Changeset 3dfd9c for src/Parser/PdbParser.cpp

Timestamp:

Feb 22, 2012, 11:27:55 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:

98c428

Parents:

ea7a50

git-author:

Frederik Heber <heber@…> (01/12/12 08:22:20)

git-committer:

Frederik Heber <heber@…> (02/22/12 11:27:55)

Message:

BUGFIX: PdbParser stumbles over CONECT because it reads space-separated token, not substring.

• FormatParser< pdb >::getToken has to work on substr(0,6) only to read the type of entry field-wise.
• added test to Parser/PdbParser load-various.
• Small fix to ::load(), prints now only parsed atoms, not all.
• This fixes ticket #160.

File:

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

src/Parser/PdbParser.cpp

@@ -87 +87 @@
 {
   // look for first space
-  const size_t space_location = line.find(' ');
-  const size_t tab_location = line.find('\t');
+  std::string token = line.substr(0,6);
+  const size_t space_location = token.find(' ');
+  const size_t tab_location = token.find('\t');
   size_t location = space_location < tab_location ? space_location : tab_location;
-  string token;
   if (location != string::npos) {
     //LOG(1, "Found space at position " << space_location);
-    token = line.substr(0,space_location);
-  } else {
-    token = line;
+    token = token.substr(0,space_location);
   }
 
@@ -164 +162 @@
     ++step;
   }
-  BOOST_FOREACH(atom *_atom, World::getInstance().getAllAtoms())
+  LOG(4, "INFO: Listing all newly parsed atoms.");
+  BOOST_FOREACH(atom *_atom, *newmol)
     LOG(4, "INFO: Atom " << _atom->getName() << " " << *dynamic_cast<AtomInfo *>(_atom) << ".");