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  • src/molecule_fragmentation.cpp

    rb34306 ra67d19  
    4444  }
    4545  FragmentCount = NoNonHydrogen*(1 << (c*order));
    46   Log() << Verbose(1) << "Upper limit for this subgraph is " << FragmentCount << " for " << NoNonHydrogen << " non-H atoms with maximum bond degree of " << c << "." << endl;
     46  DoLog(1) && (Log() << Verbose(1) << "Upper limit for this subgraph is " << FragmentCount << " for " << NoNonHydrogen << " non-H atoms with maximum bond degree of " << c << "." << endl);
    4747  return FragmentCount;
    4848};
    … …  
    6868    } // else it's "-1" or else and thus must not be added
    6969  }
    70   Log() << Verbose(1) << "The scanned KeySet is ";
     70  DoLog(1) && (Log() << Verbose(1) << "The scanned KeySet is ");
    7171  for(KeySet::iterator runner = CurrentSet.begin(); runner != CurrentSet.end(); runner++) {
    72     Log() << Verbose(0) << (*runner) << "\t";
    73   }
    74   Log() << Verbose(0) << endl;
     72    DoLog(0) && (Log() << Verbose(0) << (*runner) << "\t");
     73  }
     74  DoLog(0) && (Log() << Verbose(0) << endl);
    7575  return (status != 0);
    7676};
    … …  
    100100
    101101  // 1st pass: open file and read
    102   Log() << Verbose(1) << "Parsing the KeySet file ... " << endl;
     102  DoLog(1) && (Log() << Verbose(1) << "Parsing the KeySet file ... " << endl);
    103103  sprintf(filename, "%s/%s%s", path, FRAGMENTPREFIX, KEYSETFILE);
    104104  InputFile.open(filename);
    … …  
    113113        testGraphInsert = FragmentList->insert(GraphPair (CurrentSet,pair<int,double>(NumberOfFragments++,1)));  // store fragment number and current factor
    114114        if (!testGraphInsert.second) {
    115           eLog() << Verbose(0) << "KeySet file must be corrupt as there are two equal key sets therein!" << endl;
     115          DoeLog(0) && (eLog()<< Verbose(0) << "KeySet file must be corrupt as there are two equal key sets therein!" << endl);
    116116          performCriticalExit();
    117117        }
    … …  
    122122    InputFile.clear();
    123123    Free(&buffer);
    124     Log() << Verbose(1) << "done." << endl;
     124    DoLog(1) && (Log() << Verbose(1) << "done." << endl);
    125125  } else {
    126     Log() << Verbose(1) << "File " << filename << " not found." << endl;
     126    DoLog(1) && (Log() << Verbose(1) << "File " << filename << " not found." << endl);
    127127    status = false;
    128128  }
    … …  
    154154
    155155  // 2nd pass: open TEFactors file and read
    156   Log() << Verbose(1) << "Parsing the TEFactors file ... " << endl;
     156  DoLog(1) && (Log() << Verbose(1) << "Parsing the TEFactors file ... " << endl);
    157157  sprintf(filename, "%s/%s%s", path, FRAGMENTPREFIX, TEFACTORSFILE);
    158158  InputFile.open(filename);
    … …  
    164164        InputFile >> TEFactor;
    165165        (*runner).second.second = TEFactor;
    166         Log() << Verbose(2) << "Setting " << ++NumberOfFragments << " fragment's TEFactor to " << (*runner).second.second << "." << endl;
     166        DoLog(2) && (Log() << Verbose(2) << "Setting " << ++NumberOfFragments << " fragment's TEFactor to " << (*runner).second.second << "." << endl);
    167167      } else {
    168168        status = false;
    … …  
    172172    // 4. Free and done
    173173    InputFile.close();
    174     Log() << Verbose(1) << "done." << endl;
     174    DoLog(1) && (Log() << Verbose(1) << "done." << endl);
    175175  } else {
    176     Log() << Verbose(1) << "File " << filename << " not found." << endl;
     176    DoLog(1) && (Log() << Verbose(1) << "File " << filename << " not found." << endl);
    177177    status = false;
    178178  }
    … …  
    202202  line += KEYSETFILE;
    203203  output.open(line.c_str(), ios::out);
    204   Log() << Verbose(1) << "Saving key sets of the total graph ... ";
     204  DoLog(1) && (Log() << Verbose(1) << "Saving key sets of the total graph ... ");
    205205  if(output != NULL) {
    206206    for(Graph::iterator runner = KeySetList.begin(); runner != KeySetList.end(); runner++) {
    … …  
    212212      output << endl;
    213213    }
    214     Log() << Verbose(0) << "done." << endl;
     214    DoLog(0) && (Log() << Verbose(0) << "done." << endl);
    215215  } else {
    216     eLog() << Verbose(0) << "Unable to open " << line << " for writing keysets!" << endl;
     216    DoeLog(0) && (eLog()<< Verbose(0) << "Unable to open " << line << " for writing keysets!" << endl);
    217217    performCriticalExit();
    218218    status = false;
    … …  
    243243  line += TEFACTORSFILE;
    244244  output.open(line.c_str(), ios::out);
    245   Log() << Verbose(1) << "Saving TEFactors of the total graph ... ";
     245  DoLog(1) && (Log() << Verbose(1) << "Saving TEFactors of the total graph ... ");
    246246  if(output != NULL) {
    247247    for(Graph::iterator runner = KeySetList.begin(); runner != KeySetList.end(); runner++)
    248248      output << (*runner).second.second << endl;
    249     Log() << Verbose(1) << "done." << endl;
     249    DoLog(1) && (Log() << Verbose(1) << "done." << endl);
    250250  } else {
    251     Log() << Verbose(1) << "failed to open " << line << "." << endl;
     251    DoLog(1) && (Log() << Verbose(1) << "failed to open " << line << "." << endl);
    252252    status = false;
    253253  }
    … …  
