Re: [Open Babel] retain identifier with InChI conversions

[Francois Berenger]

Dear Sivani,

Maybe, put all the identifiers in a new file using shell commands:

$ obabel input.inchi -O output.smi
$ cut -f2 input.inchi > input.names

If the obabel conversion doesn't remove any line, it should be safe
to use the following unix command:

$ paste output.smi input.names > named_output.smi

Regards,
F.

On 29/06/2023 23:23, Sivani Baskaran via OpenBabel-discuss wrote:

Hello,

I am trying to generate a SMILES notation from standardized InChIs. I
have a long list of chemicals and would like to retain an identifier
in the output file like you do when parsing other conversions.

I've tried a few different ways of doing this based on the
documentation, but the identifier is never included in the output
file.

System/Version: Windows 11, CL Open Babel 3.1.1

Goal: Convert an InChI file with InChI followed by the name or a
number of a chemical to a .smi file with the SMILES and the identifier
(name/integer) for a set of chemicals.

Failed attempts:
* obabel "./substances.inchi" -O "./substances.SMI"
* obabel "./substances.inchi" -O "./substances.SMI" -n
* obabel -i inchi "./substances.inchi" -o smi -O "./substances.SMI"
* obabel -i inchi "./substances.inchi" -o smi -O "./substances.SMI" -n
* obabel -i inchi "./substances.inchi" -n -o smi -O "./substances.SMI"

Contents of "substances.inchi" (also attached)
InChI=1S/C6H4ClNO2/c7-5-1-3-6(4-2-5)8(9)10/h1-4Hname
InChI=1S/C6H6N2O2/c7-5-1-3-6(4-2-5)8(9)10/h1-4H,7H2 another, name
InChI=1S/C6H5NO3/c8-6-3-1-5(2-4-6)7(9)10/h1-4,8H3
InChI=1S/C6H5ClO2S/c7-5-1-3-6(4-2-5)10(8)9/h1-4H,(H,8,9)name-2

What I want the output to look like:
c1cc(ccc1Cl)N(=O)=O name
c1cc(ccc1N)N(=O)=O  another, name
c1cc(ccc1N(=O)=O)O  3
c1cc(ccc1Cl)S(=O)O  name-2

How can I ensure the output will also have the identifier without
resorting to having an individual InChI file for each chemical? Please
note, all my identifiers are integers, but for testing purposes I
included text string examples.

Thanks,
Sivani
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Re: [Open Babel] Converting from pdb to pdbqt

[Francois Berenger]

On 11/01/2023 08:06, Ilinca Flacau wrote:

I'm looking to convert a PDB file to a PDBQT file, and the website
lists it as a supported file format. However, in the OpenBabelGUI
(3.1.1 64 bit for windows) it does not appear to be an option. Is
there a way to do this?


Maybe this will help you:
https://github.com/ljmartin/pdb_to_pdbqt


Thank you,

Ilinca
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Re: [Open Babel] Question for Openbabbel installation with Python

[Francois Berenger]

On 10/06/2022 10:32, Quentin Delobelle wrote:

Hello,

 I am a French doctorate student in my second year of thesis and I had
some question regarding some problem for the installation of Openbabel
in Python.

 I work on molecular dynamics in the Laboratory of Theoretical
Chemistry run by Pr. Jean-Philip PIQUEMAL and would like to install
Openbabel for its utilisation in the Poltype software
(https://biomol.bme.utexas.edu/tinkergpu/index.php/Poltype:Poltype#POLTYPE_1.14).


 I would need some precision of the installation of Openbabel with
Python :

* Is it possible to configure the installation of Openbabel 2.3.0
(the one needed for poltype) with Python 3.7, and if not what version
of Openbabel and/or Python would you recommend ? (I linked a test of
Poltype when we tried to use Openbabel 3.1 in python 3.7 but it was
incompatible).

*
* How would you install Openbabel with Python bindings ?


On some Linux distributions, it is as simple as:

$ sudo apt install openbabel python3-openbabel


 Thank you for your attention.

