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

[OpenBabel-scripting] charge wrongly calculated

[Hannes L. <Han...@st...>]

Hi,

the following script reads the attached mol2 file but wrongly outputs 0
for the charge.  Openbabel is version 2.3.

import pybel
mol = pybel.readfile('mol2', 'amm.mol2').next()
print mol.charge

I think it should be obvious from the N.4 Sybyl atom type that there
must be a charge.  The sum of charges in the mol2 file also adds up to
+1.

Is there a way to force recalculation of charges?

Thanks,
Hannes.
-- 
Scanned by iCritical.

[OpenBabel-scripting] AllowPartiallyTrustedCallers in OBDotNet DLL?

[Håvard S. <hav...@gm...>]

Would any OpenBabel developers please consider adding the
AllowPartiallyTrustedCallers attribute to the OBDotNet DLL? This
should allow OpenBabel to be called from partially trusted code (e.g.
IIS applications).

I haven't researched further if adding this attribute is all that is
needed to enable partial trust callers, as I haven't been able to find
instructions for building the OBDotNet DLL (the bindings .lib build
just fine in the vcprojs generated from CMake, but where do I go from
there?). I would be happy to test and report back if someone could
provide me with precise detailed build instructions for OBDotNet.

-- 
Regards,

Håvard

Re: [OpenBabel-scripting] problem with Python/vector3

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

Whatever way the maths primitives are implemented in OB, they are not
suited to use from any of the language bindings. I always just call
GetX(), GetY() and GetZ(), do my thing, and then stick the result back
in a vector.

See functions t() and u() at
http://baoilleach.blogspot.com/2012/02/on-reflection-transforming-molecules-is.html

I'll put this on my list of things to look into, but given that you
can work around it, to be honest it's not going to be a priority. If
there's anyone else out there who fancy's a shot, feel free...

- Noel

On 27 March 2012 16:41, Hannes Loeffler <Han...@st...> wrote:
> Hi there,
>
> I have a problem with the Python script at the end of this email (the
> attachment contains this script and the two input files needed).
> Trying to use the -= operator obviously triggers a memory corruption
> bug:
>
> *** glibc detected *** python: double free or corruption (out):
> 0x09d122a0 ***
>
> Thanks a lot,
> Hannes.
>
>
> import openbabel as ob
>
> ob.obErrorLog.SetOutputLevel(0)
>
> conv = ob.OBConversion()
> conv.SetInAndOutFormats('pdb', 'pdb')
>
> r = ob.OBMol()
> t = ob.OBMol()
>
> conv.ReadFile(r, 'r.pdb')
> conv.ReadFile(t, 't.pdb')
>
> shift = r.GetAtom(1).GetVector()
>
> # the following line triggers the bug
> shift -= t.GetAtom(1).GetVector()
> --
> Scanned by iCritical.
>
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[OpenBabel-scripting] problem with Python/vector3

[Hannes L. <Han...@st...>]

Hi there,

I have a problem with the Python script at the end of this email (the
attachment contains this script and the two input files needed).
Trying to use the -= operator obviously triggers a memory corruption
bug:

*** glibc detected *** python: double free or corruption (out):
0x09d122a0 ***

Thanks a lot,
Hannes.


import openbabel as ob

ob.obErrorLog.SetOutputLevel(0)

conv = ob.OBConversion()
conv.SetInAndOutFormats('pdb', 'pdb')

r = ob.OBMol()
t = ob.OBMol()

conv.ReadFile(r, 'r.pdb')
conv.ReadFile(t, 't.pdb')

shift = r.GetAtom(1).GetVector()

# the following line triggers the bug
shift -= t.GetAtom(1).GetVector()
-- 
Scanned by iCritical.

Re: [OpenBabel-scripting] Get number of carbon atoms?

[Pascal M. <pas...@gm...>]

Hello,

> I am just getting started with the C# bindings for OpenBabel. How do I get
> the number of carbon atoms in a molecule I have read from an mdl file?

Iterate over atoms and increment if OBAtom IsCarbon()
http://openbabel.org/dev-api/classOpenBabel_1_1OBAtom.shtml#a1f0a167775136e911cd349cdd8923b24
or
OBMol GetFormula() or GetSpacedFormula(), keep the number following C.

Regards,
Pascal

[OpenBabel-scripting] Get number of carbon atoms?

[Håvard S <hav...@gm...>]

Hi.

I am just getting started with the C# bindings for OpenBabel. How do I get
the number of carbon atoms in a molecule I have read from an mdl file?

Thanks in advance,

-Håvard

Re: [OpenBabel-scripting] [Open Babel] Babel works in shell but not in PHP

[David H. <li...@co...>]

Also, I should add, you should see whether your PHP is using safe
mode.  As described at
http://php.net/manual/en/ini.sect.safe-mode.php#ini.safe-mode-exec-dir
, safe mode can be used to restrict what directories one can execute
programs from.

