C++ OBSmartsPattern::Match方法代码示例

  // Helper function -- handle SMARTS selections
  // Called by performAction()
  void SelectExtension::selectSMARTS(GLWidget *widget)
  {
    bool ok;
    QString pattern = QInputDialog::getText(qobject_cast<QWidget*>(parent()),
        tr("SMARTS Selection"),
        tr("SMARTS pattern to select"),
        QLineEdit::Normal,
        "", &ok);
    if (ok && !pattern.isEmpty()) {
      OBSmartsPattern smarts;
      smarts.Init(pattern.toStdString());
      OpenBabel::OBMol obmol = m_molecule->OBMol();
      smarts.Match(obmol);

      // if we have matches, select them
      if(smarts.NumMatches() != 0) {
        QList<Primitive *> matchedAtoms;

        vector< vector <int> > mapList = smarts.GetUMapList();
        vector< vector <int> >::iterator i; // a set of matching atoms
        vector<int>::iterator j; // atom ids in each match
        for (i = mapList.begin(); i != mapList.end(); ++i) {
          for (j = i->begin(); j != i->end(); ++j) {
            matchedAtoms.append(m_molecule->atom(obmol.GetAtom(*j)->GetIdx()-1));
          }
        }

        widget->clearSelected();
        widget->setSelected(matchedAtoms, true);
        widget->update();
      } // end matches
    }
    return;
  }

int main() {  
   
     OBAtom a, b, c;
      a.SetAtomicNum(8);
      b.SetAtomicNum(6);
      c.SetAtomicNum(8);

     OBMol mol;
     mol.AddAtom(a);
     mol.AddAtom(b);
     mol.AddAtom(c);
     
     mol.AddBond(1,2,2);
     mol.AddBond(2,3,2);

      OBConversion conv;
      conv.SetOutFormat("SMI");
      cout << conv.WriteString(&mol,1) << endl;
      
     OBSmartsPattern sp;
     
     sp.Init ("C~*");
     
     sp.Match (mol,false);
     
       cout << sp.NumMatches() << endl;
       
        cout << sp.GetUMapList().size() << endl;
      
      return EXIT_SUCCESS;
  }    

    double Predict(OBBase* pOb, string* param=NULL)
    {
      OBMol* pmol = dynamic_cast<OBMol*> (pOb);
      if(!pmol)
        return 0;

      OBSmartsPattern sp;
      if (sp.Init(_smarts) && sp.Match(*pmol))
        return sp.GetUMapList().size();
      else
        return 0.0;
    }

/** The descriptor name can be s or smarts and is case independent
    The operator to return true for a match can be:
    one or more spaces, =, ==,  or nothing if the SMARTS string
    starts with a letter.
    To return true for a mismatch the operator is !=
    A space or tab should follow the SMARTS string.
 **/      
bool SmartsFilter::Compare(OBBase* pOb, istream& optionText, bool noEval)
{
  OBMol* pmol = dynamic_cast<OBMol*> (pOb);
  if(!pmol)
    return false;
  
  string smarts;
  bool matchornegate = ReadStringFromFilter(optionText, smarts);
  if(noEval)
    return false;
  OBSmartsPattern sp;
  sp.Init(smarts);
  bool ret = sp.Match(*pmol,true);//single match  
  if(!matchornegate)
    ret = !ret;
  return ret;
}

  bool GetFingerprint(OBBase* pOb, vector<unsigned int>&fp, int nbits) 
  {
    OBMol* pmol = dynamic_cast<OBMol*>(pOb);
    
   	unsigned int o=0;
   	unsigned int m=0;
   	unsigned int i=0;
   	unsigned int n=0;
    
    if(!pmol)
      return false;
    
    //Read patterns file if it has not been done already
    if(smartsStrings.empty())
      ReadPatternFile(_patternsfile, smartsStrings);

