Re: [Open Babel] help with installation

[Artur Hermano]

Dear Alan,

thank you so much for your help. It all does make sense, but I am not sure how 
I could sort this out, because I intend to use autodock vina, which actually 
calls openbabel scripts... so, should I try and use Autodock Vina through 
conda? How do I do that? If that's so, shouldn't I be having problems with 
SWIG? It's all very confusing to me as I am new to this kind of tool...

You may need to manually specify the location of Open Babel include and library 
directories. For example:
  python setup.py build_ext -I/usr/local/include/openbabel3 -L/usr/local/lib
  python setup.py install

Would you know how to execute this solution that appears when SWIG fails? I've 
tried, but maybe I did something wrong, because nothing changed...

Any help is very appreciated! Thank you!


--


Artur


From: Alan 
Sent: Friday, December 3, 2021 05:06
To: Artur Hermano 
Subject: Re: [Open Babel] help with installation

It's all about in which environment you did install openbabel. In macOS for 
example, using brew, only the python shipped by brew will see the openbabel 
module, not even a virtual env from this very same python will see it. It's 
really annoying, unfortunately, because the binary "obabel" is usually 
available in any environment.

The safe solution I found so far, if I need to work with openbabel, is to use 
conda.

I've tried "openbabel-wheel"(which in principle should allow me to install it 
in a py venv) but it didn't work on my Mac.

Though I use Mac, the same logic applies to Ubuntu. Openbabel python module 
will only work with the very specific python shipped in the same distribution.

On Wed, 1 Dec 2021 at 13:43, Artur Hermano 
mailto:artur.herm...@hotmail.com>> wrote:
Hello OpenBabel users,

I've been having issues with OpenBabel and thought I might use some help from 
more experienced users.
My main problem is that I have (apparently) installed OpenBabel succesfully, 
but other softwares cannot access it. For example, when I try to run a programm 
that uses OpenBabel ('mk_prepare_ligand.py -i 1iep_ligand.sdf -o 
1iep_ligand.pdbqt --pH 7.4'), I get the following error:

'Traceback (most recent call last):
  File "/home/artur/.local/bin/mk_prepare_ligand.py", line 11, in 
from openbabel import openbabel as ob
ModuleNotFoundError: No module named 'openbabel''

Furthermore, if I try to remove openbabel from my system, I receive a message 
(in Portuguese, so I won't copy it here) saying that "openbabel isn't 
installed, so it won't be removed". However, I can easily execute the comand 
obabel through my Ubuntu 20.04 terminal.
Additionally, if I try the command pip install -U openbabel, I get the 
following error message:

Collecting openbabel
  Using cached openbabel-3.1.1.1.tar.gz (82 kB)
Building wheels for collected packages: openbabel
  Building wheel for openbabel (setup.py) ... error
  ERROR: Command errored out with exit status 1:
   command: /usr/bin/python3 -u -c 'import sys, setuptools, tokenize; 
sys.argv[0] = '"'"'/tmp/pip-install-ctx5tcrx/openbabel/setup.py'"'"'; 
__file__='"'"'/tmp/pip-install-ctx5tcrx/openbabel/setup.py'"'"';f=getattr(tokenize,
 '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', 
'"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' 
bdist_wheel -d /tmp/pip-wheel-xzrzd_1p
   cwd: /tmp/pip-install-ctx5tcrx/openbabel/
  Complete output (66 lines):
  running bdist_wheel
  running build
  running build_ext
  Warning: invalid version number '3.1.1.1'.
  Guessing Open Babel location:
  - include_dirs: ['/usr/include/python3.8', '/usr/local/include/openbabel3']
  - library_dirs: ['/usr/local/lib']
  building 'openbabel._openbabel' extension
  swigging openbabel/openbabel-python.i to openbabel/openbabel-python_wrap.cpp
  swig -python -c++ -small -O -templatereduce -naturalvar 
-I/usr/include/python3.8 -I/usr/local/include/openbabel3 -o 
openbabel/openbabel-python_wrap.cpp openbabel/openbabel-python.i

then several errors similar to these: openbabel/openbabel-python.i:246: Error: 
Unable to find 'openbabel/babelconfig.h'
  openbabel/openbabel-python.i:248: Error: Unable to find 'openbabel/data.h'
  openbabel/openbabel-python.i:249: Error: Unable to find 'openbabel/obutil.h'

And then finally: Error: SWIG failed. Is Open Babel installed?
You may need to manually specify the location of Open Babel include and 
library directories. For example:
  python setup.py build_ext -I/usr/local/include/openbabel3 -L/usr/local/lib
  python setup.py install

ERROR: Command errored out with exit status 1: /usr/bin/python3 -u -c 'import 
sys, setuptools, tokenize; sys.argv[0] = 
'"'"'/tmp/pip-install-ctx5tcrx/openbabel/setup.py'"'"'; 
__file__='"'&quo

Re: [Open Babel] Help on SMILES format

[Geoffrey Hutchison]

> I had to generate a 3D molecule from SMILES to xyz. But i have noticed that, 
> 'sometimes', if i give a SMILES input for a cyclic molecule, ('c1c1' for 
> benzene) and convert it into xyz (3d) coordinates and take the data to 
> visualize in Avogadro, it is not showing a cyclic molecule at all (showing an 
> acyclic hexatriene type of thing). I, again, want to say the word "sometimes",

This is a known bug that's much less likely to occur in OB-3.0 - which has a 
much larger set of ring fragments. When generating 3D coordinates, if a ring 
isn't matched, it falls back to the atom-by-atom builder. If you use the 
'better' or 'best' levels of 3D coordinate generation, the force field will 
clean this up before writing the XYZ file.

