[Joelib-devel] Convert() & PseudoAtoms in Smiles

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

Hi all,

	I have two questions concerning the convert() method in JOELib in
order to transform a CDK molecule in a JOEMol molecule:

Convertor conv = new Convertor();
JOEMol joemol = conv.convert(CDKmolecule);

When I try to do this, my resulting molecule contains bonds but not the
atoms:

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

instead of:

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

This second output result from a CDKmolecule to smile conversion first, and
then, a smile To JOEmol conversion.

An other problem is about the pseudoAtom R: When I try to parse this smile:
[*]CO, I have the following error:

[*]CO
14:03:55 [ERROR] joelib.molecule.JOEMol   - _mod is negative - EndModify()
called too many times
SMILES entry "[*]CO" could not be loaded.

	Thanks,

best regards,
Nico