Changeset 9d37ac

Timestamp:

Mar 1, 2011, 10:16:38 AM (14 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:

9b8387

Parents:

4afa46

git-author:

Frederik Heber <heber@…> (02/24/11 14:39:14)

git-committer:

Frederik Heber <heber@…> (03/01/11 10:16:38)

Message:

DOCUFIX: Removed *out as parameter from waaay back ...

File:

• src/molecule_graph.cpp (modified) (28 diffs)

src/molecule_graph.cpp

@@ -110 +110 @@
   }
 }
-;
 
 /** Creates an adjacency list of the molecule.
@@ -125 +124 @@
  *  -# correct the bond degree iteratively (single->double->triple bond)
  *  -# finally print the bond list to \a *out if desired
- * \param *out out stream for printing the matrix, NULL if no output
  * \param bonddistance length of linked cells (i.e. maximum minimal length checked)
  * \param IsAngstroem whether coordinate system is gauged to Angstroem or Bohr radii
@@ -269 +267 @@
 
 /** Prints a list of all bonds to \a *out.
- * \param output stream
  */
 void molecule::OutputBondsList() const
@@ -292 +289 @@
  * preferred over carbon bonds). Beforehand, we had picked the first mismatching partner, which lead to oxygenes with single instead of
  * double bonds as was expected.
- * \param *out output stream for debugging
  * \return number of bonds that could not be corrected
  */
@@ -316 +312 @@
   return (No);
 }
-;
+
 
 /** Counts all cyclic bonds and returns their number.
  * \note Hydrogen bonds can never by cyclic, thus no check for that
- * \param *out output stream for debugging
- * \return number opf cyclic bonds
+ * \return number of cyclic bonds
  */
 int molecule::CountCyclicBonds()
@@ -384 +379 @@
 
 /** Sets atom::GraphNr and atom::LowpointNr to BFSAccounting::CurrentGraphNr.
- * \param *out output stream for debugging
  * \param *Walker current node
  * \param &BFS structure with accounting data for BFS
@@ -405 +399 @@
  *  -# TreeEgde: set atom::Ancestor and continue with Walker along this edge
  * Continue until molecule::FindNextUnused() finds no more unused bonds.
- * \param *out output stream for debugging
  * \param *mol molecule with atoms and finding unused bonds
  * \param *&Binder current edge
@@ -448 +441 @@
  * Meaning that if we touch upon a node who suddenly has a smaller atom::LowpointNr than its ancestor, then we
  * have a found a new branch in the graph tree.
- * \param *out output stream for debugging
  * \param *mol molecule with atoms and finding unused bonds
  * \param *&Walker current node
@@ -495 +487 @@
  * If we are not DFSAccounting::BackStepping, then we clear the root stack by putting everything into a
  * component down till we meet DFSAccounting::Root.
- * \param *out output stream for debugging
  * \param *mol molecule with atoms and finding unused bonds
  * \param *&Walker current node
@@ -535 +526 @@
 
 /** Initializes DFSAccounting structure.
- * \param *out output stream for debugging
  * \param &DFS accounting structure to allocate
  * \param *mol molecule with AtomCount, BondCount and all atoms
@@ -551 +541 @@
 
 /** Free's DFSAccounting structure.
- * \param *out output stream for debugging
  * \param &DFS accounting structure to free
  */
@@ -571 +560 @@
  * articulations points, ...
  * We use the algorithm from [Even, Graph Algorithms, p.62].
- * \param *out output stream for debugging
  * \param *&BackEdgeStack NULL pointer to std::deque<bond *> with all the found back edges, allocated and filled on return
  * \return list of each disconnected subgraph as an individual molecule class structure
@@ -672 +660 @@
 
 /** Output graph information per atom.
- * \param *out output stream
  */
 void molecule::OutputGraphInfoPerAtom() const
@@ -682 +669 @@
 
 /** Output graph information per bond.
- * \param *out output stream
  */
 void molecule::OutputGraphInfoPerBond() const
@@ -712 +698 @@
 
 /** Initialise each vertex as white with no predecessor, empty queue, color Root lightgray.
- * \param *out output stream for debugging
  * \param &BFS accounting structure
  * \param AtomCount number of entries in the array to allocate
@@ -733 +718 @@
 
 /** Free's accounting structure.
- * \param *out output stream for debugging
  * \param &BFS accounting structure
  */
@@ -747 +731 @@
 