But again, if you have examples, that's extremely helpful. Saying 'sometimes 
this works' is extremely frustrating from a debugging perspective because it 
gives us nothing to test, debug and improve.

If you have a specific example with OB-3.0, please submit the bug report and 
example SMILES to https://github.com/openbabel/openbabel/issues

Thanks and best regards,
-Geoff

---
Prof. Geoffrey Hutchison
Department of Chemistry
University of Pittsburgh
tel: (412) 648-0492
email: geo...@pitt.edu
twitter: @ghutchis
web: https://hutchison.chem.pitt.edu/___
OpenBabel-discuss mailing list
OpenBabel-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss

Re: [Open Babel] Help on SMILES format

[Arpan Choudhury]

Dear all,
I had to generate a 3D molecule from SMILES to xyz. But i have noticed
that, 'sometimes', if i give a SMILES input for a cyclic molecule,
('c1c1' for benzene) and convert it into xyz (3d) coordinates and take
the data to visualize in Avogadro, it is not showing a cyclic molecule at
all (showing an acyclic hexatriene type of thing). I, again, want to say
the word "sometimes", because in some other times its all perfect. So i am
afraid that whether its a fault of the SMILES format or during my Openbabel
installation something went wrong.

Regards,
Arpan

Indian Association for the Cultivation of Science, Kolkata, India

On Wed, 11 Dec 2019, 12:14 pm Arpan Choudhury,  wrote:

> Dear all,
> I had to generate a 3D molecule from SMILES to xyz. But i have noticed
> that, sometimes, in 3D if i give a SMILES input for a cyclic molecule,
> ('c1c1' for benzene) and convert it into xyz (3d) coordinates and take
> the data to visualize in Avogadro, it is not showing a cyclic molecule at
> all. I, again, want to say the word "sometimes", because in some other
> times its all perfect. So i am afraid that whether its a fault of the
> SMILES format or during my Openbabel installation something went wrong.
>
> Regards,
> Arpan
>
> Indian Association for the Cultivation of Science, Kolkata, India
>
>
>
> On Tue, 10 Dec 2019, 9:21 pm Geoffrey Hutchison, <
> geoff.hutchi...@gmail.com> wrote:
>
>>
>> > I am using Openbabel GUI on windows. I am converting SMILES to xyz
>> format using 'generate 3D coordinates' option. Everything is looking fine
>> (viewing in gui.svg viewer in firefox) as expected.
>>
>>  I'm not sure why you're generating 3D coordinates to view a 2D format
>> (SVG).
>>
>> > But when i am taking the output xyz data to view in other molecular
>> editors like GaussView or Avogadro, it is not giving the structure as
>> viewed in gui.svg
>>
>> I'm not sure what that means. The XYZ file will be a 3D molecule, not a
>> 2D depiction.
>>
>> Perhaps you can give us a concrete example of the SMILES, the SVG and the
>> XYZ file?
>>
>> Thanks very much,
>> -Geoff
>>
>> ---
>> Prof. Geoffrey Hutchison
>> Department of Chemistry
>> University of Pittsburgh
>> tel: (412) 648-0492
>> email: geo...@pitt.edu
>> twitter: @ghutchis
>> web: https://hutchison.chem.pitt.edu/
>
>
___
OpenBabel-discuss mailing list
OpenBabel-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss

Re: [Open Babel] Help on SMILES format

[Geoffrey Hutchison]

> I am using Openbabel GUI on windows. I am converting SMILES to xyz format 
> using 'generate 3D coordinates' option. Everything is looking fine (viewing 
> in gui.svg viewer in firefox) as expected.

 I'm not sure why you're generating 3D coordinates to view a 2D format (SVG).

> But when i am taking the output xyz data to view in other molecular editors 
> like GaussView or Avogadro, it is not giving the structure as viewed in 
> gui.svg

I'm not sure what that means. The XYZ file will be a 3D molecule, not a 2D 
depiction.

Perhaps you can give us a concrete example of the SMILES, the SVG and the XYZ 
file?

Thanks very much,
-Geoff

---
Prof. Geoffrey Hutchison
Department of Chemistry
University of Pittsburgh
tel: (412) 648-0492
email: geo...@pitt.edu
twitter: @ghutchis
web: https://hutchison.chem.pitt.edu/

___
OpenBabel-discuss mailing list
OpenBabel-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss

Re: [Open Babel] Help

[Geoffrey Hutchison]

While it's easy for you to hack the mol2format.cpp code - I have never seen 
more than 3-4 decimal places in a mol2 file.

I've looked for the format specification, but it doesn't seem to be online.

How much is it changing the dihedral angles?

-Geoff

---
Prof. Geoffrey Hutchison
Department of Chemistry
University of Pittsburgh
tel: (412) 648-0492
email: geo...@pitt.edu
twitter: @ghutchis
web: https://hutchison.chem.pitt.edu/


> On Sep 19, 2019, at 1:06 PM, David Ricardo Figueroa Blanco 
>  wrote:
> 
> Hi, 
> 
> I am working with xyz files but I need to convert many .xyz to .mol2. I used 
> babel *.xyz - omol2 -m but the mol2 file round in the 4 decimal number and I 
> need all the decimals that came from the .xyz file. This is important because 
> it changes some dihedral angles. 
> 
> Thank you for your time and colaboration. 
> David
> ___
> OpenBabel-discuss mailing list
> OpenBabel-discuss@lists.sourceforge.net 
> 
> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss 
> 
___
OpenBabel-discuss mailing list
OpenBabel-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss

Re: [Open Babel] Help using Pybel in Microsoft Visual Studio and from within batch file

[Geoffrey Hutchison]

> My second question is regarding running python programs in command line,
> have you ever tried to run the python program that imports pybel from inside
> a batch file? For me this throws an error "ModuleNotFoundError: No module
> named pybel".

