openbabel-scripting — This list is deprecated. Please use openbabel-discuss instead.

[OpenBabel-scripting] NOTICE: Closure of the openbabel-scripting mailing list

[Noel O'B. <bao...@gm...>]

Hello all,

The openbabel-scripting mailing list will be closed for new posts by
the end of the year. If you are a subscriber, please subscribe instead
to openbabel-discuss. The discuss list will now be the single point of
contact for all queries relating to the command-line tools or the API
usage.

Note that the mailing list will not be deleted, and a full archive of
all existing posts will remain, both at SourceForge and at Nabble.

All the best,
   Noel

Re: [OpenBabel-scripting] more graceful exit for make3D on large molecules

[Noel O'B. <bao...@gm...>]

Hi Steven,

It ran out of memory setting up the VdW part of the forcefield
optimisation. The resulting segfault is handled gracefully in C++
(raising a C++ exception) but currently this doesn't cross the
boundary to Python very well except to cause trouble.

The only way around this would either be to move to a 64-bit setup
(which is a bit untested for Windows) but is working for Adrià on
Linux. Or to call obabel at the command-line from Python to read and
write from a file. If, for your purposes, you don't need to run the
forcefield, then of course you could edit the code in "make3D()" not
to run the forcefield optimisation. You would still have some sort of
a 3D structure.

- Noel

On 14 November 2011 20:58, Arturo, Steven (SG) <SGA...@do...> wrote:
> Good day all.  I understand that I use pybel to manipulate structures that
> are larger than what the code is intended to do.  So I am testing the limits
> of this.
>
>
>
> I write because if I execute a ‘make3D’ function on a molecule that is too
> large, pybel (or openbabel) crashes python.
>
>
>
> Here is what a good execution looks like when I use ‘make3D’ on a large
> molecule.
>
>
>
> Python 2.7 (r27:82525, Jul  4 2010, 09:01:59) [MSC v.1500 32 bit (Intel)] on
> win32
>
> Type "help", "copyright", "credits" or "license" for more information.
>
>>>> import pybel
>
>>>> smiles='O'+'CCO'*300
>
>>>> mol=pybel.readstring('smi',smiles)
>
>>>> mol.make3D()
>
>>>> ^Z
>
>
>
> And here is what a bad execution looks like
>
>
>
> Python 2.7 (r27:82525, Jul  4 2010, 09:01:59) [MSC v.1500 32 bit (Intel)] on
> win32
>
> Type "help", "copyright", "credits" or "license" for more information.
>
>>>> import pybel
>
>>>> smiles='O'+'CCO'*400
>
>>>> mol=pybel.readstring('smi',smiles)
>
>>>> mol.make3D()
>
>
>
> This application has requested the Runtime to terminate it in an unusual
> way.
>
> Please contact the application's support team for more information.
>
>
>
> As you can see, I am running a 32-bit version of python on Windows.  It is a
> 64-bit version of Windows 7 with 12 GB of memory.
>
>
>
> I investigated whether the error is memory-based.  It seems that this error
> is shown when python asks for about 490 MB of memory.  This is well below
> the limits of this machine, since I have run scripts on this same machine
> that fail when it is ~1.7 GB of memory, something more meaningful when I run
> a 32-bit application on Windows 7.
>
>
>
> Two questions… Why is this happening?  And is there a more graceful way to
> fail, so that I can wrap the command with a try loop and execute the rest of
> my script if ‘make3D’ fails?
>
>
>
> Thanks for your help.
>
>
>
> Steve
>
>
>
> Steven G. Arturo
>
> Core R&D – E&PS
>
> The Dow Chemical Company
>
> 727 Norristown Road
>
> Spring House, PA 19477
>
> 7B/207P  979.238.5749
>
>
>
> ------------------------------------------------------------------------------
> RSA(R) Conference 2012
> Save $700 by Nov 18
> Register now
> http://p.sf.net/sfu/rsa-sfdev2dev1
> _______________________________________________
> OpenBabel-scripting mailing list
> Ope...@li...
> https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
>
>

Re: [OpenBabel-scripting] more graceful exit for make3D on large molecules

[Adrià C. M. <sso...@gm...>]

It works for me without problems on python 2.7.2 on 64 bit ubuntu, in a
more humble machine (4 Gb of RAM),  and the usage of RAM memory is not that
big (maybe 500 Mb or less for both executions together)

Adrià

2011/11/14 Arturo, Steven (SG) <SGA...@do...>

> Good day all.  I understand that I use pybel to manipulate structures that
> are larger than what the code is intended to do.  So I am testing the
> limits of this.****
>
> ** **
>
> I write because if I execute a ‘make3D’ function on a molecule that is too
> large, pybel (or openbabel) crashes python.****
>
> ** **
>
> Here is what a good execution looks like when I use ‘make3D’ on a large
> molecule.****
>
> ** **
>
> Python 2.7 (r27:82525, Jul  4 2010, 09:01:59) [MSC v.1500 32 bit (Intel)]
> on win32****
>
> Type "help", "copyright", "credits" or "license" for more information.****
>
> >>> import pybel****
>
> >>> smiles='O'+'CCO'*300****
>
> >>> mol=pybel.readstring('smi',smiles)****
>
> >>> mol.make3D()****
>
> >>> ^Z****
>
> ** **
>
> And here is what a bad execution looks like****
>
> ** **
>
> Python 2.7 (r27:82525, Jul  4 2010, 09:01:59) [MSC v.1500 32 bit (Intel)]
> on win32****
>
> Type "help", "copyright", "credits" or "license" for more information.****
>
> >>> import pybel****
>
> >>> smiles='O'+'CCO'*400****
>
> >>> mol=pybel.readstring('smi',smiles)****
>
> >>> mol.make3D()****
>
> ** **
>
> This application has requested the Runtime to terminate it in an unusual
> way.****
>
> Please contact the application's support team for more information.****
>
> ** **
>
> As you can see, I am running a 32-bit version of python on Windows.  It is
> a 64-bit version of Windows 7 with 12 GB of memory.****
>
> ** **
>
> I investigated whether the error is memory-based.  It seems that this
> error is shown when python asks for about 490 MB of memory.  This is well
> below the limits of this machine, since I have run scripts on this same
> machine that fail when it is ~1.7 GB of memory, something more meaningful
> when I run a 32-bit application on Windows 7.****
>
> ** **
>
> Two questions… Why is this happening?  And is there a more graceful way to
> fail, so that I can wrap the command with a try loop and execute the rest
> of my script if ‘make3D’ fails?  ****
>
> ** **
>
> Thanks for your help.****
>
> ** **
>
> Steve****
>
> ** **
>
> Steven G. Arturo****
>
> Core R&D – E&PS****
>
> The Dow Chemical Company****
>
> 727 Norristown Road****
>
> Spring House, PA 19477****
>
> 7B/207P  979.238.5749****
>
> ** **
>
>
> ------------------------------------------------------------------------------
> RSA(R) Conference 2012
> Save $700 by Nov 18
> Register now
> http://p.sf.net/sfu/rsa-sfdev2dev1
> _______________________________________________
> OpenBabel-scripting mailing list
> Ope...@li...
> https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
>
>


