C++ OBMol::Clear方法代码示例

void CheckValidDipeptide(OBConversion &conv,
                         const string &test,
                         unsigned int testCount)
{
  OBMol mol;
  OBResidue *res;
  ostringstream os;

  mol.Clear();
  conv.ReadString(&mol, test);
  chainsparser.PerceiveChains(mol);
  if (mol.NumResidues() != 2) {
    os << "not ok " << testCount << " # expected 2 residues, but found "
         << mol.NumResidues() << '\n';
    os << "# ";
    FOR_RESIDUES_OF_MOL(res, mol)
      os << res->GetName() << " ";
    os << endl;
    BOOST_CHECK_MESSAGE( 0, os.str().c_str() );
  } else {
    res = mol.GetResidue(0);
    BOOST_CHECK_MESSAGE( res, "Get first AA from dipeptide" );
    res = mol.GetResidue(1);
    BOOST_CHECK_MESSAGE( res, "Get second AA from dipeptide" );
  }
}

void GenerateFormulaReference()
{
  std::ifstream ifs;
  if (!SafeOpen(ifs, smilestypes_file.c_str()))
    return;

  std::ofstream ofs;
  if (!SafeOpen(ofs, results_file.c_str()))
    return;

  OBMol mol;
  OBConversion conv(&ifs, &cout);

  if(! conv.SetInAndOutFormats("SMI","SMI"))
    {
      cerr << "SMILES format is not loaded" << endl;
      return;
    }

  for (;ifs;)
    {
      mol.Clear();
      conv.Read(&mol);
      if (mol.Empty())
        continue;

      //write out formula, molecular weight and exact mass
      ofs << mol.GetFormula() << " " << mol.GetMolWt() << " " 
          << mol.GetExactMass() << endl;
    }

	cerr << " Molecular formula results written successfully" << endl;
  return;
}

void aromatic_test()
{
  cout << endl << "# Testing aromaticity perception...  " << endl;

  string filename = "files/aromatics.smi";
  
  ifstream ifs(filename.c_str());
  BOOST_REQUIRE_MESSAGE( ifs, "Bail out! Cannot read input file!" );
  
  OBConversion conv(&ifs, &cout);
  OBFormat* pFormat;
  
  pFormat = conv.FormatFromExt(filename.c_str());
  BOOST_REQUIRE_MESSAGE( pFormat != NULL, "Bail out! Cannot read file format!" );
  
  // Finally, we can do some work!
  OBMol mol;
  
  unsigned int testCount = 0;

  BOOST_REQUIRE_MESSAGE( conv.SetInAndOutFormats(pFormat, pFormat), "Bail out! File format isn't loaded");
  
  int molCount = 0;
  char message[BUFF_SIZE];
  while(ifs.peek() != EOF && ifs.good())
    {
      mol.Clear();
      conv.Read(&mol);
      molCount++;
      
      FOR_ATOMS_OF_MOL(atom, mol)
        {
          if (atom->IsHydrogen())
            continue;

          testCount++;
          
	  snprintf(message, BUFF_SIZE, "not ok %d # atom isn't aromatic!\n"
		      "# atom idx %d in molecule %d %s", 
		      testCount, atom->GetIdx(), molCount, mol.GetTitle());
          BOOST_CHECK_MESSAGE( atom->IsAromatic(), message );
        }

      FOR_BONDS_OF_MOL(bond, mol)
        {
          if (!bond->IsInRing())
            continue;
          
	  testCount++;
        
	  snprintf(message, BUFF_SIZE, "not ok %d # bond isn't aromatic!\n"
                                       "# begin atom %d, end atom %d, bond order %d in molecule %d %s", 
                                       testCount, bond->GetBeginAtomIdx(), bond->GetEndAtomIdx(),
				       bond->GetBondOrder(), molCount, mol.GetTitle());
          BOOST_CHECK_MESSAGE( bond->IsAromatic(), message );
        }
	
