Ignore:
Timestamp:
Apr 22, 2010, 2:00:03 PM (16 years ago)
Author:
Frederik Heber <heber@…>
Children:
423c7b
Parents:
c43766
Message:

Huge change: Log() << Verbose(.) --> DoLog(.) && (Log() << Verbose(.) << ...);

Most of the files are affected, but this is necessary as if DoLog() says verbosity is not enough, all the stream operators won"t get executed which saves substantial amount of computation time.

Signed-off-by: Frederik Heber <heber@…>

File:
1 edited

Legend:

Unmodified
Added
Removed

  • molecuilder/src/molecule_fragmentation.cpp

    rc43766 r1f2e46  
    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);
    … …  
    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 {
    216216    DoeLog(0) && (eLog()<< Verbose(0) << "Unable to open " << line << " for writing keysets!" << endl);
    … …  
    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 {
    … …  
    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
    … …  
    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 {
    … …  
    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
    … …  
    720720
    721721    // free memory for bond part
    722     Log() << Verbose(1) << "Freeing bond memory" << endl;
     722    DoLog(1) && (Log() << Verbose(1) << "Freeing bond memory" << endl);
    723723    delete(FragmentList); // remove bond molecule from memory
    724724    Free(&SortIndex);
    725725  } else {
    726     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);
    727727  }
    728728  delete(BondFragments);
    729   Log() << Verbose(0) << "End of bond fragmentation." << endl;
     729  DoLog(0) && (Log() << Verbose(0) << "End of bond fragmentation." << endl);
    730730
    731731  return ((int)(!FragmentationToDo)+1);    // 1 - continue, 2 - stop (no fragmentation occured)
    … …  
    746746  line << path << "/" << FRAGMENTPREFIX << ORDERATSITEFILE;
    747747  file.open(line.str().c_str());
    748   Log() << Verbose(1) << "Writing OrderAtSite " << ORDERATSITEFILE << " ... " << endl;
     748  DoLog(1) && (Log() << Verbose(1) << "Writing OrderAtSite " << ORDERATSITEFILE << " ... " << endl);
    749749  if (file != NULL) {
    750750    ActOnAllAtoms( &atom::OutputOrder, &file );
    751751    file.close();
    752     Log() << Verbose(1) << "done." << endl;
     752    DoLog(1) && (Log() << Verbose(1) << "done." << endl);
    753753    return true;
    754754  } else {
    755     Log() << Verbose(1) << "failed to open file " << line.str() << "." << endl;
     755    DoLog(1) && (Log() << Verbose(1) << "failed to open file " << line.str() << "." << endl);
    756756    return false;
    757757  }
    … …  
    774774  ifstream file;
    775775
    776   Log() << Verbose(1) << "Begin of ParseOrderAtSiteFromFile" << endl;
     776  DoLog(1) && (Log() << Verbose(1) << "Begin of ParseOrderAtSiteFromFile" << endl);
    777777  line << path << "/" << FRAGMENTPREFIX << ORDERATSITEFILE;
    778778  file.open(line.str().c_str());
    … …  
    795795    SetAtomValueToIndexedArray( MaxArray, &atom::nr, &atom::MaxOrder );
    796796
    797     Log() << Verbose(1) << "done." << endl;
     797    DoLog(1) && (Log() << Verbose(1) << "done." << endl);
    798798    status = true;
    799799  } else {
    800     Log() << Verbose(1) << "failed to open file " << line.str() << "." << endl;
     800    DoLog(1) && (Log() << Verbose(1) << "failed to open file " << line.str() << "." << endl);
    801801    status = false;
    802802  }
    … …  
    804804  Free(&MaxArray);
    805805
    806   Log() << Verbose(1) << "End of ParseOrderAtSiteFromFile" << endl;
     806  DoLog(1) && (Log() << Verbose(1) << "End of ParseOrderAtSiteFromFile" << endl);
    807807  return status;
    808808};
    … …  
    821821  int SP, Removal;
    822822
    823   Log() << Verbose(2) << "Looking for removal candidate." << endl;
     823  DoLog(2) && (Log() << Verbose(2) << "Looking for removal candidate." << endl);
    824824  SP = -1; //0;  // not -1, so that Root is never removed
