from:"Maciek Wójcikowski"

I was wrong, the "F" option retains bonds' order and it even works for
aromatic atoms.
For future reference, to generate smiles of fragment by atom indices in
Python you can do:

> idxs = [1,2,3,4]
> mol.write('smi', opt={'F': ' '.join(map(str, idxs))}).strip()



Pozdrawiam,  |  Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl

2017-06-19 17:19 GMT+02:00 Maciek Wójcikowski <mac...@wojcikowski.pl>:

> No worries :) I planned to do Chem.FindAtomEnvironmentOfRadiusN() and
> Chem.PathToSubMol() in RDKit, but the function you've suggested is also
> feasible.
>
> @Geoff - the smiles fragment does not perserve any bond information from
> what I've tested so far.
>
> 
> Pozdrawiam,  |  Best regards,
> Maciek Wójcikowski
> mac...@wojcikowski.pl
>
> 2017-06-19 17:12 GMT+02:00 Andrew Dalke <da...@dalkescientific.com>:
>
>> Me:
>> > Perhaps you want Chem.MolFragmentToSmiles(mol, atomsToUse=idxs)?
>> >
>> > http://www.rdkit.org/docs-beta/api/rdkit.Chem.rdmolfiles-
>> module.html#MolFragmentToSmiles
>>
>> Err, umm, *blush*. Forgot which list I was reading.
>>
>> [Andrew! It says it right in the subject line! :]
>>
>> Andrew
>> da...@dalkescientific.com
>>
>>
>> 
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Re: [Open Babel] Submolecule from OBMol

No worries :) I planned to do Chem.FindAtomEnvironmentOfRadiusN() and
Chem.PathToSubMol() in RDKit, but the function you've suggested is also
feasible.

@Geoff - the smiles fragment does not perserve any bond information from
what I've tested so far.


Pozdrawiam,  |  Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl

2017-06-19 17:12 GMT+02:00 Andrew Dalke <da...@dalkescientific.com>:

> Me:
> > Perhaps you want Chem.MolFragmentToSmiles(mol, atomsToUse=idxs)?
> >
> > http://www.rdkit.org/docs-beta/api/rdkit.Chem.rdmolfiles-module.html#
> MolFragmentToSmiles
>
> Err, umm, *blush*. Forgot which list I was reading.
>
> [Andrew! It says it right in the subject line! :]
>
> Andrew
> da...@dalkescientific.com
>
>
> 
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Re: [Open Babel] Submolecule from OBMol

I'm trying to get back the ECFP environments, most preferably as smiles. So
it's literally a list of connected atoms.

The dumb solution goes as follows:

def submol(mol, idxs):
> mol_clone = mol.clone
> mol_clone.OBMol.BeginModify()
> delete_atoms = []
> for i in reversed(range(len(mol.atoms))):
> if i in idxs:
> continue
> delete_atoms.append(mol_clone.OBMol.GetAtomById(i))
> for atom in delete_atoms:
> mol_clone.OBMol.DeleteAtom(atom)
> mol_clone.OBMol.BeginModify()
> return mol_clone


----
Pozdrawiam,  |  Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl

2017-06-19 15:53 GMT+02:00 Noel O'Boyle <baoille...@gmail.com>:

> This would be a useful API function.
>
> If it's a disconnected portion of the molecule, and you wanted to
> write a smiles, there is a fragment option for the smiles writer that
> you could use.
>
> - Noel
>
> On 17 June 2017 at 21:44, Maciek Wójcikowski <mac...@wojcikowski.pl>
> wrote:
> > Hi all,
> >
> > Quick question: I have OBMol and want to create a sub-molecule from a
> subset
> > of atoms given by atom/bond indices. Is there a clever way to do it in
> > OpenBabel? I'm aware that I can make a copy and prune the unwanted atoms
> ;)
> >
> > 
> > Pozdrawiam,  |  Best regards,
> > Maciek Wójcikowski
> > mac...@wojcikowski.pl
> >
> > 
> --
> > Check out the vibrant tech community on one of the world's most
> > engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> > ___
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> > OpenBabel-discuss@lists.sourceforge.net
> > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
> >
>
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Re: [Open Babel] Submolecule from OBMol

The last BeginModify should be EndModify.


Pozdrawiam,  |  Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl

2017-06-19 16:39 GMT+02:00 Maciek Wójcikowski <mac...@wojcikowski.pl>:

> I'm trying to get back the ECFP environments, most preferably as smiles.
> So it's literally a list of connected atoms.
>
> The dumb solution goes as follows:
>
> def submol(mol, idxs):
>> mol_clone = mol.clone
>> mol_clone.OBMol.BeginModify()
>> delete_atoms = []
>> for i in reversed(range(len(mol.atoms))):
>> if i in idxs:
>> continue
>> delete_atoms.append(mol_clone.OBMol.GetAtomById(i))
>> for atom in delete_atoms:
>> mol_clone.OBMol.DeleteAtom(atom)
>> mol_clone.OBMol.BeginModify()
>> return mol_clone
>
>
> 
> Pozdrawiam,  |  Best regards,
> Maciek Wójcikowski
> mac...@wojcikowski.pl
>
> 2017-06-19 15:53 GMT+02:00 Noel O'Boyle <baoille...@gmail.com>:
>
>> This would be a useful API function.
>>
>> If it's a disconnected portion of the molecule, and you wanted to
>> write a smiles, there is a fragment option for the smiles writer that
>> you could use.
>>
>> - Noel
>>
>> On 17 June 2017 at 21:44, Maciek Wójcikowski <mac...@wojcikowski.pl>
>> wrote:
>> > Hi all,
>> >
>> > Quick question: I have OBMol and want to create a sub-molecule from a
>> subset
>> > of atoms given by atom/bond indices. Is there a clever way to do it in
>> > OpenBabel? I'm aware that I can make a copy and prune the unwanted
>> atoms ;)
>> >
>> > 
>> > Pozdrawiam,  |  Best regards,
>> > Maciek Wójcikowski
>> > mac...@wojcikowski.pl
>> >
>> > 
>> --
>> > Check out the vibrant tech community on one of the world's most
>> > engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>> > ___
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>> > OpenBabel-discuss@lists.sourceforge.net
>> > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>> >
>>
>
>
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[Open Babel] Submolecule from OBMol

2017-06-17 Thread Maciek Wójcikowski

Hi all,

Quick question: I have OBMol and want to create a sub-molecule from a
subset of atoms given by atom/bond indices. Is there a clever way to do it
in OpenBabel? I'm aware that I can make a copy and prune the unwanted atoms
;)


Pozdrawiam,  |  Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl
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Re: [Open Babel] Error when using compound.draw() in pybel installed by conda - PNG depiction support not found.

2017-05-31 Thread Maciek Wójcikowski

I've rebuilt the Python 2.7 packages for Windows (the rest is still
compiling), and the PNG should work now. Update openbabel package to 2.4.1
py27_3: `conda install -c openbabel openbabel`.


Pozdrawiam,  |  Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl

2017-05-31 13:16 GMT+02:00 Noel O'Boyle <baoille...@gmail.com>:

> That's a pity. In the meanwhile, you can still create SVG images if
> you choose this a write format, and pysvg might be able to convert to
> PNG (?).
>
> On 31 May 2017 at 10:21, Maciek Wójcikowski <mac...@wojcikowski.pl> wrote:
> > Hi,
> >
> > PNG is not supported yet on Windows - Openbabel was not compiled with
> it, as
> > there is no cairo package on Anaconda main channel for windows (note
> you're
> > using conda-forge).
> >
> > Unfortunately this is also the case in bioconda, so for now there is no
> > better conda solution yet. I will revisit this issue and try to support
> PNG
> > files.
> >
> > 
> > Pozdrawiam,  |  Best regards,
> > Maciek Wójcikowski
> > mac...@wojcikowski.pl
> >
> > 2017-05-31 11:06 GMT+02:00 Hongbin Yang <yanyangh...@163.com>:
> >>
> >> Hi，
> >>
> >> I installed openbabel via `conda install -c openbabel openbabel`.
> >>
> >> I wanted to draw the molecule like
> >> `pybel.readstring('smi','c1c1').draw()`
> >>
> >> Then the error was raised:
> >> C:\Users\yanya\Anaconda2\lib\site-packages\pybel.pyc in draw(self,
> show,
> >> filename, update, usecoords)
> >> 615 formatok = obconversion.SetOutFormat("_png2")
> >> 616 if not formatok:
> >> --> 617 raise ImportError("PNG depiction support not found. You should "
> >> 618 "compile Open Babel with support for Cairo. See "
> >> 619 "installation instructions for more "
> >>
> >> ImportError: PNG depiction support not found. You should compile Open
> >> Babel with support for Cairo. See installation instructions for more
> >> information.
> >>
> >> The installed packages includes:
> >> libpng 1.6.28 vc9_0 [vc9] conda-forge
> >> pillow 4.0.0 py27_0
> >> pycairo 1.10.0 
> >> openbabel 2.4.1 py27_2 openbabel
> >> cairo 1.14.6 vc9_4 [vc9] conda-forge
> >>
> >> I have both pillow and (py)cairo. Why can't I draw the molecule ?
> >> I guess that if I followed the suggestion and compile it with suport
> cairo
> >> it will work. But I have to work with conda. Is there any better way?
> >>
> >> Sincerely,
> >>
> >> 
> >> Hongbin Yang 杨弘宾
> >> Research: Toxicophore and Chemoinformatics
> >> Pharmaceutical Science, School of Pharmacy
> >> East China University of Science and Technology
> >>
> >>
> >> 
> --
> >> Check out the vibrant tech community on one of the world's most
> >> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> >> ___
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> >> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
> >>
> >
> >
> > 
> --
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Re: [Open Babel] Error when using compound.draw() in pybel installed by conda - PNG depiction support not found.

2017-05-31 Thread Maciek Wójcikowski

Hi,

PNG is not supported yet on Windows - Openbabel was not compiled with it,
as there is no cairo package on Anaconda main channel for windows (note
you're using conda-forge).

Unfortunately this is also the case in bioconda, so for now there is no
better conda solution yet. I will revisit this issue and try to support PNG
files.


Pozdrawiam,  |  Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl

2017-05-31 11:06 GMT+02:00 Hongbin Yang <yanyangh...@163.com>:

> Hi，
>
> I installed openbabel via `conda install -c openbabel openbabel`.
>
> I wanted to draw the molecule like
> `pybel.readstring('smi','c1c1').draw()`
>
> Then the error was raised:
> C:\Users\yanya\Anaconda2\lib\site-packages\pybel.pyc in draw(self, show,
> filename, update, usecoords)
> 615 formatok = obconversion.SetOutFormat("_png2")
> 616 if not formatok:
> --> 617 raise ImportError("PNG depiction support not found. You should "
> 618 "compile Open Babel with support for Cairo. See "
> 619 "installation instructions for more "
>
> ImportError: PNG depiction support not found. You should compile Open
> Babel with support for Cairo. See installation instructions for more
> information.
>
> The installed packages includes:
> libpng 1.6.28 vc9_0 [vc9] conda-forge
> pillow 4.0.0 py27_0
> pycairo 1.10.0 
> openbabel 2.4.1 py27_2 openbabel
> cairo 1.14.6 vc9_4 [vc9] conda-forge
>
> I have both pillow and (py)cairo. Why can't I draw the molecule ?
> I guess that if I followed the suggestion and compile it with suport cairo
> it will work. But I have to work with conda. Is there any better way?
>
> Sincerely,
>
> --
> Hongbin Yang 杨弘宾
> Research: Toxicophore and Chemoinformatics
> Pharmaceutical Science, School of Pharmacy
> East China University of Science and Technology
>
> 
> --
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
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Re: [Open Babel] About pybel module installation

2017-04-09 Thread Maciek Wójcikowski

Hello,

What you need is openbabel package not pybel: "pip install openbabel"
See https://pypi.python.org/pypi/openbabel



Pozdrawiam,  |  Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl

2017-04-06 1:23 GMT+02:00 Phuong Do <phuongdo@gmail.com>:

> Hello,
>
> I intend to use pybel module in python for my project. When I install
> pybel by "pip install pybel" and "import pybel", there is no error.
> However, now when I check for "modules installed in python", it is pyBEL
> 0.4.4, not pybel that I want.
>
> Is there any way that I can install it properly. I am using macbook.
> Thank you very much.
>
> Phuong Do
>
>
> 
> --
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Re: [Open Babel] How to Install openbabel for Python 3.6 on macOS Sierra 10.12.3

2017-02-13 Thread Maciek Wójcikowski

Hello,

Python 3.6 support is not there yet. It should be added soon.