-David

On Mon, Feb 6, 2012 at 11:51 AM, David Hall <li...@co...> wrote:
> are the environment variables correct?  As in, to run it on the
> command line, do you have special PATH or other settings?  If so, you
> should use http://www.php.net/putenv to put those variables into the
> PHP script.
>
> -David
>
> On Tue, Jan 31, 2012 at 4:25 AM, Sangeetha Subramaniam
> <srd...@gm...> wrote:
>> Dear All,
>>
>> Can someone help me to run babel  for file conversion in PhP.
>> Here is what I want to do:
>>
>> "babel -ismi compound.smi -osdf -0 com_3d.sdf --gen3d"
>>
>> This runs fine in command as well as in shell, but not in PHP. There is no
>> problem with file permission.
>>
>> Can someone please help.
>>
>> PS:I see this question was posted previously by someone, but I could not
>> locate the reply.
>>
>> Thanks
>> Sangeetha.
>>
>>
>>
>> ------------------------------------------------------------------------------
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>>

Re: [OpenBabel-scripting] [Open Babel] Babel works in shell but not in PHP

[David H. <li...@co...>]

are the environment variables correct?  As in, to run it on the
command line, do you have special PATH or other settings?  If so, you
should use http://www.php.net/putenv to put those variables into the
PHP script.

-David

On Tue, Jan 31, 2012 at 4:25 AM, Sangeetha Subramaniam
<srd...@gm...> wrote:
> Dear All,
>
> Can someone help me to run babel  for file conversion in PhP.
> Here is what I want to do:
>
> "babel -ismi compound.smi -osdf -0 com_3d.sdf --gen3d"
>
> This runs fine in command as well as in shell, but not in PHP. There is no
> problem with file permission.
>
> Can someone please help.
>
> PS:I see this question was posted previously by someone, but I could not
> locate the reply.
>
> Thanks
> Sangeetha.
>
>
>
> ------------------------------------------------------------------------------
> Try before you buy = See our experts in action!
> The most comprehensive online learning library for Microsoft developers
> is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3,
> Metro Style Apps, more. Free future releases when you subscribe now!
> http://p.sf.net/sfu/learndevnow-dev2
> _______________________________________________
> OpenBabel-discuss mailing list
> Ope...@li...
> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>

Re: [OpenBabel-scripting] how to re-render (polish, relayout) a molfile

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

On 29 January 2012 20:39, Jan Hummel <Hu...@mp...> wrote:
> Hello,
> First I want to apologize if this is a trivial question or the wrong place to ask.
>
> I'm maintain a Database for GC-MS spectra. Recently I updated the web frontend to display the chemical structures using the ChemDoodle Web Components (http://web.chemdoodle.com/) plugin. However, I notice that some structure are displayed correct
> (i.g. see here: http://gmd.mpimp-golm.mpg.de/Metabolites/f4f207ff-8ff8-4789-99a1-147ae0a36673.aspx) whereas others are displayed incorrect (http://gmd.mpimp-golm.mpg.de/Metabolites/0c450b43-c901-4435-9e74-051222d815ea.aspx). I mean they get displayed, but not very nice. I think that ChemDoodle is not the problem that the chemical structure can't be recognized from the displayed picture. The scaling of the picture (or of the mol-Files) seems somehow odd. And, other chemical software solutions seem to handle this to a better degree.

I would contact ChemDoodle - maybe there's a switch you can use to
rescale automatically.

> >From my understanding (being not a chemist) I suspect, that I have some problems in the mol-Files. The coordinates between correct and incorrect mol-Files seem to differ by an order of magnitude.

> My question is now, How can I use OpenBabel to re-render (repaint, re-layout) an "incorrect" mol-File into a "standard compliant" mol-File? mol.Center() did not the trick.

For each atom, you could scale the coordinates, e.g. (in pseudo C++)
  oldcoords = atom->GetVector();
  newcoords = oldcoords / 10.0;
  atom->SetVector(newcoords);

> Here is my C# code
> OBConversion obconv = new OBConversion();
> OBMol mol = new OBMol();
> obconv.SetInFormat("mol");
> obconv.SetOutFormat("mol");
> obconv.ReadString(mol, source);
> mol.Center();
> obconv.WriteFile(mol, dest);

If you want to generate new 2d coordinates, you need to call gen2d.
Here's some Python code:

gen2d = OBOp.FindType("gen2d") # Looks up the plugin and returns it
gen2d.Do(mymol) # Calls the plugin on your molecule

- Noel

[OpenBabel-scripting] Babel works in shell but not in PHP

[Sangeetha S. <srd...@gm...>]

Dear All,

Can someone help me to run babel  for file conversion in PhP.
Here is what I want to do:

"babel -ismi compound.smi -osdf -0 com_3d.sdf --gen3d"

This runs fine in command as well as in shell, but not in PHP. There is no
problem with file permission.

Can someone please help.

PS:I see this question was posted previously by someone, but I could not
locate the reply.

Thanks
Sangeetha.

[OpenBabel-scripting] how to re-render (polish, relayout) a molfile

[Jan H. <Hu...@mp...>]

Hello,
First I want to apologize if this is a trivial question or the wrong place to ask.

I'm maintain a Database for GC-MS spectra. Recently I updated the web frontend to display the chemical structures using the ChemDoodle Web Components (http://web.chemdoodle.com/) plugin. However, I notice that some structure are displayed correct
(i.g. see here: http://gmd.mpimp-golm.mpg.de/Metabolites/f4f207ff-8ff8-4789-99a1-147ae0a36673.aspx) whereas others are displayed incorrect (http://gmd.mpimp-golm.mpg.de/Metabolites/0c450b43-c901-4435-9e74-051222d815ea.aspx). I mean they get displayed, but not very nice. I think that ChemDoodle is not the problem that the chemical structure can't be recognized from the displayed picture. The scaling of the picture (or of the mol-Files) seems somehow odd. And, other chemical software solutions seem to handle this to a better degree.

