/**********************************************************************

fastsearchformat.cpp: Preparation and searching of fingerprint-based index files

Copyright (C) 2005-2006 by Chris Morley

This program is free software; you can redistribute it and/or modify

it under the terms of the GNU General Public License as published by

the Free Software Foundation version 2 of the License.

This program is distributed in the hope that it will be useful,

but WITHOUT ANY WARRANTY; without even the implied warranty of

MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the

GNU General Public License for more details.

***********************************************************************/

#include <openbabel/babelconfig.h>

#include <sstream>

#include <iostream>

#include <fstream>

#include <openbabel/mol.h>

#include <openbabel/obconversion.h>

#include <openbabel/fingerprint.h>

#include <openbabel/op.h>

#include <openbabel/elements.h>

#include <openbabel/bond.h>

#include <openbabel/obutil.h>

#include <cstdlib>

#include <algorithm>

using namespace std;

namespace OpenBabel {

/// \brief Prepares and searches of fingerprint-based index files. See FastSearch class for details

class FastSearchFormat : public OBFormat

{

public:

//Register this format type ID

FastSearchFormat() : fsi(nullptr)

{

  OBConversion::RegisterFormat("fs",this);

  //Specify the number of option taken by options

  OBConversion::RegisterOptionParam("S", this, 1, OBConversion::GENOPTIONS);

  OBConversion::RegisterOptionParam("S", this, 1, OBConversion::INOPTIONS);

  OBConversion::RegisterOptionParam("f", this, 1);

  OBConversion::RegisterOptionParam("N", this, 1);

  OBConversion::RegisterOptionParam("u", this, 0);

  OBConversion::RegisterOptionParam("t", this, 1, OBConversion::INOPTIONS);

  OBConversion::RegisterOptionParam("l", this, 1, OBConversion::INOPTIONS);

  OBConversion::RegisterOptionParam("a", this, 0, OBConversion::INOPTIONS);

  OBConversion::RegisterOptionParam("e", this, 0, OBConversion::INOPTIONS);

}

const char* Description() override  // required

{ return

  "Fastsearch format\n"

  "Fingerprint-aided substructure and similarity searching\n\n"

  "Writing to the fs format makes an index of a multi-molecule datafile::\n\n"

  "      obabel dataset.sdf -ofs\n\n"

  "This prepares an index :file:`dataset.fs` with default parameters, and is slow\n"

  "(~30 minutes for a 250,000 molecule file).\n\n"

  "However, when reading from the fs format searches are much faster, a few seconds,\n"

  "and so can be done interactively.\n\n"

  "The search target is the parameter of the ``-s`` option and can be\n"

  "slightly extended SMILES (with ``[#n]`` atoms and ``~`` bonds) or\n"

  "the name of a file containing a molecule.\n\n"

  "Several types of searches are possible:\n\n"

  "- Identical molecule::\n\n"

  "      obabel index.fs -O outfile.yyy -s SMILES exact\n\n"

  "- Substructure::\n\n"

  "      obabel index.fs -O outfile.yyy  -s SMILES   or\n"

  "      obabel index.fs -O outfile.yyy  -s filename.xxx\n\n"

  "  where ``xxx`` is a format id known to OpenBabel, e.g. sdf\n"

  "- Molecular similarity based on Tanimoto coefficient::\n\n"

  "      obabel index.fs -O outfile.yyy -at15  -sSMILES  # best 15 molecules\n"

  "      obabel index.fs -O outfile.yyy -at0.7 -sSMILES  # Tanimoto >0.7\n"

  "      obabel index.fs -O outfile.yyy -at0.7,0.9 -sSMILES\n"

  "      #     Tanimoto >0.7 && Tanimoto < 0.9\n\n"

  "The datafile plus the ``-ifs`` option can be used instead of the index file.\n\n"

  "NOTE on 32-bit systems the datafile MUST NOT be larger than 4GB.\n\n"

  "Dative bonds like -[N+][O-](=O) are indexed as -N(=O)(=O), and when searching\n"

  "the target molecule should be in the second form.\n\n"

  ".. seealso::\n\n"

  "    :ref:`fingerprints`\n\n"

  "Write Options (when making index) e.g. -xfFP3\n"

  " f# Fingerprint type\n"

  "     If not specified, the default fingerprint (currently FP2) is used\n"

  " N# Fold fingerprint to # bits\n"