Pozdrawiam,  |  Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl

2017-02-13 5:31 GMT+01:00 i4hashmi <i4has...@hotmail.com>:

> I am using Python for making a script to work with some chemical structures
> in my PhD. I want to install openbabel libraries for python. I tried my
> best
> but I could not install it on Windows. I posted a question earlier about
> installing it on Windows at
> http://stackoverflow.com/questions/42151301/how-do-i-
> install-openbabel-for-python-3-6-in-windows-10/42151551?
> noredirect=1#comment71470260_42151551
> but could not find a solution. The solution installed the library but it
> does not work and could not connect to SWIG.
> No I am trying to install it on my office computer which is a mac for past
> 5
> hours but I could not figure what is going on.
> I tried to install it from source code of Openbabel and link it with
> python3
> but it is making problem.
> If I use the following command:
>
>  `cmake ../ -DPYTHON_BINDINGS=ON -DRUN_SWIG=ON`
>
> It successfully links it to Python 2.7 which I do not want. When I try the
> following options, it gives the error shown below:
>
> `cmake ../ -DPYTHON_EXECUTABLE=/usr/bin/python3 -DPYTHON_BINDINGS=ON
> -DRUN_SWIG=ON`
>
> OR
>
> `cmake ../ -DRUN_SWIG=ON -DPYTHON_EXECUTABLE=/usr/bin/python3
> -DPYTHON_INCLUDE_DIR=/Library/Frameworks/Python.framework/
> Versions/3.5/include/python3.5m
> -DPYTHON_LIBRARY=/Library/Frameworks/Python.framework/
> Versions/3.5/lib/libpython3.5m.dylib
> -DPYTHON_BINDINGS=ON`
>
> It gives the following error at the end after a lot of successful output:
>
> -- Found PythonInterp: /usr/bin/python3.6 (found version "1.4")
> -- Found SWIG: /usr/local/bin/swig (found version "3.0.12")
> -- Found SWIG: /usr/local/bin/swig (found suitable version "3.0.12",
> minimum required is "2.0")
> -- Found PythonLibs:
> /usr/local/Cellar/python3/3.6.0/Frameworks/Python.framework/
> Versions/3.6/lib/libpython3.6m.dylib
> (found version "3.6.0")
> -- Python bindings will be compiled
> CMake Error at scripts/CMakeLists.txt:120 (install):
> install TARGETS given no LIBRARY DESTINATION for module target
> "bindings_python".
> CMake Error at scripts/CMakeLists.txt:123 (install):
> install FILES given no DESTINATION!
> CMake Error at scripts/CMakeLists.txt:126 (install):
> install FILES given no DESTINATION!
> -- Configuring incomplete, errors occurred!
> See also
> "/usr/local/Cellar/obabel/openbabel-master/ali/
> CMakeFiles/CMakeOutput.log".
> See also
> "/usr/local/Cellar/obabel/openbabel-master/ali/CMakeFiles/CMakeError.log".
>
>
> I am not sure why It detects the Python as v1.4 `-- Found PythonInterp:
> /usr/bin/python3.6 (found version "1.4") ` instead of finding v.3.5.
> I tried all the procedure with python 3.6 as well but the same errors
> occur.
> I am also using the openbabel obtained from github which was said to be
> working with these commands at the following post:
> http://forums.openbabel.org/OpenBabel-for-Python-3-td4659432.html
> But it doesn't work as well.
> Please help me as I require this module for my research.
> Thanks
>
>
>
> --
> View this message in context: http://forums.openbabel.org/
> How-to-Install-openbabel-for-Python-3-6-on-macOS-Sierra-10-
> 12-3-tp4659726.html
> Sent from the General discussion mailing list archive at Nabble.com.
>
> 
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Re: [Open Babel] MOPAC

2016-11-15 Thread Maciek Wójcikowski

Babel is deprecated in 2.4, maybe that's messing with your app?


Pozdrawiam,  |  Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl

2016-11-15 12:45 GMT+01:00 Chris Swain <sw...@mac.com>:

> Hi,
>
> Thanks, that works fine.
>
> Chris
>
> On 15 Nov 2016, at 11:06, Pascal Muller <pascal.jm.mul...@gmail.com>
> wrote:
>
> Hi,
>
>
> A user of iBabel reported that they could not convert sdf files to  MOPAC
>> (.mop) .
>>
>> I checked using the command line
>>
>>  /usr/local/bin/babel '/Users/Chris/Desktop/confs/temp1.sdf'  -omop
>> -xf '/Users/Chris/Desktop/confs/temp1.mop’
>>
>> and
>>
>> /usr/local/bin/obabel '/Users/Chris/Desktop/confs/temp1.sdf'  -omop
>> -xf '/Users/Chris/Desktop/confs/temp1.mop’
>>
>> and whilst output appears in the terminal window no output file is created
>>
>> Do I have the syntax wrong or something?
>>
>
> Try using the -O option (-O) e.g.
> obabel tmp.sdf -O tmp.mop
>
> Regards,
> Pascal
>
>
>> Cheers
>>
>> Chris
>>
>> 
>> --
>>
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>
>
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Re: [Open Babel] Problem with Pybel installation for Anaconda

2016-10-15 Thread Maciek Wójcikowski

Hi,

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


Pozdrawiam,  |  Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl

2016-10-15 9:30 GMT+02:00 Noel O'Boyle <baoille...@gmail.com>:

> I can't comment on the anaconda parts, but maybe Maciek can...
>
> Regarding pip, apologies, we're in the middle of releasing OB 2.4.1 and I
> haven't yet updated the "pip install" parts which need to be in synch with
> the OB install. Give me until Monday and it should be fine.
>
> Regarding uninstall, pip is lying. I guess it's a pip bug, but it doesn't
> uninstall when the pip package is a wheel. If you go to your site-packages
> directory you will see several openbabel files - I don't know if this is
> the problem though.
>
> - Noel
>
>
> On 14 Oct 2016 8:41 p.m., "Richard Marchese Robinson" <
> rmarcheserobin...@gmail.com> wrote:
>
>> Hi,
>>
>> I've been encountering difficulties getting Pybel to install for Anaconda.
>>
>> I would be grateful for any assistance you have time to provide.
>>
>> I managed to install Pybel via the following command:
>> conda install -c openbabel openbabel=2.4.1
>> [based on https://anaconda.org/openbabel/openbabel]
>>
>> However, it seems 'inchi' is not a recognised format, as shown below,
>> even though - when working with Pybel version 1.8 with Python 2.7.5
>> (vanilla Python installation) - the following sequence of commands worked
>> without error.
>>
>> 
>> Python 2.7.12 |Anaconda 4.0.0 (32-bit)| (default, Jun 29 2016, 11:42:13)
>> [MSC v.1500 32 bit (Intel)] on win32
>> Type "help", "copyright", "credits" or "license" for more information.
>> Anaconda is brought to you by Continuum Analytics.
>> Please check out: http://continuum.io/thanks and https://anaconda.org
>> >>> import pybel
>> >>> mol = pybel.readstring('smi','c1c1')
>> >>> mol.write('inchi')
>> Traceback (most recent call last):
>>   File "", line 1, in 
>>   File "C:\Anaconda2\lib\site-packages\pybel.py", line 527, in write
>> format)
>> ValueError: inchi is not a recognised Open Babel format
>> =
>>
>> Please note that I did previously try getting Pybel via the PyPi
>> openbabel package [pip install openbabel], for which import pybel failed
>> with the message ["ImportError: DLL load failed: The specified procedure
>> could not be found."]. I do hope I have not created a mess. However, as
>> "pip uninstall openbabel" reported "Cannot uninstall requirement openbabel,
>> not installed", I believe the old PyPi installation was cleared up?
>>
>>
>> Best regards,
>>
>> Richard
>>
>>
> 
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Re: [Open Babel] Question about file conversion

2016-05-09 Thread Maciek Wójcikowski

Hi,

That is a wild guess, since you gave us near to zero information, but what
is the first line of your .smi file? If it's not valid smiles, then the
reader will give up, since it has finish reading the file on first line.
Valid smiles file is: "smiles string, white-space and name", like "c1c1
benzene"


Pozdrawiam,  |  Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl

2016-05-09 4:35 GMT+02:00 Brendan M. O'Boyle <bmobo...@caltech.edu>:

> Hello,
>
> I am trying to use OpenBabel and iBabel to convert SMILES strings into sdf
> files for manipulation with Schrodinger software.
>
> I installed the OpenBabel first and then I am using iBabel.  I put in the
> SMILES string under the convert header and then use that to prepare an sdf
> file.
>
> However, the file is zero bytes and there is something wrong with the
> conversion even though a file is generated.
>
> Is this a common problem?
>
> Thank you,
> Brendan
>
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Re: [Open Babel] generating conformers with open babel

2016-05-03 Thread Maciek Wójcikowski

Hello,

I think that Confab is available only in current development branch. Check
"obabel -L confab" to see if it's there. If not then you'd have to use
conda or compile it yourself.


Pozdrawiam,  |  Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl

2016-05-03 12:14 GMT+02:00 Francois Berenger <francois.beren...@inria.fr>:

> Hello,
>
> I am running Open Babel 2.3.2.
>
> I naively thought that the command:
>
> obabel input.mol2 -O output.mol2 --confab --conf 50
>
> Would give me in output.mol2 the 50 lowest energy conformers
> of each molecule in input.mol2.
>
> Unfortunately not (output.mol2 is equal to input.mol2).
>
> What is the proper way to call confab ?
>
> Thanks,
> F.
>
>
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Re: [Open Babel] set the atom type in python interface

2016-04-13 Thread Maciek Wójcikowski

Hi,

Here you go:

from openbabel import OBAtomAtomIter,OBTypeTable

# setup typetable to translate atom types
typetable = OBTypeTable()
typetable.SetFromType('INT')
typetable.SetToType('SYB')

lig = pybel.readfile('sdf', "xxx.sdf").next()
types = [typetable.Translate(a.type) for a in lig.atoms]



Pozdrawiam,  |  Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl

2016-04-13 19:13 GMT+02:00 Yun Ding <ydi...@lsu.edu>:

> Dear all,
>
>
> I would like to get the SYB type of the atom using the python interface,
> however, it always gives the INT type, how can I set it to be SYB type?
>
>
> By studying the C++ code I know how to do it in C++. But using python is
> much more convenient for me.
>
>
> So far my code is like
>
>
> ```
>
> import pybel
>
>
> lig = pybel.readfile('sdf', "xxx.sdf").next()
>
> types = [a.type for a in lig.atoms]
>
> ```
>
>
> Thanks!
>
>
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Re: [Open Babel] problem with residue detection

2016-04-11 Thread Maciek Wójcikowski

Hi,

Add "-xl" to the command line (which ignores the residues for mol2).