-- 
*Adrià Cereto Massagué*

Universitat Rovira i Virgili

Languages: Català, Español, English, Français, Deutsch, Português, Esperanto

Nota importante
<http://www.gnu.org/philosophy/no-word-attachments.es.html>| Important
Notice <http://www.gnu.org/philosophy/no-word-attachments.html>

[OpenBabel-scripting] more graceful exit for make3D on large molecules

[Arturo, S. (SG) <SGA...@do...>]

Good day all.  I understand that I use pybel to manipulate structures
that are larger than what the code is intended to do.  So I am testing
the limits of this.

 

I write because if I execute a 'make3D' function on a molecule that is
too large, pybel (or openbabel) crashes python.

 

Here is what a good execution looks like when I use 'make3D' on a large
molecule.

 

Python 2.7 (r27:82525, Jul  4 2010, 09:01:59) [MSC v.1500 32 bit
(Intel)] on win32

Type "help", "copyright", "credits" or "license" for more information.

>>> import pybel

>>> smiles='O'+'CCO'*300

>>> mol=pybel.readstring('smi',smiles)

>>> mol.make3D()

>>> ^Z

 

And here is what a bad execution looks like

 

Python 2.7 (r27:82525, Jul  4 2010, 09:01:59) [MSC v.1500 32 bit
(Intel)] on win32

Type "help", "copyright", "credits" or "license" for more information.

>>> import pybel

>>> smiles='O'+'CCO'*400

>>> mol=pybel.readstring('smi',smiles)

>>> mol.make3D()

 

This application has requested the Runtime to terminate it in an unusual
way.

Please contact the application's support team for more information.

 

As you can see, I am running a 32-bit version of python on Windows.  It
is a 64-bit version of Windows 7 with 12 GB of memory.

 

I investigated whether the error is memory-based.  It seems that this
error is shown when python asks for about 490 MB of memory.  This is
well below the limits of this machine, since I have run scripts on this
same machine that fail when it is ~1.7 GB of memory, something more
meaningful when I run a 32-bit application on Windows 7.

 

Two questions... Why is this happening?  And is there a more graceful
way to fail, so that I can wrap the command with a try loop and execute
the rest of my script if 'make3D' fails?  

 

Thanks for your help.

 

Steve

 

Steven G. Arturo

Core R&D - E&PS

The Dow Chemical Company

727 Norristown Road

Spring House, PA 19477

7B/207P  979.238.5749

 

Re: [OpenBabel-scripting] Script for descriptor calculation

[Noel O'B. <bao...@gm...>]

['TPSA', 'HBD', 'nF', 'logP', 'MW', 'tbonds', 'bonds', 'atoms', 'HBA1', 'HBA2',
'sbonds', 'dbonds', 'MR', 'abonds']

They can be used from any language. E.g. from Python...

>>> import pybel
>>> print pybel.readstring("smi", "CC").calcdesc(["MW", "bonds"])
{'MW': 30.069040000000001, 'bonds': 1.0}

- Noel

On 10 November 2011 11:29, Vasanthanathan Poongavanam
<nat...@un...> wrote:
> Hi
>
> i am new to openbabel-script, i would like to know if the openbabel
> descriptors can be calculated using any scripting language, and how many
> descriptors can be calculated ?
>
> best regards
>
> Nathan
>
> -----------------------------------------------
> Poongavanam Vasanthanathan, M.Pharm., PhD
> PostDoc, Pharmacoinformatics Research Group
> Department für Medizinische / Pharmazeutische Chemie
> Universität Wien
> Althanstraße 14
> 1090 Wien
> T: +431427755112
> F: +43142779551
> --------------------------------------
>
>
> ------------------------------------------------------------------------------
> RSA(R) Conference 2012
> Save $700 by Nov 18
> Register now
> http://p.sf.net/sfu/rsa-sfdev2dev1
> _______________________________________________
> OpenBabel-scripting mailing list
> Ope...@li...
> https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
>

Re: [OpenBabel-scripting] OSX 6.8 Openbabel python bindings

[Geoff H. <ge...@ge...>]

> I'm running OSX 10.6.8, and I'm having trouble installing openbabel with
> python bindings. Any help would be appreciated

So there are two problems. First, your python version seems to be trying to build for Mac OS X 10.3:

> build/temp.macosx-10.3-fat-2.6/Users/PierreB/Downloads/openbabel-2.3.1/scripts/python/openbabel-python.o
...
> /usr/include/AvailabilityMacros.h:108:14: warning: #warning Building for
> Intel with Mac OS X Deployment Target < 10.4 is invalid.

Second, it looks like your libopenbabel.dylib is not built "fat":

> ld: warning: in ../lib/libopenbabel.dylib, file was built for unsupported
> file format which is not the architecture being linked (ppc)
...
> ld: warning: in ../lib/libopenbabel.dylib, file was built for unsupported
> file format which is not the architecture being linked (i386)
...
> /Users/PierreB/Downloads/openbabel-2.3.1/build/lib/libopenbabel.dylib:
> Mach-O 64-bit dynamically linked shared library x86_64

So you should probably find the "native" python, which should be /usr/bin/python-2.6 which should build for 10.6 (and handle x86_64) and consider changing the architectures for CMake / OSX for libopenbabel. (Edit the CMakeCache.txt   for CMAKE_OSX_ARCHITECTURES:STRING=…)

Hope that helps,
-Geoff

[OpenBabel-scripting] OSX 6.8 Openbabel python bindings

[pierrelb <pie...@gm...>]

I'm running OSX 10.6.8, and I'm having trouble installing openbabel with
python bindings. Any help would be appreciated

Below are the results of the build.

