bugGnome Chemistry Utils - Bugs: bug #26810, GDashed chiral bond oriented in...

 
 

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bug #26810: GDashed chiral bond oriented in one side

Submitted by:  Stefano <ntropia>
Submitted on:  Mon 15 Jun 2009 06:48:10 PM UTC  
 
Category: NoneSeverity: 3 - Normal
Item Group: NoneStatus: Fixed
Privacy: PublicAssigned to: None
Open/Closed: Closed

Tue 05 Jan 2010 09:53:07 AM UTC, comment #5:

Closed after 0.11.4 release.

Jean Bréfort <jean_brefort>
Project Administrator
Tue 22 Sep 2009 08:36:16 AM UTC, comment #4:

Fixed in the 0.12 branch. An option has been added in the preferences dialog to change GChemPaint default behavior (which does not change since I persist to consider that having the large side farest is contrary to intuition and all rules of perspective).

Jean Bréfort <jean_brefort>
Project Administrator
Mon 15 Jun 2009 09:26:00 PM UTC, comment #3:

I can see your point, but this is what I would expect (maybe because is how is already implemented in all the commercial drawing tools):

-a new bond is usually schetcked by clicking to the attach point (i.e. a corner of a cycle)
-the user point of view should be the one coded into the convention of the dashed/filled lines in chemistry: plane of view == the molecular plane (i.e. the one in which the aforementioned cycle lies).
-the bond should be oriented basing on both these assumptions: the selected chirality (over/below the plane) starts from the selected point.

As an example, you could look at the cholesterol molecule as from Wikipedia: http://en.wikipedia.org/wiki/File:Cholesterol.svg

In the current implementation, the dashed bond is (as far as I know) the only one that must be schetcked from the end to the start to obtain the right orientation. That's not user-friendly, for me.

Stefano <ntropia>
Mon 15 Jun 2009 09:12:38 PM UTC, comment #2:

The dashed bonds are oriented the way I use them. I feel that it is more ligical to have the wide end near the observer, even this is not the usual convention.
I intend to add an option to allow the opposite convention (it is planned, but for now the main work is to reimplement everything using a new canvas).
If you click on an already drawn bond when the appropriate tool is active, the bond ends are exchanged, so you can already invert them, but it is not secure since exported files will end with a wrong stereochemistry.

Jean Bréfort <jean_brefort>
Project Administrator
Mon 15 Jun 2009 06:54:47 PM UTC, comment #1:

Unfortunately it got submitted before I completed it.

The quick fix for this is to orient the dashed as the filled one, because the user tend to click on the atom from which the bond will spread (then the filled orientation is correct).

The true feature, on the other hand, would be having the chiral bonds should orientable in both directions, maybe drawing on them a second time to invert them.

Stefano <ntropia>
Mon 15 Jun 2009 06:48:10 PM UTC, original submission:

The dashed chiral bond (forth bond on the toolbar) is oriented in the opposite side than the filled chiral bond.
Both should be orientable (maye

Stefano <ntropia>

 

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Items that depend on this one: None found

 

Carbon-Copy List
  • -unavailable- added by ntropia (Submitted the item)
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    Follow 3 latest changes.

    Date Changed By Updated Field Previous Value => Replaced By
    Tue 05 Jan 2010 09:53:07 AM UTCjean_brefortOpen/ClosedOpen=>Closed
    Tue 22 Sep 2009 08:36:16 AM UTCjean_brefortStatusConfirmed=>Fixed
    Mon 15 Jun 2009 09:12:38 PM UTCjean_brefortStatusNone=>Confirmed

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