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Re: [OpenBabel-scripting] A few questions about scripting OB with Perl

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

2008/9/22 IN SUK JOUNG <i....@gm...>:
> Hello,
> I have a few questions about Perl-OB binding.
>
> 1) Objects created by
> ## Assuming $residue is a OBResidue object.
> $atom = $residue->GetAtoms;
> $bond = $residue->GetBonds;
> seem to be almost useless. When I need atoms or bonds in a specific residue,
> I iterate OBMol object and find the specific atoms/bonds. This does not seem
> to be very efficient way to me. Actually, I expected that $residue->GetAtoms
> returns Perl array/arrayref of OBAtoms objects, but it didn't. Is there a
> way to utilize the obejct created by above methods?

You should use OBResidueAtomIter instead. I'm afraid there doesn't
seem to be an equivalent BondIter. If you're interested in this,
please file a feature request.

> 2) Atom index starts from 1 but residues and bonds starts from 0. Is this
> intended?

The next version of OpenBabel, 3.0, will have all indices starting
from 0. This is a legacy issue which cannot be fixed as it would be
backwards-incompatible.

> --
> Best,
> In-Suk Joung
>
> -------------------------------------------------------------------------
> This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
> Build the coolest Linux based applications with Moblin SDK & win great
> prizes
> Grand prize is a trip for two to an Open Source event anywhere in the world
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>
>

[OpenBabel-scripting] A few questions about scripting OB with Perl

[IN S. J. <i....@gm...>]

Hello,
I have a few questions about Perl-OB binding.

1) Objects created by
## Assuming $residue is a OBResidue object.
$atom = $residue->GetAtoms;
$bond = $residue->GetBonds;
seem to be almost useless. When I need atoms or bonds in a specific residue,
I iterate OBMol object and find the specific atoms/bonds. This does not seem
to be very efficient way to me. Actually, I expected that $residue->GetAtoms
returns Perl array/arrayref of OBAtoms objects, but it didn't. Is there a
way to utilize the obejct created by above methods?

2) Atom index starts from 1 but residues and bonds starts from 0. Is this
intended?

-- 
Best,
In-Suk Joung

Re: [OpenBabel-scripting] OBPairData problem

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

Hello Loris,

This problem is due to the PairData object getting destroyed by
Python, while the C++ OBMol still wants to keep it. The solution is to
use CloneData instead of SetData. In other words, *never* use SetData
from Python or any other scripting language. I will update the Python
documentation to make this clear.

You might find it useful to look at the code of pybel.py to see how I
do things there.

Noel

On 16/09/2008, Loris Moretti <lor...@ch...> wrote:
> Hi all,
>
>  I am quite new to OpenBabel I am trying to develop a script in Python with
>  OpenBabel. The script reads a multiple sdf file, takes a molecule per time and
>  calculates some properties. It adds the property value and attribute to the
>  OBMol object with OBPairData and then, it writes out the molecules into a
>  multiple sdf file with the new field.
>
>  a very simple form of the script:
>
>  #########################################################
>  #!/usr/bin/python
>
>  import openbabel
>
>  obConversion = openbabel.OBConversion()
>  obConversion.SetInAndOutFormats("sdf", "sdf")
>
>  mol = openbabel.OBMol()
>
>  iteratorMol = obConversion.ReadFile(mol, "molecules.sdf")
>
>  while iteratorMol:
>
>     newData = openbabel.OBPairData()
>     newData.SetAttribute("NEWDATA")
>     newData.SetValue("blabla")
>     mol.SetData(newData)
>
>     print obConversion.WriteString(mol)
>
>     iteratorMol = obConversion.Read(mol)
>  #########################################################
>
>  The script works for the first molecule of the input file but fails for the
>  others with a "segmentation fault" error.
>  I tested it line by line and I saw there is a problem to reuse the OBPairData
>  object.
>
>  It might be a trivial error of mine but I cannot see it!
>  It might be an error of the system I use!
>
>  Can anyone help, please.
>
>  Thanks in advance,
>  loris...
>
>  -------------------------------------------------------------------------
>  This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
>  Build the coolest Linux based applications with Moblin SDK & win great prizes
>  Grand prize is a trip for two to an Open Source event anywhere in the world
>  http://moblin-contest.org/redirect.php?banner_id=100&url=/
>  _______________________________________________
>  OpenBabel-scripting mailing list
>  Ope...@li...
>  https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
>

[OpenBabel-scripting] OBPairData problem

[Loris M. <lor...@ch...>]

Hi all,

I am quite new to OpenBabel I am trying to develop a script in Python with
OpenBabel. The script reads a multiple sdf file, takes a molecule per time and
calculates some properties. It adds the property value and attribute to the
OBMol object with OBPairData and then, it writes out the molecules into a
multiple sdf file with the new field.

a very simple form of the script:

#########################################################
#!/usr/bin/python

import openbabel

obConversion = openbabel.OBConversion()
obConversion.SetInAndOutFormats("sdf", "sdf")

mol = openbabel.OBMol()

iteratorMol = obConversion.ReadFile(mol, "molecules.sdf")

while iteratorMol:

    newData = openbabel.OBPairData()
    newData.SetAttribute("NEWDATA")
    newData.SetValue("blabla")
    mol.SetData(newData)

    print obConversion.WriteString(mol)

    iteratorMol = obConversion.Read(mol)
#########################################################

The script works for the first molecule of the input file but fails for the
others with a "segmentation fault" error.
I tested it line by line and I saw there is a problem to reuse the OBPairData
object.

It might be a trivial error of mine but I cannot see it! 
It might be an error of the system I use!

Can anyone help, please.

Thanks in advance,
loris...

Re: [OpenBabel-scripting] Unable to set molecule name in pybel?

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

On 05/09/2008, Geoffrey Hutchison <ge...@ge...> wrote:
>
>  On Sep 5, 2008, at 7:50 AM, Noel O'Boyle wrote:
>
>
> > I can't easily check at the moment (I'm on holidays), but earlier
> > versions of Pybel didn't allow the user to set the title, just read
> > the title.
> >
>
>  Correct me if I'm wrong, but shouldn't a Pybel molecule still be an OBMol?
> Since Pybel includes the Open Babel wrapper, the C++ methods should still be
> exposed.
>
>  mol.SetTitle("Foo!")
>
>  Does that work?

Actually, it would be mol.OBMol.SetTitle("Foo!"), where mol is the
Pybel Molecule.

See line 225 of
http://code.google.com/p/cinfony/source/browse/trunk/cinfony/pybel.py
for the current pybel code using this.

>  Cheers,
>  -Geoff
>

Re: [OpenBabel-scripting] Unable to set molecule name in pybel?

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

In the 'new' version, an exception is raised (thanks to Andrew Dalke
for the patch).