    } // while reading molecules
    
}

static void WriteAgents(OBMol& mol, OBReactionFacade& rxnfacade, OBConversion* pconv, OBFormat* pformat)
{
  for(unsigned int i=0; i<rxnfacade.NumComponents(AGENT); i++) {
    mol.Clear();
    rxnfacade.GetComponent(&mol, AGENT, i);
    WriteMolFile(&mol, pconv, pformat);
  }
}

int main(int argc,char **argv)
{
  char *program_name= argv[0];
  int c;
  char *FileIn = NULL;

  if (argc != 2) {
    cerr << " Usage: " << program_name << " <input file>\n";
    exit(-1);
  }
  else {
      FileIn  = argv[1];
  }

  // Find Input filetype
  OBConversion conv(&cin, &cout);
  OBFormat *inFormat = conv.FormatFromExt(FileIn);

  if (!inFormat || !conv.SetInFormat(inFormat)) {
    cerr << program_name << ": cannot read input format!" << endl;
    exit (-1);
  }
  // If we can't also use this for an output format, use XYZ
  if (!conv.SetOutFormat(inFormat))
    conv.SetOutFormat(conv.FindFormat("xyz"));

  ifstream ifs;

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

  OBMol mol;
  OBPointGroup pg;

  for (c = 1;; ++c)
    {
      mol.Clear();
      conv.Read(&mol, &ifs);
      if (mol.Empty())
        break;

      // not needed by OBPointGroup, but useful for external programs
      pg.Setup(&mol);
      cerr << "Point Group: " << pg.IdentifyPointGroup() << endl;
      pg.Symmetrize(&mol);

      conv.Write(&mol, &cout);

    } // end for loop

  return(1);
}

void GenerateCharges()
{
  std::ifstream ifs;
  if (!SafeOpen(ifs, molecules_file.c_str()))
    return;

  std::ofstream rofs;
  if (!SafeOpen(rofs, results_file.c_str()))
    return;

  std::ofstream dofs;
  if (!SafeOpen(dofs, dipole_file.c_str()))
    return;

  OBMol mol;
  OBConversion conv(&ifs, &cout);
  char buffer[BUFF_SIZE];
  
  if(! conv.SetInAndOutFormats("SDF","SDF"))
    {
      cerr << "SDF format is not loaded" << endl;
      return;
    }

  OBChargeModel *pCM = OBChargeModel::FindType("mmff94");

  if (pCM == NULL) {
    cerr << "Cannot load charge model!" << endl;
    return;
  }

  std::vector<double> partialCharges;
  vector3 dipoleMoment;
  for (;ifs;)
    {
      mol.Clear();
      conv.Read(&mol);
      if (mol.Empty())
        continue;

      if (pCM->ComputeCharges(mol)) {
        partialCharges = pCM->GetPartialCharges();
      }

      // write out the dipole moment
      dipoleMoment = pCM->GetDipoleMoment(mol);
      sprintf(buffer, "%15.5f%15.5f%15.5f\n", dipoleMoment.x(), dipoleMoment.y(), dipoleMoment.z());
      dofs << buffer;
      
      // and write all the partial charges
      FOR_ATOMS_OF_MOL(atom, mol) {
        sprintf(buffer, "%15.5f\n", atom->GetPartialCharge());
        rofs << buffer;
      }
    }

int main(int argc,char **argv)
{
  char *program_name= argv[0];
  int c;
  char *FileIn = NULL;

  if (argc != 2) {
    cerr << " Usage: " << program_name << " <input file>\n";
    exit(-1);
  }
  else {
      FileIn  = argv[1];
  }

  // Find Input filetype
  OBConversion conv;
  OBFormat *inFormat = conv.FormatFromExt(FileIn);
    
  if (!inFormat || !conv.SetInFormat(inFormat)) {
    cerr << program_name << ": cannot read input format!" << endl;
    exit (-1);
  }

  ifstream ifs;

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

  OBMol mol;
  OBPointGroup pg;

  for (c = 1;; ++c)
    {
      mol.Clear();
      conv.Read(&mol, &ifs);
      if (mol.Empty())
        break;
      
      // not needed by OBPointGroup, but useful for external programs
      mol.Center();
      mol.ToInertialFrame();

      pg.Setup(&mol);
      cout << "Point Group: " << pg.IdentifyPointGroup() << endl;