    825825  Removal = -1;
    … …  
    909909    }
    910910    if ((LonelyFlag) && (Leaf->AtomCount > 1)) {
    911       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);
    912912    }
    913913#ifdef ADDHYDROGEN
    … …  
    10561056    TouchedList[j] = -1;
    10571057  }
    1058   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: ");
    10591059  for(KeySet::iterator runner = FragmentSet->begin(); runner != FragmentSet->end(); runner++)
    1060     Log() << Verbose(0) << (*runner) << " ";
    1061   Log() << Verbose(0) << endl;
     1060    DoLog(0) && (Log() << Verbose(0) << (*runner) << " ");
     1061  DoLog(0) && (Log() << Verbose(0) << endl);
    10621062  TouchedIndex = 0; // set Index to 0 for list of atoms added on this level
    10631063};
    … …  
    11361136        Log() << Verbose(1+verbosity) << "Enough items on stack for a fragment!" << endl;
    11371137        // store fragment as a KeySet
    1138         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: ");
    11391139        for(KeySet::iterator runner = FragmentSearch->FragmentSet->begin(); runner != FragmentSearch->FragmentSet->end(); runner++)
    1140           Log() << Verbose(0) << (*runner) << " ";
    1141         Log() << Verbose(0) << endl;
     1140          DoLog(0) && (Log() << Verbose(0) << (*runner) << " ");
     1141        DoLog(0) && (Log() << Verbose(0) << endl);
    11421142        //if (!CheckForConnectedSubgraph(FragmentSearch->FragmentSet))
    11431143          //DoeLog(1) && (eLog()<< Verbose(1) << "The found fragment is not a connected subgraph!" << endl);
    … …  
    12211221{
    12221222  bond *Binder = NULL;
    1223   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);
    12241224  for(int i=Order;i--;) {
    1225     Log() << Verbose(1) << "Current SP level is " << i << ": ";
     1225    DoLog(1) && (Log() << Verbose(1) << "Current SP level is " << i << ": ");
    12261226    Binder = FragmentSearch.BondsPerSPList[2*i];
    12271227    while (Binder->next != FragmentSearch.BondsPerSPList[2*i+1]) {
    … …  
    12341234    cleanup(FragmentSearch.BondsPerSPList[2*i], FragmentSearch.BondsPerSPList[2*i+1]);
    12351235    // also start and end node
    1236     Log() << Verbose(0) << "cleaned." << endl;
     1236    DoLog(0) && (Log() << Verbose(0) << "cleaned." << endl);
    12371237  }
    12381238};
    … …  
    12641264  int SP = -1;
    12651265
    1266   Log() << Verbose(0) << "Starting BFS analysis ..." << endl;
     1266  DoLog(0) && (Log() << Verbose(0) << "Starting BFS analysis ..." << endl);
    12671267  for (SP = 0; SP < (Order-1); SP++) {
    1268     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)");
    12691269    if (SP > 0) {
    1270       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);
    12711271      FragmentSearch.BondsPerSPCount[SP] = 0;
    12721272    } else
    1273       Log() << Verbose(0) << "." << endl;
     1273      DoLog(0) && (Log() << Verbose(0) << "." << endl);
    12741274
    12751275    RemainingWalkers = FragmentSearch.BondsPerSPCount[SP];
    … …  
    12811281      Predecessor = CurrentEdge->leftatom;    // ... and leftatom is predecessor
    12821282      AtomKeyNr = Walker->nr;
    1283       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);
    12841284      // check for new sp level
    12851285      // go through all its bonds
    1286       Log() << Verbose(1) << "Going through all bonds of Walker." << endl;
     1286      DoLog(1) && (Log() << Verbose(1) << "Going through all bonds of Walker." << endl);
    12871287      for (BondList::const_iterator Runner = Walker->ListOfBonds.begin(); Runner != Walker->ListOfBonds.end(); (++Runner)) {
    12881288        OtherWalker = (*Runner)->GetOtherAtom(Walker);
    … …  
    12921292  #endif
    12931293                                                              ) {  // skip hydrogens and restrict to fragment
    1294           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);