On 05/09/2008, Andrew Fant <fa...@po...> wrote:
> Fair enough.  I'll dig into the code and see.  If the title is immutable,
> shouldn't an attempt to change it raise some sort of exception though,
> rather than just silently dropping it on the floor?
>
>  Andy
>
>
>  Noel O'Boyle wrote:
>
> > I can't easily check at the moment (I'm on holidays), but earlier
> > versions of Pybel didn't allow the user to set the title, just read
> > the title. If it's not available in the latest Pybel (just look at the
> > source code of pybel.py in the Molecule class), for sure it's in the
> > pybel.py that's bundled with cinfony.
> >
> > Noel
> >
> > 2008/9/4 Andrew Fant <fa...@po...>:
> >
> > > OK.  I'm probably missing something really simple here, but I am
> > > converting a dataset from a bunch of grody old hyperchem files into an
> > > SD file. Along the way, I am using:
> > >
> > > mol.title=name
> > >
> > > to supposedly set the molecule's title to the value of name (just a
> > > hacked-up variant of the filename it came from).
> > >
> > > The problem is that the title doesn't get exported as I write the file
> > > to the new sd file.  I get a molblock header that looks like:
> > >
> > >  OpenBabel09030819443D
> > >
> > >  78 81  0  0  0  0  0  0  0  0999 V2000
> > >
> > > and then the molecular coordinates.  I didn't see anything obvious
> > > online about this behavior.  Am I doing something really stupid, or is
> > > this a known will-fix that I am jumping the gun on?
> > >
> > > Thanks,
> > >    Andy
> > >
> > >
> -------------------------------------------------------------------------
> > > This SF.Net email is sponsored by the Moblin Your Move Developer's
> challenge
> > > Build the coolest Linux based applications with Moblin SDK & win great
> prizes
> > > Grand prize is a trip for two to an Open Source event anywhere in the
> world
> > >
> http://moblin-contest.org/redirect.php?banner_id=100&url=/
> > > _______________________________________________
> > > OpenBabel-scripting mailing list
> > > Ope...@li...
> > >
> https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
> > >
> > >
> >
>
>

Re: [OpenBabel-scripting] OpenBabel and Chemistry::OpenBabel

[Strempel S. <seb...@ch...>]

Dear Geoffrey,

thank you very much for the hint.

New file libopenbabel.so.3 with entry /usr/local/lib created in /etc/ld.so.conf.d/.
Command /sbin/ldconfig as root to create cache again.

example.pl in ./scripts/perl/examples runs.


Have a nice day

Sebastian



-----Ursprüngliche Nachricht-----
Von: Geoffrey Hutchison [mailto:ge...@ge...]
Gesendet: Fr 05.09.2008 22:59
An: Strempel  Sebastian
Cc: openbabel-scripting
Betreff: Re: [OpenBabel-scripting] OpenBabel and Chemistry::OpenBabel
 

On Sep 5, 2008, at 4:28 AM, Strempel Sebastian wrote:

> Can't load '/usr/local/lib/perl5/site_perl/5.10.0/i686-linux/auto/ 
> Chemistry/OpenBabel/OpenBabel.so' for module Chemistry::OpenBabel:  
> libopenbabel.so.3:

I'd concentrate in the last part of that -- libopenbabel.so.3.

First, if you run "babel -H" from the command-line, does it run?

Second, where is libopenbabel.so.3? My guess is that it's in /usr/ 
local/lib and that's not in your ld path. Try "man ldconfig" and look  
at /etc/ld.so.conf since you're using Linux.

Cheers,
-Geoff

Re: [OpenBabel-scripting] OpenBabel and Chemistry::OpenBabel

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

On Sep 5, 2008, at 4:28 AM, Strempel Sebastian wrote:

> Can't load '/usr/local/lib/perl5/site_perl/5.10.0/i686-linux/auto/ 
> Chemistry/OpenBabel/OpenBabel.so' for module Chemistry::OpenBabel:  
> libopenbabel.so.3:

I'd concentrate in the last part of that -- libopenbabel.so.3.

First, if you run "babel -H" from the command-line, does it run?

Second, where is libopenbabel.so.3? My guess is that it's in /usr/ 
local/lib and that's not in your ld path. Try "man ldconfig" and look  
at /etc/ld.so.conf since you're using Linux.

Cheers,
-Geoff

Re: [OpenBabel-scripting] Unable to set molecule name in pybel?

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

On Sep 5, 2008, at 7:50 AM, Noel O'Boyle wrote:

> I can't easily check at the moment (I'm on holidays), but earlier
> versions of Pybel didn't allow the user to set the title, just read
> the title.

Correct me if I'm wrong, but shouldn't a Pybel molecule still be an  
OBMol? Since Pybel includes the Open Babel wrapper, the C++ methods  
should still be exposed.

mol.SetTitle("Foo!")

Does that work?

Cheers,
-Geoff

Re: [OpenBabel-scripting] Unable to set molecule name in pybel?

[Andrew F. <fa...@po...>]

Fair enough.  I'll dig into the code and see.  If the title is 
immutable, shouldn't an attempt to change it raise some sort of 
exception though, rather than just silently dropping it on the floor?

Andy

Noel O'Boyle wrote:
> I can't easily check at the moment (I'm on holidays), but earlier
> versions of Pybel didn't allow the user to set the title, just read
> the title. If it's not available in the latest Pybel (just look at the
> source code of pybel.py in the Molecule class), for sure it's in the
> pybel.py that's bundled with cinfony.
> 
> Noel
> 
> 2008/9/4 Andrew Fant <fa...@po...>:
>> OK.  I'm probably missing something really simple here, but I am
>> converting a dataset from a bunch of grody old hyperchem files into an
>> SD file. Along the way, I am using:
>>
>> mol.title=name
>>
>> to supposedly set the molecule's title to the value of name (just a
>> hacked-up variant of the filename it came from).
>>
>> The problem is that the title doesn't get exported as I write the file
>> to the new sd file.  I get a molblock header that looks like:
>>
>>  OpenBabel09030819443D
>>
>>  78 81  0  0  0  0  0  0  0  0999 V2000
>>
>> and then the molecular coordinates.  I didn't see anything obvious
>> online about this behavior.  Am I doing something really stupid, or is
>> this a known will-fix that I am jumping the gun on?
>>
>> Thanks,
>>     Andy
>>
>> -------------------------------------------------------------------------
>> This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
>> Build the coolest Linux based applications with Moblin SDK & win great prizes
>> Grand prize is a trip for two to an Open Source event anywhere in the world
>> http://moblin-contest.org/redirect.php?banner_id=100&url=/
>> _______________________________________________
>> OpenBabel-scripting mailing list
>> Ope...@li...
>> https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
>>

Re: [OpenBabel-scripting] Unable to set molecule name in pybel?

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

I can't easily check at the moment (I'm on holidays), but earlier
versions of Pybel didn't allow the user to set the title, just read
the title. If it's not available in the latest Pybel (just look at the
source code of pybel.py in the Molecule class), for sure it's in the
pybel.py that's bundled with cinfony.