    //Make fp size the smallest power of two to contain the patterns
    //unsigned int n=Getbitsperint();
    //while(n<smartsStrings.size())n*=2;
    //fp.resize(n/Getbitsperint());
    
    fp.resize(16);

    for(n=0;n<smartsStrings.size();++n)
		{
			OBSmartsPattern sp;
			sp.Init(smartsStrings[n]);
			
			if(sp.Match(*pmol)) {
			    m=sp.GetUMapList().size();
			    //m=sp.NumMatches();
			    o=n*8;
			    for(i=0;i<8;++i) {
			           if(i<m) {SetBit(fp, o+i);
			           //cout << "1";
			       }  
          //cout << endl;  
				}				
				}				
		}

    if(nbits)
      Fold(fp, nbits);
    return true;
  };

void CheckSmarts::checkSmarts() {

	OBSmartsPattern smartsPattern;

	for (unsigned int i = 0; i < data->num_smarts(); i++) {

		cout << *data->get_smarts(i) << "\t[ ";

		for (unsigned int j = 0; j < data->num_smiles(); j++) {

			smartsPattern.Init(*data->get_smarts(i));

			if (smartsPattern.Match(*data->get_mol(j), true))
				cout << data->get_id(j) << " ";
		}

		cout << "]\n";
	}
}

/** The descriptor name can be s or smarts and is case independent
    The operator to return true for a match can be:
    one or more spaces, =, ==,  or nothing if the SMARTS string
    starts with a letter.
    To return true for a mismatch the operator is !=
    A space or tab should follow the SMARTS string.
 **/
bool SmartsFilter::Compare(OBBase *pOb, istream &optionText, bool noEval,
                           std::string *) {
  OBMol *pmol = dynamic_cast<OBMol *>(pOb);
  if (!pmol)
    return false;

  string smarts;
  bool matchornegate = ReadStringFromFilter(optionText, smarts);
  if (noEval)
    return false;
  OBSmartsPattern sp;
  if (!sp.Init(smarts))
    return false; // can't initialize the SMARTS, so fail gracefully

  bool ret = sp.Match(*pmol, true); // single match
  if (!matchornegate)
    ret = !ret;
  return ret;
}

///////////////////////////////////////////////////////////////////////////////
//! \brief Find the molecule(s) with or without a given SMART pattern
int main(int argc,char **argv)
{
  char c;
  unsigned int ntimes=0; // number of times SMARTS matches in a molecule
  unsigned int numMatching = 0; // number of matching molecules (for -c flag)
  bool pattern_matched=false, ntimes_matched=true;
  bool count=false, invert=false, full=false, name_only=false;
  char *FileIn = NULL, *Pattern = NULL;
  char *program_name = argv[0];
  char *iext;
  bool useInFile = true;

  OBConversion conv(&cin,&cout);
  OBFormat *pFormat = conv.FindFormat("smi"); // default format is SMILES
    
  // Parse options
  while ((c = getopt(argc, argv, "t:nvcfi:-")) != -1)
    {
#ifdef _WIN32
	    char optopt = c;
#endif
      switch (c)
        {
        case 't': // request ntimes unique matches

          c = sscanf(optarg, "%d", &ntimes);
          if (c != 1 )
            {
              cerr << program_name << ": unable to parse -t option" << endl;
              exit (-1);
            }
          break;

        case 'i':
          iext = optarg;

          //The ID provided by the OBFormat class is used as 
          // the identifying file extension. This is a slight
          // reduction in flexibility (which is not currently used)
          pFormat = conv.FindFormat(iext);
            
          if(pFormat==NULL)
            {
              cerr << program_name << ": cannot read input format!" << endl;
              exit(-1);
            }

          break;
        case 'n': // print the molecule name only
          name_only = true;
          break;
        case 'c': // count the number of match
          count = true;
          break;
        case 'v': // match only the molecules without the pattern
          invert = true;
          break;

        case 'f':
          full = true;
          break;

        case '-':
          useInFile = false;
          break;

        case '?':
          if (isprint (optopt))
            fprintf (stderr, "Unknown option `-%c'.\n", optopt);
          else
            fprintf (stderr,
                     "Unknown option character `\\x%x'.\n",
                     optopt);
          return 1;
        }
    }
  int index = optind;

  if (argc-index != 2 && argc-index != 1)
    {
      string err = "Usage: ";
      err += program_name;
      err += " [options] \"PATTERN\" <filename>\n";
      err += "If no filename is supplied, then obgrep will use stdin instead.\n";
      err += "Options:\n";
      err += "   -v      Invert the matching, print non-matching molecules\n";
      err += "   -c      Print the number of matched molecules\n";
      err += "   -i <format> Specify the input and output format\n";
      err += "   -f      Full match, print matching-molecules when the number\n";
      err += "           of heavy atoms is equal to the number of PATTERN atoms\n";
      err += "   -n      Only print the name of the molecules\n";
      err += "   -t NUM  Print a molecule only if the PATTERN occurs NUM times inside the molecule\n";
      cerr << err << ends;
      exit(-1);
    }
  else
    {
      Pattern = argv[index++];
//.........这里部分代码省略.........

