Adding a selected_atoms field in an sdf export

Marvin sketch provides a very nice way to select a group of atoms in a molecule.

I would like to export that selection of atoms as an sdf field selected_atoms on sdf export.

Is there anyway to achieve this?

Many thanks,

Mike

Hi Mike,

No, it is not possible to save the selection to any file format, and it is presently not among our plans to implement such a feature. Why would this be important for you?

Best regards,

Akos

Thanks Akos,

An example might be where I have a molecule that has a group or scaffold that I wish to replace - so to identify bioisosteres. A number of programs exist such as Newlead, MOE, Biosolve's LeadIT, Cresset that require a selection of atoms to be made. I recognise that we can grab these atom numbers through the java API but I would prefer trying to standardise this as an sdf using selected_atoms. This would make it easier for workflow tools to pass the information.

A second example might be where I am trying to improve my pharmacophore model by defining a feature dictionary definition. So for example I have a set of active ligands the all contain quinoline. Instead of defining the quinoline as a 2 aromatic rings + an acceptor then just to add/define the quinoline as a single feature in the pharmacophore dictionary. For complex systems it is easier to do this graphically using msketch.

A third example might be where I have ligand docked in a protein - I want to design off a particular region of the ligand. How can I tell the de novo design program where to substitute/design off? Again I think a solution could be to use msketch with a selected_atoms field export.

All three examples demonstrate how I want to use msketch as the starting point in my workflow but require further information to pass to the programs that are executed later.

Regards,

Mike

Hi Mike,

Thanks for the examples; now I understand that it would be a nice feature if someone wants to process the structures later based on the selections. I register this feature request.

Ho do you want to get the info in the corresponding SDF field? Is it OK as a simple list of the atom numbers?

Best regards,

Akos

Akos,

a simple comma separated list would be fine.

I'm suprised that no one has asked for similar in the past and also whether there are other fields that may be of use to write out? For example if I calculate LogP then a new window is generated with the result. I have to wirte that down. But maybe it's an idea to store the result and be able to write it to the sdf too? I'm just wondering if there is a generic approach possible - but perhaps that is more for you guys to think about.

Many thanks,

Mike 

Mike,

Actually, it is just the selection which is not solved to be saved to SDF yet. Caculated properties can be saved to SDFile using cxcalc:

http://www.chemaxon.com/marvin/help/applications/calc.html:

Or you can use InstantJChem or JChem for XL.

Best regards,

Akos

Hi,

I have registered the feature request to save the selection to file. Presently it is scheduled to version 5.5. Actually, Marvin will save this info into the molecule field in MOLFiles, because this is how we can maintain the conversion between the different file formats (MRV, SKC, CDX, etc.). Since it is not supported by the original CTFile format, we will solve it using data sgroup. Is it enough for you in case of SDFiles as well, or you need an option to save the info to a separate data field?

Best regards,

Akos