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From: Noel O'B. <bao...@gm...> - 2008-03-30 20:22:58
|
That is confusing. So, it may be something to do with conflicts between different iconv.dll ? Hmmm...I wonder do the different iconv.dll have different file sizes? Noel On 30/03/2008, Steven Wathen <SW...@si...> wrote: > Noel, > > I tried installing the new openbabel-python-1.2.win32 - no luck > > When I ran from the command line, I got an error message that said "This application failed to start because iconv.dll was not found. Re-installing the application may fix this problem." This error wasn't displayed when running from IDLE. > > I did re-install openbabel-python-1.2.win32, but got the same error. It shouldn't matter that my version of Python is 2.5.2, should it? > > One other thing, openbabel/pybel does work on my wife's laptop which is running WinXP Home Edition - so that by itself isn't the issue. > > I copied the file iconv.dll from the Python25/Lib/site-packages folder on my wife's laptop and tried again - your new openbabel-python-1.2.win32 now seems to work. > > I checked my laptop - the iconv.dll file is already there. > I uninstalled the original openbabel-python, and then installed the new version: openbabel-python-1.2.win32 > openbabel/pybel now seems to work on my laptop as well. > > > > > Steve > > ------------- > Dr. Steven P. Wathen > Associate Professor of Chemistry > Siena Heights University > 1247 East Siena Heights Drive > Adrian, MI 49221 > > (517) 264-7657 > sw...@si... > ________________________________________ > > From: Noel O'Boyle [bao...@gm...] > > Sent: Sunday, March 30, 2008 2:33 PM > To: Steven Wathen > > Subject: Re: [OpenBabel-scripting] problem installing openbabel for python on windows > > I've made a version of openbabel-python using Windows Home Edition. It's at: > http://www.redbrick.dcu.ie/~noel/test/openbabel-python-1.2.win32.exe > > Note that this is based on the current development code, and is likely > to give error messages when it starts. However, if you could test it > that'd be great. I'm using Python 2.5.0 by the way, so the next thing > for me to test is to upgrade to the latest Python 2.5 and try again. > > Also, you might want to check your computer's PATH and make sure that > there are no old references to OpenBabel there... > > Noel > > On 30/03/2008, Steven Wathen <SW...@si...> wrote: > > Hi, > > > > I have access to three computers - I can get openbabel/pybel to work on only one of them. > > > > My office computer is running WinXP - Professional Edition: Python 2.5.2 and openbabel/pybel work. > > > > My Laptop is running WinXP Media Center Edition SP2, my home computer is running WinXP Home Edition SP2 - neither of these computers will run openbabel/pybel from Python 2.5.2 > > > > I hope this helps to narrow down the problem - I'm afraid I don't know why it would make a difference which version of WinXP, SP2 I am running. > > > > > > Steve > > > > > > ------------- > > Dr. Steven P. Wathen > > Associate Professor of Chemistry > > Siena Heights University > > 1247 East Siena Heights Drive > > Adrian, MI 49221 > > > > (517) 264-7657 > > sw...@si... > > > > ________________________________________ > > From: lunchbox99 [lun...@tp...] > > Sent: Saturday, March 29, 2008 6:32 PM > > > > To: 'Noel O'Boyle'; Steven Wathen > > > > Cc: ope...@li... > > > > Subject: RE: [OpenBabel-scripting] problem installing openbabel for python on windows > > > > > > To confirm from a non-developer. I just installed python 2.5.2 on vista SP1. > > I then installed the openbabel python wrappers > > "openbabel-python-1.2.2.py2.5.exe". After opening a python shell at the > > command prompt, importing openbabel or pybel works fine. I have done nothing > > special to this pc. > > > > mc > > > > > > > > -----Original Message----- > > From: ope...@li... > > [mailto:ope...@li...] On Behalf Of Noel > > O'Boyle > > Sent: Sunday, 30 March 2008 4:48 AM > > To: Steven Wathen > > Cc: ope...@li... > > Subject: Re: [OpenBabel-scripting] problem installing openbabel for python > > on windows > > > > Hello Steven, > > > > Sorry about the problem. I've just downloaded and installed the file > > myself, just to verify that it works for me. The bad news is that > > another user also reported a similar bug and we were not able to > > figure out what the problem is. Can someone (who is not a developer) > > confirm that this installation file works for them? > > > > In the meanwhile, can you test the following? Rather than using IDLE, > > could you open a command prompt and run python, and try importing > > pybel there. > > > > You could also try installing Python2.4 instead, and the corresponding > > Pybel. What version of Windows are you using exactly? > > > > This is a serious problem, but unfortunately I really have no idea how > > to reproduce the bug, or how to fix it. :-/ > > > > - Noel > > > > > > > > On 28/03/2008, Steven Wathen <SW...@si...> wrote: > > > Hello, > > > > > > I am interested in using the Open Babel module for Python on Windows, but > > it doesn't seem to install properly. > > > > > > I installed the file at > > http://downloads.sourceforge.net/openbabel/openbabel-python-1.2.2.py2.5.exe > > > then I restarted my computer. > > > > > > I then opened IDLE and tried to do some of the examples listed on the web > > site. This is what I got: > > > > > > >>> from openbabel import * > > > > > > Traceback (most recent call last): > > > File "<pyshell#0>", line 1, in <module> > > > from openbabel import * > > > File "C:\Python25\Lib\site-packages\openbabel.py", line 7, in <module> > > > import _openbabel > > > ImportError: DLL load failed: This application has failed to start > > because the application configuration is incorrect. Reinstalling the > > application may fix this problem. > > > > > > >>> from pybel import * > > > > > > Traceback (most recent call last): > > > File "<pyshell#1>", line 1, in <module> > > > from pybel import * > > > File "C:\Python25\Lib\site-packages\pybel.py", line 1, in <module> > > > import openbabel as ob > > > File "C:\Python25\Lib\site-packages\openbabel.py", line 7, in <module> > > > import _openbabel > > > ImportError: DLL load failed: This application has failed to start > > because the application configuration is incorrect. Reinstalling the > > application may fix this problem. > > > >>> > > > > > > > > > I then thought that maybe the OpenBabelGUI was needed to use the Python > > bindings. I installed the OpenBabelGUI and it seems to run by itself fine. > > But accessing Open Babel from Python gives the same error message as before. > > > > > > I uninstalled the openbabel-python-1.2.2.py2.5.exe, downloaded the > > installation file again, re-installed and rebooted my computer. Same error > > message. > > > > > > Can you tell me what I am doing wrong? > > > > > > Thanks for your help, > > > > > > Steve > > > > > > > > > ------------- > > > Dr. Steven P. Wathen > > > Associate Professor of Chemistry > > > Siena Heights University > > > 1247 East Siena Heights Drive > > > Adrian, MI 49221 > > > > > > (517) 264-7657 > > > sw...@si... > > > > > > ------------------------------------------------------------------------- > > > Check out the new SourceForge.net Marketplace. > > > It's the best place to buy or sell services for > > > just about anything Open Source. > > > > > http://ad.doubleclick.net/clk;164216239;13503038;w?http://sf.net/marketplace > > > _______________________________________________ > > > OpenBabel-scripting mailing list > > > Ope...@li... > > > https://lists.sourceforge.net/lists/listinfo/openbabel-scripting > > > > > > > ------------------------------------------------------------------------- > > Check out the new SourceForge.net Marketplace. > > It's the best place to buy or sell services for > > just about anything Open Source. > > http://ad.doubleclick.net/clk;164216239;13503038;w?http://sf.net/marketplace > > _______________________________________________ > > OpenBabel-scripting mailing list > > Ope...@li... > > https://lists.sourceforge.net/lists/listinfo/openbabel-scripting > > > > > > > |
|
From: Steven W. <SW...@si...> - 2008-03-30 14:04:17
|
Since I have a computer that won't run openbabel/pybel and one that will run it, is there something I can look for that is different on the two machines that might be the cause of the problem? Some setting or missing file? I don't know where to look, but if you have any ideas I can check it out. Steve ------------- Dr. Steven P. Wathen Associate Professor of Chemistry Siena Heights University 1247 East Siena Heights Drive Adrian, MI 49221 (517) 264-7657 sw...@si... ________________________________________ From: Noel O'Boyle [bao...@gm...] Sent: Sunday, March 30, 2008 6:00 AM To: Steven Wathen Cc: lunchbox99; ope...@li... Subject: Re: [OpenBabel-scripting] problem installing openbabel for python on windows > I'm going to try installing Python 2.5.2 on my laptop (my usual computer) and see it pybel works. Currently I have Python 2.5.1 on that computer. Thanks for helping track down the problem. It may have something to do with Home Editon vs. Professional edition...I'm not sure which one the installer was created on, but I can create a new installer using Home Edition for you to test. |
|
From: Noel O'B. <bao...@gm...> - 2008-03-30 10:00:18
|
On 29/03/2008, Steven Wathen <SW...@si...> wrote:
> Hi Noel and MC,
>
> I just installed Python 2.5.2 on my office computer, and pybel works - although I found that readlines and Smarts give errors, where pybel.readlines and pybel.Smarts work ok.
