Summary: | sci-chemistry/ghemical-2.10: import scrambles molecule structure | ||
---|---|---|---|
Product: | Gentoo Linux | Reporter: | Reinis Danne <rei4dan> |
Component: | Current packages | Assignee: | Gentoo Chemistry-Related Packages <sci-chemistry> |
Status: | RESOLVED FIXED | ||
Severity: | major | Keywords: | InOverlay |
Priority: | High | ||
Version: | unspecified | ||
Hardware: | All | ||
OS: | Linux | ||
Whiteboard: | patch and ebuild available | ||
Package list: | Runtime testing required: | --- | |
Attachments: |
working *.gpr file generated by ghemical-2.95
the same structure, but saved trough "Export.." dialog Exported as *.pdb How it should look (and in one case does) How it does look 1 How it does look 2 How it does look 3 a patch for import/export errors due to non-"C" system locale a patch for configure.ac - test for libf2c which is needed for Mopac a ebuild which works with two previously posted patches |
Description
Reinis Danne
2008-03-08 09:34:34 UTC
Does this work in 2.95? I just added it. No it still doesn't work. Coordinates are a bit different, however it doesn't help. Created attachment 163479 [details]
working *.gpr file generated by ghemical-2.95
Created attachment 163481 [details]
the same structure, but saved trough "Export.." dialog
Created attachment 163482 [details]
Exported as *.pdb
Created attachment 163487 [details]
How it should look (and in one case does)
Created attachment 163488 [details]
How it does look 1
Created attachment 163490 [details]
How it does look 2
Created attachment 163492 [details]
How it does look 3
Export doesn't work either now. Coordinates are zeroed out, regardless fail format. Found the cause for this. More precisely - Debian developer did and reported it to ghemical-devel mailing list after which the solution was posted. It turns out that only systems with non-"C" locale are affected by this bug. As ghemical-2.95 did not compile because of bug 232292, I used the modified ebuild from that bugreport and added a patch for this bug. Also made a separate patch for ghemical-2.95 building error. Tested this configuration and it works for me. There is still one issue though - ghemical-2.95 fails at a configuration step complaining about missing pkg-config. This can be worked around: >$ PKG_CONFIG=`which pkg-config` emerge -a ghemical Created attachment 171373 [details, diff]
a patch for import/export errors due to non-"C" system locale
Created attachment 171375 [details, diff]
a patch for configure.ac - test for libf2c which is needed for Mopac
Created attachment 171376 [details]
a ebuild which works with two previously posted patches
Added to science overlay *ghemical-2.99.2 (21 Jun 2010) 21 Jun 2010; Justin Lecher <jlec@gentoo.org> +files/2.99.2-docs.patch, -ghemical-2.10.ebuild, -ghemical-2.95.ebuild, -ghemical-2.98.ebuild, +ghemical-2.99.2.ebuild: Version Bump, fixing bug 212689, 232292, 246414, thanks rei4dan for working on patches, Cleaned old buggy versions, Fixed wrong path for html installation |