bugGChemPaint - Bugs: bug #50190, cdx(ml) files not rendered...

 
 

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bug #50190: cdx(ml) files not rendered correctly

Submitted by:  Bernd Speiser <berndspeiser>
Submitted on:  Mon 30 Jan 2017 09:56:00 PM UTC  
 
Category: NoneSeverity: 3 - Normal
Item Group: NoneStatus: Fixed
Privacy: PublicAssigned to: Jean Bréfort <jean_brefort>
Open/Closed: Closed

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

Mon 06 Feb 2017 05:26:42 PM UTC, comment #13:

all right, works OK now on a fresh source tree.
Thank you!

Bernd Speiser <berndspeiser>
Mon 06 Feb 2017 12:35:27 PM UTC, comment #12:

Oops, the patch contained twice the changes, my bad.

(file #39679)

Jean Bréfort <jean_brefort>
Project AdministratorIn charge of this item.
Mon 06 Feb 2017 11:36:00 AM UTC, comment #11:

Actually, I used a fresh download of 0.14.16 (gnome-chemistry-utils-0.14.16.tar.bz2) and only applied 50190-1.patch.
Then patches were correctly reported for several files (more than for the previous patch, i.e. 50190.patch) and, during the same run, then the messages appeared.
I can try tonight with another installation that has the first patch (50190.patch) already applied.

Bernd Speiser <berndspeiser>
Mon 06 Feb 2017 10:50:58 AM UTC, comment #10:

You probably applied both patches, the second one includes the first, that's why patch finds some parts have already been applied.

Jean Bréfort <jean_brefort>
Project AdministratorIn charge of this item.
Mon 06 Feb 2017 10:29:26 AM UTC, comment #9:

Thank you, the second patch helps with the exo bond issue.

When using patch 50190-1.patch, however, it seems that the patch wants to go through all the changes twice.
Upon
patch -p0 < 50190-1.patch
in the main directory, after going through a couple of succcessful patches, I get several messages like

patching file libs/gcp/bond.cc
Reversed (or previously applied) patch detected! Assume -R? [n]

answering no every time helps, but I guess this is not what is intended.

Bernd Speiser <berndspeiser>
Mon 06 Feb 2017 09:48:43 AM UTC, comment #8:

This new patch also contains the previous changes, and also fixes the exo bonds issue.

I need to investigate a strange file type issue before a new release.

(file #39678)

Jean Bréfort <jean_brefort>
Project AdministratorIn charge of this item.
Thu 02 Feb 2017 04:34:33 PM UTC, comment #7:

sorry, my fault -- I used the patch command in the wrong way.
Your suggested command works fine, after recompiling, the substituents are shown correctly. Thanks.

The crossing exo bonds are still bad.

Bernd Speiser <berndspeiser>
Thu 02 Feb 2017 10:01:39 AM UTC, comment #6:

The patch should change both files. In the gchemutils root directory just use:
patch -p0 < 50190.patch

Jean Bréfort <jean_brefort>
Project AdministratorIn charge of this item.
Thu 02 Feb 2017 09:55:42 AM UTC, comment #5:

maybe I did this wrong - is it indeed a patch for cdxml.cc and NOT for cdx.cc?
In the first lines of the patch file, only cdx.cc is mentioned.
Do I need to apply this to cdxml.cc?

Bernd Speiser <berndspeiser>
Thu 02 Feb 2017 09:04:01 AM UTC, comment #4:

Very strange, the patch for cdxml.cc is applied to cdx.cc and, of course, it fails. I tested on a fresh repository and things work for me.

Jean Bréfort <jean_brefort>
Project AdministratorIn charge of this item.
Wed 01 Feb 2017 07:46:57 PM UTC, comment #3:

thanks for the patch - however, when I try to use it,
I get:

loaders/cdx> /usr/bin/patch -i ~/Downloads/GChemPaint/50190.patch cdx.cc
patching file cdx.cc
patching file cdx.cc
Hunk #1 FAILED at 194.
Hunk #2 FAILED at 506.
Hunk #3 FAILED at 783.
Hunk #4 FAILED at 794.
Hunk #5 FAILED at 813.
Hunk #6 FAILED at 824.
Hunk #7 FAILED at 1283.
Hunk #8 FAILED at 1332.
8 out of 8 hunks FAILED -- saving rejects to file cdx.cc.rej

What's going wrong?

Bernd Speiser <berndspeiser>
Tue 31 Jan 2017 10:00:16 PM UTC, comment #2:

yes, indeed the two exo bonds are incorrect.

Bernd Speiser <berndspeiser>
Tue 31 Jan 2017 08:41:24 AM UTC, comment #1:

Thanks for the samples. I see another issue, the exo bonds are behind the main cycle, which is just impossible (and not what is seen in the png image). The string issue should be somewhat easy to fix (but not today), but no idea about the bonds issue.

Jean Bréfort <jean_brefort>
Project AdministratorIn charge of this item.
Mon 30 Jan 2017 09:56:00 PM UTC, original submission:

Hi,

I am using GChemPaint either version 0.14.14 and 0.14.16 and found a case of a cdx drawing where in both versions part of the graphics is not shown.
I attach a png file that shows how the result should look like, and the cdx as well as the cdxml files that cause the error:
the cdx file does not show the substituent R', while the cdxml file does not show R' but also it does not show substituent R three times.

I'd be happy to test any improvements of the code. Thanks.

Best regards
Bernd

Bernd Speiser <berndspeiser>

 

Attached Files
file #39679:  50190-2.patch added by jean_brefort (14KiB - text/x-patch - updated patch)
file #39678:  50190-1.patch added by jean_brefort (29KiB - text/x-patch - new enhanced patch)
file #39639:  50190.patch added by jean_brefort (4KiB - text/x-patch - Proposed patch for the string issue.)
file #39617:  Dimer5.cdx added by berndspeiser (6KiB - x-chemical/x-cdx)
file #39618:  Dimer5.png added by berndspeiser (32KiB - image/png)
file #39619:  Dimer5.cdxml added by berndspeiser (11KiB - application/vnd.chemdraw+xml)

 

Depends on the following items: None found

Items that depend on this one: None found

 

Carbon-Copy List
  • -unavailable- added by berndspeiser (Submitted the item)
  • -unavailable- added by berndspeiser
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    Follow 11 latest changes.

    Date Changed By Updated Field Previous Value => Replaced By
    Sat 15 Apr 2017 06:37:54 AM UTCjean_brefortStatusConfirmed=>Fixed
      Open/ClosedOpen=>Closed
    Mon 06 Feb 2017 12:35:27 PM UTCjean_brefortAttached File-=>Added 50190-2.patch, #39679
    Mon 06 Feb 2017 09:48:43 AM UTCjean_brefortAttached File-=>Added 50190-1.patch, #39678
    Wed 01 Feb 2017 12:28:58 PM UTCjean_brefortAttached File-=>Added 50190.patch, #39639
    Tue 31 Jan 2017 08:41:39 AM UTCjean_brefortStatusNone=>Confirmed
      Assigned toNone=>jean_brefort
    Mon 30 Jan 2017 09:56:00 PM UTCberndspeiserAttached File-=>Added Dimer5.cdx, #39617
      Attached File-=>Added Dimer5.png, #39618
      Attached File-=>Added Dimer5.cdxml, #39619
      Carbon-Copy-=>Added -unavailable-

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