One way or another, the environment is different. While you mention including 
the Pybel and openbabel.py files in the site-packages directory, my guess is 
that they're not being loaded somehow.

Since there aren't a whole lot of Windows users on here, I'm afraid we can't be 
much help. But you're doing the right thing - checking that things run from the 
command-line first. Somehow, the environment of the batch file is different 
than the command-line.

-Geoff

___
OpenBabel-discuss mailing list
OpenBabel-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss

Re: [Open Babel] Help with compiling the language bindings

[Tayeb Kakeshpour]

If you want to install on a Linux system, I find the conda installer the 
easiest way. First, you need to install anaconda, then, you can install 
openbabel simply using the command in the following link:
https://anaconda.org/openbabel/openbabel

-Tayeb

Tayeb Kakeshpour
Graduate Research Assistant
Jackson Research Group
Michigan State University
Department of Chemistry
578 S. Shaw Lane, room 535
East Lansing, MI 48824
kakes...@msu.edu



> On Oct 8, 2018, at 4:53 AM, Christina Frances Sandall  
> wrote:
> 
> Hi there,
> 
> I am very new to all of this, and am looking for help with the install.  I 
> followed the instructions on the page below:
> 
> http://openbabel.org/wiki/Install_(source_code)
> 
> specifically the section on Installing globally with root access.  I also 
> installed a GNU compiler according to these instructions: 
> https://wiki.helsinki.fi/display/HUGG/GNU+compiler+install+on+Mac+OS+X and 
> cmake prior to running these commands.
> 
> I used the following commands:
> 
> tar zxvf openbabel-2.4.1.tar.gz
> mv openbabel-2.4.1 ob-src
> mkdir ob-build
> cd ob-build
> cmake ../ob-src 2>&1 | tee cmake.out
> sudo make install
> 
> Everything seemed to install, but I am looking to run the optimize plugin in 
> pymol, and I got an error there: "Optimize plug-in needs openbabel to be 
> installed in your system, please follow the instructions at
> http://openbabel.org/wiki/Get_Open_Babel”.  I realized I still did not have 
> it completely installed, so I tried the following command:
> export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/lib
> which “ran” with no errors.  I now have several files and folders in the 
> following directory:
> /usr/local/lib
> They are:
> pkgconfig (FOLDER)
> 
> libinchi.dylib
> 
> libinchi.0.4.1.dylib
> 
> libinchi.0.dylib
> 
> openbabel (FOLDER)
> 
> libopenbabel.dylib
> 
> libopenbabel.5.0.0.dylib
> 
> libopenbabel.5.dylib
> 
> cmake (FOLDER)
> 
> 
> I believe open babel is still not completely installed because I did not 
> compile the language bindings at the time of install.  I now have installed 
> python (2.7.10), but am looking for how I can finish this install.  As I said 
> above, I’m looking to use the optimize plugin in pymol.  I’m working on a Mac 
> (running MacOS Mojave version 10.14).  Would very much appreciate any help.  
> Thanks very much!
> 
> 
> 
> 
> ___
> OpenBabel-discuss mailing list
> OpenBabel-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
___
OpenBabel-discuss mailing list
OpenBabel-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss

Re: [Open Babel] Help

[Jeff Janes]

On Tue, May 29, 2018 at 8:42 AM, Haddadi Kiandokht 
wrote:

> Hello!
>
> There might be different smiles for a compound due to existence of
> tautomers. I need to convert canonical smiles of a compound to all possible
> smiles of its tautomers.
>
> I dig into tautomer.h library and tried to obtain all possible tautomer
> smiles of a compound but the algorithm just output one specific canonical
> smiles for each tautomers.
>
> For example this KEGG compound with the KEGG id of C00544 has two tautomer.


I don't think this molecule has two tautomers.  If you count phenol /
ketones and ene-1,1-diol / carboxylic acids (neither of which I think
obabel supports as tautomers) than there are more than two, and if you
don't count them there is only one form.


> Therefore, it must have two different smiles. TautomerFunctor (a class of
> tautomer.h) converts all smiles to one specific smiles.
> I want to have all two distinct smiles structure so I can take into
> account all possible states of a molecule that can be happened.
>

I don't know how the exact interface works between the obtautomer binary
program and the TautomerFunctor function, but obtautomer without the -c
option is supposed to enumerate all tautomers.  With the -c option it is
supposed to provide a single canonical tautomer, but it is known to be
buggy.  Perhaps you can look at how obtautomer invokes the c functions to
see how that interface works.

