User 6f58eb8616
30-07-2009 09:09:45
JChem Version: 5.1.3_2
Environment: WinXP
Problem: I have a SMILES which I would expect to not match a particluar SMARTS but instead I am getting a hit. I would expect the non-aromatic C in the SMARTS to prevent the match. Is there something I have missed?
Eg:
Molecule target = MolImporter.importMol("c1c(O)ccc1=O","smiles");
Molecule smartsFilter;
smartsFilter = MolImporter.importMol("[OH]-a~a~C=[OX1]", "smarts");
MolSearch ms = new MolSearch();
ms.setTarget(target);
ms.setQuery(smartsFilter);
hits = ms.findAll();
ChemAxon 42004978e8
30-07-2009 14:43:46
Hi,
There is a bug regarding the SMARTS import of such inputs. The atom
with the double bond connecting to an oxigen is not ensured to be
aliphatic.
If the structure is opened by marvin sketch then it's apparent that
this atom doesn't have aliphatic query property. Until the bug is fixed
as a work-around you can import the query from mrv format and there you
can specify the problematic carbon atom to be aliphatic.
My colleague responsible for smarts import will handle this bug.
Thanks for reporting it,
Regards,
Robert
User 6f58eb8616
31-07-2009 18:14:36
Thanks for looking into this.
Best wishes
Derek
ChemAxon 25dcd765a3
11-08-2009 11:51:16
Hi,
I have corrected the bug.
Thank you for the report.
Marvin 5.2.5 will contain the fix.
Andras