    293293        (*PresentItem).second.first = fabs(Value);
    294294        (*PresentItem).second.second = FragOrder;
    295         Log() << Verbose(2) << "Updated element (" <<  (*PresentItem).first << ",[" << (*PresentItem).second.first << "," << (*PresentItem).second.second << "])." << endl;
     295        DoLog(2) && (Log() << Verbose(2) << "Updated element (" <<  (*PresentItem).first << ",[" << (*PresentItem).second.first << "," << (*PresentItem).second.second << "])." << endl);
    296296      } else {
    297         Log() << Verbose(2) << "Did not update element " <<  (*PresentItem).first << " as " << FragOrder << " is less than or equal to " << (*PresentItem).second.second << "." << endl;
     297        DoLog(2) && (Log() << Verbose(2) << "Did not update element " <<  (*PresentItem).first << " as " << FragOrder << " is less than or equal to " << (*PresentItem).second.second << "." << endl);
    298298      }
    299299    } else {
    300       Log() << Verbose(2) << "Inserted element (" <<  (*PresentItem).first << ",[" << (*PresentItem).second.first << "," << (*PresentItem).second.second << "])." << endl;
     300      DoLog(2) && (Log() << Verbose(2) << "Inserted element (" <<  (*PresentItem).first << ",[" << (*PresentItem).second.first << "," << (*PresentItem).second.second << "])." << endl);
    301301    }
    302302  } else {
    303     Log() << Verbose(1) << "No Fragment under No. " << No << "found." << endl;
     303    DoLog(1) && (Log() << Verbose(1) << "No Fragment under No. " << No << "found." << endl);
    304304  }
    305305};
    … …  
    360360  atom *Walker = mol->start;
    361361  map<double, pair<int,int> > *FinalRootCandidates = new map<double, pair<int,int> > ;
    362   Log() << Verbose(1) << "Root candidate list is: " << endl;
     362  DoLog(1) && (Log() << Verbose(1) << "Root candidate list is: " << endl);
    363363  for(map<int, pair<double,int> >::iterator runner = AdaptiveCriteriaList->begin(); runner != AdaptiveCriteriaList->end(); runner++) {
    364364    Walker = mol->FindAtom((*runner).first);
    … …  
    366366      //if ((*runner).second.second >= Walker->AdaptiveOrder) { // only insert if this is an "active" root site for the current order
    367367      if (!Walker->MaxOrder) {
    368         Log() << Verbose(2) << "(" << (*runner).first << ",[" << (*runner).second.first << "," << (*runner).second.second << "])" << endl;
     368        DoLog(2) && (Log() << Verbose(2) << "(" << (*runner).first << ",[" << (*runner).second.first << "," << (*runner).second.second << "])" << endl);
    369369        FinalRootCandidates->insert( make_pair( (*runner).second.first, pair<int,int>((*runner).first, (*runner).second.second) ) );
    370370      } else {
    371         Log() << Verbose(2) << "Excluding (" << *Walker << ", " << (*runner).first << ",[" << (*runner).second.first << "," << (*runner).second.second << "]), as it has reached its maximum order." << endl;
     371        DoLog(2) && (Log() << Verbose(2) << "Excluding (" << *Walker << ", " << (*runner).first << ",[" << (*runner).second.first << "," << (*runner).second.second << "]), as it has reached its maximum order." << endl);
    372372      }
    373373    } else {
    374       eLog() << Verbose(0) << "Atom No. " << (*runner).second.first << " was not found in this molecule." << endl;
     374      DoeLog(0) && (eLog()<< Verbose(0) << "Atom No. " << (*runner).second.first << " was not found in this molecule." << endl);
    375375      performCriticalExit();
    376376    }
    … …  
    397397    Walker = mol->FindAtom(No);
    398398    //if (Walker->AdaptiveOrder < MinimumRingSize[Walker->nr]) {
    399       Log() << Verbose(2) << "Root " << No << " is still above threshold (10^{" << Order <<"}: " << runner->first << ", setting entry " << No << " of Atom mask to true." << endl;
     399      DoLog(2) && (Log() << Verbose(2) << "Root " << No << " is still above threshold (10^{" << Order <<"}: " << runner->first << ", setting entry " << No << " of Atom mask to true." << endl);
    400400      AtomMask[No] = true;
    401401      status = true;
    … …  
    413413void PrintAtomMask(bool *AtomMask, int AtomCount)
    414414{
    415   Log() << Verbose(2) << "              ";
     415  DoLog(2) && (Log() << Verbose(2) << "              ");
    416416  for(int i=0;i<AtomCount;i++)
    417     Log() << Verbose(0) << (i % 10);
    418   Log() << Verbose(0) << endl;
    419   Log() << Verbose(2) << "Atom mask is: ";
     417    DoLog(0) && (Log() << Verbose(0) << (i % 10));
     418  DoLog(0) && (Log() << Verbose(0) << endl);
     419  DoLog(2) && (Log() << Verbose(2) << "Atom mask is: ");
    420420  for(int i=0;i<AtomCount;i++)
    421     Log() << Verbose(0) << (AtomMask[i] ? "t" : "f");
    422   Log() << Verbose(0) << endl;
     421    DoLog(0) && (Log() << Verbose(0) << (AtomMask[i] ? "t" : "f"));
     422  DoLog(0) && (Log() << Verbose(0) << endl);
    423423};
    424424
    … …  
    447447    // transmorph graph keyset list into indexed KeySetList
    448448    if (GlobalKeySetList == NULL) {
    449       eLog() << Verbose(1) << "Given global key set list (graph) is NULL!" << endl;
     449      DoeLog(1) && (eLog()<< Verbose(1) << "Given global key set list (graph) is NULL!" << endl);
    450450      return false;
    451451    }
    … …  
    455455    map<int, pair<double,int> > *AdaptiveCriteriaList = ScanAdaptiveFileIntoMap(path, *IndexKeySetList); // (Root No., (Value, Order)) !