    } // end for loop
  
  return(1);
}

  int ReadPQS_geom(istream &ifs, OBMol &mol, const char *title,
                   int input_style, double bohr_to_angstrom)
  {
    int atom_count=0;
    double x, y, z;
    char buffer[BUFF_SIZE];
    string str;
    OBAtom *atom;
    vector<string> vs;

    mol.Clear();
    mol.BeginModify();

    while (ifs.getline(buffer,BUFF_SIZE) && !card_found(buffer))
      {
        if (buffer[0]!='$')
          {
            tokenize(vs, buffer);
            if (vs.size() < 1) return false; // timvdm 18/06/2008
            atom=mol.NewAtom();
            str=vs[0];
            if (input_style==0)
              {
                if (vs.size() < 4) return false; // timvdm 18/06/2008
                atom->SetAtomicNum(OBElements::GetAtomicNum(str.c_str()));
                x=atof((char*) vs[1].c_str())*bohr_to_angstrom;
                y=atof((char*) vs[2].c_str())*bohr_to_angstrom;
                z=atof((char*) vs[3].c_str())*bohr_to_angstrom;
              }
            else
              {
                if (vs.size() < 5) return false; // timvdm 18/06/2008
                str.replace (0,2,"");
                atom->SetAtomicNum(OBElements::GetAtomicNum(str.c_str()));
                x=atof((char*) vs[2].c_str())*bohr_to_angstrom;
                y=atof((char*) vs[3].c_str())*bohr_to_angstrom;
                z=atof((char*) vs[4].c_str())*bohr_to_angstrom;
              }
            atom->SetVector(x, y, z);
            atom_count++;
          }
      }

    mol.ConnectTheDots();
    mol.PerceiveBondOrders();

    mol.EndModify();
    mol.SetTitle(title);

    return atom_count;
  }

void GenerateEnergies()
{
  std::ifstream ifs;
  if (!SafeOpen(ifs, molecules_file.c_str()))
    return;

  std::ofstream ofs;
  if (!SafeOpen(ofs, results_file.c_str()))
    return;

  OBMol mol;
  OBConversion conv(&ifs, &cout);
  char buffer[BUFF_SIZE];
  
  if(! conv.SetInAndOutFormats("SDF","SDF"))
    {
      cerr << "SDF format is not loaded" << endl;
      return;
    }

  OBForceField* pFF = OBForceField::FindForceField("Ghemical");

  if (pFF == NULL) {
    cerr << "Cannot load force field!" << endl;
    return;
  }

  pFF->SetLogFile(&cout);
  pFF->SetLogLevel(OBFF_LOGLVL_NONE);

  for (;ifs;)
    {
      mol.Clear();
      conv.Read(&mol);
      if (mol.Empty())
        continue;

      if (!pFF->Setup(mol)) {
        cerr << "Could not setup force field on molecule: " << mol.GetTitle() << endl;
        return;
      }
      
      // Don't compute gradients
      sprintf(buffer, "%15.5f\n", pFF->Energy(false));
      ofs << buffer;
    }

	cerr << " Ghemical force field energies written successfully" << endl;
  return;
}

void CheckInvalidResidue(OBConversion &conv,
                         const string &test,
                         unsigned int testCount)
{
  OBMol mol;
  
  mol.Clear();
  conv.ReadString(&mol, test);
  chainsparser.PerceiveChains(mol);
  if (mol.NumResidues() != 0) {
    OBResidue *res = mol.GetResidue(0);
    if (res->GetName() == "LIG") { // ligand, not residue
      cout << "ok " << testCount << " # found ligand, not residue "
           << test << '\n';
    } else {
      cout << "not ok " << testCount << " # expected 0 residues, found "
           << mol.NumResidues() << '\n';
      cout << "# " << res->GetName() << endl;
    }
  } else
    cout << "ok " << testCount << " # correctly rejected " << test << '\n';
}

void CheckInvalidResidue(OBConversion &conv,
                         const string &test,
                         unsigned int testCount)
{
  OBMol mol;
  ostringstream os;
  