running build_py
creating build/lib.macosx-10.3-fat-2.6
copying openbabel.py -> build/lib.macosx-10.3-fat-2.6
copying pybel.py -> build/lib.macosx-10.3-fat-2.6
running build_ext
building '_openbabel' extension
gcc-4.0 -fno-strict-aliasing -fno-common -dynamic -arch ppc -arch i386 -g
-O2 -DNDEBUG -g -O3 -I/usr/local/include/eigen2
-I/Users/PierreB/Downloads/openbabel-2.3.1/scripts/python/../../include
-I../include
-I/Library/Frameworks/Python.framework/Versions/2.6/include/python2.6 -c
/Users/PierreB/Downloads/openbabel-2.3.1/scripts/python/openbabel-python.cpp
-o
build/temp.macosx-10.3-fat-2.6/Users/PierreB/Downloads/openbabel-2.3.1/scripts/python/openbabel-python.o
In file included from /usr/include/architecture/i386/math.h:626,
                 from /usr/include/math.h:28,
                 from
/Library/Frameworks/Python.framework/Versions/2.6/include/python2.6/pyport.h:235,
                 from
/Library/Frameworks/Python.framework/Versions/2.6/include/python2.6/Python.h:58,
                 from
/Users/PierreB/Downloads/openbabel-2.3.1/scripts/python/openbabel-python.cpp:150:
/usr/include/AvailabilityMacros.h:108:14: warning: #warning Building for
Intel with Mac OS X Deployment Target < 10.4 is invalid.

c++ -arch ppc -arch i386 -g -bundle -undefined dynamic_lookup
-I/usr/local/include/eigen2
build/temp.macosx-10.3-fat-2.6/Users/PierreB/Downloads/openbabel-2.3.1/scripts/python/openbabel-python.o
-L/Users/PierreB/Downloads/openbabel-2.3.1/scripts/python/../../lib
-L/Users/PierreB/Downloads/openbabel-2.3.1/scripts/python/../../lib64
-L../lib -lopenbabel -o build/lib.macosx-10.3-fat-2.6/_openbabel.so
ld: warning: directory
'/Users/PierreB/Downloads/openbabel-2.3.1/scripts/python/../../lib'
following -L not found
ld: warning: directory
'/Users/PierreB/Downloads/openbabel-2.3.1/scripts/python/../../lib64'
following -L not found
ld: warning: in ../lib/libopenbabel.dylib, file was built for unsupported
file format which is not the architecture being linked (ppc)
ld: warning: directory
'/Users/PierreB/Downloads/openbabel-2.3.1/scripts/python/../../lib'
following -L not found
ld: warning: directory
'/Users/PierreB/Downloads/openbabel-2.3.1/scripts/python/../../lib64'
following -L not found
ld: warning: in ../lib/libopenbabel.dylib, file was built for unsupported
file format which is not the architecture being linked (i386)
running install_lib
copying build/lib.macosx-10.3-fat-2.6/_openbabel.so ->
/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages
copying build/lib.macosx-10.3-fat-2.6/openbabel.py ->
/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages
copying build/lib.macosx-10.3-fat-2.6/pybel.py ->
/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages
byte-compiling
/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/openbabel.py
to openbabel.pyc
byte-compiling
/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/pybel.py
to pybel.pyc
running install_egg_info
Writing
/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/openbabel-1.7-py2.6.egg-info
Pierre-Bhoorasinghs-MacBook-Pro:build PierreB$
Pierre-Bhoorasinghs-MacBook-Pro:build PierreB$ python
Python 2.6.6 (r266:84374, Aug 31 2010, 11:00:51)
[GCC 4.0.1 (Apple Inc. build 5493)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import pybel
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File
"/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/pybel.py",
line 16, in <module>
    import openbabel as ob
  File
"/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/openbabel.py",
line 65, in <module>
    _openbabel = swig_import_helper()
  File
"/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/openbabel.py",
line 61, in swig_import_helper
    _mod = imp.load_module('_openbabel', fp, pathname, description)
ImportError:
dlopen(/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/_openbabel.so,
2): Symbol not found: __ZN9OpenBabel8OBPlugin7DisplayERSsPKcS3_
  Referenced from:
/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/_openbabel.so
  Expected in: dynamic lookup



Here's my attempt to link

Pierre-Bhoorasinghs-MacBook-Pro:build PierreB$ file
/Users/PierreB/Downloads/openbabel-2.3.1/build/lib/libopenbabel.dylib
/Users/PierreB/Downloads/openbabel-2.3.1/build/lib/libopenbabel.dylib:
Mach-O 64-bit dynamically linked shared library x86_64
Pierre-Bhoorasinghs-MacBook-Pro:build PierreB$ otool -L
/Users/PierreB/Downloads/openbabel-2.3.1/build/lib/libopenbabel.dylib
/Users/PierreB/Downloads/openbabel-2.3.1/build/lib/libopenbabel.dylib:
     /Users/PierreB/Downloads/openbabel-2.3.1/build/lib/libopenbabel.4.dylib
(compatibility version 4.0.0, current version 4.0.1)
     /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current
version 125.2.11)
     /usr/lib/libz.1.dylib (compatibility version 1.0.0, current version
1.2.3)
     /usr/lib/libstdc++.6.dylib (compatibility version 7.0.0, current
version 7.9.0)
Pierre-Bhoorasinghs-MacBook-Pro:build PierreB$ 
 


--
View this message in context: http://forums.openbabel.org/OSX-6-8-Openbabel-python-bindings-tp4027870p4027870.html
Sent from the openbabel-scripting mailing list archive at Nabble.com.

[OpenBabel-scripting] Script for descriptor calculation

[Vasanthanathan P. <nat...@un...>]

Hi

i am new to openbabel-script, i would like to know if the openbabel 
descriptors can be calculated using any scripting language, and how many 
descriptors can be calculated ?

best regards

Nathan

-----------------------------------------------
Poongavanam Vasanthanathan, M.Pharm., PhD
PostDoc, Pharmacoinformatics Research Group
Department für Medizinische / Pharmazeutische Chemie
Universität Wien
Althanstraße 14
1090 Wien
T: +431427755112
F: +43142779551
--------------------------------------

Re: [OpenBabel-scripting] pybel ring numbering

[Noel O'B. <bao...@gm...>]

Have you read the OpenSMILES spec? It's at
http://opensmiles.org/spec/open-smiles-3-input.html#3.4: "It is
permissable to re-use ring-closure numbers. Once a particular number
has been encountered twice, that number is available again for
subsequent ring closures."