    456456    if (AdaptiveCriteriaList->empty()) {
    457       eLog() << Verbose(2) << "Unable to parse file, incrementing all." << endl;
     457      DoeLog(2) && (eLog()<< Verbose(2) << "Unable to parse file, incrementing all." << endl);
    458458      while (Walker->next != end) {
    459459        Walker = Walker->next;
    … …  
    493493    if (!status) {
    494494      if (Order == 0)
    495         Log() << Verbose(1) << "Single stepping done." << endl;
     495        DoLog(1) && (Log() << Verbose(1) << "Single stepping done." << endl);
    496496      else
    497         Log() << Verbose(1) << "Order at every site is already equal or above desired order " << Order << "." << endl;
     497        DoLog(1) && (Log() << Verbose(1) << "Order at every site is already equal or above desired order " << Order << "." << endl);
    498498    }
    499499  }
    … …  
    512512{
    513513  if (SortIndex != NULL) {
    514     Log() << Verbose(1) << "SortIndex is " << SortIndex << " and not NULL as expected." << endl;
     514    DoLog(1) && (Log() << Verbose(1) << "SortIndex is " << SortIndex << " and not NULL as expected." << endl);
    515515    return false;
    516516  }
    … …  
    563563  bool *AtomMask = NULL;
    564564
    565   Log() << Verbose(0) << endl;
     565  DoLog(0) && (Log() << Verbose(0) << endl);
    566566#ifdef ADDHYDROGEN
    567   Log() << Verbose(0) << "I will treat hydrogen special and saturate dangling bonds with it." << endl;
     567  DoLog(0) && (Log() << Verbose(0) << "I will treat hydrogen special and saturate dangling bonds with it." << endl);
    568568#else
    569   Log() << Verbose(0) << "Hydrogen is treated just like the rest of the lot." << endl;
     569  DoLog(0) && (Log() << Verbose(0) << "Hydrogen is treated just like the rest of the lot." << endl);
    570570#endif
    571571
    … …  
    593593    // fill the bond structure of the individually stored subgraphs
    594594  MolecularWalker->FillBondStructureFromReference(this, FragmentCounter, ListOfLocalAtoms, false);  // we want to keep the created ListOfLocalAtoms
    595     Log() << Verbose(0) << "Analysing the cycles of subgraph " << MolecularWalker->Leaf << " with nr. " << FragmentCounter << "." << endl;
     595    DoLog(0) && (Log() << Verbose(0) << "Analysing the cycles of subgraph " << MolecularWalker->Leaf << " with nr. " << FragmentCounter << "." << endl);
    596596    LocalBackEdgeStack = new StackClass<bond *> (MolecularWalker->Leaf->BondCount);
    597597//    // check the list of local atoms for debugging
    … …  
    602602//      else
    603603//        Log() << Verbose(0) << "\t" << ListOfLocalAtoms[FragmentCounter][i]->Name;
    604     Log() << Verbose(0) << "Gathering local back edges for subgraph " << MolecularWalker->Leaf << " with nr. " << FragmentCounter << "." << endl;
     604    DoLog(0) && (Log() << Verbose(0) << "Gathering local back edges for subgraph " << MolecularWalker->Leaf << " with nr. " << FragmentCounter << "." << endl);
    605605    MolecularWalker->Leaf->PickLocalBackEdges(ListOfLocalAtoms[FragmentCounter++], BackEdgeStack, LocalBackEdgeStack);
    606     Log() << Verbose(0) << "Analysing the cycles of subgraph " << MolecularWalker->Leaf << " with nr. " << FragmentCounter << "." << endl;
     606    DoLog(0) && (Log() << Verbose(0) << "Analysing the cycles of subgraph " << MolecularWalker->Leaf << " with nr. " << FragmentCounter << "." << endl);
    607607    MolecularWalker->Leaf->CyclicStructureAnalysis(LocalBackEdgeStack, MinimumRingSize);
    608     Log() << Verbose(0) << "Done with Analysing the cycles of subgraph " << MolecularWalker->Leaf << " with nr. " << FragmentCounter << "." << endl;
     608    DoLog(0) && (Log() << Verbose(0) << "Done with Analysing the cycles of subgraph " << MolecularWalker->Leaf << " with nr. " << FragmentCounter << "." << endl);
    609609    delete(LocalBackEdgeStack);
    610610  }
    … …  
    637637    while (MolecularWalker->next != NULL) {
    638638      MolecularWalker = MolecularWalker->next;
    639       Log() << Verbose(1) << "Fragmenting subgraph " << MolecularWalker << "." << endl;
     639      DoLog(1) && (Log() << Verbose(1) << "Fragmenting subgraph " << MolecularWalker << "." << endl);
    640640      //MolecularWalker->Leaf->OutputListOfBonds(out);  // output atom::ListOfBonds for debugging
    641641      if (MolecularWalker->Leaf->first->next != MolecularWalker->Leaf->last) {
    642642        // call BOSSANOVA method
    643         Log() << Verbose(0) << endl << " ========== BOND ENERGY of subgraph " << FragmentCounter << " ========================= " << endl;
     643        DoLog(0) && (Log() << Verbose(0) << endl << " ========== BOND ENERGY of subgraph " << FragmentCounter << " ========================= " << endl);