 /** Clean the accounting structure.
- * \param *out output stream for debugging
  * \param &BFS accounting structure
  */
@@ -763 +746 @@
 
 /** Resets shortest path list and BFSStack.
- * \param *out output stream for debugging
  * \param *&Walker current node, pushed onto BFSAccounting::BFSStack and BFSAccounting::TouchedStack
  * \param &BFS accounting structure
@@ -776 +758 @@
 
 /** Performs a BFS from \a *Root, trying to find the same node and hence a cycle.
- * \param *out output stream for debugging
  * \param *&BackEdge the edge from root that we don't want to move along
  * \param &BFS accounting structure
@@ -864 +845 @@
 
 /** Climb back the BFSAccounting::PredecessorList and find cycle members.
- * \param *out output stream for debugging
  * \param *&OtherAtom
  * \param *&BackEdge denotes the edge we did not want to travel along when doing CyclicBFSFromRootToRoot()
@@ -907 +887 @@
 
 /** From a given node performs a BFS to touch the next cycle, for whose nodes \a *&MinimumRingSize is set and set it accordingly.
- * \param *out output stream for debugging
  * \param *&Root node to look for closest cycle from, i.e. \a *&MinimumRingSize is set for this node
  * \param *&MinimumRingSize minimum distance from this node possible without encountering oneself, set on return for each atom
@@ -962 +941 @@
 
 /** All nodes that are not in cycles get assigned a \a *&MinimumRingSizeby BFS to next cycle.
- * \param *out output stream for debugging
  * \param *&MinimumRingSize array with minimum distance without encountering onself for each atom
  * \param &MinRingSize global minium distance
@@ -997 +975 @@
  * we have found the Root via BFS, we may climb back the closed cycle via the Predecessors. Thereby we mark atoms and bonds
  * as cyclic and print out the cycles.
- * \param *out output stream for debugging
  * \param *BackEdgeStack stack with all back edges found during DFS scan. Beware: This stack contains the bonds from the total molecule, not from the subgraph!
  * \param *&MinimumRingSize contains smallest ring size in molecular structure on return or -1 if no rings were found, if set is maximum search distance
  * \todo BFS from the not-same-LP to find back to starting point of tributary cycle over more than one bond
  */
-void molecule::CyclicStructureAnalysis(std::deque<bond *> * BackEdgeStack, int *&MinimumRingSize) const
+void molecule::CyclicStructureAnalysis(
+    std::deque<bond *> * BackEdgeStack,
+    int *&MinimumRingSize
+    ) const
 {
   struct BFSAccounting BFS;
@@ -1102 +1082 @@
 
 /** Output a list of flags, stating whether the bond was visited or not.
- * \param *out output stream for debugging
- * \param *list
+ * \param *list list to print
  */
 void OutputAlreadyVisited(int *list)
@@ -1236 +1215 @@
 
 /** Checks contents of adjacency file against bond structure in structure molecule.
- * \param *out output stream for debugging
  * \param *path path to file
  * \param **ListOfAtoms allocated (molecule::AtomCount) and filled lookup table for ids (Atom::nr) to *Atom
@@ -1294 +1272 @@
 
 /** Picks from a global stack with all back edges the ones in the fragment.
- * \param *out output stream for debugging
  * \param **ListOfLocalAtoms array of father atom::nr to local atom::nr (reverse of atom::father)
  * \param *ReferenceStack stack with all the back egdes
@@ -1442 +1419 @@
  * Gray vertices are always enqueued in an std::deque<atom *> FIFO queue, the rest is usual BFS with adding vertices found was
  * white and putting into queue.
- * \param *out output stream for debugging
  * \param *Mol Molecule class to add atoms to
  * \param **AddedAtomList list with added atom pointers, index is atom father's number
@@ -1568 +1544 @@
  * with end points present in this molecule, bond is created in this molecule.
  * Special care was taken to ensure that this is of complexity O(N), where N is the \a Father's molecule::AtomCount.
- * \param *out output stream for debugging
  * \param *Father father molecule
  * \return true - is induced subgraph, false - there are atoms with fathers not in \a Father
  * \todo not checked, not fully working probably
  */
-bool molecule::BuildInducedSubgraph(const molecule *Father)
-{
+bool molecule::BuildInducedSubgraph(const molecule *Father){
   bool status = true;
   atom **ParentList = NULL;