HTH,
   Noel

On 4 November 2011 21:12, giovannicianchetta
<gio...@gm...> wrote:
> Hi,
> I am having a strange problem with openbabel and pybel.
> look at the code below, please:
>
>
>>>> import pybel
>>>> mol=pybel.readstring('smi','c1ccccc1CCc2ccccc2')
>>>> print mol
> c1ccccc1CCc1ccccc1
>
> as you can notice the second ring has been renumbered as 1 so now I have two
> rings with the same index.
> has anyone found this problem before?
> is there a solution for this?
>
> thanks
>
> Giovanni
>
> --
> View this message in context: http://forums.openbabel.org/pybel-ring-numbering-tp3991497p3991497.html
> Sent from the openbabel-scripting mailing list archive at Nabble.com.
>
> ------------------------------------------------------------------------------
> RSA(R) Conference 2012
> Save $700 by Nov 18
> Register now
> http://p.sf.net/sfu/rsa-sfdev2dev1
> _______________________________________________
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> Ope...@li...
> https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
>

[OpenBabel-scripting] pybel ring numbering

[giovannicianchetta <gio...@gm...>]

Hi,
I am having a strange problem with openbabel and pybel.
look at the code below, please:


>>> import pybel
>>> mol=pybel.readstring('smi','c1ccccc1CCc2ccccc2')
>>> print mol
c1ccccc1CCc1ccccc1	

as you can notice the second ring has been renumbered as 1 so now I have two
rings with the same index.
has anyone found this problem before?
is there a solution for this?

thanks

Giovanni

--
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Re: [OpenBabel-scripting] [Open Babel] ANNOUNCE: Open Babel 2.3.1 Release

[Giovanni C. <gci...@gm...>]

Congratulation to everybody guys!!!

2011/10/17 Geoffrey Hutchison <ge...@pi...>

> I am very happy to finally announce the release of Open Babel 2.3.1, a
> major update release of the open source chemistry toolbox.
>
> Open Babel has been downloaded nearly 200,000 times and is used in over 45
> projects and over 400 publications.
> http://www.jcheminf.com/content/3/1/33
>
> This release represents a major bug-fix-release and should be a stable
> upgrade, strongly recommended for all users of Open Babel. Many bugs and
> enhancements have been added in the last year since the 2.3.0 release.
>
> What's new? See the full release notes at:
> http://openbabel.org/wiki/Open_Babel_2.3.1
>
> See the new user guide at:
> http://openbabel.org/docs/2.3.1/
>
> See the updated developer documentation at:
> http://openbabel.org/api/2.3/
>
> To download, see:
> http://sourceforge.net/projects/openbabel/files/
>
> For more information, see the project website at:
> http://openbabel.org/
>
> I'd particularly like to thank Chris Morley, Noel O'Boyle, and many others
> who put large amounts of time testing and improving this release.
>
> This is a community project and we couldn't have made this release without
> you. Many thanks to all the contributors to Open Babel including those of
> you who submitted feedback, bug reports, and code.
>
> Cheers,
> -Geoff
>
> ---
> Prof. Geoffrey Hutchison
> Department of Chemistry
> University of Pittsburgh
> tel: (412) 648-0492
> email: ge...@pi...
> web: http://hutchison.chem.pitt.edu/
>
>
>
> ------------------------------------------------------------------------------
> All the data continuously generated in your IT infrastructure contains a
> definitive record of customers, application performance, security
> threats, fraudulent activity and more. Splunk takes this data and makes
> sense of it. Business sense. IT sense. Common sense.
> http://p.sf.net/sfu/splunk-d2d-oct
> _______________________________________________
> OpenBabel-discuss mailing list
> Ope...@li...
> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>

[OpenBabel-scripting] ANNOUNCE: Open Babel 2.3.1 Release

[Geoffrey H. <ge...@pi...>]

I am very happy to finally announce the release of Open Babel 2.3.1, a major update release of the open source chemistry toolbox.

Open Babel has been downloaded nearly 200,000 times and is used in over 45 projects and over 400 publications.
http://www.jcheminf.com/content/3/1/33

This release represents a major bug-fix-release and should be a stable upgrade, strongly recommended for all users of Open Babel. Many bugs and enhancements have been added in the last year since the 2.3.0 release.

What's new? See the full release notes at:
http://openbabel.org/wiki/Open_Babel_2.3.1

See the new user guide at:
http://openbabel.org/docs/2.3.1/

See the updated developer documentation at:
http://openbabel.org/api/2.3/

To download, see:
http://sourceforge.net/projects/openbabel/files/

For more information, see the project website at:
http://openbabel.org/

I'd particularly like to thank Chris Morley, Noel O'Boyle, and many others who put large amounts of time testing and improving this release.

This is a community project and we couldn't have made this release without you. Many thanks to all the contributors to Open Babel including those of you who submitted feedback, bug reports, and code.

Cheers,
-Geoff

---
Prof. Geoffrey Hutchison
Department of Chemistry
University of Pittsburgh
tel: (412) 648-0492
email: ge...@pi...
web: http://hutchison.chem.pitt.edu/

[OpenBabel-scripting] Open Babel Paper Published in J Cheminf

[Geoffrey H. <ge...@pi...>]

I'm glad to announce that after 10 years, we finally got around to publishing a paper on Open Babel. :-)

Noel M. O’Boyle , Michael Banck , Craig A. James , Chris Morley , Tim Vandermeersch, Geoffrey R. Hutchison. “Open Babel: An open chemical toolbox.” J. Cheminf. 2011 3:33.
http://www.jcheminf.com/content/3/1/33

The article is open access, so we hope you'll grab a copy and cite it whenever you publish work using Open Babel. So far, over 400 publications have used OB, and the article covers some of the most interesting and diverse uses, in addition to the development, structure, and features of the toolkit.

Thanks to Noel M. O'Boyle, Michael Banck, Craig A. James, Chris Morley, and Tim Vandermeersch!

-Geoff

---
Prof. Geoffrey Hutchison
Department of Chemistry
University of Pittsburgh
tel: (412) 648-0492
email: ge...@pi...
web: http://hutchison.chem.pitt.edu/

Re: [OpenBabel-scripting] Question about OBFIT and SMART pattern

[Geoffrey H. <ge...@ge...>]

> I wonder that is it possible to indentify atoms by indecies ( ie. atom
> number in xyz file) with SMART pattern? I am trying to fit two molecules
> with OBFIT and would like to do it by atom number.  

Well, you can script the fitting, but it wouldn't be by OBFIT or SMARTS pattern, because those don't consider atom indices.

But there are multiple ways to align if you have a set of atoms. I'd suggest looking at the tools/obfit.cpp code yourself -- the key bit is the call to qtrfit() which just takes an array of coordinates for the alignment.