 DELOBELLE Quentin

06.10.12.34.01

quentin3e...@hotmail.fr

 Doctorant 2ème année ED394

 Equipe Biologie et Thérapeutiques du cancer

 Centre de Recherche Saint-Antoine - Bâtiment Kourilsky, 8ème étage


 Laboratoire de Chimie Théorique

 Barre 12-13 - Campus Pierre et Marie Curie - Sorbonne Université

Envoyé à partir d’Outlook [1]


Links:
--
[1] http://aka.ms/weboutlook
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Re: [Open Babel] convert SMILE to Mol

[Francois Berenger]

On 05/05/2022 05:50, Mohammad Goodarzi wrote:

Hello guys,

It has been sometimes that I used obabel but now I cannot use it to
convert lots of molecules to mol format.

I have a MAC and I am trying to convert SMILE to Mol

I do this

obabel .smi -omol -m

This is one example that I save it into a file with format .smi
CC1=CC=C(C=C1)C(=O)N1N=C(CC1C1=CC=CO1)C1=CC=C(NS(C)(=O)=O)C=C1

but the answer is empty


Here is an example command-line session:

# obabel in.smi -O out.mol
==
*** Open Babel Warning  in WriteMolecule
  No 2D or 3D coordinates exist. Stereochemical information will be 
stored using an Open Babel extension. To generate 2D or 3D coordinates 
instead use --gen2D or --gen3D.

1 molecule converted

# cat in.smi
CC1=CC=C(C=C1)C(=O)N1N=C(CC1C1=CC=CO1)C1=CC=C(NS(C)(=O)=O)C=C1  mol1

# cat out.mol
mol1
 OpenBabel05092210342D

 30 33  0  0  0  0  0  0  0  0999 V2000
0.0.0. C   0  0  0  0  0  0  0  0  0  0  0  0
0.0.0. C   0  0  0  0  0  0  0  0  0  0  0  0
0.0.0. C   0  0  0  0  0  0  0  0  0  0  0  0
0.0.0. C   0  0  0  0  0  0  0  0  0  0  0  0
0.0.0. C   0  0  0  0  0  0  0  0  0  0  0  0
0.0.0. C   0  0  0  0  0  0  0  0  0  0  0  0
0.0.0. C   0  0  0  0  0  0  0  0  0  0  0  0
0.0.0. C   0  0  0  0  0  0  0  0  0  0  0  0
0.0.0. O   0  0  0  0  0  0  0  0  0  0  0  0
0.0.0. N   0  0  0  0  0  0  0  0  0  0  0  0
0.0.0. N   0  0  0  0  0  0  0  0  0  0  0  0
0.0.0. C   0  0  0  0  0  0  0  0  0  0  0  0
0.0.0. C   0  0  0  0  0  0  0  0  0  0  0  0
0.0.0. C   0  0  0  0  0  0  0  0  0  0  0  0
0.0.0. C   0  0  0  0  0  0  0  0  0  0  0  0
0.0.0. C   0  0  0  0  0  0  0  0  0  0  0  0
0.0.0. C   0  0  0  0  0  0  0  0  0  0  0  0
0.0.0. C   0  0  0  0  0  0  0  0  0  0  0  0
0.0.0. O   0  0  0  0  0  0  0  0  0  0  0  0
0.0.0. C   0  0  0  0  0  0  0  0  0  0  0  0
0.0.0. C   0  0  0  0  0  0  0  0  0  0  0  0
0.0.0. C   0  0  0  0  0  0  0  0  0  0  0  0
0.0.0. C   0  0  0  0  0  0  0  0  0  0  0  0
0.0.0. N   0  0  0  0  0  0  0  0  0  0  0  0
0.0.0. S   0  0  0  0  0  0  0  0  0  0  0  0
0.0.0. C   0  0  0  0  0  0  0  0  0  0  0  0
0.0.0. O   0  0  0  0  0  0  0  0  0  0  0  0
0.0.0. O   0  0  0  0  0  0  0  0  0  0  0  0
0.0.0. C   0  0  0  0  0  0  0  0  0  0  0  0
0.0.0. C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  7  1  0  0  0  0
  2  3  2  0  0  0  0
  3  4  1  0  0  0  0
  4  5  2  0  0  0  0
  5  6  1  0  0  0  0
  5  8  1  0  0  0  0
  6  7  2  0  0  0  0
  8  9  2  0  0  0  0
  8 10  1  0  0  0  0
 10 14  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  2  0  0  0  0
 12 13  1  0  0  0  0
 12 20  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 19  1  0  0  0  0
 15 16  2  0  0  0  0
 16 17  1  0  0  0  0
 17 18  2  0  0  0  0
 18 19  1  0  0  0  0
 20 30  1  0  0  0  0
 20 21  2  0  0  0  0
 21 22  1  0  0  0  0
 22 23  2  0  0  0  0
 23 24  1  0  0  0  0
 23 29  1  0  0  0  0
 24 25  1  0  0  0  0
 25 26  1  0  0  0  0
 25 27  2  0  0  0  0
 25 28  2  0  0  0  0
 29 30  2  0  0  0  0
M  END