>From my understanding (being not a chemist) I suspect, that I have some problems in the mol-Files. The coordinates between correct and incorrect mol-Files seem to differ by an order of magnitude.

My question is now, How can I use OpenBabel to re-render (repaint, re-layout) an "incorrect" mol-File into a "standard compliant" mol-File? mol.Center() did not the trick.

Here is my C# code
OBConversion obconv = new OBConversion();
OBMol mol = new OBMol();
obconv.SetInFormat("mol");
obconv.SetOutFormat("mol");
obconv.ReadString(mol, source);
mol.Center();
obconv.WriteFile(mol, dest);
       

Thank you very much for any help.

Jan
 

Re: [OpenBabel-scripting] [Open Babel] pybel - (howto) calculation of RMSD for two molecules (but different conformers)

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

Oh yes, I forgot. I've already done this some time ago...I was just
waiting for 2.3.1 to be released...

https://gist.github.com/974477

- Noel

On 17 January 2012 09:48, Visvaldas K. <coy...@ya...> wrote:
> Dear Noel,
>
>
> Thank you for your answers!
>
> For my 1st question, I had in mind something along the lines of openbabel python bindings. However, a "standalone" version of the rmsd calculation could be probably useful for quite a few people.
>
> Vis
>
>
>
>
> ________________________________
> From: Noel O'Boyle <bao...@gm...>
> To: Visvaldas K. <coy...@ya...>
> Sent: Tuesday, January 17, 2012 11:40 AM
> Subject: Re: [OpenBabel-scripting] [Open Babel] pybel - (howto) calculation of RMSD for two molecules (but different conformers)
>
> Regarding (2), it does handle what you call "local symmetry" (automorphisms).
>
> Regarding (1), it wouldn't take long to write a C++ program (not sure
> about Python) that used Open Babel to calculate the RMSD in the way
> you describe. But I guess you are asking for an option to obabel,
> right?
>
> - Noel
>
> On 16 January 2012 20:25, Visvaldas K. <coy...@ya...> wrote:
>> Perhaps this should have gone a to a new thread...
>>
>> I have a couple of questions about RMSD. Maybe they could lead to "requested
>> features":)
>>
>> 1) from the documentation, it seems that rmsd calc _always_ does
>> superposition of the molecules before calculating RMSD.  From some older
>> (2007) openbabel thread it seams there is no way to compute RMSD without
>> superposition. This would be very useful, say, in ligand-protein docking
>> calculations.
>>
>> 2) The computed RMSDs are "symmetry corrected". There is a global symmetry
>> and a local symmetry. Is the local symmetry also calculated for the purposes
>> of symmetry correction when doing RMSD? Actually, it's not a trivial
>> problem; one way to tackle it is to permute rotations around all rotatable
>> dihedrals in a reference molecule, and to try to obtain a nearly identical
>> molecule ("nearly" because of imperfections). Perhaps other algorithms
>> exist. An example would be a local symmetry of the phenyl ring in
>> phenylalanine: phenylalanine is non-symmetric, but phenyl inside it has two
>> pairs of equivalent carbons.
>>
>> Best regards,
>>
>> Vis
>>
>> ------------------------------------------------------------------------------
>> RSA(R) Conference 2012
>> Mar 27 - Feb 2
>> Save $400 by Jan. 27
>> Register now!
>> http://p.sf.net/sfu/rsa-sfdev2dev2
>> _______________________________________________
>> OpenBabel-scripting mailing list
>> Ope...@li...
>> https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
>>

Re: [OpenBabel-scripting] [Open Babel] pybel - (howto) calculation of RMSD for two molecules (but different conformers)

[Visvaldas K. <coy...@ya...>]

Dear Noel,


Thank you for your answers!

For my 1st question, I had in mind something along the lines of openbabel python bindings. However, a "standalone" version of the rmsd calculation could be probably useful for quite a few people.

Vis




________________________________
From: Noel O'Boyle <bao...@gm...>
To: Visvaldas K. <coy...@ya...> 
Sent: Tuesday, January 17, 2012 11:40 AM
Subject: Re: [OpenBabel-scripting] [Open Babel] pybel - (howto) calculation of RMSD for two molecules (but different conformers)

Regarding (2), it does handle what you call "local symmetry" (automorphisms).

Regarding (1), it wouldn't take long to write a C++ program (not sure
about Python) that used Open Babel to calculate the RMSD in the way
you describe. But I guess you are asking for an option to obabel,
right?