-Geoff

Re: [OpenBabel-scripting] "pdb" not a recognised OpenBabel format (error)

[Daniel S. <sin...@gm...>]

OK sorry for taking so much time. I did get it to work. Basically I had to
get gcc 4.6 off my system. After that it worked (with gcc 4.5.3)
Thanks all again for the help.
-Dan

On Fri, Sep 9, 2011 at 3:50 PM, Daniel Sindhikara <sin...@gm...>wrote:

> Geoff,
>   That's basically the problem, but reversed. It does find the correct
> Enthought version of python, but for some reason Enthought chose to use gcc
> 4.0.1 to compile. This is getting difficult now. I don't think I can change
> the compiler in Enthought and recompile. Do the two versions of gcc need to
> be compatible? I can't find where this "-arch" option is to change it.  I
> can change the specs for cmake to point to gcc4.0.1 but I end up with other
> problems.
> e.g.:
> [ 49%] Building CXX object src/formats/CMakeFiles/cdxmlformat.dir/xml/xml.o
> Linking CXX shared module ../../lib/cdxmlformat.so
> ld: warning: in /opt/local/lib/libxml2.dylib, file was built for
> unsupported file format which is not the architecture being linked (i386)
> Undefined symbols:
>   "_xmlResetError", referenced from:
>       OpenBabel::XMLConversion::ReadXML(OpenBabel::XMLBaseFormat*,
> OpenBabel::OBBase*)in xml.o
>   "_xmlOutputBufferFlush", referenced from:
> ....
>
>
>
>
>
>
> On Wed, Sep 7, 2011 at 5:03 PM, Geoff Hutchison <ge...@ge...>wrote:
>
>>   Thanks for the help. I deleted all versions of Openbabel then started
>> from scratch. I now get a new error (after "100%" installing). I believe
>> there is some incompatibility with my version of gcc (4.6). I'm not sure,
>> however which version I should use, and which file to modify to point to a
>> different gcc.
>> The error is: cc1plus: error: unrecognized command line option "-arch"
>>
>>
>> Well, I don't know much about the Enthought version of python, but that's
>> an issue with a non-Apple version of gcc when compiling the Python
>> extension. I'd look at the CMakeCache.txt file in your build directory and
>> see:
>>
>> PYTHON_EXECUTABLE:FILEPATH=/usr/bin/python2.7
>>
>> My guess is that it's not the python you expect from Enthought, but the
>> rest of Open Babel has been compiled by the GCC provided by either Enthought
>> or MacPorts.
>>
>> That's the confusion.
>>
>> -Geoff
>>
>
>
>
> --
> Dr. Daniel J. Sindhikara
> Institute for Molecular Science
> E-mail: sin...@gm...
> Website: http://sites.google.com/site/dansindhikara/
> --
>



-- 
Dr. Daniel J. Sindhikara
Institute for Molecular Science
E-mail: sin...@gm...
Website: http://sites.google.com/site/dansindhikara/
--

Re: [OpenBabel-scripting] OBConversion of mol object without input format

[Noel O'B. <bao...@gm...>]

Works for me as follows:

>>> import openbabel as ob
>>> mol = ob.OBMol()
>>> atom = mol.NewAtom()
>>> atom.SetAtomicNum(6)
>>> atom.SetVector( 1, 1, 1)
>>> conv = ob.OBConversion()
>>> success = conv.SetOutFormat("inchi")
>>> assert success
>>> conv.WriteString(mol)
'InChI=1S/CH4/h1H4\n'
>>>

- Noel


On 12 September 2011 22:12, vulcan[omni] <sam...@gm...> wrote:
> Hello,
>
> I am using the openbabel python module to compute the InChi string of an
> obmol object. However, I have to construct the obmol manually like so:
>
>  # Coordinates is this format:
> ((O,(0.0,0.0,0.0)),(H,(1.0,0.0,0.0)),(H,(-1.0,0.0,0.0))
>  mol = openbabel.OBMol()
>  for entry in coordinates:
>        newAtom = mol.NewAtom()
>        newAtom.SetAtomicNum(symbolToNumber(entry[0]))
>        newAtom.SetVector(*(map(float,entry[1])))
>
> Therefore, I need to have an OBConverter object with no input format and
> output format, ideally like this:
>
> converter.SetInAndOutFormats(None,"inchi")
>
> However, calling this and then doing:
>
> inchi = converter.WriteString(mol)
>
> just returns a blank string, even when mol is populated correctly. Is my
> problem with the setup of OBConverter or is it something else? I appreciate
> any insight.
>
> Thank you,
>
> Sam Manzer
>
> --
> View this message in context: http://forums.openbabel.org/OBConversion-of-mol-object-without-input-format-tp3808639p3808639.html
> Sent from the openbabel-scripting mailing list archive at Nabble.com.
>
> ------------------------------------------------------------------------------
> Doing More with Less: The Next Generation Virtual Desktop
> What are the key obstacles that have prevented many mid-market businesses
> from deploying virtual desktops?   How do next-generation virtual desktops
> provide companies an easier-to-deploy, easier-to-manage and more affordable
> virtual desktop model.http://www.accelacomm.com/jaw/sfnl/114/51426474/
> _______________________________________________
> OpenBabel-scripting mailing list
> Ope...@li...
> https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
>

[OpenBabel-scripting] Question about OBFIT and SMART pattern

[Ledius <ro...@fh...>]

Hi

I wonder that is it possible to indentify atoms by indecies ( ie. atom
number in xyz file) with SMART pattern? I am trying to fit two molecules
with OBFIT and would like to do it by atom number.  

Best regards,
Matti

--
View this message in context: http://forums.openbabel.org/Question-about-OBFIT-and-SMART-pattern-tp3809595p3809595.html
Sent from the openbabel-scripting mailing list archive at Nabble.com.

[OpenBabel-scripting] OBConversion of mol object without input format

[vulcan[omni] <sam...@gm...>]

Hello,

I am using the openbabel python module to compute the InChi string of an
obmol object. However, I have to construct the obmol manually like so: 

 # Coordinates is this format:
((O,(0.0,0.0,0.0)),(H,(1.0,0.0,0.0)),(H,(-1.0,0.0,0.0)) 
 mol = openbabel.OBMol() 
 for entry in coordinates: 
        newAtom = mol.NewAtom()
        newAtom.SetAtomicNum(symbolToNumber(entry[0]))
        newAtom.SetVector(*(map(float,entry[1])))

Therefore, I need to have an OBConverter object with no input format and
output format, ideally like this:

converter.SetInAndOutFormats(None,"inchi")

However, calling this and then doing:

inchi = converter.WriteString(mol)

just returns a blank string, even when mol is populated correctly. Is my
problem with the setup of OBConverter or is it something else? I appreciate
any insight. 

Thank you,

Sam Manzer

--
View this message in context: http://forums.openbabel.org/OBConversion-of-mol-object-without-input-format-tp3808639p3808639.html
Sent from the openbabel-scripting mailing list archive at Nabble.com.

Re: [OpenBabel-scripting] "pdb" not a recognised OpenBabel format (error)

[Geoff H. <ge...@ge...>]

>   Thanks for the help. I deleted all versions of Openbabel then started from scratch. I now get a new error (after "100%" installing). I believe there is some incompatibility with my version of gcc (4.6). I'm not sure, however which version I should use, and which file to modify to point to a different gcc.
> The error is: cc1plus: error: unrecognized command line option "-arch"


Well, I don't know much about the Enthought version of python, but that's an issue with a non-Apple version of gcc when compiling the Python extension. I'd look at the CMakeCache.txt file in your build directory and see:

PYTHON_EXECUTABLE:FILEPATH=/usr/bin/python2.7

My guess is that it's not the python you expect from Enthought, but the rest of Open Babel has been compiled by the GCC provided by either Enthought or MacPorts.

