Changeset fa649a for src/molecule.hpp

Timestamp:

Nov 2, 2009, 12:50:57 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, Candidate_v1.7.0, Candidate_v1.7.1, 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:

7218f8

Parents:

34e0013

Message:

Small changes.

• VolumeOfConvexEnvelope() - setprecision corrected
• BUGFIX: PrepareClustersinWater() - IsAngstroem was set to NULL instead of true
• config::Load(), ..LoadOld() - get MoleculeListClass instead of molecule
• config::TestSyntax() - removed unncessary molecule parameter
• ParseCommandLineOptions() - no mol is created anymore, this is done when parsing in config::Load(), mol is set to first active instead
• config.cpp: Lots of ^{M (dos EOL) removed}
• have const molecule * const ref now: MoleculeLeafClass::FillBondStructureFromReference(), molecule::PickLocalBackEdges(), DepthFirstSearchAnalysis_CheckForaNewComponent(), DepthFirstSearchAnalysis_ProbeAlongUnusedBond()
• are const member functions now - necessary due to periodentafel being a const pointer: molecule::ResetAllBondsToUnused(), molecule::FindNextUnused(), molecule::SetNextComponentNumber(), molecule::CyclicStructureAnalysis(), CyclicStructureAnalysis_AssignRingSizetoNonCycleMembers(), molecule::OutputGraphInfoPerBond(), molecule::OutputGraphInfoPerAtom(), molecule::CyclicBondAnalysis(), molecule::CyclicStructureAnalysis(), molecule::GetColor(), molecule::CorrectBondDegree(), molecule::OutputBondsList()
• in molecule NoNonHydrogen, NoNonBonds and NoCyclicBonds are mutable
• molecule constructor rewritten with respect to ticket #4 (shorten constructors)

File:

• src/molecule.hpp (modified) (5 diffs)

src/molecule.hpp

@@ -83 +83 @@
   public:
     double cell_size[6];//!< cell size
-    periodentafel *elemente; //!< periodic table with each element
+    const periodentafel * const elemente; //!< periodic table with each element
     atom *start;        //!< start of atom list
     atom *end;          //!< end of atom list
@@ -93 +93 @@
     int ElementCount;       //!< how many unique elements are therein
     int ElementsInMolecule[MAX_ELEMENTS]; //!< list whether element (sorted by atomic number) is alread present or not
-    int NoNonHydrogen;  //!< number of non-hydrogen atoms in molecule
-    int NoNonBonds;     //!< number of non-hydrogen bonds in molecule
-    int NoCyclicBonds;  //!< number of cyclic bonds in molecule, by DepthFirstSearchAnalysis()
+    mutable int NoNonHydrogen;  //!< number of non-hydrogen atoms in molecule
+    mutable int NoNonBonds;     //!< number of non-hydrogen bonds in molecule
+    mutable int NoCyclicBonds;  //!< number of cyclic bonds in molecule, by DepthFirstSearchAnalysis()
     double BondDistance;  //!< typical bond distance used in CreateAdjacencyList() and furtheron
     bool ActiveFlag;    //!< in a MoleculeListClass used to discern active from inactive molecules
@@ -102 +102 @@
     int IndexNr;        //!< index of molecule in a MoleculeListClass
 
-  molecule(periodentafel *teil);
+  molecule(const periodentafel * const teil);
   virtual ~molecule();
 
@@ -241 +241 @@
   void CreateAdjacencyListFromDbondFile(ofstream *out, ifstream *output);
   void CreateAdjacencyList(ofstream *out, double bonddistance, bool IsAngstroem, void (BondGraph::*f)(BondedParticle * const , BondedParticle * const , double &, double &, bool), BondGraph *BG = NULL);
-  int CorrectBondDegree(ofstream *out);
-  void OutputBondsList(ofstream *out);
-  void CyclicBondAnalysis();
-  void OutputGraphInfoPerAtom(ofstream *out);
-  void OutputGraphInfoPerBond(ofstream *out);
+  int CorrectBondDegree(ofstream *out) const;
+  void OutputBondsList(ofstream *out) const;
+  void CyclicBondAnalysis() const;
+  void OutputGraphInfoPerAtom(ofstream *out) const;
+  void OutputGraphInfoPerBond(ofstream *out) const;
 
 
   // Graph analysis
-  MoleculeLeafClass * DepthFirstSearchAnalysis(ofstream *out, class StackClass<bond *> *&BackEdgeStack);
-  void CyclicStructureAnalysis(ofstream *out, class StackClass<bond *> *BackEdgeStack, int *&MinimumRingSize);
-  bool PickLocalBackEdges(ofstream *out, atom **ListOfLocalAtoms, class StackClass<bond *> *&ReferenceStack, class StackClass<bond *> *&LocalStack);
-  bond * FindNextUnused(atom *vertex);
-  void SetNextComponentNumber(atom *vertex, int nr);
-  void InitComponentNumbers();
-  void ResetAllBondsToUnused();
+  MoleculeLeafClass * DepthFirstSearchAnalysis(ofstream *out, class StackClass<bond *> *&BackEdgeStack) const;
+  void CyclicStructureAnalysis(ofstream *out, class StackClass<bond *> *BackEdgeStack, int *&MinimumRingSize) const;
+  bool PickLocalBackEdges(ofstream *out, atom **ListOfLocalAtoms, class StackClass<bond *> *&ReferenceStack, class StackClass<bond *> *&LocalStack) const;
+  bond * FindNextUnused(atom *vertex) const;
+  void SetNextComponentNumber(atom *vertex, int nr) const;
+  void ResetAllBondsToUnused() const;
   int CountCyclicBonds(ofstream *out);
   bool CheckForConnectedSubgraph(ofstream *out, KeySet *Fragment);
-  string GetColor(enum Shading color);
+  string GetColor(enum Shading color) const;
   bond * CopyBond(atom *left, atom *right, bond *CopyBond);
 
@@ -351 +350 @@
 
   bool AddLeaf(molecule *ptr, MoleculeLeafClass *Previous);
-  bool FillBondStructureFromReference(ofstream *out, molecule *reference, int &FragmentCounter, atom ***&ListOfLocalAtoms, bool FreeList = false);
+  bool FillBondStructureFromReference(ofstream *out, const molecule * const reference, int &FragmentCounter, atom ***&ListOfLocalAtoms, bool FreeList = false);
   bool FillRootStackForSubgraphs(ofstream *out, KeyStack *&RootStack, bool *AtomMask, int &FragmentCounter);
   bool AssignKeySetsToFragment(ofstream *out, molecule *reference, Graph *KeySetList, atom ***&ListOfLocalAtoms, Graph **&FragmentList, int &FragmentCounter, bool FreeList = false);