Noel

2008/9/4 Andrew Fant <fa...@po...>:
> OK.  I'm probably missing something really simple here, but I am
> converting a dataset from a bunch of grody old hyperchem files into an
> SD file. Along the way, I am using:
>
> mol.title=name
>
> to supposedly set the molecule's title to the value of name (just a
> hacked-up variant of the filename it came from).
>
> The problem is that the title doesn't get exported as I write the file
> to the new sd file.  I get a molblock header that looks like:
>
>  OpenBabel09030819443D
>
>  78 81  0  0  0  0  0  0  0  0999 V2000
>
> and then the molecular coordinates.  I didn't see anything obvious
> online about this behavior.  Am I doing something really stupid, or is
> this a known will-fix that I am jumping the gun on?
>
> Thanks,
>     Andy
>
> -------------------------------------------------------------------------
> This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
> Build the coolest Linux based applications with Moblin SDK & win great prizes
> Grand prize is a trip for two to an Open Source event anywhere in the world
> http://moblin-contest.org/redirect.php?banner_id=100&url=/
> _______________________________________________
> OpenBabel-scripting mailing list
> Ope...@li...
> https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
>

Re: [OpenBabel-scripting] OpenBabel and Chemistry::OpenBabel

[Strempel S. <seb...@ch...>]

Dear Geoffrey,

thank you for your fast response. The contents in "./scripts/perl" can be compiled indeed.
However "make test" fails on every single test. Make install seems to work and copies the files
but a test with your example.pl tells me that:

Can't load '/usr/local/lib/perl5/site_perl/5.10.0/i686-linux/auto/Chemistry/OpenBabel/OpenBabel.so' for module Chemistry::OpenBabel: libopenbabel.so.3:

The contents of the directory "/usr/local/lib/perl5/site_perl/5.10.0/i686-linux/auto/Chemistry/OpenBabel/" are:

-r--r--r-- 1 root root       0  5. Sep 09:35 OpenBabel.bs
-r-xr-xr-x 1 root root 2725483  5. Sep 09:35 OpenBabel.so
-rw-r--r-- 1 root root     246  5. Sep 10:10 .packlist

So Chemistry::OpenBabel seems ok but not its dependent libraries. 

Where is my error or misunderstanding? 
Shall I wait for the next release as you proposed?
Thank you again for your time and help.

Sebastian


-----Ursprüngliche Nachricht-----
Von: Geoffrey Hutchison [mailto:ge...@pi...]
Gesendet: Do 04.09.2008 15:06
An: Strempel  Sebastian
Cc: openbabel-scripting
Betreff: Re: OpenBabel and Chemistry::OpenBabel
 
Dear Sebastian,

The OpenBabel scripting modules are updated with every release of the  
main library. Particularly with Perl, it's difficult for the scripting  
module to detect which version of the library is installed.

In short, Chemistry::OpenBabel is at 1.3 -- this corresponds to the  
OB-2.2 release. If you've compiled the release from source, go into  
the scripts/perl directory and you'll find the appropriate Perl module.

Cheers,
-Geoff


On Sep 4, 2008, at 5:24 AM, Strempel Sebastian wrote:

> Dear Geoffrey,
>
> I have downloaded Openbabel 2.2.0 and Chemistry::OpenBabel 1.2.0.
> I first installed the OpenBabel libraries and then tried to install  
> the perl module
> that unfortunately failed ("OpenBabel not defined"). It seems that  
> the module did
> not find the preinstalled libraries. I called the installation  
> commands from the
> respective directories.
>
> OpenBabel:
> decompress files; go to new directory; ./configure; make; make  
> install;
>
> Chemistry:
> decompress files; go to this new folder (not in openbabel folder);  
> perl Makefile.pl; make --> error
>
> Where is my mistake or misunderstanding.
> Thank you for your help and time.
>
> Regards
>
> Sebastian Strempel
>
> -- 
> Sebastian Strempel
> Diplom-Bioinformatiker Univ. (M.Sc.)
>
> ETH Zürich
> Institute for Chemical and Bioengineering
> Safety and Environmental Technology Group
> HCI G138
> Wolfgang-Pauli-Strasse 10
> 8093 Zürich, Switzerland
>
> phone: 0041446326885
> fax: 0041446321189
> homepage: http://proto-sustchem.ethz.ch/
> mailto:seb...@ch...
>

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

[OpenBabel-scripting] GetMIMEType() returns None in python

[TJ O'D. <tj...@ac...>]

I'm using openbabel 2.2.0 for windows (also fails on Mac)
This python script prints None for MIME types,
but the Description and GetID are fine.
Is GetMIMEType busted or maybe the swig?

Thanks,
TJ O'Donnell

import openbabel

obc=openbabel.OBConversion()
for ext in ('sdf','pdb','xyz','mol2'):
   f = obc.FindFormat(ext)
   print          f.Description()
   print 'ext=',  f.GetID()
   print 'mime=', f.GetMIMEType()

[OpenBabel-scripting] Unable to set molecule name in pybel?

[Andrew F. <fa...@po...>]

OK.  I'm probably missing something really simple here, but I am 
converting a dataset from a bunch of grody old hyperchem files into an 
SD file. Along the way, I am using:

mol.title=name

to supposedly set the molecule's title to the value of name (just a 
hacked-up variant of the filename it came from).

The problem is that the title doesn't get exported as I write the file 
to the new sd file.  I get a molblock header that looks like:

  OpenBabel09030819443D

  78 81  0  0  0  0  0  0  0  0999 V2000

and then the molecular coordinates.  I didn't see anything obvious 
online about this behavior.  Am I doing something really stupid, or is 
this a known will-fix that I am jumping the gun on?

Thanks,
     Andy

Re: [OpenBabel-scripting] OpenBabel and Chemistry::OpenBabel

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

Dear Sebastian,

The OpenBabel scripting modules are updated with every release of the  
main library. Particularly with Perl, it's difficult for the scripting  
module to detect which version of the library is installed.

In short, Chemistry::OpenBabel is at 1.3 -- this corresponds to the  
OB-2.2 release. If you've compiled the release from source, go into  
the scripts/perl directory and you'll find the appropriate Perl module.

Cheers,
-Geoff


On Sep 4, 2008, at 5:24 AM, Strempel Sebastian wrote:

> Dear Geoffrey,
>
> I have downloaded Openbabel 2.2.0 and Chemistry::OpenBabel 1.2.0.
> I first installed the OpenBabel libraries and then tried to install  
> the perl module
> that unfortunately failed ("OpenBabel not defined"). It seems that  
> the module did
> not find the preinstalled libraries. I called the installation  
> commands from the
> respective directories.
>
> OpenBabel:
> decompress files; go to new directory; ./configure; make; make  
> install;
>
> Chemistry:
> decompress files; go to this new folder (not in openbabel folder);  
> perl Makefile.pl; make --> error
>
> Where is my mistake or misunderstanding.
> Thank you for your help and time.
>
> Regards
>
> Sebastian Strempel
>
> -- 
> Sebastian Strempel
> Diplom-Bioinformatiker Univ. (M.Sc.)
>
> ETH Zürich
> Institute for Chemical and Bioengineering
> Safety and Environmental Technology Group
> HCI G138
> Wolfgang-Pauli-Strasse 10
> 8093 Zürich, Switzerland
>
> phone: 0041446326885
> fax: 0041446321189
> homepage: http://proto-sustchem.ethz.ch/
> mailto:seb...@ch...
>

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

[OpenBabel-scripting] Unable to set molecule name in pybel?

[Andrew F. <fa...@mo...>]

OK.  I'm probably missing something really simple here, but I am 
converting a dataset from a bunch of grody old hyperchem files into an 
SD file. Along the way, I am using:

mol.title=name

to supposedly set the molecule's title to the value of name (just a 
hacked-up variant of the filename it came from).

The problem is that the title doesn't get exported as I write the file 
to the new sd file.  I get a molblock header that looks like:

  OpenBabel09030819443D

  78 81  0  0  0  0  0  0  0  0999 V2000

and then the molecular coordinates.  I didn't see anything obvious 
online about this behavior.  Am I doing something really stupid, or is 
this a known will-fix that I am jumping the gun on?