//.........这里部分代码省略.........
		{
			// No incompleted jobs. Sleep for a while.
			if (!sleeping) cout << local_time() << "Sleeping" << endl;
			sleeping = true;
			this_thread::sleep_for(chrono::seconds(10));
			continue;
		}
		sleeping = false;
		const auto job = value.Obj();

		// Obtain job properties.
		const auto _id = job["_id"].OID();
		cout << local_time() << "Executing job " << _id.str() << endl;
		const auto job_path = jobs_path / _id.str();
		const auto format = job["format"].String();
		const auto email = job["email"].String();

		// Parse the user-supplied ligand.
		OBMol obMol;
		OBConversion obConversion;
		obConversion.SetInFormat(format.c_str());
		obConversion.ReadFile(&obMol, (job_path / ("ligand." + format)).string());
		const auto num_atoms = obMol.NumAtoms();
//		obMol.AddHydrogens(); // Adding hydrogens does not seem to affect SMARTS matching.

		// Classify subset atoms.
		array<vector<int>, num_subsets> subsets;
		for (size_t k = 0; k < num_subsets; ++k)
		{
			auto& subset = subsets[k];
			subset.reserve(num_atoms);
			OBSmartsPattern smarts;
			smarts.Init(SubsetSMARTS[k]);
			smarts.Match(obMol);
			for (const auto& map : smarts.GetMapList())
			{
				subset.push_back(map.front());
			}
		}
		const auto& subset0 = subsets.front();

		// Check user-provided ligand validity.
		if (subset0.empty())
		{
			// Record job completion time stamp.
			const auto millis_since_epoch = duration_cast<std::chrono::milliseconds>(system_clock::now().time_since_epoch()).count();
			conn.update(collection, BSON("_id" << _id), BSON("$set" << BSON("done" << Date_t(millis_since_epoch))));

			// Send error notification email.
			cout << local_time() << "Sending an error notification email to " << email << endl;
			MailMessage message;
			message.setSender("usr <[email protected]>");
			message.setSubject("Your usr job has failed");
			message.setContent("Description: " + job["description"].String() + "\nSubmitted: " + to_simple_string(ptime(epoch, boost::posix_time::milliseconds(job["submitted"].Date().millis))) + " UTC\nFailed: " + to_simple_string(ptime(epoch, boost::posix_time::milliseconds(millis_since_epoch))) + " UTC\nReason: failed to parse the provided ligand.");
			message.addRecipient(MailRecipient(MailRecipient::PRIMARY_RECIPIENT, email));
			SMTPClientSession session("137.189.91.190");
			session.login();
			session.sendMessage(message);
			session.close();
			continue;
		}

		// Calculate the four reference points.
		const auto n = subset0.size();
		const auto v = 1.0 / n;
		array<vector3, num_references> references{};

///////////////////////////////////////////////////////////////////////////////
//! \brief Set a tortional bond to a given angle
int main(int argc,char **argv)
{
  const char *Pattern=NULL;
  unsigned int i, t, errflg = 0;
  int c;
  char flags[255];
  string err;
  bool graphOutput=false;

  // parse the command line -- optional -a flag to change all matching torsions
  if (argc < 3 || argc > 4) {
    errflg++;
  } else {
    FileIn = argv[1];
    Pattern = "[!$(*#*)&!D1][email protected][!$(*#*)&!D1]";
    // Read the atom position
    c = sscanf(argv[2], "%d", &angleSum);
	angle = 360./angleSum;
    if (argc == 4)
	{
    		c = sscanf(argv[3], "%s", flags);
		int flagid=1;
    		while (flags[flagid]!=0)
			switch (flags[flagid++])
			{
			case 'g':
				graphOutput=true;
			case 'e':
				forceField=OBForceField::FindForceField("MMFF94");
				isEnergyCalcing=true;
				break;
    			}
 	}
  }
  if (errflg) {
    cerr << "Usage: rkrotate <filename> <angle> [options]" << endl;
    exit(-1);
  }

