Hi, I've been encountering difficulties getting Pybel to install for Anaconda.I would be grateful for any assistance you have time to provide. I managed to install Pybel via the following command: conda install -c openbabel openbabel=2.4.1 However, it seems 'inchi' is not a recognised format, as shown below, even though - when working with Pybel version 1.8 with Python 2.7.5 (vanilla Python installation) - the following sequence of commands worked without error. ======================================== Python 2.7.12 |Anaconda 4.0.0 (32-bit)| (default, Jun 29 2016, 11:42:13) [MSC v.1500 32 bit (Intel)] on win32 Type "help", "copyright", "credits" or "license" for more information. Anaconda is brought to you by Continuum Analytics. Please check out: http://continuum.io/thanks and https://anaconda.org >>> import pybel >>> mol = pybel.readstring('smi','c1ccccc1') >>> mol.write('inchi') Traceback (most recent call last): File "<stdin>", line 1, in <module> File "C:\Anaconda2\lib\site-packages\pybel.py", line 527, in write format) ValueError: inchi is not a recognised Open Babel format ========================================= Please note that I did previously try getting Pybel via the PyPi openbabel package [pip install openbabel], for which import pybel failed with the message ["ImportError: DLL load failed: The specified procedure could not be found."]. I do hope I have not created a mess. However, as "pip uninstall openbabel" reported "Cannot uninstall requirement openbabel, not installed", I believe the old PyPi installation was cleared up? Best regards, Richard ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, SlashDot.org! http://sdm.link/slashdot _______________________________________________ OpenBabel-discuss mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/openbabel-discuss |
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I can't comment on the anaconda parts, but maybe Maciek can... Regarding pip, apologies, we're in the middle of releasing OB 2.4.1 and I haven't yet updated the "pip install" parts which need to be in synch with the OB install. Give me until Monday and it should be fine. Regarding uninstall, pip is lying. I guess it's a pip bug, but it doesn't uninstall when the pip package is a wheel. If you go to your site-packages directory you will see several openbabel files - I don't know if this is the problem though. - Noel On 14 Oct 2016 8:41 p.m., "Richard Marchese Robinson" <[hidden email]> wrote:
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Hi, Indeed for some reason InCHI is not built on windows. I'll have to fix it, stay tuned for updates. 2016-10-15 9:30 GMT+02:00 Noel O'Boyle <[hidden email]>:
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Hi Noel, Maciek, Thank you very much for your quick and helpful response!On Sat, Oct 15, 2016 at 9:00 AM, Maciek Wójcikowski <[hidden email]> wrote:
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