Thanks,
	Andy

[OpenBabel-scripting] .Net bindings

[Matt S. <mes...@gm...>]

I've been finishing up the .net bindings and I'm wondering if we
should make them CLS compliant. The only thing standing in the way is
methods that return unsigned numeric types.

Before I make any changes I wanted to ask what languages other than
IronPython are people interested in seeing compatibility for.


-Matt

[OpenBabel-scripting] Using OpenBabel from Jython

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

Hello all,

I've just released a new version of Cinfony with full documentation.
If there is anyone out there who is interested in using OpenBabel from
Jython (on Windows or Linux), I would really appreciate feedback on
the installation
instructions and general documentation.

It's all available at http://cinfony.googlecode.com

Regards,
  Noel

P.S. The Pybel in Cinfony is the same as the one that comes with
OpenBabel (actually, slightly newer)

Re: [OpenBabel-scripting] Pybel - localopt() error?!

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

> Hi Noel,
>
> as far as i know are you one of the main developer behind the great
> pybel bindungs for openbabel. I'm unable to find an irc channel or
> something like this, so i'm trying to cantact you directly. Hope that is
> ok.

Google "Pybel". :-) 4th line:
"If you have any problems or want to ask a question, please send an
email to the openbabel-scripting mailing list."

> I'm playing around with the new functions draw, localopt, addh etc. And
> i get a strange error if i try to generate 3D structures from inchis.
> Attached you can find a inchi.txt with several inchis from chemid-plus.
> The script inchi23dmolfile.py tries to read each inchi and generate 3D
> structures. With one inchi i get a segmentation fault, with an other i
> get a small backtrace (see below). If i try these procedure in ipython i
> can't reproduce it. But with the script i get every time the same error.
> Do you have any clue what is causing by error? Any hint to debug it
> further, or how i can absorb these error, to proceed with the script (my
> initial script have a few hundred inchis)?

The problem isn't reading the inchis but generating the 3D structures.
There's some weird memory stuff going on. There's no short term
solution I'm afraid. I'll file a bug and one of the other developers
will look into it.