Cheers,

Jeff
--
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot___
OpenBabel-discuss mailing list
OpenBabel-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss

Re: [Open Babel] Help with generation of atom names in mol2 format

[Maciek Wójcikowski]

Hi Antionio,

OpenBabel generates new labels, unless there are already OBResiude info on
that. You can set it to whatever you want with OBResiude.SetAtomID().
Checkout the script below:

import pybel
> ob = pybel.ob
> mol = pybel.readstring('smi', 'c1c1')
> res = ob.OBResidue()
> for atom in ob.OBMolAtomIter(mol.OBMol):
> res.AddAtom(atom)
> res.SetAtomID(atom, '%s%i' %
> (ob.OBElementTable().GetSymbol(atom.GetAtomicNum()), atom.GetIdx()))
>


print(mol.write('mol2'))


Note that if you use the -xl option the residue will be ignored, but you
can name the residue to whatever you want via res.SetName('BLAH')



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

2018-01-18 23:57 GMT+01:00 Antonio Jesus Banegas Luna <
ajbane...@alu.ucam.edu>:

> Hello all,
>
> I'm a newby in obabel and I need a bit of help.
> I use obabel to convert a file from sdf to mol2 format because another
> program requires such conversion.
> The conversion is fine, and I get something like this (I only show the
> ATOM block):
>
> @ATOM
>   1 C   0.5825   -1.49430.8613 C.ar1  LIG1
> 0.0063
>   2 C  -0.4113   -2.11971.6364 C.ar1  LIG1
> 0.0421
>   3 C  -1.7701   -1.87081.3728 C.ar1  LIG1
> 0.1957
>   4 O  -2.7253   -2.46432.1262 O.3 1  LIG1
> -0.2866
>   5 C  -2.1325   -1.00440.3248 C.ar1  LIG1
> 0.0421
>
> However, the third-party software requires something like this:
>
> @ATOM
>   1 C*1*   0.5825   -1.49430.8613 C.ar1  LIG1
> 0.0063
>   2 C*2* -0.4113   -2.11971.6364 C.ar1  LIG1
> 0.0421
>   3 C*3*  -1.7701   -1.87081.3728 C.ar1  LIG1
> 0.1957
>   4 O*1*  -2.7253   -2.46432.1262 O.3 1  LIG1
> -0.2866
>   5 C*4*  -2.1325   -1.00440.3248 C.ar1  LIG1
> 0.0421
>
> Now, my question is: is there any way of forcing obabel to generate atom
> names in the required format?
> Maybe someone has some experience with this.
>
> Thanks in advance,
> Antonio
>
> --
> Antonio J. Banegas Luna
> Bioinformatics and High Performance Computing Research 
> groupajbane...@alu.ucam.edu
> http://orcid.org/-0003-1158-8877http://www.researcherid.com/rid/O-7331-2016https://scholar.google.es/citations?user=EWtHIUMJhttps://www.researchgate.net/profile/Antonio_Jesus_Banegas_Luna
>
>
> 
> --
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> ___
> OpenBabel-discuss mailing list
> OpenBabel-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>
>
--
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot___
OpenBabel-discuss mailing list
OpenBabel-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss

Re: [Open Babel] Help to conversion format cif_to_pdb

[Dimitri Maziuk]

On 04/14/2014 08:51 AM, David Hall wrote:
 Can you explain what parts of the file are not compatible that you are
 looking at? Residue numbering? Temperature Factors? Testing briefly, it
 appears the coordinates agree, so knowing that fields you are looking to
 preserve would be useful.

SEQRES, temperature factors, the whole header from TITLE to MTRIX... The
diff is almost 7MB, I don't think you want to look.

IMO even half-way complete conversion is way beyond OpenBabel's job
description so I wouldn't bother wasting any time on it. Extracting
OBMol from PDB entry is probably hard enough (e.g. what do you do with
NMR structure with 50 models and REMARK 210 BEST REPRESENTATIVE
CONFORMER IN THIS ENSEMBLE : 19,23,42).

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



signature.asc
Description: OpenPGP digital signature
--
Learn Graph Databases - Download FREE O'Reilly Book
Graph Databases is the definitive new guide to graph databases and their
applications. Written by three acclaimed leaders in the field,
this first edition is now available. Download your free book today!
http://p.sf.net/sfu/NeoTech___
OpenBabel-discuss mailing list
OpenBabel-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss

Re: [Open Babel] Help to conversion format cif_to_pdb

[Wellisson Gonçalves]

Sorry but i don't understand your answer
What's OBMol and what can it do ?
in fact babel in openbabel don't translate the file completely
it's omits a lot of information.
I don't worried about this
The point is how different and reliable it is


2014-04-15 14:14 GMT-03:00 Dimitri Maziuk dmaz...@bmrb.wisc.edu:

 On 04/14/2014 08:51 AM, David Hall wrote:
  Can you explain what parts of the file are not compatible that you are
  looking at? Residue numbering? Temperature Factors? Testing briefly, it
  appears the coordinates agree, so knowing that fields you are looking to
  preserve would be useful.

 SEQRES, temperature factors, the whole header from TITLE to MTRIX... The
 diff is almost 7MB, I don't think you want to look.

 IMO even half-way complete conversion is way beyond OpenBabel's job
 description so I wouldn't bother wasting any time on it. Extracting
 OBMol from PDB entry is probably hard enough (e.g. what do you do with
 NMR structure with 50 models and REMARK 210 BEST REPRESENTATIVE
 CONFORMER IN THIS ENSEMBLE : 19,23,42).

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



 --
 Learn Graph Databases - Download FREE O'Reilly Book
 Graph Databases is the definitive new guide to graph databases and their
 applications. Written by three acclaimed leaders in the field,
 this first edition is now available. Download your free book today!
 http://p.sf.net/sfu/NeoTech
 ___
 OpenBabel-discuss mailing list
 OpenBabel-discuss@lists.sourceforge.net
 https://lists.sourceforge.net/lists/listinfo/openbabel-discuss




-- 


Obrigado,
Wellison Gonçalves
--
Learn Graph Databases - Download FREE O'Reilly Book
Graph Databases is the definitive new guide to graph databases and their
applications. Written by three acclaimed leaders in the field,
this first edition is now available. Download your free book today!
http://p.sf.net/sfu/NeoTech___
OpenBabel-discuss mailing list
OpenBabel-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss

Re: [Open Babel] Help to conversion format cif_to_pdb

[Dimitri Maziuk]

On 04/15/2014 03:59 PM, Wellisson Gonçalves wrote:
 Sorry but i don't understand your answer

OpenBabel deals with molecules.

