Does Marvin contain preset variable queries?

Hi,





Does MarvinSketch 5.1 contain any preset lists of variables, such as 'any heterocycle', 'any carbocycle', 'all alkyl groups', etc? We have a client that normally uses STN, which does offer such preset lists. I realize you can specify lists of atoms for a particular position on a ring, but this client would ideally like to be able to insert a preset variable list (something more specific than 'any hetero atom').





Thanks,





Nicko

Hi Nicko,





No, unfortunately this feature is currently not available in Marvin and JChem the same way as in STN. Instead, there are a number of query features that are relevant here:


- Ring atom query property (R) http://www.chemaxon.com/jchem/doc/user/query_features.html#atprop


- R-group queries http://www.chemaxon.com/jchem/doc/user/query_special_types.html#rgroupquery


etc.





See the above links to relevant parts of the JChem Query Guide for more details, or the whole guide for a general overview:


http://www.chemaxon.com/jchem/doc/user/Query.html





However, we are working on the handling of these generic groups as part of our Markush project. (We usually refer to them as homology variation.)





With release 5.2 (due within a few months), we will be able to enumerate and register Markush structures containing homology variation atoms. The support for homology atoms in queries will be solved in a later version.





In 5.2, we will represent these homology atoms as pseudo atoms in Marvin. (Marvin Sketch: "More" or "Periodic System" window > "Query" tab > Pseudo button, with "alkyl", "aryl", "heteroaryl" etc. values in the text box below.)





Let us know if you have any further questions.





Regards,


Szabolcs

Hi Szabolcs,





Thanks for the quick response, and for the links. I have seen the R-Group drawing instructions in the Marvin Help Guide. Is there a similar guide that describes an easy, reasonably intuitive way for a MarvinSketch user to refine their query using Atom Properties? The link you sent to the JChem help file seemed more like instructions for someone using the JChem API.





Thanks,





Nicko

Well, the JChem Query Guide tries to cater for end-users also, but you are right that it does not contain instructions about MarvinSketch query drawing features.





There is some limited material about query drawing in Marvin Sketch help:


http://www.chemaxon.com/marvin/help/sketch/gui/dialogs.html#periodic


http://www.chemaxon.com/marvin/help/sketch/sketch-chem.html#query-guide





But we will improve these in the 5.2 release.





Best regards,


Szabolcs

Hi,





Users of SureChem only have access to MarvinSketch - we don't expose any JChem functionality to them - so I'm looking for search methods that are exposed in the Marvin UI.





So with that in mind, how can I draw a query structure that contains a heterocyclic ring of any size, with any number of hetero atoms, which can be monocyclic or fused, and saturatred or unsaturated?





Thanks,





Nicko

Hi Nicko,


First, please note that Marvin is only the sketcher, and the search engine must support the particular query features to be used and translate them to results. So anything I suggest here is also dependent on the search engine at the back-end.


I am not aware of any method that currently easily describes this query in a simple way, but it can be done by list logic:


For example, let's assume that you want to realize the following substructure search: (see first attached picture, heterocycle_query).

1. Do a substructure search for the specific parts plus any ring (Any atom and R query atom property - meaning: "part of ring" - see query_R below.)


2. Then search with all-carbon rings (variable size ring with a link node) - the kind of rings we want to avoid - see query_carbocycle


3. Then take the difference of the two result sets.