    644644        MolecularWalker->Leaf->FragmentBOSSANOVA(FragmentList[FragmentCounter], RootStack[FragmentCounter], MinimumRingSize);
    645645      } else {
    646         eLog() << Verbose(1) << "Subgraph " << MolecularWalker << " has no atoms!" << endl;
     646        DoeLog(1) && (eLog()<< Verbose(1) << "Subgraph " << MolecularWalker << " has no atoms!" << endl);
    647647      }
    648648      FragmentCounter++;  // next fragment list
    649649    }
    650650  }
    651   Log() << Verbose(2) << "CheckOrder is " << CheckOrder << "." << endl;
     651  DoLog(2) && (Log() << Verbose(2) << "CheckOrder is " << CheckOrder << "." << endl);
    652652  delete[](RootStack);
    653653  delete[](AtomMask);
    … …  
    680680  for(Graph::iterator runner = TotalGraph.begin(); runner != TotalGraph.end(); runner++) {
    681681    KeySet test = (*runner).first;
    682     Log() << Verbose(0) << "Fragment No." << (*runner).second.first << " with TEFactor " << (*runner).second.second << "." << endl;
     682    DoLog(0) && (Log() << Verbose(0) << "Fragment No." << (*runner).second.first << " with TEFactor " << (*runner).second.second << "." << endl);
    683683    BondFragments->insert(StoreFragmentFromKeySet(test, configuration));
    684684    k++;
    685685  }
    686   Log() << Verbose(0) << k << "/" << BondFragments->ListOfMolecules.size() << " fragments generated from the keysets." << endl;
     686  DoLog(0) && (Log() << Verbose(0) << k << "/" << BondFragments->ListOfMolecules.size() << " fragments generated from the keysets." << endl);
    687687
    688688  // ===== 9. Save fragments' configuration and keyset files et al to disk ===
    … …  
    691691    CreateMappingLabelsToConfigSequence(SortIndex);
    692692
    693     Log() << Verbose(1) << "Writing " << BondFragments->ListOfMolecules.size() << " possible bond fragmentation configs" << endl;
     693    DoLog(1) && (Log() << Verbose(1) << "Writing " << BondFragments->ListOfMolecules.size() << " possible bond fragmentation configs" << endl);
    694694    if (BondFragments->OutputConfigForListOfFragments(configuration, SortIndex))
    695       Log() << Verbose(1) << "All configs written." << endl;
     695      DoLog(1) && (Log() << Verbose(1) << "All configs written." << endl);
    696696    else
    697       Log() << Verbose(1) << "Some config writing failed." << endl;
     697      DoLog(1) && (Log() << Verbose(1) << "Some config writing failed." << endl);
    698698
    699699    // store force index reference file
    … …  
    704704
    705705    // store Adjacency file
    706     StoreAdjacencyToFile(configuration->configpath);
     706    char *filename = Malloc<char> (MAXSTRINGSIZE, "molecule::FragmentMolecule - *filename");
     707    strcpy(filename, FRAGMENTPREFIX);
     708    strcat(filename, ADJACENCYFILE);
     709    StoreAdjacencyToFile(configuration->configpath, filename);
     710    Free(&filename);
    707711
    708712    // store Hydrogen saturation correction file
    … …  
    716720
    717721    // free memory for bond part
    718     Log() << Verbose(1) << "Freeing bond memory" << endl;
     722    DoLog(1) && (Log() << Verbose(1) << "Freeing bond memory" << endl);
    719723    delete(FragmentList); // remove bond molecule from memory
    720724    Free(&SortIndex);
    721725  } else {
    722     Log() << Verbose(1) << "FragmentList is zero on return, splitting failed." << endl;
     726    DoLog(1) && (Log() << Verbose(1) << "FragmentList is zero on return, splitting failed." << endl);
    723727  }
    724728  delete(BondFragments);
    725   Log() << Verbose(0) << "End of bond fragmentation." << endl;
     729  DoLog(0) && (Log() << Verbose(0) << "End of bond fragmentation." << endl);
    726730
    727731  return ((int)(!FragmentationToDo)+1);    // 1 - continue, 2 - stop (no fragmentation occured)
    … …  
    742746  line << path << "/" << FRAGMENTPREFIX << ORDERATSITEFILE;
    743747  file.open(line.str().c_str());
    744   Log() << Verbose(1) << "Writing OrderAtSite " << ORDERATSITEFILE << " ... " << endl;
     748  DoLog(1) && (Log() << Verbose(1) << "Writing OrderAtSite " << ORDERATSITEFILE << " ... " << endl);
    745749  if (file != NULL) {
    746750    ActOnAllAtoms( &atom::OutputOrder, &file );
    747751    file.close();
    748     Log() << Verbose(1) << "done." << endl;
     752    DoLog(1) && (Log() << Verbose(1) << "done." << endl);
    749753    return true;
    750754  } else {
    751     Log() << Verbose(1) << "failed to open file " << line.str() << "." << endl;
     755    DoLog(1) && (Log() << Verbose(1) << "failed to open file " << line.str() << "." << endl);
