To show the aromatic bond, you have to modify 2
classes :
AtomContainer
public void addBond(int atom1, int atom2, double order,
int stereo) {
Bond bond = new Bond(getAtomAt(atom1),
getAtomAt(atom2), order, stereo);
if (contains(bond)) { return; } if (bondCount >= bonds.length) { growBondArray(); } addBond(bond);
}
MDLReader in method readMolecule() in the last for loop
if (stereo == 1) {
// MDL up bond
stereo = CDKConstants.STEREO_BOND_UP;
}
else if (stereo == 6) {
// MDL down bond
stereo =
CDKConstants.STEREO_BOND_DOWN;
}
// added hvanderz
if (order == 4)
molecule.addBond(atom1 - 1, atom2 - 1,
CDKConstants.BONDORDER_AROMATIC, stereo);
else
molecule.addBond(atom1 - 1, atom2 - 1, order,
stereo);
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Bug is fixed: the current CVS version no longer has this
problem.