As mc said, this is a feature of python. If you "import pybel", you
need to put pybel in front of readstring and Smarts, etc. But if you
"from pybel import *", you don't need to do this (but the names may
clash with names in your program, and it can make things a little
confusing sometimes).
> An odd thing I noticed, when I tried the example:
> >>> mymol = readstring("smi", "CCCC")
> >>> print mymol.molwt
> 45
>
>
> the MW that I got was 58! I'm not sure if I did something strange, or pybel is doing something strange.
Looks like an error in the docs - thanks for pointing this out. The
correct MW is 58.
> I'm going to try installing Python 2.5.2 on my laptop (my usual computer) and see it pybel works. Currently I have Python 2.5.1 on that computer.
Thanks for helping track down the problem. It may have something to do
with Home Editon vs. Professional edition...I'm not sure which one the
installer was created on, but I can create a new installer using Home
Edition for you to test.
> Thanks,
>
>
> Steve
> -------------
> Dr. Steven P. Wathen
> Associate Professor of Chemistry
> Siena Heights University
> 1247 East Siena Heights Drive
> Adrian, MI 49221
>
> (517) 264-7657
> sw...@si...
>
> ________________________________________
> From: lunchbox99 [lun...@tp...]
> Sent: Saturday, March 29, 2008 6:32 PM
> To: 'Noel O'Boyle'; Steven Wathen
>
> Cc: ope...@li...
>
> Subject: RE: [OpenBabel-scripting] problem installing openbabel for python on windows
>
>
> To confirm from a non-developer. I just installed python 2.5.2 on vista SP1.
> I then installed the openbabel python wrappers
> "openbabel-python-1.2.2.py2.5.exe". After opening a python shell at the
> command prompt, importing openbabel or pybel works fine. I have done nothing
> special to this pc.
>
> mc
>
>
>
> -----Original Message-----
> From: ope...@li...
> [mailto:ope...@li...] On Behalf Of Noel
> O'Boyle
> Sent: Sunday, 30 March 2008 4:48 AM
> To: Steven Wathen
> Cc: ope...@li...
> Subject: Re: [OpenBabel-scripting] problem installing openbabel for python
> on windows
>
> Hello Steven,
>
> Sorry about the problem. I've just downloaded and installed the file
> myself, just to verify that it works for me. The bad news is that
> another user also reported a similar bug and we were not able to
> figure out what the problem is. Can someone (who is not a developer)
> confirm that this installation file works for them?
>
> In the meanwhile, can you test the following? Rather than using IDLE,
> could you open a command prompt and run python, and try importing
> pybel there.
>
> You could also try installing Python2.4 instead, and the corresponding
> Pybel. What version of Windows are you using exactly?
>
> This is a serious problem, but unfortunately I really have no idea how
> to reproduce the bug, or how to fix it. :-/
>
> - Noel
>
>
>
> On 28/03/2008, Steven Wathen <SW...@si...> wrote:
> > Hello,
> >
> > I am interested in using the Open Babel module for Python on Windows, but
> it doesn't seem to install properly.
> >
> > I installed the file at
> http://downloads.sourceforge.net/openbabel/openbabel-python-1.2.2.py2.5.exe
> > then I restarted my computer.
> >
> > I then opened IDLE and tried to do some of the examples listed on the web
> site. This is what I got:
> >
> > >>> from openbabel import *
> >
> > Traceback (most recent call last):
> > File "<pyshell#0>", line 1, in <module>
> > from openbabel import *
> > File "C:\Python25\Lib\site-packages\openbabel.py", line 7, in <module>
> > import _openbabel
> > ImportError: DLL load failed: This application has failed to start
> because the application configuration is incorrect. Reinstalling the
> application may fix this problem.
> >
> > >>> from pybel import *
> >
> > Traceback (most recent call last):
> > File "<pyshell#1>", line 1, in <module>
> > from pybel import *
> > File "C:\Python25\Lib\site-packages\pybel.py", line 1, in <module>
> > import openbabel as ob
> > File "C:\Python25\Lib\site-packages\openbabel.py", line 7, in <module>
> > import _openbabel
> > ImportError: DLL load failed: This application has failed to start
> because the application configuration is incorrect. Reinstalling the
> application may fix this problem.
> > >>>
> >
> >
> > I then thought that maybe the OpenBabelGUI was needed to use the Python
> bindings. I installed the OpenBabelGUI and it seems to run by itself fine.
> But accessing Open Babel from Python gives the same error message as before.
> >
> > I uninstalled the openbabel-python-1.2.2.py2.5.exe, downloaded the
> installation file again, re-installed and rebooted my computer. Same error
> message.
> >
> > Can you tell me what I am doing wrong?
> >
> > Thanks for your help,
> >
> > Steve
> >
> >
> > -------------
> > Dr. Steven P. Wathen
> > Associate Professor of Chemistry
> > Siena Heights University
> > 1247 East Siena Heights Drive
> > Adrian, MI 49221
> >
> > (517) 264-7657
> > sw...@si...
> >
> > -------------------------------------------------------------------------
> > Check out the new SourceForge.net Marketplace.
> > It's the best place to buy or sell services for
> > just about anything Open Source.
> >
> http://ad.doubleclick.net/clk;164216239;13503038;w?http://sf.net/marketplace
> > _______________________________________________
> > OpenBabel-scripting mailing list
> > Ope...@li...
> > https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
> >
>
> -------------------------------------------------------------------------
> Check out the new SourceForge.net Marketplace.
> It's the best place to buy or sell services for
> just about anything Open Source.
> http://ad.doubleclick.net/clk;164216239;13503038;w?http://sf.net/marketplace
> _______________________________________________
> OpenBabel-scripting mailing list
> Ope...@li...
> https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
>
>
>
|
|
From: lunchbox99 <lun...@tp...> - 2008-03-30 02:23:48
|
Steve,
I was just re-reading a post of yours and just want to clarify something.
QUOTE FROM STEVE: "I just installed Python 2.5.2 on my office computer, and
pybel works - although I found that readlines and Smarts give errors, where
pybel.readlines and pybel.Smarts work ok."
If you import a python module like pybel using "import pybel", you will need
to specify the module name to access any methods. This is not an error.
For example:
import pybel
mol = pybel.readstring('SMI', 'CCCC')
print mol.molwt
However if you import the pybel module via "from pybel import *", you can
use the name identifier directly ie mol = readstring('SMI', 'CCCC'). The
reason for this is that a "from-import" loads the identifiers into the
current namespace.
Here is a quote from Core Python (2nd Ed) by Wesley Chun - an excellent
python book by the way: "In practice, using from module import * is
considered poor style because it "pollutes" the current namespace and has
the potential of overriding names in the current namespace"
I don't know how familiar you are with python but in effect this means you
run the risk of naming clashes if importing large modules.
mc
|
|
From: lunchbox99 <lun...@tp...> - 2008-03-30 00:53:34
|
Are you saying that you got a molwt of 45? I ran the same commands and got a
molwt of 58.1222, which is correct for butane.
mc
-----Original Message-----
From: Steven Wathen [mailto:SW...@si...]
Sent: Sunday, 30 March 2008 8:54 AM
To: lunchbox99; 'Noel O'Boyle'
Cc: ope...@li...
Subject: RE: [OpenBabel-scripting] problem installing openbabel for python
on windows
Hi Noel and MC,
I just installed Python 2.5.2 on my office computer, and pybel works -
although I found that readlines and Smarts give errors, where
pybel.readlines and pybel.Smarts work ok.
An odd thing I noticed, when I tried the example:
>>> mymol = readstring("smi", "CCCC")
>>> print mymol.molwt
45
the MW that I got was 58! I'm not sure if I did something strange, or pybel
is doing something strange.
I'm going to try installing Python 2.5.2 on my laptop (my usual computer)
and see it pybel works. Currently I have Python 2.5.1 on that computer.
Thanks,
Steve
-------------
Dr. Steven P. Wathen
Associate Professor of Chemistry
Siena Heights University
1247 East Siena Heights Drive
Adrian, MI 49221
(517) 264-7657
sw...@si...
________________________________________
From: lunchbox99 [lun...@tp...]
Sent: Saturday, March 29, 2008 6:32 PM
To: 'Noel O'Boyle'; Steven Wathen
Cc: ope...@li...
Subject: RE: [OpenBabel-scripting] problem installing openbabel for python
on windows
To confirm from a non-developer. I just installed python 2.5.2 on vista SP1.
