Molekel

synss · 07-09-2009, 05:07 PM

Is anyone using this software on Linux, and if yes, what distro? I may benefit from having a look at the patches or the versions used...

I am trying to install "Molekel", http://molekel.cscs.ch/wiki/pmwiki.php/Main/Build and I have some problems. I think I have all dependencies, including glew, which is not mentioned on the website, but I have a problem compiling:

Code:

/usr/include/Inventor/actions/SoRayPickAction.h: In constructor ‘MoleculeActorPickCommand::MoleculeActorPickCommand()’:
/usr/include/Inventor/actions/SoRayPickAction.h:90: error: ‘SoRayPickAction::SoRayPickAction(const SoRayPickAction&)’ is private

I understand what that means: trying to copy with a private copy-const is forbidden. This Inventor is actually OpenMOIV, which does not seem to have been updated for years: can't be a new problem. So I do not really know what to do...

knudfl · 07-28-2009, 09:30 PM

SoRayPickAction.h : is a Coin2 header.

Your problems probably origin from a poor VTK.
These are my notes from July 10' :

VTK........
"cmake_command="

Code:

cmake with-soxt -DBUILD_SHARED_LIBS:BOOL=ON -DBUILD_EXAMPLES:BOOL=ON -DBUILD_TESTING:BOOL=ON -DVTK_USE_GL2PS:BOOL=ON -DVTK_USE_GUISUPPORT:BOOL=ON -DVTK_USE_SYSTEM_EXPAT=ON -DVTK_USE_SYSTEM_FREETYPE=ON -DVTK_USE_SYSTEM_JPEG=ON -DVTK_USE_SYSTEM_PNG=ON -DVTK_USE_SYSTEM_TIFF=ON -DVTK_USE_SYSTEM_ZLIB=ON -DVTK_USE_QVTK=ON -DDESIRED_QT_VERSION=4 ..

And the real problems appear, when you pass 100% compiling :
Problems with linking to libChemKit2.so.
I found no solution.
.....

Google .. libChemKit2.so ..
http://stuff.mit.edu/afs/athena/soft..._glibc2_4/lib/

http://stuff.mit.edu/afs/athena/soft...libChemKit2.so

Google .. molelel ..
http://www.debian.org/devel/debian-m...#official-debs
.....

synss · 07-29-2009, 03:20 AM

Thank you, I managed to compile everything, filed a couple bugs to Molekel, but it still crashes when I start it. It segfaults! And I am not really sure what crashes, Molekel, VTK, some other thing…

So for now, I plot my molecules + vibrations in Matlab. It is better than nothing. Although if anyone managed to get Molekel working, I would appreciate help.

Or pointers to other molecule visualization software than can show IR vibrations with arrows or something similar. I already know Molden and use it for creating animated gifs of the vibrations. But animated gifs are not good for a paper.

knudfl · 07-29-2009, 07:54 AM

I used the suggested CentOS 4.2 ( = RH EL 4.x )
for the compiling.
Did you use Arch ? Which version ?

And did you manage to Create libChemKit2.so ?
Or just using one of the pre compiled binaries,
libChemKit2.so ?
.....

synss · 07-30-2009, 12:37 AM

I used Arch x86_64, up to date. I pretty much had to compile everything, I also compiled libChemKit2.so. I have been using the AUR where available or wrote the build script otherwise. I tried to compile Molekel from SVN, revision 649. All the dependencies at the latest version available (Coin2.5, etc.).

I will try to recompile VTK. How can I add the debug symbols in cmake? At least I would know whether Molekel or the GUI crashes…

knudfl · 07-31-2009, 05:44 AM

Quote:

How can I add the debug symbols in cmake?

I sometimes read in the cmake documentation.
( It is huge.) But usually I don't find, what I need.

Examples from other application is often more usable.
And can be found with some luck and some 'Googling'.

This one is from 'kde' and may be what you are looking for :
cmake -DCMAKE_BUILD_TYPE=debugfull ..
http://techbase.kde.org/Development/...ugging_symbols
.....

Molekel : I read somewhere, that it would be replaced
by OpenBabel.
.....

knudfl · 08-03-2009, 01:04 AM

Just saw this : " Linux4Chemistry "

http://www.redbrick.dcu.ie/~noel/linux4chemistry/