Beispiel #1
0
  void OBBond::SetLength(double length)
  {
    OBAtom *atom1 = GetBeginAtom();
    OBAtom *atom2 = GetEndAtom();

    //split the length difference in half, and modify the bond twice
    double firstLength = length + ((GetLength() - length) / 2);

    SetLength(atom1, firstLength);
    SetLength(atom2, length);
  }
Beispiel #2
0
  double OBBond::GetLength() const
  {
    double	d2;
    const OBAtom *begin, *end;
    begin = GetBeginAtom();
    end = GetEndAtom();

    d2 = SQUARE(begin->GetX() - end->GetX());
    d2 += SQUARE(begin->GetY() - end->GetY());
    d2 += SQUARE(begin->GetZ() - end->GetZ());

    return(sqrt(d2));
  }
Beispiel #3
0
  double OBBond::GetEquibLength() const
  {
    const OBAtom *begin, *end;

    begin = GetBeginAtom();
    end = GetEndAtom();
    double length = CorrectedBondRad(begin->GetAtomicNum(), begin->GetHyb())
                  + CorrectedBondRad(end->GetAtomicNum(), end->GetHyb());

    if (IsAromatic())
      return length * 0.93;
    
    switch (_order) {
    case 3:
      return length * 0.87;
    case 2:
      return length * 0.91;
    }
    return length;
  }
Beispiel #4
0
  double OBBond::GetEquibLength() const
  {
    double length;
    const OBAtom *begin, *end;
    // CorrectedBondRad will always return a # now
    //  if (!CorrectedBondRad(GetBeginAtom(),rad1)) return(0.0);
    //  if (!CorrectedBondRad(GetEndAtom(),rad2))   return(0.0);

    begin = GetBeginAtom();
    end = GetEndAtom();
    length = etab.CorrectedBondRad(begin->GetAtomicNum(), begin->GetHyb())
      + etab.CorrectedBondRad(end->GetAtomicNum(), end->GetHyb());

    if (IsAromatic())
      length *= 0.93;
    else if (GetBO() == 2)
      length *= 0.91;
    else if (GetBO() == 3)
      length *= 0.87;
    return(length);
  }