PDB deals with studies of crystal structures, extended (with varying
degree of success) to structures obtained from EM, NMR, and other methods.

The study includes much more than molecule: there's citations,
secondary structure, NMR models, sample details and so on and so forth.
Dep. on your definition of molecule, it can include more than one. Etc.

I don't believe you can reasonably expect OpenBabel to convert all of
that information between 2 PDB formats: it's not what it's for.

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



signature.asc
Description: OpenPGP digital signature
--
Learn Graph Databases - Download FREE O'Reilly Book
Graph Databases is the definitive new guide to graph databases and their
applications. Written by three acclaimed leaders in the field,
this first edition is now available. Download your free book today!
http://p.sf.net/sfu/NeoTech___
OpenBabel-discuss mailing list
OpenBabel-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss

Re: [Open Babel] Help to conversion format cif_to_pdb

[Wellisson Gonçalves]

Ok
Thanks for the interest
Now, i need to convert the format, only
and it's necessary that it has the best fidelity possible with the original
structure
I think it's openbabel can't help me
I'm going to research more


2014-04-15 19:09 GMT-03:00 Dimitri Maziuk dmaz...@bmrb.wisc.edu:

 On 04/15/2014 03:59 PM, Wellisson Gonçalves wrote:
  Sorry but i don't understand your answer

 OpenBabel deals with molecules.

 PDB deals with studies of crystal structures, extended (with varying
 degree of success) to structures obtained from EM, NMR, and other methods.

 The study includes much more than molecule: there's citations,
 secondary structure, NMR models, sample details and so on and so forth.
 Dep. on your definition of molecule, it can include more than one. Etc.

 I don't believe you can reasonably expect OpenBabel to convert all of
 that information between 2 PDB formats: it's not what it's for.

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




-- 


Obrigado,
Wellison Gonçalves
--
Learn Graph Databases - Download FREE O'Reilly Book
Graph Databases is the definitive new guide to graph databases and their
applications. Written by three acclaimed leaders in the field,
this first edition is now available. Download your free book today!
http://p.sf.net/sfu/NeoTech___
OpenBabel-discuss mailing list
OpenBabel-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss

Re: [Open Babel] Help to conversion format cif_to_pdb

[Wellisson Gonçalves]

I know about that
But i don't get compile
I receive a lot of compilation errors

But a find a other tool
http://sw-tools.pdb.org/apps/CIFTr/index.html
It's very simple

But i'm developing a bioinformatics tool using C++ with QT
for platforms linux, MAC OS X and windows

It's necessary to me put a function that convert .cif to .pdb
I'm already using openbabel for other functions.
And I would very much like to use it to babel

I have no idea how to integrate
http://sw-tools.pdb.org/apps/CIFTr/index.html
or
http://sw-tools.rcsb.org/apps/MAXIT/index.html
in my aplication.
They are using a lot of directories in the project.

Thanks
Wellisson


2014-04-13 12:55 GMT-03:00 Dimitri Maziuk dmaz...@bmrb.wisc.edu:

 On 4/12/2014 2:20 PM, Wellisson Gonçalves wrote:

  A use the executable babel with parameters
  babel -icif '4POQ.cif'  -opdb '4POQ_cif_to_pdb.pdb'
 
  And i received the file that not compatible with the original file.
 
  I know becouse i downloaded the original file in website 4POQ.pdb and
  It's different

 I doubt OB can deal with a complete pdb file -- either pdb or mmcif. Try
 http://sw-tools.rcsb.org/apps/MAXIT/index.html

 Dimitri





 --
 Put Bad Developers to Shame
 Dominate Development with Jenkins Continuous Integration
 Continuously Automate Build, Test  Deployment
 Start a new project now. Try Jenkins in the cloud.
 http://p.sf.net/sfu/13600_Cloudbees
 ___
 OpenBabel-discuss mailing list
 OpenBabel-discuss@lists.sourceforge.net
 https://lists.sourceforge.net/lists/listinfo/openbabel-discuss




-- 


Obrigado,
Wellison Gonçalves
--
Learn Graph Databases - Download FREE O'Reilly Book
Graph Databases is the definitive new guide to graph databases and their
applications. Written by three acclaimed leaders in the field,
this first edition is now available. Download your free book today!
http://p.sf.net/sfu/NeoTech___
OpenBabel-discuss mailing list
OpenBabel-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss

Re: [Open Babel] Help to conversion format cif_to_pdb

[Dimitri Maziuk]

On 4/12/2014 2:20 PM, Wellisson Gonçalves wrote:

 A use the executable babel with parameters
 babel -icif '4POQ.cif'  -opdb '4POQ_cif_to_pdb.pdb'

 And i received the file that not compatible with the original file.