I then installed the openbabel python wrappers
"openbabel-python-1.2.2.py2.5.exe". After opening a python shell at the
command prompt, importing openbabel or pybel works fine. I have done nothing
special to this pc.
mc
-----Original Message-----
From: ope...@li...
[mailto:ope...@li...] On Behalf Of Noel
O'Boyle
Sent: Sunday, 30 March 2008 4:48 AM
To: Steven Wathen
Cc: ope...@li...
Subject: Re: [OpenBabel-scripting] problem installing openbabel for python
on windows
Hello Steven,
Sorry about the problem. I've just downloaded and installed the file
myself, just to verify that it works for me. The bad news is that
another user also reported a similar bug and we were not able to
figure out what the problem is. Can someone (who is not a developer)
confirm that this installation file works for them?
In the meanwhile, can you test the following? Rather than using IDLE,
could you open a command prompt and run python, and try importing
pybel there.
You could also try installing Python2.4 instead, and the corresponding
Pybel. What version of Windows are you using exactly?
This is a serious problem, but unfortunately I really have no idea how
to reproduce the bug, or how to fix it. :-/
- Noel
On 28/03/2008, Steven Wathen <SW...@si...> wrote:
> Hello,
>
> I am interested in using the Open Babel module for Python on Windows, but
it doesn't seem to install properly.
>
> I installed the file at
http://downloads.sourceforge.net/openbabel/openbabel-python-1.2.2.py2.5.exe
> then I restarted my computer.
>
> I then opened IDLE and tried to do some of the examples listed on the web
site. This is what I got:
>
> >>> from openbabel import *
>
> Traceback (most recent call last):
> File "<pyshell#0>", line 1, in <module>
> from openbabel import *
> File "C:\Python25\Lib\site-packages\openbabel.py", line 7, in <module>
> import _openbabel
> ImportError: DLL load failed: This application has failed to start
because the application configuration is incorrect. Reinstalling the
application may fix this problem.
>
> >>> from pybel import *
>
> Traceback (most recent call last):
> File "<pyshell#1>", line 1, in <module>
> from pybel import *
> File "C:\Python25\Lib\site-packages\pybel.py", line 1, in <module>
> import openbabel as ob
> File "C:\Python25\Lib\site-packages\openbabel.py", line 7, in <module>
> import _openbabel
> ImportError: DLL load failed: This application has failed to start
because the application configuration is incorrect. Reinstalling the
application may fix this problem.
> >>>
>
>
> I then thought that maybe the OpenBabelGUI was needed to use the Python
bindings. I installed the OpenBabelGUI and it seems to run by itself fine.
But accessing Open Babel from Python gives the same error message as before.
>
> I uninstalled the openbabel-python-1.2.2.py2.5.exe, downloaded the
installation file again, re-installed and rebooted my computer. Same error
message.
>
> Can you tell me what I am doing wrong?
>
> Thanks for your help,
>
> Steve
>
>
> -------------
> Dr. Steven P. Wathen
> Associate Professor of Chemistry
> Siena Heights University
> 1247 East Siena Heights Drive
> Adrian, MI 49221
>
> (517) 264-7657
> sw...@si...
>
> -------------------------------------------------------------------------
> Check out the new SourceForge.net Marketplace.
> It's the best place to buy or sell services for
> just about anything Open Source.
>
http://ad.doubleclick.net/clk;164216239;13503038;w?http://sf.net/marketplace
> _______________________________________________
> OpenBabel-scripting mailing list
> Ope...@li...
> https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
>
-------------------------------------------------------------------------
Check out the new SourceForge.net Marketplace.
It's the best place to buy or sell services for
just about anything Open Source.
http://ad.doubleclick.net/clk;164216239;13503038;w?http://sf.net/marketplace
_______________________________________________
OpenBabel-scripting mailing list
Ope...@li...
https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
|
|
From: Steven W. <SW...@si...> - 2008-03-30 00:14:19
|
Hi, I have access to three computers - I can get openbabel/pybel to work on only one of them. My office computer is running WinXP - Professional Edition: Python 2.5.2 and openbabel/pybel work. My Laptop is running WinXP Media Center Edition SP2, my home computer is running WinXP Home Edition SP2 - neither of these computers will run openbabel/pybel from Python 2.5.2 I hope this helps to narrow down the problem - I'm afraid I don't know why it would make a difference which version of WinXP, SP2 I am running. Steve ------------- Dr. Steven P. Wathen Associate Professor of Chemistry Siena Heights University 1247 East Siena Heights Drive Adrian, MI 49221 (517) 264-7657 sw...@si... ________________________________________ From: lunchbox99 [lun...@tp...] Sent: Saturday, March 29, 2008 6:32 PM To: 'Noel O'Boyle'; Steven Wathen Cc: ope...@li... Subject: RE: [OpenBabel-scripting] problem installing openbabel for python on windows To confirm from a non-developer. I just installed python 2.5.2 on vista SP1. I then installed the openbabel python wrappers "openbabel-python-1.2.2.py2.5.exe". After opening a python shell at the command prompt, importing openbabel or pybel works fine. I have done nothing special to this pc. mc -----Original Message----- From: ope...@li... [mailto:ope...@li...] On Behalf Of Noel O'Boyle Sent: Sunday, 30 March 2008 4:48 AM To: Steven Wathen Cc: ope...@li... Subject: Re: [OpenBabel-scripting] problem installing openbabel for python on windows Hello Steven, Sorry about the problem. I've just downloaded and installed the file myself, just to verify that it works for me. The bad news is that another user also reported a similar bug and we were not able to figure out what the problem is. Can someone (who is not a developer) confirm that this installation file works for them? In the meanwhile, can you test the following? Rather than using IDLE, could you open a command prompt and run python, and try importing pybel there. You could also try installing Python2.4 instead, and the corresponding Pybel. What version of Windows are you using exactly? This is a serious problem, but unfortunately I really have no idea how to reproduce the bug, or how to fix it. :-/ - Noel On 28/03/2008, Steven Wathen <SW...@si...> wrote: > Hello, > > I am interested in using the Open Babel module for Python on Windows, but it doesn't seem to install properly. > > I installed the file at http://downloads.sourceforge.net/openbabel/openbabel-python-1.2.2.py2.5.exe > then I restarted my computer. > > I then opened IDLE and tried to do some of the examples listed on the web site. This is what I got: > > >>> from openbabel import * > > Traceback (most recent call last): > File "<pyshell#0>", line 1, in <module> > from openbabel import * > File "C:\Python25\Lib\site-packages\openbabel.py", line 7, in <module> > import _openbabel > ImportError: DLL load failed: This application has failed to start because the application configuration is incorrect. Reinstalling the application may fix this problem. > > >>> from pybel import * > > Traceback (most recent call last): > File "<pyshell#1>", line 1, in <module> > from pybel import * > File "C:\Python25\Lib\site-packages\pybel.py", line 1, in <module> > import openbabel as ob > File "C:\Python25\Lib\site-packages\openbabel.py", line 7, in <module> > import _openbabel > ImportError: DLL load failed: This application has failed to start because the application configuration is incorrect. Reinstalling the application may fix this problem. > >>> > > > I then thought that maybe the OpenBabelGUI was needed to use the Python bindings. I installed the OpenBabelGUI and it seems to run by itself fine. But accessing Open Babel from Python gives the same error message as before. > > I uninstalled the openbabel-python-1.2.2.py2.5.exe, downloaded the installation file again, re-installed and rebooted my computer. Same error message. > > Can you tell me what I am doing wrong? > > Thanks for your help, > > Steve > > > ------------- > Dr. Steven P. Wathen > Associate Professor of Chemistry > Siena Heights University > 1247 East Siena Heights Drive > Adrian, MI 49221 > > (517) 264-7657 > sw...@si... > > ------------------------------------------------------------------------- > Check out the new SourceForge.net Marketplace. > It's the best place to buy or sell services for > just about anything Open Source. > http://ad.doubleclick.net/clk;164216239;13503038;w?http://sf.net/marketplace > _______________________________________________ > OpenBabel-scripting mailing list > Ope...@li... > https://lists.sourceforge.net/lists/listinfo/openbabel-scripting > ------------------------------------------------------------------------- Check out the new SourceForge.net Marketplace. It's the best place to buy or sell services for just about anything Open Source. http://ad.doubleclick.net/clk;164216239;13503038;w?http://sf.net/marketplace _______________________________________________ OpenBabel-scripting mailing list Ope...@li... https://lists.sourceforge.net/lists/listinfo/openbabel-scripting |
|
From: Steven W. <SW...@si...> - 2008-03-29 22:54:19
|
Hi Noel and MC,
I just installed Python 2.5.2 on my office computer, and pybel works - although I found that readlines and Smarts give errors, where pybel.readlines and pybel.Smarts work ok.