> I would be happy to provide you with more informations if you like.
>
> Thank you very much,
> Bjoern
>
> P.S. Is their any irc channel, or mailing list for pybel?
>
> Segmentation fault
> InChI=1/C10H18O6/c1-9(11)15-7-5-13-3-4-14-6-8-16-10(2)12/h3-8H2,1-2H3
>
>
> InChI=1/2Cr.2Na.7O/q;;2*
> +1;;;;;;2*-1/rCr2O7.2Na/c3-1(4,5)9-2(6,7)8;;/q-2;2*+1
> -------------- backtrace ------------------------
> *** glibc detected *** python: corrupted double-linked list:
> 0x00000000010f3420 ***
> ======= Backtrace: =========
> /lib/libc.so.6[0x7f2f822bc28c]
> /lib/libc.so.6(cfree+0x8c)[0x7f2f822bfc1c]
> python[0x435ed7]
> python[0x434944]
> python(PyEval_EvalFrameEx+0x85c)[0x4837fc]
> python(PyEval_EvalCodeEx+0x776)[0x48a376]
> python(PyEval_EvalCode+0x32)[0x48a492]
> python(PyRun_FileExFlags+0x10e)[0x4abdce]
> python(PyRun_SimpleFileExFlags+0x1a9)[0x4ac069]
> python(Py_Main+0x8fd)[0x4145ad]
> /lib/libc.so.6(__libc_start_main+0xf4)[0x7f2f822661c4]
> python[0x413b29]
> ======= Memory map: ========
> 00400000-00522000 r-xp 00000000 08:02
> 574300                             /usr/bin/python2.5
> 00721000-00753000 rw-p 00121000 08:02
> 574300                             /usr/bin/python2.5
> 00753000-011c7000 rw-p 00753000 00:00 0
> [heap]
> 401d3000-401d4000 ---p 401d3000 00:00 0
> 401d4000-409d4000 rw-p 401d4000 00:00 0
> 7f2f6c000000-7f2f6c021000 rw-p 7f2f6c000000 00:00 0
> 7f2f6c021000-7f2f70000000 ---p 7f2f6c021000 00:00 0
> 7f2f700b3000-7f2f700b8000 r-xp 00000000 08:02
> 781861                     /usr/lib/openbabel/2.2/2.2.0/zindoformat.so
> 7f2f700b8000-7f2f702b8000 ---p 00005000 08:02
> 781861                     /usr/lib/openbabel/2.2/2.2.0/zindoformat.so
> 7f2f702b8000-7f2f702b9000 rw-p 00005000 08:02
> 781861                     /usr/lib/openbabel/2.2/2.2.0/zindoformat.so
> 7f2f702b9000-7f2f702c4000 r-xp 00000000 08:02
> 781720                     /usr/lib/openbabel/2.2/2.2.0/fchkformat.so
> 7f2f702c4000-7f2f704c4000 ---p 0000b000 08:02
> 781720                     /usr/lib/openbabel/2.2/2.2.0/fchkformat.so
> 7f2f704c4000-7f2f704c5000 rw-p 0000b000 08:02
> 781720                     /usr/lib/openbabel/2.2/2.2.0/fchkformat.so
> 7f2f704c5000-7f2f704cf000 r-xp 00000000 08:02
> 781604                     /usr/lib/openbabel/2.2/2.2.0/fastsearchformat.so
> 7f2f704cf000-7f2f706ce000 ---p 0000a000 08:02
> 781604                     /usr/lib/openbabel/2.2/2.2.0/fastsearchformat.so
> 7f2f706ce000-7f2f706cf000 rw-p 00009000 08:02
> 781604                     /usr/lib/openbabel/2.2/2.2.0/fastsearchformat.so
> 7f2f706cf000-7f2f706d7000 r-xp 00000000 08:02
> 781676                     /usr/lib/openbabel/2.2/2.2.0/cacaoformat.so
> 7f2f706d7000-7f2f708d6000 ---p 00008000 08:02
> 781676                     /usr/lib/openbabel/2.2/2.2.0/cacaoformat.so
> 7f2f708d6000-7f2f708d7000 rw-p 00007000 08:02
> 781676                     /usr/lib/openbabel/2.2/2.2.0/cacaoformat.so
> 7f2f708d7000-7f2f708dd000 r-xp 00000000 08:02
> 781856                     /usr/lib/openbabel/2.2/2.2.0/mpqcformat.so
> 7f2f708dd000-7f2f70add000 ---p 00006000 08:02
> 781856                     /usr/lib/openbabel/2.2/2.2.0/mpqcformat.so
> 7f2f70add000-7f2f70ade000 rw-p 00006000 08:02
> 781856                     /usr/lib/openbabel/2.2/2.2.0/mpqcformat.so
> 7f2f70ade000-7f2f70ae7000 r-xp 00000000 08:02
> 781606                     /usr/lib/openbabel/2.2/2.2.0/thermoformat.so
> 7f2f70ae7000-7f2f70ce6000 ---p 00009000 08:02
> 781606                     /usr/lib/openbabel/2.2/2.2.0/thermoformat.so
> 7f2f70ce6000-7f2f70ce7000 rw-p 00008000 08:02
> 781606                     /usr/lib/openbabel/2.2/2.2.0/thermoformat.so
> 7f2f70ce7000-7f2f70cf5000 r-xp 00000000 08:02
> 781879                     /usr/lib/openbabel/2.2/2.2.0/pdbformat.so
> 7f2f70cf5000-7f2f70ef5000 ---p 0000e000 08:02
> 781879                     /usr/lib/openbabel/2.2/2.2.0/pdbformat.so
> 7f2f70ef5000-7f2f70ef6000 rw-p 0000e000 08:02
> 781879                     /usr/lib/openbabel/2.2/2.2.0/pdbformat.so
> 7f2f70ef6000-7f2f70efd000 r-xp 00000000 08:02
> 781867                     /usr/lib/openbabel/2.2/2.2.0/reportformat.so
> 7f2f70efd000-7f2f710fd000 ---p 00007000 08:02
> 781867                     /usr/lib/openbabel/2.2/2.2.0/reportformat.so
> 7f2f710fd000-7f2f710fe000 rw-p 00007000 08:02
> 781867                     /usr/lib/openbabel/2.2/2.2.0/reportformat.so
> 7f2f710fe000-7f2f71104000 r-xp 00000000 08:02
> 780096                     /usr/lib/openbabel/2.2/2.2.0/unichemformat.so
> 7f2f71104000-7f2f71303000 ---p 00006000 08:02
> 780096                     /usr/lib/openbabel/2.2/2.2.0/unichemformat.so
> 7f2f71303000-7f2f71304000 rw-p 00005000 08:02
> 780096                     /usr/lib/openbabel/2.2/2.2.0/unichemformat.so
> 7f2f71304000-7f2f71309000 r-xp 00000000 08:02
> 781868                     /usr/lib/openbabel/2.2/2.2.0/fhformat.so
> 7f2f71309000-7f2f71509000 ---p 00005000 08:02
> 781868                     /usr/lib/openbabel/2.2/2.2.0/fhformat.so
> 7f2f71509000-7f2f7150a000 rw-p 00005000 08:02
> 781868                     /usr/lib/openbabel/2.2/2.2.0/fhformat.so
> 7f2f7150a000-7f2f71607000 r-xp 00000000 08:02
> 781612                     /usr/lib/openbabel/2.2/2.2.0/inchiformat.so
> 7f2f71607000-7f2f71806000 ---p 000fd000 08:02
> 781612                     /usr/lib/openbabel/2.2/2.2.0/inchiformat.so
> 7f2f71806000-7f2f7181b000 rw-p 000fc000 08:02
> 781612                     /usr/lib/openbabel/2.2/2.2.0/inchiformat.so
> 7f2f7181b000-7f2f71820000 r-xp 00000000 08:02
> 781885                     /usr/lib/openbabel/2.2/2.2.0/molreportformat.so
> 7f2f71820000-7f2f71a20000 ---p 00005000 08:02
> 781885                     /usr/lib/openbabel/2.2/2.2.0/molreportformat.so
> 7f2f71a20000-7f2f71a21000 rw-p 00005000 08:02
> 781885                     /usr/lib/openbabel/2.2/2.2.0/molreportformat.so
> 7f2f71a21000-7f2f71a26000 r-xp 00000000 08:02
> 781857                     /usr/lib/openbabel/2.2/2.2.0/CSRformat.so
> 7f2f71a26000-7f2f71c26000 ---p 00005000 08:02
> 781857                     /usr/lib/openbabel/2.2/2.2.0/CSRformat.so
> 7f2f71c26000-7f2f71c27000 rw-p 00005000 08:02
> 781857                     /usr/lib/openbabel/2.2/2.2.0/CSRformat.so
> 7f2f71c27000-7f2f71c30000 r-xp 00000000 08:02
> 781866                     /usr/lib/openbabel/2.2/2.2.0/crkformat.so
> 7f2f71c30000-7f2f71e2f000 ---p 00009000 08:02
> 781866                     /usr/lib/openbabel/2.2/2.2.0/crkformat.so
> 7f2f71e2f000-7f2f71e30000 rw-p 00008000 08:02
> 781866                     /usr/lib/openbabel/2.2/2.2.0/crkformat.so
> 7f2f71e30000-7f2f71e37000 r-xp 00000000 08:02
> 781860                     /usr/lib/openbabel/2.2/2.2.0/chem3dformat.so
> 7f2f71e37000-7f2f72037000 ---p 00007000 08:02
> 781860                     /usr/lib/openbabel/2.2/2.2.0/chem3dformat.so
> 7f2f72037000-7f2f72038000 rw-p 00007000 08:02
> 781860                     /usr/lib/openbabel/2.2/2.2.0/chem3dformat.so
> 7f2f72038000-7f2f7203e000 r-xp 00000000 08:02
> 780115                     /usr/lib/openbabel/2.2/2.2.0/ghemicalformat.so
> 7f2f7203e000-7f2f7223e000 ---p 00006000 08:02
> 780115                     /usr/lib/openbabel/2.2/2.2.0/ghemicalformat.so
> 7f2f7223e000-7f2f7223f000 rw-p 00006000 08:02
> 780115                     /usr/lib/openbabel/2.2/2.2.0/ghemicalformat.so
> 7f2f7223f000-7f2f72245000 r-xp 00000000 08:02
> 781882                     /usr/lib/openbabel/2.2/2.2.0/fastaformat.so
> 7f2f72245000-7f2f72444000 ---p 00006000 08:02
> 781882                     /usr/lib/openbabel/2.2/2.2.0/fastaformat.so
> 7f2f72444000-7f2f72445000 rw-p 00005000 08:02
> 781882                     /usr/lib/openbabel/2.2/2.2.0/fastaformat.so
> 7f2f72445000-7f2f7244a000 r-xp 00000000 08:02
> 781869                     /usr/lib/openbabel/2.2/2.2.0/cssrformat.so
> 7f2f7244a000-7f2f7264a000 ---p 00005000 08:02
> 781869                     /usr/lib/openbabel/2.2/2.2.0/cssrformat.so
> 7f2f7264a000-7f2f7264b000 rw-p 00005000 08:02
> 781869                     /usr/lib/openbabel/2.2/2.2.0/cssrformat.so
> 7f2f7264b000-7f2f72651000 r-xp 00000000 08:02
> 780107                     /usr/lib/openbabel/2.2/2.2.0/hinformat.so
> 7f2f72651000-7f2f72850000 ---p 00006000 08:02
> 780107                     /usr/lib/openbabel/2.2/2.2.0/hinformat.so
> 7f2f72850000-7f2f72851000 rw-p 00005000 08:02
> 780107                     /usr/lib/openbabel/2.2/2.2.0/hinformat.so
> 7f2f72851000-7f2f72857000 r-xp 00000000 08:02
> 781881                     /usr/lib/openbabel/2.2/2.2.0/carformat.so
> 7f2f72857000-7f2f72a56000 ---p 00006000 08:02
> 781881                     /usr/lib/openbabel/2.2/2.2.0/carformat.so
> 7f2f72a56000-7f2f72a57000 rw-p 00005000 08:02
> 781881                     /usr/lib/openbabel/2.2/2.2.0/carformat.so
> 7f2f72a57000-7f2f72a5d000 r-xp 00000000 08:02
> 781608                     /usr/lib/openbabel/2.2/2.2.0/cacheformat.so
> 7f2f72a5d000-7f2f72c5c000 ---p 00006000 08:02
> 781608                     /usr/lib/openbabel/2.2/2.2.0/cacheformat.so
> 7f2f72c5c000-7f2f72c5d000 rw-p 00005000 08:02
> 781608                     /usr/lib/openbabel/2.2/2.2.0/cacheformat.so
> 7f2f72c5d000-7f2f72c66000 r-xp 00000000 08:02
> 781865                     /usr/lib/openbabel/2.2/2.2.0/opendxformat.so
> 7f2f72c66000-7f2f72e65000 ---p 00009000 08:02
> 781865                     /usr/lib/openbabel/2.2/2.2.0/opendxformat.so
> 7f2f72e65000-7f2f72e66000 rw-p 00008000 08:02
> 781865                     /usr/lib/openbabel/2.2Aborted
>
> --
> ==========================================
> Björn Grüning
> D-14612 Falkensee, Germany
> Tel. +49-3322-212968, Fax +49-3322-4287528
> email: bj...@gr...
> jid:   ba...@gr...
>

[OpenBabel-scripting] Fwd: Pybel - localopt() error?!