    12951295          // set the label if not set (and push on root stack as well)
    12961296          if ((OtherWalker != Predecessor) && (OtherWalker->GetTrueFather()->nr > RootKeyNr)) { // only pass through those with label bigger than Root's
    12971297            FragmentSearch.ShortestPathList[OtherWalker->nr] = SP+1;
    1298             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);
    12991299            // add the bond in between to the SP list
    13001300            Binder = new bond(Walker, OtherWalker); // create a new bond in such a manner, that bond::rightatom is always the one more distant
    13011301            add(Binder, FragmentSearch.BondsPerSPList[2*(SP+1)+1]);
    13021302            FragmentSearch.BondsPerSPCount[SP+1]++;
    1303             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);
    13041304          } else {
    13051305            if (OtherWalker != Predecessor)
    1306               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);
    13071307            else
    1308               Log() << Verbose(3) << "This is my predecessor " << *Predecessor << "." << endl;
     1308              DoLog(3) && (Log() << Verbose(3) << "This is my predecessor " << *Predecessor << "." << endl);
    13091309          }
    13101310        } else Log() << Verbose(2) << "Is not in the restricted keyset or skipping hydrogen " << *OtherWalker << "." << endl;
    … …  
    13221322{
    13231323  bond *Binder = NULL;
    1324   Log() << Verbose(0) << "Printing all found lists." << endl;
     1324  DoLog(0) && (Log() << Verbose(0) << "Printing all found lists." << endl);
    13251325  for(int i=1;i<Order;i++) {    // skip the root edge in the printing
    13261326    Binder = FragmentSearch.BondsPerSPList[2*i];
    1327     Log() << Verbose(1) << "Current SP level is " << i << "." << endl;
     1327    DoLog(1) && (Log() << Verbose(1) << "Current SP level is " << i << "." << endl);
    13281328    while (Binder->next != FragmentSearch.BondsPerSPList[2*i+1]) {
    13291329      Binder = Binder->next;
    1330       Log() << Verbose(2) << *Binder << endl;
     1330      DoLog(2) && (Log() << Verbose(2) << *Binder << endl);
    13311331    }
    13321332  }
    … …  
    13721372  int Counter = FragmentSearch.FragmentCounter; // mark current value of counter
    13731373
    1374   Log() << Verbose(0) << endl;
    1375   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);
    13761376
    13771377  SetSPList(Order, FragmentSearch);
    … …  
    13851385  // creating fragments with the found edge sets  (may be done in reverse order, faster)
    13861386  int SP = CountNumbersInBondsList(Order, FragmentSearch);
    1387   Log() << Verbose(0) << "Total number of edges is " << SP << "." << endl;
     1387  DoLog(0) && (Log() << Verbose(0) << "Total number of edges is " << SP << "." << endl);
    13881388  if (SP >= (Order-1)) {
    13891389    // start with root (push on fragment stack)
    1390     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);
    13911391    FragmentSearch.FragmentSet->clear();
    1392     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);
    13931393
    13941394    // prepare the subset and call the generator
    … …  
    14001400    Free(&BondsList);
    14011401  } else {
    1402     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);
    14031403  }
    14041404
    14051405  // as FragmentSearch structure is used only once, we don't have to clean it anymore
    14061406  // remove root from stack
    1407   Log() << Verbose(0) << "Removing root again from stack." << endl;
     1407  DoLog(0) && (Log() << Verbose(0) << "Removing root again from stack." << endl);
    14081408  FragmentSearch.FragmentSet->erase(FragmentSearch.Root->nr);
    14091409
    … …  
    14121412
    14131413  // return list
    1414   Log() << Verbose(0) << "End of PowerSetGenerator." << endl;
     1414  DoLog(0) && (Log() << Verbose(0) << "End of PowerSetGenerator." << endl);