    752756    return false;
    753757  }
    … …  
    770774  ifstream file;
    771775
    772   Log() << Verbose(1) << "Begin of ParseOrderAtSiteFromFile" << endl;
     776  DoLog(1) && (Log() << Verbose(1) << "Begin of ParseOrderAtSiteFromFile" << endl);
    773777  line << path << "/" << FRAGMENTPREFIX << ORDERATSITEFILE;
    774778  file.open(line.str().c_str());
    … …  
    791795    SetAtomValueToIndexedArray( MaxArray, &atom::nr, &atom::MaxOrder );
    792796
    793     Log() << Verbose(1) << "done." << endl;
     797    DoLog(1) && (Log() << Verbose(1) << "done." << endl);
    794798    status = true;
    795799  } else {
    796     Log() << Verbose(1) << "failed to open file " << line.str() << "." << endl;
     800    DoLog(1) && (Log() << Verbose(1) << "failed to open file " << line.str() << "." << endl);
    797801    status = false;
    798802  }
    … …  
    800804  Free(&MaxArray);
    801805
    802   Log() << Verbose(1) << "End of ParseOrderAtSiteFromFile" << endl;
     806  DoLog(1) && (Log() << Verbose(1) << "End of ParseOrderAtSiteFromFile" << endl);
    803807  return status;
    804808};
    … …  
    817821  int SP, Removal;
    818822
    819   Log() << Verbose(2) << "Looking for removal candidate." << endl;
     823  DoLog(2) && (Log() << Verbose(2) << "Looking for removal candidate." << endl);
    820824  SP = -1; //0;  // not -1, so that Root is never removed
    821825  Removal = -1;
    … …  
    902906      }
    903907    } else {
    904       eLog() << Verbose(1) << "Son " << Runner->Name << " has father " << FatherOfRunner->Name << " but its entry in SonList is " << SonList[FatherOfRunner->nr] << "!" << endl;
     908      DoeLog(1) && (eLog()<< Verbose(1) << "Son " << Runner->Name << " has father " << FatherOfRunner->Name << " but its entry in SonList is " << SonList[FatherOfRunner->nr] << "!" << endl);
    905909    }
    906910    if ((LonelyFlag) && (Leaf->AtomCount > 1)) {
    907       Log() << Verbose(0) << *Runner << "has got bonds only to hydrogens!" << endl;
     911      DoLog(0) && (Log() << Verbose(0) << *Runner << "has got bonds only to hydrogens!" << endl);
    908912    }
    909913#ifdef ADDHYDROGEN
    … …  
    10521056    TouchedList[j] = -1;
    10531057  }
    1054   Log() << Verbose(2) << "Remaining local nr.s on snake stack are: ";
     1058  DoLog(2) && (Log() << Verbose(2) << "Remaining local nr.s on snake stack are: ");
    10551059  for(KeySet::iterator runner = FragmentSet->begin(); runner != FragmentSet->end(); runner++)
    1056     Log() << Verbose(0) << (*runner) << " ";
    1057   Log() << Verbose(0) << endl;
     1060    DoLog(0) && (Log() << Verbose(0) << (*runner) << " ");
     1061  DoLog(0) && (Log() << Verbose(0) << endl);
    10581062  TouchedIndex = 0; // set Index to 0 for list of atoms added on this level
    10591063};
    … …  
    11321136        Log() << Verbose(1+verbosity) << "Enough items on stack for a fragment!" << endl;
    11331137        // store fragment as a KeySet
    1134         Log() << Verbose(2) << "Found a new fragment[" << FragmentSearch->FragmentCounter << "], local nr.s are: ";
     1138        DoLog(2) && (Log() << Verbose(2) << "Found a new fragment[" << FragmentSearch->FragmentCounter << "], local nr.s are: ");
    11351139        for(KeySet::iterator runner = FragmentSearch->FragmentSet->begin(); runner != FragmentSearch->FragmentSet->end(); runner++)
    1136           Log() << Verbose(0) << (*runner) << " ";
    1137         Log() << Verbose(0) << endl;
     1140          DoLog(0) && (Log() << Verbose(0) << (*runner) << " ");
     1141        DoLog(0) && (Log() << Verbose(0) << endl);
    11381142        //if (!CheckForConnectedSubgraph(FragmentSearch->FragmentSet))
    1139           //eLog() << Verbose(1) << "The found fragment is not a connected subgraph!" << endl;
     1143          //DoeLog(1) && (eLog()<< Verbose(1) << "The found fragment is not a connected subgraph!" << endl);
    11401144        InsertFragmentIntoGraph(FragmentSearch);
    11411145      }
    … …  
    12171221{
    12181222  bond *Binder = NULL;
    1219   Log() << Verbose(0) << "Free'ing all found lists. and resetting index lists" << endl;
     1223  DoLog(0) && (Log() << Verbose(0) << "Free'ing all found lists. and resetting index lists" << endl);
    12201224  for(int i=Order;i--;) {
    1221     Log() << Verbose(1) << "Current SP level is " << i << ": ";
     1225    DoLog(1) && (Log() << Verbose(1) << "Current SP level is " << i << ": ");
    12221226    Binder = FragmentSearch.BondsPerSPList[2*i];
    12231227    while (Binder->next != FragmentSearch.BondsPerSPList[2*i+1]) {
    … …  
    12301234    cleanup(FragmentSearch.BondsPerSPList[2*i], FragmentSearch.BondsPerSPList[2*i+1]);
