Changeset fd4905 for src/Parser

Timestamp:

Aug 28, 2010, 1:45:13 AM (15 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:

6c438f

Parents:

8fd934 (diff), 653542 (diff)
Note: this is a merge changeset, the changes displayed below correspond to the merge itself.
Use the (diff) links above to see all the changes relative to each parent.

Message:

Merge branch 'stable' into StructureRefactoring

Location:

src/Parser

Files:

• FormatParserStorage.cpp (modified) (8 diffs)
• FormatParserStorage.hpp (modified) (4 diffs)
• Makefile.am (modified) (2 diffs)
• PdbParser.cpp (added)
• PdbParser.hpp (added)
• TremoloParser.cpp (modified) (8 diffs)
• TremoloParser.hpp (modified) (2 diffs)

src/Parser/FormatParserStorage.cpp

@@ -28 +28 @@
 #include "Parser/MpqcParser.hpp"
 #include "Parser/PcpParser.hpp"
+#include "Parser/PdbParser.hpp"
 #include "Parser/TremoloParser.hpp"
 #include "Parser/XyzParser.hpp"
@@ -56 +57 @@
   ParserSuffix.resize(ParserTypes_end, "");
 
+  ParserNames[mpqc] = "mpqc";
+  ParserNames[pcp] = "pcp";
+  ParserNames[pdb] = "pdb";
+  ParserNames[tremolo] = "tremolo";
+  ParserNames[xyz] = "xyz";
+
+  for (std::map<ParserTypes, std::string>::const_iterator it = ParserNames.begin(); it != ParserNames.end(); ++it)
+    ParserLookupNames.insert(pair<std::string, ParserTypes>(it->second,it->first) );
+
   ParserSuffix[mpqc] = "in";
   ParserSuffix[pcp] = "conf";
+  ParserSuffix[pdb] = "pdb";
   ParserSuffix[tremolo] = "data";
   ParserSuffix[xyz] = "xyz";
+
+  ParserAddFunction[mpqc] = &FormatParserStorage::addMpqc;
+  ParserAddFunction[pcp] = &FormatParserStorage::addPcp;
+  ParserAddFunction[pdb] = &FormatParserStorage::addPdb;
+  ParserAddFunction[tremolo] = &FormatParserStorage::addTremolo;
+  ParserAddFunction[xyz] = &FormatParserStorage::addXyz;
 }
 
@@ -112 +129 @@
 }
 
+
 /** Adds an PcpParser to the storage.
  */
@@ -124 +142 @@
 
 
+/** Adds an PdbParser to the storage.
+ */
+void FormatParserStorage::addPdb()
+{
+  if (!ParserPresent[pdb]) {
+    ParserList[pdb] = new PdbParser();
+    ParserPresent[pdb] = true;
+  } else
+    DoeLog(1) && (eLog() << Verbose(1) << "Parser pdb is already present." << endl);
+}
+
+
 /** Adds an TremoloParser to the storage.
  */
@@ -146 +176 @@
     DoeLog(1) && (eLog() << Verbose(1) << "Parser xyz is already present." << endl);
 }
+
+ParserTypes FormatParserStorage::getType(std::string type)
+{
+  if (ParserLookupNames.find(type) == ParserLookupNames.end()) {
+    DoeLog(1) && (eLog() << Verbose(1) << "Unknown type " << type << "." << endl);
+    return ParserTypes_end;
+  } else
+    return ParserLookupNames[type];
+}
+
+bool FormatParserStorage::add(ParserTypes ptype)
+{
+  if (ptype != ParserTypes_end) {
+    if (ParserAddFunction.find(ptype) != ParserAddFunction.end()) {
+      DoLog(0) && (Log() << Verbose(0) << "Adding " << ParserNames[ptype] << " type to output." << endl);
+      (getInstance().*(ParserAddFunction[ptype]))(); // we still need an object to work on ...
+      return true;
+    } else {
+      DoeLog(1) && (eLog() << Verbose(1) << "No parser to add for this known type " << ParserNames[ptype] << ", not implemented?" << endl);
+      return false;
+    }
+  } else {
+    return false;
+  }
+}
+
+bool FormatParserStorage::add(std::string type)
+{
+  return add(getType(type));
+}
+
 
 /** Parses an istream depending on its suffix
@@ -158 +219 @@
   } else if (suffix == ParserSuffix[pcp]) {
     getPcp().load(&input);
+  } else if (suffix == ParserSuffix[pdb]) {
+    getPdb().load(&input);
   } else if (suffix == ParserSuffix[tremolo]) {
     getTremolo().load(&input);
@@ -163 +226 @@
     getXyz().load(&input);
   } else {
-    DoeLog(1) && (eLog() << Verbose(1) << "Unknown suffix to for FormatParserStorage::get()." << endl);
+    DoeLog(1) && (eLog() << Verbose(1) << "Unknown suffix " << suffix << " to for FormatParserStorage::get()." << endl);
     return false;
   }
@@ -189 +252 @@
 }
 
+/** Returns reference to the output PdbParser, adds if not present.
+ * \return reference to the output PdbParser
+ */
+PdbParser &FormatParserStorage::getPdb()
+{
+  if (!ParserPresent[pdb])
+    addPdb();
+  return dynamic_cast<PdbParser &>(*ParserList[pdb]);
+}
+
 /** Returns reference to the output TremoloParser, adds if not present.
  * \return reference to the output TremoloParser

src/Parser/FormatParserStorage.hpp

@@ -17 +17 @@
 
 #include <string>
+#include <map>
 #include <vector>
 
 class FormatParser;
 class MpqcParser;
+class PdbParser;
 class PcpParser;
 class TremoloParser;
@@ -26 +28 @@
 