Pozdrawiam,  |  Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl

2016-04-11 19:08 GMT+02:00 Fredy Quevedo <maquevedo@gmail.com>:

> Dear all:
>
> I am having some problem with the conversion of a .smi file to a .mol2
> structure. The .smi notation is:
>
> OC[C@@H]1CCCN1C(=O)[C@H](Cc1c[nH]c2c12)Nc1ccc(Nc2ccncc2)cc1
>
>
> after applying the following script:
>
> obabel -ismi file.smi -omol2 -O file.mol2
>
>
> I obtain a .mol2 file in which residues are named TRP and UNK, and it
> seems like the molecule es detected as containing 2 residues. Is obable
> recognizing a tryptophan residue in my organic molecule and it is
> assignig it as a residue?
> How can I skip this detection?
>
> thank you very much in advance for the help,
>
> best regards
>
> Alfredo
>
>
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Re: [Open Babel] PAINS filtering

2016-03-15 Thread Maciek Wójcikowski

Hi,
There are improved SMARTS for PAINS in RDKit.
https://github.com/rdkit/rdkit/tree/master/Data/Pains
http://rdkit.blogspot.com/2015/08/curating-pains-filters.html


You can also use ODDT to do the filtering
http://oddt.readthedocs.org/en/latest/#oddt-command-line-interface-cli
example #2. (although currently it uses Rajarshi's SMARTS definition). I
have to update those to Greg's revised version.

Pozdrawiam,  |  Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl

2016-03-15 18:54 GMT+01:00 Stefano Forli <fo...@scripps.edu>:

> About that, a while ago I had compiled an OB-compatible data file with the
> three pattern
> classes (L15, L150 and M150) from Raj Gua [1].
>
> Dirt cheap implementation with Pybel works fine, but the main issue is
> timing. Processing
> a Mol2 file with 1000 random molecules from the ZINC database takes about
> 13 seconds.
> Not bad, but not even fast: to process a pretty large library for virtual
> screning  (e.g,
> ChemBridge library, 1.5M compounds) would take about 5.4 hours.
>
> I'm not sure if there's a way to speed up the process, but if so, it
> should be definitely
> considered.
>
> Anyway, let me know what would be the best way to share the files, and
> I'll do it.
>
> Cheers,
>
> S
>
>
> [1] http://blog.rguha.net/?p=850
>
>
> On 03/15/2016 08:21 AM, mirix wrote:
> > There you go:
> >
> > http://pastebin.ca/raw/3401877 <http://pastebin.ca/raw/3401877>
> >
> > This comes from here:
> >
> > http://blog.rguha.net/?p=850
> >
> >
> >
> >
> > --
> > View this message in context:
> http://forums.openbabel.org/PAINS-filtering-tp4659223p4659226.html
> > Sent from the General discussion mailing list archive at Nabble.com.
> >
> >
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>   Dept. of Integrative Structural
>and Computational Biology, MB-112A
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Re: [Open Babel] pdf export

2016-01-22 Thread Maciek Wójcikowski

If you need this badly there is na option to write CSV file in ODDT's
virtual screening module. You can choose a delimiter and quotation signs,
but unfortunately it does not write smiles to CSV. If you need it badly i
can add parameter to include smiles in CSV. Sorry for off-OpenBabel mail.

from oddt.virtualscreening import virtualscreening as vs
pipeline = vs()
pipeline.load_ligands('sdf', 'ampc/actives_final.sdf.gz')
pipeline.write_csv('ampc_docked.csv')



Pozdrawiam,  |  Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl

2016-01-22 14:17 GMT+01:00 Chris Swain <sw...@mac.com>:

> Apologies the title should be sdf export.
>
> A couple of additional comments.
>
> It would be useful to have options for the delimiter. It is possible the
> content may contain commas, so options for tab or pipe might be useful
> and/or putting quotes around text.
>
> Not every record in a sdf will have all fields so the usual strategy is to
> first scan the sdf file to identify all fields and then go back to the
> start to do the export.
>
> Cheers,
>
> Chris
>
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Re: [Open Babel] azoxy

2016-01-05 Thread Maciek Wójcikowski

Hi Stefano,

I might suggest trying VS module in oddt (https://github.com/oddt/oddt)
which is based on Pybel (DISCLAIMER: I'm the author of oddt). To overcome
the connectivity problem it just copy the coordinates of docked
conformationson the input molecules. This way you should retain the
connectivity.[
https://github.com/oddt/oddt/blob/master/oddt/docking/AutodockVina.py#L199]

Sample docking pipeline is below. Note that comments (which allow you to
save scores) in mol2 files are available in development version of
OpenBabel. If you use stable, then use SDF.

from oddt.virtualscreening import virtualscreening as vs
# Initiate virtual screening pipeline using 8 CPUs
pipeline = vs(n_cpu=8)
# Load ligands from a mol2 file
pipeline.load_ligands('mol2', 'ampc/actives_final.mol2.gz')
# Dock entire library to receptor, autocenter docking box on  ligand
pipeline.dock('autodock_vina', 'ampc/receptor.pdbqt',
'ampc/crystal_ligand.mol2')
# Write docked ligands conformations to a file (including scores)
pipeline.write('mol2', 'ampc_docked.mol2', overwrite=True, opt={'c':None})


The arguments for dock method:
http://oddt.readthedocs.org/en/latest/rst/oddt.docking.html#module-oddt.docking.AutodockVina


Pozdrawiam,  |  Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl

2016-01-05 12:14 GMT+01:00 Stefano Forli <fo...@scripps.edu>:

> Hi Stefano,
> the problem with the PDBQT format is that connectivity is implicit and
> bond order is lost.
> If your atom coordinates are close to ideal (i.e., bond lengths are
> optimal, non-distorted) you have a good chance of OB to be able to re-build
> the correct bond order.
> Although, there's been some discussion in the mailing list about similar
> problems using PDB files as well.
> My advice is to manually correct the issues, hoping you don't have too
> many files to process.
>
> Best,
>
> S
>
> --
>
>  Stefano Forli, PhD
>
>  Assistant Professor of Integrative
>  Structural and Computational Biology,
>  Molecular Graphics Laboratory
>
>  Dept. of Integrative Structural
>   and Computational Biology, MB-112F
>  The Scripps Research Institute
>  10550  North Torrey Pines Road
>  La Jolla,  CA 92037-1000,  USA.
>
> tel: +1 (858)784-2055
> fax: +1 (858)784-2860
> email: fo...@scripps.edu
> http://www.scripps.edu/~forli/
> 
> From: Stefano Guglielmo [stefano.guglie...@unito.it]
> Sent: Monday, January 04, 2016 4:12 PM
> To: openbabel-discuss@lists.sourceforge.net
> Subject: [Open Babel] azoxy
>
> Dear opnebabel users,
>
> I've made docking with autodock of some molecules containing an azoxy
> function; I need to generate sdf file from pdbqt, but openbabel seems to
> manage the molecules not so well as it adds hydrogens to the azoxy group.
> Any suggestion about generating a correct sdf file?
>
> Thanks a lot
>
> --
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> Assistant Professor of Medicinal Chemistry
> Department of Drug Science and Technology
> Via P. Giuria 9
> 10125 Turin, ITALY
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>
> 
>
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Re: [Open Babel] splitting molecule file - the hard case

2015-11-10 Thread Maciek Wójcikowski

Hi Filip,

OBMol has a Separate method, which does exactly what you'd like.
http://openbabel.org/dev-api/classOpenBabel_1_1OBMol.shtml#a1e5c6955a32c0ec2317a8de12ab7ba5a

import pybel
> mol = pybel.readfile('mol2', 'ligand.mol2').next()
> for m in mol.OBMol.Separate():
> print m


Note that m is an OBMol object, so to get pybel molecule you need to
initiate it via Molecule class:

for m in mol.OBMol.Separate():
> print pybel.Molecule(m)





Pozdrawiam,  |  Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl

2015-11-10 16:59 GMT+01:00 Filip Stefaniak <stefan...@gmail.com>:

> Hi,
> I have a mol2 file:
> https://gist.github.com/filipsPL/0b936f4d416bdc45ebea
>
> There are three apparently separate molecules inside. But I'm not able
> to separate them. obabel -m doesn't solve the problem.
>
> I've tried to do it in python with pybel, but I don't know how to
> exactly code it (it is not the simple case as described here:
>
> https://openbabel.org/docs/dev/UseTheLibrary/PythonExamples.html#split-an-sdf-file-using-the-molecule-titles
> )
>
> In pybel I can see that the molecules are actually separated somehow:
>
> from pybel import *
> mol = readfile("mol2", "ligand.mol2").next()
> print mol
>
> result is:
> [Rh](N)(N)(N)(N)(N)N.[Rh](N)(N)(N)(N)(N)N.[Rh](N)(N)(N)(N)(N)N
>
> so my question is: how to separate this mol2 file into separate
> components? python or shell methods are acceptable.
>
> thank you for any tips,
> Filip
>
>
> --
> Filip Stefaniak
> Uptime: 13185 dni 16 godzin
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Re: [Open Babel] access all properties from mol2 file

2015-04-30 Thread Maciek Wójcikowski

Got it. OpenBabel currently does not support @TRIPOSCOMMENT, where the
data sit from Gold. You can save docked conformations as SDF file and
normalize them. There is no other solution, as Gold embeds SDF style
variables in @TRIPOSCOMMENT.


Pozdrawiam,  |  Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl

2015-04-30 18:45 GMT+02:00 Hitesh Patel hiteshpatel...@gmail.com:

 Hi Maciek,
 Attached is an example file. It is GOLD output file, and I want to
 normalize  Gold.PLP.Fitness.

 Regards,
 Hitesh Patel

 On Thu, Apr 30, 2015 at 6:24 PM, Maciek Wójcikowski mac...@wojcikowski.pl
  wrote:

 Hi,

 Currently only UCSF Dock-style data fields are supported in mol2 files,
 and you have to specify -ac or -xc option to read/write it from/to a file.
 Can you give example of such mol2?

 
 Pozdrawiam,  |  Best regards,
 Maciek Wójcikowski
 mac...@wojcikowski.pl

 2015-04-30 17:16 GMT+02:00 Hitesh Patel hiteshpatel...@gmail.com:

 Hi,

 I want to read a mol2 file containing thousands of molecules. Each
 molecule has some additional information specified by tags like below.

  MyProperty
 31.8104

 I tried to read file using pybel But, I can access only Formula. There
 are no additional information from above tags.

 mol.data
 Out[80]: {'Formula': 'C27H37N2O4'}

 I want to modify the MyProperty value and re-write the mol2 file
 without any more changes. Kindly suggest how to do that?


 Regards,
 Hitesh Patel



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Re: [Open Babel] access all properties from mol2 file

2015-04-30 Thread Maciek Wójcikowski

Hi,

Currently only UCSF Dock-style data fields are supported in mol2 files, and
you have to specify -ac or -xc option to read/write it from/to a file. Can
you give example of such mol2?


Pozdrawiam,  |  Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl

2015-04-30 17:16 GMT+02:00 Hitesh Patel hiteshpatel...@gmail.com:

 Hi,

 I want to read a mol2 file containing thousands of molecules. Each
 molecule has some additional information specified by tags like below.

  MyProperty
 31.8104

 I tried to read file using pybel But, I can access only Formula. There are
 no additional information from above tags.

 mol.data
 Out[80]: {'Formula': 'C27H37N2O4'}

 I want to modify the MyProperty value and re-write the mol2 file without
 any more changes. Kindly suggest how to do that?


 Regards,
 Hitesh Patel



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Re: [Open Babel] Compressed pybel.Outputfile output

2015-04-25 Thread Maciek Wójcikowski

Hi Matthew,

In latest version of OB (master branch on github) automatically detects .gz
extensions and compresses the output - adds -z option to converter.
https://github.com/openbabel/openbabel/blob/master/scripts/python/pybel.py#L253
If you're using newest OB it should work out of the box. Otherwise
Stefano's solution is the one you go for.


Pozdrawiam,  |  Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl

2015-04-25 0:45 GMT+02:00 Matthew Lardy mla...@gmail.com:

 Hi Stefano,

 That worked!  Thanks!
 Matthew

 On Fri, Apr 24, 2015 at 3:34 PM, Stefano Forli fo...@scripps.edu wrote:

 Hi Matthew,
 I guess something like this could do the trick:
 -
 import gzip
 import pybel

 mol = pybel.readfile('sdf', 'filename.sdf').next()
 outfilename = 'example.sdf.gz'
 output = gzip.open(outfilename, 'wb')
 molString = mol.write(format='sdf')
 output.write(molString)
 output.close()
 -
 I didn't tested but I don't see why it shouldn't work(TM)

 S



 On 04/24/2015 03:12 PM, Matthew Lardy wrote:

 Hi all,

 Does anyone have a route to write compressed sdf.gz files that are
 compatible with
 pybel.Outputfile?

