extraBonds MarvinSketch parameter

I had the following line in my MarvinSketch invocation:

    msketch_param('extraBonds', 

            among([appletName, 'targetapplet', 'queryapplet', 

                    'synthAuthApplet', 'evalApplet'])

                ? 'wedge,either,coordinate,arom,any,aromany,1or2,ctu'

                : 'wedge,either,arom,coordinate');

and I was also using a configuration file that omitted any mention of bond types.  In MarvinSketch 5.11, all of the bond types were displaying.  

I added these lines to the configuration file:

<remove path="menubar/bond-menu/boldBond"/>

<remove path="menubar/bond-menu/hashedBond"/>

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

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

<remove path="menubar/bond-menu/bond-type-menu/sep-1"/>

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

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

<remove path="menubar/bond-menu/bond-type-menu/sep-2"/>

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

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

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

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

<remove path="menubar/bond-menu/bond-type-menu/sep-3"/>

<remove path="popup/bond/boldBond"/>

<remove path="popup/bond/hashedBond"/>

<remove path="popup/bond/bond-topology-menu"/>

<remove path="popup/bond/bond-reacting-center-menu"/>

<remove path="popup/bond/bondStereoSearch"/>

<remove path="popup/bond/bond-sep-2"/>

<remove path="popup/bond/bond-type-menu/bondType.aromatic"/>

<remove path="popup/bond/bond-type-menu/sep-1"/>

<remove path="popup/bond/bond-type-menu/bondType.cisOrTrans"/>

<remove path="popup/bond/bond-type-menu/bondType.cisOrTransOrUnspec"/>

<remove path="popup/bond/bond-type-menu/sep-2"/>

<remove path="popup/bond/bond-type-menu/bondType.singleOrDouble"/>

<remove path="popup/bond/bond-type-menu/bondType.singleOrAromatic"/>

<remove path="popup/bond/bond-type-menu/bondType.doubleOrAromatic"/>

<remove path="popup/bond/bond-type-menu/bondType.any"/>

<remove path="popup/bond/bond-type-menu/sep-3"/>

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

Now the unwanted bond types don't display.  So I'm wondering, is the extraBonds parameter ineffective when a configuration file is specified?

Dear Bob!

   Unfortunatelly these solutions do not do the same. The extra bond prorety hides all bonds, and shows the listed ones. If you remove a bond type with the customisation xml, you can not enable it. We will think about a better solution for you to solve this bond question.

Regards:
Balázs 

I still don't understand.  What is the difference between omitting a bond from the extraBonds property (causing it to be hidden) and using a configuration file to remove the bond from the menu bar and the contextual menu?

The differenece is like covering a cup on the table and throwing a cup into the dustbin. If you remove the sheet from parts of the table some cup will be visible, but the dusbin and its content will not.

As I've said we have to find a better solution for you...

I still don't understand.  Let me try again.  I can use a configuration file to create a toolbar that does not have a button for the bond in question.  I can also use the configuration file to prevent a user from accessing the query bond from the atom popup menu or the menu bar.  

If I omit a query bond from the extraBonds parameter, does Marvin remove that bond from:

• the menu bar?  


• the atom popup menu?  


• a toolbar that, without the extraBonds parameter, would normally show that button?  


• the bond selection button?

Dear Bob!

The extraBonds property was not working correctly in the recent releases, it is fixed by now, and it will be working again in the next major release (Marvin 6.1).  

Also, if you omit a query bond from the extraBonds parameter, it simply disables that action (well, it disables those actions which are not listed), so it won't be accessible. Removing it from the configuration by remove path, then it won't appear on that part of the gui (eg. removing it from menu path then it won't be in the menu).

Regards:
Tamás