any idea?
Thanks
Mo
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Re: [Open Babel] Run obabel with n cpu cores?

[Francois Berenger]

On 28/02/2022 05:45, Rudy Richardson wrote:

1. Is there a straightforward way to run obabel with n cpu cores?


Straightforward, I am not sure.

However, there are several ways:
- xargs and its -L option
- https://github.com/UnixJunkie/PAR
- https://github.com/UnixJunkie/pardi

If you show us the obabel command you want to use, plus an example
input file, we might give you a runable example.



2. What about obabel on GPUs?

Thanks.

-- Rudy
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Re: [Open Babel] Identical Fingerprints for three compounds

[Francois Berenger]

On 06/12/2021 22:59, Wolcott, Chris (NIH/NCI) [C] wrote:

Francois,

   I apologize upfront if I am not using the correct verbiage
(compounds, molecules, ...).  I am a software developer writing a new
web application for the project staff.  The old web application
(developed in .NET) stored 370,000+ compounds and related information
generated from oBabel 2.4 in our MongoDB database.  I did find an
error that the C#/MongoDB interface did not understand Unsigned
Integers and stored everything as signed.  Doesn't look like it was a
big problem because when the data was retrieved it was converted back
to unsigned before being passed to Tanimoto.

In the new website I am using oBabel 3.1.1 and regenerated the
information for the 370k+ compounds plus added another 30k+ compounds
from a new library we have begun to use in the labs.  The fingerprints
are generated using fp2 [32 bit unsigned arrays) via OBFingerprint.  I
then use Tanimoto for similarity analysis. It takes about 5 seconds to
compare a single compound to the 400k+ pre-generated fingerprints.

With your questions I will attempt to educate myself a little bit more
on molecular fingerprints.
Any comments, references, prayers would be appreciated.


Here is a venerable reference on molecular fingerprints:

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




Fingerprints being lossy encodings of molecules:
it is possible that different molecules end-up
with the same fingerprint.

If you use an unfolded-counted fingerprint (instead of 
folded-uncounted,

usually),
this "funny" event should occur less frequently.

Another possibility might be to use a fingerprints with more bits.
Which fingerprint are you using by the way?

Regards,
F.



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Re: [Open Babel] Identical Fingerprints for three compounds

[Francois Berenger]

Dear Chris,

Fingerprints being lossy encodings of molecules:
it is possible that different molecules end-up
with the same fingerprint.

If you use an unfolded-counted fingerprint (instead of folded-uncounted, 
usually),

this "funny" event should occur less frequently.

Another possibility might be to use a fingerprints with more bits.
Which fingerprint are you using by the way?

Regards,
F.

On 06/12/2021 01:37, Wolcott, Chris (NIH/NCI) [C] via OpenBabel-discuss 
wrote:

Is it expected or is there any easy explanation why three different
smiles create the same fingerprint?  Are compounds come from the same
synthetic library.

