bugGChemPaint - Bugs: bug #21112, .CDX files open but structures...

 
 

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bug #21112: .CDX files open but structures disoriented and text deleted

Submitted by:  Takashi Suyama <tak1150>
Submitted on:  Tue 18 Sep 2007 04:33:17 PM UTC  
 
Category: NoneSeverity: 1 - Wish
Item Group: NoneStatus: Fixed
Privacy: PublicAssigned to: Jean Bréfort <jean_brefort>
Open/Closed: Closed

(Jump to the original submission Jump to the original submission)

Sat 08 Nov 2008 10:35:49 AM UTC, comment #16:

closed after 0.10.0 release.

Jean Bréfort <jean_brefort>
Project AdministratorIn charge of this item.
Tue 29 Jul 2008 02:35:19 PM UTC, comment #15:

For the essential, this bug seems fixed in svn trunk version. Things are not absolutely perfect, but good enough for 0.10 and the samples attached to this bug. I consider it fixed and I'll close it after 0.10.0 release.

If other files fail to open correctly with the development branch, please file as many bugs reports as necessary.

(file #16209)

Jean Bréfort <jean_brefort>
Project AdministratorIn charge of this item.
Mon 28 Apr 2008 07:58:15 AM UTC, comment #14:

The current screenshot shows that things now mostly work. I'll not close this bug because it is not perfect yet and some chemistry is still lost.
I think that cdx export will not be possible for 0.10 because of time constraints unless the release waits until 2009. cdxml export will still use the openbabel version with much data loss.

(file #15536)

Jean Bréfort <jean_brefort>
Project AdministratorIn charge of this item.
Sat 23 Feb 2008 09:46:31 PM UTC, comment #13:

I am so sorry for not getting back to you sooner. Thank you, Jean, for your patience and your work.

Here are the samples:

Hope they help!

(file #15100)

Takashi Suyama <tak1150>
Mon 18 Feb 2008 08:43:52 PM UTC, comment #12:

As can be seen in the screenshot, the new cdx plugin code is already somewhat better than the previous openbabel based one. At the moment, all fragments are replaced by a carbon atom as can be seen, for example, in the second molecule where OBn is missing. This is my priority at the moment, but it is all but simple.
Next, I'll have to address text decorations and alignment.
The two reaction schemes are not still perceived as such, because GChemPaint support is not yet sufficient, and because there is no pagination either, so that, if I tried to make them reactions in GChempaint, they would end on one very large line, clearly inappropriate.
So even if things are in progress, we are still far from perfection.
I'm still interested by the samples I asked in comment #11.

(file #15072)

Jean Bréfort <jean_brefort>
Project AdministratorIn charge of this item.
Sun 30 Dec 2007 10:14:01 AM UTC, comment #11:

I'd like to have the same samples but in cdxml format if possible to be certain that it will work too, also a sample with a chemical nick (as Ph-Cl) or so would be useful (in oth format).
Current state is a correct loading of simple structures with no stereochemical bonds and basic text (no rich text) import. No export yet.

Jean Bréfort <jean_brefort>
Project AdministratorIn charge of this item.
Wed 28 Nov 2007 05:04:12 PM UTC, comment #10:

Thanks. We evacuated to be cautious, but our neighborhood was completely intact.

Let me know if you need any more ChemDraw files.

Takashi Suyama <tak1150>
Wed 07 Nov 2007 08:48:54 AM UTC, comment #9:

Thanks for the samples. I hope fires had only minor consequences for you.

Jean Bréfort <jean_brefort>
Project AdministratorIn charge of this item.
Tue 06 Nov 2007 05:27:20 PM UTC, comment #8:

Sorry it's been taking so long.
I've been busy trying to catch up after the San Diego fires (in California, USA, which is where I live).
I made ChemDraw files and PNG files of what the CD files should look like. Hope this helps. If you want more complicated examples, let me know. Thanks.

Tak

(file #14330)

Takashi Suyama <tak1150>
Sun 28 Oct 2007 02:07:45 PM UTC, comment #7:

Yes, I can help with that for sure. I'll be on it later this afternoon or tomorrow. Thank you for your work!

Takashi Suyama <tak1150>
Sun 28 Oct 2007 08:41:55 AM UTC, comment #6:

In the end the issue is more critical than I initially thought. May be Openbabel is just inappropriate to import cdx or cdxml files in GChemPaint. I proposed a first patch to the openbabel-devel list adne I'm waiting for comments, but, most probably, I'll have to write a direct import/export procedure.
You might help by providing little sample files illustrating only a few features at once, hopefully in both formats and with an associated screenshot.

Jean Bréfort <jean_brefort>
Project AdministratorIn charge of this item.
Fri 21 Sep 2007 10:14:01 AM UTC, comment #5:

The triple -> quadruple bond issue is an OpenBabel issue too (fixed in svn, both trunk ans 2.1 branch).

