Thanks Kristian,
Not sure if that was what fixed me up or not but it's working now. smi
appears in the list and I can load smiles with pybel.
I've said it before but I think NOW, I'm functional. ;) (knocking on
wood)
Thanks everyone.
Dale
On 2014-11-24 10:59, Kristian Kaufmann wrote:
> 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-vc2008build_x64binRelease 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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