C++ OBMol::ReserveAtoms方法代码示例

bool ReadFeat(istream &ifs,OBMol &mol, const char *title)
{
  char buffer[BUFF_SIZE];
  int i,natoms;

  ifs.getline(buffer,BUFF_SIZE);
  sscanf(buffer,"%d",&natoms);

  mol.ReserveAtoms(natoms);
  mol.BeginModify();

  if (!ifs.getline(buffer,BUFF_SIZE)) return(false);
  mol.SetTitle(buffer);

  double x,y,z;
  char type[20];
  OBAtom *atom;
  for (i = 0; i < natoms;i++)
  {
    if (!ifs.getline(buffer,BUFF_SIZE)) return(false);
    sscanf(buffer,"%s %lf %lf %lf",
	   type,
	   &x,
	   &y,
	   &z);
    CleanAtomType(type);
    atom = mol.NewAtom();
    atom->SetVector(x,y,z);
    atom->SetAtomicNum(etab.GetAtomicNum(type));
  }

  mol.EndModify();
  return(true);
}

bool ReadAlchemy(istream &ifs,OBMol &mol, const char *title)
{
  int i;
  int natoms,nbonds;
  char buffer[BUFF_SIZE];

  ifs.getline(buffer,BUFF_SIZE);
  sscanf(buffer,"%d %*s %d", &natoms, &nbonds);
  if (!natoms) return(false);

  mol.ReserveAtoms(natoms);
  ttab.SetFromType("ALC");

  string str;
  double x,y,z;
  OBAtom *atom;
  vector<string> vs;

  for (i = 1; i <= natoms; i ++)
  {
    if (!ifs.getline(buffer,BUFF_SIZE)) return(false);
    tokenize(vs,buffer);
    if (vs.size() != 6) return(false);
    atom = mol.NewAtom();
    x = atof((char*)vs[2].c_str());
    y = atof((char*)vs[3].c_str());
    z = atof((char*)vs[4].c_str());
    atom->SetVector(x,y,z); //set coordinates

    //set atomic number
    ttab.SetToType("ATN"); ttab.Translate(str,vs[1]);
    atom->SetAtomicNum(atoi(str.c_str()));
    //set type
    ttab.SetToType("INT"); ttab.Translate(str,vs[1]); 
    atom->SetType(str);
  }

  char bobuf[100];
  string bostr;
  int bgn,end,order;

  for (i = 0; i < nbonds; i++)
  {
    if (!ifs.getline(buffer,BUFF_SIZE)) return(false);
    sscanf(buffer,"%*d%d%d%s",&bgn,&end,bobuf);
    bostr = bobuf; order = 1;
    if      (bostr == "DOUBLE")   order = 2;
    else if (bostr == "TRIPLE")   order = 3;
    else if (bostr == "AROMATIC") order = 5;
    mol.AddBond(bgn,end,order);
  }

  mol.SetTitle(title);
  return(true);
}

bool ReadXYZ(istream &ifs,OBMol &mol,const char *title)
{
  char buffer[BUFF_SIZE];

  // Read the first line, which should contain the number of atoms in
  // the molecule.
  if (!ifs.getline(buffer,BUFF_SIZE)) {
    cerr << "WARNING: Problems reading an XYZ file, method 'bool ReadXYZ(istream &,OBMol &,const char *)'" << endl
	 << "  Could not read the first line, file error." << endl;
    return(false);
  }
  unsigned int natoms;	// [ejk] assumed natoms could not be -ve
  if (sscanf(buffer,"%d", &natoms) == 0) {
    cerr << "WARNING: Problems reading an XYZ file, method 'bool ReadXYZ(istream &,OBMol &,const char *)'" << endl
	 << "  Problems reading the first line. The first line must contain the number of atoms." << endl
	 << "  OpenBabel found the line '" << buffer << "'" << endl
	 << "  which could not be interpreted as a number." << endl;
    return(false);
  }
  if (!natoms) {
    cerr << "WARNING: Problems reading an XYZ file, method 'bool ReadXYZ(istream &,OBMol &,const char *)'" << endl
	 << "  Problems reading the first line. The first line must contain the number of atoms." << endl
	 << "  OpenBabel found the number '0' which obviously does not work." << endl;
    return(false);
  }
  mol.ReserveAtoms(natoms);
  
  // The next line contains a title string for the molecule. Use this
  // as the title for the molecule if the line is not
  // empty. Otherwise, use the title given by the calling function.
  if (!ifs.getline(buffer,BUFF_SIZE)) {
    cerr << "WARNING: Problems reading an XYZ file, method 'bool ReadXYZ(istream &,OBMol &,const char *)'" << endl
	 << "  Could not read the second line, file error." << endl;
    return(false);
  }
  if (strlen(buffer) == 0)
    mol.SetTitle(buffer);
  else
    mol.SetTitle(title);
  
  // The next lines contain four items each, separated by white
  // spaces: the atom type, and the coordinates of the atom
  vector<string> vs;
  for (unsigned int i = 1; i <= natoms; i ++) {
    if (!ifs.getline(buffer,BUFF_SIZE)) {
      cerr << "WARNING: Problems reading an XYZ file, method 'bool ReadXYZ(istream &,OBMol &,const char *)'" << endl
	   << "  Could not read line #" << i+2 << ", file error." << endl
	   << "  According to line one, there should be " << natoms << " atoms, and therefore " << natoms+2 << " lines in the file" << endl;
      return(false);
    }
    tokenize(vs,buffer);
    if (vs.size() != 4) {
      cerr << "WARNING: Problems reading an XYZ file, method 'bool ReadXYZ(istream &,OBMol &,const char *)'" << endl
	   << "  Could not read line #" << i+2 << "." << endl
	   << "  OpenBabel found the line '" << buffer << "'" << endl
	   << "  According to the specifications, this line should contain exactly 4 entries, separated by white space." << endl
	   << "  However, OpenBabel found " << vs.size() << " items." << endl;
      return(false);
    }
    
