Rgroup definition with Mouse operation

Hi,


I got a question regarding R group definition. Suppose you draw three fragments and try to define them as R1. It seems that the only way is to select fragments and type R1 from keyboard. So my question is


1. Can I difine them through mouse operation? The reason is that I can not input R1 from keyboard if I create a new default MSketchPane() and add into my application, however if I start marvin sketch from executable, input from keyboard is aceepted.


2. Do I MISS some parameters when I create new MSketchPane?





Thanks a lot,


Hongzhou

You can define R-groups with mouse by the following way.


1. Select the fragments (substituents) for the R-group.


2. Press the "More" button on the toolbar to open the "More" window.


3. Choose an R-group ID (from R1 to R32) in the "More" window.


The selected substituents will be the definition of the chosen R-group.


4. Create attachment points by clicking at atoms in the substituents.


Alternatively, you can use shortcuts: type R1 (R2, R3, ...) instead of using the More window.





Movie: http://www.chemaxon.com/demosite/jchem_base/structure_search/jchem_base_r_groups/R-group.html





If you would like to use shortcuts in your application embedding MSketchPane, you should add a new keylistener to pass key events of the frame (in which MSketchPane is) to Marvin.

Code:

MSketchPane sketchPane = new MSketchPane(); frame.setContentPane(sketchPane); // Keyboard events are received by the JFrame but processed by the bean frame.addKeyListener(sketchPane);

See the SketchCustomized example in the Marvin Beans package:


http://www.chemaxon.com/marvin/examples/sketch-customized/SketchCustomized.java.txt

We can define R group attach point by clicking More panel and then select R1 or R2. Since we use this function very often, so can we move R1, R2 ..buttons to the main toolbar area?





Thanks a lot for your help,


Hongzhou

In the current Marvin, you can not move R1, R2 buttons to the toolbar.


But we will implement this feature.

I have to correct myself. There is a way in the current Marvin to put R1, R2 buttons to the toolbar. You should collect R-groups in an a extra templates file and specify "xtmpls" parameter: http://www.chemaxon.com/marvin/doc/dev/sketchman.html#parameters.xtmpls





In the following example, a new MSketchPane initialized and placed into a frame. The "xtmpls" parameter was specified (that contains R-groups), the canvas color was set. Then, a keylistener was added to the frame to pass its key events to Marvin.

Code:

JFrame frame = ... MSketchPane sketchPane = new MSketchPane(); sketchPane.setParams("xtmpls=rgroups.sdf\n"); sketchPane.setMolbg(new Color(0xffffcc)); frame.setContentPane(sketchPane); frame.addKeyListener(sketchPane);

Thanks Tamas:





When I add the rgroups.sdf into code as provided, it keep conplaining url is malformed. It seems that I have to put this sdf file into webserver and specify it in url format


sketcher.setParams("xtmpls=http://localhost:8080/axis/rgroups.sdf") to make it work.





Another question is how can I adjust size of this button? I like R1 have the same size as the element C, H, O, but what I got is like benzene size and R1 filling all the space of the button. Can I do some customization?





Thank you very much

Quote:

Another question is how can I adjust size of this button? I like R1 have the same size as the element C, H, O, but what I got is like benzene size and R1 filling all the space of the button. Can I do some customization?

In the current Marvin you can not customize buttons size.

We plan to rewrite the toolbar of the sketcher. The new toolbar will be customizable. Propably, it will solve your problem.


The toolbar rewriting is a big work and I can not promise to do this in the near future.

You can define R-groups with mouse by the following way.


1. Select the fragments (substituents) for the R-group.


(...)


Alternatively, you can use shortcuts: type R1 (R2, R3, ...) instead of using the More window.


---------------------





When I use the shortcuts I am able to enter Rn up to R9, an attempt to enter R10 or higher results in R1. I do not see a way how to enter two-digit number. When pressing "R" and "1" the action is completed already. Version in use: MarvinSketch 3.5.1

Dear Jiri,





This bug has been fixed in our development version. In the next minor release of Marvin (4.0.4) this will work.





Best regards,





Szabolcs

I understood that Rgroup numbers can be selected in the range R1-R32. However, I found that MarvinSketch (3.5.1) is capable to display Rgroup definitions in the range R1-R63 correctly, R64 being displayed as R0, R65 as R1 etc. The R group itself, as attached to the core, is limited to the range R1-R32. Any way how to expand this definition as well ?

We already extended the range, R0-R32767 will work correctly in the next major release, Marvin 4.1.

cspeter wrote:

We already extended the range, R0-R32767 will work correctly in the next major release, Marvin 4.1.

Thanks for fast reply. When do you expect the release ?

In a few weeks, hopefully.

Hello Jiri,





If you urgently need this feature, a recent alpha release of Marvin can be downloaded here:





http://www.chemaxon.com/shared/alpha/marvin/download.html





Best regards,


Szabolcs

Szabolcs wrote:

Hello Jiri, (...)a recent alpha release of Marvin can be downloaded Best regards, Szabolcs

THX

About year ago, you said about rewriting toolbar section, such that we can customize the size of R1, R2. Did you put it in your schedule? Just checking.





Thanks

I hope, it will be ready in Marvin 4.2.