Changeset 74a444 for src/Parser

Timestamp:

Aug 28, 2010, 12:58:44 AM (14 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:

653542

Parents:

dc1d9e

git-author:

Frederik Heber <heber@…> (08/28/10 00:31:59)

git-committer:

Frederik Heber <heber@…> (08/28/10 00:58:44)

Message:

TremoloParser can now deal with copied molecules/atoms.

• as some information of atoms is not stored in the World but in an internal struct, we can not easily have this information in place when atoms have been copied. Default values would be used instead those of the original atoms. Instead, we now use the father to take its values.

File:

• src/Parser/TremoloParser.cpp (modified) (2 diffs)

src/Parser/TremoloParser.cpp

@@ -34 +34 @@
 #include <vector>
 
+#include <iostream>
+#include <iomanip>
 
 using namespace std;
@@ -176 +178 @@
         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;