An odd thing I noticed, when I tried the example:
>>> mymol = readstring("smi", "CCCC")
>>> print mymol.molwt
45
the MW that I got was 58! I'm not sure if I did something strange, or pybel is doing something strange.
I'm going to try installing Python 2.5.2 on my laptop (my usual computer) and see it pybel works. Currently I have Python 2.5.1 on that computer.
Thanks,
Steve
-------------
Dr. Steven P. Wathen
Associate Professor of Chemistry
Siena Heights University
1247 East Siena Heights Drive
Adrian, MI 49221
(517) 264-7657
sw...@si...
________________________________________
From: lunchbox99 [lun...@tp...]
Sent: Saturday, March 29, 2008 6:32 PM
To: 'Noel O'Boyle'; Steven Wathen
Cc: ope...@li...
Subject: RE: [OpenBabel-scripting] problem installing openbabel for python on windows
To confirm from a non-developer. I just installed python 2.5.2 on vista SP1.
I then installed the openbabel python wrappers
"openbabel-python-1.2.2.py2.5.exe". After opening a python shell at the
command prompt, importing openbabel or pybel works fine. I have done nothing
special to this pc.
mc
-----Original Message-----
From: ope...@li...
[mailto:ope...@li...] On Behalf Of Noel
O'Boyle
Sent: Sunday, 30 March 2008 4:48 AM
To: Steven Wathen
Cc: ope...@li...
Subject: Re: [OpenBabel-scripting] problem installing openbabel for python
on windows
Hello Steven,
Sorry about the problem. I've just downloaded and installed the file
myself, just to verify that it works for me. The bad news is that
another user also reported a similar bug and we were not able to
figure out what the problem is. Can someone (who is not a developer)
confirm that this installation file works for them?
In the meanwhile, can you test the following? Rather than using IDLE,
could you open a command prompt and run python, and try importing
pybel there.
You could also try installing Python2.4 instead, and the corresponding
Pybel. What version of Windows are you using exactly?
This is a serious problem, but unfortunately I really have no idea how
to reproduce the bug, or how to fix it. :-/
- Noel
On 28/03/2008, Steven Wathen <SW...@si...> wrote:
> Hello,
>
> I am interested in using the Open Babel module for Python on Windows, but
it doesn't seem to install properly.
>
> I installed the file at
http://downloads.sourceforge.net/openbabel/openbabel-python-1.2.2.py2.5.exe
> then I restarted my computer.
>
> I then opened IDLE and tried to do some of the examples listed on the web
site. This is what I got:
>
> >>> from openbabel import *
>
> Traceback (most recent call last):
> File "<pyshell#0>", line 1, in <module>
> from openbabel import *
> File "C:\Python25\Lib\site-packages\openbabel.py", line 7, in <module>
> import _openbabel
> ImportError: DLL load failed: This application has failed to start
because the application configuration is incorrect. Reinstalling the
application may fix this problem.
>
> >>> from pybel import *
>
> Traceback (most recent call last):
> File "<pyshell#1>", line 1, in <module>
> from pybel import *
> File "C:\Python25\Lib\site-packages\pybel.py", line 1, in <module>
> import openbabel as ob
> File "C:\Python25\Lib\site-packages\openbabel.py", line 7, in <module>
> import _openbabel
> ImportError: DLL load failed: This application has failed to start
because the application configuration is incorrect. Reinstalling the
application may fix this problem.
> >>>
>
>
> I then thought that maybe the OpenBabelGUI was needed to use the Python
bindings. I installed the OpenBabelGUI and it seems to run by itself fine.
But accessing Open Babel from Python gives the same error message as before.
>
> I uninstalled the openbabel-python-1.2.2.py2.5.exe, downloaded the
installation file again, re-installed and rebooted my computer. Same error
message.
>
> Can you tell me what I am doing wrong?
>
> Thanks for your help,
>
> Steve
>
>
> -------------
> Dr. Steven P. Wathen
> Associate Professor of Chemistry
> Siena Heights University
> 1247 East Siena Heights Drive
> Adrian, MI 49221
>
> (517) 264-7657
> sw...@si...
>
> -------------------------------------------------------------------------
> Check out the new SourceForge.net Marketplace.
> It's the best place to buy or sell services for
> just about anything Open Source.
>
http://ad.doubleclick.net/clk;164216239;13503038;w?http://sf.net/marketplace
> _______________________________________________
> OpenBabel-scripting mailing list
> Ope...@li...
> https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
>
-------------------------------------------------------------------------
Check out the new SourceForge.net Marketplace.
It's the best place to buy or sell services for
just about anything Open Source.
http://ad.doubleclick.net/clk;164216239;13503038;w?http://sf.net/marketplace
_______________________________________________
OpenBabel-scripting mailing list
Ope...@li...
https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
|
|
From: lunchbox99 <lun...@tp...> - 2008-03-29 22:32:32
|
To confirm from a non-developer. I just installed python 2.5.2 on vista SP1. I then installed the openbabel python wrappers "openbabel-python-1.2.2.py2.5.exe". After opening a python shell at the command prompt, importing openbabel or pybel works fine. I have done nothing special to this pc. mc -----Original Message----- From: ope...@li... [mailto:ope...@li...] On Behalf Of Noel O'Boyle Sent: Sunday, 30 March 2008 4:48 AM To: Steven Wathen Cc: ope...@li... Subject: Re: [OpenBabel-scripting] problem installing openbabel for python on windows Hello Steven, Sorry about the problem. I've just downloaded and installed the file myself, just to verify that it works for me. The bad news is that another user also reported a similar bug and we were not able to figure out what the problem is. Can someone (who is not a developer) confirm that this installation file works for them? In the meanwhile, can you test the following? Rather than using IDLE, could you open a command prompt and run python, and try importing pybel there. You could also try installing Python2.4 instead, and the corresponding Pybel. What version of Windows are you using exactly? This is a serious problem, but unfortunately I really have no idea how to reproduce the bug, or how to fix it. :-/ - Noel On 28/03/2008, Steven Wathen <SW...@si...> wrote: > Hello, > > I am interested in using the Open Babel module for Python on Windows, but it doesn't seem to install properly. > > I installed the file at http://downloads.sourceforge.net/openbabel/openbabel-python-1.2.2.py2.5.exe > then I restarted my computer. > > I then opened IDLE and tried to do some of the examples listed on the web site. This is what I got: > > >>> from openbabel import * > > Traceback (most recent call last): > File "<pyshell#0>", line 1, in <module> > from openbabel import * > File "C:\Python25\Lib\site-packages\openbabel.py", line 7, in <module> > import _openbabel > ImportError: DLL load failed: This application has failed to start because the application configuration is incorrect. Reinstalling the application may fix this problem. > > >>> from pybel import * > > Traceback (most recent call last): > File "<pyshell#1>", line 1, in <module> > from pybel import * > File "C:\Python25\Lib\site-packages\pybel.py", line 1, in <module> > import openbabel as ob > File "C:\Python25\Lib\site-packages\openbabel.py", line 7, in <module> > import _openbabel > ImportError: DLL load failed: This application has failed to start because the application configuration is incorrect. Reinstalling the application may fix this problem. > >>> > > > I then thought that maybe the OpenBabelGUI was needed to use the Python bindings. I installed the OpenBabelGUI and it seems to run by itself fine. But accessing Open Babel from Python gives the same error message as before. > > I uninstalled the openbabel-python-1.2.2.py2.5.exe, downloaded the installation file again, re-installed and rebooted my computer. Same error message. > > Can you tell me what I am doing wrong? > > Thanks for your help, > > Steve > > > ------------- > Dr. Steven P. Wathen > Associate Professor of Chemistry > Siena Heights University > 1247 East Siena Heights Drive > Adrian, MI 49221 > > (517) 264-7657 > sw...@si... > > ------------------------------------------------------------------------- > Check out the new SourceForge.net Marketplace. > It's the best place to buy or sell services for > just about anything Open Source. > http://ad.doubleclick.net/clk;164216239;13503038;w?http://sf.net/marketplace > _______________________________________________ > OpenBabel-scripting mailing list > Ope...@li... > https://lists.sourceforge.net/lists/listinfo/openbabel-scripting > ------------------------------------------------------------------------- Check out the new SourceForge.net Marketplace. It's the best place to buy or sell services for just about anything Open Source. http://ad.doubleclick.net/clk;164216239;13503038;w?http://sf.net/marketplace _______________________________________________ OpenBabel-scripting mailing list Ope...@li... https://lists.sourceforge.net/lists/listinfo/openbabel-scripting |
|
From: Steven W. <SW...@si...> - 2008-03-29 19:57:54
|