  " u  Update an existing index\n\n"

  "Read Options (when searching) e.g. -at0.7\n"

  " t# Do similarity search:#mols or # as min Tanimoto\n"

  " a  Add Tanimoto coeff to title in similarity search\n"

  " l# Maximum number of candidates. Default<4000>\n"

  " e  Exact match\n"

  "     Alternative to using exact in ``-s`` parameter, see above\n"

  " n  No further SMARTS filtering after fingerprint phase\n\n"

  ;

}

  unsigned int Flags() override { return READBINARY | READONEONLY | WRITEBINARY; }

  public:

    bool ReadChemObject(OBConversion* pConv) override;

    bool WriteChemObject(OBConversion* pConv) override;

  private:

    bool ObtainTarget(OBConversion* pConv, std::vector<OBMol>& patternMols, const std::string& indexname);

    void AddPattern(vector<OBMol>& patternMols, OBMol patternMol, int idx);

  private:

    ///big data structure which will remain in memory after it is loaded

    //until the program ends.

    FastSearch fs;

    FastSearchIndexer* fsi;

    streampos LastSeekpos; //used during update

    OBStopwatch sw; //used when preparing index

    int nmols; //number mols in data file

  };

  ///////////////////////////////////////////////////////////////

  //Make an instance of the format class

  FastSearchFormat theFastSearchFormat;

  ///////////////////////////////////////////////////////////////

  bool FastSearchFormat::ReadChemObject(OBConversion* pConv)

  {

    //Searches index file for structural matches

    //This function is called only once per search

    std::string auditMsg = "OpenBabel::Read fastsearch index ";

    std::string description(Description());

    auditMsg += description.substr(0,description.find('\n'));

    obErrorLog.ThrowError(__FUNCTION__,

                          auditMsg,

                          obAuditMsg);

    //Derive index name

    string indexname = pConv->GetInFilename();

    string::size_type pos=indexname.find_last_of('.');

    if(pos!=string::npos)

      {

        indexname.erase(pos);

        indexname += ".fs";

      }

    //Have to open input stream again because needs to be in binary mode

    ifstream ifs;

    stringstream errorMsg;

    if(!indexname.empty())

      ifs.open(indexname.c_str(),ios::binary);

    if(!ifs)

      {

        errorMsg << "Couldn't open " << indexname << endl;

        obErrorLog.ThrowError(__FUNCTION__, errorMsg.str(), obError);

        return false;

      }

    string datafilename = fs.ReadIndex(&ifs);

    if(datafilename.empty())

      {

        errorMsg << "Difficulty reading from index " << indexname << endl;

        obErrorLog.ThrowError(__FUNCTION__, errorMsg.str(), obError);

        return false;

      }

    vector<OBMol> patternMols;

    if(!ObtainTarget(pConv, patternMols, indexname))

      return false;

    bool exactmatch = pConv->IsOption("e", OBConversion::INOPTIONS) != nullptr; // -ae option

    //Open the datafile and put it in pConv

    //datafile name derived from index file probably won't have a file path

    //but indexname may. Derive a full datafile name

    string path;

    pos = indexname.find_last_of("/\\");

    if(pos==string::npos)

      path = datafilename;

    else

      path = indexname.substr(0,pos+1) + datafilename;

    ifstream datastream(path.c_str());

    if(!datastream)

      {

        errorMsg << "Difficulty opening " << path << endl;

        obErrorLog.ThrowError(__FUNCTION__, errorMsg.str(), obError);

        return false;

      }

    pConv->SetInStream(&datastream);

    //Input format is currently fs; set it appropriately

    bool isgzip = false;

    if(!pConv->SetInAndOutFormats(pConv->FormatFromExt(datafilename.c_str(), isgzip), pConv->GetOutFormat()))

      return false;

    if (isgzip)

      {

  errorMsg << "Index datafile must not be in gzip format: " << path << endl;

        obErrorLog.ThrowError(__FUNCTION__, errorMsg.str(), obError);

        return false;

      }

    // If target has dative bonds like -[N+](=O)[O-] convert it to the uncharged form

    // (-N(=O)=O and add uncharged form to vector of mols which are sent to

    // the -s (SMARTS)filter.

    // Also check whether the target has dative bonds in the uncharged form and supply

    // the charged form to the -s filter.