  // create pattern
  OBSmartsPattern sp;
  sp.Init(Pattern);

  OBFormat* format = conv.FormatFromExt(FileIn);
  if(!(format && conv.SetInAndOutFormats(format, format))) { //in and out formats same
    cerr << "obrotate: cannot read and/or write this file format!" << endl;
    exit (-1);
  } //...NF

  //Open the molecule file
  ifstream ifs;

  // Read the file
  ifs.open(FileIn);
  if (!ifs) {
    cerr << "obrotate: cannot read input file!" << endl;
    exit (-1);
  }

  OBMol mol;
  vector< vector <int> > maplist;      // list of matched atoms
//  vector< vector <int> >::iterator m;  // and its iterators
  //   int tindex;
  
  // Set the angles
  for (;;) {
    mol.Clear();
    //NF      ifs >> mol;                   // Read molecule
    conv.Read(&mol,&ifs); //NF
    if (mol.Empty())
      break;

    if (sp.Match(mol)) {          
      // if match perform rotation
      maplist = sp.GetUMapList(); // get unique matches
      
      if (maplist.size() > 1)
        cerr << "obrotate: Found " << maplist.size() << " matches." << endl;

	energySheet=new MultiVector<double>(degrees=maplist.size(),angleSum);
	indexSheet=new int[maplist.size()];

      for (int EXO=0;EXO<maplist.size();++EXO)
	totalSum*=angleSum+EXO;
      // look at all the mapping atom but save only the last one.
	turnMol(mol,maplist,maplist.size()-1);
	
      if (graphOutput)
      {
	ofstream ofs("energyGraph.mlog");
	int ind[degrees];
	for (int i=0;i<degrees;++i)
		ind[i]=0;
	do
	{
		for (int i=0;i<degrees;++i)
			ofs<<ind[i]<<'\t';
		ofs<<energySheet->getVectorValue(ind)<<endl;
//.........这里部分代码省略.........

//.........这里部分代码省略.........
        nPatternAtoms = patmol.NumHvyAtoms();
      }
    }
    else
      nPatternAtoms = 0;
    
    //disable old versions
    pConv->AddOption(GetID(), OBConversion::GENOPTIONS, "");
  }

  bool match;
  //These are a vector of each mapping, each containing atom indxs.
  vector<vector<int> > vecatomvec;
  vector<vector<int> >* pMappedAtoms = NULL;
  OBSmartsPattern sp;

  if(nPatternAtoms)
    if(pmol->NumHvyAtoms() != nPatternAtoms)
      return false;

  int imol=0; //index of mol in pattern file
  if(!queries.empty()) //filename supplied
  {
    //match is set true if any of the structures match - OR behaviour
    for(qiter=queries.begin();qiter!=queries.end();++qiter, ++imol) 
    {
      OBIsomorphismMapper* mapper = OBIsomorphismMapper::GetInstance(*qiter);
      OBIsomorphismMapper::Mappings mappings;
      mapper->MapUnique(pmol, mappings);
      if( (match = !mappings.empty()) ) // extra parens to indicate truth value
      {
        OBIsomorphismMapper::Mappings::iterator ita;
        OBIsomorphismMapper::Mapping::iterator itb;
        for(ita=mappings.begin(); ita!=mappings.end();++ita)//each mapping
        {
          vector<int> atomvec;
          for(itb=ita->begin(); itb!=ita->end();++itb)//each atom index
            atomvec.push_back(itb->second+1);
          vecatomvec.push_back(atomvec);
          atomvec.clear();
        }
        pMappedAtoms = &vecatomvec;
        break;
      }
    }
  }
  else //SMARTS supplied
  {
    if(!sp.Init(vec[0]))
    {
      string msg = vec[0] + " cannot be interpreted as either valid SMARTS "
        "or the name of a file with an extension known to OpenBabel "
        "that contains one or more pattern molecules.";
      obErrorLog.ThrowError(__FUNCTION__, msg, obError, onceOnly);
      delete pmol;
      pmol = NULL;
      pConv->SetOneObjectOnly(); //stop conversion
      return false;
    }

    if( (match = sp.Match(*pmol)) ) // extra parens to indicate truth value
      pMappedAtoms = &sp.GetMapList();
  }

  if((!match && !inv) || (match && inv))
  {
    //delete a non-matching mol
    delete pmol;
    pmol = NULL;
    return false;
  }

  if(!inv && vec.size()>=2 && !vec[1].empty() && !nPatternAtoms)
  {
    vector<vector<int> >::iterator iter;

    if(vec[1]=="extract")
    {
      //Delete all unmatched atoms. Use only the first match
      ExtractSubstruct(pmol, *pMappedAtoms->begin());
      return true;
    }