 I know becouse i downloaded the original file in website 4POQ.pdb and
 It's different

I doubt OB can deal with a complete pdb file -- either pdb or mmcif. Try 
http://sw-tools.rcsb.org/apps/MAXIT/index.html

Dimitri




--
Put Bad Developers to Shame
Dominate Development with Jenkins Continuous Integration
Continuously Automate Build, Test  Deployment 
Start a new project now. Try Jenkins in the cloud.
http://p.sf.net/sfu/13600_Cloudbees
___
OpenBabel-discuss mailing list
OpenBabel-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss

Re: [Open Babel] Help please

[Geoffrey Hutchison]

 hi.I wanted to know is how this article was composed or found a way to
 synthesize it?

That's not really our thing. We write software that helps people index, 
convert, etc. chemicals. Your best bet is to find an organic synthesis forum.

A quick Google search suggested:
http://www.chemicalforums.com/index.php?board=3.0
http://www.scienceforums.net/forum/59-organic-chemistry/

Good luck!
-Geoff


--
Minimize network downtime and maximize team effectiveness.
Reduce network management and security costs.Learn how to hire 
the most talented Cisco Certified professionals. Visit the 
Employer Resources Portal
http://www.cisco.com/web/learning/employer_resources/index.html
___
OpenBabel-discuss mailing list
OpenBabel-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss

Re: [Open Babel] help in using molprint2D

[Noel O'Boyle]

It's not possible, and the code will have to be rewritten to allow an
arbitary number of layers. In the meanwhile, you may want to check out
my implementation in Python:
http://baoilleach.blogspot.co.uk/2008/07/calculate-circular-fingerprints-with.html

On 12 November 2012 16:15, green69 gcinci...@gmail.com wrote:
 Hi everybody,

 I'm running Open Babel 2.3.1 in GNU/LinuxDebian OS. I'm interested in using
 molprint2D fingerprints. As described in openbabel manual the following
 command should gives the list of molprint2D fingerprint for each molecule:

 /obabel -ismi test.smi -ompd/

 As described in manual the format of the output is as follow:
 /[Molec_name]\t[atomtype];[layer]-[frequency]-[neighbour_type];/

 Anyway I noted that the fingerprints provided are only those for the layer
 #1 and layer #2 which, for each atom, provide the information about the atom
 itself and those at a distance of 1 bond. Please, do you know if it would be
 possible to grow the depth of the fingerprints provided? That is to say to
 obtain fingerprints of layer #3 or more, which provide for each atom the
 information about atoms laying at 2 (or more) bonds distance?

 Moreover, it would be possible to obtain the molecular similarity using
 molprint2D fingerprint? This is possible in the case of FP2, FP3, FP4 and
 MACCS using the following command:

 /obabel -ismi comp1.smi  -ofpt/

 Many thanks,

 Gio





 --
 View this message in context: 
 http://forums.openbabel.org/help-in-using-molprint2D-tp4655661.html
 Sent from the General discussion mailing list archive at Nabble.com.

 --
 Everyone hates slow websites. So do we.
 Make your web apps faster with AppDynamics
 Download AppDynamics Lite for free today:
 http://p.sf.net/sfu/appdyn_d2d_nov
 ___
 OpenBabel-discuss mailing list
 OpenBabel-discuss@lists.sourceforge.net
 https://lists.sourceforge.net/lists/listinfo/openbabel-discuss

--
Monitor your physical, virtual and cloud infrastructure from a single
web console. Get in-depth insight into apps, servers, databases, vmware,
SAP, cloud infrastructure, etc. Download 30-day Free Trial.
Pricing starts from $795 for 25 servers or applications!
http://p.sf.net/sfu/zoho_dev2dev_nov
___
OpenBabel-discuss mailing list
OpenBabel-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss

Re: [Open Babel] help

[Craig James]

On Thu, Jul 5, 2012 at 3:06 AM, 蓝鱼在嘴里 807409...@qq.com wrote:

 Hello，
 I want to understand the fingerprint type of FP2 in Openbabel,where can I
 find the information?For example,0616670,I know which fragment it
 represents,but for 0 6 5 6 5 6 1 6 936,I do not know.So where can I
 find the instruction.
 If there is someone know,please tell me.Thanks!


The bits in a fingerprint don't represent anything specifically.  Certain
features in a molecule will cause a particular bit to be set (you can go
from features to bits), but you can't go the reverse direction (bits to
features).  Any particular bit can theoretically represent thousands of
different features.

For a general introduction to fingerprints, see the Daylight Theory Manual:

   http://www.daylight.com/dayhtml/doc/theory/theory.finger.html

Another resource is Cheminformatics 101: Similarity from eMolecules:

  http://www.emolecules.com/doc/cheminformatics-101-molecular-similarity.php

FP2 is a slight varient of the general principles discussed in the Daylight
Manual:

   http://openbabel.org/wiki/FP2

Craig




 --
 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


--
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

Re: [Open Babel] Help: everything compile well... But no results

[Tim Vandermeersch]

Hi,

On Mon, Jun 27, 2011 at 4:03 PM, Marianne marianne.se...@epfl.ch wrote:
 Hello

 I am new to using the openbabel API and really exciting to use OB. I have an
 existing C++ program in MSVC2008, I would like to use some of the functions
 in Openbabel (Isomorphism).