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

---------- Forwarded message ----------
From: Bjoern Gruening <bj...@gr...>
Date: 2008/7/27
Subject: Pybel - localopt() error?!
To: Noel O'Boyle <bao...@gm...>



Hi Noel,

as far as i know are you one of the main developer behind the great
pybel bindungs for openbabel. I'm unable to find an irc channel or
something like this, so i'm trying to cantact you directly. Hope that is
ok.
I'm playing around with the new functions draw, localopt, addh etc. And
i get a strange error if i try to generate 3D structures from inchis.
Attached you can find a inchi.txt with several inchis from chemid-plus.
The script inchi23dmolfile.py tries to read each inchi and generate 3D
structures. With one inchi i get a segmentation fault, with an other i
get a small backtrace (see below). If i try these procedure in ipython i
can't reproduce it. But with the script i get every time the same error.
Do you have any clue what is causing by error? Any hint to debug it
further, or how i can absorb these error, to proceed with the script (my
initial script have a few hundred inchis)?
I would be happy to provide you with more informations if you like.

Thank you very much,
Bjoern

P.S. Is their any irc channel, or mailing list for pybel?

Segmentation fault
InChI=1/C10H18O6/c1-9(11)15-7-5-13-3-4-14-6-8-16-10(2)12/h3-8H2,1-2H3


