bugGChemPaint - Bugs: bug #21728, R Group not recognised

 
 

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bug #21728: R Group not recognised

Submitted by:  Steve Hughes <huggies15>
Submitted on:  Wed 05 Dec 2007 03:36:30 PM UTC  
 
Category: NoneSeverity: 1 - Wish
Item Group: NoneStatus: Fixed
Privacy: PublicAssigned to: Jean Bréfort <jean_brefort>
Open/Closed: Closed

Sat 08 Nov 2008 10:35:20 AM UTC, comment #3:

clsed after 0.10.0 release.

Jean Bréfort <jean_brefort>
Project AdministratorIn charge of this item.
Mon 21 Apr 2008 08:19:50 AM UTC, comment #2:

I now consider it's mostly working in 0.9.x. Just needs some testing. Marked as fixed, and will be closed after first 0.10 beta release.

Jean Bréfort <jean_brefort>
Project AdministratorIn charge of this item.
Wed 05 Dec 2007 03:54:46 PM UTC, comment #1:

Hi, generic symbols are not possible in gchempaint-0.8.x, but will be implemented in 0.10.x, although it might possible in some cases, as OR. It's not that simple because gchempaint try to check the content of any string you type with the CH2 tool. 0.8.x is happy only if it finds the atom to which a bond can be added, and does not parse the remaining symbols. 0.10.x will parse the whole string and accepts nicks as Ph, Et, and so on, and also generic ones, as R and X (I need to add M) which might be expanded to their default value (methyl for R, Cl for X). At the moment, it is possible to define the nicknames, in 0.9, but not to use them. There is some code in gchemcalc, but it is blocking on ambiguous symbols as Pr and Ac. Seems the solution is to guess the connectivity to decide which is the meaning of these symbols. Note that once we have the connectivity, it becomes possible to build a 3D structure.
All that code is just not trivial, that's why it is not implemented yet.
Both standard and user defined symbols will be supported.

Jean Bréfort <jean_brefort>
Project AdministratorIn charge of this item.
Wed 05 Dec 2007 03:36:30 PM UTC, original submission:

Hi, thanks for sorting out so many problems, but having been using this for sometime now i find a few things are still a bit 'dodgy'.
these include opening gchempaint files, but i see there is a bug report ope for that already, the other is there is no option of adding generic symbals to chemicals.
i find i often need to add R (generic side chain), X (halide), or M (metal) symbals eg M(CO)6 where M=Mn,Ru etc etc, but there is no support for such an option and i keep having to blag my way through such problems.
is there any chance of adding these in, i imagine its a simple thing to do, but i dont know much about programming :)

nice work tho!
Steve Hughes

Steve Hughes <huggies15>

 

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Carbon-Copy List
  • -unavailable- added by jean_brefort (Posted a comment)
  • -unavailable- added by huggies15 (Submitted the item)
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    Follow 6 latest changes.

    Date Changed By Updated Field Previous Value => Replaced By
    Sat 08 Nov 2008 10:35:20 AM UTCjean_brefortOpen/ClosedOpen=>Closed
    Mon 21 Apr 2008 08:19:50 AM UTCjean_brefortStatusIn Progress=>Fixed
    Tue 18 Mar 2008 11:28:05 AM UTCjean_brefortStatusConfirmed=>In Progress
    Wed 05 Dec 2007 03:54:46 PM UTCjean_brefortSeverity3 - Normal=>1 - Wish
      StatusNone=>Confirmed
      Assigned toNone=>jean_brefort

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