C++ OBMol::NumResidues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 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';
  }
}

//.........这里部分代码省略.........
                resname == "GPG" || resname == "NAD" || resname == "NAL" ||
                resname == "NDP" || resname == "ABA") {
              if (type.size() > 1)
                type = type.substr(0,1);
              //type.erase(1,type.size()-1);
            } else // other residues
              if (isdigit(type[0])){
                type = type.substr(1,1);
              }
              else
                if (type.size() > 1 && isdigit(type[1]))
                  type = type.substr(0,1);
                else
                  if (type.size() > 1 && isalpha(type[1])) {
                    if (type[0] == 'O' && type[1] == 'H')
                      type = type.substr(0,1); // no "Oh" element (e.g. 1MBN)
                    else if(isupper(type[1])) {
                      type[1] = tolower(type[1]);
                    }
                  }
        }

      } // HETATM records
    } // no element column to use

    OBAtom atom;
    /* X, Y, Z */
    string xstr = sbuf.substr(24,8);
    string ystr = sbuf.substr(32,8);
    string zstr = sbuf.substr(40,8);
    vector3 v(atof(xstr.c_str()),atof(ystr.c_str()),atof(zstr.c_str()));
    atom.SetVector(v);
    atom.ForceImplH();

    // useful for debugging unknown atom types (e.g., PR#1577238)
    //    cout << mol.NumAtoms() + 1  << " : '" << element << "'" << " " << etab.GetAtomicNum(element.c_str()) << endl;
    if (elementFound)
      atom.SetAtomicNum(etab.GetAtomicNum(element.c_str()));
    else // use our old-style guess from athe atom type
      atom.SetAtomicNum(etab.GetAtomicNum(type.c_str()));

    if ( (! scharge.empty()) && "  " != scharge )
      {
        if ( isdigit(scharge[0]) && ('+' == scharge[1] || '-' == scharge[1]) )
          {
            const char reorderCharge[3] = { scharge[1], scharge[0], '\0' };
            const int charge = atoi(reorderCharge);
            atom.SetFormalCharge(charge);
          }
        else
          {
            stringstream errorMsg;
            errorMsg << "WARNING: Problems reading a PDB file\n"
                     << "  Problems reading a HETATM or ATOM record.\n"
                     << "  According to the PDB specification,\n"
                     << "  columns 79-80 should contain charge of the atom\n"
                     << "  but OpenBabel found '" << scharge << "' (atom " << mol.NumAtoms()+1 << ").";
            obErrorLog.ThrowError(__FUNCTION__, errorMsg.str(), obWarning);
          }
      }
    else {
      atom.SetFormalCharge(0);
    }

    /* residue sequence number */
    string resnum = sbuf.substr(16,4);
    OBResidue *res  = (mol.NumResidues() > 0) ? mol.GetResidue(mol.NumResidues()-1) : NULL;
    if (res == NULL
        || res->GetName() != resname
        || res->GetNumString() != resnum
        || res->GetChain() != chain)
      {
        vector<OBResidue*>::iterator ri;
        for (res = mol.BeginResidue(ri) ; res ; res = mol.NextResidue(ri))
          if (res->GetName() == resname
              && res->GetNumString() == resnum
              && static_cast<int>(res->GetChain()) == chain)
            break;

        if (res == NULL) {
          res = mol.NewResidue();
          res->SetChain(chain);
          res->SetName(resname);
          res->SetNum(resnum);
        }
      }

    if (!mol.AddAtom(atom))
      return(false);
    else {
      OBAtom *atom = mol.GetAtom(mol.NumAtoms());

      res->AddAtom(atom);
      res->SetSerialNum(atom, atoi(serno.c_str()));
      res->SetAtomID(atom, sbuf.substr(6,4));
      res->SetHetAtom(atom, hetatm);

      return(true);
    }
  } // end reading atom records

//.........这里部分代码省略.........
      exit (-1);
    }

  ifstream ifs;

  // Read the file
  ifs.open(FileIn);
  if (!ifs)
    {
      cerr << program_name << ": cannot read input file!" << endl;
      exit (-1);
    }
  
  OBMol mol;
  OBFormat *canSMIFormat = conv.FindFormat("can");
  OBFormat *inchiFormat = conv.FindFormat("inchi");


  ////////////////////////////////////////////////////////////////////////////
  // List of properties
  // Name
  // Molecular weight (Standard molar mass given by IUPAC atomic masses)
  // Number of rings : the size of the smallest set of smallest rings (SSSR)
  
  //.....ADD YOURS HERE.....
  
  for (c = 1;; ++c)
    {
      mol.Clear();
      conv.Read(&mol, &ifs);
      if (mol.Empty())
        break;
      
      if (!mol.HasHydrogensAdded())
        mol.AddHydrogens();
      // Print the properties
      if (strlen(mol.GetTitle()) != 0)
        cout << "name             " << mol.GetTitle() << endl;
      else 
        cout << "name             " << FileIn << " " << c << endl;

      cout << "formula          " << mol.GetFormula() << endl;
      cout << "mol_weight       " << mol.GetMolWt() << endl;
      cout << "exact_mass       " << mol.GetExactMass() << endl;

      string smilesString = "-";
      if (canSMIFormat) {
        conv.SetOutFormat(canSMIFormat);
        smilesString = conv.WriteString(&mol);
        if ( smilesString.length() == 0 )
        {
          smilesString = "-";
        }
      }
      cout << "canonical_SMILES " << smilesString << endl;

      string inchiString = "-";
      if (inchiFormat) {
        conv.SetOutFormat(inchiFormat);
        inchiString = conv.WriteString(&mol);
        if ( inchiString.length() == 0 )
        {
          inchiString = "-";
        }
      }
      cout << "InChI            " << inchiString << endl;

      cout << "num_atoms        " << mol.NumAtoms() << endl;
      cout << "num_bonds        " << mol.NumBonds() << endl;
      cout << "num_residues     " << mol.NumResidues() << endl;
      cout << "num_rotors       " << mol.NumRotors() << endl;
      if (mol.NumResidues() > 0)
        cout << "sequence         " << sequence(mol) << endl;
      else
        cout << "sequence         " << "-" << endl;

      cout << "num_rings        " << nrings(mol) << endl;

      OBDescriptor* pDesc;
      pDesc= OBDescriptor::FindType("logP");
      if(pDesc)
        cout << "logP             " << pDesc->Predict(&mol) << endl;

      pDesc = OBDescriptor::FindType("TPSA");
      if(pDesc)
        cout << "PSA              " << pDesc->Predict(&mol) << endl;

      pDesc = OBDescriptor::FindType("MR");
      if(pDesc)
        cout << "MR               " << pDesc->Predict(&mol) << endl;

      cout << "$$$$" << endl; // SDF like end of compound descriptor list
      
      //Other OBDescriptors could be output here, even ones that were rarely
      // used. Since these are plugin classes, they may not be loaded, but
      // then with code like the above they are just ignored.
    } // end for loop
  
  return(0);
}