- Noel

On 16 January 2012 20:25, Visvaldas K. <coy...@ya...> wrote:
> Perhaps this should have gone a to a new thread...
>
> I have a couple of questions about RMSD. Maybe they could lead to "requested
> features":)
>
> 1) from the documentation, it seems that rmsd calc _always_ does
> superposition of the molecules before calculating RMSD.  From some older
> (2007) openbabel thread it seams there is no way to compute RMSD without
> superposition. This would be very useful, say, in ligand-protein docking
> calculations.
>
> 2) The computed RMSDs are "symmetry corrected". There is a global symmetry
> and a local symmetry. Is the local symmetry also calculated for the purposes
> of symmetry correction when doing RMSD? Actually, it's not a trivial
> problem; one way to tackle it is to permute rotations around all rotatable
> dihedrals in a reference molecule, and to try to obtain a nearly identical
> molecule ("nearly" because of imperfections). Perhaps other algorithms
> exist. An example would be a local symmetry of the phenyl ring in
> phenylalanine: phenylalanine is non-symmetric, but phenyl inside it has two
> pairs of equivalent carbons.
>
> Best regards,
>
> Vis
>
> ------------------------------------------------------------------------------
> RSA(R) Conference 2012
> Mar 27 - Feb 2
> Save $400 by Jan. 27
> Register now!
> http://p.sf.net/sfu/rsa-sfdev2dev2
> _______________________________________________
> OpenBabel-scripting mailing list
> Ope...@li...
> https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
>

Re: [OpenBabel-scripting] [Open Babel] pybel - (howto) calculation of RMSD for two molecules (but different conformers)

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

Regarding (2), it does handle what you call "local symmetry" (automorphisms).

Regarding (1), it wouldn't take long to write a C++ program (not sure
about Python) that used Open Babel to calculate the RMSD in the way
you describe. But I guess you are asking for an option to obabel,
right?

- Noel

On 16 January 2012 20:25, Visvaldas K. <coy...@ya...> wrote:
> Perhaps this should have gone a to a new thread...
>
> I have a couple of questions about RMSD. Maybe they could lead to "requested
> features":)
>
> 1) from the documentation, it seems that rmsd calc _always_ does
> superposition of the molecules before calculating RMSD.  From some older
> (2007) openbabel thread it seams there is no way to compute RMSD without
> superposition. This would be very useful, say, in ligand-protein docking
> calculations.
>
> 2) The computed RMSDs are "symmetry corrected". There is a global symmetry
> and a local symmetry. Is the local symmetry also calculated for the purposes
> of symmetry correction when doing RMSD? Actually, it's not a trivial
> problem; one way to tackle it is to permute rotations around all rotatable
> dihedrals in a reference molecule, and to try to obtain a nearly identical
> molecule ("nearly" because of imperfections). Perhaps other algorithms
> exist. An example would be a local symmetry of the phenyl ring in
> phenylalanine: phenylalanine is non-symmetric, but phenyl inside it has two
> pairs of equivalent carbons.
>
> Best regards,
>
> Vis
>
> ------------------------------------------------------------------------------
> RSA(R) Conference 2012
> Mar 27 - Feb 2
> Save $400 by Jan. 27
> Register now!
> http://p.sf.net/sfu/rsa-sfdev2dev2
> _______________________________________________
> OpenBabel-scripting mailing list
> Ope...@li...
> https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
>

Re: [OpenBabel-scripting] [Open Babel] pybel - (howto) calculation of RMSD for two molecules (but different conformers)

[Visvaldas K. <coy...@ya...>]

Perhaps this should have gone a to a new thread...

I have a couple of questions about RMSD. Maybe they could lead to "requested features":)


1) from the documentation, it seems that rmsd calc _always_ does superposition of the molecules before calculating RMSD.  From some older (2007) openbabel thread it seams there is no way to compute RMSD without superposition. This would be very useful, say, in ligand-protein docking calculations.

2) The computed RMSDs are "symmetry corrected". There is a global symmetry and a local symmetry. Is the local symmetry also calculated for the purposes of symmetry correction when doing RMSD? Actually, it's not a trivial problem; one way to tackle it is to permute rotations around all rotatable dihedrals in a reference molecule, and to try to obtain a nearly identical molecule ("nearly" because of imperfections). Perhaps other algorithms exist. An example would be a local symmetry of the phenyl ring in phenylalanine: phenylalanine is non-symmetric, but phenyl inside it has two pairs of equivalent carbons. 

Best regards,

Vis

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

[Visvaldas K. <coy...@ya...>]

Actually, the python which I used when trying to install openbabel python bindings, was from Xcode disk. I will use fink to install another version of python. (It seems that in fink one can install openbabel-py if the the fink-version of python is downloaded, but I was hoping I could compile openbabel bindings from scratch using "native" python).

Thank you,

Visvaldas



________________________________
 From: Noel O'Boyle <bao...@gm...>
To: Visvaldas K. <coy...@ya...> 
Cc: "ope...@li..." <ope...@li...> 
Sent: Thursday, January 5, 2012 3:34 PM
Subject: Re: [OpenBabel-scripting] OSX 6.8 Openbabel python bindings
 
Can you try using a different version of Python, e.g. your system
installation of Python. (I forget where this is located, check on
Google.)

To do this, set the CMake variables (using -D) PYTHON_EXECUTABLE,
PYTHON_INCLUDE_PATH and PYTHON_LIBRARY appropriately, and force a SWIG
rebuild by "touch $OBSRC/scripts/openbabel-python.i" (with the
appropriate value for $OBSRC). To see the current values of the Python
variables, use "grep -i python CMakeCache.txt".