Hi Noel, I tried running Python from the command line. When I try to import openbabel or pybel, I get the same error as before. For some reason it is unable to access the file _openbabel.pyd properly. I will try installing Python 2.4 and see if that works. I'll let you know what happens. Thanks, Steve ------------- Dr. Steven P. Wathen Associate Professor of Chemistry Siena Heights University 1247 East Siena Heights Drive Adrian, MI 49221 (517) 264-7657 sw...@si... ________________________________________ From: Noel O'Boyle [bao...@gm...] Sent: Saturday, March 29, 2008 2:47 PM To: Steven Wathen Cc: ope...@li... Subject: Re: [OpenBabel-scripting] problem installing openbabel for python on windows Hello Steven, Sorry about the problem. I've just downloaded and installed the file myself, just to verify that it works for me. The bad news is that another user also reported a similar bug and we were not able to figure out what the problem is. Can someone (who is not a developer) confirm that this installation file works for them? In the meanwhile, can you test the following? Rather than using IDLE, could you open a command prompt and run python, and try importing pybel there. You could also try installing Python2.4 instead, and the corresponding Pybel. What version of Windows are you using exactly? This is a serious problem, but unfortunately I really have no idea how to reproduce the bug, or how to fix it. :-/ - Noel On 28/03/2008, Steven Wathen <SW...@si...> wrote: > Hello, > > I am interested in using the Open Babel module for Python on Windows, but it doesn't seem to install properly. > > I installed the file at http://downloads.sourceforge.net/openbabel/openbabel-python-1.2.2.py2.5.exe > then I restarted my computer. > > I then opened IDLE and tried to do some of the examples listed on the web site. This is what I got: > > >>> from openbabel import * > > Traceback (most recent call last): > File "<pyshell#0>", line 1, in <module> > from openbabel import * > File "C:\Python25\Lib\site-packages\openbabel.py", line 7, in <module> > import _openbabel > ImportError: DLL load failed: This application has failed to start because the application configuration is incorrect. Reinstalling the application may fix this problem. > > >>> from pybel import * > > Traceback (most recent call last): > File "<pyshell#1>", line 1, in <module> > from pybel import * > File "C:\Python25\Lib\site-packages\pybel.py", line 1, in <module> > import openbabel as ob > File "C:\Python25\Lib\site-packages\openbabel.py", line 7, in <module> > import _openbabel > ImportError: DLL load failed: This application has failed to start because the application configuration is incorrect. Reinstalling the application may fix this problem. > >>> > > > I then thought that maybe the OpenBabelGUI was needed to use the Python bindings. I installed the OpenBabelGUI and it seems to run by itself fine. But accessing Open Babel from Python gives the same error message as before. > > I uninstalled the openbabel-python-1.2.2.py2.5.exe, downloaded the installation file again, re-installed and rebooted my computer. Same error message. > > Can you tell me what I am doing wrong? > > Thanks for your help, > > Steve > > > ------------- > Dr. Steven P. Wathen > Associate Professor of Chemistry > Siena Heights University > 1247 East Siena Heights Drive > Adrian, MI 49221 > > (517) 264-7657 > sw...@si... > > ------------------------------------------------------------------------- > Check out the new SourceForge.net Marketplace. > It's the best place to buy or sell services for > just about anything Open Source. > http://ad.doubleclick.net/clk;164216239;13503038;w?http://sf.net/marketplace > _______________________________________________ > OpenBabel-scripting mailing list > Ope...@li... > https://lists.sourceforge.net/lists/listinfo/openbabel-scripting > |
|
From: Noel O'B. <bao...@gm...> - 2008-03-29 18:47:31
|
Hello Steven, Sorry about the problem. I've just downloaded and installed the file myself, just to verify that it works for me. The bad news is that another user also reported a similar bug and we were not able to figure out what the problem is. Can someone (who is not a developer) confirm that this installation file works for them? In the meanwhile, can you test the following? Rather than using IDLE, could you open a command prompt and run python, and try importing pybel there. You could also try installing Python2.4 instead, and the corresponding Pybel. What version of Windows are you using exactly? This is a serious problem, but unfortunately I really have no idea how to reproduce the bug, or how to fix it. :-/ - Noel On 28/03/2008, Steven Wathen <SW...@si...> wrote: > Hello, > > I am interested in using the Open Babel module for Python on Windows, but it doesn't seem to install properly. > > I installed the file at http://downloads.sourceforge.net/openbabel/openbabel-python-1.2.2.py2.5.exe > then I restarted my computer. > > I then opened IDLE and tried to do some of the examples listed on the web site. This is what I got: > > >>> from openbabel import * > > Traceback (most recent call last): > File "<pyshell#0>", line 1, in <module> > from openbabel import * > File "C:\Python25\Lib\site-packages\openbabel.py", line 7, in <module> > import _openbabel > ImportError: DLL load failed: This application has failed to start because the application configuration is incorrect. Reinstalling the application may fix this problem. > > >>> from pybel import * > > Traceback (most recent call last): > File "<pyshell#1>", line 1, in <module> > from pybel import * > File "C:\Python25\Lib\site-packages\pybel.py", line 1, in <module> > import openbabel as ob > File "C:\Python25\Lib\site-packages\openbabel.py", line 7, in <module> > import _openbabel > ImportError: DLL load failed: This application has failed to start because the application configuration is incorrect. Reinstalling the application may fix this problem. > >>> > > > I then thought that maybe the OpenBabelGUI was needed to use the Python bindings. I installed the OpenBabelGUI and it seems to run by itself fine. But accessing Open Babel from Python gives the same error message as before. > > I uninstalled the openbabel-python-1.2.2.py2.5.exe, downloaded the installation file again, re-installed and rebooted my computer. Same error message. > > Can you tell me what I am doing wrong? > > Thanks for your help, > > Steve > > > ------------- > Dr. Steven P. Wathen > Associate Professor of Chemistry > Siena Heights University > 1247 East Siena Heights Drive > Adrian, MI 49221 > > (517) 264-7657 > sw...@si... > > ------------------------------------------------------------------------- > Check out the new SourceForge.net Marketplace. > It's the best place to buy or sell services for > just about anything Open Source. > http://ad.doubleclick.net/clk;164216239;13503038;w?http://sf.net/marketplace > _______________________________________________ > OpenBabel-scripting mailing list > Ope...@li... > https://lists.sourceforge.net/lists/listinfo/openbabel-scripting > |
|
From: Chris M. <c.m...@ds...> - 2008-03-29 09:15:42
|
Noel O'Boyle wrote:
> pybel just uses the default options of each format. But even OpenBabel
> currently doesn't seem to have the option you are looking for:
> "InChI format\n"
> "IUPAC/NIST molecular identifier\n"
> "Write options, e.g. -xat\n"
> " X <Option string> List of InChI options:\n"
On 27/03/2008, yez...@tp... <yez...@tp...> wrote:
> > I am trying to generate InChi codes using pybel like this:
> >
> > descriptor={}
> > descriptor['INCHI']=mol.write('INCHI')
> >
> > While running, the output window reports an InChi warning that
protons have been added or
> > removed. When I examine the structures, the InChi generation has
produced a new tautomeric form
> > for many molecules eg amides as imine-alcohols. The corresponding
smiles representation using
> > mol.write('CAN') works as expected ie the same tautomer as the
input structure.
> >
> > I am aware that InChi allows the generation of mobile H atom and
fixed H atom models - can I pass
> > something to mol.write('INCHI') to generate a fixed-H atom
representation?
> >
On the babel commandline adding the option -xX "FixedH" would include a
fixed hydrogen layer in the InChI. This is a bit cumbersome so I have
added a couple of other options to the development code.
F include fixed hydrogen layer
M include bonds to metal
You can now call simple output options like these from C++ code like
conv.AddOption("F");
where conv is the OBConversion object.
I guess the syntax from Python is similar. Maybe Pybel could wrap option
calls for output formats somehow?
Chris
|
|
From: Steven W. <SW...@si...> - 2008-03-28 19:32:42
|
Hi Thanks for responding.
Python works fine on my computer
import openbabel
and
import pybel
give the same error message I got before.
I looked in c:\python25\lib\site-packages
there are several files with openbabel or pybel in the names present, as well as a folder named openbabel_data
_openbabel.pyd, openbabel.py, openbabel.pyc, openbabel.pyo, openbabel_python-1.2.2-py2.5.egg-info, OpenBabelDLL.dll
pybel.py, pybel.pyc, pybel.pyo
Steve
-------------
Dr. Steven P. Wathen
Associate Professor of Chemistry
Siena Heights University
1247 East Siena Heights Drive
Adrian, MI 49221
(517) 264-7657
sw...@si...
________________________________________
From: Lunchbox99 [lun...@tp...]