That's the confusion.

-Geoff

Re: [OpenBabel-scripting] "pdb" not a recognised OpenBabel format (error)

[Daniel S. <sin...@gm...>]

Noel,
  Thanks for the help. I deleted all versions of Openbabel then started from
scratch. I now get a new error (after "100%" installing). I believe there is
some incompatibility with my version of gcc (4.6). I'm not sure, however
which version I should use, and which file to modify to point to a different
gcc.
The error is: cc1plus: error: unrecognized command line option "-arch"

Sorry for all the questions!

Here are my commands and the full error info:

cmake ../openbabel-2.3.0 -DCMAKE_INSTALL_PREFIX=~/Tools/OBabel
-DCMAKE_BUILD_TYPE=DEBUG -DEIGEN2_INCLUDE_DIR=/opt/local/include/eigen2
-DPYTHON_BINDINGS=ON

Using included inchi library.
GUI will not be built
-- Python bindings will be compiled
-- Configuring done
-- Generating done
-- Build files have been written to: /Users/sindhikara/Downloads/build

13:26:36 [danpc: ~/Downloads/build]$ make && make install
[  0%] Building CXX object src/CMakeFiles/openbabel.dir/alias.o
...
[100%] Building CXX object test/CMakeFiles/test_unitcell.dir/unitcell.o
Linking CXX executable ../bin/test_unitcell
[100%] Built target test_unitcell
running build
running build_py
copying openbabel.py -> /Users/sindhikara/Downloads/build/scripts/pybuild
copying pybel.py -> /Users/sindhikara/Downloads/build/scripts/pybuild
running build_ext
building '_openbabel' extension
gcc -fno-strict-aliasing -fno-common -dynamic -arch x86_64 -isysroot
/Developer/SDKs/MacOSX10.5.sdk -DNDEBUG -g -O3 -arch x86_64 -isysroot
/Developer/SDKs/MacOSX10.5.sdk
-I/Users/sindhikara/Downloads/openbabel-2.3.0/scripts/python/../../include
-I../include
-I/Library/Frameworks/EPD64.framework/Versions/7.1/include/python2.7 -c
/Users/sindhikara/Downloads/openbabel-2.3.0/scripts/python/openbabel-python.cpp
-o
build/temp.macosx-10.5-x86_64-2.7/Users/sindhikara/Downloads/openbabel-2.3.0/scripts/python/openbabel-python.o
cc1plus: error: unrecognized command line option "-arch"
cc1plus: error: unrecognized command line option "-arch"
error: command 'gcc' failed with exit status 1
make[2]: *** [scripts/CMakeFiles/_openbabel] Error 1
make[1]: *** [scripts/CMakeFiles/_openbabel.dir/all] Error 2
make: *** [all] Error 2




On Tue, Sep 6, 2011 at 9:26 PM, Noel O'Boyle <bao...@gm...> wrote:

> Well, that's the reason right there. You have several Open Babel
> installations, and there is interference. My advice is to delete all
> of your Open Babel installations, including related Python files. Then
> install the whole thing locally (including the Python bindings), set
> your environment variables appropriately, and then test "obabel -H
> pdb".
>
> - Noel
>
> On 6 September 2011 11:22, Daniel Sindhikara <sin...@gm...> wrote:
> > Yes it recognizes it, when I check the binary in my unzip directory,
> > however, it does not.
> >
> > 19:21:35 [danpc: ~/Downloads/openbabel-2.3.0/bin]$ obabel -H pdb
> >   Protein Data Bank format
> > Read Options e.g. -as
> >   s  Output single bonds only
> >   b  Disable bonding entirely
> >   c  Ignore CONECT records
> >
> >
> > Specification at: http://www.wwpdb.org/docs.html
> > 19:21:39 [danpc: ~/Downloads/openbabel-2.3.0/bin]$ ./obabel -H pdb
> > Format type:  was not recognized
> >
> >
> > On Tue, Sep 6, 2011 at 7:07 PM, Noel O'Boyle <bao...@gm...>
> wrote:
> >>
> >> Does "obabel -H pdb" show the PDB format?
> >>
> >> On 6 September 2011 07:16, Daniel Sindhikara <sin...@gm...>
> wrote:
> >> > Hello,
> >> >   After a long hiatus I got back on this project. After following the
> >> > instructions I successfully installed openbabel/pybel.
> >> > However, when I tried testing the program I got a funny error, "pdb is
> >> > not a
> >> > recognised OpenBabel format".
> >> >
> >> > Enthought Python Distribution -- www.enthought.com
> >> > Version: 7.1-1 (64-bit)
> >> >
> >> > Python 2.7.2 |EPD 7.1-1 (64-bit)| (default, Jul  3 2011, 15:56:02)
> >> > [GCC 4.0.1 (Apple Inc. build 5493)] on darwin
> >> > Type "packages", "demo" or "enthought" for more information.
> >> >>>> import pybel as pb
> >> >>>> testmolecule = pb.readfile("pdb","mai.pdb").next()
> >> > Traceback (most recent call last):
> >> >   File "<stdin>", line 1, in <module>
> >> >   File
> >> >
> >> >
> "/Users/sindhikara/Tools/openbabel-install/lib/python2.7/site-packages/pybel.py",
> >> > line 90, in readfile
> >> >     raise ValueError("%s is not a recognised OpenBabel format" %
> format)
> >> > ValueError: pdb is not a recognised OpenBabel format
> >> >
> >> >
> >> > Further, checking the formats variable:
> >> >>>> pb.informats
> >> > {}
> >> >
> >> > It was empty.
> >> > Any clues into why this would happen?
> >> >
> >> > Thanks in advance!
> >> > -Dan
> >> >
> >> >
> >> > --
> >> > Dr. Daniel J. Sindhikara
> >> > Institute for Molecular Science
> >> > E-mail: sin...@gm...
> >> > Website: http://sites.google.com/site/dansindhikara/
> >> > --
> >> >
> >> >
> >> >
> ------------------------------------------------------------------------------
> >> > Special Offer -- Download ArcSight Logger for FREE!
> >> > Finally, a world-class log management solution at an even better
> >> > price-free! And you'll get a free "Love Thy Logs" t-shirt when you
> >> > download Logger. Secure your free ArcSight Logger TODAY!
> >> > http://p.sf.net/sfu/arcsisghtdev2dev
> >> > _______________________________________________
> >> > OpenBabel-scripting mailing list
> >> > Ope...@li...
> >> > https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
> >> >
> >> >
> >
> >
> >
> > --
> > Dr. Daniel J. Sindhikara
> > Institute for Molecular Science
> > E-mail: sin...@gm...
> > Website: http://sites.google.com/site/dansindhikara/
> > --
> >
>



-- 
Dr. Daniel J. Sindhikara
Institute for Molecular Science
E-mail: sin...@gm...
Website: http://sites.google.com/site/dansindhikara/
--

Re: [OpenBabel-scripting] "pdb" not a recognised OpenBabel format (error)

[Noel O'B. <bao...@gm...>]

Well, that's the reason right there. You have several Open Babel
installations, and there is interference. My advice is to delete all
of your Open Babel installations, including related Python files. Then
install the whole thing locally (including the Python bindings), set
your environment variables appropriately, and then test "obabel -H
pdb".

