Changeset 07a47e for src/Graph

Timestamp:

Oct 26, 2011, 3:02:53 PM (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:

41d023

Parents:

99b0dc

Message:

Replaced enable/disable-hydrogen by internal switch.

• changes in Fragmentation, Graph and molecule structures.
• switch is now enum HydrogenSaturation that is constant everywhere except in the Actions. FragmentMoleculeAction and DepthFirstSearchAction have new parameter DoSaturation with default value of true.

Location:

src/Graph

Files:

• BreadthFirstSearchAdd.cpp (modified) (3 diffs)
• BreadthFirstSearchAdd.hpp (modified) (3 diffs)
• CyclicStructureAnalysis.cpp (modified) (2 diffs)
• CyclicStructureAnalysis.hpp (modified) (3 diffs)

src/Graph/BreadthFirstSearchAdd.cpp

@@ -32 +32 @@
 
 
-BreadthFirstSearchAdd::BreadthFirstSearchAdd(atom *&_Root, int _BondOrder, bool _IsAngstroem) :
+BreadthFirstSearchAdd::BreadthFirstSearchAdd(atom *&_Root, int _BondOrder, bool _IsAngstroem, const enum HydrogenSaturation _saturation) :
   BondOrder(_BondOrder),
   Root(_Root),
+  saturation(_saturation),
   IsAngstroem(_IsAngstroem)
 {
@@ -100 +101 @@
         AddedBondList[Binder] = Mol->CopyBond(AddedAtomList[Walker->getNr()], AddedAtomList[OtherAtom->getNr()], Binder);
       } else {
-#ifdef ADDHYDROGEN
-        if (!Mol->AddHydrogenReplacementAtom(Binder, AddedAtomList[Walker->getNr()], Walker, OtherAtom, IsAngstroem))
-        exit(1);
-#endif
+        if (saturation == DoSaturate)
+          if (!Mol->AddHydrogenReplacementAtom(Binder, AddedAtomList[Walker->getNr()], Walker, OtherAtom, IsAngstroem))
+            exit(1);
       }
     }
@@ -118 +118 @@
       AddedBondList[Binder] = Mol->CopyBond(AddedAtomList[Walker->getNr()], AddedAtomList[OtherAtom->getNr()], Binder);
     } else { // if it's root bond it has to broken (otherwise we would not create the fragments)
-#ifdef ADDHYDROGEN
-      if(!Mol->AddHydrogenReplacementAtom(Binder, AddedAtomList[Walker->getNr()], Walker, OtherAtom, IsAngstroem))
-      exit(1);
-#endif
+      if (saturation == DoSaturate)
+        if(!Mol->AddHydrogenReplacementAtom(Binder, AddedAtomList[Walker->getNr()], Walker, OtherAtom, IsAngstroem))
+          exit(1);
     }
   }

src/Graph/BreadthFirstSearchAdd.hpp

@@ -18 +18 @@
 
 #include "Bond/GraphEdge.hpp"
+#include "Fragmentation/HydrogenSaturation_enum.hpp"
 #include "Helpers/defs.hpp"
 #include "types.hpp"
@@ -28 +29 @@
 {
 public:
-  BreadthFirstSearchAdd(atom *&_Root, int _BondOrder, bool _IsAngstroem);
+  BreadthFirstSearchAdd(atom *&_Root, int _BondOrder, bool _IsAngstroem, const enum HydrogenSaturation _saturation);
   ~BreadthFirstSearchAdd();
 
@@ -71 +72 @@
   std::map<bond *, bond *> AddedBondList; //!< maps from father bond to son
 
+  //!> whether to treat hydrogen special or not
+  const enum HydrogenSaturation saturation;
+
+  //!> is angstroem our unit of length
   bool IsAngstroem;
 };

src/Graph/CyclicStructureAnalysis.cpp

@@ -31 +31 @@
 #include "molecule.hpp"
 
-CyclicStructureAnalysis::CyclicStructureAnalysis()
+CyclicStructureAnalysis::CyclicStructureAnalysis(const enum HydrogenSaturation _saturation) :
+  saturation(_saturation)
 {}
 