    12311235    // also start and end node
    1232     Log() << Verbose(0) << "cleaned." << endl;
     1236    DoLog(0) && (Log() << Verbose(0) << "cleaned." << endl);
    12331237  }
    12341238};
    … …  
    12601264  int SP = -1;
    12611265
    1262   Log() << Verbose(0) << "Starting BFS analysis ..." << endl;
     1266  DoLog(0) && (Log() << Verbose(0) << "Starting BFS analysis ..." << endl);
    12631267  for (SP = 0; SP < (Order-1); SP++) {
    1264     Log() << Verbose(1) << "New SP level reached: " << SP << ", creating new SP list with " << FragmentSearch.BondsPerSPCount[SP] << " item(s)";
     1268    DoLog(1) && (Log() << Verbose(1) << "New SP level reached: " << SP << ", creating new SP list with " << FragmentSearch.BondsPerSPCount[SP] << " item(s)");
    12651269    if (SP > 0) {
    1266       Log() << Verbose(0) << ", old level closed with " << FragmentSearch.BondsPerSPCount[SP-1] << " item(s)." << endl;
     1270      DoLog(0) && (Log() << Verbose(0) << ", old level closed with " << FragmentSearch.BondsPerSPCount[SP-1] << " item(s)." << endl);
    12671271      FragmentSearch.BondsPerSPCount[SP] = 0;
    12681272    } else
    1269       Log() << Verbose(0) << "." << endl;
     1273      DoLog(0) && (Log() << Verbose(0) << "." << endl);
    12701274
    12711275    RemainingWalkers = FragmentSearch.BondsPerSPCount[SP];
    … …  
    12771281      Predecessor = CurrentEdge->leftatom;    // ... and leftatom is predecessor
    12781282      AtomKeyNr = Walker->nr;
    1279       Log() << Verbose(0) << "Current Walker is: " << *Walker << " with nr " << Walker->nr << " and SP of " << SP << ", with " << RemainingWalkers << " remaining walkers on this level." << endl;
     1283      DoLog(0) && (Log() << Verbose(0) << "Current Walker is: " << *Walker << " with nr " << Walker->nr << " and SP of " << SP << ", with " << RemainingWalkers << " remaining walkers on this level." << endl);
    12801284      // check for new sp level
    12811285      // go through all its bonds
    1282       Log() << Verbose(1) << "Going through all bonds of Walker." << endl;
     1286      DoLog(1) && (Log() << Verbose(1) << "Going through all bonds of Walker." << endl);
    12831287      for (BondList::const_iterator Runner = Walker->ListOfBonds.begin(); Runner != Walker->ListOfBonds.end(); (++Runner)) {
    12841288        OtherWalker = (*Runner)->GetOtherAtom(Walker);
    … …  
    12881292  #endif
    12891293                                                              ) {  // skip hydrogens and restrict to fragment
    1290           Log() << Verbose(2) << "Current partner is " << *OtherWalker << " with nr " << OtherWalker->nr << " in bond " << *(*Runner) << "." << endl;
     1294          DoLog(2) && (Log() << Verbose(2) << "Current partner is " << *OtherWalker << " with nr " << OtherWalker->nr << " in bond " << *(*Runner) << "." << endl);
    12911295          // set the label if not set (and push on root stack as well)
    12921296          if ((OtherWalker != Predecessor) && (OtherWalker->GetTrueFather()->nr > RootKeyNr)) { // only pass through those with label bigger than Root's
    12931297            FragmentSearch.ShortestPathList[OtherWalker->nr] = SP+1;
    1294             Log() << Verbose(3) << "Set Shortest Path to " << FragmentSearch.ShortestPathList[OtherWalker->nr] << "." << endl;
     1298            DoLog(3) && (Log() << Verbose(3) << "Set Shortest Path to " << FragmentSearch.ShortestPathList[OtherWalker->nr] << "." << endl);
    12951299            // add the bond in between to the SP list
    12961300            Binder = new bond(Walker, OtherWalker); // create a new bond in such a manner, that bond::rightatom is always the one more distant
    12971301            add(Binder, FragmentSearch.BondsPerSPList[2*(SP+1)+1]);
    12981302            FragmentSearch.BondsPerSPCount[SP+1]++;
    1299             Log() << Verbose(3) << "Added its bond to SP list, having now " << FragmentSearch.BondsPerSPCount[SP+1] << " item(s)." << endl;
     1303            DoLog(3) && (Log() << Verbose(3) << "Added its bond to SP list, having now " << FragmentSearch.BondsPerSPCount[SP+1] << " item(s)." << endl);
    13001304          } else {
    13011305            if (OtherWalker != Predecessor)
    1302               Log() << Verbose(3) << "Not passing on, as index of " << *OtherWalker << " " << OtherWalker->GetTrueFather()->nr << " is smaller than that of Root " << RootKeyNr << "." << endl;
     1306              DoLog(3) && (Log() << Verbose(3) << "Not passing on, as index of " << *OtherWalker << " " << OtherWalker->GetTrueFather()->nr << " is smaller than that of Root " << RootKeyNr << "." << endl);
    13031307            else
