Changeset 8990879 for src

Timestamp:

Oct 6, 2011, 7:10:04 AM (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:

473237

Parents:

f6ba43

git-author:

Frederik Heber <heber@…> (04/30/11 12:31:44)

git-committer:

Frederik Heber <heber@…> (10/06/11 07:10:04)

Message:

FIX: PdbParser - symbol is now parsed and written in capital letters.

• This fixes ticket #146.
• Added regression test to check this behavior.

File:

• src/Parser/PdbParser.cpp (modified) (3 diffs)

src/Parser/PdbParser.cpp

@@ -260 +260 @@
         }
         // change element and charge if changed
-        if (atomInfo.get<std::string>(PdbKey::element) != (*atomIt)->getType()->getSymbol())
-          atomInfo.set(PdbKey::element, (*atomIt)->getType()->getSymbol());
+        if (atomInfo.get<std::string>(PdbKey::element) != (*atomIt)->getType()->getSymbol()) {
+          std::string symbol = (*atomIt)->getType()->getSymbol();
+          if ((symbol[1] >= 'a') && (symbol[1] <= 'z'))
+            symbol[1] = (symbol[1] - 'a') + 'A';
+          atomInfo.set(PdbKey::element, symbol);
+        }
 
         // finally save the line
@@ -408 +412 @@
 size_t PdbParser::getSerial(const size_t atomid) const
 {
-  ASSERT(atomIdMap.find(atomid) != atomIdMap.end(), "PdbParser::getAtomId: atomid not present in Map.");
+  ASSERT(atomIdMap.find(atomid) != atomIdMap.end(),
+      "PdbParser::getSerial() - atomid "+toString(atomid)+" not present in Map.");
   return (atomIdMap.find(atomid)->second);
 }
@@ -570 +575 @@
     newAtom->setPosition(tempVector);
     // set element
+    std::string value = atomInfo.get<std::string>(PdbKey::element);
+    // make second character lower case if not
+    if ((value[1] >= 'A') && (value[1] <= 'Z'))
+      value[1] = (value[1] - 'A') + 'a';
     const element *elem = World::getInstance().getPeriode()
-        ->FindElement(atomInfo.get<std::string>(PdbKey::element));
+        ->FindElement(value);
     ASSERT(elem != NULL,
         "PdbParser::readAtomDataLine() - element "+atomInfo.get<std::string>(PdbKey::element)+" is unknown!");