Problem with Pybel installation for Anaconda

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Problem with Pybel installation for Anaconda

RichardMR
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


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Re: Problem with Pybel installation for Anaconda

Noel O'Boyle
Administrator
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:
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


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Re: Problem with Pybel installation for Anaconda

mwojcikowski
Hi,

Indeed for some reason InCHI is not built on windows. I'll have to fix it, stay tuned for updates.

----
Pozdrawiam,  |  Best regards,
Maciek Wójcikowski
[hidden email]

2016-10-15 9:30 GMT+02:00 Noel O'Boyle <[hidden email]>:
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:
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


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Re: Problem with Pybel installation for Anaconda

RichardMR
Hi Noel, Maciek,

Thank you very much for your quick and helpful response!

Best regards,

Richard

On Sat, Oct 15, 2016 at 9:00 AM, Maciek Wójcikowski <[hidden email]> wrote:
Hi,

Indeed for some reason InCHI is not built on windows. I'll have to fix it, stay tuned for updates.

----
Pozdrawiam,  |  Best regards,
Maciek Wójcikowski
[hidden email]

2016-10-15 9:30 GMT+02:00 Noel O'Boyle <[hidden email]>:
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:
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


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