- Noel

On 6 September 2011 11:22, Daniel Sindhikara <sin...@gm...> wrote:
> Yes it recognizes it, when I check the binary in my unzip directory,
> however, it does not.
>
> 19:21:35 [danpc: ~/Downloads/openbabel-2.3.0/bin]$ obabel -H pdb
>   Protein Data Bank format
> Read Options e.g. -as
>   s  Output single bonds only
>   b  Disable bonding entirely
>   c  Ignore CONECT records
>
>
> Specification at: http://www.wwpdb.org/docs.html
> 19:21:39 [danpc: ~/Downloads/openbabel-2.3.0/bin]$ ./obabel -H pdb
> Format type:  was not recognized
>
>
> On Tue, Sep 6, 2011 at 7:07 PM, Noel O'Boyle <bao...@gm...> wrote:
>>
>> Does "obabel -H pdb" show the PDB format?
>>
>> On 6 September 2011 07:16, Daniel Sindhikara <sin...@gm...> wrote:
>> > Hello,
>> >   After a long hiatus I got back on this project. After following the
>> > instructions I successfully installed openbabel/pybel.
>> > However, when I tried testing the program I got a funny error, "pdb is
>> > not a
>> > recognised OpenBabel format".
>> >
>> > Enthought Python Distribution -- www.enthought.com
>> > Version: 7.1-1 (64-bit)
>> >
>> > Python 2.7.2 |EPD 7.1-1 (64-bit)| (default, Jul  3 2011, 15:56:02)
>> > [GCC 4.0.1 (Apple Inc. build 5493)] on darwin
>> > Type "packages", "demo" or "enthought" for more information.
>> >>>> import pybel as pb
>> >>>> testmolecule = pb.readfile("pdb","mai.pdb").next()
>> > Traceback (most recent call last):
>> >   File "<stdin>", line 1, in <module>
>> >   File
>> >
>> > "/Users/sindhikara/Tools/openbabel-install/lib/python2.7/site-packages/pybel.py",
>> > line 90, in readfile
>> >     raise ValueError("%s is not a recognised OpenBabel format" % format)
>> > ValueError: pdb is not a recognised OpenBabel format
>> >
>> >
>> > Further, checking the formats variable:
>> >>>> pb.informats
>> > {}
>> >
>> > It was empty.
>> > Any clues into why this would happen?
>> >
>> > Thanks in advance!
>> > -Dan
>> >
>> >
>> > --
>> > Dr. Daniel J. Sindhikara
>> > Institute for Molecular Science
>> > E-mail: sin...@gm...
>> > Website: http://sites.google.com/site/dansindhikara/
>> > --
>> >
>> >
>> > ------------------------------------------------------------------------------
>> > Special Offer -- Download ArcSight Logger for FREE!
>> > Finally, a world-class log management solution at an even better
>> > price-free! And you'll get a free "Love Thy Logs" t-shirt when you
>> > download Logger. Secure your free ArcSight Logger TODAY!
>> > http://p.sf.net/sfu/arcsisghtdev2dev
>> > _______________________________________________
>> > OpenBabel-scripting mailing list
>> > Ope...@li...
>> > https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
>> >
>> >
>
>
>
> --
> Dr. Daniel J. Sindhikara
> Institute for Molecular Science
> E-mail: sin...@gm...
> Website: http://sites.google.com/site/dansindhikara/
> --
>

Re: [OpenBabel-scripting] "pdb" not a recognised OpenBabel format (error)

[Daniel S. <sin...@gm...>]

Yes it recognizes it, when I check the binary in my unzip directory,
however, it does not.

19:21:35 [danpc: ~/Downloads/openbabel-2.3.0/bin]$ obabel -H pdb
  Protein Data Bank format
Read Options e.g. -as
  s  Output single bonds only
  b  Disable bonding entirely
  c  Ignore CONECT records


Specification at: http://www.wwpdb.org/docs.html
19:21:39 [danpc: ~/Downloads/openbabel-2.3.0/bin]$ ./obabel -H pdb
Format type:  was not recognized


On Tue, Sep 6, 2011 at 7:07 PM, Noel O'Boyle <bao...@gm...> wrote:

> Does "obabel -H pdb" show the PDB format?
>
> On 6 September 2011 07:16, Daniel Sindhikara <sin...@gm...> wrote:
> > Hello,
> >   After a long hiatus I got back on this project. After following the
> > instructions I successfully installed openbabel/pybel.
> > However, when I tried testing the program I got a funny error, "pdb is
> not a
> > recognised OpenBabel format".
> >
> > Enthought Python Distribution -- www.enthought.com
> > Version: 7.1-1 (64-bit)
> >
> > Python 2.7.2 |EPD 7.1-1 (64-bit)| (default, Jul  3 2011, 15:56:02)
> > [GCC 4.0.1 (Apple Inc. build 5493)] on darwin
> > Type "packages", "demo" or "enthought" for more information.
> >>>> import pybel as pb
> >>>> testmolecule = pb.readfile("pdb","mai.pdb").next()
> > Traceback (most recent call last):
> >   File "<stdin>", line 1, in <module>
> >   File
> >
> "/Users/sindhikara/Tools/openbabel-install/lib/python2.7/site-packages/pybel.py",
> > line 90, in readfile
> >     raise ValueError("%s is not a recognised OpenBabel format" % format)
> > ValueError: pdb is not a recognised OpenBabel format
> >
> >
> > Further, checking the formats variable:
> >>>> pb.informats
> > {}
> >
> > It was empty.
> > Any clues into why this would happen?
> >
> > Thanks in advance!
> > -Dan
> >
> >
> > --
> > Dr. Daniel J. Sindhikara
> > Institute for Molecular Science
> > E-mail: sin...@gm...
> > Website: http://sites.google.com/site/dansindhikara/
> > --
> >
> >
> ------------------------------------------------------------------------------
> > Special Offer -- Download ArcSight Logger for FREE!
> > Finally, a world-class log management solution at an even better
> > price-free! And you'll get a free "Love Thy Logs" t-shirt when you
> > download Logger. Secure your free ArcSight Logger TODAY!
> > http://p.sf.net/sfu/arcsisghtdev2dev
> > _______________________________________________
> > OpenBabel-scripting mailing list
> > Ope...@li...
> > https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
> >
> >
>



-- 
Dr. Daniel J. Sindhikara
Institute for Molecular Science
E-mail: sin...@gm...
Website: http://sites.google.com/site/dansindhikara/
--

Re: [OpenBabel-scripting] "pdb" not a recognised OpenBabel format (error)

[Noel O'B. <bao...@gm...>]

Does "obabel -H pdb" show the PDB format?

