export with chiral frag in SDF

export to SDF with 'chiral frag'





Hello All,





I would like to export to SDF with 'chiral flag'.





I inserted following "mrv" structure into table:

Code:

strmol = MSketchPane.getMol("mrv"); UpdateHandler.setStructure(strmol); ... ===== strmol value ===== Start >> <?xml version="1.0" ?> <MDocument atomSetRGB="0:N,1:#ff0000" bondSetRGB="0:N">   <MChemicalStruct>     <molecule title="test" molID="m1">       <atomArray>         <atom id="a1" elementType="O"               x2="1.592771417695844" y2="1.157216172347424" />         <atom id="a2" elementType="N"               x2="1.5927714176958458" y2="-0.3827838276525757" />         <atom id="a3" elementType="C" mrvSetSeq="1"               x2="0.12814438260130956" y2="-0.8586699989899964" />         <atom id="a4" elementType="C"               x2="-0.7770449059290998" y2="0.38721617234742167" />         <atom id="a5" elementType="C"               x2="0.1281443826013069" y2="1.6331023436848406" />         <atom id="a6" elementType="N"               x2="-2.317044905929099" y2="0.38721617234742123" />         <atom id="a7" elementType="O"               x2="-0.3477417887361067" y2="-2.3232970340845327" />       </atomArray>       <bondArray>         <bond atomRefs2="a3 a4" order="1" />         <bond atomRefs2="a4 a5" order="1" />         <bond atomRefs2="a5 a1" order="1" />         <bond atomRefs2="a1 a2" order="1" />         <bond atomRefs2="a4 a6" order="1">           <bondStereo>H</bondStereo>         </bond>         <bond atomRefs2="a2 a3" order="1" />         <bond atomRefs2="a3 a7" order="2" />       </bondArray>     </molecule>   </MChemicalStruct> </MDocument> << End ===== strmol value =====

and exported.





However, exported SDF's chiral flag is false.





Export code:

Code:

Exporter.setFormat(Exporter.SDFILE); Exporter.writeNext(); ===== sdf ===== Start >> test   Marvin  01290718002D            6  5  0  0  0  0            999 V2000             ~~~    -2.8750    1.3125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0    -2.1605    1.7250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0    -3.5895    1.7250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0    -2.8750    0.4875    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0    -2.1605    0.0750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0    -3.5895    0.0750    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0   1  2  2  0  0  0  0   1  3  1  0  0  0  0   1  4  1  0  0  0  0   4  5  1  0  0  0  0   4  6  1  1  0  0  0 M  END $$$$ << End ===== sdf =====

Can structures export to SDF with chiral frag, using JChem?

Hi Chiaki,





It seems to me that chiral flag in your source mrv file is not set, accordingly your imported file will neither contain that setting.


If you import a structure with JChem Manager, you have an option to check "set chiral flags for MDL formats", but it works only with MDL format. See this link: http://www.chemaxon.com/jchem/doc/admin/index.html#import





We suggest you might use our standardizer tool after export to set the chiral flag in your compound. You can make a new configuration, with "absolute stereo" action. (I have attached a sample configuration file.) You can find more information in this site: http://www.chemaxon.com/jchem/doc/user/StandardizerConfiguration.html#config


(Look the 10th item <Absolute stereo> below Configuration XML section)





Best regards,


Edvard

Hello, and thank you for your comment.





I got an idea from your sample, and solved my question.





I set the absolute stereo before insert method.

Code:

mol.setAbsStereo(true);

Best regards,


Chiaki