Bug 680292
| Summary: | Molecular mechanics not supported | ||||||||||||
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| Product: | [Fedora] Fedora | Reporter: | lg <gvlatyshev> | ||||||||||
| Component: | openbabel | Assignee: | Kevin Kofler <kevin> | ||||||||||
| Status: | CLOSED ERRATA | QA Contact: | Fedora Extras Quality Assurance <extras-qa> | ||||||||||
| Severity: | medium | Docs Contact: | |||||||||||
| Priority: | unspecified | ||||||||||||
| Version: | rawhide | CC: | dominik, itamar, kevin, paul | ||||||||||
| Target Milestone: | --- | Keywords: | Patch | ||||||||||
| Target Release: | --- | ||||||||||||
| Hardware: | i686 | ||||||||||||
| OS: | Linux | ||||||||||||
| Whiteboard: | |||||||||||||
| Fixed In Version: | openbabel-2.3.0-3.fc15 | Doc Type: | Bug Fix | ||||||||||
| Doc Text: | Story Points: | --- | |||||||||||
| Clone Of: | Environment: | ||||||||||||
| Last Closed: | 2011-03-27 03:10:54 UTC | Type: | --- | ||||||||||
| Regression: | --- | Mount Type: | --- | ||||||||||
| Documentation: | --- | CRM: | |||||||||||
| Verified Versions: | Category: | --- | |||||||||||
| oVirt Team: | --- | RHEL 7.3 requirements from Atomic Host: | |||||||||||
| Cloudforms Team: | --- | Target Upstream Version: | |||||||||||
| Embargoed: | |||||||||||||
| Attachments: |
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Yeah, I'd blame obenergy there. $ strace obenergy -L
[skipped]
open("/usr//usr/lib/openbabel/2.3.0", O_RDONLY|O_NONBLOCK|O_LARGEFILE|O_DIRECTORY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
write(2, "obenergy", 8) = 8
write(2, ": cannot read input format!", 27) = 27
write(2, "\n", 1) = 1
exit_group(-1) = ?
Note /usr//usr/
Created attachment 486409 [details]
quick fix for plugin directory location
%cmake macros in openbabel.spec sets -DCMAKE_INSTALL_LIBDIR:PATH=/usr/lib which breaks openbabel build system.
Created attachment 486410 [details]
show forcefields list in obenergy output
The patch fixes "forcefields is not a recognized plugin type. Those with instances of sub-types loaded are:" message when obenergy is called without parameters
These patches don't fix the problem described in https://bugzilla.redhat.com/show_bug.cgi?id=680292#c0 but without them all openbabel binaries will do not work Created attachment 486493 [details]
fix for forcefield extension
This was fixed in avogadro commit 9653f3769f985926c1021f3480df7a253f4ff71d. The patch is simply diff between avogadro 1.0.1 and current git version. It also includes commit 50acbbeba91236a1387a10011438a32ce73ce69e
Created attachment 486495 [details]
fix autooptimization tool
The patch is essentially the same as for forcefield extension. With these patches both openbabel binaries (babel, obenergy, obminimize) and avogadro work as expected. Tested on fedora 14
Oh fun, so we have 2 OpenBabel bugs and 2 Avogadro bugs. I'm going to apply the fixes for all. I cannot reproduce any of these issues on F14 with openbabel-2.2.3-4.fc14, so I'm going to assume that those are all regressions caused by OpenBabel 2.3.0, and thus need fixing only in F15 and Rawhide. BTW, I wonder if other OpenBabel users also need fixing for this silent incompatible change in 2.3.0. openbabel-2.3.0-3.fc15,avogadro-1.0.1-14.fc15 has been submitted as an update for Fedora 15. https://admin.fedoraproject.org/updates/openbabel-2.3.0-3.fc15,avogadro-1.0.1-14.fc15 openbabel-2.3.0-3.fc15, avogadro-1.0.1-14.fc15 has been pushed to the Fedora 15 stable repository. If problems still persist, please make note of it in this bug report. |
Description of problem: Molecular mechanics is not available and autooptimization tool doesn't work. The start button is greyed out Version-Release number of selected component (if applicable): avogadro-1.0.1-13.fc15.i686 openbabel-libs-2.3.0-2.fc15.i686 How reproducible: Always Steps to Reproduce: 1. open avogadro 2. draw any molecule 3. make sure that Tool settings display is turned on 4. click autooptimization tool on toolbar (leter E with down arrow) Actual results: Force field cannot be selected and start button is greyed out Expected results: The force field should contain at least 2 entries (UFF and MMF94). The start button should be active Additional info: May actually be openbabel bug since obenergy produces strange output $ obenergy Usage: obenergy [options] <filename> options: description: -v verbose: print out indivual energy interactions -h add hydrogens before calculating energy -ff ffid select a forcefield available forcefields: forcefields is not a recognized plugin type. Those with instances of sub-types loaded are: