[Joelib-devel] convert() method (org.openscience.cdk.libio.joelib.Convertor)

[<nic...@sy...>]

Hi Egon, Hi Joerg,

	I have parsed a smile string, C(=N)C(=O)C, into a CDK molecule. All
was ok until I used the convert method to obtains a JOEMol object. This is
the result I found:

  -ISIS-            3D
Used JOELib chemistry kernel (expert systems) ID is 715333816
  5  4  0  0  0  0  0  0  0  0  1 V2000
    0.0000    0.0000    0.0000 Xx  0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 Xx  0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 Xx  0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 Xx  0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 Xx  0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  1  3  1  0  0  0  0
  3  4  2  0  0  0  0
  3  5  1  0  0  0  0
M  END
$$$$

As you could see, the convert method forget the atoms symbol. On the other
hand, if H atoms are present in the molecule, they are well deferred.

	I have a second question concerning the numbering of atoms; if you
asked for the getAtomNumber() method in CDK, it gives you a different number
than the getIdx() method from JOELib. So I have supposed that they were not
correlated. But, If you want to keep in memory the position of one atome in
CDK molecule, how could I retrieved this in my new JOEMol ?

Thanks for your help,
Nico