 Thanks in advance!
 Matthew


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Re: [Open Babel] MACCS key 44

2014-10-20 Thread Maciek Wójcikowski

Hello Andrew,

I created pull request on github [
https://github.com/openbabel/openbabel/pull/96]


Pozdrawiam,  |  Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl

2014-10-20 15:14 GMT+02:00 Andrew Dalke da...@dalkescientific.com:

 Hi all,

   Open Babel's MACCS definitions derive from RDKit's. As such, it doesn't
 define key 44 because Greg didn't know what OTHER meant.

 You can see that in
   https://github.com/openbabel/openbabel/blob/master/data/MACCS.txt
 with
   44:('?',0), # OTHER

 Since that time, Accelrys has published a white paper which clarifies
 a few things, including what other means. See my essay at


 http://www.dalkescientific.com/writings/diary/archive/2014/10/17/maccs_key_44.html

 for details.

 As a result, I proposed and Greg agreed that that definition be
 added to RDKit's implementation. The issues report is at

   https://github.com/rdkit/rdkit/issues/352

 the commit message is at


 https://github.com/rdkit/rdkit/commit/f48812238d6e7eb89cdb62920b176a242e1561d9

 and the pattern is

[!#1;!#6;!#7;!#8;!#9;!#14;!#15;!#16;!#17;!#35;!#53]

 My argument for making a change is that so many people expect that
 a MACCS keys implementation means one thing (at least up to
 chemistry perception differences), and key 44 will affect the
 a chemical similarity measure, in a non-trivial and chemically
 relevant way (the other missing key, isotope, doesn't have a real
 chemical difference in the same way).

 I think Open Babel should also make that change.

 Cheers,

 Andrew
 da...@dalkescientific.com




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Re: [Open Babel] Generating a diverse set of conformers

2014-05-07 Thread Maciek Wójcikowski

Hi,

Is the input molecule flexible? It would be much easier to test if you
could sent it to the list.


Pozdrawiam,  |  Best regards,
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mac...@wojcikowski.pl


2014-05-07 11:19 GMT+02:00 Fredrik Wallner fred...@wallner.nu:

 Continue by running
 obabel -L formats
 and
 obabel -L ops

 Kind regards,
 Fredrik

 Skickat från min iPhone

  7 maj 2014 kl. 11:06 skrev Douglas Houston dhous...@staffmail.ed.ac.uk
 :
 
  /usr/people/douglas/programs/openbabel-2.3.2/build/bin/obabel -L
 
  outputs:
 
  charges
  descriptors
  fingerprints
  forcefields
  formats
  loaders
  ops
 
  How do I tell?
 
 
 
  --
  View this message in context:
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  Sent from the General discussion mailing list archive at Nabble.com.
 
 
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Re: [Open Babel] running Open Babel in parallel / distributed mode

2014-02-04 Thread Maciek Wójcikowski

Francois, could you please elaborate on the log argument? Because, that
might be the only difference here. Using either gnu parallel or xargs
standard output and error are FIFO, which makes them useless.
Other than that I cant see any advantage, since parallel line would be:

cat commands.sh | parallel -P 8  log 2 error.log
(or 21 if someone prefers joint log)


Pozdrawiam,  |  Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl


2014-02-04 11:58 GMT+01:00 Francois Berenger beren...@riken.jp:

 On 2/4/14, 6:28 PM, Noel O'Boyle wrote:

 It would be nice to see some explicit examples of how Open Babel might
 be used in this way, using one or all of these tools.


 Let's say you have a file commmands.sh:
 ---
 obabel some_file1 -Osome_other_file1.other_format
 ...
 obabel some_file2 -Osome_other_file2.other_format
 ---

 With PAR, you run them like this in parallel:

 par -i commands.sh -v -o log # all your cores will be used by default

 to check the logs (in case you are really careful about
 what you are doing, e.g. when preparing datasets for scientific use),
 I recommend:

 sort -u log | less


 - Noel

 On 4 February 2014 00:52, Francois Berenger beren...@riken.jp wrote:

 On 02/04/2014 12:14 AM, Maciek Wójcikowski wrote:

 You can also use xargs.


 Yes, xargs with the -P option, but the command lines are not trivial
 then.

 
 Pozdrawiam,  |  Best regards,
 Maciek Wójcikowski
 mac...@wojcikowski.pl mailto:mac...@wojcikowski.pl


 2014-02-03 16:10 GMT+01:00 Igor Filippov igor.v.filip...@gmail.com
 mailto:igor.v.filip...@gmail.com:

  How is it different from GNU parallel?
  http://www.gnu.org/software/bash/manual/html_node/GNU-
 Parallel.html


 It should be quite similar in functionality.

  Igor


  On Mon, Feb 3, 2014 at 1:37 AM, Francois Berenger 
 beren...@riken.jp
  mailto:beren...@riken.jp wrote:

  Hello,

  I do this almost everyday so I think I should share it with
 this
  list.

  In case you need to execute many Open Babel commands
  and don't want to wait, you can execute them in parallel
  on a multi-core computer.
  Of course, the commands should be independent, for example
  processing different datasets.

  Let's say the commands are in a file called for_par.sh.
  I developped a tool called PAR years ago that can do this:

  par -i for_par.sh -v -o log

  It will use all cores of the computer, display a completion
  percentage and store all output messages in the file log.

  If your user can connect to several computers e.g. via
  SSH then you can even run commands in a distributed manner.
  I use it daily on Linux but know some people used it on Mac OS
 X
  as well.

  The project is there:

  https://savannah.nongnu.org/projects/par

  The paper is freely available there:

  http://bioinformatics.oxfordjournals.org/content/26/
 22/2918.long

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Re: [Open Babel] missing obabel executable when compiling by sources on HPC

2014-01-15 Thread Maciek Wójcikowski

I think you should build with SHARED = True and append correct directory
to LD_LIBRARY_PATH, which probably should look like:

export
LD_LIBRARY_PATH=$LD_LIBRARY_PATH:~/openbabel/openbabel-2.3.2-install/lib

Pozdrawiam, | Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl

2014/1/15 Vedat Durmaz dur...@zib.de

Am 14.01.2014 19:10, schrieb Dimitri Maziuk:

On 01/14/2014 11:21 AM, Vedat Durmaz wrote:
...

i really don't
understand, why obabel building is deactivated by default in the static
case. however, i also don't have that much experience with that
cmake/configure stuff.

Looks like a braino to me, perhaps the endif(BUILD_SHARED) was supposed
to be about 10 lines above where it is now?

but then still no obabel executable would have been compiled/linked in
case of a static build. maybe i haven't explained (and understood) well
enough. i don't know whether this will work, but i'll try to attach the
CMakeLists.txt file from the ./tools directory before and after
modification (concerning the last 1-15 lines only) ..

vedat

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Re: [Open Babel] Bindings - first and last molecule option

2013-12-12 Thread Maciek Wójcikowski

I think, I've pin-pointed the issue in the source - OBConversion class. The
first and last molecule is set by SetStartAndEnd method. It's being called
only by Convert method, not by Read nor ReadFile, hence the binding dont
use -f and -l. I figure if i't called SetStartAndEnd in Read or ReadFile,
then it should work. Unfortunately I struggle to find the spot. Tried to
add it to ReadFile, but it does not work.

Any better ideas?


Pozdrawiam,  |  Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl


2013/12/5 Geoffrey Hutchison geoff.hutchi...@gmail.com

 This only proves, that I really want to use it. Is the proof.py script
 working correctly for anybody (attached in previous mail)? It should ouptut
 molecules no. 5-10 out of 100 in proof.sdf


 No, it doesn't work.

 % python proof.py | wc
  100 1001300

 Hmm. Chris, any idea why this wouldn't work from Python?

 obconversion = OBConversion()
 obconversion.SetInFormat(sdf)
 obconversion.AddOption('f', obconversion.GENOPTIONS, 5)
 obconversion.AddOption('l', obconversion.GENOPTIONS, 10)
 obmol = OBMol()

 notatend = obconversion.ReadFile(obmol,proof.sdf)
 while notatend:
 print obmol.GetTitle()
 obmol = OBMol()
 notatend = obconversion.Read(obmol)



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Re: [Open Babel] Bindings - first and last molecule option

2013-12-04 Thread Maciek Wójcikowski

This only proves, that I really want to use it. Is the proof.py script
working correctly for anybody (attached in previous mail)? It should ouptut
molecules no. 5-10 out of 100 in proof.sdf


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2013/12/3 Chris Morley c.mor...@gaseq.co.uk

  On 2013-12-03 04:28, Maciek Wójcikowski wrote:
  You're probably right, C also has to read therm, but other than
 recognizing
 the beginning and the end of the molecule it wouldn't do anything
 especially
 kekulization and bonding etc.
 
 On 03/12/2013 18:11, Geoffrey Hutchison wrote:
  Actually no. Indeed this would be a useful lazy optimization, but is
 not
  currently implemented this way. The C++ library does in fact read the
 file,
  but the molecules go through the parsers, which means that things like
  kekulization, bond perception, etc. are generally done.

 In fact it is implemented this way for most common multi-molecule file
 formats. The molecules before the one specified by the -f option are
 skipped without being parsed. (The format's virtual SkipObjects()
 function is used.)

 Chris


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Re: [Open Babel] Bindings - first and last molecule option

2013-12-03 Thread Maciek Wójcikowski

Hi Dimitri,

Try to do that for 20mln molecules, I guarantee you it'll kill your
machine. The point is to skip n molecules at the beginning of the file, and
do it efficiently(aka, read only desired range on n-m molecules). You're
probably right, C also has to read therm, but other than recognizing the
beginning and the end of the molecule it wouldn't do anything especially
kekulization and bonding etc.


Pozdrawiam,  |  Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl


2013/12/3 Dimitri Maziuk dmaz...@bmrb.wisc.edu

 On 2013-12-03 04:28, Maciek Wójcikowski wrote:
  Hello,
 
  I'd like to ask, if it's somehow possible to use first [-f] and last
  [-l] options via python bindings?

 last = list(mols)[-1] ? -- I haven't tried myself. I suspect even in c++
 you still have to actually read them all in to get random access...

 Dima




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[Open Babel] Openbabel and Lone Pairs

2013-11-08 Thread Maciek Wójcikowski

Hi,

Currently I'm working on GOLD docking results, and try to process them
through OB. Unfortunately OB doesn't understand GOLD's explicit lone pair
pseudo atoms (atom type: Lp). For mol2 - mol2 conversion it changes it to
Xx type atoms, for sdf (sdf defines them as * type) - mol2 they are
changed as dummy atoms (Du). There is probably no way to remove them at
conversion, unless I didn't found one, but maybe it should be fixed? From
brief code analysis the lone pairs are defined implicitly, but maybe OB
should also understand explicit representations as valid, or at least
recognise Lp/*, as in mol2/sdf, atom types and ignore them.


Pozdrawiam,  |  Best regards,
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Re: [Open Babel] Can we just copy the compiled files to another account ?

2013-10-30 Thread Maciek Wójcikowski

Hi,

You also have to copy the bash variables you've set. Have you done that?
There is no reason it shouldn't work, unless you've configured it right.


Pozdrawiam,  |  Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl


2013/10/30 Zhengyh swanboi...@gmail.com

 Greetings,

 I compiled openbabel with python binding and I have 3 account on a HPC
 cluster.
 So I just copy the compiled files to the other 2 account and make the
 environment correct.
 But I got the same error in the 2 account when I was running a python
 program imported pybel:
  Traceback (most recent call last):
  File /public/home/xzren/zhengyh/bin/st, line 201, in ?
  mola = pybel.readfile('g09', 'a.log').next()
  File
 
 /public/home/xzren/zhengyh/usr/openbabel/lib64/python2.4/site-packages/pybel.py,
  line 84, in readfile
  raise ValueError(%s is not a recognised OpenBabel format % format)
  ValueError: g09 is not a recognised OpenBabel format

 Why can't we just copy the compiled files to another account of the same
 system?