- Noel

On 4 January 2012 20:58, Visvaldas K. <coy...@ya...> wrote:
> Dear colleagues,
>
> I tried to compile openbabel python bindings for trunk version of openbabel
> on December 30 on my mac, os version 10.6.8 (with python 2.5 - perhaps it's
> too old!), with the following error:
> ng error:
>
> {visvaldas}~/openbabel/build% make bindings_python -j2
> [  4%] [  4%] Building CXX object src/CMakeFiles/openbabel.dir/atom.o
> Building CXX object src/CMakeFiles/openbabel.dir/base.o
> [  4%] Building CXX object src/CMakeFiles/openbabel.dir/bitvec.o
> [  9%] Building CXX object src/CMakeFiles/openbabel.dir/bond.o
> [  9%] Building CXX object src/CMakeFiles/openbabel.dir/bondtyper.o
> [  9%] Building CXX object src/CMakeFiles/openbabel.dir/builder.o
> [ 14%] Building CXX object src/CMakeFiles/openbabel.dir/canon.o
>
> <similar part chopped off - VK>
>
> [ 95%] Building CXX
>  object src/CMakeFiles/openbabel.dir/stereo/perception.o
> [100%] Building CXX object src/CMakeFiles/openbabel.dir/stereo/facade.o
> Linking CXX shared library ../lib/libopenbabel.dylib
> [100%] Built target openbabel
> [100%] Generating ../../scripts/python/openbabel-python.cpp,
> ../../scripts/python/openbabel.py
> /Users/visvaldas/openbabel/include/openbabel/isomorphism.h:159: Warning 325:
> Nested class not currently supported (Functor ignored)
> Scanning dependencies of target bindings_python
> [100%] Building CXX object
> scripts/CMakeFiles/bindings_python.dir/python/openbabel-python.cpp.o
> In file included from
> /Library/Frameworks/Python.framework/Headers/Python.h:57,
>                  from
> /Users/visvaldas/openbabel/scripts/python/openbabel-python.cpp:150:
> /Library/Frameworks/Python.framework/Headers/pyport.h:730:2: error: #error
> "LONG_BIT definition appears wrong for platform (bad gcc/glibc config?)."
>
>
> make[3]: ***
>  [scripts/CMakeFiles/bindings_python.dir/python/openbabel-python.cpp.o]
> Error 1
> make[2]: *** [scripts/CMakeFiles/bindings_python.dir/all] Error 2
> make[1]: *** [scripts/CMakeFiles/bindings_python.dir/rule] Error 2
> make: *** [bindings_python] Error 2
>
>
> Best regards,
>
> Visvaldas
>
>
>
>
> Hello Pierre,
>
> I've been doing some work on the Python bindings getting them to work
> on MacOSX 64-bit. Please try our development code (trunk). You will
> need to recreate the bindings using -DRUN_SWIG=TRUE with a recent
> version of Swig (>=2.0.1) on the path.
>
> You should also "grep -i python CMakeCache.txt" and check that all of
> the Python related variables are pointing to the same desired Python
> installation. If not, you can edit CMakeCache.txt directly or else
> specify the correct values when calling CMake.
>
> - Noel
>
>
> ------------------------------------------------------------------------------
> Ridiculously easy VDI. With Citrix VDI-in-a-Box, you don't need a complex
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> _______________________________________________
> OpenBabel-scripting mailing list
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> https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
>

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

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

Can you try using a different version of Python, e.g. your system
installation of Python. (I forget where this is located, check on
Google.)

To do this, set the CMake variables (using -D) PYTHON_EXECUTABLE,
PYTHON_INCLUDE_PATH and PYTHON_LIBRARY appropriately, and force a SWIG
rebuild by "touch $OBSRC/scripts/openbabel-python.i" (with the
appropriate value for $OBSRC). To see the current values of the Python
variables, use "grep -i python CMakeCache.txt".