    // color the substructure if there is a second parameter which is not "exact" or "extract"
    // with multiple color parameters use the one corresponding to the query molecule, or the last
    if(imol>vec.size()-2)
      imol = vec.size()-2;
    for(iter=pMappedAtoms->begin();iter!=pMappedAtoms->end();++iter)//each match
       AddDataToSubstruct(pmol, *iter, "color", vec[imol+1]);
    return true;
  }

  if(pConv && pConv->IsLast())
  {
    for(qiter=queries.begin();qiter!=queries.end();++qiter)
      delete *qiter;
    queries.clear();
  }
  return true;
}

//.........这里部分代码省略.........
          {
            string attr(txt.substr(0,pos)), val(txt.substr(pos+1));
            //Update value if it already exists
            OBPairData* dp = dynamic_cast<OBPairData*>(GetData(attr));
            if(dp) {
              dp->SetValue(val);
              dp->SetOrigin(userInput);
            }
            else {
              // Pair did not exist; make new one
              dp = new OBPairData;
              dp->SetAttribute(attr);
              dp->SetValue(val);
              dp->SetOrigin(userInput);
              SetData(dp);
            }
          }
      }

    itr = pOptions->find("add");  //adds new properties from descriptors in list
    if(itr!=pOptions->end())
      OBDescriptor::AddProperties(this, itr->second);

    itr = pOptions->find("delete"); //deletes the specified properties
    if(itr!=pOptions->end())
      OBDescriptor::DeleteProperties(this, itr->second);

    itr = pOptions->find("append"); //Appends values of descriptors or properties to title
    if(itr!=pOptions->end())
      {
        string title(GetTitle());
        title += OBDescriptor::GetValues(this, itr->second);
        if(ispunct(title[0]))
          title[0]=' ';//a leading punct char is used only as a separator, not at start
        SetTitle(Trim(title).c_str());
      }



      //Filter using OBDescriptor comparison and (older) SMARTS tests
    //Continue only if previous test was true.
    bool fmatch = true;
    itr = pOptions->find("filter");
    if(itr!=pOptions->end())
      {
        std::istringstream optionText(itr->second);
        fmatch = OBDescriptor::FilterCompare(this, optionText, false);
      }

    if(fmatch)
      {
        itr = pOptions->find("v");
        if(itr!=pOptions->end() && !itr->second.empty())
          {
            //inverse match quoted SMARTS string which follows
            OBSmartsPattern sp;
            sp.Init(itr->second);
            fmatch = !sp.Match(*this); //(*pmol) ;
          }
      }
    if(fmatch)
    {
      itr = pOptions->find("s");
      if(itr!=pOptions->end() && !itr->second.empty())
        {
          //SMARTS filter
          //If exactmatch option set (probably in fastsearchformat) the
          //number of atoms in the pattern (passed as a string in the option text)
          //has to be the same as in the molecule.
          itr2 = pOptions->find("exactmatch");
          if(itr2!=pOptions->end() && NumHvyAtoms()!=atoi(itr2->second.c_str()))
            fmatch=false;
          else
            {
              //match quoted SMARTS string which follows
              OBSmartsPattern sp;
                sp.Init(itr->second.c_str());
                fmatch = sp.Match(*this);
            }
        }
    }

    if(!fmatch)
      {
        //filter failed: delete OBMol and return NULL
        delete this;
        return NULL;
      }
    else
      {
        if(ret==false)
          {
            obErrorLog.ThrowError(__FUNCTION__, "Error executing an option", obError);
            delete this; //added 9March2006
            return NULL;
          }
        else
          return this;
      }
  }

  void OBBondTyper::AssignFunctionalGroupBonds(OBMol &mol)
  {
    if (!_init)
      Init();