  mol.Clear();
  conv.ReadString(&mol, test);
  chainsparser.PerceiveChains(mol);
  if (mol.NumResidues() != 0) {
    OBResidue *res = mol.GetResidue(0);
    if (res->GetName() == "LIG") { // ligand, not residue
      BOOST_CHECK( 1 );
    } else {
      os << "not ok " << testCount << " # expected 0 residues, found "
           << mol.NumResidues() << '\n';
      os << "# " << res->GetName() << endl;
      BOOST_CHECK_MESSAGE( 0, os.str().c_str() );
    }
  } else
    BOOST_CHECK( 1 );
}

void CheckValidDipeptide(OBConversion &conv,
                         const string &test,
                         unsigned int testCount)
{
  OBMol mol;

  mol.Clear();
  conv.ReadString(&mol, test);
  chainsparser.PerceiveChains(mol);
  if (mol.NumResidues() != 2) {
    cout << "not ok " << testCount << " # expected 2 residues, but found "
         << mol.NumResidues() << '\n';
    cout << "# ";
    FOR_RESIDUES_OF_MOL(res, mol)
      cout << res->GetName() << " ";
    cout << endl;
  } else {
    OBResidue *res;
    res = mol.GetResidue(0);
    cout << "ok " << testCount << " # " << res->GetName();
    res = mol.GetResidue(1);
    cout << " " << res->GetName() << '\n';
  }
}

int main(int argc,char *argv[])
{
  if (argc != 2)
    {
      cout << "Usage: obrotamer <file>" << endl;
      cout << "  Outputs the number of rotable bonds and generate a random"
           << " rotamer" << endl;
      return(-1);
    }

  ifstream ifs(argv[1]);
  if (!ifs)
    {
      cerr << "Error! Cannot read input file!" << endl;
      return(-1);
    }
  
  OBConversion conv(&ifs, &cout);
  OBFormat* pFormat;
  
  pFormat = conv.FormatFromExt(argv[1]);
  if ( pFormat == NULL )
    {
      cerr << "Error! Cannot read file format!" << endl;
      return(-1);
    }
  
  // Finally, we can do some work!
  OBMol mol;
  if (! conv.SetInAndOutFormats(pFormat, pFormat))
    {
      cerr << "Error! File format isn't loaded" << endl;
      return (-1);
    }
  
  OBRotorList rl;
  OBRotamerList rotamers;
  int *rotorKey = NULL;
  OBRandom rand;
  rand.TimeSeed();

  while(ifs.peek() != EOF && ifs.good())
    {
      mol.Clear();
      conv.Read(&mol);

      rl.Setup(mol);
      
      cerr << " Number of rotatable bonds: " << rl.Size() << endl;

      // indexed from 1, rotorKey[0] = 0
      std::vector<int> rotorKey(rl.Size() + 1, 0);

      // each entry represents the configuration of a rotor
      // e.g. indexes into OBRotor::GetResolution()
      //       (the different angles to sample from the OBRotorRules database)
      OBRotorIterator ri;
      OBRotor *rotor = rl.BeginRotor(ri);
      for (int i = 1; i < rl.Size() + 1; ++i, rotor = rl.NextRotor(ri))
        rotorKey[i] = rand.NextInt() % rotor->GetResolution().size();

      rotamers.SetBaseCoordinateSets(mol);
      rotamers.Setup(mol, rl);
      rotamers.AddRotamer(rotorKey);

      // This is more useful when you have added many rotamers
      // rather than the one in this example
      rotamers.ExpandConformerList(mol, mol.GetConformers());
      
      // Change the molecule conformation -- from 0 .. rotamers.NumRotamers()
      mol.SetConformer(0);
      conv.Write(&mol);
    } // while reading molecules
  
  return(0);
}

void GenerateSmartsReference()
{
  std::ifstream ifs;
  if (!SafeOpen(ifs,smarts_file.c_str()))
    return;

  char buffer[BUFF_SIZE];
  vector<OBSmartsPattern*> vsp;
  for (;ifs.getline(buffer,BUFF_SIZE);)
    {
      if (buffer[0] == '#') // skip comment line
        continue;

