
-void FormatParser< pdb >::readPdbAtomInfoContainer(PdbAtomInfoContainer &atomInfo, std::string &line) const
+void PdbParser::readPdbAtomInfoContainer(PdbAtomInfoContainer &atomInfo, std::string &line) const
 {
   const size_t length = line.length();
   if (length < 80)
-    ELOG(2, "FormatParser< pdb >::readPdbAtomInfoContainer() - pdb is mal-formed, containing less than 80 chars!");
+    ELOG(2, "PdbParser::readPdbAtomInfoContainer() - pdb is mal-formed, containing less than 80 chars!");
   if (length >= 6) {
     LOG(4,"INFO: Parsing token from "+line.substr(0,6)+".");
@@ -538 +530 @@
     atomInfo.set(PdbKey::serial, line.substr(6,5));
     ASSERT(atomInfo.get<int>(PdbKey::serial) != 0,
-        "FormatParser< pdb >::readPdbAtomInfoContainer() - serial 0 is invalid (filler id for conect entries).");
+        "PdbParser::readPdbAtomInfoContainer() - serial 0 is invalid (filler id for conect entries).");
   }
 
@@ -599 +591 @@
  * \param newmol molecule to add parsed atoms to
  */
-void FormatParser< pdb >::readAtomDataLine(const unsigned int _step, std::string &line, molecule *newmol = NULL) {
+void PdbParser::readAtomDataLine(const unsigned int _step, std::string &line, molecule *newmol = NULL) {
   vector<string>::iterator it;
 
@@ -606 +598 @@
   bool FirstTimestep = isPresentadditionalAtomData(newAtom->getId()) ? false : true;
   ASSERT((FirstTimestep && (_step == 0)) || (!FirstTimestep && (_step !=0)),
-      "FormatParser< pdb >::readAtomDataLine() - additionalAtomData present though atom is newly parsed.");
+      "PdbParser::readAtomDataLine() - additionalAtomData present though atom is newly parsed.");
   if (FirstTimestep) {
     LOG(3,"INFO: Parsing new atom.");
@@ -654 +646 @@
       SerialSet.insert(toSize_t(atomInfo.get<std::string>(PdbKey::serial)));
     ASSERT(Inserter.second,
-        "FormatParser< pdb >::readAtomDataLine() - ATOM contains entry with serial "
+        "PdbParser::readAtomDataLine() - ATOM contains entry with serial "
         +atomInfo.get<std::string>(PdbKey::serial)+" already present!");
     setSerial(toSize_t(atomInfo.get<std::string>(PdbKey::serial)), newAtom->getId());
@@ -675 +667 @@
         ->FindElement(value);
     ASSERT(elem != NULL,
-        "FormatParser< pdb >::readAtomDataLine() - element "+atomInfo.get<std::string>(PdbKey::element)+" is unknown!");
+        "PdbParser::readAtomDataLine() - element "+atomInfo.get<std::string>(PdbKey::element)+" is unknown!");
     newAtom->setType(elem);
 