    OBSmartsPattern *currentPattern;
    OBBond *b1, *b2;
    OBAtom *a1,*a2, *a3;
    double angle, dist1, dist2;
    vector<int> assignments;
    vector<vector<int> > mlist;
    vector<vector<int> >::iterator matches, l;
    vector<pair<OBSmartsPattern*, vector<int> > >::iterator i;
    unsigned int j;

    // Loop through for all the functional groups and assign bond orders
    for (i = _fgbonds.begin();i != _fgbonds.end();++i)
      {
        currentPattern = i->first;
        assignments = i->second;

        if (currentPattern && currentPattern->Match(mol))
          {
            mlist = currentPattern->GetUMapList();
            for (matches = mlist.begin(); matches != mlist.end(); ++matches)
              {
                // Now loop through the bonds to assign from _fgbonds
                for (j = 0; j < assignments.size(); j += 3)
                  {
                    // along the assignments vector: atomID1 atomID2 bondOrder
                    a1 = mol.GetAtom((*matches)[ assignments[j] ]);
                    a2 = mol.GetAtom((*matches)[ assignments[j+1 ] ]);
                    if (!a1 || !a2) continue;

                    b1 = a1->GetBond(a2);

                    if (!b1) continue;
                    b1->SetBO(assignments[j+2]);
                  } // bond order assignments
              } // each match
          } // current pattern matches

      } // for(functional groups)

    // FG with distance and/or bond criteria
    // Carbonyl oxygen C=O
    OBSmartsPattern carbo; carbo.Init("[#8D1][#6](*)(*)");

    if (carbo.Match(mol))
      {
        mlist = carbo.GetUMapList();
        for (l = mlist.begin(); l != mlist.end(); ++l)
          {
            a1 = mol.GetAtom((*l)[0]);
            a2 = mol.GetAtom((*l)[1]);

            angle = a2->AverageBondAngle();
            dist1 = a1->GetDistance(a2);

            // carbonyl geometries ?
            if (angle > 115 && angle < 150 && dist1 < 1.28) {

              if ( !a1->HasDoubleBond() ) {// no double bond already assigned
                b1 = a1->GetBond(a2);

                if (!b1 ) continue;
                b1->SetBO(2);
              }
            }
          }
      } // Carbonyl oxygen

    // thione C=S
    OBSmartsPattern thione; thione.Init("[#16D1][#6](*)(*)");

    if (thione.Match(mol))
      {
        mlist = thione.GetUMapList();
        for (l = mlist.begin(); l != mlist.end(); ++l)
          {
            a1 = mol.GetAtom((*l)[0]);
            a2 = mol.GetAtom((*l)[1]);

            angle = a2->AverageBondAngle();
            dist1 = a1->GetDistance(a2);

            // thione geometries ?
            if (angle > 115 && angle < 150 && dist1 < 1.72) {

              if ( !a1->HasDoubleBond() ) {// no double bond already assigned
                b1 = a1->GetBond(a2);

                if (!b1 ) continue;
                b1->SetBO(2);
              }
            }
          }
      } // thione

    // Isocyanate N=C=O or Isothiocyanate
//.........这里部分代码省略.........