      OBSmartsPattern *sp = new OBSmartsPattern;

      if (sp->Init(buffer))
        vsp.push_back(sp);
      else
        delete sp;
    }

  std::ofstream ofs;
  if (!SafeOpen(ofs, results_file.c_str()))
    return;

  ofs << vsp.size() << " patterns" << endl;
  std::ifstream mifs;
  if (!SafeOpen(mifs, smilestypes_file.c_str()))
    return;

  vector<int> vm;
  vector<vector<int> > mlist;
  vector<vector<int> >::iterator j;
  vector<OBSmartsPattern*>::iterator i;
  OBMol mol;
  OBConversion conv(&mifs, &cout);

  if(! conv.SetInAndOutFormats("SMI","SMI"))
    {
      cerr << "SMILES format is not loaded" << endl;
      return;
    }

  for (;mifs;)
    {
      mol.Clear();
      conv.Read(&mol);

      if (mol.Empty())
        continue;
      for (i = vsp.begin();i != vsp.end();i++)
        {
          (*i)->Match(mol);
          mlist = (*i)->GetMapList();
          for (j = mlist.begin();j != mlist.end();j++)
            {
              sprintf(buffer,"%3d",*(j->begin()));
              ofs << buffer;
            }
          ofs << endl;
        }
    }


  cerr << " SMARTS test results written successfully" << endl;
  return;
}

bool RXNFormat::WriteMolecule(OBBase* pOb, OBConversion* pConv)
{
    OBMol* pmol = dynamic_cast<OBMol*>(pOb);
    if (pmol == NULL || !pmol->IsReaction())
      return false;

    pConv->AddOption("no$$$$",OBConversion::OUTOPTIONS);

    OBFormat* pMolFormat = pConv->FindFormat("MOL");
    if(pMolFormat==NULL)
    {
      obErrorLog.ThrowError(__FUNCTION__, "MDL MOL format not available", obError);
        return false;
    }

    OBReactionFacade rxnfacade(pmol);

    HandleAgent handleagent = ReadAgentOption(pConv->IsOption("G"));
    bool hasAgent = rxnfacade.NumComponents(AGENT) > 0;
    bool agentInReactants, agentInProducts;
    if (hasAgent && (handleagent==BOTH_REACT_AND_PROD || handleagent==AS_REACT))
      agentInReactants = true;
    else
      agentInReactants = false;
    if (hasAgent && (handleagent==BOTH_REACT_AND_PROD || handleagent==AS_PROD))
      agentInProducts = true;
    else
      agentInProducts = false;

    ostream &ofs = *pConv->GetOutStream();

    ofs << "$RXN" << '\n';
    ofs << pmol->GetTitle() << '\n';
    ofs << "      OpenBabel" << '\n';
    //ofs << pReact->GetComment() << '\n';
    ofs << "\n";

    ofs << setw(3);
    if (agentInReactants)
      ofs << rxnfacade.NumComponents(REACTANT) + rxnfacade.NumComponents(AGENT);
    else
      ofs << rxnfacade.NumComponents(REACTANT);
    ofs << setw(3);
    if (agentInProducts)
      ofs << rxnfacade.NumComponents(PRODUCT) + rxnfacade.NumComponents(AGENT);
    else
      ofs << rxnfacade.NumComponents(PRODUCT);
    if (hasAgent && handleagent==AS_AGENT)
      ofs << setw(3) << rxnfacade.NumComponents(AGENT);
    ofs << '\n';

    // Write reactants
    OBMol mol;
    for(unsigned int i=0; i<rxnfacade.NumComponents(REACTANT); i++) {
      mol.Clear();
      rxnfacade.GetComponent(&mol, REACTANT, i);
      WriteMolFile(&mol, pConv, pMolFormat);
    }
    if (agentInReactants)
      WriteAgents(mol, rxnfacade, pConv, pMolFormat);

    // Write products
    for(unsigned int i=0; i<rxnfacade.NumComponents(PRODUCT); i++) {
      mol.Clear();
      rxnfacade.GetComponent(&mol, PRODUCT, i);
      WriteMolFile(&mol, pConv, pMolFormat);
    }
    if (agentInProducts)
      WriteAgents(mol, rxnfacade, pConv, pMolFormat);

    // Write agent out (if treating AS_AGENT)
    if(hasAgent && handleagent==AS_AGENT)
      WriteAgents(mol, rxnfacade, pConv, pMolFormat);
    
    return true;
}