    // Together with the automatic conversion to the uncharged form when the fs index is made,

    // this ensures that both forms are found however they occur in the datafile or the taget.

    vector<OBBase*> extraSMARTSMols;

    vector<OBMol>extraUnchargedMols;

    for(unsigned i=0;i<patternMols.size();++i)

    {

      if(patternMols[i].ConvertDativeBonds())

        extraSMARTSMols.push_back(&patternMols[i]);

      else 

      {

        // If target has uncharged dative bonds, still use it for fastsearching,

        // but add the charged form for -s filter.

        extraUnchargedMols.push_back(patternMols[i]);

        if(extraUnchargedMols.back().MakeDativeBonds())

          extraSMARTSMols.push_back(&extraUnchargedMols.back());

      }

    }

    OBOp* sFilter = OBOp::FindType("s");

    if(sFilter)

      sFilter->ProcessVec(extraSMARTSMols);

    //Now do searching

    const char* p = pConv->IsOption("t",OBConversion::INOPTIONS);

    if(p)

      {

        //Do a similarity search

        multimap<double, unsigned long> SeekposMap;

        string txt=p;

        if(txt.find('.')==string::npos)

          {

            //Finds n molecules with largest Tanimoto

            int n = atoi(p);

            fs.FindSimilar(&patternMols[0], SeekposMap, n);

          }

        else

          {

            //Finds molecules with Tanimoto > MinTani

            double MaxTani = 1.1;

            size_t pos = txt.find(',');

            if( pos != string::npos ) {

              MaxTani = atof( txt.substr( pos + 1 ).c_str() );

            }

            double MinTani = atof( txt.substr( 0, pos ).c_str() );

            fs.FindSimilar(&patternMols[0], SeekposMap, MinTani, MaxTani);

          }

        //Don't want to filter through SMARTS filter

        pConv->RemoveOption("s", OBConversion::GENOPTIONS);

        //also because op names are case independent

        pConv->RemoveOption("S", OBConversion::GENOPTIONS);

        multimap<double, unsigned long>::reverse_iterator itr;

        for(itr=SeekposMap.rbegin();itr!=SeekposMap.rend();++itr)

          {

            datastream.seekg(itr->second);

            if(pConv->IsOption("a", OBConversion::INOPTIONS))

              {

                //Adds Tanimoto coeff to title

                //First remove any previous value

                pConv->RemoveOption("addtotitle", OBConversion::GENOPTIONS);

                stringstream ss;

                ss << " " << itr->first;

                pConv->AddOption("addtotitle",OBConversion::GENOPTIONS, ss.str().c_str());

              }

            pConv->SetOneObjectOnly();

            if(itr != --SeekposMap.rend())

              pConv->SetMoreFilesToCome();//so that not seen as last on output

            pConv->Convert(nullptr, nullptr);

          }

      }

    else

    {

      //Structure search

      int MaxCandidates = 4000;

      p = pConv->IsOption("l",OBConversion::INOPTIONS);

      if(p && atoi(p))

        MaxCandidates = atoi(p);

      vector<unsigned long> SeekPositions;

      if(exactmatch)

      {

        //Find mols where all fingerprint bits are the same as the target

        fs.FindMatch(&patternMols[0], SeekPositions, MaxCandidates);

        // ensure that SMARTS filter in transform.cpp looks only for an exact match

        // by setting an option with the number of heavy atoms in the pattern mol included.

        stringstream ss;

        ss << patternMols[0].NumHvyAtoms();

        pConv->AddOption("exactmatch", OBConversion::GENOPTIONS, ss.str().c_str());

      }

      else

      {

        //Do a substructure search for each target

        vector<OBMol>::iterator iter;

        for(iter=patternMols.begin();iter!=patternMols.end();++iter)

          fs.Find(&*iter, SeekPositions, MaxCandidates);

        clog << SeekPositions.size() << " candidates from fingerprint search phase" << endl;

      }

      vector<unsigned long>::iterator seekitr,

          begin = SeekPositions.begin(), end = SeekPositions.end();

      if(patternMols.size()>1)//only sort and eliminate duplicates if necessary

      {

        sort(begin, end);

        end = unique(begin, end); //removed duplicates are after new end

      }

      //Output the candidate molecules, filtering through s filter, unless it was not requested

      if(pConv->IsOption("n", OBConversion::INOPTIONS) )

        pConv->RemoveOption("s",OBConversion::GENOPTIONS);

      pConv->SetLast(false);

      for(seekitr=begin; seekitr!=end; ++seekitr)