 // enum has to be outside of class for operator++ to be possible
-enum ParserTypes { mpqc, pcp, tremolo, xyz, ParserTypes_end, ParserTypes_begin = mpqc };
+enum ParserTypes { mpqc, pcp, pdb, tremolo, xyz, ParserTypes_end, ParserTypes_begin = mpqc };
 typedef enum ParserTypes ParserTypes;
 
@@ -35 +37 @@
 public:
 
-
   void addMpqc();
   void addPcp();
+  void addPdb();
   void addTremolo();
   void addXyz();
+  bool add(std::string type);
+  bool add(ParserTypes type);
 
   bool get(std::istream &input, std::string suffix);
   MpqcParser &getMpqc();
   PcpParser &getPcp();
+  PdbParser &getPdb();
   TremoloParser &getTremolo();
   XyzParser &getXyz();
+
+  ParserTypes getType(std::string type);
 
   void SetOutputPrefixForAll(std::string &_prefix);
@@ -67 +74 @@
   std::vector<std::string> ParserSuffix;
 
+  // function pointers to each add...()
+  std::map< ParserTypes, void (FormatParserStorage::*)() > ParserAddFunction;
+
+  // type name of each parser type and reverse lookup
+  std::map<ParserTypes, std::string> ParserNames;
+  std::map<std::string, ParserTypes> ParserLookupNames;
+
+
   // prefix of the filenames to use on save
   std::string prefix;

src/Parser/Makefile.am

@@ -13 +13 @@
   MpqcParser.cpp \
   PcpParser.cpp \
+  PdbParser.cpp \
   TremoloParser.cpp \
   XyzParser.cpp
@@ -22 +23 @@
   MpqcParser.hpp \
   PcpParser.hpp \
+  PdbParser.hpp \
   TremoloParser.hpp \
   XyzParser.hpp

src/Parser/TremoloParser.cpp

@@ -26 +26 @@
 #include "World.hpp"
 #include "atom.hpp"
+#include "bond.hpp"
 #include "element.hpp"
-#include "bond.hpp"
+#include "molecule.hpp"
 #include "periodentafel.hpp"
 #include "Descriptors/AtomIdDescriptor.hpp"
@@ -33 +34 @@
 #include <vector>
 
+#include <iostream>
+#include <iomanip>
 
 using namespace std;
@@ -88 +91 @@
 
   usedFields.clear();
+  molecule *newmol = World::getInstance().createMolecule();
   while (file->good()) {
     std::getline(*file, line, '\n');
@@ -97 +101 @@
     }
     if (line.length() > 0 && line.at(0) != '#') {
-      readAtomDataLine(line);
+      readAtomDataLine(line, newmol);
     }
   }
@@ -169 +173 @@
         break;
       case TremoloKey::Id :
-        *file << currentAtom->getId() << "\t";
+        *file << currentAtom->getId()+1 << "\t";
         break;
       case TremoloKey::neighbors :
         writeNeighbors(file, atoi(it->substr(it->find("=") + 1, 1).c_str()), currentAtom);
         break;
+      case TremoloKey::resSeq :
+        if (additionalAtomData.find(currentAtom->getId()) != additionalAtomData.end()) {
+          *file << additionalAtomData[currentAtom->getId()].get(currentField);
+        } else if (currentAtom->getMolecule() != NULL) {
+          *file << setw(4) << currentAtom->getMolecule()->getId()+1;
+        } else {
+          *file << defaultAdditionalData.get(currentField);
+        }
+        *file << "\t";
+      break;
       default :
-        *file << (additionalAtomData.find(currentAtom->getId()) != additionalAtomData.end()
-          ? additionalAtomData[currentAtom->getId()].get(currentField)
-          : defaultAdditionalData.get(currentField));
+        if (additionalAtomData.find(currentAtom->getId()) != additionalAtomData.end()) {
+          *file << additionalAtomData[currentAtom->getId()].get(currentField);
+        } else if (additionalAtomData.find(currentAtom->GetTrueFather()->getId()) != additionalAtomData.end()) {
+          *file << additionalAtomData[currentAtom->GetTrueFather()->getId()].get(currentField);
+        } else {
+          *file << defaultAdditionalData.get(currentField);
+        }
         *file << "\t";
         break;
@@ -197 +215 @@
   for (int i = 0; i < numberOfNeighbors; i++) {
     *file << (currentBond != currentAtom->ListOfBonds.end()
-        ? (*currentBond)->GetOtherAtom(currentAtom)->getId() : 0) << "\t";
+        ? (*currentBond)->GetOtherAtom(currentAtom)->getId()+1 : 0) << "\t";
+    if (currentBond != currentAtom->ListOfBonds.end())
+      currentBond++;
   }
 }
@@ -229 +249 @@
  *
  * \param line to parse as an atom
- */
-void TremoloParser::readAtomDataLine(string line) {
+ * \param *newmol molecule to add atom to
+ */
+void TremoloParser::readAtomDataLine(string line, molecule *newmol = NULL) {
   vector<string>::iterator it;
   stringstream lineStream;
@@ -279 +300 @@
     }
   }
+  if (newmol != NULL)
+    newmol->AddAtom(newAtom);
 }
 

src/Parser/TremoloParser.hpp

@@ -11 +11 @@
 #include <string>
 #include "Parser/FormatParser.hpp"
+
+class molecule;
 
 /**
@@ -85 +87 @@
 private:
   void readAtomDataLine(string line);
+  void readAtomDataLine(string line, molecule *newmol);
   void parseAtomDataKeysLine(string line, int offset);
   void readNeighbors(std::stringstream* line, int numberOfNeighbors, int atomId);