1st Compound

   Canonical Smile:
O=C1N[C@H]2C[C@H](N(C2)Cc2ccncc2)C(=O)N2CCO[C@@H](C2)CN(C[C@H]2O[C@@H](C1)[C@H](O)[C@@H]2O)C(=O)C1CC1


   InchiKey:  FQBFZRAABMTECZ-BLZXGSKESA-N

   Formula:   C27H37N5O7

   Mol Weight: 543.612

2nd Compound

   Canonical Smile:
O=C1N[C@@H]2CN([C@@H](C2)C(=O)N2CCO[C@@H](C2)CN(C[C@H]2O[C@@H](C1)[C@H](O)[C@@H]2O)C(=O)CC(C)(C)C)Cc1ccncc1


   InchiKey:  MGQQDDGDXATMAK-QEHADNFDSA-N

   Formula:   C29H43N5O7

   Mol Weight: 573.681

3rd Compound

   Canonical Smile:
O=C1N[C@H]2C[C@H](N(C2)Cc2ccncc2)C(=O)N2CCO[C@@H](C2)CN(C[C@H]2O[C@@H](C1)[C@H](O)[C@@H]2O)C(=O)C


   InchiKey:  VCBCUIGRWFWUDB-KDTKDTIDSA-N

   Formula:   C25H35N5O7

   Mol Weight: 517.575

The Fingerprint generated for all three compounds is the same:

   8399392, 537051136, 393233, 134218496, 2415919137, 8388608,
1073741824, 805323777,

   168820760, 931135619, 941393456, 1073741856, 513, 31465472,
33554432, 270532616,

   1016076, 2151158792, 25698305, 2516617274, 1073983488, 2097156,
16843232, 2097152,

   536875016, 0, 2097168, 1835200, 2214659584, 1065216, 16808960,
491586

Using OpenBabel 3.1.1 via the PHP extension
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Re: [Open Babel] Question regarding your software

[Francois Berenger]

On 06/10/2021 05:38, Evgeny Akkuratov wrote:

Good afternoon,

I have a question regarding your software.
I have two datasets of chemical molecules and I would like to know
whether there is any similar molecule in dataset #2 for the each
molecule from dataset #1. I was planning to use MolPrint2D score to
judge whether they are similar or not however I find out that I can do
it in Open Bable. Can I kindly ask you to guide me how to do it?
Both datasets are in sdf format.


Something like this should work; I assume you have access to a UNIX-like 
command line.


# convert both files to canonical SMILES
obabel f1.sdf -O f1.can
obabel f2.sdf -O f2.can
# only keep the SMILES and sort them
cut -f1 f1.can | sort > f1_sorted.can
cut -f1 f2.can | sort > f2_sorted.can
# find the intersection between the two sets of canonical SMILES
comm -12 f1_sorted.can f2_sorted.can

Regards,
F.


Best,
Evgeny

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Re: [Open Babel] Library not loaded

[Francois Berenger]

On 13/08/2021 00:29, Chris Swain via OpenBabel-discuss wrote:

Hi,

I’m sure I’ve seen mention of this error in the past but I can’t find 
it.


An iBabel user has installed openbabel using home-brew on a Mac and
they report this error

Dyld: Library not loaded: 
Usr/local/opt/boost/lib/libbost_iostreams-mt.dylib

Referenced from :/usr/local/bin/obabel
Reason image not found
Abort trap: 6

Does this need to be installed separately?


The formula doesn't mention any boost-related _direct_ dependencies:

cf.

https://github.com/Homebrew/homebrew-core/blob/f225ce6dce2cab361b835c5c7471405a05a83a67/Formula/open-babel.rb

If brew can install the missing dependency (that was detected at 
runtime),

then the formula should be corrected.


Cheers,

Chris

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Re: [Open Babel] pdb to mol2 bonding

[Francois Berenger]

Dear Richard,

Others might know more, but as a workaround you might try UCSF Chimera 
in order

to do the PDB to MOL2 conversion.

Regards,
F.

On 09/07/2021 19:52, Richard Gillilan wrote:

Hello all,

I'm actually back to this list after nearly twenty years. Nice to see
this package is still actively maintained!

It will take me a while to get back up to speed, but my needs are the
same as they were back then when I published some docking work using
the code:

I use openbabel to convert pdb files to mol2 adding bond orders and
protonation states for proteins. My code then uses the bond orders to
assign forcefield parameters for simulation purposes.

I did a preliminary conversion of lysozyme:  obabel -p 7.0 -ipdb
6lyz_no_wat.pdb -omol2 >! test.mol2

Seems like there are a number of incorrect bonds formed. I have a very
old note that openbabel often failed to assign carbonyl oxygens a
double bond. In principle, knowledge of the amino acid 3-letter code
should solve the bonding problems.

