date:20131007

Re: [Open Babel] SDF M-block

2013-10-07 Thread Geoffrey Hutchison

 M  CHG  2   3   1   6  -1
 
 is illegal. Is there a way to make openbabel understand this line?

What on earth is it trying to indicate?

It seems like you have a lot of non-standard SDF files. What is the source?

-Geoff

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Re: [Open Babel] problems with python libraries

2013-10-07 Thread Noel O'Boyle

If that solved your problem, then your problem was the PATH. You can
check the path that Python sees with import sys; print(sys.path).

If the Open Babel directory is on the PATH, then the only thing I can
think of is that you opened a command prompt window before the PATH
was updated.

If want to go ahead with your workaround, copy the .obf files also and
see if it works.

- Noel

On 7 October 2013 16:11, Michal Krompiec michal.kromp...@gmail.com wrote:
 Hello, this problem is solved (by copying openbabel's dlls to python
 directory. I'm able to import openbabel now, but when I try to import
 pybel, I get the following error:
 Traceback (most recent call last):
   File pyshell#1, line 1, in module
 import pybel
   File C:\Python33\lib\site-packages\pybel.py, line 69, in module
 informats = _formatstodict(_obconv.GetSupportedInputFormat())
   File C:\Python33\lib\site-packages\pybel.py, line 65, in _formatstodict
 broken = [(x,y.strip()) for x,y in broken]
   File C:\Python33\lib\site-packages\pybel.py, line 65, in listcomp
 broken = [(x,y.strip()) for x,y in broken]
 ValueError: need more than 1 value to unpack

 Can anybody help??
 Thanks,
 Michal Krompiec

 On 7 October 2013 12:37, Michal Krompiec michal.kromp...@gmail.com wrote:
 Hello, I need urgent help with the openbabel python library. I can't
 get it  to work (on 3 different Windows 7 computers).
 I installed OpenBabel GUI 2.3.2 first, then Python 3.3 32-bit, then
 OpenBabel python bindings 1.8 for python 3.3.

 When I try to import openabel or pybel, I get the following error message:
 import pybel
 Traceback (most recent call last):
   File pyshell#0, line 1, in module
 import pybel
   File C:\Python33\lib\site-packages\pybel.py, line 52, in module
 import openbabel as ob
   File C:\Python33\lib\site-packages\openbabel.py, line 37, in module
 _openbabel = swig_import_helper()
   File C:\Python33\lib\site-packages\openbabel.py, line 33, in
 swig_import_helper
 _mod = imp.load_module('_openbabel', fp, pathname, description)
   File C:\Python33\lib\imp.py, line 183, in load_module
 return load_dynamic(name, filename, file)
 ImportError: DLL load failed: The specified module could not be found.

 What to do? openbabel directory is in the path, copying openbabel's
 dlls into windows/system doesn't help.
 I tried again with Python 2.7, but got exactly the same problem.
 I know that some people reported this issue previously, but their
 solutions don't work for me.
 Thanks in advance,
 Michal Krompiec

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Re: [Open Babel] problems with python libraries

2013-10-07 Thread Dimitri Maziuk

On 10/07/2013 12:58 PM, Michal Krompiec wrote:

 import sys; print(sys.path)
 ['', 'C:\\Python27\\Lib\\idlelib',
 'C:\\Windows\\system32\\python27.zip', 'C:\\Python27\\DLLs',
 'C:\\Python27\\lib', 'C:\\Python27\\lib\\plat-win',
 'C:\\Python27\\lib\\lib-tk', 'C:\\Python27',
 'C:\\Python27\\lib\\site-packages', 'C:\\Program Files
 (x86)\\OpenBabel-2.3.2']

 Traceback (most recent call last):
   File pyshell#1, line 1, in module
 import pybel
   File C:\Python33\lib\site-packages\pybel.py, line 69, in module
 informats = _formatstodict(_obconv.GetSupportedInputFormat())

I think you should first figure out your python: is it 3.3 or 2.7?

-- 
Dimitri Maziuk
Programmer/sysadmin
BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu



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Re: [Open Babel] problems with python libraries

2013-10-07 Thread Noel O'Boyle

Regarding the difference between the paths, that's my mistake. One is
the system PATH, the other is where Python searches for .py files..

- Noel

On 7 October 2013 18:47, Michal Krompiec michal.kromp...@gmail.com wrote:
 Dear Noel,
 Yes, but the system path is OK:
 C:\Users\Michalecho %path%
 C:\Program Files\Common Files\Microsoft Shared\Windows Live;C:\Program Files 
 (x8
 6)\Common Files\Microsoft Shared\Windows Live;C:\Windows\system32;C:\
 Windows;C:\
 Windows\System32\Wbem;C:\Windows\System32\WindowsPowerShell\v1.0\;C:\Program 
 Fil
 es (x86)\EgisTec MyWinLocker\x86;C:\Program Files (x86)\EgisTec 
 MyWinLocker\x64;
 C:\Program Files (x86)\ATI Technologies\ATI.ACE\Core-Static;C:\Program Files 
 (x8
 6)\Windows Live\Shared;C:\Program Files (x86)\Common Files\MDL 
 Shared\ISIS;c:\Pr
 ogram Files (x86)\Microsoft SQL Server\90\Tools\binn\;C:\Program Files 
 (x86)\Qui
 ckTime\QTSystem\;C:\Program Files (x86)\Avogadro\bin;C:\Program Files 
 (x86)\Open
 Babel-2.3.2;C:\Program Files (x86)\Mozilla Firefox

 whereas python's path is different:
 import sys; print(sys.path)
 ['', 'C:\\Python27\\Lib\\idlelib',
 'C:\\Windows\\system32\\python27.zip', 'C:\\Python27\\DLLs',
 'C:\\Python27\\lib', 'C:\\Python27\\lib\\plat-win',
 'C:\\Python27\\lib\\lib-tk', 'C:\\Python27',
 'C:\\Python27\\lib\\site-packages']


