Changeset 13a953

Timestamp:

Mar 11, 2011, 12:38:30 PM (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:

61775a

Parents:

2d4334

git-author:

Frederik Heber <heber@…> (03/03/11 01:28:42)

git-committer:

Frederik Heber <heber@…> (03/11/11 12:38:30)

Message:

Moved molecule::CheckAdjacencyAgainstFile() into functor in Graph/.

• Note that this is currently not working because there is no correct mapping from indices in the adjacency file to the indices of the atoms (and without some fixed mean of aligning atoms, this will never be possible).

Location:

src

Files:

• Graph/CheckAgainstAdjacencyFile.cpp (added)
• Graph/CheckAgainstAdjacencyFile.hpp (added)
• Graph/Makefile.am (modified) (2 diffs)
• molecule.hpp (modified) (1 diff)
• molecule_fragmentation.cpp (modified) (4 diffs)
• molecule_graph.cpp (modified) (2 diffs)

src/Graph/Makefile.am

@@ -10 +10 @@
         BreadthFirstSearchAdd.cpp \
         BuildInducedSubgraph.cpp \
+        CheckAgainstAdjacencyFile.cpp \
         ConnectedSubgraph.cpp \
         CyclicStructureAnalysis.cpp \
@@ -17 +18 @@
         BreadthFirstSearchAdd.hpp \
         BuildInducedSubgraph.hpp \
+        CheckAgainstAdjacencyFile.hpp \
         ConnectedSubgraph.hpp \
         CyclicStructureAnalysis.hpp \

src/molecule.hpp

@@ -216 +216 @@
   bool StoreBondsToFile(std::string filename, std::string path = "");
   bool StoreAdjacencyToFile(std::string filename, std::string path = "");
-  bool CheckAdjacencyFileAgainstMolecule(std::string &path, atom **ListOfAtoms);
   bool ParseOrderAtSiteFromFile(std::string &path);
   bool StoreOrderAtSiteFile(std::string &path);

src/molecule_fragmentation.cpp

@@ -30 +30 @@
 #include "element.hpp"
 #include "Graph/BondGraph.hpp"
+#include "Graph/CheckAgainstAdjacencyFile.hpp"
 #include "Graph/CyclicStructureAnalysis.hpp"
 #include "Graph/DepthFirstSearchAnalysis.hpp"
@@ -609 +610 @@
 };
 
+
 /** Performs a many-body bond order analysis for a given bond order.
  * -# parses adjacency, keysets and orderatsite files
@@ -640 +642 @@
   Graph TotalGraph;     // graph with all keysets however local numbers
   int TotalNumberOfKeySets = 0;
-  atom **ListOfAtoms = NULL;
   atom ***ListOfLocalAtoms = NULL;
   bool *AtomMask = NULL;
@@ -655 +656 @@
   // ===== 1. Check whether bond structure is same as stored in files ====
 
-  // create lookup table for Atom::Nr
-  FragmentationToDo = FragmentationToDo && CreateFatherLookupTable(ListOfAtoms, getAtomCount());
-
   // === compare it with adjacency file ===
-  FragmentationToDo = FragmentationToDo && CheckAdjacencyFileAgainstMolecule(prefix, ListOfAtoms);
-  delete[](ListOfAtoms);
+  {
+    std::ifstream File;
+    string filename;
+    filename = prefix + ADJACENCYFILE;
+    File.open(filename.c_str(), ios::out);
+    DoLog(1) && (Log() << Verbose(1) << "Looking at bond structure stored in adjacency file and comparing to present one ... " << endl);
+    std::map<int, atom*> ListOfAtoms;
+    std::pair<std::map<int, atom*>::iterator, bool> inserter;
+    for (const_iterator iter = begin();
+        iter != end();
+        ++iter) {
+      atom *Walker = *iter;
+      inserter = ListOfAtoms.insert( make_pair( Walker->GetTrueFather()->getNr(), Walker) );
+      FragmentationToDo = FragmentationToDo && inserter.second;
+    }
+    CheckAgainstAdjacencyFile FileChecker;
+    FragmentationToDo = FragmentationToDo && FileChecker(File, ListOfAtoms);
+  }
 
   // === reset bond degree and perform CorrectBondDegree ===

src/molecule_graph.cpp

@@ -43 +43 @@
 #include "WorldTime.hpp"
 
-#define MAXBONDS 8
-
 
 /** Fills the bond structure of this chain list subgraphs that are derived from a complete \a *reference molecule.
@@ -198 +196 @@
 ;
 
