Changeset 74a65e for src/molecules.cpp

Timestamp:

Oct 11, 2008, 4:07:28 PM (16 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:

9fc556

Parents:

617b53

Message:

molecule::AddHydrogenReplacementAtom() returns false on missing parameters, molecule::FragmentMolecule() less output

molecule::AddHydrogenReplacementAtom(): Gave only a warning when either typical hydrogen bond length or angle was missing, now the adding stops, error instead of warning message and false is returned instead.
molecule::BreadthFirstSearchAdd() exits, when AddHydrogenReplacementAtom() returns false
molecule::StoreFragmentFromKeySet() exits, when AddHydrogenReplacementAtom() returns false

File:

• src/molecules.cpp (modified) (6 diffs)

src/molecules.cpp

@@ -220 +220 @@
   BondRescale = TopOrigin->type->HBondDistance[TopBond->BondDegree-1];
   if (BondRescale == -1) {
-    cerr << Verbose(3) << "WARNING: There is no typical bond distance for bond (" << TopOrigin->Name << "<->" << TopReplacement->Name << ") of degree " << TopBond->BondDegree << "!" << endl;
+    cerr << Verbose(3) << "ERROR: There is no typical hydrogen bond distance in replacing bond (" << TopOrigin->Name << "<->" << TopReplacement->Name << ") of degree " << TopBond->BondDegree << "!" << endl;
+    return false;
     BondRescale = bondlength; 
   } else {
@@ -299 +300 @@
       bondangle = TopOrigin->type->HBondAngle[1];
       if (bondangle == -1) {
-        *out << Verbose(3) << "WARNING: There is no typical bond angle for bond (" << TopOrigin->Name << "<->" << TopReplacement->Name << ") of degree " << TopBond->BondDegree << "!" << endl;
+        *out << Verbose(3) << "ERROR: There is no typical hydrogen bond angle in replacing bond (" << TopOrigin->Name << "<->" << TopReplacement->Name << ") of degree " << TopBond->BondDegree << "!" << endl;
+        return false;
         bondangle = 0;
       }
@@ -2982 +2984 @@
       MolecularWalker = MolecularWalker->next;
       *out << Verbose(1) << "Fragmenting subgraph " << MolecularWalker << "." << endl;
-      // output ListOfBondsPerAtom for debugging
-      MolecularWalker->Leaf->OutputListOfBonds(out);
+      //MolecularWalker->Leaf->OutputListOfBonds(out);  // output ListOfBondsPerAtom for debugging
       if (MolecularWalker->Leaf->first->next != MolecularWalker->Leaf->last) {
-      
         // call BOSSANOVA method
         *out << Verbose(0) << endl << " ========== BOND ENERGY of subgraph " << FragmentCounter << " ========================= " << endl;
@@ -3358 +3358 @@
               } else {
 #ifdef ADDHYDROGEN
-                Mol->AddHydrogenReplacementAtom(out, Binder, AddedAtomList[Walker->nr], Walker, OtherAtom, ListOfBondsPerAtom[Walker->nr], NumberOfBondsPerAtom[Walker->nr], IsAngstroem);
+                if (!Mol->AddHydrogenReplacementAtom(out, Binder, AddedAtomList[Walker->nr], Walker, OtherAtom, ListOfBondsPerAtom[Walker->nr], NumberOfBondsPerAtom[Walker->nr], IsAngstroem))
+                  exit(1);
 #endif
               }
@@ -3373 +3374 @@
             } else { // if it's root bond it has to broken (otherwise we would not create the fragments)
 #ifdef ADDHYDROGEN
-              Mol->AddHydrogenReplacementAtom(out, Binder, AddedAtomList[Walker->nr], Walker, OtherAtom, ListOfBondsPerAtom[Walker->nr], NumberOfBondsPerAtom[Walker->nr], IsAngstroem);
+              if(!Mol->AddHydrogenReplacementAtom(out, Binder, AddedAtomList[Walker->nr], Walker, OtherAtom, ListOfBondsPerAtom[Walker->nr], NumberOfBondsPerAtom[Walker->nr], IsAngstroem))
+                exit(1);
 #endif
             }
@@ -3535 +3537 @@
 #ifdef ADDHYDROGEN
           //*out << Verbose(3) << "Adding Hydrogen to " << Runner->Name << " and a bond in between." << endl;
-          Leaf->AddHydrogenReplacementAtom(out, ListOfBondsPerAtom[FatherOfRunner->nr][i], Runner, FatherOfRunner, OtherFather, ListOfBondsPerAtom[FatherOfRunner->nr],NumberOfBondsPerAtom[FatherOfRunner->nr], IsAngstroem);
+          if(!Leaf->AddHydrogenReplacementAtom(out, ListOfBondsPerAtom[FatherOfRunner->nr][i], Runner, FatherOfRunner, OtherFather, ListOfBondsPerAtom[FatherOfRunner->nr],NumberOfBondsPerAtom[FatherOfRunner->nr], IsAngstroem))
+            exit(1);
 #endif
           //NumBonds[Runner->nr] += ListOfBondsPerAtom[FatherOfRunner->nr][i]->BondDegree;