- Noel

On 4 January 2012 20:58, Visvaldas K. <coy...@ya...> wrote:
> Dear colleagues,
>
> I tried to compile openbabel python bindings for trunk version of openbabel
> on December 30 on my mac, os version 10.6.8 (with python 2.5 - perhaps it's
> too old!), with the following error:
> ng error:
>
> {visvaldas}~/openbabel/build% make bindings_python -j2
> [  4%] [  4%] Building CXX object src/CMakeFiles/openbabel.dir/atom.o
> Building CXX object src/CMakeFiles/openbabel.dir/base.o
> [  4%] Building CXX object src/CMakeFiles/openbabel.dir/bitvec.o
> [  9%] Building CXX object src/CMakeFiles/openbabel.dir/bond.o
> [  9%] Building CXX object src/CMakeFiles/openbabel.dir/bondtyper.o
> [  9%] Building CXX object src/CMakeFiles/openbabel.dir/builder.o
> [ 14%] Building CXX object src/CMakeFiles/openbabel.dir/canon.o
>
> <similar part chopped off - VK>
>
> [ 95%] Building CXX
>  object src/CMakeFiles/openbabel.dir/stereo/perception.o
> [100%] Building CXX object src/CMakeFiles/openbabel.dir/stereo/facade.o
> Linking CXX shared library ../lib/libopenbabel.dylib
> [100%] Built target openbabel
> [100%] Generating ../../scripts/python/openbabel-python.cpp,
> ../../scripts/python/openbabel.py
> /Users/visvaldas/openbabel/include/openbabel/isomorphism.h:159: Warning 325:
> Nested class not currently supported (Functor ignored)
> Scanning dependencies of target bindings_python
> [100%] Building CXX object
> scripts/CMakeFiles/bindings_python.dir/python/openbabel-python.cpp.o
> In file included from
> /Library/Frameworks/Python.framework/Headers/Python.h:57,
>                  from
> /Users/visvaldas/openbabel/scripts/python/openbabel-python.cpp:150:
> /Library/Frameworks/Python.framework/Headers/pyport.h:730:2: error: #error
> "LONG_BIT definition appears wrong for platform (bad gcc/glibc config?)."
>
>
> make[3]: ***
>  [scripts/CMakeFiles/bindings_python.dir/python/openbabel-python.cpp.o]
> Error 1
> make[2]: *** [scripts/CMakeFiles/bindings_python.dir/all] Error 2
> make[1]: *** [scripts/CMakeFiles/bindings_python.dir/rule] Error 2
> make: *** [bindings_python] Error 2
>
>
> Best regards,
>
> Visvaldas
>
>
>
>
> Hello Pierre,
>
> I've been doing some work on the Python bindings getting them to work
> on MacOSX 64-bit. Please try our development code (trunk). You will
> need to recreate the bindings using -DRUN_SWIG=TRUE with a recent
> version of Swig (>=2.0.1) on the path.
>
> You should also "grep -i python CMakeCache.txt" and check that all of
> the Python related variables are pointing to the same desired Python
> installation. If not, you can edit CMakeCache.txt directly or else
> specify the correct values when calling CMake.
>
> - Noel
>
>
> ------------------------------------------------------------------------------
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> infrastructure or vast IT resources to deliver seamless, secure access to
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>

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

[Visvaldas K. <coy...@ya...>]

Dear colleagues,

I tried to compile openbabel python bindings for trunk version of openbabel on December 30 on my mac, os version 10.6.8 (with python 2.5 - perhaps it's too old!), with the following error:
ng error:

{visvaldas}~/openbabel/build% make bindings_python -j2
[  4%] [  4%] Building CXX object src/CMakeFiles/openbabel.dir/atom.o
Building CXX object src/CMakeFiles/openbabel.dir/base.o
[  4%] Building CXX object src/CMakeFiles/openbabel.dir/bitvec.o
[  9%] Building CXX object src/CMakeFiles/openbabel.dir/bond.o
[  9%] Building CXX object src/CMakeFiles/openbabel.dir/bondtyper.o
[  9%] Building CXX object src/CMakeFiles/openbabel.dir/builder.o
[ 14%] Building CXX object src/CMakeFiles/openbabel.dir/canon.o

<similar part chopped off - VK>

[ 95%] Building CXX object src/CMakeFiles/openbabel.dir/stereo/perception.o
[100%] Building CXX object src/CMakeFiles/openbabel.dir/stereo/facade.o
Linking CXX shared library ../lib/libopenbabel.dylib
[100%] Built target openbabel
[100%] Generating ../../scripts/python/openbabel-python.cpp, ../../scripts/python/openbabel.py
/Users/visvaldas/openbabel/include/openbabel/isomorphism.h:159: Warning 325: Nested class not currently supported (Functor ignored)
Scanning dependencies of target bindings_python
[100%] Building CXX object scripts/CMakeFiles/bindings_python.dir/python/openbabel-python.cpp.o
In file included from /Library/Frameworks/Python.framework/Headers/Python.h:57,
from /Users/visvaldas/openbabel/scripts/python/openbabel-python.cpp:150:
/Library/Frameworks/Python.framework/Headers/pyport.h:730:2: error: #error "LONG_BIT definition appears wrong for platform (bad gcc/glibc config?)."


make[3]: *** [scripts/CMakeFiles/bindings_python.dir/python/openbabel-python.cpp.o] Error 1
make[2]: *** [scripts/CMakeFiles/bindings_python.dir/all] Error 2
make[1]: *** [scripts/CMakeFiles/bindings_python.dir/rule] Error 2
make: *** [bindings_python] Error 2


Best regards,

Visvaldas




Hello Pierre,

I've been doing some work on the Python bindings getting them to work
on MacOSX 64-bit. Please try our development code (trunk). You will
need to recreate the bindings using -DRUN_SWIG=TRUE with a recent
version of Swig (>=2.0.1) on the path.

You should also "grep -i python CMakeCache.txt" and check that all of
the Python related variables are pointing to the same desired Python
installation. If not, you can edit CMakeCache.txt directly or else
specify the correct values when calling CMake.

- Noel 

Re: [OpenBabel-scripting] API for generating 2D coordinates or 3D->2D conversion?

[Ilya B. <ba...@gm...>]

Marianne - thank you very much! Actually, I need to do the reverse (convert
3D coordinates to 2D coordinates), but hopefully there is the "gen2D" option
as well.

Regards,
Ilya

-- 
    Ilya Balabin, Ph. D.
    Department of Chemistry
    Duke University
    Durham, NC 27708-0349
    http://www.duke.edu/~ilya  

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Re: [OpenBabel-scripting] API for generating 2D coordinates or 3D->2D conversion?