      {

        datastream.seekg(*seekitr);

        if(!pConv->GetInFormat()->ReadChemObject(pConv))

          return false;

        pConv->SetFirstInput(false); //needed for OpSort

      }

    }

    return false; //To finish

  }

  /////////////////////////////////////////////////////

  bool FastSearchFormat::WriteChemObject(OBConversion* pConv)

  {

    //Prepares or updates an index file. Called for each molecule indexed

    bool update = pConv->IsOption("u") != nullptr;

    static ostream* pOs;

    static bool NewOstreamUsed;

    if (fsi == nullptr)

      {

  // Warn that compressed files cannot be used. It's hard to seek

  // inside of a gzip file.

  if(pConv->GetInGzipped())

    {

      obErrorLog.ThrowError(__FUNCTION__,

        "Fastindex search requires an uncompressed input file so it can quickly seek to a record.",

        obWarning);

    }

        //First pass sets up FastSearchIndexer object

        pOs = pConv->GetOutStream();// with named index it is already open

        NewOstreamUsed=false;

        string mes("prepare an");

        if(update)

          mes = "update the";

        clog << "This will " << mes << " index of " << pConv->GetInFilename()

             <<  " and may take some time..." << flush;

        if(!pConv->IsLastFile())

        {

          obErrorLog.ThrowError(__FUNCTION__,

            "There should not be multiple input files. A .fs file is an index of a single datafile.",

            obError);

          return false;

        }

        std::string auditMsg = "OpenBabel::Write fastsearch index ";

        std::string description(Description());

        auditMsg += description.substr( 0, description.find('\n') );

        obErrorLog.ThrowError(__FUNCTION__,auditMsg,obAuditMsg);

        FptIndex* pidx = nullptr; //used with update

        //if(pOs==&cout) did not work with GUI

        if(!dynamic_cast<ofstream*>(pOs))

          {

            //No index filename specified

            //Derive index name from datafile name

            string indexname=pConv->GetInFilename();

            string::size_type pos=indexname.find_last_of('.');

            if(pos!=string::npos)

              indexname.erase(pos);

            indexname += ".fs";

            bool idxok=true;

            if(update)

              {

                LastSeekpos = 0;

                //Read in existing index

                idxok=false;

                ifstream ifs(indexname.c_str(),ifstream::binary);

                if(ifs.good())

                  {

                    pidx = new FptIndex;

                    idxok = pidx->Read(&ifs);

                  }

              }//ifs closed here

            pOs = new ofstream(indexname.c_str(),ofstream::binary);

            if(!pOs->good() || !idxok)

              {

                stringstream errorMsg;

                errorMsg << "Trouble opening or reading " << indexname << endl;

                obErrorLog.ThrowError(__FUNCTION__, errorMsg.str(), obError);

                static_cast<ofstream *>(pOs)->close(); // close the file before quitting

                delete pOs;

                delete pidx; // remove possible memory leak

                return false;

              }

            NewOstreamUsed=true;

          }

        else // not cout

          {

            if(update)

              {

                obErrorLog.ThrowError(__FUNCTION__,

                  "Currently, updating is only done on index files that"

                  "have the same name as the datafile.\n"

                  "Do not specify an output file; use the form:\n"

                  "   obabel datafile.xxx -ofs -xu", obError);

                return false;

              }

          }

        int nbits = 0;

        const char* p = pConv->IsOption("N");

        if(p)

          nbits = atoi(p);

        string fpid; //fingerprint type

        p=pConv->IsOption("f");

        if(p)

          fpid=p;

        //Prepare name without path

        string datafilename = pConv->GetInFilename();

        if(datafilename.empty())

          {

            obErrorLog.ThrowError(__FUNCTION__, "No datafile!", obError);

            delete pidx;

            return false;

          }

        string::size_type pos = datafilename.find_last_of("/\\");

        if(pos!=string::npos)

          datafilename=datafilename.substr(pos+1);

        nmols = pConv->NumInputObjects();

        if(nmols>0)

          clog << "\nIt contains " << nmols << " molecules" << flush;

        if(nmols>500000)

        {

          istream* is = pConv->GetInStream();

          streampos origpos = is->tellg();

          is->seekg(0,ios_base::end);

          long long filesize = is->tellg();

          if(sizeof(void*) < 8 && filesize > 4294967295u)