    1304               Log() << Verbose(3) << "This is my predecessor " << *Predecessor << "." << endl;
     1308              DoLog(3) && (Log() << Verbose(3) << "This is my predecessor " << *Predecessor << "." << endl);
    13051309          }
    13061310        } else Log() << Verbose(2) << "Is not in the restricted keyset or skipping hydrogen " << *OtherWalker << "." << endl;
    … …  
    13181322{
    13191323  bond *Binder = NULL;
    1320   Log() << Verbose(0) << "Printing all found lists." << endl;
     1324  DoLog(0) && (Log() << Verbose(0) << "Printing all found lists." << endl);
    13211325  for(int i=1;i<Order;i++) {    // skip the root edge in the printing
    13221326    Binder = FragmentSearch.BondsPerSPList[2*i];
    1323     Log() << Verbose(1) << "Current SP level is " << i << "." << endl;
     1327    DoLog(1) && (Log() << Verbose(1) << "Current SP level is " << i << "." << endl);
    13241328    while (Binder->next != FragmentSearch.BondsPerSPList[2*i+1]) {
    13251329      Binder = Binder->next;
    1326       Log() << Verbose(2) << *Binder << endl;
     1330      DoLog(2) && (Log() << Verbose(2) << *Binder << endl);
    13271331    }
    13281332  }
    … …  
    13681372  int Counter = FragmentSearch.FragmentCounter; // mark current value of counter
    13691373
    1370   Log() << Verbose(0) << endl;
    1371   Log() << Verbose(0) << "Begin of PowerSetGenerator with order " << Order << " at Root " << *FragmentSearch.Root << "." << endl;
     1374  DoLog(0) && (Log() << Verbose(0) << endl);
     1375  DoLog(0) && (Log() << Verbose(0) << "Begin of PowerSetGenerator with order " << Order << " at Root " << *FragmentSearch.Root << "." << endl);
    13721376
    13731377  SetSPList(Order, FragmentSearch);
    … …  
    13811385  // creating fragments with the found edge sets  (may be done in reverse order, faster)
    13821386  int SP = CountNumbersInBondsList(Order, FragmentSearch);
    1383   Log() << Verbose(0) << "Total number of edges is " << SP << "." << endl;
     1387  DoLog(0) && (Log() << Verbose(0) << "Total number of edges is " << SP << "." << endl);
    13841388  if (SP >= (Order-1)) {
    13851389    // start with root (push on fragment stack)
    1386     Log() << Verbose(0) << "Starting fragment generation with " << *FragmentSearch.Root << ", local nr is " << FragmentSearch.Root->nr << "." << endl;
     1390    DoLog(0) && (Log() << Verbose(0) << "Starting fragment generation with " << *FragmentSearch.Root << ", local nr is " << FragmentSearch.Root->nr << "." << endl);
    13871391    FragmentSearch.FragmentSet->clear();
    1388     Log() << Verbose(0) << "Preparing subset for this root and calling generator." << endl;
     1392    DoLog(0) && (Log() << Verbose(0) << "Preparing subset for this root and calling generator." << endl);
    13891393
    13901394    // prepare the subset and call the generator
    … …  
    13961400    Free(&BondsList);
    13971401  } else {
    1398     Log() << Verbose(0) << "Not enough total number of edges to build " << Order << "-body fragments." << endl;
     1402    DoLog(0) && (Log() << Verbose(0) << "Not enough total number of edges to build " << Order << "-body fragments." << endl);
    13991403  }
    14001404
    14011405  // as FragmentSearch structure is used only once, we don't have to clean it anymore
    14021406  // remove root from stack
    1403   Log() << Verbose(0) << "Removing root again from stack." << endl;
     1407  DoLog(0) && (Log() << Verbose(0) << "Removing root again from stack." << endl);
    14041408  FragmentSearch.FragmentSet->erase(FragmentSearch.Root->nr);
    14051409
    … …  
    14081412
    14091413  // return list
    1410   Log() << Verbose(0) << "End of PowerSetGenerator." << endl;
     1414  DoLog(0) && (Log() << Verbose(0) << "End of PowerSetGenerator." << endl);
    14111415  return (FragmentSearch.FragmentCounter - Counter);
    14121416};
    … …  
    14541458  atom *Walker = NULL;
    14551459
    1456   Log() << Verbose(0) << "Combining the lists of all orders per order and finally into a single one." << endl;
     1460  DoLog(0) && (Log() << Verbose(0) << "Combining the lists of all orders per order and finally into a single one." << endl);
    14571461  if (FragmentList == NULL) {
    14581462    FragmentList = new Graph;
    … …  
    14871491void FreeAllOrdersList(Graph ***FragmentLowerOrdersList, KeyStack &RootStack, molecule *mol)
    14881492{
    1489   Log() << Verbose(1) << "Free'ing the lists of all orders per order." << endl;
     1493  DoLog(1) && (Log() << Verbose(1) << "Free'ing the lists of all orders per order." << endl);
    14901494  int RootNr = 0;
    14911495  int RootKeyNr = 0;
    … …  
    15401544  struct UniqueFragments FragmentSearch;
