[Cdk-devel] HINReader error

[Yap C. W. <ph...@nu...>]

Dear Rajarshi and Egon,

One of my collaborators is having trouble reading hyperchem files (HIN files) with CDK. As I was tracing through the code, I noticed that the code to identify aromatic atoms and bonds in the HINReader.java may not be correct. I have modified it as shown below (lines which were changed were highlighted in red). I am not sure whether this modification is correct but it is working for me so far.

Best regards,
Chun Wei

                          case 'a':
                                bo = IBond.Order.SINGLE;
                                atom.setFlag(CDKConstants.ISAROMATIC, true);
                                break;
                        }
                        List<Object> ar = new ArrayList<Object>(3);
                        ar.add(atomSerial);
                        ar.add(s);
                        ar.add(bo);
                        cons.add( ar );
                    }
                    m.addAtom(atom);
                    atomSerial++;
                    line = input.readLine();
                }

                // now just store all the bonds we have
                for (List<Object> ar : cons) {
                    IAtom s = m.getAtom((Integer) ar.get(0));
                    IAtom e = m.getAtom((Integer) ar.get(1));
                    IBond.Order bo = (IBond.Order) ar.get(2);
                    if (!isConnected(m, s, e))
                    {
                        IBond newBond = null;
                        if (s.getFlag(CDKConstants.ISAROMATIC) || e.getFlag(CDKConstants.ISAROMATIC))
                        {
                            newBond = file.getBuilder().newInstance(IBond.class,s, e, bo);
                            newBond.setFlag(CDKConstants.ISAROMATIC, true);
                        }
                        else
                        {
                            newBond = file.getBuilder().newInstance(IBond.class,s, e, bo);
                        }
                        m.addBond(newBond);
                    }
                }