On 6 September 2011 07:16, Daniel Sindhikara <sin...@gm...> wrote:
> Hello,
>   After a long hiatus I got back on this project. After following the
> instructions I successfully installed openbabel/pybel.
> However, when I tried testing the program I got a funny error, "pdb is not a
> recognised OpenBabel format".
>
> Enthought Python Distribution -- www.enthought.com
> Version: 7.1-1 (64-bit)
>
> Python 2.7.2 |EPD 7.1-1 (64-bit)| (default, Jul  3 2011, 15:56:02)
> [GCC 4.0.1 (Apple Inc. build 5493)] on darwin
> Type "packages", "demo" or "enthought" for more information.
>>>> import pybel as pb
>>>> testmolecule = pb.readfile("pdb","mai.pdb").next()
> Traceback (most recent call last):
>   File "<stdin>", line 1, in <module>
>   File
> "/Users/sindhikara/Tools/openbabel-install/lib/python2.7/site-packages/pybel.py",
> line 90, in readfile
>     raise ValueError("%s is not a recognised OpenBabel format" % format)
> ValueError: pdb is not a recognised OpenBabel format
>
>
> Further, checking the formats variable:
>>>> pb.informats
> {}
>
> It was empty.
> Any clues into why this would happen?
>
> Thanks in advance!
> -Dan
>
>
> --
> Dr. Daniel J. Sindhikara
> Institute for Molecular Science
> E-mail: sin...@gm...
> Website: http://sites.google.com/site/dansindhikara/
> --
>
> ------------------------------------------------------------------------------
> Special Offer -- Download ArcSight Logger for FREE!
> Finally, a world-class log management solution at an even better
> price-free! And you'll get a free "Love Thy Logs" t-shirt when you
> download Logger. Secure your free ArcSight Logger TODAY!
> http://p.sf.net/sfu/arcsisghtdev2dev
> _______________________________________________
> OpenBabel-scripting mailing list
> Ope...@li...
> https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
>
>

[OpenBabel-scripting] "pdb" not a recognised OpenBabel format (error)

[Daniel S. <sin...@gm...>]

Hello,
  After a long hiatus I got back on this project. After following the
instructions I successfully installed openbabel/pybel.
However, when I tried testing the program I got a funny error, "pdb is not a
recognised OpenBabel format".

Enthought Python Distribution -- www.enthought.com
Version: 7.1-1 (64-bit)

Python 2.7.2 |EPD 7.1-1 (64-bit)| (default, Jul  3 2011, 15:56:02)
[GCC 4.0.1 (Apple Inc. build 5493)] on darwin
Type "packages", "demo" or "enthought" for more information.
>>> import pybel as pb
>>> testmolecule = pb.readfile("pdb","mai.pdb").next()
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File
"/Users/sindhikara/Tools/openbabel-install/lib/python2.7/site-packages/pybel.py",
line 90, in readfile
    raise ValueError("%s is not a recognised OpenBabel format" % format)
ValueError: pdb is not a recognised OpenBabel format


Further, checking the formats variable:
>>> pb.informats
{}

It was empty.
Any clues into why this would happen?

Thanks in advance!
-Dan


-- 
Dr. Daniel J. Sindhikara
Institute for Molecular Science
E-mail: sin...@gm...
Website: http://sites.google.com/site/dansindhikara/
--

Re: [OpenBabel-scripting] Fwd: importing pybel

[Daniel S. <sin...@gm...>]

Hi,
  Sorry for the extremely late reply. After installing Eigen2 I got it to
work. Thanks for the help!
-Dan

On Tue, Jul 26, 2011 at 5:22 PM, Noel O'Boyle <bao...@gm...> wrote:

> The Python bindings require OB to be compiled with Eigen2. See the
> install instructions at
> http://openbabel.org/docs/2.3.0/Installation/install.html
>
> - Noel
>
> On 26 July 2011 03:53, Daniel Sindhikara <sin...@gm...> wrote:
> > Hi,
> > I downloaded "openbabel-2.3.0.tar.gz"
> > When I run that command, I get:
> > otool -L
> >
> /Users/sindhikara/Tools/openbabel-install/lib/python2.7/site-packages/_openbabel.so
> >
> /Users/sindhikara/Tools/openbabel-install/lib/python2.7/site-packages/_openbabel.so:
> >     /Users/sindhikara/Downloads/openbabel-2.3.0/lib/libopenbabel.4.dylib
> > (compatibility version 4.0.0, current version 4.0.0)
> >     /usr/lib/libstdc++.6.dylib (compatibility version 7.0.0, current
> version
> > 7.9.0)
> >     /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current
> version
> > 125.2.11)
> >
> > Thanks!
> >
> >
> >
> > On Mon, Jul 25, 2011 at 11:49 PM, Geoffrey Hutchison
> > <ge...@ge...> wrote:
> >>
> >> > I am running Mac OSX 10.6.8. When I e-mailed you originally I had
> >> > installed "iBabel" the mac version. Since then tried installing the
> linux
> >> > version and I suppose it installed correctly, but I still cannot
> import it:
> >>
> >> What "linux version" did you install?
> >>
> >> Can you run "otool -L
> >>
> /Users/sindhikara/Tools/openbabel-install/lib/python2.7/site-packages/_openbabel.so"
> >> for me?
> >>
> >> Thanks,
> >> -Geoff
> >
> >
> > --
> > Dr. Daniel J. Sindhikara
> > Institute for Molecular Science
> > E-mail: sin...@gm...
> > Website: http://sites.google.com/site/dansindhikara/
> > --
> >
> >
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> > analysis on the changes within the DLP market, and the criteria used to
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>



-- 
Dr. Daniel J. Sindhikara
Institute for Molecular Science
E-mail: sin...@gm...
Website: http://sites.google.com/site/dansindhikara/
--