"Structure can not be converted to smiles/cxsmiles ...&

Importing the structure below with JChemManager 3.0.8 I got the message "structure can not ne converted to smiles/cxsmiles Use the smarts or cxsmiles format".








Marvin 02280513442D





6 4 0 0 0 0 999 V2000


-0.3164 0.0417 0.0000 N 0 3 0 0 0 0 0 0 0 0 0 0


-0.9033 0.6327 0.0000 R# 0 0 0 0 0 0 0 0 0 0 0 0


-1.1156 -0.1665 0.0000 R# 0 0 0 0 0 0 0 0 0 0 0 0


-0.3205 -0.7785 0.0000 R# 0 0 0 0 0 0 0 0 0 0 0 0


0.4663 0.2997 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0


2.1771 -0.0167 0.0000 Cl 0 5 0 0 0 0 0 0 0 0 0 0


2 1 1 0 0 0 0


3 1 1 0 0 0 0


4 1 1 0 0 0 0


5 1 1 0 0 0 0


M CHG 2 1 1 6 -1


M RGP 3 2 1 3 1 4 1


M END


$$$$





How can this structure be imported with JChemManager ?





Thank you





ps : the smile of this structure was C[N+]([R1])([R1])[R1] with JCHEM 2.1

Please send the structure using the Code tag, because the spaces have been lost.


BBCode details

please find enclosed an sdf file

The SMILES code generated using using JChem 2.1 was not correct. R1 R2, ... have different meanings in SMARTS and shouldn't be used in SMILES at all. We are working on the representation of structures with R-groups using the cxsmiles/cxsmarts formats. This will be available in the upcoming major version. Sorry about the difficulty.

OK thank you Ferenc,





Have you got an idea of when you plan to deliver the next major version ? will this version correct the problem with resin-like molecules and pseudo types atoms registration as well ?





Pierre-Olivier

It is very difficult to estimate the date of the next major release, because we have a tough technical issue (about converting some components to ActiveX).


I hope it will happen before May, but this can be very optimistic. Yes, the resin issue will also be solved in that release.

OK thank you

Hi,





Actually, structures containing R1, R2 ... atoms (like your adogen.sdf) will import fine in our next bugfix release (3.0.9).


We expect to release this version in 1-2 days.





Since we do not have support for this in the cxsmiles format yet, the cd_smiles column will be NULL for these structures.


It means, that if there are many structures like this, the search process will be slower.


Later, when upgrading to the next major version (3.1), the NULL values in the cd_smiles column will be replaced by the appropriate values.





Szilard