[Marianne <mar...@ep...>]

Hello Ilya,

I make some test some times ago, normally it is ok:

// Transformation of 2D mol file to a 3D mol file, (with 3D conversion)
    OBConversion conv;
    conv.OpenInAndOutFiles("test2D.mol","test3D.mol");
    conv.SetInAndOutFormats("mol","mol");
    conv.AddOption("gen3D",conv.GENOPTIONS);
    conv.Convert();
    conv.CloseOutFile();

Best regards,

Marianne 

--
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Re: [OpenBabel-scripting] API for generating 2D coordinates or 3D->2D conversion?

[Marianne <mar...@ep...>]

Hello Ilya,

I make some test some times ago, normally it is ok:

// Transformation of 2D mol file to a unique 3D sdf file, (with 3D
conversion)
    OBConversion conv;
    conv.OpenInAndOutFiles("test2D.mol","test3D.mol");
    conv.SetInAndOutFormats("mol","mol");
    conv.AddOption("gen3D",conv.GENOPTIONS);
    conv.Convert();
    conv.CloseOutFile();

Best regards,

Marianne

--
View this message in context: http://forums.openbabel.org/API-for-generating-2D-coordinates-or-3D-2D-conversion-tp4197679p4201588.html
Sent from the openbabel-scripting mailing list archive at Nabble.com.

[OpenBabel-scripting] API for generating 2D coordinates or 3D->2D conversion?

[Ilya B. <ba...@gm...>]

Ladies and gentlemen,

I would greatly appreciate any hint on the API for 2D coordinate generation
or 3D to 2D coordinate conversion, assuming those exist. That can be done
from the command line using the '--gen2d' option, which makes me think there
could be an API as well. I have not found one yet, though... any
suggestions?

Many thanks in advance,
Ilya

-- 
    Ilya Balabin, Ph. D.
    Department of Chemistry
    Duke University
    Durham, NC 27708-0349
    http://www.duke.edu/~ilya 

--
View this message in context: http://forums.openbabel.org/API-for-generating-2D-coordinates-or-3D-2D-conversion-tp4197679p4197679.html
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Re: [OpenBabel-scripting] more graceful exit for make3D on large molecules

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

Hi Noel.  Thanks for the ideas.  I have been able to increase the size of molecules by editing make3D().  I make the addh() line optional. The force field optimization still works without hydrogen atoms.  I then later addh().  This makes larger molecules accessible; it still has a limit, and I am in the process of exploring that limit.

I will look into using obabel from a command line and its gen3d() argument.

Thanks.

Steve

Steven G. Arturo
7B/207P  979.238.5749


-----Original Message-----
From: Noel O'Boyle [mailto:bao...@gm...] 
Sent: Tuesday, November 15, 2011 5:40 AM
To: Arturo, Steven (SG)
Cc: ope...@li...
Subject: Re: [OpenBabel-scripting] more graceful exit for make3D on large molecules

Hi Steven,

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

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

- Noel

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

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

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

Hello Pierre,

I've been doing some work on the Python bindings getting them to work
on MacOSX 64-bit. Please try our development code (trunk). You will
need to recreate the bindings using -DRUN_SWIG=TRUE with a recent
version of Swig (>=2.0.1) on the path.

You should also "grep -i python CMakeCache.txt" and check that all of
the Python related variables are pointing to the same desired Python
installation. If not, you can edit CMakeCache.txt directly or else
specify the correct values when calling CMake.

