"Some features of cannot be converted to smiles" problem

User abedee28b0

23-07-2014 08:12:55

I've recently discovered several chemical using  chemaxon.formats.MolExporter , chemaxon.reaction.Reactor class. but library throw exception .


I think that my smiles has error. above my smiles .  



[#6:3][C:2](=[O:1])[Cs]>>[O:6][C:4](=[O:5])[C:3][C:2]([#1,#6:8])=[O:1] 



 


I want to modify my smile.


help me please. 


 


java source :


Reactor reactor = new Reactor();


reactor.setReaction(MolImporter.importMol(smiles));  // my smiles string set 


reactor.setReactant(reactant); 


Molecule[] products;


while ((products = reactor.react()) != null) {


     for (Molecule product : products) {


         String productSmiles = MolExporter.exportToFormat(product , "smiles");  //this line throw exception 


     }


 }


AND exception message :


 



Some features of OCCC(C(O)=O)C([#1,#6])=O cannot be converted to smiles. Use the cxsmiles, smarts or cxsmarts format. 


Some features of OC(=O)CC(C(O)=O)C([#1,#6])=O cannot be converted to smiles. Use the cxsmiles, smarts or cxsmarts format.


ChemAxon e08c317633

23-07-2014 08:36:04

Your reaction scheme is incorrect: it adds a list atom to the product, so it will create a query molecule as product. Molecules with query features (like list atoms) cannot be exported to SMILES, because SMILES format does not support query features. 


Fix: replace the list atom on the right side of your reaction scheme with a normal atom.