Standardizer Clear Stereo / Clear Isotope

Hi,





I trying to use Standardizer with the "Clean Stereo" option and it works fine for Standard Smiles, but it does not remove the additional features when I use extended smiles, i.e.

Code:

MolImporter importer = new MolImporter();    Molecule mol = importer.importMol("N[C@H](O)CCCCCC1CC[C@H](O)[C@@H]1O |a:1|");    Standardizer standardizer = new Standardizer("clearstereo");    standardizer.standardize(mol);        System.out.println("mol = " + mol.toFormat("cxsmiles"));    System.out.println("mol = " + mol.toFormat("cxsmarts"));

Ouput is


mol = NC(O)CCCCCC1CCC(O)C1O |a:1|


mol = [#7]C(O)CCCCCC1CCC(O)C1O |a:1|





Is this expected or is this a problem?


Can I use another way to get a Smiles without stereochemistry ? I have used the Smiles (non-stereo) in Marvin, is there an equivalent with the API?





Can I also suggest a "Clear Isotopes" option for Standardizer ?





Thanks in advance for your help


Catherine

Hi,

ctravers wrote:

Hi, I trying to use Standardizer with the "Clean Stereo" option and it works fine for Standard Smiles, but it does not remove the additional features when I use extended smiles, i.e. Code: MolImporter importer = new MolImporter();    Molecule mol = importer.importMol("N[C@H](O)CCCCCC1CC[C@H](O)[C@@H]1O |a:1|");    Standardizer standardizer = new Standardizer("clearstereo");    standardizer.standardize(mol);        System.out.println("mol = " + mol.toFormat("cxsmiles"));    System.out.println("mol = " + mol.toFormat("cxsmarts")); Ouput is mol = NC(O)CCCCCC1CCC(O)C1O |a:1| mol = [#7]C(O)CCCCCC1CCC(O)C1O |a:1| Is this expected or is this a problem? Can I use another way to get a Smiles without stereochemistry ? I have used the Smiles (non-stereo) in Marvin, is there an equivalent with the API?

This is a problem (a bug). The "clearstereo" action in Standardizer does not removes enhanced stereo information. The fix of this bug will be available in the next JChem version (JChem 3.2.4).





Till then:





I have added a few lines to your code (attached) that will remove all enhanced stereo information. After this information is removed, the molecule can be exported to SMILES format (SMILES does not support enhanced stereo information representation - see documentation).





Output of the attached code example:

Code:

$ java ClearStereoInformationTest smiles: NC(O)CCCCCC1CCC(O)C1O cxsmiles NC(O)CCCCCC1CCC(O)C1O cxsmarts [#7]C(O)CCCCCC1CCC(O)C1O

Quote:

Can I also suggest a "Clear Isotopes" option for Standardizer ?

It's already on the requested features list, but now it gets higher priority :)





Best regards,


Zsolt

Thanks for your help. That's very useful.


Catherine