InChI=1/2Cr.2Na.7O/q;;2*
+1;;;;;;2*-1/rCr2O7.2Na/c3-1(4,5)9-2(6,7)8;;/q-2;2*+1
-------------- backtrace ------------------------
*** glibc detected *** python: corrupted double-linked list:
0x00000000010f3420 ***
======= Backtrace: =========
/lib/libc.so.6[0x7f2f822bc28c]
/lib/libc.so.6(cfree+0x8c)[0x7f2f822bfc1c]
python[0x435ed7]
python[0x434944]
python(PyEval_EvalFrameEx+0x85c)[0x4837fc]
python(PyEval_EvalCodeEx+0x776)[0x48a376]
python(PyEval_EvalCode+0x32)[0x48a492]
python(PyRun_FileExFlags+0x10e)[0x4abdce]
python(PyRun_SimpleFileExFlags+0x1a9)[0x4ac069]
python(Py_Main+0x8fd)[0x4145ad]
/lib/libc.so.6(__libc_start_main+0xf4)[0x7f2f822661c4]
python[0x413b29]
======= Memory map: ========
00400000-00522000 r-xp 00000000 08:02
574300                             /usr/bin/python2.5
00721000-00753000 rw-p 00121000 08:02
574300                             /usr/bin/python2.5
00753000-011c7000 rw-p 00753000 00:00 0
[heap]
401d3000-401d4000 ---p 401d3000 00:00 0
401d4000-409d4000 rw-p 401d4000 00:00 0
7f2f6c000000-7f2f6c021000 rw-p 7f2f6c000000 00:00 0
7f2f6c021000-7f2f70000000 ---p 7f2f6c021000 00:00 0
7f2f700b3000-7f2f700b8000 r-xp 00000000 08:02
781861                     /usr/lib/openbabel/2.2/2.2.0/zindoformat.so
7f2f700b8000-7f2f702b8000 ---p 00005000 08:02
781861                     /usr/lib/openbabel/2.2/2.2.0/zindoformat.so
7f2f702b8000-7f2f702b9000 rw-p 00005000 08:02
781861                     /usr/lib/openbabel/2.2/2.2.0/zindoformat.so
7f2f702b9000-7f2f702c4000 r-xp 00000000 08:02
781720                     /usr/lib/openbabel/2.2/2.2.0/fchkformat.so
7f2f702c4000-7f2f704c4000 ---p 0000b000 08:02
781720                     /usr/lib/openbabel/2.2/2.2.0/fchkformat.so
7f2f704c4000-7f2f704c5000 rw-p 0000b000 08:02
781720                     /usr/lib/openbabel/2.2/2.2.0/fchkformat.so
7f2f704c5000-7f2f704cf000 r-xp 00000000 08:02
781604                     /usr/lib/openbabel/2.2/2.2.0/fastsearchformat.so
7f2f704cf000-7f2f706ce000 ---p 0000a000 08:02
781604                     /usr/lib/openbabel/2.2/2.2.0/fastsearchformat.so
7f2f706ce000-7f2f706cf000 rw-p 00009000 08:02
781604                     /usr/lib/openbabel/2.2/2.2.0/fastsearchformat.so
7f2f706cf000-7f2f706d7000 r-xp 00000000 08:02
781676                     /usr/lib/openbabel/2.2/2.2.0/cacaoformat.so
7f2f706d7000-7f2f708d6000 ---p 00008000 08:02
781676                     /usr/lib/openbabel/2.2/2.2.0/cacaoformat.so
7f2f708d6000-7f2f708d7000 rw-p 00007000 08:02
781676                     /usr/lib/openbabel/2.2/2.2.0/cacaoformat.so
7f2f708d7000-7f2f708dd000 r-xp 00000000 08:02
781856                     /usr/lib/openbabel/2.2/2.2.0/mpqcformat.so
7f2f708dd000-7f2f70add000 ---p 00006000 08:02
781856                     /usr/lib/openbabel/2.2/2.2.0/mpqcformat.so
7f2f70add000-7f2f70ade000 rw-p 00006000 08:02
781856                     /usr/lib/openbabel/2.2/2.2.0/mpqcformat.so
7f2f70ade000-7f2f70ae7000 r-xp 00000000 08:02
781606                     /usr/lib/openbabel/2.2/2.2.0/thermoformat.so
7f2f70ae7000-7f2f70ce6000 ---p 00009000 08:02
781606                     /usr/lib/openbabel/2.2/2.2.0/thermoformat.so
7f2f70ce6000-7f2f70ce7000 rw-p 00008000 08:02
781606                     /usr/lib/openbabel/2.2/2.2.0/thermoformat.so
7f2f70ce7000-7f2f70cf5000 r-xp 00000000 08:02
781879                     /usr/lib/openbabel/2.2/2.2.0/pdbformat.so
7f2f70cf5000-7f2f70ef5000 ---p 0000e000 08:02
781879                     /usr/lib/openbabel/2.2/2.2.0/pdbformat.so
7f2f70ef5000-7f2f70ef6000 rw-p 0000e000 08:02
781879                     /usr/lib/openbabel/2.2/2.2.0/pdbformat.so
7f2f70ef6000-7f2f70efd000 r-xp 00000000 08:02
781867                     /usr/lib/openbabel/2.2/2.2.0/reportformat.so
7f2f70efd000-7f2f710fd000 ---p 00007000 08:02
781867                     /usr/lib/openbabel/2.2/2.2.0/reportformat.so
7f2f710fd000-7f2f710fe000 rw-p 00007000 08:02
781867                     /usr/lib/openbabel/2.2/2.2.0/reportformat.so
7f2f710fe000-7f2f71104000 r-xp 00000000 08:02
780096                     /usr/lib/openbabel/2.2/2.2.0/unichemformat.so
7f2f71104000-7f2f71303000 ---p 00006000 08:02
780096                     /usr/lib/openbabel/2.2/2.2.0/unichemformat.so
7f2f71303000-7f2f71304000 rw-p 00005000 08:02
780096                     /usr/lib/openbabel/2.2/2.2.0/unichemformat.so
7f2f71304000-7f2f71309000 r-xp 00000000 08:02
781868                     /usr/lib/openbabel/2.2/2.2.0/fhformat.so
7f2f71309000-7f2f71509000 ---p 00005000 08:02
781868                     /usr/lib/openbabel/2.2/2.2.0/fhformat.so
7f2f71509000-7f2f7150a000 rw-p 00005000 08:02
781868                     /usr/lib/openbabel/2.2/2.2.0/fhformat.so
7f2f7150a000-7f2f71607000 r-xp 00000000 08:02
781612                     /usr/lib/openbabel/2.2/2.2.0/inchiformat.so
7f2f71607000-7f2f71806000 ---p 000fd000 08:02
781612                     /usr/lib/openbabel/2.2/2.2.0/inchiformat.so
7f2f71806000-7f2f7181b000 rw-p 000fc000 08:02
781612                     /usr/lib/openbabel/2.2/2.2.0/inchiformat.so
7f2f7181b000-7f2f71820000 r-xp 00000000 08:02
781885                     /usr/lib/openbabel/2.2/2.2.0/molreportformat.so
7f2f71820000-7f2f71a20000 ---p 00005000 08:02
781885                     /usr/lib/openbabel/2.2/2.2.0/molreportformat.so
7f2f71a20000-7f2f71a21000 rw-p 00005000 08:02
781885                     /usr/lib/openbabel/2.2/2.2.0/molreportformat.so
7f2f71a21000-7f2f71a26000 r-xp 00000000 08:02
781857                     /usr/lib/openbabel/2.2/2.2.0/CSRformat.so
7f2f71a26000-7f2f71c26000 ---p 00005000 08:02
781857                     /usr/lib/openbabel/2.2/2.2.0/CSRformat.so
7f2f71c26000-7f2f71c27000 rw-p 00005000 08:02
781857                     /usr/lib/openbabel/2.2/2.2.0/CSRformat.so
7f2f71c27000-7f2f71c30000 r-xp 00000000 08:02
781866                     /usr/lib/openbabel/2.2/2.2.0/crkformat.so
7f2f71c30000-7f2f71e2f000 ---p 00009000 08:02
781866                     /usr/lib/openbabel/2.2/2.2.0/crkformat.so
7f2f71e2f000-7f2f71e30000 rw-p 00008000 08:02
781866                     /usr/lib/openbabel/2.2/2.2.0/crkformat.so
7f2f71e30000-7f2f71e37000 r-xp 00000000 08:02
781860                     /usr/lib/openbabel/2.2/2.2.0/chem3dformat.so
7f2f71e37000-7f2f72037000 ---p 00007000 08:02
781860                     /usr/lib/openbabel/2.2/2.2.0/chem3dformat.so
7f2f72037000-7f2f72038000 rw-p 00007000 08:02
781860                     /usr/lib/openbabel/2.2/2.2.0/chem3dformat.so
7f2f72038000-7f2f7203e000 r-xp 00000000 08:02
780115                     /usr/lib/openbabel/2.2/2.2.0/ghemicalformat.so
7f2f7203e000-7f2f7223e000 ---p 00006000 08:02
780115                     /usr/lib/openbabel/2.2/2.2.0/ghemicalformat.so
7f2f7223e000-7f2f7223f000 rw-p 00006000 08:02
780115                     /usr/lib/openbabel/2.2/2.2.0/ghemicalformat.so
7f2f7223f000-7f2f72245000 r-xp 00000000 08:02
781882                     /usr/lib/openbabel/2.2/2.2.0/fastaformat.so
7f2f72245000-7f2f72444000 ---p 00006000 08:02
781882                     /usr/lib/openbabel/2.2/2.2.0/fastaformat.so
7f2f72444000-7f2f72445000 rw-p 00005000 08:02
781882                     /usr/lib/openbabel/2.2/2.2.0/fastaformat.so
7f2f72445000-7f2f7244a000 r-xp 00000000 08:02
781869                     /usr/lib/openbabel/2.2/2.2.0/cssrformat.so
7f2f7244a000-7f2f7264a000 ---p 00005000 08:02
781869                     /usr/lib/openbabel/2.2/2.2.0/cssrformat.so
7f2f7264a000-7f2f7264b000 rw-p 00005000 08:02
781869                     /usr/lib/openbabel/2.2/2.2.0/cssrformat.so
7f2f7264b000-7f2f72651000 r-xp 00000000 08:02
780107                     /usr/lib/openbabel/2.2/2.2.0/hinformat.so
7f2f72651000-7f2f72850000 ---p 00006000 08:02
780107                     /usr/lib/openbabel/2.2/2.2.0/hinformat.so
7f2f72850000-7f2f72851000 rw-p 00005000 08:02
780107                     /usr/lib/openbabel/2.2/2.2.0/hinformat.so
7f2f72851000-7f2f72857000 r-xp 00000000 08:02
781881                     /usr/lib/openbabel/2.2/2.2.0/carformat.so
7f2f72857000-7f2f72a56000 ---p 00006000 08:02
781881                     /usr/lib/openbabel/2.2/2.2.0/carformat.so
7f2f72a56000-7f2f72a57000 rw-p 00005000 08:02
781881                     /usr/lib/openbabel/2.2/2.2.0/carformat.so
7f2f72a57000-7f2f72a5d000 r-xp 00000000 08:02
781608                     /usr/lib/openbabel/2.2/2.2.0/cacheformat.so
7f2f72a5d000-7f2f72c5c000 ---p 00006000 08:02
781608                     /usr/lib/openbabel/2.2/2.2.0/cacheformat.so
7f2f72c5c000-7f2f72c5d000 rw-p 00005000 08:02
781608                     /usr/lib/openbabel/2.2/2.2.0/cacheformat.so
7f2f72c5d000-7f2f72c66000 r-xp 00000000 08:02
781865                     /usr/lib/openbabel/2.2/2.2.0/opendxformat.so
7f2f72c66000-7f2f72e65000 ---p 00009000 08:02
781865                     /usr/lib/openbabel/2.2/2.2.0/opendxformat.so
7f2f72e65000-7f2f72e66000 rw-p 00008000 08:02
781865                     /usr/lib/openbabel/2.2Aborted

--
==========================================
Björn Grüning
D-14612 Falkensee, Germany
Tel. +49-3322-212968, Fax +49-3322-4287528
email: bj...@gr...
jid:   ba...@gr...