Anyone worked on this aspect of openbabel in the past?

Richard Gillilan
HP-Bio/BioSAXS
Cornell High Energy Synchrotron Source
Ithaca, NY






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Re: [Open Babel] Converting SDF to PDBQT using OpenBabel

[Francois Berenger]

On 17/04/2021 18:52, Roy Batty wrote:

I want to convert several molecules from sdf format to pdbqt using
OpenBabel.


obabel input.sdf -O output.pdbqt

PS: though I am not sure autodock will be able to read those
without any error...


However, I can't find pdbqt format neither in the output format
options nor in the input.

I tried reinstalling MGLTools, as it has AutoDock, but the issue
remains.

I would really appreciate any help.

Kind regards, Roy
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[Open Babel] If someone know how to migrate en OpenBabel-2.0 cmake project to OpenBabel-3.0.0 ...

[Francois Berenger]

Your help would be welcome:

https://github.com/gertthijs/stripper/issues/1

I naively tried to replace -2.0 everywhere to -3.0.0
in the file cmake/modules/FindOpenBabel2.cmake, but that doesn't cut it.

Regards,
F.

PS: honestly, whenever I try to do something with cmake, it never 
works...

¯\_(ツ)_/¯


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Re: [Open Babel] Openbabel Mac install

[Francois Berenger]

On 23/03/2021 07:11, Brian Levandowski wrote:

Hello babel support team,

I installed openbabel 3.1.1_1 through homebrew on MacOS (catalina).
When I try to use any babel command such as "babel -h" the output is
"zsh: command not found: babel"


Try obabel instead of babel.


Thank you for the help,
Brian
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Re: [Open Babel] OpenBabel-discuss Digest, Vol 167, Issue 10

[Francois Berenger]

Maybe try this:

convert the SDF file to SMILES.

$ obabel input.sdf -O output.smi

Then, add the names in the SMILES file with some unix commands (provided 
you
have the list of names in the same order than the molecules in your SDF 
file,

then convert back to SDF).
Note that this will loose the 3D coordinates, if you have them in the 
input SDF file.


Then, back to sdf:

$ obabel output_w_names.smi -O input_w_names.sdf

I think I have done something like this in the past,
and openbabel was placing the name as the first line in each
SDF block (which is what I expect, and is more useful
than a name property with I don't know what tag someone gave it,
and tag name always changing depending on which software generated the 
SDF file)...


Regards,
F.

On 16/04/2020 03:13, Bennion, Brian via OpenBabel-discuss wrote:

More context.  I have 500K ligands in a single sdf file.  The names
for each ligand was found after the sdf file was created.  I would
like to either replace the label at the top with the appropriate title
or add to a property value.  Unfortunately, I and others at LLNL have
never been able to compile python bindings to obabel.
I am not familiar with pybabel but can look at it.
Due to the source of the sdf files RDKit chokes on about 50% of them
so manipulation is not easy there.

Brian


-Original Message-
From: openbabel-discuss-requ...@lists.sourceforge.net

Sent: Tuesday, April 14, 2020 6:55 AM
To: openbabel-discuss@lists.sourceforge.net
Subject: OpenBabel-discuss Digest, Vol 167, Issue 10

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Today's Topics:

   1. Re: Operating on multi molecule sdf files (Geoffrey Hutchison)
   2. Structure size scaling in 2D depiction (Bakary N'tji Diallo)


--

Message: 1
Date: Tue, 14 Apr 2020 09:53:59 -0400
From: Geoffrey Hutchison 
To: "Bennion, Brian" 
Cc: "openbabel-discuss@lists.sourceforge.net"

Subject: Re: [Open Babel] Operating on multi molecule sdf files
Message-ID: 
Content-Type: text/plain; charset="utf-8"

After reading the docs I think that adding individual properties to 
individual molecules in a multi molecule sdf files is probably not 
possible?
I have an sdf file with 500k molecules and I would like to add a 
little unique identifier that isn?t a supported descriptor to each 
molecule and then write out the altered sdf file.