-bool CheckAdjacencyFileAgainstMolecule_Init(std::string &path, ifstream &File, int *&CurrentBonds)
-{
-  string filename;
-  filename = path + ADJACENCYFILE;
-  File.open(filename.c_str(), ios::out);
-  DoLog(1) && (Log() << Verbose(1) << "Looking at bond structure stored in adjacency file and comparing to present one ... " << endl);
-  if (File.fail())
-    return false;
-
-  // allocate storage structure
-  CurrentBonds = new int[MAXBONDS]; // contains parsed bonds of current atom
-  for(int i=0;i<MAXBONDS;i++)
-    CurrentBonds[i] = 0;
-  return true;
-}
-;
-
-void CheckAdjacencyFileAgainstMolecule_Finalize(ifstream &File, int *&CurrentBonds)
-{
-  File.close();
-  File.clear();
-  delete[](CurrentBonds);
-}
-;
-
-void CheckAdjacencyFileAgainstMolecule_CompareBonds(bool &status, int &NonMatchNumber, atom *&Walker, size_t &CurrentBondsOfAtom, int AtomNr, int *&CurrentBonds, atom **ListOfAtoms)
-{
-  size_t j = 0;
-  int id = -1;
-
-  //Log() << Verbose(2) << "Walker is " << *Walker << ", bond partners: ";
-  const BondList& ListOfBonds = Walker->getListOfBonds();
-  if (CurrentBondsOfAtom == ListOfBonds.size()) {
-    for (BondList::const_iterator Runner = ListOfBonds.begin();
-        Runner != ListOfBonds.end();
-        ++Runner) {
-      id = (*Runner)->GetOtherAtom(Walker)->getNr();
-      j = 0;
-      for (; (j < CurrentBondsOfAtom) && (CurrentBonds[j++] != id);)
-        ; // check against all parsed bonds
-      if (CurrentBonds[j - 1] != id) { // no match ? Then mark in ListOfAtoms
-        ListOfAtoms[AtomNr] = NULL;
-        NonMatchNumber++;
-        status = false;
-        DoeLog(2) && (eLog() << Verbose(2) << id << " can not be found in list." << endl);
-      } else {
-        //Log() << Verbose(0) << "[" << id << "]\t";
-      }
-    }
-    //Log() << Verbose(0) << endl;
-  } else {
-    DoLog(0) && (Log() << Verbose(0) << "Number of bonds for Atom " << *Walker << " does not match, parsed " << CurrentBondsOfAtom << " against " << ListOfBonds.size() << "." << endl);
-    status = false;
-  }
-}
-;
-
-/** Checks contents of adjacency file against bond structure in structure molecule.
- * \param *path path to file
- * \param **ListOfAtoms allocated (molecule::AtomCount) and filled lookup table for ids (Atom::Nr) to *Atom
- * \return true - structure is equal, false - not equivalence
- */
-bool molecule::CheckAdjacencyFileAgainstMolecule(std::string &path, atom **ListOfAtoms)
-{
-  ifstream File;
-  bool status = true;
-  atom *Walker = NULL;
-  int *CurrentBonds = NULL;
-  int NonMatchNumber = 0; // will number of atoms with differing bond structure
-  size_t CurrentBondsOfAtom = -1;
-  const int AtomCount = getAtomCount();
-
-  if (!CheckAdjacencyFileAgainstMolecule_Init(path, File, CurrentBonds)) {
-    DoLog(1) && (Log() << Verbose(1) << "Adjacency file not found." << endl);
-    return true;
-  }
-
-  char buffer[MAXSTRINGSIZE];
-  int tmp;
-  // Parse the file line by line and count the bonds
-  while (!File.eof()) {
-    File.getline(buffer, MAXSTRINGSIZE);
-    stringstream line;
-    line.str(buffer);
-    int AtomNr = -1;
-    line >> AtomNr;
-    CurrentBondsOfAtom = -1; // we count one too far due to line end
-    // parse into structure
-    if ((AtomNr >= 0) && (AtomNr < AtomCount)) {
-      Walker = ListOfAtoms[AtomNr];
-      while (line >> ws >> tmp) {
-        std::cout << "Recognized bond partner " << tmp << std::endl;
-        CurrentBonds[++CurrentBondsOfAtom] = tmp;
-        ASSERT(CurrentBondsOfAtom < MAXBONDS,
-            "molecule::CheckAdjacencyFileAgainstMolecule() - encountered more bonds than allowed: "
-            +toString(CurrentBondsOfAtom)+" >= "+toString(MAXBONDS)+"!");
-      }
-      // compare against present bonds
-      CheckAdjacencyFileAgainstMolecule_CompareBonds(status, NonMatchNumber, Walker, CurrentBondsOfAtom, AtomNr, CurrentBonds, ListOfAtoms);
-    } else {
-      if (AtomNr != -1)
-        DoeLog(2) && (eLog() << Verbose(2) << AtomNr << " is not valid in the range of ids [" << 0 << "," << AtomCount << ")." << endl);
-    }
-  }
-  CheckAdjacencyFileAgainstMolecule_Finalize(File, CurrentBonds);
-
-  if (status) { // if equal we parse the KeySetFile
-    DoLog(1) && (Log() << Verbose(1) << "done: Equal." << endl);
-  } else
-    DoLog(1) && (Log() << Verbose(1) << "done: Not equal by " << NonMatchNumber << " atoms." << endl);
-  return status;
-}
-;
-
 /** Adds a bond as a copy to a given one
  * \param *left leftatom of new bond