Hi,
I have the following question about processing SMILES format structures +
2D Generation + serialization in Mol format. I am using CDK 1.5.8.
My goal is to process an structure in SMILES format, generate 2D
coordinates and save it as in Mol format. The problem where I am stuck is
that the input SMILES has the no stereochemistry defined, but the final mol
output _has_ the stereochemestry defined.
Following I have prepared a simple example to describe my problem:
The input structure is the following one:
ON=CC1=CC=C(O)C=C1
The structure is read and parsed using the following code (snippet):
[...]
IAtomContainer iAtomContainer = null;
final SmilesParser smilesParser = new
SmilesParser(DefaultChemObjectBuilder.getInstance());
iAtomContainer = smilesParser.parseSmiles(molecule);
[...]
then the 2D coordinates are generated.
[...]
sdg.setMolecule(iAtomContainer, true);
sdg.generateCoordinates();
iAtomContainerWCoordinates = sdg.getMolecule();
[...]
and finally the 'IAtomContainer' object is serialized as 'mol' file,
producing the following output:
CDK 0116150922
10 10 0 0 0 0 0 0 0 0999 V2000
3.9132 3.7394 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
2.6112 2.9947 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
2.6051 1.4947 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.3030 0.7500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.3030 -0.7500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0280 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.3220 -0.7500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.6148 -1.5107 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
-1.3220 0.7500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0280 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
2 3 2 0 0 0 0
3 4 1 0 0 0 0
4 5 2 0 0 0 0
5 6 1 0 0 0 0
6 7 2 0 0 0 0
7 8 1 0 0 0 0
7 9 1 0 0 0 0
9 10 2 0 0 0 0
4 10 1 0 0 0 0
M END
If you render the structure before (SMILES) and after (MOL) the process, it
is possible to watch how initially the double bond between N and C has not
the stereo defined, but at the end of the process is arbitrarily defined
(E). I have also attached two snapshots two further describe this
(SMILES_before.png) and (MOL_after.png).
Why is this happening ? Is there any way to control, and keep the flag of
stereochemistry not defined during the transformation from SMILES to MOL?
(I would like that the two depictions produce the same image)
Thanks in advance
Oscar
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