Hi,
is there a way to keep the annotations for stereoisomerism when printing
SMILES with CDK1.4?
Example is below.
Thanks,
Martin
String smiles = "C[C@@]1(F)[C@H](O)[C@H](O[C@H]1n1ccc(=O)[nH]c1=O)C=O";
IAtomContainer compound = new
SmilesParser(SilentChemObjectBuilder.getInstance()).parseSmiles(smiles);
SmilesGenerator smilesGenerator = new SmilesGenerator();
smilesGenerator.setUseAromaticityFlag(true);
System.out.println(smilesGenerator.createSMILES(compound));
StructureDiagramGenerator sdg = new StructureDiagramGenerator();
sdg.setMolecule((IMolecule) compound);
sdg.generateCoordinates();
compound = sdg.getMolecule();
boolean b[] = new boolean[compound.getBondCount()];
for (int i = 0; i < b.length; i++)
b[i] = true;
System.out.println(smilesGenerator.createChiralSMILES(compound, b));
Output is:
[H]C2(OC([H])(N1CCC(=O)NC1(=O))C(F)(C)C2([H])(O))(C=O)
[H]C2(OC([H])(N1CCC(=O)NC1(=O))C(F)(C)C2([H])(O))(C=O)
--
Dipl-Inf. Martin Gütlein
Phone:
+49 (0)6131 39 23336 (office)
+49 (0)177 623 9499 (mobile)
Email:
[email protected]
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