Summary: | sci-chemistry/avogadro-1.0.1 copy & paste structures does not work | ||
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Product: | Gentoo Linux | Reporter: | urcindalo <urcindalo> |
Component: | Current packages | Assignee: | Gentoo Chemistry-Related Packages <sci-chemistry> |
Status: | RESOLVED TEST-REQUEST | ||
Severity: | normal | ||
Priority: | High | ||
Version: | unspecified | ||
Hardware: | All | ||
OS: | Linux | ||
Whiteboard: | |||
Package list: | Runtime testing required: | --- | |
Attachments: | example disaccharide |
Description
urcindalo
2010-06-03 19:02:04 UTC
I forgot to add the error I get in a terminal when pasting a methane molecule from a window to another: ===== ============================== *** Open Babel Warning in ReadMolecule Problems reading an XYZ file: The first line must contain the number of atoms. Format is: "sssssss" setOBMol called. Other atom has a position list of size zero! Other atom has a position list of size zero! Other atom has a position list of size zero! Downgrading the version to 1.0.0 removes the issue in my boxes. I can provide all the necessary tests. Since I use mostly stable systems, maybe a dependency version has to be updated? Still no news? I am able to reproduce this bug in THREE different boxes. Avogadro is an extremely important package for me. (In reply to comment #3) > Still no news? > > I am able to reproduce this bug in THREE different boxes. Avogadro is an > extremely important package for me. > Could you please report the bug upstream and added the url here? I only just saw your bug report, this looks like a regression in Avogadro. I don't seem to be able to reproduce the issue in 1.0 or master. I am hoping to put out a 1.0.2_rc0 next week, perhaps you could test that and let me know if you still see the issue there. Otherwise, an example of what is actually in your clipboard would also be helpful (it should be an XYZ file). Please retest with avogadro-1.0.2_rc1 and report if the issue is fixed. Sorry for the delay in my answer. I was busy with other tasks. I'm really confused here. When I first filed the bug, I was having the issue with v1.0.1 on my two boxes, laptop and desktop, whereas both of them worked well with 1.0.0. Before upgrading to 1.0.2_rc1 I checked again, and to my surprise the issue was gone with 1.0.1 on my laptop, but still present on my desktop. v1.0.2_rc1 behaves the same: laptop OK, desktop can't copy & paste. Somehow the issue was resolved on my laptop over the weeks after daily world updates. Both boxes are almost identical configuration-wise, but evidently there has to be something causing the issue. Since I'm now at my desktop, here is the clipboard output when I create a methane in an Avogadro's window and select and copy it: === 5 C -9.72186 4.89279 0.00000 H -8.65186 4.89279 0.00000 H -10.07904 5.90142 0.00000 H -10.09231 4.36863 0.85611 H -10.07359 4.39511 -0.87948 === When I open a new window with Avogadro and paste the clipboard, nothing happens. However, I can paste it into KWrite, for instance. Any clues? To make matters even stranger, copy & paste is working today on my desktop machine!!! I really don't know why. No, wait!! I think I may know why it was working on my laptop but not on my desktop. I rebooted my desktop today after a very long while, whilst I reboot my laptop more often (for obvious reasons). Maybe there was some change in a deep Avogadro's dependency that needed a reboot. Anyway, whatever the problem was, it seems to be over now. I think maybe Avogadro needed a particular version for some of its dependencies. See whether everything is fine with 1.0.3 and close the bug. This looks like a neverending story. The bug is still present. Here is the output from the terminal when I create a methane and try to paste it into a new window: === $ avogadro "Avogadro version: 1.0.3 Git: LibAvogadro version: 1.0.3 Git: " Locale: "es_ES" Translation successfully loaded. "El sistema permite OpenGL" "A punto de probar funcionalidades OpenGL." "Funcionalidades OpenGL encontradas: " "Doble bĂșfer." "Renderizado directo." "Antialias." Loading plugins: "/usr/bin/../lib64/avogadro/1_0" Searching for plugins in "/usr/lib64/avogadro/1_0/colors" Searching for plugins in "/usr/lib64/avogadro/1_0/engines" Searching for plugins in "/usr/lib64/avogadro/1_0/extensions" Searching for plugins in "/usr/lib64/avogadro/1_0/tools" Searching for plugins in "" Loading plugins: "/home/ramiro/.avogadro/1_0/plugins" Searching for plugins in "" Searching for plugins in "" Searching for plugins in "" Searching for plugins in "" Searching for plugins in "" QStackedLayout::setCurrentWidget: Widget 0x2cc8800 not contained in stack Avogadro(31707)/ KSycocaPrivate::openDatabase: Trying to open ksycoca from "/var/tmp/kdecache-ramiro/ksycoca4" GLWidget initialisation... GLSL support enabled, OpenGL 2.0 support confirmed. GLWidget initialised... createObjects() libpng warning: Ignoring attempt to set cHRM RGB triangle with zero area QStackedLayout::setCurrentWidget: Widget 0x4c8eff0 not contained in stack GLWidget initialisation... GLSL support enabled, OpenGL 2.0 support confirmed. GLWidget initialised... createObjects() ============================== *** Open Babel Warning in ReadMolecule Problems reading an XYZ file: The first line must contain the number of atoms. Format is: "s" setOBMol called. Other atom has a position list of size zero! Other atom has a position list of size zero! Other atom has a position list of size zero! === This happens with both stable openbabel v2.2.3 and ~amd64 v2.3.0. The clipboard content is: === 5 C -7.71030 2.87870 0.00000 H -6.64030 2.87870 0.00000 H -8.10763 2.19209 0.71805 H -8.07364 2.63420 -0.97627 H -8.03654 3.86069 0.27233 === It is still not here. Could you please bug upstream and paste the url here? What about version 1.1.0? Created attachment 331676 [details]
example disaccharide
Mixed results. It does not seem to work when you copy/paste a molecular fragment, due to an incorrect xzy file format passed to the clipper.
For instance, take the molecule I attach. Select one of the sugar rings plus the central sulphur atom, leaving the second ring unselected. Then copy that and paste it into another avogadro instance. Nothing happens. In the terminal you can see an error related to an incorrect number of atoms defined in the zxy file format.
I got some hypothesis:
* Maybe this happens because it is a fragment with an atom other than C's and H's, because it does not seem to happen with a fragment selected from an avogadro-built butane.
* Maybe this happens because there are no H's to complete the valences in the fragment. Again, this does not happen in the case of an avogadro-built butane.
* Maybe both conditions at the same time.
* But, if you add the missing H's and copy the fragment, avogadro exits with a segmentation fault. I just discovered it. A different bug?
So, I really don't know what to answer. There are improvements compared to previous versions where you simply couldn't copy/paste normally, but there are still issues, upstream or Gentoo related.
Thanks for your efforts.
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