 Regards!
 Abruzzi


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Re: [Open Babel] Can't make it work on a Redhat X64 platform!

2013-10-25 Thread Maciek Wójcikowski

Hi,

Besides PYTHON_PATH please try adding the directory with openbabel.so.4
to $LD_LIBRARY_PATH


Pozdrawiam,  |  Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl


2013/10/25 Zhengyh swanboi...@gmail.com

  Greetings,
 I was compiling the openbabel 2.3.1 version with binding for Python on
 'Red Hat Enterprise Linux Server release 5.6 (Tikanga)' .
 I installed openbabel locally and this is the path below:
 *
 *

  *babel:   '/public/home/zhengyh/usr/openbabel/bin/babel'*
 *Python binding:
 '/public/home/zhengyh/usr/openbabel/lib64/python2.4/site-packages/'*



 I appended the Python binding path to $PYTHONPATH as the doc tells but it
 did not work when  I imported openbabel in Python:

 In .bashrc :*
 *

  *
 PYTHONPATH=/public/home/zhengyh/usr/openbabel/lib:/public/home/zhengyh/usr/openbabel/lib64/python2.4/site-packages:$PYTHONPATH
 *

   But:

  * import openbabel*
 *Traceback (most recent call last):*
 *  File stdin, line 1, in ?*
 *ImportError: No module named openbabel*
 * *

   *
 *And again I did this in another scheme:

  * import sys,pprint**
 ** pprint.pprint(sys.path)**
 **['',**
 ** '/usr/lib64/python24.zip',**
 ** '/usr/lib64/python2.4',**
 ** '/usr/lib64/python2.4/plat-linux2',**
 ** '/usr/lib64/python2.4/lib-tk',**
 ** '/usr/lib64/python2.4/lib-dynload',**
 ** '/usr/lib64/python2.4/site-packages',**
 ** '/usr/lib64/python2.4/site-packages/Numeric',**
 ** '/usr/lib64/python2.4/site-packages/PIL',**
 ** '/usr/lib64/python2.4/site-packages/gtk-2.0',**
 ** '/usr/lib/python2.4/site-packages']**
 **
 sys.path.append('/public/home/zhengyh/usr/openbabel/lib64/python2.4/site-packages')
 **
 ** import openbabel**
 **Traceback (most recent call last):**
 **  File stdin, line 1, in ?**
 **  File
 /public/home/zhengyh/usr/openbabel/lib64/python2.4/site-packages/openbabel.py,
 line 47, in ?**
 **import _openbabel**
 **ImportError: libopenbabel.so.4: cannot open shared object file: No such
 file or directory**
 ** sys.path.append('/public/home/zhengyh/usr/openbabel/lib')**
 ** import openbabel**
 **Traceback (most recent call last):**
 **  File stdin, line 1, in ?**
 **  File
 /public/home/zhengyh/usr/openbabel/lib64/python2.4/site-packages/openbabel.py,
 line 47, in ?**
 **import _openbabel**
 **ImportError: libopenbabel.so.4: cannot open shared object file: No such
 file or directory**
 ** pprint.pprint(sys.path)**
 **['',**
 ** '/usr/lib64/python24.zip',**
 ** '/usr/lib64/python2.4',**
 ** '/usr/lib64/python2.4/plat-linux2',**
 ** '/usr/lib64/python2.4/lib-tk',**
 ** '/usr/lib64/python2.4/lib-dynload',**
 ** '/usr/lib64/python2.4/site-packages',**
 ** '/usr/lib64/python2.4/site-packages/Numeric',**
 ** '/usr/lib64/python2.4/site-packages/PIL',**
 ** '/usr/lib64/python2.4/site-packages/gtk-2.0',**
 ** '/usr/lib/python2.4/site-packages',**
 ** '/public/home/zhengyh/usr/openbabel/lib64/python2.4/site-packages',**
 ** '/public/home/zhengyh/usr/openbabel/lib']**
 *

   It seems that openbabel.py could not find libopenbabel.so.4 in the
 convention place.




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Re: [Open Babel] Which is the function in API doing the same thing as --join

2013-10-25 Thread Maciek Wójcikowski

Hi,

Have you tried mol1 += mol2? I use it for joining proteins with ligands,
but should work in any case.


Pozdrawiam,  |  Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl


2013/10/25 Zhengyh swanboi...@gmail.com

 Hello,

 Thank you all who are helping me with this openbabel.
 We use --join to join all input molecules into a single output
 moleculeentry.
 But which is the right function to do this in the pybel or openbable API?
 I just can't find it...

 Regards!



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Re: [Open Babel] create a database with openbabel

2013-08-22 Thread Maciek Wójcikowski

Hello,

The other choice, if you prefer MySQL, is Mychem
http://mychem.sourceforge.net/. But I'd say neither of them is easy to use
for unexperienced user (unless you have at least some DB knowledge).



Pozdrawiam,  |  Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl


2013/8/22 Steffen Neumann sneum...@ipb-halle.de

 Hi,

 you could check out
 https://github.com/ergo70/pgchem_tigress

 Also check out the blog at
 http://theplateisbad.blogspot.de/

 Yours,
 Steffen


 On Sat, 2013-06-29 at 15:06 -0700, Juan F Sánchez wrote:
  Hello, my name is Juan Francisco Sánchez
 
 
  I am a professor of the university of Mèxico
 
 
  I'm interested in knowing how to build a database of chemical
  structures with openbabel, (file. SDF) but I do not know how to do it
  I'd like you to help me:
  Where do I find instructions or tutorial  for building a database of
  chemical structures with openbabel, (file. SDF)?
 
  Thanks
 
 
 
 
 
 
 
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Re: [Open Babel] SMILES, SMARTS, and PDB

2013-07-08 Thread Maciek Wójcikowski

I think you need custom code. For python, you could use pybel. There are
three lines that do what you want (
http://openbabel.org/docs/dev/UseTheLibrary/Python_PybelAPI.html#pybel.Smarts.findall).
You only miss one or two lines to get the atoms by their indices.

Although searching pdb files with it could be a demanding and time
consuming task. It's really made for small molecules, i guess. I'd
personally would loop through atoms check if they are HETATOMs and then
check SMARTS pattern. Alternatively, you can filter them by name, if you
can suspect what's your residues name could be (although it's the most
error prone).


Pozdrawiam,  |  Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl


2013/7/8 Brett Hannigan godot_gil...@yahoo.com

 Unfortunately, I don't think that's quite what I need.  The obabel filter
 command will look at the given pdb and then output the entire pdb if it
 matches the given SMARTS query, right?  What I would like to do is only get
 the atoms that match the SMARTS query.

 For example, let's say I have a pdb with a single phospho-serine residue.
  What I would like to do is get only the phosphate atoms from the pdb, and
 not get the rest of the residue atoms.

 Really what I am going for here is I'd like specify some groups that I
 find interesting, say a phosphate group, a phenyl group, etc.  And then I
 have a database of protein + ligand pdbs.  I'd like to loop through those
 pdbs and look for my groups that I am interested in.  Rather than just
 identify the pdbs that have the sub-structure I am interested in (i.e.
 identify all pdbs with phosphates), I want to know which atoms in the pdb
 constitute the interesting sub-structure.  That way I could then align all
 phosphate groups and look at the residues surrounding the phophates to see
 if I see common modes of binding etc.  Phosphate would just be one example,
 you can imagine identifying many other interesting sub-structures.

 -Brett

   --
  *From:* Maciek Wójcikowski mac...@wojcikowski.pl
 *To:* Brett T. Hannigan bret...@mail.med.upenn.edu
 *Cc:* openbabel-discuss@lists.sourceforge.net
 *Sent:* Saturday, July 6, 2013 6:21 AM
 *Subject:* Re: [Open Babel] SMILES, SMARTS, and PDB

 Hello,

 You can convert from PDB to PDB using filter option (
 http://openbabel.org/wiki/--filter_option)
 obabel input.pdb -O output.pdb --filter s='CN'

 If your database is really large, or you want to search multiple times,
 then I'd suggest using FastSearch for performance reasons. For further
 lecture: http://openbabel.org/wiki/FastSearch

 
 Pozdrawiam,  |  Best regards,
 Maciek Wójcikowski
 mac...@wojcikowski.pl


 2013/7/5 Brett T. Hannigan bret...@mail.med.upenn.edu

 I have a database of molecules in pdb files.  I'd like to go through each
 molecule and see if it has certain substructures, and if they do identify
 which atoms are part of that substructure.  So it's easy enough to read the
 pdb file in, convert it to SMILES representation, and then do a SMARTS
 query to look for my substructures.  However, if the SMARTS query reports
 that the substructure is present in the molecule, I'm not sure how to
 identify the atoms in the pdb file which make up the match.  Any ideas?

 --
 **
 Brett T. Hannigan
 8011 Ardleigh St.
 Philadelphia, PA 19118
 brett.hanni...@gmail.com
 **


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Re: [Open Babel] SMILES, SMARTS, and PDB

2013-07-08 Thread Maciek Wójcikowski

You could also look into ProDy, if you use PDB files.
http://www.csb.pitt.edu/prody/reference/atomic/flags.html#term-hetero


Pozdrawiam,  |  Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl


2013/7/8 Maciek Wójcikowski mac...@wojcikowski.pl

 I think you need custom code. For python, you could use pybel. There are
 three lines that do what you want (
 http://openbabel.org/docs/dev/UseTheLibrary/Python_PybelAPI.html#pybel.Smarts.findall).
 You only miss one or two lines to get the atoms by their indices.

 Although searching pdb files with it could be a demanding and time
 consuming task. It's really made for small molecules, i guess. I'd
 personally would loop through atoms check if they are HETATOMs and then
 check SMARTS pattern. Alternatively, you can filter them by name, if you
 can suspect what's your residues name could be (although it's the most
 error prone).

 
 Pozdrawiam,  |  Best regards,
 Maciek Wójcikowski
 mac...@wojcikowski.pl


 2013/7/8 Brett Hannigan godot_gil...@yahoo.com

 Unfortunately, I don't think that's quite what I need.  The obabel filter
 command will look at the given pdb and then output the entire pdb if it
 matches the given SMARTS query, right?  What I would like to do is only get
 the atoms that match the SMARTS query.

 For example, let's say I have a pdb with a single phospho-serine residue.
  What I would like to do is get only the phosphate atoms from the pdb, and
 not get the rest of the residue atoms.

 Really what I am going for here is I'd like specify some groups that I
 find interesting, say a phosphate group, a phenyl group, etc.  And then I
 have a database of protein + ligand pdbs.  I'd like to loop through those
 pdbs and look for my groups that I am interested in.  Rather than just
 identify the pdbs that have the sub-structure I am interested in (i.e.
 identify all pdbs with phosphates), I want to know which atoms in the pdb
 constitute the interesting sub-structure.  That way I could then align all
 phosphate groups and look at the residues surrounding the phophates to see
 if I see common modes of binding etc.  Phosphate would just be one example,
 you can imagine identifying many other interesting sub-structures.

 -Brett

   --
  *From:* Maciek Wójcikowski mac...@wojcikowski.pl
 *To:* Brett T. Hannigan bret...@mail.med.upenn.edu
 *Cc:* openbabel-discuss@lists.sourceforge.net
 *Sent:* Saturday, July 6, 2013 6:21 AM
 *Subject:* Re: [Open Babel] SMILES, SMARTS, and PDB

 Hello,

 You can convert from PDB to PDB using filter option (
 http://openbabel.org/wiki/--filter_option)
 obabel input.pdb -O output.pdb --filter s='CN'

 If your database is really large, or you want to search multiple times,
 then I'd suggest using FastSearch for performance reasons. For further
 lecture: http://openbabel.org/wiki/FastSearch

 
 Pozdrawiam,  |  Best regards,
 Maciek Wójcikowski
 mac...@wojcikowski.pl


 2013/7/5 Brett T. Hannigan bret...@mail.med.upenn.edu

 I have a database of molecules in pdb files.  I'd like to go through each
 molecule and see if it has certain substructures, and if they do identify
 which atoms are part of that substructure.  So it's easy enough to read the
 pdb file in, convert it to SMILES representation, and then do a SMARTS
 query to look for my substructures.  However, if the SMARTS query reports
 that the substructure is present in the molecule, I'm not sure how to
 identify the atoms in the pdb file which make up the match.  Any ideas?