Sent: Friday, March 28, 2008 3:10 PM
To: Steven Wathen
Cc: ope...@li...
Subject: Re: [OpenBabel-scripting] problem installing openbabel for python on windows
First, you do not need the GUI apps installed to use the python
wrappers. Does your python 2.5 work otherwise ie does "import os"
return an error?
Try importing openbabel with the simple form to avoid namespace
problems:
import openbabel
import pybel
If it works, you can combine on one line "import openbabel, pybel"
Do the openbabel files exist in "c:\python25\lib\site-packages"? If
not, they are possibly not installed properly.
I apologize for any spelling mistakes, this email was sent from my
iPod touch at 5am!!
On 29/03/2008, at 1:01 AM, Steven Wathen <SW...@si...>
wrote:
> Hello,
>
> I am interested in using the Open Babel module for Python on
> Windows, but it doesn't seem to install properly.
>
> I installed the file at http://downloads.sourceforge.net/openbabel/openbabel-python-1.2.2.py2.5.exe
> then I restarted my computer.
>
> I then opened IDLE and tried to do some of the examples listed on
> the web site. This is what I got:
>
>>>> from openbabel import *
>
> Traceback (most recent call last):
> File "<pyshell#0>", line 1, in <module>
> from openbabel import *
> File "C:\Python25\Lib\site-packages\openbabel.py", line 7, in
> <module>
> import _openbabel
> ImportError: DLL load failed: This application has failed to start
> because the application configuration is incorrect. Reinstalling the
> application may fix this problem.
>
>>>> from pybel import *
>
> Traceback (most recent call last):
> File "<pyshell#1>", line 1, in <module>
> from pybel import *
> File "C:\Python25\Lib\site-packages\pybel.py", line 1, in <module>
> import openbabel as ob
> File "C:\Python25\Lib\site-packages\openbabel.py", line 7, in
> <module>
> import _openbabel
> ImportError: DLL load failed: This application has failed to start
> because the application configuration is incorrect. Reinstalling the
> application may fix this problem.
>>>>
>
>
> I then thought that maybe the OpenBabelGUI was needed to use the
> Python bindings. I installed the OpenBabelGUI and it seems to run
> by itself fine. But accessing Open Babel from Python gives the same
> error message as before.
>
> I uninstalled the openbabel-python-1.2.2.py2.5.exe, downloaded the
> installation file again, re-installed and rebooted my computer.
> Same error message.
>
> Can you tell me what I am doing wrong?
>
> Thanks for your help,
>
> Steve
>
>
> -------------
> Dr. Steven P. Wathen
> Associate Professor of Chemistry
> Siena Heights University
> 1247 East Siena Heights Drive
> Adrian, MI 49221
>
> (517) 264-7657
> sw...@si...
>
> ---
> ----------------------------------------------------------------------
> Check out the new SourceForge.net Marketplace.
> It's the best place to buy or sell services for
> just about anything Open Source.
> http://ad.doubleclick.net/clk;164216239;13503038;w?http://sf.net/marketplace
> _______________________________________________
> OpenBabel-scripting mailing list
> Ope...@li...
> https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
>
>
|
|
From: Lunchbox99 <lun...@tp...> - 2008-03-28 19:15:34
|
First, you do not need the GUI apps installed to use the python wrappers. Does your python 2.5 work otherwise ie does "import os" return an error? Try importing openbabel with the simple form to avoid namespace problems: import openbabel import pybel If it works, you can combine on one line "import openbabel, pybel" Do the openbabel files exist in "c:\python25\lib\site-packages"? If not, they are possibly not installed properly. I apologize for any spelling mistakes, this email was sent from my iPod touch at 5am!! On 29/03/2008, at 1:01 AM, Steven Wathen <SW...@si...> wrote: > Hello, > > I am interested in using the Open Babel module for Python on > Windows, but it doesn't seem to install properly. > > I installed the file at http://downloads.sourceforge.net/openbabel/openbabel-python-1.2.2.py2.5.exe > then I restarted my computer. > > I then opened IDLE and tried to do some of the examples listed on > the web site. This is what I got: > >>>> from openbabel import * > > Traceback (most recent call last): > File "<pyshell#0>", line 1, in <module> > from openbabel import * > File "C:\Python25\Lib\site-packages\openbabel.py", line 7, in > <module> > import _openbabel > ImportError: DLL load failed: This application has failed to start > because the application configuration is incorrect. Reinstalling the > application may fix this problem. > >>>> from pybel import * > > Traceback (most recent call last): > File "<pyshell#1>", line 1, in <module> > from pybel import * > File "C:\Python25\Lib\site-packages\pybel.py", line 1, in <module> > import openbabel as ob > File "C:\Python25\Lib\site-packages\openbabel.py", line 7, in > <module> > import _openbabel > ImportError: DLL load failed: This application has failed to start > because the application configuration is incorrect. Reinstalling the > application may fix this problem. >>>> > > > I then thought that maybe the OpenBabelGUI was needed to use the > Python bindings. I installed the OpenBabelGUI and it seems to run > by itself fine. But accessing Open Babel from Python gives the same > error message as before. > > I uninstalled the openbabel-python-1.2.2.py2.5.exe, downloaded the > installation file again, re-installed and rebooted my computer. > Same error message. > > Can you tell me what I am doing wrong? > > Thanks for your help, > > Steve > > > ------------- > Dr. Steven P. Wathen > Associate Professor of Chemistry > Siena Heights University > 1247 East Siena Heights Drive > Adrian, MI 49221 > > (517) 264-7657 > sw...@si... > > --- > ---------------------------------------------------------------------- > Check out the new SourceForge.net Marketplace. > It's the best place to buy or sell services for > just about anything Open Source. > http://ad.doubleclick.net/clk;164216239;13503038;w?http://sf.net/marketplace > _______________________________________________ > OpenBabel-scripting mailing list > Ope...@li... > https://lists.sourceforge.net/lists/listinfo/openbabel-scripting > > |
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From: Steven W. <SW...@si...> - 2008-03-28 15:01:57
|
Hello, I am interested in using the Open Babel module for Python on Windows, but it doesn't seem to install properly. I installed the file at http://downloads.sourceforge.net/openbabel/openbabel-python-1.2.2.py2.5.exe then I restarted my computer. I then opened IDLE and tried to do some of the examples listed on the web site. This is what I got: >>> from openbabel import * Traceback (most recent call last): File "<pyshell#0>", line 1, in <module> from openbabel import * File "C:\Python25\Lib\site-packages\openbabel.py", line 7, in <module> import _openbabel ImportError: DLL load failed: This application has failed to start because the application configuration is incorrect. Reinstalling the application may fix this problem. >>> from pybel import * Traceback (most recent call last): File "<pyshell#1>", line 1, in <module> from pybel import * File "C:\Python25\Lib\site-packages\pybel.py", line 1, in <module> import openbabel as ob File "C:\Python25\Lib\site-packages\openbabel.py", line 7, in <module> import _openbabel ImportError: DLL load failed: This application has failed to start because the application configuration is incorrect. Reinstalling the application may fix this problem. >>> I then thought that maybe the OpenBabelGUI was needed to use the Python bindings. I installed the OpenBabelGUI and it seems to run by itself fine. But accessing Open Babel from Python gives the same error message as before. I uninstalled the openbabel-python-1.2.2.py2.5.exe, downloaded the installation file again, re-installed and rebooted my computer. Same error message. Can you tell me what I am doing wrong? Thanks for your help, Steve ------------- Dr. Steven P. Wathen Associate Professor of Chemistry Siena Heights University 1247 East Siena Heights Drive Adrian, MI 49221 (517) 264-7657 sw...@si... |
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From: Noel O'B. <bao...@gm...> - 2008-03-28 10:03:28
|
On 28/03/2008, lunchbox99 <lun...@tp...> wrote:
> Thanks Noel. Perhaps I should also declare my relative newbie status when it
> comes to matters InChi related. I usually use canonical smiles.
>
> I am aware that mobile H treatment is deliberate and the default behavior to
> presumably facilitate comparisons between tautomers from various sources. I
> am using openbabel via the python wrappers to write a structural profiler
> script for a sample registration tool. The InChi code is being tested as a
> structure storage mechanism for a database of ~200k samples (real samples,
> not virtual). I will also store canonical smiles to provide a backup
> solution if the InChi proves problematic.
>
> If the stored InChi structure is read from the database and viewed,
> chemists/biologists will not understand why the structures are "wrong"...
> they would expect amides to look like amides, not imino-alcohols. If
> openbabel does not support fixed-H InChi, maybe I will just stick with
> cansmiles for structure viewing and only use InChi internally to facilitate
> duplicate checking.