 Why?
 Best wishes,
 Michal

 On 7 October 2013 17:12, Noel O'Boyle baoille...@gmail.com wrote:
 If that solved your problem, then your problem was the PATH. You can
 check the path that Python sees with import sys; print(sys.path).

 If the Open Babel directory is on the PATH, then the only thing I can
 think of is that you opened a command prompt window before the PATH
 was updated.

 If want to go ahead with your workaround, copy the .obf files also and
 see if it works.

 - Noel

 On 7 October 2013 16:11, Michal Krompiec michal.kromp...@gmail.com wrote:
 Hello, this problem is solved (by copying openbabel's dlls to python
 directory. I'm able to import openbabel now, but when I try to import
 pybel, I get the following error:
 Traceback (most recent call last):
   File pyshell#1, line 1, in module
 import pybel
   File C:\Python33\lib\site-packages\pybel.py, line 69, in module
 informats = _formatstodict(_obconv.GetSupportedInputFormat())
   File C:\Python33\lib\site-packages\pybel.py, line 65, in _formatstodict
 broken = [(x,y.strip()) for x,y in broken]
   File C:\Python33\lib\site-packages\pybel.py, line 65, in listcomp
 broken = [(x,y.strip()) for x,y in broken]
 ValueError: need more than 1 value to unpack

 Can anybody help??
 Thanks,
 Michal Krompiec

 On 7 October 2013 12:37, Michal Krompiec michal.kromp...@gmail.com wrote:
 Hello, I need urgent help with the openbabel python library. I can't
 get it  to work (on 3 different Windows 7 computers).
 I installed OpenBabel GUI 2.3.2 first, then Python 3.3 32-bit, then
 OpenBabel python bindings 1.8 for python 3.3.

 When I try to import openabel or pybel, I get the following error message:
 import pybel
 Traceback (most recent call last):
   File pyshell#0, line 1, in module
 import pybel
   File C:\Python33\lib\site-packages\pybel.py, line 52, in module
 import openbabel as ob
   File C:\Python33\lib\site-packages\openbabel.py, line 37, in module
 _openbabel = swig_import_helper()
   File C:\Python33\lib\site-packages\openbabel.py, line 33, in
 swig_import_helper
 _mod = imp.load_module('_openbabel', fp, pathname, description)
   File C:\Python33\lib\imp.py, line 183, in load_module
 return load_dynamic(name, filename, file)
 ImportError: DLL load failed: The specified module could not be found.

 What to do? openbabel directory is in the path, copying openbabel's
 dlls into windows/system doesn't help.
 I tried again with Python 2.7, but got exactly the same problem.
 I know that some people reported this issue previously, but their
 solutions don't work for me.
 Thanks in advance,
 Michal Krompiec

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Re: [Open Babel] problems with python libraries

2013-10-07 Thread Michal Krompiec

This is not a mistake. As I wrote in my first post, I was trying to
install python and ob on 3 different computers, and these two error
messages are from different computers: one running python 3.3 and the
other running 2.7.

But coming back to the point: adding openbabel's directory to windows
path did not solve the problem (at least on one of the systems,
haven't checked the others). Copying all openbabel's dll and obf files
to python directory is perhaps a messy workaround, but it works, so I
don't care ;)




On 7 October 2013 19:06, Dimitri Maziuk dmaz...@bmrb.wisc.edu wrote:
 On 10/07/2013 12:58 PM, Michal Krompiec wrote:

 import sys; print(sys.path)
 ['', 'C:\\Python27\\Lib\\idlelib',
 'C:\\Windows\\system32\\python27.zip', 'C:\\Python27\\DLLs',
 'C:\\Python27\\lib', 'C:\\Python27\\lib\\plat-win',
 'C:\\Python27\\lib\\lib-tk', 'C:\\Python27',
 'C:\\Python27\\lib\\site-packages', 'C:\\Program Files
 (x86)\\OpenBabel-2.3.2']

 Traceback (most recent call last):
   File pyshell#1, line 1, in module
 import pybel
   File C:\Python33\lib\site-packages\pybel.py, line 69, in module
 informats = _formatstodict(_obconv.GetSupportedInputFormat())

 I think you should first figure out your python: is it 3.3 or 2.7?

 --
 Dimitri Maziuk
 Programmer/sysadmin
 BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu


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Re: [Open Babel] SDF M-block

Re: [Open Babel] problems with python libraries

Re: [Open Babel] problems with python libraries

Re: [Open Babel] problems with python libraries

Re: [Open Babel] problems with python libraries

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