C++ OBSmartsPattern::GetMapList方法代码示例

//.........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.........
			// 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{};
		auto& ctd = references[0];

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.........