Save disconnected molecules separately in MarvinSketch

Hi -





Is there a way to save multiple molecules drawn on the same page in MarvinSketch as separate molecules in any format?  (SDF is preferred but MRV is fine.)  This is the standard functionality of ChemDraw when saving as SDF.





As an example, in the attached image I would like the three fragments in the window to be saved as 3 separate molecules not as one large molecule.  To test, my preference (or option) would be opening the MRV or SDF from MarvinSketch in MarvinView would give three separate entries not one entry with an image contain the 3 fragments.








To get around the fact that MarvinSketch saves everything as one molecule with disconnected pieces, I have to feed the open thru OpenBabel and use the "Output disconnected fragments separately" functionality.








Any help would be appreciated.





Thanks.





David

Hi David,





Sorry for the delayed answer.











Unfortunately, this is not currently possible in MarvinSketch. We do have Java methods to break a molecule into its separate fragments, but it is not accessible from MarvinSketch GUI.








We will consider this feature for future development. Thank you for drawing our attention to it.








Best regards,





Szabolcs

If the Java methods are available (which I assumed because the calculators can treat the individual pieces as fragments) does that mean it would be possible for me to write a plugin that uses them to save files the way I would like?





I have started looking into creating my own plugins and am comfortable enough to try something like this unless you expect to be able to offer this option in the 5.2 release this quarter?








Thanks.





David

Hi David,





some of my colleagues are on holiday now, they will answer when they are back next week.





Kind regards,


Judit

Hi David,





5.2 is going to be released in a week, so we have no time to implement this feature. In addition, I cannot promise it to happen very soon either. The other way round (to import the separate structure records in an SDFile to the same canvas) is already under development, and scheduled to be available in 5.2.1, but the export will come only later.





Thank you for your understanding.








Best regards,





Akos

Hi David,





I forget to answer the section related to the creation of a calculator plugin doing this job. As far as I know it is possible: you probably need to create a plugin which brings up a MarvinView where the fragments are in different cells, and then you can save it to any multimolecular format.





Alternatively, if it is not important to have this functionality form the MarvinSketch GUI, in 5.2 there will be a new Chemical Terms function named "fragments()" will be available, which returns the fragments of a molecule as separate molecules.








Best regards,





Akos

Hi Akos -





Thanks.  I appreciate that you can't get this functionality into a short term release.





I will look into the new chemical terms feature because that should do what I need.  However,  not having to leave the GUI would be preferential so I may try to implement it as a GUI plugin anyway.





David

Hi David,





If you have any difficulties when creating the plugin, just drop a message here, and our expert will help you.





Best regards,





Akos

Has any further consideration been given to this feature?  It would still be useful to me to be able to draw multiple molecules and have them save as separate disconnected molecules in the output file.

 

Thanks.

David

Hi,

Unfortunately, we still had no capacity for this. On the other hand, it is a useful feature, so we will take it into account when planning version 5.4.

Best regards,

Akos

akospapp wrote:

Hi, Unfortunately, we still had no capacity for this. On the other hand, it is a useful feature, so we will take it into account when planning version 5.4. Best regards, Akos

Hi,

 

We have now version 5.8. Is it now possible to save disconected molecules as separated entries in sdf or mrv?

Best regards,

Ania

Sorry. We are planning to implement it in the version 5.10.

Maybe you could add a getFragments() method to chemaxon.marvin.beans.MarvinPane so that it can be called by Javascript?

Hi Bob,

yes we can do this, but what should this method return to the javascript side? The source with multiple molecules crated from fragments in a given format can be suitable for you?

Regards,
Istvan

I would return an array of Strings containing the MRV for each individual molecule.

All right, that's fine for us. I have added this request to the issue in our issue tracker, and they will be developed together for 5.10 then.