 I followed the instructions on the website and built the windows-vc2008 and
 then tried to add the sample code in C++  to make test of the results first:

 --
 *#include lt;openbabel/obconversion.hgt;
 #include lt;openbabel/mol.hgt;

 using namespace std;
 using namespace OpenBabel;

 int _tmain(int argc,char **argv) {
       // Read molecule from SMILES string

       OBConversion conv;
       OBMol mol;
       conv.SetInFormat(smi);
           conv.ReadString(mol, C(Cl)(=O)CCC(=O)Cl);



       // Print out some general information

           conv.SetOutFormat(can);
       coutCanonical SMILES:
 lt;conv.WriteString(amp;mol)lt;lt;endl;
       coutlt;lt;quot;The molecular weight is quot;lt;lt;
 mol.GetMolWt();


         return 0; // exit with success
  }lt;/bgt;
 ---

 Everything compile fine but when I execute the code, I obtain

I don't see anything wrong with the code but you could try to check
the return values from some functions. OBConversion::SetInFormat,
OBConversion::SetOutFormat and OBConversion::ReadString all return
true on success. For example, if the format plugins are not found
SetInFormat will return false.

Tim

 ---
 *Canonical SMILES:
 The molecular weight is 0*

 ---

 I link this small program with
 1) Include files:
 openbabel-2.3.0\windows-vc2008\build\include
 openbabel-2.3.0\windows-vc2008\include
 openbabel-2.3.0\include

 2) Source file:
 openbabel-2.3.0\src

 3) Lib file:
 openbabel-2.3.0\windows-vc2008\build\src\Release\openbabel-2.lib


 openbabel-2.dll is added  in the exe folder.


 Help will be really appreciate. Thank you


 Marianne

 --
 View this message in context: 
 http://forums.openbabel.org/Help-everything-compile-well-But-no-results-tp3627796p3627796.html
 Sent from the General discussion mailing list archive at Nabble.com.

 --
 All of the data generated in your IT infrastructure is seriously valuable.
 Why? It contains a definitive record of application performance, security
 threats, fraudulent activity, and more. Splunk takes this data and makes
 sense of it. IT sense. And common sense.
 http://p.sf.net/sfu/splunk-d2d-c2
 ___
 OpenBabel-discuss mailing list
 OpenBabel-discuss@lists.sourceforge.net
 https://lists.sourceforge.net/lists/listinfo/openbabel-discuss


--
All of the data generated in your IT infrastructure is seriously valuable.
Why? It contains a definitive record of application performance, security 
threats, fraudulent activity, and more. Splunk takes this data and makes 
sense of it. IT sense. And common sense.
http://p.sf.net/sfu/splunk-d2d-c2
___
OpenBabel-discuss mailing list
OpenBabel-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss

Re: [Open Babel] Help with FastSearch

[Andrew Dalke]

On May 27, 2011, at 11:58 PM, A. Heifets wrote:
 I'm trying to follow http://openbabel.org/wiki/Tutorial:Fingerprints
 and obabel -H fs on my data but I have some strange digressions from
 the tutorial.

Are you interested in trying out my new chemfp package?
  http://code.google.com/p/chem-fingerprints/

It currently generates a text file, but it does support gzip'ed
files, so:

   ob2fps --FP2 DB.sdf -o DB_manual.fps.gz

should generate all the FP2 fingerprints from OpenBabel.


Then to search, make a fingerprint and send it to the
simsearch program

   ob2fs --FP2 last_mol.sdf | simsearch DB_manual.fs

(I'm working on the code to support the simpler

   simsearch --queries last_mol.sdf DB_manual.fs

)

Do note that if you give it more than a few compounds
at a time (more than the batch size, which is a tunable
parameter) then it will load all of the targets into
memory. For your data set and if I did my math right,
that will take about 1.5GB of memory for that case.


I'm curious to know how fast it is with your data set,
and if it's fast enough for you.


Andrew
da...@dalkescientific.com



--
Simplify data backup and recovery for your virtual environment with vRanger. 
Installation's a snap, and flexible recovery options mean your data is safe,
secure and there when you need it. Data protection magic?
Nope - It's vRanger. Get your free trial download today. 
http://p.sf.net/sfu/quest-sfdev2dev
___
OpenBabel-discuss mailing list
OpenBabel-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss

Re: [Open Babel] Help with FastSearch

[Chris Morley]

On 27/05/2011 22:58, A. Heifets wrote:
 I'm trying to follow http://openbabel.org/wiki/Tutorial:Fingerprints
 and obabel -H fs on my data but I have some strange digressions from
 the tutorial.

 First, I'm not convinced that the index was built correctly (although
 there were no error messages to imply that it failed).

I suspect that the problem is the size of your datafile, which I guess 
is probably about 18GB. fs index files contain displacements into this 
file but they are only 32 bits, making the maximum file size 4GB. This 
means that the maximum number of molecules might be about 2 million for 
sdf files although much greater for SMILES files.

This limitation is not documented and needs to be. There also needs to 
be a warning when preparing the index when the datafile is found to be 
too large. And, of course, the deficiency needs to be eliminated by 
changing the structure of the index file, which will not happen in the 
next release, but maybe will later.

I don't understand your difficulty with  the -s parameter being 
interpreted as SMILES instead of a file name. Possibly it could be 
because of a corrupted fs file. Can you try again with a nice small 
dataset? Thanks for the detailed reporting.

Chris

   If you look at
 the first log below [1], you can see that OpenBabel found 8.2 million
 molecules and converted 7 thousand.  Is there a way to tell why it
 didn't convert the rest.  Invalid structures?  Abort after the Expand
 Warning?  I'm also unsure why OB reports taking 39 seconds when the
 date stamps report 20 minutes.

 I tested whether the entire database was converted by pulling the last
 molecule and querying the index for it.  If the whole file was
 successfully converted, then the search would find it (or, at least,
 other molecules with Tanimoto coefficient = 1).  So, I copy and pasted
 the last molecule into a file [2].  My second problem (see log [3])
 was that OpenBabel interprets the '-s' parameter as a SMILES string,
 unlike the obabel -H fs help which says I can pass in a filename.

