Changeset bdb143 for src/analysis_bonds.cpp

Timestamp:

Jun 28, 2010, 3:38:05 PM (15 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:

13892b, 51a5c8

Parents:

b2531f (diff), c39cc4 (diff)
Note: this is a merge changeset, the changes displayed below correspond to the merge itself.
Use the (diff) links above to see all the changes relative to each parent.

git-author:

Frederik Heber <heber@…> (06/28/10 14:53:18)

git-committer:

Frederik Heber <heber@…> (06/28/10 15:38:05)

Message:

Merge branch 'StructureRefactoring' into stable

Conflicts:

molecuilder/src/analysis_bonds.cpp
molecuilder/src/analysis_bonds.hpp
molecuilder/src/builder.cpp
molecuilder/src/unittests/Makefile.am
molecuilder/src/unittests/TestRunnerMain.cpp

• TESTFIX: Tesselations/heptan - Due to different implementations of GetCircumCenter() sequence of triangles nodes has changed in degenerate case
• TESTFIX: Tesselation/1-3 - Due to convexity criterion fourth argument (i.e. the value at the node) has changed.

Signed-off-by: Frederik Heber <heber@…>

File:

• src/analysis_bonds.cpp (modified) (5 diffs)

src/analysis_bonds.cpp

@@ -121 +121 @@
  * \param *molecules molecules to count bonds
  * \param *InterfaceElement or NULL
- */
-int CountHydrogenBridgeBonds(MoleculeListClass *molecules, const element * InterfaceElement = NULL)
+ * \param *Interface2Element or NULL
+ */
+int CountHydrogenBridgeBonds(MoleculeListClass *molecules, const element * InterfaceElement = NULL, const element * Interface2Element = NULL)
 {
   int count = 0;
@@ -128 +129 @@
   double Otherangle = 0.;
   bool InterfaceFlag = false;
+  bool Interface2Flag = false;
   bool OtherHydrogenFlag = true;
   for (MoleculeList::const_iterator MolWalker = molecules->ListOfMolecules.begin();MolWalker != molecules->ListOfMolecules.end(); ++MolWalker) {
@@ -145 +147 @@
               OtherHydrogens = 0;
               InterfaceFlag = (InterfaceElement == NULL);
+              Interface2Flag = (Interface2Element == NULL);
               for (BondList::const_iterator BondRunner = (*Runner)->ListOfBonds.begin(); BondRunner != (*Runner)->ListOfBonds.end(); BondRunner++) {
                 atom * const OtherAtom = (*BondRunner)->GetOtherAtom(*Runner);
@@ -155 +158 @@
                 }
                 InterfaceFlag = InterfaceFlag || (OtherAtom->type == InterfaceElement);
+                Interface2Flag = Interface2Flag || (OtherAtom->type == Interface2Element);
               }
               DoLog(1) && (Log() << Verbose(1) << "Otherangle is " << Otherangle << " for " << OtherHydrogens << " hydrogens." << endl);
@@ -168 +172 @@
                   break;
               }
-              if (InterfaceFlag && OtherHydrogenFlag) {
+              if (InterfaceFlag && Interface2Flag && OtherHydrogenFlag) {
                 // on this element (Walker) we check for bond to hydrogen, i.e. part of water molecule
                 for (BondList::const_iterator BondRunner = (*Walker)->ListOfBonds.begin(); BondRunner != (*Walker)->ListOfBonds.end(); BondRunner++) {