Yes, I install the 32-bit openbabel. And yes, a lot of formats are missing. However the GUI version can handle these format very well. I think there is something wrong when binding the obabel to python in " pythong-binding: openbabel-2.4.0-cp27-cp27m-win32.whl" However, I am not familiar with this part. So I don't know where goes wrong. The only thing I can ensure is that the binding is for 2.40 version and python2.7
I have no idea what is going on in pybel. Sad. :( On Thu, Sep 29, 2016 at 11:00 PM, Noel O'Boyle <[email protected]> wrote: > (ccing to openbabel-discuss as this mailing list is closed) > > I notice that others formats are missing such as Mol file. There are 6 > or 7 common formats loaded from formats_common.obf and these are all > missing. It must be that your virus checker or Windows firewall is > blocking that .obf file. I don't understand how the GUI can handle it > correctly though in that case. ?? > > - Noel > > On 29 September 2016 at 15:54, Noel O'Boyle <[email protected]> wrote: > > Did you install the 32-bit version of Open Babel? > > > > - Noel > > > > On 29 September 2016 at 15:07, Jianshu Hu <[email protected]> > wrote: > >> Hi everyone, > >> > >> I met a problem while trying to use openbabel in Python. > >> > >> Env: > >> python: Python 2.7.12 (v2.7.12:d33e0cf91556, Jun 27 2016, > 15:19:22) > >> [MSC v.1500 32 bit (Intel)] on win32 > >> obabel: Open Babel 2.4.0 -- Sep 22 2016 -- 18:19:48 > >> OS: win10 > >> pythong-binding: openbabel-2.4.0-cp27-cp27m-win32.whl > >> > >> Problem: > >>>>> from pybel import * > >>>>> mymol=readstring("smi","CCCC") > >> Traceback (most recent call last): > >> File "<stdin>", line 1, in <module> > >> File "C:\Python27\lib\site-packages\pybel.py", line 199, in > readstring > >> raise ValueError("%s is not a recognised Open Babel format" % > format) > >> ValueError: smi is not a recognised Open Babel format > >> > >> Trying to find out what happend: > >> >>> sorted(informats) > >> ['CONFIG', 'CONTCAR', 'CONTFF', 'HISTORY', 'MDFF', 'POSCAR', 'POSFF', > >> 'VASP', 'abinit', 'acesout', 'acr', 'adfout', 'alc', 'aoforce', 'arc', > >> 'axsf', 'bgf', 'box', 'bs', 'c09out', 'c3d1', 'c3d2', 'caccrt', 'car', > >> 'castep', 'ccc', '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', 'jin', 'jout', > >> 'log', 'lpmd', 'mcdl', 'mcif', 'mmcif', 'mmd', 'mmod', 'mold', 'molden', > >> 'molf', 'moo', 'mop', 'mopcrt', 'mopin', 'mopout', 'mpc', 'mpo', 'mpqc', > >> 'msi', 'nwo', 'orca', 'out', 'outmol', 'output', 'pcm', 'pdbqt', 'png', > >> 'pos', 'pqr', 'pqs', 'prep', 'pwscf', 'qcout', 'res', 'rsmi', 'rxn', > >> 'siesta', 'smy', 't41', 'tdd', 'text', 'therm', 'tmol', 'txt', 'txyz', > >> 'unixyz', 'vmol', 'xsf', 'xyz', 'yob'] > >> > >> I found there is no smi in pybel.informats, however the Openbabel > GUI > >> can read or write smi format correctly. > >> > >> Where goes wrong? The pybel no loner support smi format? > >> > >> PS: the openbabel in python has the same problem > >> > >> Thank you for helps, > >> > >> JS Hu > >> > >> ------------------------------------------------------------ > ------------------ > >> > >> _______________________________________________ > >> OpenBabel-scripting mailing list > >> [email protected] > >> https://lists.sourceforge.net/lists/listinfo/openbabel-scripting > >> >
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