 --
 **
 Brett T. Hannigan
 8011 Ardleigh St.
 Philadelphia, PA 19118
 brett.hanni...@gmail.com
 **


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Re: [Open Babel] SMILES, SMARTS, and PDB

2013-07-06 Thread Maciek Wójcikowski

Hello,

You can convert from PDB to PDB using filter option (
http://openbabel.org/wiki/--filter_option)
obabel input.pdb -O output.pdb --filter s='CN'

If your database is really large, or you want to search multiple times,
then I'd suggest using FastSearch for performance reasons. For further
lecture: http://openbabel.org/wiki/FastSearch


Pozdrawiam,  |  Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl


2013/7/5 Brett T. Hannigan bret...@mail.med.upenn.edu

 I have a database of molecules in pdb files.  I'd like to go through each
 molecule and see if it has certain substructures, and if they do identify
 which atoms are part of that substructure.  So it's easy enough to read the
 pdb file in, convert it to SMILES representation, and then do a SMARTS
 query to look for my substructures.  However, if the SMARTS query reports
 that the substructure is present in the molecule, I'm not sure how to
 identify the atoms in the pdb file which make up the match.  Any ideas?

 --
 **
 Brett T. Hannigan
 8011 Ardleigh St.
 Philadelphia, PA 19118
 brett.hanni...@gmail.com
 **


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Re: [Open Babel] python api question

Hello,

Sure - try atom.atomicnum (pybel) or OBAtom.GetAtomicNum() (openbabel). It
returns atomic number of element (fe. C - 6).


Pozdrawiam,  |  Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl


2013/6/5 Dimitri Maziuk dmaz...@bmrb.wisc.edu

 Hi all,

 I'm after the atom (element) type letter. What I get from pybel's
 atom.type or atom.OBAtom.GetType() are O3, O2, C3, C2, etc. Is there a
 function or property that returns just O's and C's?

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



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Re: [Open Babel] python api question

If you realy need symbol of an element in automated fassion, then there is
OBElementTable.GetSymbol( atomicnum ) that you can use.

http://openbabel.org/dev-api/classOpenBabel_1_1OBElementTable.shtml#a18907ad1590deb926b43c4f08cac9405


Pozdrawiam,  |  Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl


2013/6/5 Maciek Wójcikowski mac...@wojcikowski.pl

 Hello,

 Sure - try atom.atomicnum (pybel) or OBAtom.GetAtomicNum() (openbabel). It
 returns atomic number of element (fe. C - 6).

 
 Pozdrawiam,  |  Best regards,
 Maciek Wójcikowski
 mac...@wojcikowski.pl


 2013/6/5 Dimitri Maziuk dmaz...@bmrb.wisc.edu

  Hi all,

 I'm after the atom (element) type letter. What I get from pybel's
 atom.type or atom.OBAtom.GetType() are O3, O2, C3, C2, etc. Is there a
 function or property that returns just O's and C's?

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



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Re: [Open Babel] python api question

Yes.
etab = ob.OBElementTable()
etab.GetSymbol(6)


Pozdrawiam,  |  Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl


2013/6/5 Dimitri Maziuk dmaz...@bmrb.wisc.edu

 On 2013-06-05 02:54, Maciek Wójcikowski wrote:
  If you realy need symbol of an element in automated fassion, then there
  is OBElementTable.GetSymbol( atomicnum ) that you can use.
 
 
 http://openbabel.org/dev-api/classOpenBabel_1_1OBElementTable.shtml#a18907ad1590deb926b43c4f08cac9405

 So it's exported as openbabel.OBElementTable, right? The Fine Manual is
 a bit sketchy.

 Thanks
 Dimitri




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Re: [Open Babel] Atom numbers again, this time from python

There is an undocumented option in molecule.write() and .readfile() which
allows of passing options to reading/writing. You must pass opt with
dictionary of options. For line you gave: opt = {'b' : None, 'i' : None,
'a' : None} although I believe that 'b' : None should be 'b' : '' if you
wish to pass empty value, since None is reserved for options without value.
You could look into that in pybel.py file.


Pozdrawiam,  |  Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl


2013/6/5 Dimitri Maziuk dmaz...@bmrb.wisc.edu

 Hi everyone,

 one more python question: I'm trying to do

 obabel -h --canonical -xb none -xi -xa -xP1000 -osvg ...

 All I can see in TFM is pybel.Molecule.addh() for -h -- is there way
 to get to the rest? Specifically, -xa and -xi, as I can
 post-process the SVG to change the size and the background.

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



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[Open Babel] PHP bindings

2013-04-12 Thread Maciek Wójcikowski

Hello,

Since it seam, that pull requests are not read by everybody, I decided to
post also here. I've included PHP bindings into my branch on github and
would kindly ask anybody to test it on their environment. There is example
PHP file which should depict one molecule.

Here is the pull request: https://github.com/openbabel/openbabel/pull/7 and
the branch I'm talking about:
https://github.com/mwojcikowski/openbabel/tree/php-binding

With this binding writing webapps for cheminformatics should be easier and
more accessible to web developers. It can also by highly useful for
importing data and molecules depiction.

Pozdrawiam,  |  Best regards,
Maciek Wójcikowski
mac...@wojcikowski.plhttps://mail.google.com/mail/u/0/?view=cmfs=1tf=1to=mac...@wojcikowski.pl
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Re: [Open Babel] openbabel + confab

2013-03-19 Thread Maciek Wójcikowski

Try cherry-picking a commit.


Pozdrawiam,  |  Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl


2013/3/18 Noel O'Boyle baoille...@gmail.com

 Hi David,

 Can you put all of the Confab-related code on a branch so I can get at
 them without pulling the other unrelated code on your master?
 Alternatively I can just copy+paste the files locally or if you know
 some other way I can get these changes using Git I'm happy to hear it.

 - Noel

 On 15 March 2013 20:10, Noel O'Boyle baoille...@gmail.com wrote:
  Looks good, but not all the Confab code is in there. If it going to be
  called Confab I want to make sure it works the same as the original.
  So...what do you think about merging this onto a branch? I hereby
  commit to sorting it out :-)
 
  - Noel
 
  On 15 March 2013 19:26, Geoffrey Hutchison geoff.hutchi...@gmail.com
 wrote:
  I dug up old versions of tree.hh from Cadabra . Luckily, it actually
  has the exact same files as Confab, but with a GPLv2-compliant
  license. Since the author of Cadabra is the same person as the author
  of tree.hh, I think these files should be considered cleanly under
  GPLv2.
 
  If the file header is labeled as GPLv2, the file is released (to the
 wild) under GPLv2. Thanks for the investigation.
 
  changeset at
 https://github.com/cowsandmilk/openbabel/commit/d27bb24dd2efa4304b369f4c3923c0ce43de97bb
 
  If Noel gives the go-ahead, I'd be happy to merge this into openbabel
 master. I think it's much better to avoid an unmaintained confab fork.
 
  Thanks!
  -Geoff


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Re: [Open Babel] obminimize

2013-02-27 Thread Maciek Wójcikowski

Try:
obminimize -ff MMFF94 -sd source.sdf  target.sdf


Pozdrawiam,  |  Best regards,
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mac...@wojcikowski.pl


2013/2/27 Оги Боги alchemist...@abv.bg

  Hi guys,

 I am trying to use obminimize under 64bit windows 7 in order to minimize
 geometry of molecules inside multimolecule sdf file. I'm using the
 following command:

 obminimize -ff MMFF94 -sd path-to-sdf

 The problem is that obminimize prints results from minimization procedure
 in console but nothing happens with atom coordinates in sdf file. Is that
 normal or I've made some mistake?





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[Open Babel] Residue support in Pybel

2013-02-20 Thread Maciek Wójcikowski

Hi,

I've added few lines to pybel to make life easier while working with files
containing proteins, f.e. PDB structures. With this capability you could do
something like that:

for residue in protein.residues:
print residue.name
for atom in residue:
print atom.name

If you think it's a good idea would it be possible to add it to trunk?

PS.
How is github/git integration going? Github repo seams to be forgotten
since initial sync somewhere in October 2012...


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pybel.diff
Description: Binary data
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Re: [Open Babel] Problem with --gen3D Open Babel 2.3.1

2013-01-20 Thread Maciek Wójcikowski

Have you tried it with OB 2.3.2?


Pozdrawiam,  |  Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl


2013/1/20 David García Aristegui ariste...@cbm.uam.es

 OK, is an open bug http://sourceforge.net/p/openbabel/bugs/833/

  Hello, i'm trying to assign 3D coordinates to this SMILES structure
 
  OP(=O)(O)OC[C@H]1O[C@H]([C@@H]([C@
 @H]1O)OCC(=O)c1c2cc3c3cc2ccc1)n1cnc2c(=O)[nH]c(N)nc12
 
  obabel is unable to resolve the structure
 
  time obabel --gen3D -ismi 3.3_30.smi -omol2 -O 3.3_30.mol2
  1 molecule converted
 
  real  6m8.107s
  user  6m7.947s
  sys   0m0.020s
 
  But the mol2 files looks like...
 
  @TRIPOSMOLECULE
  *
   65 70 0 0 0
  SMALL
  GASTEIGER
 
  @TRIPOSATOM
1 O -nan  -nan  -nan O.3 1  LIG1
  -0.3026
2 P -nan  -nan  -nan P.3 1  LIG1
  0.4724
3 O -nan  -nan  -nan O.2 1  LIG1
  -0.2275
  (...)
 
  Any ideas, is this a known bug?
  Best
 
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Re: [Open Babel] Problem with --gen3D Open Babel 2.3.1

2013-01-20 Thread Maciek Wójcikowski

   -3.5196 H   1  LIG10.0625
 63 H   8.7236   -2.60070.3194 H   1  LIG10.1030
 64 H  10.6816   -1.8859   -6.7791 H   1  LIG10.1451
 65 H  10.4817   -0.4112   -6.0074 H   1  LIG10.1451
@TRIPOSBOND
 1 1 21
 2 2 32
 3 2 41
 4 2 51
 5 5 61
 6 6 71
 7 7 81
 8 7 91
 9 9101
1010121
1112131
1212141
1314151
14 7141
1514161
1612171
1717181
1818191
1919202
2019211
212122   ar
222223   ar
232324   ar
242425   ar
252526   ar
262627   ar
272728   ar
282829   ar
292429   ar
302930   ar
313031   ar
322231   ar
333132   ar
343233   ar
353334   ar
362134   ar
373536   ar
383637   ar
393738   ar
403839   ar
4139402
423941   ar
4341421
444143   ar
4543441
464345   ar
474546   ar
483546   ar
493846   ar
5010351
5110111
52 1471
53 4481
54 6491
55 6501
5616511
5718521
5818531
5923541
6025551
6126561
6227571
6328581
6430591
6532601
6633611
6734621
6836631
6944641
7044651
1 molecule converted



Pozdrawiam,  |  Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl


2013/1/20 David García Aristegui ariste...@cbm.uam.es

 OK, in the News section of the Openbabel main page is announced
 2011-10-17 Open Babel 2.3.1 Released only, i'm downloading the 2.3.2
 release.

 I will try to do the conversion with the new release, but the bug is
 Milestone: 2.3.x.

 By the way, would you be so kind to try to do the conversion, if you have
 a 2.3.2 version available?

 Best regards.

  Have you tried it with OB 2.3.2?
 