 Fortunately, I had a copy of the SMILES string, so I tried querying
 with that.  As you can see in log [4], no Tanimoto coefficient 1
 molecules were pulled out, so I take that to confirm my initial
 suspicions that the index didn't get all of the molecules.  This
 surprises me since, as you can see in log [2] below, the molecule
 seems fine to me; I'm not sure why it didn't get added to the index.

 My question:  what am I doing wrong?

 Thanks!

 Cheers,
 Abe


 [1] The log of making the index.  The SVN build is fresh:
 nohup bash -c date
 /home/aheifets/opt/openbabel-svn/build/bin/obabel --errorlevel 5 -isdf
 DB.sdf -ofs -ODB_manual.fs  dateindex1.log 2index1.err
 $ cat index1.*
 ==
 *** Open Babel Warning  in Expand
Alias CH3. was not chemically interpreted

 This will prepare an index of RXN_db.sdf and may take some time...
 It contains 8271991 molecules Estimated completion time 7e+02 minutes

   It took 39 seconds
 7151 molecules converted
 Fri May 27 16:36:35 EDT 2011
 Fri May 27 16:57:04 EDT 2011

 [2] The contents of last_mol.sdf:
 $ cat last_mol.sdf
 0028.mol#1
   OpenBabel05201115292D

   21 21  0  0  0  0  0  0  0  0999 V2000
 -0.2826   -1.44370. C   0  0  0  0  0  0  0  0  0  0  0  0
  0.5424   -1.44370. S   0  0  0  0  0  0  0  0  0  0  0  0
  0.5424   -0.61870. N   0  0  0  0  0  0  0  0  0  0  0  0
 -0.1721   -0.20620. C   0  0  0  0  0  0  0  0  0  0  0  0
 -0.17210.61880. C   0  0  0  0  0  0  0  0  0  0  0  0
 -0.88651.03130. C   0  0  0  0  0  0  0  0  0  0  0  0
 -0.88651.85620. O   0  0  0  0  0  0  0  0  0  0  0  0
 -1.60102.26870. C   0  0  0  0  0  0  0  0  0  0  0  0
 -2.31551.85620. C   0  0  0  0  0  0  0  0  0  0  0  0
  3.9796   -1.44370. C   0  0  0  0  0  0  0  0  0  0  0  0
  3.1546   -2.26870. C   0  0  0  0  0  0  0  0  0  0  0  0
  2.9149   -0.61870. O   0  0  0  0  0  0  0  0  0  0  0  0
  1.3674   -1.44370. O   0  0  0  0  0  0  0  0  0  0  0  0
  0.5424   -2.26870. O   0  0  0  0  0  0  0  0  0  0  0  0
 -0.6951   -2.15820. C   0  0  0  0  0  0  0  0  0  0  0  0
 -1.5201   -2.15820. C   0  0  0  0  0  0  0  0  0  0  0  0
 -1.9326   -1.44370. C   0  0  0  0  0  0  0  0  0  0  0  0
 -2.7576   -1.44370. S   0  0  0  0  0  0  0  0  0  0  0  0
 -3.5826   -1.44370. C   0  0  0  0  0  0  0  0  0  0  0  0
 -1.5201   -0.72930. C   0  0  0  0  0  0  0  0  0  0  0  0
 -0.6951   -0.72930. C   0  0  0  0  0  0  0  0  0  0  0  0
1 21  2  0  0  0  0
1  2  1  0  0  0  0
2 14  2  0  0  0  0
2 13  2  0  0  0  0
2  3  1  0  0  0  0
3  4  1  0  0  0  0
4  5  1  0  0  0  0
5  6  1  0  0  0  0
6  7  1  0  0  0  0
7  8  1  0  0  0  0
   

Re: [Open Babel] help - segmentation fault with Pybel on Mac OS x

[Geoffrey Hutchison]

 I have managed to compile OpenBabel with the python bindings on my Mac by 
 following the instructions on the OpenBabel website.  OpenBabel works fine 
 form the command line, and I can import pybel into python.  However whenever 
 I try to use pybel I get a segmentation error  For example:

Yes, I need to fix up the build script for the Mac python bindings (and 
probably other scripting bindings as well). The problem is that the 
openbabel.so build for the Python binding will link to the files in your build 
directory, not the installed libopenbabel.dylib. :-(

So what you want to do is this:

otool -L /Library/Python/2.6/site-packages/_openbabel.so

You should see something like this:
/Library/Python/2.6/site-packages/_openbabel.so:
/Users/ghutchis/Devel/build/openbabel/lib/libopenbabel.4.dylib 
(compatibility version 4.0.0, current version 4.0.0)
/usr/lib/libstdc++.6.dylib (compatibility version 7.0.0, current 
version 7.9.0)
/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current 
version 125.2.1)

Make a note of the first path (to libopenbabel.dylib) and copy that text.

Then run:

sudo install_name_tool -change [old path] /usr/local/lib/libopenbabel.4.dylib 
/Library/Python/2.6/site-packages/_openbabel.so

That should do it. If not, please let me know.

Hope that helps,
-Geoff--
Free Software Download: Index, Search  Analyze Logs and other IT data in 
Real-Time with Splunk. Collect, index and harness all the fast moving IT data 
generated by your applications, servers and devices whether physical, virtual
or in the cloud. Deliver compliance at lower cost and gain new business 
insights. http://p.sf.net/sfu/splunk-dev2dev ___
OpenBabel-discuss mailing list
OpenBabel-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss