Hi Dale,
I had this problem a couple of years ago on win x64. I don't remember
exactly what I had to do to make all the formats load, but I think I recall
having to add the site-packages folder to the PATH environment variable.
Kristian Kaufmann
On Mon, Nov 24, 2014 at 12:42 PM, Dale R. Cameron <
dcame...@westcoastchemist.ca> wrote:
> Sigh, I spoke too soon. I now have an "un-empty" list of formats but
> unfortunately all of thew formats in formats_common are not showing up. No
> pdb, no sdf, no smi, etc.
>
> Here is the results of the print sorted(pybel.informats) command
>
> ['CONFIG', 'CONTCAR', 'CONTFF', 'HISTORY', 'MDFF', 'POSCAR', 'POSFF',
> 'VASP', 'abinit', 'acesout', 'acr', 'adfout', 'alc', 'arc', 'axsf', 'bgf',
> 'box', 'bs', 'c09out', 'c3d1', 'c3d2', 'caccrt', 'car', 'castep', 'ccc',
> 'cdjson', 'cdx', 'cif', 'ck', 'crk2d', 'crk3d', 'ct', 'cub', 'cube',
> 'dallog', 'dalmol', 'dat', 'dmol', 'dx', 'exyz', 'fa', 'fasta', 'fch',
> 'fchk', 'fck', 'feat', 'fhiaims', 'fract', 'fs', 'fsa', 'g03', 'g09',
> 'g92', 'g94', 'g98', 'gal', 'gam', 'gamess', 'gamin', 'gamout', 'got',
> 'gpr', 'gro', 'gukin', 'gukout', 'gzmat', 'hin', 'inp', 'ins', 'jout',
> 'log', 'lpmd', 'mcdl', 'mcif', 'mmcif', 'mmd', 'mmod', 'mold', 'molden',
> 'molf', 'moo', 'mop', 'mopcrt', 'mopin', 'mopout', 'mpc', 'mpo', 'mpqc',
> 'msi', 'nwo', 'out', 'outmol', 'output', 'pcjson', 'pcm', 'pdbqt', 'png',
> 'pos', 'pqr', 'pqs', 'prep', 'pwscf', 'qcout', 'res', 'rsmi', 'rxn', 'smy',
> 't41', 'tdd', 'text', 'therm', 'tmol', 'txt', 'txyz', 'unixyz', 'vmol',
> 'xsf', 'xyz', 'yob']
>
> I see no relevant build errors for these. The function works with babel
> from the command line. The obf files are all copied to site packages (as
> well as all the others from previous emails.
>
> At least for now, I can likely get on with what I wanted openbabel loaded
> for in the first place (I believe... yet to test if the other functions are
> all working) but without common formats, I have to convert structures to
> one of the ones available first on the command line and that is going to
> get tiresome very quickly. Any idea what is left for me to do? I'm really
> at my wits end for what was supposed to be a rather straightforward
> project. I'll keep digging myself.
>
> Thanks in advance again,
>
> Dale
>
> On 2014-11-24 07:27, Dale R. Cameron wrote:
>
> Thanks Noel, Your help has been very appreciated. Looks like I'm finally
> functional.
>
> Best wishes,
>
> Dale
>
> On 2014-11-22 13:34, Noel O'Boyle wrote:
>
> All of the plugins are in the .obf files. You need to copy these to
> the same directory as the .dll.
>
> - Noel
>
> On 21 November 2014 18:26, Dale R. Cameron <dcame...@westcoastchemist.ca>
> wrote:
>
> Thanks Noel, Had to also copy over openbabel-2.dll to site-packages but
> the modules did load after that exercise. I was smiling... was... First
> test was to see if I could load an sdf. No success. "ValueError: sdf is not
> a recognized Open Babel format". Checked informats and was surprised to see
> it was empty. print sorted(pybel.informats) [] Tried the following as
> well... obconversion = openbabel.OBConversion() for i in
> obconversion.GetSupportedInputFormat(): print repr(i) The above gives me
> nothing, confirming the pybel result above for ob itself. So, that's when I
> lost my smile. :( Have I excluded something to get it to build that is
> causing no input formats to be available? The only format that wouldn't
> compile was the orcaformat, from formats_compchem, which I excluded from
> the build. To confirm if it was a universal problem, I went to a cmd shell
> and tried to run a simple conversion "babel -isdf test.sdf -omol2
> test.mol". This works fine. Checked the file and the mol2 is perfect... So
> I'm not sure what is left to try. Seems like babel is built correctly and
> it must be python related. Or it's me... Which is always a possibility I
> think everything is pointing where it belongs. BABEL_DATADIR is pointing to
> the top level data directory in the ob folder. BABEL_LIBDIR is pointing to
> the libs folder inside the newest x64 release build. The
> windows-vc2008\build_x64\bin\Release is in the path (Am I missing others?)
> I had trouble with babel (in a cmd window) recognizing where libinchi.dll
> was so I added the libs folder directly in the path as well. No chnges here
> affect the problem. Baby steps progress is still progress... Thanks, Dale
> On 2014-11-21 08:05, Noel O'Boyle wrote: Just copy the relevant files to
> site-packages: pybel.py, openbabel.py, _openbabel.pyd. Then add your
> release build to the front of the windows PATH (or else copy everything to
> site-packages but that's not very nice) and "import pybel". - Noel On 21
> November 2014 15:45, Dale R. Cameron <dcame...@westcoastchemist.ca>
> wrote: I had no trouble with SWIG. Installed the latest version for
> Windows, told cmake where it would be and no troubles at all. My trouble is
> installing them afterwards to be importable in python. Dale On 2014-11-21
> 04:33, Mathias Laurin wrote: My only remaining issue is how to install the
> python bindings for this newly built set. I have not found instructions for
> how to perform that last task to get me where I want to be. In theory, you
> need to call cmake with -DPYTHON_BINDINGS=ON -DRUN_SWIG=ON -DSWIG_DIR=/bin
> The last one must be adapted to wherever you actually installed swig; I put
> mine in /bin using MSYS. Now, I did that on my own 32 bit install and make
> complains that it does not find swig.swg and python.swg. Any clue? Does it
> run on 64 bits? Best regards Mathias
>
>
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