Changeset 765f16 for src/Parser/PdbParser.cpp

Timestamp:

Oct 14, 2011, 3:15:30 PM (13 years ago)

Author:

Frederik Heber <heber@…>

Branches:

Action_Thermostats, Add_AtomRandomPerturbation, Add_FitFragmentPartialChargesAction, Add_RotateAroundBondAction, Add_SelectAtomByNameAction, Added_ParseSaveFragmentResults, AddingActions_SaveParseParticleParameters, Adding_Graph_to_ChangeBondActions, Adding_MD_integration_tests, Adding_ParticleName_to_Atom, Adding_StructOpt_integration_tests, AtomFragments, Automaking_mpqc_open, AutomationFragmentation_failures, Candidate_v1.5.4, Candidate_v1.6.0, Candidate_v1.6.1, ChangeBugEmailaddress, ChangingTestPorts, ChemicalSpaceEvaluator, CombiningParticlePotentialParsing, Combining_Subpackages, Debian_Package_split, Debian_package_split_molecuildergui_only, Disabling_MemDebug, Docu_Python_wait, EmpiricalPotential_contain_HomologyGraph, EmpiricalPotential_contain_HomologyGraph_documentation, Enable_parallel_make_install, Enhance_userguide, Enhanced_StructuralOptimization, Enhanced_StructuralOptimization_continued, Example_ManyWaysToTranslateAtom, Exclude_Hydrogens_annealWithBondGraph, FitPartialCharges_GlobalError, Fix_BoundInBox_CenterInBox_MoleculeActions, Fix_ChargeSampling_PBC, Fix_ChronosMutex, Fix_FitPartialCharges, Fix_FitPotential_needs_atomicnumbers, Fix_ForceAnnealing, Fix_IndependentFragmentGrids, Fix_ParseParticles, Fix_ParseParticles_split_forward_backward_Actions, Fix_PopActions, Fix_QtFragmentList_sorted_selection, Fix_Restrictedkeyset_FragmentMolecule, Fix_StatusMsg, Fix_StepWorldTime_single_argument, Fix_Verbose_Codepatterns, Fix_fitting_potentials, Fixes, ForceAnnealing_goodresults, ForceAnnealing_oldresults, ForceAnnealing_tocheck, ForceAnnealing_with_BondGraph, ForceAnnealing_with_BondGraph_continued, ForceAnnealing_with_BondGraph_continued_betteresults, ForceAnnealing_with_BondGraph_contraction-expansion, FragmentAction_writes_AtomFragments, FragmentMolecule_checks_bonddegrees, GeometryObjects, Gui_Fixes, Gui_displays_atomic_force_velocity, ImplicitCharges, IndependentFragmentGrids, IndependentFragmentGrids_IndividualZeroInstances, IndependentFragmentGrids_IntegrationTest, IndependentFragmentGrids_Sole_NN_Calculation, JobMarket_RobustOnKillsSegFaults, JobMarket_StableWorkerPool, JobMarket_unresolvable_hostname_fix, MoreRobust_FragmentAutomation, ODR_violation_mpqc_open, PartialCharges_OrthogonalSummation, PdbParser_setsAtomName, PythonUI_with_named_parameters, QtGui_reactivate_TimeChanged_changes, Recreated_GuiChecks, Rewrite_FitPartialCharges, RotateToPrincipalAxisSystem_UndoRedo, SaturateAtoms_findBestMatching, SaturateAtoms_singleDegree, StoppableMakroAction, Subpackage_CodePatterns, Subpackage_JobMarket, Subpackage_LinearAlgebra, Subpackage_levmar, Subpackage_mpqc_open, Subpackage_vmg, Switchable_LogView, ThirdParty_MPQC_rebuilt_buildsystem, TrajectoryDependenant_MaxOrder, TremoloParser_IncreasedPrecision, TremoloParser_MultipleTimesteps, TremoloParser_setsAtomName, Ubuntu_1604_changes, stable

Children:

d3d6c6

Parents:

9a6b76e

git-author:

Frederik Heber <heber@…> (09/27/11 19:04:36)

git-committer:

Frederik Heber <heber@…> (10/14/11 15:15:30)

Message:

Huge Refactoring of FormatParserStorage and all FormatParser's.

FormatParser:

• FormatParser is now a template, specialized by enum ParserTypes.
• new struct FormatParserTrait is as well a template of same type, containing parser-specific information in static entities.
• all FormatParsers are now specializations of this FormatParser.
• all Parsers can be accessed in a unified manner, given in the new class FormatParserInterface.
• common functions are placed in FormatParser_common.hpp as one cannot partially specialize a function class.
• some boost preprocessor magic is used in ParserTypes and FormatParserTraits to define the template specialization or to create the ParserTypes enumeration.

FormatParserStorage:

• We construct all lookup tables and alikes via boost preprocessor magic from a list of all available parser (enums).
• we use the templated getParser() and addParser() functions to serve parsers to the outside. Instances are as usual created only once.

Tests:

• tests only had to be changed because of the "renaming" of the Parsers.

File:

• src/Parser/PdbParser.cpp (modified) (28 diffs)

src/Parser/PdbParser.cpp

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