From: <no...@so...> - 2002-10-09 12:08:15
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Bugs item #620731, was opened at 2002-10-09 12:08 You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=120024&aid=620731&group_id=20024 Category: None Group: None Status: Open Resolution: None Priority: 5 Submitted By: Hans Vanderzijl (hansvdz) Assigned to: Nobody/Anonymous (nobody) Summary: addBond() should have double bond order Initial Comment: 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); ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=120024&aid=620731&group_id=20024 |