@@ -687 +679 @@
     // then check additional info for consistency
     ASSERT(atomInfo.get<std::string>(PdbKey::token) == consistencyInfo.get<std::string>(PdbKey::token),
-        "FormatParser< pdb >::readAtomDataLine() - difference in token on multiple time step for atom with id "
+        "PdbParser::readAtomDataLine() - difference in token on multiple time step for atom with id "
         +atomInfo.get<std::string>(PdbKey::serial)+"!");
     ASSERT(atomInfo.get<std::string>(PdbKey::name) == consistencyInfo.get<std::string>(PdbKey::name),
-        "FormatParser< pdb >::readAtomDataLine() - difference in name on multiple time step for atom with id "
+        "PdbParser::readAtomDataLine() - difference in name on multiple time step for atom with id "
         +atomInfo.get<std::string>(PdbKey::serial)+":"
         +atomInfo.get<std::string>(PdbKey::name)+"!="
         +consistencyInfo.get<std::string>(PdbKey::name)+".");
     ASSERT(atomInfo.get<std::string>(PdbKey::altLoc) == consistencyInfo.get<std::string>(PdbKey::altLoc),
-        "FormatParser< pdb >::readAtomDataLine() - difference in altLoc on multiple time step for atom with id "
+        "PdbParser::readAtomDataLine() - difference in altLoc on multiple time step for atom with id "
         +atomInfo.get<std::string>(PdbKey::serial)+"!");
     ASSERT(atomInfo.get<std::string>(PdbKey::resName) == consistencyInfo.get<std::string>(PdbKey::resName),
-        "FormatParser< pdb >::readAtomDataLine() - difference in resName on multiple time step for atom with id "
+        "PdbParser::readAtomDataLine() - difference in resName on multiple time step for atom with id "
         +atomInfo.get<std::string>(PdbKey::serial)+"!");
     ASSERT(atomInfo.get<std::string>(PdbKey::chainID) == consistencyInfo.get<std::string>(PdbKey::chainID),
-        "FormatParser< pdb >::readAtomDataLine() - difference in chainID on multiple time step for atom with id "
+        "PdbParser::readAtomDataLine() - difference in chainID on multiple time step for atom with id "
         +atomInfo.get<std::string>(PdbKey::serial)+"!");
     ASSERT(atomInfo.get<std::string>(PdbKey::resSeq) == consistencyInfo.get<std::string>(PdbKey::resSeq),
-        "FormatParser< pdb >::readAtomDataLine() - difference in resSeq on multiple time step for atom with id "
+        "PdbParser::readAtomDataLine() - difference in resSeq on multiple time step for atom with id "
         +atomInfo.get<std::string>(PdbKey::serial)+"!");
     ASSERT(atomInfo.get<std::string>(PdbKey::iCode) == consistencyInfo.get<std::string>(PdbKey::iCode),
-        "FormatParser< pdb >::readAtomDataLine() - difference in iCode on multiple time step for atom with id "
+        "PdbParser::readAtomDataLine() - difference in iCode on multiple time step for atom with id "
         +atomInfo.get<std::string>(PdbKey::serial)+"!");
     ASSERT(atomInfo.get<std::string>(PdbKey::occupancy) == consistencyInfo.get<std::string>(PdbKey::occupancy),
-        "FormatParser< pdb >::readAtomDataLine() - difference in occupancy on multiple time step for atom with id "
+        "PdbParser::readAtomDataLine() - difference in occupancy on multiple time step for atom with id "
         +atomInfo.get<std::string>(PdbKey::serial)+"!");
     ASSERT(atomInfo.get<std::string>(PdbKey::tempFactor) == consistencyInfo.get<std::string>(PdbKey::tempFactor),
-        "FormatParser< pdb >::readAtomDataLine() - difference in tempFactor on multiple time step for atom with id "
+        "PdbParser::readAtomDataLine() - difference in tempFactor on multiple time step for atom with id "
         +atomInfo.get<std::string>(PdbKey::serial)+"!");
     ASSERT(atomInfo.get<std::string>(PdbKey::charge) == consistencyInfo.get<std::string>(PdbKey::charge),
-        "FormatParser< pdb >::readAtomDataLine() - difference in charge on multiple time step for atom with id "
+        "PdbParser::readAtomDataLine() - difference in charge on multiple time step for atom with id "
         +atomInfo.get<std::string>(PdbKey::serial)+"!");
     ASSERT(atomInfo.get<std::string>(PdbKey::element) == consistencyInfo.get<std::string>(PdbKey::element),
-        "FormatParser< pdb >::readAtomDataLine() - difference in element on multiple time step for atom with id "
+        "PdbParser::readAtomDataLine() - difference in element on multiple time step for atom with id "
         +atomInfo.get<std::string>(PdbKey::serial)+"!");
     // and parse in trajectory
@@ -742 +734 @@
  *
  */
-void FormatParser< pdb >::printAtomInfo(const atom * const newAtom) const
+void PdbParser::printAtomInfo(const atom * const newAtom) const
 {
   const PdbAtomInfoContainer &atomInfo = additionalAtomData.at(newAtom->getId()); // operator[] const does not exist
@@ -770 +762 @@
  * \param line to parse as an atom
  */
-void FormatParser< pdb >::readNeighbors(const unsigned int _step, std::string &line)
+void PdbParser::readNeighbors(const unsigned int _step, std::string &line)
 {
   const size_t length = line.length();
@@ -780 +772 @@
   string output;
   ASSERT(length >=16,
-      "FormatParser< pdb >::readNeighbors() - CONECT entry has not enough entries: "+line+"!");
-//  output = "Split line:|";
-//  output += line.substr(6,5) + "|";
+      "PdbParser::readNeighbors() - CONECT entry has not enough entries: "+line+"!");
+  output = "Split line:|";
+  output += line.substr(6,5) + "|";
   const size_t id = toSize_t(line.substr(6,5));
   for (size_t index = 11; index <= 26; index+=5) {
@@ -793 +785 @@
         ListOfNeighbors.push_back(otherid);
       else
-        ELOG(2, "FormatParser< pdb >::readNeighbors() - discarding conect entry with id 0.");
+        ELOG(2, "PdbParser::readNeighbors() - discarding conect entry with id 0.");
     } else  {
       break;
@@ -821 +813 @@
  * \return input string with modified atom IDs
  */
-//string  FormatParser< pdb >::adaptIdDependentDataString(string data) {
+//string PdbParser::adaptIdDependentDataString(string data) {
 //  // there might be no IDs
 //  if (data == "-") {
@@ -844 +836 @@
 
 
-bool FormatParser< pdb >::operator==(const FormatParser< pdb >& b) const
+bool PdbParser::operator==(const PdbParser& b) const
 {
   bool status = true;