Personally,  I'd do this with a quick Python script, since a Pybel
molecule has a data property:
https://open-babel.readthedocs.io/en/latest/UseTheLibrary/Python_PybelAPI.html#pybel.Molecule.data


-Geoff

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Message: 2
Date: Mon, 13 Apr 2020 21:07:56 +0200
From: "Bakary N'tji Diallo" 
To: "openbabel-discuss@lists.sourceforge.net mailinglist"

Subject: [Open Babel] Structure size scaling in 2D depiction
Message-ID:

Content-Type: text/plain; charset="utf-8"

Dear all,

I have the following depiction for a structure file. As you can see
the first compound is scaled up.

[image: image.png]
Is there way to maintain a uniform structure size.
I am using the following command: "obabel structure.smi -O out.svg -xC 
-xe -d"


Thanks
Best regards
--

Bakary N?tji DIALLO

PhD Student (Bioinformatics) ,
Research Unit in Bioinformatics (RUBi) 

Mail: diallobaka...@gmail.com |  Skype: diallobakary4

Tel:  +27798233845 | +223 74 56 57 22 | +223 97 39 77 14
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Re: [Open Babel] How to convert inchikey to other formats?

[Francois Berenger]

On 23/03/2020 12:21, Peng Yu wrote:

Hi,

I don't find how to take inchikey input and convert it to other 
formats.


You should read about what really is an inchikey:

https://en.wikipedia.org/wiki/International_Chemical_Identifier#InChIKey

While you are at it, maybe you can read about what is a one way
hash function.

PS: there is an unpractical way though: compute the inchikey of all 
possible

molecules, until you hit the key that you were looking for.


http://openbabel.org/docs/current/FileFormats/Overview.html

I got the following error. Could anybody show me the correct way to
make the conversion? Thanks.

$ obabel -iinchikey <(echo GFAUNYMRSKVDJL-UHFFFAOYSA-N) -o smiles -O 
/dev/stdout

Invalid input format
Open Babel 3.0.0 -- Oct 27 2019 -- 13:55:24
Usage:
obabel [-i]  [-o] -O 
[Options]

Try  -H option for more information.



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Re: [Open Babel] obspectrophore

[Francois Berenger]

On 14/03/2020 23:24, Chris Swain via OpenBabel-discuss wrote:

One of the tools is to calculate spectrophores

Described in details here.

https://open-babel.readthedocs.io/en/latest/Fingerprints/spectrophore.html

I’ve tried this and this gives the following output

ID_02 1.49538 2.12033 1.7562 3.27156 4.92821 3.76685 3.61875
3.729173.76939 6.28893 6.30063 3.72489 2.83871 2.85013 10.5265 10.5304
15.5199 13.969411.3836 20.0744 16.3271 16.501 20.8502 15.5603 28.4983
31.3098 29.2032 24.146220.224 20.7701 6.87111 23.1492 21.7416 26.0935
9.92935 25.4605 0.9371 0.873542.92003 2.92001 0.822645 0.846267
0.396603 3.15673 1.981910.922839 0.768973 3.02225
ID_03 6.84965 6.85544 6.72281 6.48777 12.8201 7.05141 6.9188
10.509210.2884 13.2464 13.4809 10.6597 10.729 8.80592 12.2808 12.2669
19.0122 10.959 10.9159 18.9153 18.8156 17.8466 19.1632 15.8986 77.1334
88.843 73.3087 63.837371.6235 62.2845 31.3721 64.6271 66.3996 70.8296
43.6268 77.404 1.96881 1.815534.38761 4.86641 2.14023 2.06807 1.30172
4.25882 4.07622 2.78876 2.91516 4.7208
ID_04 2.09153 2.57848 3.0399 5.28119 7.0974 6.31162 4.99044
5.058176.08685 7.89896 9.2356 6.84507 1.6726 3.06771 11.507 11.5015
4.95658 5.794594.36526 14.4005 10.6234 6.90563 6.90318 11.5636 45.1809
70.8286 70.3362 87.037378.0632 85.3583 54.6045 87.5461 82.7769 101.74
94.1001 97.7448 1.58159 1.825885.28398 5.281 2.00404 2.0139 1.04747
5.43697 4.41786 2.00631 1.78719 4.85954

How does one use/search using these fingerprints?