This may be a good solution. My understanding of InChI is that they
are intended for creating a unique string for each molecule. In other
words, they are not ready meant to be read and interpreted. It may be
possible to use OpenBabel to generate the various tautomers
corresponding to a particular structure though. Also, if storage space
is a problem, and you are not going to be reading the InChI, you may
want to use InChiKeys instead.
HTH
> mc
>
>
>
> -----Original Message-----
> From: Noel O'Boyle [mailto:bao...@gm...]
> Sent: Friday, 28 March 2008 6:52 AM
> To: yez...@tp...
> Cc: ope...@li...; Chris Morley
> Subject: Re: [OpenBabel-scripting] InChi generation options
>
> Just to clarify, I assume that you are aware that the current
> behaviour is the correct default. Different tautomers of the same
> molecule should have the same InChI. That is one of the core ideas of
> the InChI.
>
> Noel
>
> On 27/03/2008, Noel O'Boyle <bao...@gm...> wrote:
> > pybel just uses the default options of each format. But even OpenBabel
> > currently doesn't seem to have the option you are looking for:
> > "InChI format\n"
> > "IUPAC/NIST molecular identifier\n"
> > "Write options, e.g. -xat\n"
> > " X <Option string> List of InChI options:\n"
> > " t add molecule name\n"
> > " a output auxilliary information\n"
> > " K output InChIKey\n"
> > " u output only unique molecules\n"
> > " U output only unique molecules and sort them\n"
> > " e compare first molecule to others\n"
> > " w don't warn on undef stereo or charge rearrangement\n\n"
> >
> > I am not very familiar with InChI beyond the basics. Perhaps Geoff or
> > Chris can comment on whether this option could be added.
> >
> >
> > Noel
> >
> >
> > On 27/03/2008, yez...@tp... <yez...@tp...> wrote:
> > > I am trying to generate InChi codes using pybel like this:
> > >
> > > descriptor={}
> > > descriptor['INCHI']=mol.write('INCHI')
> > >
> > > While running, the output window reports an InChi warning that protons
> have been added or
> > > removed. When I examine the structures, the InChi generation has
> produced a new tautomeric form
> > > for many molecules eg amides as imine-alcohols. The corresponding
> smiles representation using
> > > mol.write('CAN') works as expected ie the same tautomer as the input
> structure.
> > >
> > > I am aware that InChi allows the generation of mobile H atom and fixed
> H atom models - can I pass
> > > something to mol.write('INCHI') to generate a fixed-H atom
> representation?
> > >
> > >
> > >
> > >
> -------------------------------------------------------------------------
> > > Check out the new SourceForge.net Marketplace.
> > > It's the best place to buy or sell services for
> > > just about anything Open Source.
> > >
> http://ad.doubleclick.net/clk;164216239;13503038;w?http://sf.net/marketplace
> > > _______________________________________________
> > > OpenBabel-scripting mailing list
> > > Ope...@li...
> > > https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
> > >
> >
>
>
>
|
|
From: Noel O'B. <bao...@gm...> - 2008-03-27 20:51:58
|
Just to clarify, I assume that you are aware that the current
behaviour is the correct default. Different tautomers of the same
molecule should have the same InChI. That is one of the core ideas of
the InChI.
Noel
On 27/03/2008, Noel O'Boyle <bao...@gm...> wrote:
> pybel just uses the default options of each format. But even OpenBabel
> currently doesn't seem to have the option you are looking for:
> "InChI format\n"
> "IUPAC/NIST molecular identifier\n"
> "Write options, e.g. -xat\n"
> " X <Option string> List of InChI options:\n"
> " t add molecule name\n"
> " a output auxilliary information\n"
> " K output InChIKey\n"
> " u output only unique molecules\n"
> " U output only unique molecules and sort them\n"
> " e compare first molecule to others\n"
> " w don't warn on undef stereo or charge rearrangement\n\n"
>
> I am not very familiar with InChI beyond the basics. Perhaps Geoff or
> Chris can comment on whether this option could be added.
>
>
> Noel
>
>
> On 27/03/2008, yez...@tp... <yez...@tp...> wrote:
> > I am trying to generate InChi codes using pybel like this:
> >
> > descriptor={}
> > descriptor['INCHI']=mol.write('INCHI')
> >
> > While running, the output window reports an InChi warning that protons have been added or
> > removed. When I examine the structures, the InChi generation has produced a new tautomeric form
> > for many molecules eg amides as imine-alcohols. The corresponding smiles representation using
> > mol.write('CAN') works as expected ie the same tautomer as the input structure.
> >
> > I am aware that InChi allows the generation of mobile H atom and fixed H atom models - can I pass
> > something to mol.write('INCHI') to generate a fixed-H atom representation?
> >
> >
> >
> > -------------------------------------------------------------------------
> > Check out the new SourceForge.net Marketplace.
> > It's the best place to buy or sell services for
> > just about anything Open Source.
> > http://ad.doubleclick.net/clk;164216239;13503038;w?http://sf.net/marketplace
> > _______________________________________________
> > OpenBabel-scripting mailing list
> > Ope...@li...
> > https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
> >
>
|
|
From: Noel O'B. <bao...@gm...> - 2008-03-27 20:50:17
|
pybel just uses the default options of each format. But even OpenBabel
currently doesn't seem to have the option you are looking for:
"InChI format\n"
"IUPAC/NIST molecular identifier\n"
"Write options, e.g. -xat\n"
" X <Option string> List of InChI options:\n"
" t add molecule name\n"
" a output auxilliary information\n"
" K output InChIKey\n"
" u output only unique molecules\n"
" U output only unique molecules and sort them\n"
" e compare first molecule to others\n"
" w don't warn on undef stereo or charge rearrangement\n\n"
I am not very familiar with InChI beyond the basics. Perhaps Geoff or
Chris can comment on whether this option could be added.
Noel
On 27/03/2008, yez...@tp... <yez...@tp...> wrote:
> I am trying to generate InChi codes using pybel like this:
>
> descriptor={}
> descriptor['INCHI']=mol.write('INCHI')
>
> While running, the output window reports an InChi warning that protons have been added or
> removed. When I examine the structures, the InChi generation has produced a new tautomeric form
> for many molecules eg amides as imine-alcohols. The corresponding smiles representation using
> mol.write('CAN') works as expected ie the same tautomer as the input structure.
>
> I am aware that InChi allows the generation of mobile H atom and fixed H atom models - can I pass
> something to mol.write('INCHI') to generate a fixed-H atom representation?
>
>
>
> -------------------------------------------------------------------------
> Check out the new SourceForge.net Marketplace.
> It's the best place to buy or sell services for
> just about anything Open Source.
> http://ad.doubleclick.net/clk;164216239;13503038;w?http://sf.net/marketplace
> _______________________________________________
> OpenBabel-scripting mailing list
> Ope...@li...
> https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
>
|
|
From: <yez...@tp...> - 2008-03-27 01:18:00
|
I am trying to generate InChi codes using pybel like this:
descriptor={}
descriptor['INCHI']=mol.write('INCHI')
While running, the output window reports an InChi warning that protons have been added or
removed. When I examine the structures, the InChi generation has produced a new tautomeric form
for many molecules eg amides as imine-alcohols. The corresponding smiles representation using
mol.write('CAN') works as expected ie the same tautomer as the input structure.
I am aware that InChi allows the generation of mobile H atom and fixed H atom models - can I pass
something to mol.write('INCHI') to generate a fixed-H atom representation?
