MarvinSketch 10.3 and 10.4 "Copy as Smiles" problem

At least for MarvinSketch 10.3 and 10.4 (and maybe others), there is a problem copying as SMILES. If a structure has an element of SMARTS (say, a bond specified In Chain), the smiles (smarts) string is not copied at all.

I don't remember this being an issue before.

Thank you for reporting this issue. We are investigate it.

Best Regards,

Efi

Unfortunately, you cannot copy a structure containing SMARTS elements in SMILES, because SMILES is not able to handle these elements. We are planning to include SMARTS among the available formats of the "Edit>Copy As…” menu in a future version of Marvin.
However, you can copy in SMARTS if you choose the "Edit>Source" menu. In the "Source" window use the "View" menu and choose "SMARTS".

Could you please write the version number of Marvin in which you were able to do "Copy As SMILES" with a structure containing SMARTS elements?

Best regards,

Dora

Hmmm. Guess I'm wrong about being about to copy as SMARTS.

Thanks for the tip about how to actually do it. I do strongly suggest you add this to the Edit menu.

Hi,

can you tell me where do you would like to paste the copied smarts just to make sure that the feature could work properly with the target applications? Do you want to use the Chemaxon extension for the smarts format also?

Regards,
Istvan

Istvan

A typical use case would be to craft the query in Sketch and then copy into a .sma (text) file.

I see, in this case, this will be possible to implement it easily, and I think this new feature can be part of the 5.12 release. The SMARTS and CxSMARTS format will be accessible on the Copy as dialog.

Thank you for the suggestion.

Regards,
Istvan

Hi,

I can tell this for sure now, the SMARTS format will be included as a format available on the Copy as dialog in the 5.12 version.

We will send you a notification here if we have the first public beta build, if you would like to try or check it before the final release.

Regards,
Istvan