    // Atom Type: get the atomic number from the element table, using
    // the first entry in the currently read line. If the entry makes
    // sense, set the atomic number and leave the atomic type open
    // (the type is then later faulted in when atom->GetType() is
    // called). If the entry does not make sense to use, set the atom
    // type manually, assuming that the author of the xyz-file had
    // something "special" in mind.
    OBAtom *atom  = mol.NewAtom();
    int atomicNum = etab.GetAtomicNum(vs[0].c_str());
    atom->SetAtomicNum(etab.GetAtomicNum(vs[0].c_str())); //set atomic number, or '0' if the atom type is not recognized
    if (atomicNum == 0)
      atom->SetType(vs[0]);

    // Read the atom coordinates
    char *endptr;
    double x = strtod((char*)vs[1].c_str(),&endptr);
    if (endptr == (char*)vs[1].c_str()) {
      cerr << "WARNING: Problems reading an XYZ file, method 'bool ReadXYZ(istream &,OBMol &,const char *)'" << endl
	   << "  Could not read line #" << i+2 << "." << endl
	   << "  OpenBabel found the line '" << buffer << "'" << endl
	   << "  According to the specifications, this line should contain exactly 4 entries, separated by white space." << endl
	   << "  Item #0: Atom Type, Items #1-#3 cartesian coordinates in Angstrom." << endl
	   << "  OpenBabel could not interpret item #1 as a number." << endl;
      return(false);
    }
    double y = strtod((char*)vs[2].c_str(),&endptr);
    if (endptr == (char*)vs[2].c_str()) {
      cerr << "WARNING: Problems reading an XYZ file, method 'bool ReadXYZ(istream &,OBMol &,const char *)'" << endl
	   << "  Could not read line #" << i+2 << "." << endl
	   << "  OpenBabel found the line '" << buffer << "'" << endl
	   << "  According to the specifications, this line should contain exactly 4 entries, separated by white space." << endl
	   << "  Item #0: Atom Type, Items #1-#3 cartesian coordinates in Angstrom." << endl
	   << "  OpenBabel could not interpret item #2 as a number." << endl;
      return(false);
    }
    double z = strtod((char*)vs[3].c_str(),&endptr);
    if (endptr == (char*)vs[3].c_str()) {
      cerr << "WARNING: Problems reading an XYZ file, method 'bool ReadXYZ(istream &,OBMol &,const char *)'" << endl
	   << "  Could not read line #" << i+2 << "." << endl
	   << "  OpenBabel found the line '" << buffer << "'" << endl
//.........这里部分代码省略.........

  bool CHEM3D1Format::ReadChem3d(istream &ifs,OBMol &mol,bool mmads,const char *type_key)
  {
    char buffer[BUFF_SIZE];
    int natoms,i;
    char tmp[16],tmp1[16];
    char atomic_type[16];
    double exponent = 0.0;
    double divisor = 1.0;
    double Alpha,Beta,Gamma,A,B,C;
    bool has_fractional = false, has_divisor = false;
    matrix3x3 m;

    vector<string> vs;
    ifs.getline(buffer,BUFF_SIZE);
    tokenize(vs,buffer);

    if (mmads)
      {
        if (vs.empty())
          return(false);
        natoms = atoi((char*)vs[0].c_str());
        if (vs.size() == 2)
          mol.SetTitle(vs[1]);
      }
    else
      {
        switch(vs.size())
          {
          case 7 :
            sscanf(buffer,"%d%lf%lf%lf%lf%lf%lf",
                   &natoms,&Alpha,&Beta,&Gamma,&A,&B,&C);
            m.FillOrth(Alpha,Beta,Gamma,A,B,C);
            has_fractional = true;
            break;
          case 8 :
            sscanf(buffer,"%d%lf%lf%lf%lf%lf%lf%lf",
                   &natoms,&Alpha,&Beta,&Gamma,&A,&B,&C,&exponent);
            m.FillOrth(Alpha,Beta,Gamma,A,B,C);
            has_fractional = true;
            has_divisor = true;
            break;
          default :
            sscanf(buffer,"%d",&natoms);
            break;
          }
      }

    if (!natoms)
      return(false);
    divisor = pow(10.0,exponent);
    mol.ReserveAtoms(natoms);

    ttab.SetToType("INT");
    ttab.SetFromType(type_key);

    OBAtom *atom;
    double x,y,z;
    vector3 v;

    unsigned int k;
    for (i = 1; i <= natoms; i++)
      {
        ifs.getline(buffer,BUFF_SIZE);
        sscanf(buffer,"%15s%*d%lf%lf%lf%15s",
               atomic_type,
               &x,
               &y,
               &z,
               tmp);
        v.Set(x,y,z);
        if (has_fractional)
          v *= m;
        if (has_divisor)
          v/= divisor;

        tokenize(vs,buffer);
        if (vs.empty())
          return(false);

        atom = mol.NewAtom();
        ttab.Translate(tmp1,tmp);
        atom->SetType(tmp1);
        atom->SetVector(v);
        atom->SetAtomicNum(etab.GetAtomicNum(atomic_type));

        for (k = 6;k < vs.size(); k++)
          mol.AddBond(atom->GetIdx(),atoi((char*)vs[k].c_str()),1);
      }

    // clean out remaining blank lines
    while(ifs.peek() != EOF && ifs.good() &&
          (ifs.peek() == '\n' || ifs.peek() == '\r'))
      ifs.getline(buffer,BUFF_SIZE);

    mol.PerceiveBondOrders();

    return(true);
  }