Hi Jean-Marc,
if the molecules you are writing contain properties, those should be written
out as molecular properties lines.
The respective code in the CDK SDFWriter looks like
// write the properties
Map<Object,Object> sdFields = container.getProperties();
if(sdFields != null){
for (Object propKey : sdFields.keySet()) {
if (!isCDKInternalProperty(propKey)) {
writer.write("> <" + propKey + ">");
writer.newLine();
writer.write("" + sdFields.get(propKey));
writer.newLine();
writer.newLine();
You can set those properties with
public void setProperty(Object description, Object property);
Let me know if that helps?
Kind regards,
Chris
--
Dr. Christoph Steinbeck
Head of Cheminformatics and Metabolism
European Bioinformatics Institute (EBI)
Wellcome Trust Genome Campus
Hinxton, Cambridge CB10 1SD UK
Phone +44 1223 49 2640
What is man but that lofty spirit - that sense of enterprise.
... Kirk, "I, Mudd," stardate 4513.3..
On 12 Mar 2012, at 15:40, Jean-Marc Nuzillard wrote:
> Dear CDK users,
>
> I would like to know which is the way to append molecular property lines to
> molecules in SD files.
> There is an old post on this list, dated 2006, about this topic.
> I guess the procedure has changed since then.
> I have not seen setSdFields() as a MDLWriter method in the CDK documentation.
>
> Best regards,
>
>
> Dr. Jean-Marc Nuzillard
> Institute of Molecular Chemistry
> CNRS UMR 7312
> Moulin de la Housse
> CPCBAI, Bâtiment 18
> BP 1039
> 51687 REIMS Cedex 2
> France
>
> Tel : 33 3 26 91 82 10
> Fax :33 3 26 91 31 66
> http://www.univ-reims.fr/ICMR
>
> http://www.univ-reims.fr/LSD/
> http://www.univ-reims.fr/LSD/JmnSoft/
>
>
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