Changeset fd4905 for src/Parser/TremoloParser.cpp

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, Candidate_v1.7.0, 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

File:

• src/Parser/TremoloParser.cpp (modified) (8 diffs)

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);
 }