    14151415  return (FragmentSearch.FragmentCounter - Counter);
    14161416};
    … …  
    14581458  atom *Walker = NULL;
    14591459
    1460   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);
    14611461  if (FragmentList == NULL) {
    14621462    FragmentList = new Graph;
    … …  
    14911491void FreeAllOrdersList(Graph ***FragmentLowerOrdersList, KeyStack &RootStack, molecule *mol)
    14921492{
    1493   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);
    14941494  int RootNr = 0;
    14951495  int RootKeyNr = 0;
    … …  
    15441544  struct UniqueFragments FragmentSearch;
    15451545
    1546   Log() << Verbose(0) << "Begin of FragmentBOSSANOVA." << endl;
     1546  DoLog(0) && (Log() << Verbose(0) << "Begin of FragmentBOSSANOVA." << endl);
    15471547
    15481548  // FragmentLowerOrdersList is a 2D-array of pointer to MoleculeListClass objects, one dimension represents the ANOVA expansion of a single order (i.e. 5)
    … …  
    15941594
    15951595      // create top order where nothing is reduced
    1596       Log() << Verbose(0) << "==============================================================================================================" << endl;
    1597       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 << "
    15981598
    15991599      // Create list of Graphs of current Bond Order (i.e. F_{ij})
    … …  
    16051605
    16061606      // output resulting number
    1607       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);
    16081608      if (NumMoleculesOfOrder[RootNr] != 0) {
    16091609        NumMolecules = 0;
    … …  
    16221622    }
    16231623  }
    1624   Log() << Verbose(0) << "==============================================================================================================" << endl;
    1625   Log() << Verbose(1) << "Total number of resulting molecules is: " << TotalNumMolecules << "." << endl;
    1626   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);
    16271627
    16281628  // cleanup FragmentSearch structure
    … …  
    16421642  Free(&NumMoleculesOfOrder);
    16431643
    1644   Log() << Verbose(0) << "End of FragmentBOSSANOVA." << endl;
     1644  DoLog(0) && (Log() << Verbose(0) << "End of FragmentBOSSANOVA." << endl);
    16451645};
    16461646
    … …  
    16661666  bool flag = true;
    16671667
    1668   Log() << Verbose(2) << "Begin of ScanForPeriodicCorrection." << endl;
     1668  DoLog(2) && (Log() << Verbose(2) << "Begin of ScanForPeriodicCorrection." << endl);
    16691669
    16701670  ColorList = Calloc<enum Shading>(AtomCount, "molecule::ScanForPeriodicCorrection: *ColorList");
    … …  
    16841684          OtherBinder = Binder->next; // note down binding partner for later re-insertion
    16851685          unlink(Binder);   // unlink bond
    1686           Log() << Verbose(2) << "Correcting at bond " << *Binder << "." << endl;
     1686          DoLog(2) && (Log() << Verbose(2) << "Correcting at bond " << *Binder << "." << endl);
    16871687          flag = true;
    16881688          break;
    … …  
    17001700      //Log() << Verbose(3) << "Translation vector is ";
    17011701      Translationvector.Output();
    1702       Log() << Verbose(0) << endl;
     1702      DoLog(0) && (Log() << Verbose(0) << endl);
    17031703      // apply to all atoms of first component via BFS
    17041704      for (int i=AtomCount;i--;)
    … …  
    17221722      link(Binder, OtherBinder);
    17231723    } else {
    1724       Log() << Verbose(3) << "No corrections for this fragment." << endl;
     1724      DoLog(3) && (Log() << Verbose(3) << "No corrections for this fragment." << endl);
    17251725    }
    17261726    //delete(CompStack);
    … …  
    17311731  Free(&ColorList);
    17321732  Free(&matrix);
    1733   Log() << Verbose(2) << "End of ScanForPeriodicCorrection." << endl;
    1734 };
     1733  DoLog(2) && (Log() << Verbose(2) << "End of ScanForPeriodicCorrection." << endl);
     1734};
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