[OpenBabel-scripting] ANN: OpenBabel Python bindings 1.3 available

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

Announcing the release of the OpenBabel module for Python, version
1.3, available from
   http://openbabel.org/wiki/Install.

OpenBabel is a chemical toolbox designed to speak the many languages
of chemical data. It's an open, collaborative project allowing anyone
to search, convert, analyze, or store data from molecular modeling,
chemistry, solid-state materials, biochemistry, or related areas. This
Python module allows you to access the OpenBabel library in your
Python scripts.

New features in 1.3:
 (1) Additions to Pybel Molecules to take advantage of new features of
the OpenBabel toolkit: make3D() for generation of 3D structures,
localopt() for geometry optimisation using forcefields, addh() and
removeh() for adding and removing hydrogens
 (2) The draw() method of a Molecule allows 2D structure diagram
generation and depiction using an interface to OASA
(http://bkchem.zirael.org/oasa_en.html)
 (3) Breadth-first iteration over molecules with depth information
(OBMolAtomBFSIter)
 (4) Integration with cinfony (http://code.google.com/p/cinfony),
enabling data to exchanged between OpenBabel and other open source
cheminformatics toolkits

Core features:
 (1) Read and write over 90 file formats including InChI and SMILES
 (2) Access molecular properties like molecular weight, formula, charge
 (3) Access and edit data fields formats like SDF, MOL2 and CIF
 (4) Daylight-type fingerprints and calculation of the Tanimoto coefficient
 (5) SMARTS pattern matching
 (6) Graph algorithms such as the Smallest Set of Smallest Rings (SSSR)

Documentation:
 (1) The Python module: http://openbabel.org/wiki/Python
 (2) The C++ toolkit: http://openbabel.org/api/2.2.0/
 (3) A paper describing Pybel: http://dx.doi.org/10.1186/1752-153X-2-5
 (4) The OpenBabel web site: http://openbabel.org

Support:
 (1) If you have any questions, send an email to
       ope...@li...
 (2) Report a bug at http://sourceforge.net/tracker/?atid=428740&group_id=40728

 Regards,
    Noel

[OpenBabel-scripting] ANNOUNCE: Open Babel 2.2.0 Release

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

I am very happy to finally announce the release of Open Babel 2.2.0,  
the latest stable version of the open source chemistry toolbox.

This release represents a major update and should be a stable upgrade,  
strongly recommended for all users of Open Babel. Highlights include  
improved force fields and coordinate generation, conformer searching,  
enhanced plugins including molecular descriptors, filters, and command- 
line transformations. Many formats are improved or added, including  
CIF, mmCIF, Gaussian cube, PQR, OpenDX cubes, and more. Improved  
developer API and scripting support and many, many bug fixes are also  
included.

What's new? See the full release notes at:
http://openbabel.org/wiki/Open_Babel_2.2.0

To download, see:
http://sourceforge.net/project/showfiles.php?group_id=40728&package_id=32894

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

I would like to personally thank a few people for making this release  
a great one. In alphabetical order, Jean Bréfort, Andrew Dalke, Marcus  
Hanwell, Chris Morley, Noel O'Boyle, Kevin Shepherd, Tim  
Vandermeersch, and Ugo Varetto.

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

Re: [OpenBabel-scripting] reg:ruby installation

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

On Jun 18, 2008, at 8:03 AM, Noel O'Boyle wrote:

> OpenBabel cannot generate images. The input format makes no
> difference. I mentioned pybel as an alternative solution in my
> previous email.

I think he's also referring to Rich Apodaca's articles.
http://depth-first.com/

I think Depth-First.com goes into great detail about creating the  
images. It's a combination of Open Babel and CDK in Ruby.

Cheers,
-Geoff

Re: [OpenBabel-scripting] reg:ruby installation

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

2008/6/18 Anand <an...@av...>:
> Thankyou for the information. I am using openbabel 2.1.1 version.
>
> My problem is to generate images at least from inchi format as given in
> tutorials will that help or any alternative solution to this.
OpenBabel cannot generate images. The input format makes no
difference. I mentioned pybel as an alternative solution in my
previous email.

> Regards
> Anand
> ----- Original Message ----- From: "Noel O'Boyle" <bao...@gm...>
> To: "Anand" <an...@av...>
> Cc: <Ope...@li...>
> Sent: Wednesday, June 18, 2008 5:04 PM
> Subject: Re: [OpenBabel-scripting] reg:ruby installation
>
>
>> 2008/6/18 Anand <an...@av...>:
>>>
>>> Dear users,
>>>
>>> I have trouble installing obruby.
>>>
>>> I have successfullt installed openbabel in linux and also ruby
>>>
>>> But the interactive ruby irb is prompted and when I say require
>>> 'openbabel'
>>>
>>> it prompts Load error openbabel.so  /.......openbabel.so
>>
>> What version of OpenBabel? How did you build/install obruby?
>>
>>> Kindly provide a solution.
>>>
>>> I am inetersted in generating PNG images either from smiles or any other
>>> formats as indiviual files
>>
>> It's currently not possible to generate PNG images from SMILES using
>> OpenBabel. Pybel can do it (in the development version), but it uses a
>> third-party library (OASA).
>>
>>> Please suggest
>>>
>>> Thank you
>>>
>>> Regards
>>> Anand
>>>
>>>
>>>
>>> -------------------------------------------------------------------------
>>> Check out the new SourceForge.net Marketplace.
>>> It's the best place to buy or sell services for
>>> just about anything Open Source.
>>> http://sourceforge.net/services/buy/index.php
>>> _______________________________________________
>>> OpenBabel-scripting mailing list
>>> Ope...@li...
>>> https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
>>>
>>>
>>
>
>
>

Re: [OpenBabel-scripting] reg:ruby installation

[Anand <an...@av...>]

Thankyou for the information. I am using openbabel 2.1.1 version.

My problem is to generate images at least from inchi format as given in 
tutorials will that help or any alternative solution to this.

Regards
Anand
----- Original Message ----- 
From: "Noel O'Boyle" <bao...@gm...>
To: "Anand" <an...@av...>
Cc: <Ope...@li...>
Sent: Wednesday, June 18, 2008 5:04 PM
Subject: Re: [OpenBabel-scripting] reg:ruby installation


> 2008/6/18 Anand <an...@av...>:
>> Dear users,
>>
>> I have trouble installing obruby.
>>
>> I have successfullt installed openbabel in linux and also ruby
>>
>> But the interactive ruby irb is prompted and when I say require 
>> 'openbabel'
>>
>> it prompts Load error openbabel.so  /.......openbabel.so
>
> What version of OpenBabel? How did you build/install obruby?
>
>> Kindly provide a solution.
>>
>> I am inetersted in generating PNG images either from smiles or any other
>> formats as indiviual files
>
> It's currently not possible to generate PNG images from SMILES using
> OpenBabel. Pybel can do it (in the development version), but it uses a
> third-party library (OASA).
>
>> Please suggest
>>
>> Thank you
>>
>> Regards
>> Anand
>>
>>
>>
>> -------------------------------------------------------------------------
>> Check out the new SourceForge.net Marketplace.
>> It's the best place to buy or sell services for
>> just about anything Open Source.
>> http://sourceforge.net/services/buy/index.php
>> _______________________________________________
>> OpenBabel-scripting mailing list
>> Ope...@li...
>> https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
>>
>>
>