Changeset 473237 for src

Timestamp:

Oct 6, 2011, 7:11:55 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:

8b8a5b

Parents:

8990879

git-author:

Frederik Heber <heber@…> (04/30/11 13:10:10)

git-committer:

Frederik Heber <heber@…> (10/06/11 07:11:55)

Message:

FIX: PdbParser - CONECTs with full 80 chars were not parsed correctly.

• this fixes ticket #147.
• also, we now write full length CONECTs.
• added regression test to check on this behavior.
• TESTFIX: Parser/Pdb/with-conects now diffs with '-w' to ignore white spaces errors. CONECT lines need not have full length.
• TESTFIX: Molecules/BondFile/Fragmentation now diffs with '-w' as well.

File:

• src/Parser/PdbParser.cpp (modified) (4 diffs)

src/Parser/PdbParser.cpp

@@ -382 +382 @@
  * Note that ListOfBonds of WorldTime::CurrentTime is used.
  *
+ * Also, we fill up the CONECT line to extend over 80 chars.
+ *
  * \param *file  where to write neighbor information to
  * \param MaxnumberOfNeighbors of neighbors
@@ -388 +390 @@
 void PdbParser::writeNeighbors(ostream* file, int MaxnumberOfNeighbors, atom* currentAtom) {
   int MaxNo = MaxnumberOfNeighbors;
+  int charsleft = 80;
   const BondList & ListOfBonds = currentAtom->getListOfBonds();
   if (!ListOfBonds.empty()) {
@@ -394 +397 @@
         *file << "CONECT";
         *file << setw(5) << getSerial(currentAtom->getId());
+        charsleft = 80-6-5;
         MaxNo = 0;
       }
       *file << setw(5) << getSerial((*currentBond)->GetOtherAtom(currentAtom)->getId());
+      charsleft -= 5;
       MaxNo++;
-      if (MaxNo == MaxnumberOfNeighbors)
+      if (MaxNo == MaxnumberOfNeighbors) {
+        for (;charsleft > 0; charsleft--)
+          *file << ' ';
         *file << "\n";
+      }
     }
-    if (MaxNo != MaxnumberOfNeighbors)
+    if (MaxNo != MaxnumberOfNeighbors) {
+      for (;charsleft > 0; charsleft--)
+        *file << ' ';
       *file << "\n";
+    }
   }
 }
@@ -688 +699 @@
   ASSERT(length >=16,
       "PdbParser::readNeighbors() - CONECT entry has not enough entries: "+line+"!");
-//  output = "Split line:|";
-//  output += line.substr(6,5) + "|";
+  output = "Split line:|";
+  output += line.substr(6,5) + "|";
   const size_t id = toSize_t(line.substr(6,5));
   for (size_t index = 11; index <= 26; index+=5) {
     if (index+5 <= length) {
-//      output += line.substr(index,5) + "|";
-      const size_t otherid = toSize_t(line.substr(index,5));
-      ListOfNeighbors.push_back(otherid);
+      output += line.substr(index,5) + "|";
+      // search for digits
+      int otherid = -1;
+      PdbAtomInfoContainer::ScanKey(otherid, line.substr(index,5));
+      if (otherid >= 0)
+        ListOfNeighbors.push_back((size_t)otherid);
     } else  {
       break;
     }
   }
-//  DoLog(2) && (Log() << Verbose(2) << output << std::endl);
+  LOG(4, output);
 
   // add neighbours
   atom *_atom = World::getInstance().getAtom(AtomById(getSerial(id)));
+  LOG(2, "STATUS: Atom " << _atom->getId() << " gets " << ListOfNeighbors.size() << " more neighbours.");
   for (std::list<size_t>::const_iterator iter = ListOfNeighbors.begin();
       iter != ListOfNeighbors.end();
       ++iter) {
-//    DoLog(1) && (Log() << Verbose(1) << "Adding Bond (" << getAtomId(id) << "," << getAtomId(*iter) << ")" << std::endl);
     atom * const _Otheratom = World::getInstance().getAtom(AtomById(getSerial(*iter)));
+    LOG(3, "INFO: Adding Bond (" << *_atom << "," << *_Otheratom << ")");
     _atom->addBond(_step, _Otheratom);
   }