Mol Importer

Hello





I am using MolImporter to import an SD file, which contains chiral flags.


The molecule contain many stereocenters.





I would like to convert the molecule to extended Smiles with absolute on all chiral centers.





Is there a way to make all the chiral centers absolute in the Molecule, by using a flag in MolImporter or molecule.exportToFormat("cxsmiles")





Thanks


Catherine

Dear Catherine,





If the molecule has chiral flag, then all the stereocenters have absolute stereoconfiguration.


( http://www.chemaxon.com/jchem/doc/user/query_stereochemistry.html MDL old stereo representation (chiral flag))





Moreover if you export it to extended SMILES all chiral centers will have also absolute stereoconfiguration.


( http://www.chemaxon.com/marvin/help/formats/cxsmiles-doc.html )





So this is the default behavior.





Andras

Hi





I am using version 5.1.1.


I have attached my example file and the code I am using

Code:

fis = new FileInputStream(file);             mi = new MolImporter(fis);             while ((mol = mi.read()) != null) {                 System.out.println(mol.toFormat("smiles"));                 System.out.println(mol.toFormat("mol"));                 System.out.println(mol.toFormat("cxsmiles"));              }

The output to the console is as follow

Code:

C[C@@H]1CCCN1   Marvin  11140815272D            6  6  0  0  1  0            999 V2000    -0.5334   -2.0959    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0     0.2916   -2.0959    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0     0.5484   -1.3117    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0    -0.1209   -0.8250    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0    -0.7859   -1.3117    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0    -0.1292    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0   2  3  1  0  0  0  0   3  4  1  0  0  0  0   4  5  1  0  0  0  0   5  1  1  0  0  0  0   1  2  1  0  0  0  0   4  6  1  1  0  0  0 M  END C[C@@H]1CCCN1

The chiral flag is set in the SD file but the Absolute flag is not set in the Extended Smiles as I expected.





What else can I do ?





Thanks


Catherine

Dear Catherine,





From our extended SMILES documentation:

Quote:

The absolute stereoconfiguration is the default, which is not marked. (Absolute stereoconfiguration known also as "Chiral flag" in MDL molfiles. )

http://www.chemaxon.com/marvin/help/formats/cxsmiles-doc.html





So

Quote:

C[C@@H]1CCCN1

means absolute stereoconfiguration.





I hope this is what you wanted.





Andras