- Noel

On 10 November 2011 20:58, pierrelb <pie...@gm...> wrote:
> I'm running OSX 10.6.8, and I'm having trouble installing openbabel with
> python bindings. Any help would be appreciated
>
> Below are the results of the build.
>
> running build_py
> creating build/lib.macosx-10.3-fat-2.6
> copying openbabel.py -> build/lib.macosx-10.3-fat-2.6
> copying pybel.py -> build/lib.macosx-10.3-fat-2.6
> running build_ext
> building '_openbabel' extension
> gcc-4.0 -fno-strict-aliasing -fno-common -dynamic -arch ppc -arch i386 -g
> -O2 -DNDEBUG -g -O3 -I/usr/local/include/eigen2
> -I/Users/PierreB/Downloads/openbabel-2.3.1/scripts/python/../../include
> -I../include
> -I/Library/Frameworks/Python.framework/Versions/2.6/include/python2.6 -c
> /Users/PierreB/Downloads/openbabel-2.3.1/scripts/python/openbabel-python.cpp
> -o
> build/temp.macosx-10.3-fat-2.6/Users/PierreB/Downloads/openbabel-2.3.1/scripts/python/openbabel-python.o
> In file included from /usr/include/architecture/i386/math.h:626,
>                 from /usr/include/math.h:28,
>                 from
> /Library/Frameworks/Python.framework/Versions/2.6/include/python2.6/pyport.h:235,
>                 from
> /Library/Frameworks/Python.framework/Versions/2.6/include/python2.6/Python.h:58,
>                 from
> /Users/PierreB/Downloads/openbabel-2.3.1/scripts/python/openbabel-python.cpp:150:
> /usr/include/AvailabilityMacros.h:108:14: warning: #warning Building for
> Intel with Mac OS X Deployment Target < 10.4 is invalid.
>
> c++ -arch ppc -arch i386 -g -bundle -undefined dynamic_lookup
> -I/usr/local/include/eigen2
> build/temp.macosx-10.3-fat-2.6/Users/PierreB/Downloads/openbabel-2.3.1/scripts/python/openbabel-python.o
> -L/Users/PierreB/Downloads/openbabel-2.3.1/scripts/python/../../lib
> -L/Users/PierreB/Downloads/openbabel-2.3.1/scripts/python/../../lib64
> -L../lib -lopenbabel -o build/lib.macosx-10.3-fat-2.6/_openbabel.so
> ld: warning: directory
> '/Users/PierreB/Downloads/openbabel-2.3.1/scripts/python/../../lib'
> following -L not found
> ld: warning: directory
> '/Users/PierreB/Downloads/openbabel-2.3.1/scripts/python/../../lib64'
> following -L not found
> ld: warning: in ../lib/libopenbabel.dylib, file was built for unsupported
> file format which is not the architecture being linked (ppc)
> ld: warning: directory
> '/Users/PierreB/Downloads/openbabel-2.3.1/scripts/python/../../lib'
> following -L not found
> ld: warning: directory
> '/Users/PierreB/Downloads/openbabel-2.3.1/scripts/python/../../lib64'
> following -L not found
> ld: warning: in ../lib/libopenbabel.dylib, file was built for unsupported
> file format which is not the architecture being linked (i386)
> running install_lib
> copying build/lib.macosx-10.3-fat-2.6/_openbabel.so ->
> /Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages
> copying build/lib.macosx-10.3-fat-2.6/openbabel.py ->
> /Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages
> copying build/lib.macosx-10.3-fat-2.6/pybel.py ->
> /Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages
> byte-compiling
> /Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/openbabel.py
> to openbabel.pyc
> byte-compiling
> /Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/pybel.py
> to pybel.pyc
> running install_egg_info
> Writing
> /Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/openbabel-1.7-py2.6.egg-info
> Pierre-Bhoorasinghs-MacBook-Pro:build PierreB$
> Pierre-Bhoorasinghs-MacBook-Pro:build PierreB$ python
> Python 2.6.6 (r266:84374, Aug 31 2010, 11:00:51)
> [GCC 4.0.1 (Apple Inc. build 5493)] on darwin
> Type "help", "copyright", "credits" or "license" for more information.
>>>> import pybel
> Traceback (most recent call last):
>  File "<stdin>", line 1, in <module>
>  File
> "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/pybel.py",
> line 16, in <module>
>    import openbabel as ob
>  File
> "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/openbabel.py",
> line 65, in <module>
>    _openbabel = swig_import_helper()
>  File
> "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/openbabel.py",
> line 61, in swig_import_helper
>    _mod = imp.load_module('_openbabel', fp, pathname, description)
> ImportError:
> dlopen(/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/_openbabel.so,
> 2): Symbol not found: __ZN9OpenBabel8OBPlugin7DisplayERSsPKcS3_
>  Referenced from:
> /Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/_openbabel.so
>  Expected in: dynamic lookup
>
>
>
> Here's my attempt to link
>
> Pierre-Bhoorasinghs-MacBook-Pro:build PierreB$ file
> /Users/PierreB/Downloads/openbabel-2.3.1/build/lib/libopenbabel.dylib
> /Users/PierreB/Downloads/openbabel-2.3.1/build/lib/libopenbabel.dylib:
> Mach-O 64-bit dynamically linked shared library x86_64
> Pierre-Bhoorasinghs-MacBook-Pro:build PierreB$ otool -L
> /Users/PierreB/Downloads/openbabel-2.3.1/build/lib/libopenbabel.dylib
> /Users/PierreB/Downloads/openbabel-2.3.1/build/lib/libopenbabel.dylib:
>     /Users/PierreB/Downloads/openbabel-2.3.1/build/lib/libopenbabel.4.dylib
> (compatibility version 4.0.0, current version 4.0.1)
>     /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current
> version 125.2.11)
>     /usr/lib/libz.1.dylib (compatibility version 1.0.0, current version
> 1.2.3)
>     /usr/lib/libstdc++.6.dylib (compatibility version 7.0.0, current
> version 7.9.0)
> Pierre-Bhoorasinghs-MacBook-Pro:build PierreB$
>
>
>
> --
> View this message in context: http://forums.openbabel.org/OSX-6-8-Openbabel-python-bindings-tp4027870p4027870.html
> Sent from the openbabel-scripting mailing list archive at Nabble.com.
>
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[OpenBabel-scripting] OBForceField Java

[Alexander K. <ale...@sc...>]

Hi there,

I am trying to get an OpenBabel ForceField up and running in Java, I managed to install the java language bindings and can load the library now.

However, calling:

ff = OBForceField.FindForceField("MMFF94");

returns null.

Using  OBPlugin.List("forcefields");

returns: forcefields is not a recognized plugin type. Those with instances of sub-types loaded are:

I cannot find any documentation on this, only the C++ API specs, which don't help much at this point.

Is there something I am missing?

Regards,

Alex

PS: Sorry for cross posting, I posted to the wrong mailing list first 'openbabel-discuss'


--
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Schloss Birlinghoven, D-53754 Sankt Augustin
Tel.: +49 - 2241 - 14 - 2736
E-mail: ale...@sc...
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