|
|
From: TJ O'D. <tj...@ac...> - 2008-03-23 22:53:54
|
Noel This worked fine for me. It was the "configure --enable-maintainer-mode" step that I was missing. After that, everything went without a hitch. And the Canonical Atom Order is working fine too. Thanks, TJ Noel O'Boyle wrote: > Sorry - I beg your pardon. The problem is the documentation (which I > now remember I was supposed to update). If you are using the trunk, > there is a file missing which you need to create yourself. > > You need to do two things: > (1) install SWIG (we recommend you download the latest version and > compile it yourself) > (2) run "configure --enable-maintainer-mode" instead of just > "configure" (see the last line in > http://openbabel.org/wiki/Install_%28source_code%29#Advanced_Notes) > > When you run 'make' it will create the SWIG bindings as the file > openbabel_python.cpp. After running "make install", "python setup.py > build" should hopefully work. > > Noel > >> wrote: >> I think it must be those recent, um, improvements to the setup.py. >> Could you do me a favour and send me (off-list) the output of "ls >> -alR" in the top openbabel directory (where the ChangeLog and so on >> are)? This will help me fix this problem. Also, what is your exact >> operating system? Is that a regular Ubuntu? >> >> In the meanwhile, you can just set the environment variable >> OPENBABEL_INSTALL to the location where you installed OpenBabel, e.g. >> /usr/local. Then it should work for you. >> >> >> Noel >> >> >> On 21/03/2008, TJ O'Donnell <tj...@ac...> wrote: >> > Hi Noel - another O'Person :) >> > >> > I downloaded the latest via svn. It seems to have compiled and >> > installed OK. But the python setup fails. >> > >> > tj@vmubuntu:~/openbabel/trunk/scripts/python$ python setup.py build >> > WARNING: Environment variable OPENBABEL_INSTALL is not set >> > INFO: Looking for library and include files in ../../src and ../../include >> > running build >> > running build_py >> > file openbabel.py (for module openbabel) not found >> > file openbabel.py (for module openbabel) not found >> > running build_ext >> > building '_openbabel' extension >> > gcc -pthread -fno-strict-aliasing -DNDEBUG -g -O2 -Wall >> > -Wstrict-prototypes -fPIC -I../../include -I/usr/include/python2.5 -c >> > openbabel_python.cpp -o build/temp.linux-i686-2.5/openbabel_python.o >> > gcc: openbabel_python.cpp: No such file or directory >> > gcc: no input files >> > error: command 'gcc' failed with exit status 1 >> > >> > I've attached the configure.out and make.out. >> > >> > Can you figure out why python setup is not working? >> > >> > Thanks, >> > >> > TJ >> > >> > >> > >> > >> > > Geoff - it might be a good idea to document these side-effects...I >> > > wasn't aware of this one. >> > > >> > > TJ, from O'person to another: >> > > >> > >>>> a = pybel.readstring("smi", "CCCC(=O)") >> > >>>> a.data.keys() >> > > [] >> > >>>> print a.write("can") >> > > CCCC=O >> > >>>> a.data.keys() >> > > ['PartialCharges', 'canonical order'] >> > >>>> a.data['canonical order'] >> > > '1 2 3 4 5' >> > > >> > >>>> a = pybel.readstring("smi", "C(=O)CCC") >> > >>>> a.data.keys() >> > > [] >> > >>>> print a.write("can") >> > >>>> print b >> > > CCCC=O >> > >>>> a.data['canonical order'] >> > > '5 4 3 1 2' >> > > >> > > If you have any further questions, please let us know. >> > > >> > > - Noel >> > > >> > > On 21/03/2008, Geoffrey Hutchison <ge...@ge...> wrote: >> > >> >> > >> On Mar 21, 2008, at 2:05 PM, TJ O'Donnell wrote: >> > >> >> > >> > Is it possible to get the canonical atom re-ordering, >> > >> > say as an int vector, after conversion to canonical smiles? >> > >> >> > >> >> > >> As a matter of fact, yes. The current SVN trunk has this feature -- >> > >> after conversion to canonical SMILES, the ordering is available as an >> > >> OBPairData called "Canonical Atom Order" >> > >> >> > >> For a C++ example, of this, check out tools/obfragment.cpp. >> > >> >> > >> This should be accessible from Python directly, although I defer to >> > >> Noel on the Pybel syntax for this. >> > >> >> > >> Cheers, >> > >> -Geoff >> > >> >> > >> >> > >> ------------------------------------------------------------------------- >> > >> This SF.net email is sponsored by: Microsoft >> > >> Defy all challenges. Microsoft(R) Visual Studio 2008. >> > >> http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ >> > >> _______________________________________________ >> > >> OpenBabel-scripting mailing list >> > >> Ope...@li... >> > >> https://lists.sourceforge.net/lists/listinfo/openbabel-scripting >> > >> >> > > >> > >> > >> |
|
From: Geoffrey H. <ge...@ge...> - 2008-03-21 20:41:03
|
> Geoff - it might be a good idea to document these side-effects...I > wasn't aware of this one. Well.. it just went in recently. I promise it'll be on the wiki when 2.2 is released. I waited because Craig was arguing (successfully) for a different name than I used. Cheers, -Geoff |
|
From: Noel O'B. <bao...@gm...> - 2008-03-21 20:29:03
|
Geoff - it might be a good idea to document these side-effects...I
wasn't aware of this one.
TJ, from O'person to another:
>>> a = pybel.readstring("smi", "CCCC(=O)")
>>> a.data.keys()
[]
>>> print a.write("can")
CCCC=O
>>> a.data.keys()
['PartialCharges', 'canonical order']
>>> a.data['canonical order']
'1 2 3 4 5'
>>> a = pybel.readstring("smi", "C(=O)CCC")
>>> a.data.keys()
[]
>>> print a.write("can")
>>> print b
CCCC=O
>>> a.data['canonical order']
'5 4 3 1 2'
If you have any further questions, please let us know.
- Noel
On 21/03/2008, Geoffrey Hutchison <ge...@ge...> wrote:
>
> On Mar 21, 2008, at 2:05 PM, TJ O'Donnell wrote:
>
> > Is it possible to get the canonical atom re-ordering,
> > say as an int vector, after conversion to canonical smiles?
>
>
> As a matter of fact, yes. The current SVN trunk has this feature --
> after conversion to canonical SMILES, the ordering is available as an
> OBPairData called "Canonical Atom Order"
>
> For a C++ example, of this, check out tools/obfragment.cpp.
>
> This should be accessible from Python directly, although I defer to
> Noel on the Pybel syntax for this.
>
> Cheers,
> -Geoff
>
>
> -------------------------------------------------------------------------
> This SF.net email is sponsored by: Microsoft
> Defy all challenges. Microsoft(R) Visual Studio 2008.
> http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/
> _______________________________________________
> OpenBabel-scripting mailing list
> Ope...@li...
> https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
>
|
|
From: Geoffrey H. <ge...@ge...> - 2008-03-21 19:13:00
|
On Mar 21, 2008, at 2:05 PM, TJ O'Donnell wrote: > Is it possible to get the canonical atom re-ordering, > say as an int vector, after conversion to canonical smiles? As a matter of fact, yes. The current SVN trunk has this feature -- after conversion to canonical SMILES, the ordering is available as an OBPairData called "Canonical Atom Order" For a C++ example, of this, check out tools/obfragment.cpp. This should be accessible from Python directly, although I defer to Noel on the Pybel syntax for this. Cheers, -Geoff |
|
From: TJ O'D. <tj...@ac...> - 2008-03-21 18:05:08
|
Is it possible to get the canonical atom re-ordering, say as an int vector, after conversion to canonical smiles? I tried GetGIDVector, but this is not what I need. Thanks, TJ O'Donnell |
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From: Jerome P. <j.p...@pa...> - 2008-03-12 19:42:03
|
Dear Jurgens, In addition to the answer of Geoffrey, I inform you that for dealing with SQL databases of small libraries, you can take a look on : - Pgchem (Open Babel functions for PostgreSQL) : http://pgfoundry.org/projects/pgchem/ - Mychem (Open Babel functions for MySQL) : http://sourceforge.net/projects/mychem/ Cheers, Jerome Le Tuesday 11 March 2008 15:41:20 Geoffrey Hutchison, vous avez écrit : > On Mar 11, 2008, at 4:36 AM, Jurgens de Bruin wrote: > > was wondering if OB has any functionalities that can be applied to > > a library of small molecules?? > > I'm not sure what you mean. Certainly Open Babel can handle libraries, > doing splitting, merging, batch conversion, etc. Almost all functions > can be run across a library file. That's what Open Babel is designed > to do. > > If, however, what you mean is to run "clustering" statistical > analysis, then no. We do not have any functions for statistical > analysis at all. Other packages (e.g., R) are better suited for this > IMHO. > > Cheers, > -Geoff > > ------------------------------------------------------------------------- > This SF.net email is sponsored by: Microsoft > Defy all challenges. Microsoft(R) Visual Studio 2008. > http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ > _______________________________________________ > OpenBabel-scripting mailing list > Ope...@li... > https://lists.sourceforge.net/lists/listinfo/openbabel-scripting |
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From: Noel O'B. <bao...@gm...> - 2008-03-11 23:15:33
|
To add to Geoff's comments, there's also filtering by SMARTS. Maybe also filtering by descriptor values such as LogP and MR (I'm not sure is this released yet). What is it you are interested in doing? Noel On 11/03/2008, Jurgens de Bruin <deb...@gm...> wrote: > Hi > > I was wondering if OB has any functionalities that can be applied to a > library of small molecules?? > > Thanx > > -- > Regards/Groete/Mit freundlichen Grüßen/recuerdos/meilleures salutations/ > distinti saluti/siong/duì yú/привет > > Jurgens de Bruin > ------------------------------------------------------------------------- > This SF.net email is sponsored by: Microsoft > Defy all challenges. Microsoft(R) Visual Studio 2008. > http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ > _______________________________________________ > OpenBabel-scripting mailing list > Ope...@li... > https://lists.sourceforge.net/lists/listinfo/openbabel-scripting > > |
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