Maybe you can ask the authors to be sure:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3083603/pdf/1758-2946-3-S1-P7.pdf

As a first guess, maybe treat them as a vector of floats and use 
Tanimoto.

Tani(X,Y) = sum(min(x_i, y_i)) / sum(max(x_i, y_i))


Cheers
Chris
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Re: [Open Babel] Other ob tools

[Francois Berenger]

On 03/03/2020 17:46, Noel O'Boyle wrote:

Well, I don't really agree. They could just add it to obabel in the
first place and get the feedback from the development version. The
problem is that people find it easier to add new executables, rather
than spending a bit of time figuring out how to add a plugin for
obabel.


I once worked somewhere where there was a very big chemoinformatics 
executable

able to do many things; instead of having a nice library used by several
rather simple programs.

Trying to do any task using the big executable was a nightmare in terms 
of

finding the long list of options and values that you had to pass to it.

The one big program/executable approach is against the Unix philosophy 
of

having rather simple programs that can be combined easily.

For those interested in the Unix philosophy and its not so trivial many 
implications,

there is an interesting book:
---
Raymond, E. S. (2003). The art of Unix programming. Addison-Wesley 
Professional.

---

Regards,
F.


Regards,

- Noel

On Tue, 3 Mar 2020 at 07:52, Chris Swain  wrote:


Hi,

It is clear that a number of the obtools have been incorporated into
obabel, however I’m not sure they are all suitable for every file
type.

It is perhaps better to think of obtools as way to develop new tools
that others can hopefully try out and provide feedback. Tools that
are regularly used and prove to be robust and useful could then be
rolled into obabel.

And no I don’t know of a process to do this.

Cheers,

Chris

On 2 Mar 2020, at 20:11, Noel O'Boyle  wrote:

It's not a popular opinion, but I think we should have a single
robust executable. I've never used any of the others, and they are
mostly untested.

On Sat, 29 Feb 2020, 18:21 Chris Swain via OpenBabel-discuss,
 wrote:
Hi,

I’m working on an update to iBabel, and was hoping to clear out
the tools tab particularly as I’m not sure if some are now
supported with OpenBabel 3.0

Looking through the directory of openbabel tools that are installed
we have

obconformer  equiv to  obabel --conformer
obdistgen  (generate rough 3D coordinates) now use obabel --gen3D
obenergy  equiv to obabel  --energy
obfit equiv to --obabel --align
obfitall not sure what this is?
obgen   equiv to obabel --gen3D (fastest --ff MMFF94s)
obgrep equiv to obabel structure searching
obminimize  equiv to obabel --minimize (--ff MMFF94s --steps 1000
--sd)
obmm apparently this is a this is a 'full featured' MM program but
may not be generally useful
obprobe (create electrostatic probe grid)
obprop (print standard molecular properties), would be more useful
if we could get individual properties,e.g. obabel —props
  (MW LogP TPSA HBA  HBD RBC)
obrms (Calculate the heavy-atom RMSD between two chemically
identical structures) perhaps this should be an obabel option?
obrotamer (generate conformer/rotamer coordinates, not minimized)
better to use —conformer?
obrotate  (batch-rotate dihedral angles matching SMARTS patterns)
obspectrophore (calculate spectrophore)
obsym (detect 3D point group symmetry, only cif files?) sounds like
it is to deprecated
obtautomer (enumerate tautomer SMILES and canonical tautomer SMILES)
obthermo (extract the thermochemistry for a molecule, what file
format is needed?)

Any insights very welcome,

Cheers,

Chris

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[Open Babel] if you are an Open Babel user in Japan and you are free between Mar. 19-20 2020

[Francois Berenger]

Dear Open Babel users,

You might consider joining "The 8th French-Japanese Workshop
on Computational Methods in Chemistry" (FJCMC2020).

Date:  Mar. 19-20, 2020
Venue: 100th Anniversary Hall of Engineering Faculty,
   Kurokami South Campus, Kumamoto University.

