MSketch.getMol does not return smiles of structure with list

User 173254b396

21-12-2006 11:59:54

Hi,

It seems that the MSketch.getMol does not return smiles if the structure contains list of atoms. It returns marvin (mrv) ok. I have tried with version 4.0.4 and 4.1.4.

Take care, Péter

ChemAxon 7c2d26e5cf

21-12-2006 12:17:13

I am not chemist but as I know SMILES format does not support atom lists.

http://www.chemaxon.com/marvin/doc/user/smiles-doc.html

Andris, please correct me if I mistake.

User 173254b396

21-12-2006 12:22:31

It makes a nice smiles when I use copy as smiles. I am not sure it is a standard smiles but you can paste it back to marvin and get the same structure.

Péter

ChemAxon 7c2d26e5cf

21-12-2006 12:34:28

Actually, "Copy as SMILES" does not copy always SMILES to the clipboard. If the structure is not exportable as SMILES (e.g. includes atom lists), Marvin chooses a SMILES like format which can describe the structure (SMARTS, cxsmiles, cxsmarts).

ChemAxon 25dcd765a3

21-12-2006 18:28:25

Hi Peter,

You can use SMARTS in this case. It has the same compact form as SMILES, but it can handle query fetures also.

You can use the following as a rule of thumb: use SMILES for molecules and use SMARTS for queries.

Andras

User 173254b396

22-12-2006 08:08:24

Tamás, András,

You are right. What I got with copy as smiles was actually smarts. So, I am going to use smarts.

Thanks, Péter

ChemAxon 43e6884a7a

22-12-2006 11:32:58

Péter,

If you have query substructures then generate SMARTS using the Edit > Source menu option.

Please note that in some cases the SMILES and SMARTS strings are different for the same drawing.