    15411545
    1542   Log() << Verbose(0) << "Begin of FragmentBOSSANOVA." << endl;
     1546  DoLog(0) && (Log() << Verbose(0) << "Begin of FragmentBOSSANOVA." << endl);
    15431547
    15441548  // FragmentLowerOrdersList is a 2D-array of pointer to MoleculeListClass objects, one dimension represents the ANOVA expansion of a single order (i.e. 5)
    … …  
    15901594
    15911595      // create top order where nothing is reduced
    1592       Log() << Verbose(0) << "==============================================================================================================" << endl;
    1593       Log() << Verbose(0) << "Creating KeySets of Bond Order " << Order << " for " << *Walker << ", " << (RootStack.size()-RootNr) << " Roots remaining." << endl; // , NumLevels is " << NumLevels << "
     1596      DoLog(0) && (Log() << Verbose(0) << "==============================================================================================================" << endl);
     1597      DoLog(0) && (Log() << Verbose(0) << "Creating KeySets of Bond Order " << Order << " for " << *Walker << ", " << (RootStack.size()-RootNr) << " Roots remaining." << endl); // , NumLevels is " << NumLevels << "
    15941598
    15951599      // Create list of Graphs of current Bond Order (i.e. F_{ij})
    … …  
    16011605
    16021606      // output resulting number
    1603       Log() << Verbose(1) << "Number of resulting KeySets is: " << NumMoleculesOfOrder[RootNr] << "." << endl;
     1607      DoLog(1) && (Log() << Verbose(1) << "Number of resulting KeySets is: " << NumMoleculesOfOrder[RootNr] << "." << endl);
    16041608      if (NumMoleculesOfOrder[RootNr] != 0) {
    16051609        NumMolecules = 0;
    … …  
    16181622    }
    16191623  }
    1620   Log() << Verbose(0) << "==============================================================================================================" << endl;
    1621   Log() << Verbose(1) << "Total number of resulting molecules is: " << TotalNumMolecules << "." << endl;
    1622   Log() << Verbose(0) << "==============================================================================================================" << endl;
     1624  DoLog(0) && (Log() << Verbose(0) << "==============================================================================================================" << endl);
     1625  DoLog(1) && (Log() << Verbose(1) << "Total number of resulting molecules is: " << TotalNumMolecules << "." << endl);
     1626  DoLog(0) && (Log() << Verbose(0) << "==============================================================================================================" << endl);
    16231627
    16241628  // cleanup FragmentSearch structure
    … …  
    16381642  Free(&NumMoleculesOfOrder);
    16391643
    1640   Log() << Verbose(0) << "End of FragmentBOSSANOVA." << endl;
     1644  DoLog(0) && (Log() << Verbose(0) << "End of FragmentBOSSANOVA." << endl);
    16411645};
    16421646
    … …  
    16621666  bool flag = true;
    16631667
    1664   Log() << Verbose(2) << "Begin of ScanForPeriodicCorrection." << endl;
     1668  DoLog(2) && (Log() << Verbose(2) << "Begin of ScanForPeriodicCorrection." << endl);
    16651669
    16661670  ColorList = Calloc<enum Shading>(AtomCount, "molecule::ScanForPeriodicCorrection: *ColorList");
    … …  
    16801684          OtherBinder = Binder->next; // note down binding partner for later re-insertion
    16811685          unlink(Binder);   // unlink bond
    1682           Log() << Verbose(2) << "Correcting at bond " << *Binder << "." << endl;
     1686          DoLog(2) && (Log() << Verbose(2) << "Correcting at bond " << *Binder << "." << endl);
    16831687          flag = true;
    16841688          break;
    … …  
    16961700      //Log() << Verbose(3) << "Translation vector is ";
    16971701      Translationvector.Output();
    1698       Log() << Verbose(0) << endl;
     1702      DoLog(0) && (Log() << Verbose(0) << endl);
    16991703      // apply to all atoms of first component via BFS
    17001704      for (int i=AtomCount;i--;)
    … …  
    17181722      link(Binder, OtherBinder);
    17191723    } else {
    1720       Log() << Verbose(3) << "No corrections for this fragment." << endl;
     1724      DoLog(3) && (Log() << Verbose(3) << "No corrections for this fragment." << endl);
    17211725    }
    17221726    //delete(CompStack);
    … …  
    17271731  Free(&ColorList);
    17281732  Free(&matrix);
    1729   Log() << Verbose(2) << "End of ScanForPeriodicCorrection." << endl;
    1730 };
     1733  DoLog(2) && (Log() << Verbose(2) << "End of ScanForPeriodicCorrection." << endl);
     1734};
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