Jean Bréfort <jean_brefort>
Project AdministratorIn charge of this item.
Thu 20 Sep 2007 12:45:03 PM UTC, comment #4:

Partly understand what happens: only molecules are imported, so reaction arrows and text are discarded; abbreviations are replaced at some point (not in gchempaint) by a semi-developed formula (the case for Bn, Tf, TMSO,...), but the new atoms are put sometimes at silly places. If this is fixable, it is at the OpenBabel level (I partly maintain the cdk format plugin there).
I do not understand at the moment how we end with quadruple bonds instead of triple.
Seems this bug will remain opened for a long time. The attached sample is a very interesting use case. I diminish the severity to wish, as it concerns essentially missing features.

Jean Bréfort <jean_brefort>
Project AdministratorIn charge of this item.
Tue 18 Sep 2007 05:45:01 PM UTC, comment #3:

Thanks. I'll first fix the molecules issue, then see how it is possible to load the reactions too, but this will need enhancements in gchempaint (no support for multi steps reactions, planned for 0.10) and a large change in OpenBabel.

Jean Bréfort <jean_brefort>
Project AdministratorIn charge of this item.
Tue 18 Sep 2007 05:19:14 PM UTC, comment #2:

Here is the screenshot in WinXP

(file #13983)

Takashi Suyama <tak1150>
Tue 18 Sep 2007 05:04:18 PM UTC, comment #1:

Thanks for reporting. Do you have access to chemdraw ? If so, please attach a screenshot of that file. I'm not sure it is a gchempaint or an openbabel bug (or both). Anyway, I'll manage to fix it.

Jean Bréfort <jean_brefort>
Project AdministratorIn charge of this item.
Tue 18 Sep 2007 04:33:17 PM UTC, original submission:

Hi Jean,

Thank you for 0.8.3! It fixed all the problems mentioned earlier. It opens .gchempaint files perfectly.
It does not open .cdx (chemdraw) files correctly though. The structures look like they've been shaken in a bag and the texts are gone. I vaguely remember that you mentioned that installing the latest openbabel may solve the problem?

I have uninstalled everything and recompiled openbabel 2.1.1, goffice 0.4.3, etc. I still have this problem.

sample .cdx file attached

Thank you!

Takashi Suyama <tak1150>

 

Attached Files
file #16209:  dhoya.png added by jean_brefort (70KiB - image/png - new and final screenshot)
file #15536:  dhoya-synthesis.png added by jean_brefort (123KiB - image/png - update screenshot)
file #15100:  chemdraw-samples.tar.gz added by tak1150 (1KiB - application/x-gzip)
file #14330:  chemdraw_samples.tar.gz added by tak1150 (32KiB - application/x-gzip)
file #13983:  DHOYA-synthesis.PNG added by tak1150 (113KiB - image/png)
file #13979:  DHOYA-synthesis.cdx added by tak1150 (35KiB - chemical/x-cdx)

 

Depends on the following items: None found

Items that depend on this one: None found

 

Carbon-Copy List
  • -unavailable- added by jean_brefort (Posted a comment)
  • -unavailable- added by tak1150 (Submitted the item)
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    Follow 14 latest changes.

    Date Changed By Updated Field Previous Value => Replaced By
    Sat 08 Nov 2008 10:35:49 AM UTCjean_brefortOpen/ClosedOpen=>Closed
    Tue 29 Jul 2008 02:35:19 PM UTCjean_brefortAttached File-=>Added dhoya.png, #16209
      StatusIn Progress=>Fixed
    Mon 28 Apr 2008 07:58:15 AM UTCjean_brefortAttached File-=>Added dhoya-synthesis.png, #15536
    Mon 28 Apr 2008 07:53:36 AM UTCjean_brefortAttached File#15072=>Removed
    Tue 18 Mar 2008 11:28:24 AM UTCjean_brefortStatusConfirmed=>In Progress
    Sat 23 Feb 2008 09:46:31 PM UTCtak1150Attached File-=>Added chemdraw-samples.tar.gz, #15100
    Mon 18 Feb 2008 08:43:52 PM UTCjean_brefortAttached File-=>Added dhoya.png, #15072
    Tue 06 Nov 2007 05:27:20 PM UTCtak1150Attached File-=>Added chemdraw_samples.tar.gz, #14330
    Thu 20 Sep 2007 12:45:03 PM UTCjean_brefortSeverity3 - Normal=>1 - Wish
    Tue 18 Sep 2007 05:19:14 PM UTCtak1150Attached File-=>Added DHOYA-synthesis.PNG, #13983
    Tue 18 Sep 2007 05:04:18 PM UTCjean_brefortStatusNone=>Confirmed
      Assigned toNone=>jean_brefort
    Tue 18 Sep 2007 04:33:17 PM UTCtak1150Attached File-=>Added DHOYA-synthesis.cdx, #13979

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