Unable to change the bond type menu appearance

User 8c948fd5ba

10-04-2013 16:36:14

So I'm attempting to alter the bond type menu options in 5.12.1 so that certain bond types are not present.  I understand that changes to the gui are done via xml first and then js/applet params second.  That being said, I'm not able to produce any kind of change on this specific sub-menu through either means.  


Lines in the xml file such as 



<remove path="menubar/bond-menu/bond-type-menu/bondType.coord"/>



seem to do nothing, even though manipulating other areas of the gui through xml still works (IE the xml template is being loaded properly).  The "extraBonds" param, which from my understanding of the documentation should remove all bond types (or some leave the user with some default subset) seems to have no effect regardless of what it is set to (empty sting, "arom", "single_bond, arom", etc). I'm doing this via a param tag as the applet is being loaded in via an applet tag rather than through the js loader (<param name="extraBonds" value="arom,wedge,any">).


As I mentioned earlier, I am able to fully control the appearance of the applet via both of these means (xml & params) in every aspect EXCEPT on this bond-type-menu. Is there something specific that needs to happen for this menu to be customized?

ChemAxon 2c555f5717

11-04-2013 12:40:48

Dear Chess!


   Have you use dour customisation tools (View > Customize... menu) to generate that xml? Are you sure that xml is correct? Can you sand me your file to let me check it? Now I have used the menu and I got this result:


<?xml version="1.0" encoding="UTF-8"?>
<customization active="default">
<scheme id="default">
<remove path="menubar/bond-menu/bond-type-menu/sep-3"/>
<remove path="menubar/bond-menu/bond-type-menu/bondType.coord"/>
<modify path="toolbar/atoms" row="0"/>
<modify path="toolbar/tools" row="0"/>
<modify path="toolbar/templates" row="0"/>
<modify path="toolbar/chemical" row="0"/>
<modify path="toolbar/markush" row="0"/>
<modify path="toolbar/mytemplates" row="0"/>
<modify path="toolbar/general" row="0"/>
<modify path="toolbar/edit3D" row="0"/>
</scheme>
</customization>


This seams to work.  Even after I have removed the unnecessarry rows:



<?xml version="1.0" encoding="UTF-8"?>
<customization active="default">
<scheme id="default">
<remove path="menubar/bond-menu/bond-type-menu/bondType.coord"/>
</scheme>
</customization>


I have also attached the file. I hope, I could help. If you have any further questions, please do not hesitate to ask!


Regards:
Balázs 

User 8c948fd5ba

11-04-2013 14:02:44

Balázs, I did use the MarvinSketch customization tools to generate that xml. I tried your xml file but it didn't seem to have an effect. To make sure I'm not missing anything, here are the steps I followed to customize the bond type menu:


 


1.) Deleted ~/.chemaxon/5.12.1/customization.xml 


2.) Opened and closed MarvinSketch 5.12.1 to generate a fresh customization.xml


3.) Opened MarvinSketch 5.12.1 and was presented with attached image "1 Fresh config.png"


4.) Clicked on View -> Customize… 


5.) Clicked on the Popups tab and selected Bond | Type (attached image "2 Modify Screen.png")


6.) Deleted an entry by clicking on it, clicking Modify, and clicking Delete (attached image "3 Deleting entry.png")


7.) Repeated step 6 for Double C/T or Unspec, Single or Double, Single or Aromatic, Double or Aromatic, Coordinate, and the last separator (attached image "4 Final Menu Contents.png")


8.) Clicked OK


9.) Expanded the Bond Popup (attached image "5 End Result.png")


 


I can follow the above steps to remove other GUI elements, such as buttons from the edit popup, but I can't seem to get it to work for the bond types. I have attached the XML file that was generated from the above steps in the following post (I hit the 5 attachment limit). 


 


Thanks!

User 8c948fd5ba

11-04-2013 14:03:41

Attached is the generated XML from the previous post

ChemAxon 2c555f5717

11-04-2013 14:08:01

Dear Chess!


   You can edit Bond menu, but you can not edit Bond button group. Button groups are not editable at all. 


Regards:
Balázs 

ChemAxon 2c555f5717

11-04-2013 14:09:36

p.s.: There are some feature request to make Bond button group to be editable. This question is not decied by the management yet.

User 8c948fd5ba

11-04-2013 14:23:30

Alright, so I'm confused then because this functionality exists in 5.3.8.  Maybe theres a misunderstanding about what I'm asking for?  I've attached some screenshots of the custom menu from 5.3.8, as well as a clear screenshot of what should not be present. This is being done via the extraBonds parameter (A param which is documented in your documentation specifically as a way to modify the bond types that show up).  Has the functionality of this param changed? 

ChemAxon 2c555f5717

11-04-2013 16:02:32

Thank you! You have reported a bug that we have to handle. We will contact you if we know anything else.

ChemAxon 4fa3cf533c

22-04-2013 09:35:07

Dear Chess!

The extraBonds param was indeed broken, it has been fixed, and the fix will be in the next major release (Marvin 6.1). Thanks again for reporting this issue. 


Regards:
Tamás