@@ -101 +102 @@
       if ((*Runner) != BackEdge) { // only walk along DFS spanning tree (otherwise we always find SP of one being backedge Binder)
         OtherAtom = (*Runner)->GetOtherAtom(Walker);
-#ifdef ADDHYDROGEN
-        if (OtherAtom->getType()->getAtomicNumber() != 1) {
-#endif
-        LOG(2, "INFO: Current OtherAtom is: " << OtherAtom->getName() << " for bond " << *(*Runner) << "." << endl);
-        if (ColorList[OtherAtom->getNr()] == GraphEdge::white) {
-          TouchedStack.push_front(OtherAtom);
-          ColorList[OtherAtom->getNr()] = GraphEdge::lightgray;
-          PredecessorList[OtherAtom->getNr()] = Walker; // Walker is the predecessor
-          ShortestPathList[OtherAtom->getNr()] = ShortestPathList[Walker->getNr()] + 1;
-          LOG(2, "INFO: Coloring OtherAtom " << OtherAtom->getName() << " lightgray, its predecessor is " << Walker->getName() << " and its Shortest Path is " << ShortestPathList[OtherAtom->getNr()] << " egde(s) long." << endl);
-          //if (ShortestPathList[OtherAtom->getNr()] < MinimumRingSize[Walker->GetTrueFather()->getNr()]) { // Check for maximum distance
-          LOG(3, "ACCEPT: Putting OtherAtom into queue." << endl);
-          BFSStack.push_front(OtherAtom);
-          //}
+        if ((saturation == DontSaturate) || (OtherAtom->getType()->getAtomicNumber() != 1)) {
+          LOG(2, "INFO: Current OtherAtom is: " << OtherAtom->getName() << " for bond " << *(*Runner) << "." << endl);
+          if (ColorList[OtherAtom->getNr()] == GraphEdge::white) {
+            TouchedStack.push_front(OtherAtom);
+            ColorList[OtherAtom->getNr()] = GraphEdge::lightgray;
+            PredecessorList[OtherAtom->getNr()] = Walker; // Walker is the predecessor
+            ShortestPathList[OtherAtom->getNr()] = ShortestPathList[Walker->getNr()] + 1;
+            LOG(2, "INFO: Coloring OtherAtom " << OtherAtom->getName() << " lightgray, its predecessor is " << Walker->getName() << " and its Shortest Path is " << ShortestPathList[OtherAtom->getNr()] << " egde(s) long." << endl);
+            //if (ShortestPathList[OtherAtom->getNr()] < MinimumRingSize[Walker->GetTrueFather()->getNr()]) { // Check for maximum distance
+            LOG(3, "ACCEPT: Putting OtherAtom into queue." << endl);
+            BFSStack.push_front(OtherAtom);
+            //}
+          } else {
+            LOG(3, "REJECT: Not Adding, has already been visited." << endl);
+          }
+          if (OtherAtom == Root)
+            break;
         } else {
-          LOG(3, "REJECT: Not Adding, has already been visited." << endl);
+          LOG(2, "INFO: Skipping hydrogen atom " << *OtherAtom << "." << endl);
+          ColorList[OtherAtom->getNr()] = GraphEdge::black;
         }
-        if (OtherAtom == Root)
-          break;
-#ifdef ADDHYDROGEN
-      } else {
-        LOG(2, "INFO: Skipping hydrogen atom " << *OtherAtom << "." << endl);
-        ColorList[OtherAtom->getNr()] = GraphEdge::black;
-      }
-#endif
       } else {
         LOG(2, "REJECT: Bond " << *(*Runner) << " not Visiting, is the back edge." << endl);

src/Graph/CyclicStructureAnalysis.hpp

@@ -18 +18 @@
 
 #include "Bond/GraphEdge.hpp"
+#include "Fragmentation/HydrogenSaturation_enum.hpp"
 #include "Helpers/defs.hpp"
 #include "types.hpp"
@@ -28 +29 @@
 {
 public:
-  CyclicStructureAnalysis();
+  explicit CyclicStructureAnalysis(const enum HydrogenSaturation _saturation);
   ~CyclicStructureAnalysis();
 
@@ -58 +59 @@
   atom *Root;
 
+  //!> whether to treat hydrogen special or not
+  const enum HydrogenSaturation saturation;
+
   bool BackStepping;
   int CurrentGraphNr;