int main(int argc, char* argv[])
{
	const array<string, 5> SmartsPatterns =
	{
		"[!#1]", // heavy
		"[#6+0!$(*~[#7,#8,F]),SH0+0v2,s+0,S^3,Cl+0,Br+0,I+0]", // hydrophobic
		"[a]", // aromatic
		"[$([O,S;H1;v2]-[!$(*=[O,N,P,S])]),$([O,S;H0;v2]),$([O,S;-]),$([N&v3;H1,H2]-[!$(*=[O,N,P,S])]),$([N;v3;H0]),$([n,o,s;+0]),F]", // acceptor
		"[N!H0v3,N!H0+v4,OH+0,SH+0,nH+0]", // donor
	};
	OBConversion obConversion;
	obConversion.SetInFormat("pdbqt");
	while (true)
	{
		vector<array<double, 3>> atoms;
		atoms.reserve(80);
		stringstream ss;
		for (string line; getline(cin, line);)
		{
			ss << line << endl;
			const auto record = line.substr(0, 6);
			if (record == "TORSDO") break;
			if (record != "ATOM  " && record != "HETATM") continue;
			atoms.push_back({ stod(line.substr(30, 8)), stod(line.substr(38, 8)), stod(line.substr(46, 8)) });
		}
		if (atoms.empty()) break;
		OBMol obMol;
		obConversion.Read(&obMol, &ss);
		array<vector<int>, 5> subsets;
		for (size_t k = 0; k < 5; ++k)
		{
			auto& subset = subsets[k];
			subset.reserve(atoms.size());
			OBSmartsPattern smarts;
			smarts.Init(SmartsPatterns[k]);
			smarts.Match(obMol);
			for (const auto& map : smarts.GetMapList())
			{
				subset.push_back(map.front() - 1);
			}
		}
		const auto& subset0 = subsets.front();
		const auto n = subset0.size();
		const auto v = 1.0 / n;
		array<double, 3> ctd{};
		array<double, 3> cst{};
		array<double, 3> fct{};
		array<double, 3> ftf{};
		for (size_t k = 0; k < 3; ++k)
		{
			for (const auto i : subset0)
			{
				const auto& a = atoms[i];
				ctd[k] += a[k];
			}
			ctd[k] *= v;
		}
		double cst_dist = numeric_limits<double>::max();
		double fct_dist = numeric_limits<double>::lowest();
		double ftf_dist = numeric_limits<double>::lowest();
		for (const auto i : subset0)
		{
			const auto& a = atoms[i];
			const auto this_dist = dist2(a, ctd);
			if (this_dist < cst_dist)
			{
				cst = a;
				cst_dist = this_dist;
			}
			if (this_dist > fct_dist)
			{
				fct = a;
				fct_dist = this_dist;
			}
		}
		for (const auto i : subset0)
		{
			const auto& a = atoms[i];
			const auto this_dist = dist2(a, fct);
			if (this_dist > ftf_dist)
			{
				ftf = a;
				ftf_dist = this_dist;
			}
		}
		for (const auto& subset : subsets)
		{
			const auto n = subset.size();
			const auto v = 1.0 / n;
			for (const auto& rpt : { ctd, cst, fct, ftf })
			{
				vector<double> dists(n);
				for (size_t i = 0; i < n; ++i)
				{
					dists[i] = sqrt(dist2(atoms[subset[i]], rpt));
				}
				array<double, 3> m{};
				for (size_t i = 0; i < n; ++i)
				{
					const auto d = dists[i];
//.........这里部分代码省略.........

int main(int argc,char *argv[])
{
  // turn off slow sync with C-style output (we don't use it anyway).
  std::ios::sync_with_stdio(false);

  if (argc != 1)
    {
      cout << "Usage: smilesmatch\n";
      cout << "   Tests Open Babel SMILES/SMARTS pattern matching." << endl;
      return 0;
    }
  
  cout << endl << "# Testing SMILES self-matching using SMARTS...  \n";
  
  std::ifstream mifs;
  if (!SafeOpen(mifs, smilestypes_file.c_str()))
    {
      cout << "Bail out! Cannot read test data " << smilestypes_file << endl;
      return -1; // test failed
    }

  OBConversion conv(&mifs, &cout);
  if (! conv.SetInAndOutFormats("SMI","SMI"))
    {
      cout << "Bail out! SMILES format is not loaded" << endl;
      return -1;
    }

  unsigned int currentMol = 0;
  OBSmartsPattern smarts;
  OBMol mol;
  string buffer;

  //read in molecules and see if their SMARTS matches themselves
  while (getline(mifs, buffer))
    {
      mol.Clear();
      conv.ReadString(&mol, buffer);
      if (mol.Empty())
        continue;

      // trim off any title, etc.
      string::size_type pos = buffer.find_first_of(" \t\n\r");
      if (pos != string::npos)
        buffer.erase(pos);

      pos = buffer.find_first_of('.');
      if (pos != string::npos)
        continue;

      smarts.Init(buffer);
      if (smarts.Match(mol))
        cout << "ok " << ++currentMol << " # SMARTS matched the"
             << " SMILES molecule\n";
      else
        cout << "not ok " << ++currentMol << " # SMARTS did not match"
             << " for molecule " << buffer << "\n";
    }

  // output the number of tests run
  cout << "1.." << currentMol << endl;

  // Passed Test
  return 0;
}