Changeset 451148

Timestamp:

Apr 29, 2008, 7:55:34 AM (17 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:

c750cc

Parents:

1fa5b7

Message:

Store/CheckAdj...() now also incorporate bond order to check against.

Location:

src

Files:

• molecules.cpp (modified) (6 diffs)
• molecules.hpp (modified) (1 diff)

src/molecules.cpp

@@ -1942 +1942 @@
  * \return true - file written successfully, false - writing failed
  */
-bool molecule::StoreAdjacencyToFile(ofstream *out, char *path)
+bool molecule::StoreAdjacencyToFile(ofstream *out, char *path, int bondorder)
 {
   ofstream AdjacencyFile;
@@ -1953 +1953 @@
   cout << Verbose(1) << "Saving adjacency list ... ";
   if (AdjacencyFile != NULL) {
+    AdjacencyFile << "Order\t" << bondorder << endl;
     Walker = start;
     while(Walker->next != end) {
@@ -1976 +1977 @@
  * \param *path path to file
  * \param **ListOfAtoms allocated (molecule::AtomCount) and filled lookup table for ids (Atom::nr) to *Atom
+ * \param bondorder check whether files matches desired bond order
  * \return true - structure is equal, false - not equivalence
  */ 
-bool molecule::CheckAdjacencyFileAgainstMolecule(ofstream *out, char *path, atom **ListOfAtoms)
+bool molecule::CheckAdjacencyFileAgainstMolecule(ofstream *out, char *path, atom **ListOfAtoms, int bondorder)
 {
   char *filename = (char *) Malloc(sizeof(char)*255, "molecule::CheckAdjacencyFileAgainstMolecule - filename");
@@ -1992 +1994 @@
     int *CurrentBonds = (int *) Malloc(sizeof(int)*8, "molecule::CheckAdjacencyFileAgainstMolecule - CurrentBonds"); // contains parsed bonds of current atom
     int CurrentBondsOfAtom;
-    // Parse the file line by line and count the bonds
-    while (!File.eof()) {
-      File.getline(filename, 255);
-      stringstream line;
-      line.str(filename);
-      int AtomNr = -1;
-      line >> AtomNr;
-      CurrentBondsOfAtom = -1; // we count one too far due to line end
-      // parse into structure
-      if ((AtomNr >= 0) && (AtomNr < AtomCount)) {
-        while (!line.eof())
-          line >> CurrentBonds[ ++CurrentBondsOfAtom ];
-        // compare against present bonds
-        //cout << Verbose(2) << "Walker is " << *Walker << ", bond partners: ";
-        if (CurrentBondsOfAtom == NumberOfBondsPerAtom[AtomNr]) {
-          for(int i=0;i<NumberOfBondsPerAtom[AtomNr];i++) {
-            int id = ListOfBondsPerAtom[AtomNr][i]->GetOtherAtom(ListOfAtoms[AtomNr])->nr;
-            int 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;
-              //out << "[" << id << "]\t";
-            } else {
-              //out << id << "\t";
+
+    // determine order from file
+    File.getline(filename, 255);    
+    if (bondorder != atoi(&filename[5])) {
+      *out << "Bond order desired is " << bondorder << " and does not match one in file " << filename[6] << "." << endl;
+      status = false;
+    } else {
+      // Parse the file line by line and count the bonds
+      while (!File.eof()) {
+        File.getline(filename, 255);
+        stringstream line;
+        line.str(filename);
+        int AtomNr = -1;
+        line >> AtomNr;
+        CurrentBondsOfAtom = -1; // we count one too far due to line end
+        // parse into structure
+        if ((AtomNr >= 0) && (AtomNr < AtomCount)) {
+          while (!line.eof())
+            line >> CurrentBonds[ ++CurrentBondsOfAtom ];
+          // compare against present bonds
+          //cout << Verbose(2) << "Walker is " << *Walker << ", bond partners: ";
+          if (CurrentBondsOfAtom == NumberOfBondsPerAtom[AtomNr]) {
+            for(int i=0;i<NumberOfBondsPerAtom[AtomNr];i++) {
+              int id = ListOfBondsPerAtom[AtomNr][i]->GetOtherAtom(ListOfAtoms[AtomNr])->nr;
+              int 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;
+                //out << "[" << id << "]\t";
+              } else {
+                //out << id << "\t";
+              }
             }
+            //out << endl;
+          } else {
+            *out << "Number of bonds for Atom " << *ListOfAtoms[AtomNr] << " does not match, parsed " << CurrentBondsOfAtom << " against " << NumberOfBondsPerAtom[AtomNr] << "." << endl;
+            status = false;
           }
-          //out << endl;
-        } else {
-          *out << "Number of bonds for Atom " << *ListOfAtoms[AtomNr] << " does not match, parsed " << CurrentBondsOfAtom << " against " << NumberOfBondsPerAtom[AtomNr] << "." << endl;
-          status = false;
         }
       }
-    }
-    File.close();
-    File.clear();
-    if (status) { // if equal we parse the KeySetFile
-      *out << " done: Equal." << endl;
-      status = true;
-    } else
-      *out << " done: Not equal by " << NonMatchNumber << " atoms." << endl;
+      File.close();
+      File.clear();
+      if (status) { // if equal we parse the KeySetFile
+        *out << " done: Equal." << endl;
+        status = true;
+      } else
+        *out << " done: Not equal by " << NonMatchNumber << " atoms." << endl;
+    }
     Free((void **)&CurrentBonds, "molecule::CheckAdjacencyFileAgainstMolecule - **CurrentBonds");
   } else {
@@ -2093 +2103 @@
     status = false;
   }
-  status = status && CheckAdjacencyFileAgainstMolecule(out, configuration->configpath, ListOfAtoms); 
+  status = status && CheckAdjacencyFileAgainstMolecule(out, configuration->configpath, ListOfAtoms, BottomUpOrder); 
   if (status) {  // NULL entries in ListOfAtoms contain NonMatches
     status = status && ParseKeySetFile(out, configuration->configpath, ListOfAtoms, FragmentList, configuration->GetIsAngstroem());
@@ -2102 +2112 @@
   if (!status) {
     // === store Adjacency file ===
-    StoreAdjacencyToFile(out, configuration->configpath);
+    StoreAdjacencyToFile(out, configuration->configpath, BottomUpOrder);
 
     // === first perform a DFS analysis to gather info on cyclic structure and a list of disconnected subgraphs ===

src/molecules.hpp

@@ -520 +520 @@
   /// Fragment molecule by two different approaches:
   void FragmentMolecule(ofstream *out, int BottomUpOrder, int TopDownOrder, enum BondOrderScheme Scheme, config *configuration, enum CutCyclicBond CutCyclic);
-  bool StoreAdjacencyToFile(ofstream *out, char *path);
-  bool CheckAdjacencyFileAgainstMolecule(ofstream *out, char *path, atom **ListOfAtoms);
+  bool StoreAdjacencyToFile(ofstream *out, char *path, int bondorder);
+  bool CheckAdjacencyFileAgainstMolecule(ofstream *out, char *path, atom **ListOfAtoms, int bondorder);
   bool ParseKeySetFile(ofstream *out, char *filename, atom **ListOfAtoms, MoleculeListClass *&FragmentList, bool IsAngstroem);
   bool ScanBufferIntoKeySet(ofstream *out, char *buffer, KeySet &CurrentSet);