  
  Pozdrawiam,  |  Best regards,
  Maciek Wójcikowski
  mac...@wojcikowski.pl
 
 
  2013/1/20 David García Aristegui ariste...@cbm.uam.es
 
  OK, is an open bug http://sourceforge.net/p/openbabel/bugs/833/
 
   Hello, i'm trying to assign 3D coordinates to this SMILES structure
  
   OP(=O)(O)OC[C@H]1O[C@H]([C@@H]([C@
  @H]1O)OCC(=O)c1c2cc3c3cc2ccc1)n1cnc2c(=O)[nH]c(N)nc12
  
   obabel is unable to resolve the structure
  
   time obabel --gen3D -ismi 3.3_30.smi -omol2 -O 3.3_30.mol2
   1 molecule converted
  
   real  6m8.107s
   user  6m7.947s
   sys   0m0.020s
  
   But the mol2 files looks like...
  
   @TRIPOSMOLECULE
   *
65 70 0 0 0
   SMALL
   GASTEIGER
  
   @TRIPOSATOM
 1 O -nan  -nan  -nan O.3 1  LIG1
   -0.3026
 2 P -nan  -nan  -nan P.3 1  LIG1
   0.4724
 3 O -nan  -nan  -nan O.2 1  LIG1
   -0.2275
   (...)
  
   Any ideas, is this a known bug?
   Best
  
 
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[Open Babel] OB binginds segfault on EL5

2012-11-29 Thread Maciek Wójcikowski

Hi,

Does anybody have a problem with bindings (both perl and python) have
problems - segfault - on CentOS 5? I'm building latest SVN, with latest
swig, eigen 2  3 (but also tried without eigen) and latest cmake. Is it
possible that old gcc is the problem here? Same build on CentOS 6 works
fine on the same set of compounds.


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Re: [Open Babel] Copy format in Pybel

2012-11-09 Thread Maciek Wójcikowski

That was just a proof of concept piece of code. I wanted to process some
molecules and try to leave them intact. Thanks for information.


Pozdrawiam,  |  Best regards,
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mac...@wojcikowski.pl


2012/11/8 Geoffrey Hutchison geo...@pitt.edu

  Is pybel suppose to support 'copy' format? I try to make it work, but it
 generates empty string.

 No, the copy format relies on the C++ stream code. But why would you need
 it? In Python, you *have* the original file or string.

 So I'm a bit confused.

 -Geoff


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[Open Babel] Copy format in Pybel

2012-11-08 Thread Maciek Wójcikowski

Is pybel suppose to support 'copy' format? I try to make it work, but it
generates empty string.
Proof of concept:
 mol = pybel.readstring(smi, c1=CC=CC=c1)
 mol.write('copy')
''

I'm on latest SVN openbabel + CentOS 6.

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Re: [Open Babel] OpenBabel to split multimol2 file but without changing bond types?

2012-10-04 Thread Maciek Wójcikowski

Have you tried copy output format?

-ocopy

Pozdrawiam,  |  Best regards,
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mac...@wojcikowski.pl


2012/10/4 Juliette Pradon pra...@ccdc.cam.ac.uk

 Hello,

 I am using OpenBabel to split a multimol2 file into separate mol2 files
 (i.e. one mol2 file per compound). I use the following command:

 babel my_ligands.mol2 ligandPart.mol2 -m

 such that each single ligand mol2 file will be called ligandPart1.mol2,
 ligandPart2.mol2, etc

 The issue is that for some compounds, I have noticed that some bond types
 have been changed in the process, particularly aromatic bonds appearing
 where there should not be any.

 Is there another option to add to the command above that would tell
 OpenBabel not to modify the bond types?

 Thank you in advance for any help!

 Juliette

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Re: [Open Babel] Openbabel in Python in concurrent processes

2012-07-21 Thread Maciek Wójcikowski

Oh, I forgot to mention that. I use CentOS and ScientificLinux 6, both HVM.

Pozdrawiam,  |  Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl


2012/7/20 Craig James cja...@emolecules.com

 Did you see this article?  You didn't say what Linux you are using, but if
 it's Ubuntu, this may be of interest.

 http://blog.xen.org/index.php/2011/11/29/baremetal-vs-xen-vs-kvm-redux/

 Craig


 On Fri, Jul 20, 2012 at 1:01 PM, Maciek Wójcikowski mac...@wojcikowski.pl
  wrote:

 I also thought about L1 and L2 caches. But underlying problem seams to be
 much simpler. The server is VM on modern AMD server (4x 12 core opteron +
 96gigs of DDR3 ECC ram). Due to virtualisation heavy memory IO (memory
 usage was less tan 50% including caches) minimization was running so slow.
 I've done same test on Intel Desktop (i7-2600) and process execution time
 changed from 18 min (single proc.) to 21 min (8 concurrent proc.). I'd say
 that the bias is due to Intel Turbo technology and HT (4 physical cores).

 The bottom line should be: don't use virtualisation (at least Xen) for
 memory intensive computing. I must say that I'm pretty disappointed with
 those results, although it's quite obvious...

 Out of curiosity I'm going to rerun the tests on KVM and probably on
 OpenVZ to see how it goes there.
 
 Pozdrawiam,  |  Best regards,
 Maciek Wójcikowski
 mac...@wojcikowski.pl


 2012/7/20 Craig James cja...@emolecules.com



 On Fri, Jul 20, 2012 at 2:16 AM, Maciek Wójcikowski 
 mac...@wojcikowski.pl wrote:

 Hi,
 I'm doing some scripting in Python to minimize ligands and want to run
 them concurrently on SMP server (many processes, one core per proc.). The
 problem that I hit is that when I run one instance, process take 100% CPU
 and runs for ~25min. For the same set if I run 32 concurrent processes it
 runs from 60-130 min. Why is that? Server has 32 phisical cores (AMD
 Opteron) so there is no turbo mode, like in intel, to produce such power
 increase. Script is not doing any IO (at least I don't know of it, it gets
 data from MySQL, doing only SELECTs).

 How can I debug this issue? Any thoughts?


 There are many reasons why this might happen.  You should do an
 experiment starting with two process, then four, eight, etc ... and see
 where it starts to slow down.

 You say 32 CPUs, but now many CPU chips?  Is this  4x8-core CPUs,
 8x4core, or something else?

 When you run each process, how much memory does it use?  How much memory
 do you have?

 My first guess is that you are running into problems with memory
 contention -- processors fighting each other for memory.  This can be
 either cache memory (for small processes) or main memory (if the ligand
 minimization is a very large process).

 Modern CPUs are *much* faster than modern memory, which is why they have
 multi-level (L1 and L2) caches (see
 http://en.wikipedia.org/wiki/CPU_cache), and also have NUMA memory
 architecture (see http://en.wikipedia.org/wiki/Non-Uniform_Memory_Access).
 When you run a single process, it gets full access to all cache memory and
 all main memory.  When you run up to N processes where N is the number of
 CPU chips (not cores), then each CPU has full access to its caches, but
 there may be contention for main memory.  When you run N processes where N
 is the total number of CPUs (in your case, 32), then each CPU has to share
 access to both main memory and to the on-chip memory caches and data
 channels.

 The only time a process will scale from 1 to 32 on a 32-CPU system is if
 each process is compute-bound and uses so little memory that all 32
 processors are mostly working from their internal caches and don't ever
 have to wait for memory access.

 If you want to read a long but fascinating article about how this
 affects other projects, check this one out.  It's about MySQL running very
 slowly on very fast CPUs because of memory contention.


 http://blog.jcole.us/2010/09/28/mysql-swap-insanity-and-the-numa-architecture/


 Craig



 
 Pozdrawiam,  |  Best regards,
 Maciek Wójcikowski
 mac...@wojcikowski.pl


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[Open Babel] Openbabel in Python in concurrent processes

2012-07-20 Thread Maciek Wójcikowski

Hi,
I'm doing some scripting in Python to minimize ligands and want to run them
concurrently on SMP server (many processes, one core per proc.). The
problem that I hit is that when I run one instance, process take 100% CPU
and runs for ~25min. For the same set if I run 32 concurrent processes it
runs from 60-130 min. Why is that? Server has 32 phisical cores (AMD
Opteron) so there is no turbo mode, like in intel, to produce such power
increase. Script is not doing any IO (at least I don't know of it, it gets
data from MySQL, doing only SELECTs).

How can I debug this issue? Any thoughts?

Pozdrawiam,  |  Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl
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Re: [Open Babel] Openbabel in Python in concurrent processes

2012-07-20 Thread Maciek Wójcikowski

I also thought about L1 and L2 caches. But underlying problem seams to be
much simpler. The server is VM on modern AMD server (4x 12 core opteron +
96gigs of DDR3 ECC ram). Due to virtualisation heavy memory IO (memory
usage was less tan 50% including caches) minimization was running so slow.
I've done same test on Intel Desktop (i7-2600) and process execution time
changed from 18 min (single proc.) to 21 min (8 concurrent proc.). I'd say
that the bias is due to Intel Turbo technology and HT (4 physical cores).

The bottom line should be: don't use virtualisation (at least Xen) for
memory intensive computing. I must say that I'm pretty disappointed with
those results, although it's quite obvious...

Out of curiosity I'm going to rerun the tests on KVM and probably on OpenVZ
to see how it goes there.

Pozdrawiam,  |  Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl


2012/7/20 Craig James cja...@emolecules.com



 On Fri, Jul 20, 2012 at 2:16 AM, Maciek Wójcikowski mac...@wojcikowski.pl
  wrote:

 Hi,
 I'm doing some scripting in Python to minimize ligands and want to run
 them concurrently on SMP server (many processes, one core per proc.). The
 problem that I hit is that when I run one instance, process take 100% CPU
 and runs for ~25min. For the same set if I run 32 concurrent processes it
 runs from 60-130 min. Why is that? Server has 32 phisical cores (AMD
 Opteron) so there is no turbo mode, like in intel, to produce such power
 increase. Script is not doing any IO (at least I don't know of it, it gets
 data from MySQL, doing only SELECTs).

 How can I debug this issue? Any thoughts?


 There are many reasons why this might happen.  You should do an experiment
 starting with two process, then four, eight, etc ... and see where it
 starts to slow down.

 You say 32 CPUs, but now many CPU chips?  Is this  4x8-core CPUs, 8x4core,
 or something else?

 When you run each process, how much memory does it use?  How much memory
 do you have?

 My first guess is that you are running into problems with memory
 contention -- processors fighting each other for memory.  This can be
 either cache memory (for small processes) or main memory (if the ligand
 minimization is a very large process).

 Modern CPUs are *much* faster than modern memory, which is why they have
 multi-level (L1 and L2) caches (see http://en.wikipedia.org/wiki/CPU_cache),
 and also have NUMA memory architecture (see
 http://en.wikipedia.org/wiki/Non-Uniform_Memory_Access).  When you run a
 single process, it gets full access to all cache memory and all main
 memory.  When you run up to N processes where N is the number of CPU chips
 (not cores), then each CPU has full access to its caches, but there may be
 contention for main memory.  When you run N processes where N is the total
 number of CPUs (in your case, 32), then each CPU has to share access to
 both main memory and to the on-chip memory caches and data channels.

 The only time a process will scale from 1 to 32 on a 32-CPU system is if
 each process is compute-bound and uses so little memory that all 32
 processors are mostly working from their internal caches and don't ever
 have to wait for memory access.

 If you want to read a long but fascinating article about how this affects
 other projects, check this one out.  It's about MySQL running very slowly
 on very fast CPUs because of memory contention.


 http://blog.jcole.us/2010/09/28/mysql-swap-insanity-and-the-numa-architecture/


 Craig



 
 Pozdrawiam,  |  Best regards,
 Maciek Wójcikowski
 mac...@wojcikowski.pl


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Re: [Open Babel] Weighted-rotor search

2012-07-13 Thread Maciek Wójcikowski

Hello,

You should use:

ff.GetCoordinates(mol)

Where ff is your OBForceField class and mol is OBMol.

Pozdrawiam,  |  Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl


2012/7/13 scott_m js...@cam.ac.uk

 That's great, many thanks for the help. One other thing, I mentioned pybel
 because I haven't got the OBMol conversion from input smiles string to
 output file with 3D coordinates. Would you mind giving a quick example of
 this (or directing me to online documentation, I couldn't find much here)?

