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
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