          {

            obErrorLog.ThrowError(__FUNCTION__, "The datafile must not be larger than 4GB", obError);

            return false;

          }

          is->seekg(origpos);

        }

        sw.Start();

        if(update)

          {

            fsi = new FastSearchIndexer(pidx, pOs, nmols);//using existing index

            //Seek to position in datafile of last of old objects

            LastSeekpos = *(pidx->seekdata.end()-1);

            pConv->GetInStream()->seekg(LastSeekpos);

          }

        else

          fsi = new FastSearchIndexer(datafilename, pOs, fpid, nbits, nmols);

        obErrorLog.StopLogging();

      }

    //All passes provide an object for indexing

    OBBase* pOb = pConv->GetChemObject();

    OBMol* pmol = dynamic_cast<OBMol*> (pOb);

    if(pmol)

      pmol->ConvertDativeBonds();//use standard form for dative bonds

    streampos seekpos = pConv->GetInPos();

    if(!update || seekpos>LastSeekpos)

    {

      fsi->Add(pOb, seekpos );

      if(pConv->GetOutputIndex()==400 && nmols>1000)

      {

        clog << " Estimated completion time ";

        double secs = sw.Elapsed() * nmols / 400; //

        if(secs>150)

          clog << secs/60 << " minutes" << endl;

    else

          clog << secs << " seconds" << endl;

      }

    }

    else

      //Don't index old objects during update. Don't increment pConv->Index.

      pConv->SetOutputIndex(pConv->GetOutputIndex()-1);

    if(pConv->IsLast())

      {

        //Last pass

        delete fsi; //saves index file

        if(NewOstreamUsed)

          delete pOs;

        //return to starting conditions

        fsi=nullptr;

        obErrorLog.StartLogging();

        double secs = sw.Elapsed();

        if(secs>150)

          clog << "\n It took " << secs/60 << " minutes" << endl;

        else

          clog << "\n It took " << secs << " seconds" << endl;

      }

    delete pOb;

    return true;

  }

///////////////////////////////////////////////////////////////

  bool FastSearchFormat::ObtainTarget(OBConversion* pConv, vector<OBMol>& patternMols, const string& indexname)

  {

    //Obtains an OBMol from:

    // the filename in the -s option or

    // the SMARTS string in the -s option or

    // by converting the file in the -S or -aS options (deprecated).

    // If there is no -s -S or -aS option, information on the index file is displayed.

    OBMol patternMol;

    patternMol.SetIsPatternStructure();

    const char* p = pConv->IsOption("s",OBConversion::GENOPTIONS);

    bool OldSOption=false;

    //If no -s option, make OBMol from file in -S option or -aS option (both deprecated)

    if(!p)

    {

      p = pConv->IsOption("S",OBConversion::GENOPTIONS);

      if(!p)

        p = pConv->IsOption("S",OBConversion::INOPTIONS);//for GUI mainly

      OldSOption = true;

    }

    if(p)

    {

      vector<string> vec;

      tokenize(vec, p);

      if(vec.size() == 0)

      {

        obErrorLog.ThrowError(__FUNCTION__,

            "Missing argument for -s/-S", obError);

          return false;

      }

      //ignore leading ~ (not relevant to fastsearch)

      if(vec[0][0]=='~')

        vec[0].erase(0,1);

      if(vec.size()>1 && vec[1]=="exact")

        pConv->AddOption("e", OBConversion::INOPTIONS);

      OBConversion patternConv;

      OBFormat* pFormat;

      //Interpret as a filename if possible

      string& txt =vec [0];

      if( txt.empty() ||

          txt.find('.')==string::npos ||

          !(pFormat = patternConv.FormatFromExt(txt.c_str())) ||

          !patternConv.SetInFormat(pFormat) ||

          !patternConv.ReadFile(&patternMol, txt) ||

          patternMol.NumAtoms()==0)

        //if false, have a valid patternMol from a file

      {

        //is SMARTS/SMILES

        //Replace e.g. [#6] in SMARTS by C so that it can be converted as SMILES

        //for the fingerprint phase, but allow more generality in the SMARTS phase.

        for(;;)