 What I have been trying:

 mol = openbabel.OBMol()
 conversion = openbabel.OBConversion()
 conversion.SetInAndOutFormats('smi', 'com')
 conversion.ReadString(mol, 'cc')
 mol.AddHydrogens()

 #Next step is what I'm not sure of, how do I get the coordinates so that I
 can optimize and write to file??

 cv.GetCoordinates()
 cv.WriteFile(mol, 'test.com')

 # But this just gives the coordinates as 0

 With pybel I found the make3d() and localopt() functions very handy for
 this
 but can't get a similar setup going with openbabel.

 Apologies if this is a bit of a new thread.

 Cheers,

 Scott

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[Open Babel] Perl bindings in current SVN

Hi,

I have trouble building Perl bindings in openbabel SVN branch. My system is
running 64bit CentOS 6.

To compile i use following command:

cmake ../openbabel \
-DRUN_SWIG=ON \
-DPERL_BINDINGS=ON \
-DPERL_LIBRARY=/usr/lib64/perl5/CORE/libperl.so \
-DPERL_INCLUDE_PATH=/usr/lib64/perl5/CORE/ \
-DPERL_PREFIX=/usr/lib64/perl5/ \
-DPYTHON_BINDINGS=ON \
-DPYTHON_LIBRARY=/usr/lib64/libpython2.6.so \
-DPYTHON_INCLUDE_PATH=/usr/include/python2.6/

Which leads to error:
Linking CXX shared module ../lib/OpenBabel.so
CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o: In function
`_wrap_resdat_get':
/home/maciek/openbabel/openbabel/scripts/perl/openbabel-perl.cpp:2641:
undefined reference to `pthread_getspecific'
CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o: In function
`_wrap_chainsparser_get':
/home/maciek/openbabel/openbabel/scripts/perl/openbabel-perl.cpp:2633:
undefined reference to `pthread_getspecific'
CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o: In function
`_wrap_atomtyper_get':
/home/maciek/openbabel/openbabel/scripts/perl/openbabel-perl.cpp:2625:
undefined reference to `pthread_getspecific'
CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o: In function
`_wrap_aromtyper_get':
/home/maciek/openbabel/openbabel/scripts/perl/openbabel-perl.cpp:2617:
undefined reference to `pthread_getspecific'
CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o: In function
`_wrap_isotab_get':
/home/maciek/openbabel/openbabel/scripts/perl/openbabel-perl.cpp:2609:
undefined reference to `pthread_getspecific'
CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o:/home/maciek/openbabel/openbabel/scripts/perl/openbabel-perl.cpp:2601:
more undefined references to `pthread_getspecific' follow
collect2: ld returned 1 exit status
make[2]: *** [lib/OpenBabel.so] Błąd 1
make[1]: *** [scripts/CMakeFiles/bindings_perl.dir/all] Błąd 2

To clarify, given cmake command build 2.3.1 version without problem.


Pozdrawiam,  |  Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl
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Re: [Open Babel] Perl bindings in current SVN

Apparently it seams to be SWIG's fault. CentOS has SWIG in version 1.x.
Compiling latest SWIG 2.x fixed the issue. Maybe we should ad a note about
that in wiki, since that could potentially lead to some other undiscovered
errors.

Curiously cmake calls for SWIG in version 2.0 and loads successfully 1.x.

Pozdrawiam,  |  Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl


2012/5/31 Maciek Wójcikowski mac...@wojcikowski.pl

 It worked.

 The failing line was:
 /usr/bin/c++  -fPIC -O2 -g -O2 -g -Wl,--enable-new-dtags
 -Wl,--enable-new-dtags -Wl,--fatal-warnings -Wl,--no-undefined -lc  -shared
 -Wl,-soname,OpenBabel.so -o ../lib/OpenBabel.so
 CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o
 -L/usr/lib64/perl5/CORE -lperl ../lib/libopenbabel.so.4.0.0 -lm -ldl -lz
 -Wl,-rpath,/usr/lib64/perl5/CORE:/home/maciek/openbabel/build/lib

 Adding -lpthread leads to succesful compilation.

 
 Pozdrawiam,  |  Best regards,
 Maciek Wójcikowski
 mac...@wojcikowski.pl


 2012/5/31 Noel O'Boyle baoille...@gmail.com

 We changed to compiling the bindings directly rather than use Perl's
 build system. It seems to work fine on some Linux OSes but not on
 others. I haven't tracked down the problem but you could try
 VERBOSE=1 make to see the command that we are using to compile, and
 repeating it manually but adding -lpthread to see what happens.

 - Noel

 On 31 May 2012 09:56, Maciek Wójcikowski mac...@wojcikowski.pl wrote:
  Hi,
 
  I have trouble building Perl bindings in openbabel SVN branch. My
 system is
  running 64bit CentOS 6.
 
  To compile i use following command:
 
  cmake ../openbabel \
  -DRUN_SWIG=ON \
  -DPERL_BINDINGS=ON \
  -DPERL_LIBRARY=/usr/lib64/perl5/CORE/libperl.so \
  -DPERL_INCLUDE_PATH=/usr/lib64/perl5/CORE/ \
  -DPERL_PREFIX=/usr/lib64/perl5/ \
  -DPYTHON_BINDINGS=ON \
  -DPYTHON_LIBRARY=/usr/lib64/libpython2.6.so \
  -DPYTHON_INCLUDE_PATH=/usr/include/python2.6/
 
  Which leads to error:
  Linking CXX shared module ../lib/OpenBabel.so
  CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o: In function
  `_wrap_resdat_get':
  /home/maciek/openbabel/openbabel/scripts/perl/openbabel-perl.cpp:2641:
  undefined reference to `pthread_getspecific'
  CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o: In function
  `_wrap_chainsparser_get':
  /home/maciek/openbabel/openbabel/scripts/perl/openbabel-perl.cpp:2633:
  undefined reference to `pthread_getspecific'
  CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o: In function
  `_wrap_atomtyper_get':
  /home/maciek/openbabel/openbabel/scripts/perl/openbabel-perl.cpp:2625:
  undefined reference to `pthread_getspecific'
  CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o: In function
  `_wrap_aromtyper_get':
  /home/maciek/openbabel/openbabel/scripts/perl/openbabel-perl.cpp:2617:
  undefined reference to `pthread_getspecific'
  CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o: In function
  `_wrap_isotab_get':
  /home/maciek/openbabel/openbabel/scripts/perl/openbabel-perl.cpp:2609:
  undefined reference to `pthread_getspecific'
 
 CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o:/home/maciek/openbabel/openbabel/scripts/perl/openbabel-perl.cpp:2601:
  more undefined references to `pthread_getspecific' follow
  collect2: ld returned 1 exit status
  make[2]: *** [lib/OpenBabel.so] Błąd 1
  make[1]: *** [scripts/CMakeFiles/bindings_perl.dir/all] Błąd 2
 
  To clarify, given cmake command build 2.3.1 version without problem.
 
  
  Pozdrawiam,  |  Best regards,
  Maciek Wójcikowski
  mac...@wojcikowski.pl
 
 
 --
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  threat landscape has changed and how IT managers can respond.
 Discussions
  will include endpoint security, mobile security and the latest in
 malware
  threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
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  https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
 



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Re: [Open Babel] Perl bindings in current SVN

I was wrong. something went wrong and SWIG wasnt recognized at all. I'm
looking for another problem. Do you have any Idea where first to look?

Pozdrawiam,  |  Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl


2012/5/31 Maciek Wójcikowski mac...@wojcikowski.pl

 Apparently it seams to be SWIG's fault. CentOS has SWIG in version 1.x.
 Compiling latest SWIG 2.x fixed the issue. Maybe we should ad a note about
 that in wiki, since that could potentially lead to some other undiscovered
 errors.

 Curiously cmake calls for SWIG in version 2.0 and loads successfully 1.x.

 
 Pozdrawiam,  |  Best regards,
 Maciek Wójcikowski
 mac...@wojcikowski.pl


 2012/5/31 Maciek Wójcikowski mac...@wojcikowski.pl

 It worked.

 The failing line was:
 /usr/bin/c++  -fPIC -O2 -g -O2 -g -Wl,--enable-new-dtags
 -Wl,--enable-new-dtags -Wl,--fatal-warnings -Wl,--no-undefined -lc  -shared
 -Wl,-soname,OpenBabel.so -o ../lib/OpenBabel.so
 CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o
 -L/usr/lib64/perl5/CORE -lperl ../lib/libopenbabel.so.4.0.0 -lm -ldl -lz
 -Wl,-rpath,/usr/lib64/perl5/CORE:/home/maciek/openbabel/build/lib

 Adding -lpthread leads to succesful compilation.

 
 Pozdrawiam,  |  Best regards,
 Maciek Wójcikowski
 mac...@wojcikowski.pl


 2012/5/31 Noel O'Boyle baoille...@gmail.com

 We changed to compiling the bindings directly rather than use Perl's
 build system. It seems to work fine on some Linux OSes but not on
 others. I haven't tracked down the problem but you could try
 VERBOSE=1 make to see the command that we are using to compile, and
 repeating it manually but adding -lpthread to see what happens.

 - Noel

 On 31 May 2012 09:56, Maciek Wójcikowski mac...@wojcikowski.pl wrote:
  Hi,
 
  I have trouble building Perl bindings in openbabel SVN branch. My
 system is
  running 64bit CentOS 6.
 
  To compile i use following command:
 
  cmake ../openbabel \
  -DRUN_SWIG=ON \
  -DPERL_BINDINGS=ON \
  -DPERL_LIBRARY=/usr/lib64/perl5/CORE/libperl.so \
  -DPERL_INCLUDE_PATH=/usr/lib64/perl5/CORE/ \
  -DPERL_PREFIX=/usr/lib64/perl5/ \
  -DPYTHON_BINDINGS=ON \
  -DPYTHON_LIBRARY=/usr/lib64/libpython2.6.so \
  -DPYTHON_INCLUDE_PATH=/usr/include/python2.6/
 
  Which leads to error:
  Linking CXX shared module ../lib/OpenBabel.so
  CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o: In function
  `_wrap_resdat_get':
  /home/maciek/openbabel/openbabel/scripts/perl/openbabel-perl.cpp:2641:
  undefined reference to `pthread_getspecific'
  CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o: In function
  `_wrap_chainsparser_get':
  /home/maciek/openbabel/openbabel/scripts/perl/openbabel-perl.cpp:2633:
  undefined reference to `pthread_getspecific'
  CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o: In function
  `_wrap_atomtyper_get':
  /home/maciek/openbabel/openbabel/scripts/perl/openbabel-perl.cpp:2625:
  undefined reference to `pthread_getspecific'
  CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o: In function
  `_wrap_aromtyper_get':
  /home/maciek/openbabel/openbabel/scripts/perl/openbabel-perl.cpp:2617:
  undefined reference to `pthread_getspecific'
  CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o: In function
  `_wrap_isotab_get':
  /home/maciek/openbabel/openbabel/scripts/perl/openbabel-perl.cpp:2609:
  undefined reference to `pthread_getspecific'
 
 CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o:/home/maciek/openbabel/openbabel/scripts/perl/openbabel-perl.cpp:2601:
  more undefined references to `pthread_getspecific' follow
  collect2: ld returned 1 exit status
  make[2]: *** [lib/OpenBabel.so] Błąd 1
  make[1]: *** [scripts/CMakeFiles/bindings_perl.dir/all] Błąd 2
 
  To clarify, given cmake command build 2.3.1 version without problem.
 
  
  Pozdrawiam,  |  Best regards,
  Maciek Wójcikowski
  mac...@wojcikowski.pl
 
 
 --
  Live Security Virtual Conference
  Exclusive live event will cover all the ways today's security and
  threat landscape has changed and how IT managers can respond.
 Discussions
  will include endpoint security, mobile security and the latest in
 malware
  threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
  ___
  OpenBabel-discuss mailing list
  OpenBabel-discuss@lists.sourceforge.net
  https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
 




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Re: [Open Babel] Perl bindings in current SVN