        {

          string::size_type pos1, pos2;

          pos1 = txt.find("[#");

          if(pos1==string::npos)

            break;

          pos2 = txt.find(']');

          int atno;

          if(pos2!=string::npos &&  (atno = atoi(txt.substr(pos1+2, pos2-pos1-2).c_str())) && atno>0)

            txt.replace(pos1, pos2-pos1+1, OBElements::GetSymbol(atno));

          else

          {

            obErrorLog.ThrowError(__FUNCTION__,"Ill-formed [#n] atom in SMARTS", obError);

            return false;

          }

        }

        bool hasTildeBond;

        if( (hasTildeBond = (txt.find('~')!=string::npos)) ) // extra parens to indicate truth value

        {

          //Find ~ bonds and make versions of query molecule with a single and aromatic bonds

          //To avoid having to parse the SMILES here, replace ~ by $ (quadruple bond)

          //and then replace this in patternMol. Check first that there are no $ already

          //Sadly, isocynanides may have $ bonds.

          if(txt.find('$')!=string::npos)

          {

            obErrorLog.ThrowError(__FUNCTION__,

              "Cannot use ~ bonds in patterns with $ (quadruple) bonds.)", obError);

            return false;

          }

          replace(txt.begin(),txt.end(), '~' , '$');

        }

        //read as standard SMILES

        patternConv.SetInFormat("smi");

        if(!patternConv.ReadString(&patternMol, vec[0]))

        {

          obErrorLog.ThrowError(__FUNCTION__,"Cannot read the SMILES string",obError);

          return false;

        }

        if(hasTildeBond)

        {

          AddPattern(patternMols, patternMol, 0); //recursively add all combinations of tilde bond values

          return true;

        }

      }

      else

      {

        // target(s) are in a file

        patternMols.push_back(patternMol);

        while(patternConv.Read(&patternMol))

          patternMols.push_back(patternMol);

        return true;

      }

    }

    if(OldSOption) //only when using deprecated -S and -aS options

    {

      //make -s option for later SMARTS test

      OBConversion conv;

      if(conv.SetOutFormat("smi"))

      {

        string optiontext = conv.WriteString(&patternMol, true);

        pConv->AddOption("s", OBConversion::GENOPTIONS, optiontext.c_str());

      }

    }

    if(!p)

    {

      //neither -s or -S options provided. Output info rather than doing search

      const FptIndexHeader& header = fs.GetIndexHeader();

      string id(header.fpid);

      if(id.empty())

        id = "default";

      clog << indexname << " is an index of\n " << header.datafilename

           << ".\n It contains " << header.nEntries

           << " molecules. The fingerprint type is " << id << " with "

           << OBFingerprint::Getbitsperint() * header.words << " bits.\n"

           << "Typical usage for a substructure search:\n"

           << "obabel indexfile.fs -osmi -sSMILES\n"

           << "(-s option in GUI is 'Convert only if match SMARTS or mols in file')" << endl;

      return false;

    }

    patternMols.push_back(patternMol);

    return true;

  }

  void FastSearchFormat::AddPattern(vector<OBMol>& patternMols, OBMol patternMol, int idx)

  {

    //Recursive function to generate all combinations of aromatic/single bonds for each tilde bond

    //Copying an OBMol, which happens when adding it to a vector, kekulizes it,

    // changing aromatic (bo=5) bonds. So set order after adding. Should work here,

    // but is dangerous if the vector needs to be reallocated.

    if(idx>=patternMol.NumBonds())

      return;

    if(patternMol.GetBond(idx)->GetBondOrder()==4)

    {

      patternMol.GetBond(idx)->SetBondOrder(1);

      patternMols.push_back(patternMol);

      AddPattern(patternMols, patternMol,idx+1);

      patternMols.push_back(patternMol);

      patternMols.back().GetBond(idx)->SetBondOrder(5);

    }

    AddPattern(patternMols, patternMol,idx+1);

  }

  /* Accept ~ bonds. Need to generate two PatternMols for each '~'

  i.e. '-' or nothing for single and ':' for aromatic

  or 2^n patterns for n bonds. SMILES format will accept : but cannot

  provide an isolated aromatic bond. So need to edit OBMol. Retain the atom

  indices of the bond's atoms and change the bond's order.

  ObtainTarget() will return a vector of OBMol and the Find() in L260 will be done

  for each. All fs matches will go into SeekPositions. At the end this

  will be sorted and duplicates removed with unique.

  */

}//Openbabel

//! \file fastsearchformat.cpp

//! \brief Preparation and searching of fingerprint-based index files