Website: https://www.chem.kumamoto-u.ac.jp/~frjp2020/index.html

Here is an excerpt of a message from the local organizer, Dr. Sugimoto:
---
For the lecture titles, see

https://www.chem.kumamoto-u.ac.jp/~frjp2020/invited-speakers.html

Now we have 33 invited speakers including 6 young researchers.

Herein, we have 6 female and 25 male speakers. Although the balance is 
not still good, please understand that

originally I had invited 6 more female researchers.
---

The lecture hall has more than 200 seats, so there is certainly room for
interested people.

Best regards,
Francois.


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Re: [Open Babel] Error to load pybel

[Francois Berenger]

On 10/11/2019 08:51, Matthew Swain via OpenBabel-discuss wrote:

The homebrew open-babel package requires python also from homebrew,
which somehow has been uninstalled (did you run “brew uninstall
--ignore-dependencies python”?). I presume “brew install python” will


More precisely:
```
brew install python3
```

according to our Travis script:

https://github.com/rdkit/homebrew-rdkit/blob/master/.travis.yml

Regards,
F.


bring it back. Open Babel from homebrew won’t work with the separate
python 3.8 you appear to also have installed.



On 6 Nov 2019, at 16:30, Peng Yu  wrote:

Hi,

I got the following error to load pybel in openbabel python module. 
Does anybody know what is wrong? Thanks.


$ brew info open-babel
open-babel: stable 3.0.0 (bottled), HEAD
Chemical toolbox
https://openbabel.org
/usr/local/Cellar/open-babel/3.0.0 (328 files, 19.5MB) *
 Poured from bottle on 2019-11-02 at 02:42:41
From: 
https://github.com/Homebrew/homebrew-core/blob/master/Formula/open-babel.rb

==> Dependencies
Build: cmake ✘, pkg-config ✔, rapidjson ✘, swig ✔
Required: cairo ✔, eigen ✔, python ✘
==> Options
--HEAD
Install HEAD version
$ pip3 install -U openbabel
Requirement already up-to-date: openbabel in 
/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages 
(2.4.1)

$ python3
Python 3.8.0a3 (v3.8.0a3:9a448855b5, Mar 25 2019, 17:05:20)
[Clang 6.0 (clang-600.0.57)] on darwin
Type "help", "copyright", "credits" or "license" for more information.

from openbabel import pybel

Traceback (most recent call last):
 File "", line 1, in 
 File 
"/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/openbabel.py", 
line 15, in 

   import _openbabel
ImportError: 
dlopen(/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/_openbabel.cpython-38m-darwin.so, 
2): Library not loaded: 
/usr/local/opt/open-babel/lib/libopenbabel.5.dylib
 Referenced from: 
/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/_openbabel.cpython-38m-darwin.so

 Reason: image not found


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Re: [Open Babel] tanimoto coefficient for obspectrophores

[Francois Berenger]

On 23/05/2019 22:07, Moritz Beber wrote:

Just a comment that Python supports sets which make this more
efficient and easier to read:

a = set(list1)

b = set(list2)

intersection = a & b

union = a | b

len(intersection) / float(union)


Inspired by your contribution, this is probably faster (because you
don't need to compute the set union):

---
s1 = set(list1)
s2 = set(list2)
intersection = s1 & s2
a = len(s1)
b = len(s2)
c = len(intersection)
return (c / (a + b - c))
---

Note that a and b can be computed once and for all for each molecule, if 
required

by performance constraints.

Regards,
F.


On Tue, 2019-05-21 at 15:15 +0200, Bakary N'tji Diallo wrote:


Hello there,
Hope you are doing very well.

I would like to compute tanimoto similarity using obspectrophore
fingerprint. I have found a formula on the net for the tanimoto
similarity:
def tanimoto(list1, list2):

#list1 and list2 #spectrophore fingerprint
intersection = [common_item for common_item in list1 if
common_item in list2]
return float(len(intersection))/(len(list1) + len(list2) -
len(intersection))

For now, I tested this using the same compound as input and the
result is 1.
Just wanted to confirm this is the right formula for Tanimoto
coefficient for spectrophore.

Thanks
Best regards--

Bakary N’tji DIALLO

PhD Student (Bioinformatics) [1], Research Unit in Bioinformatics
(RUBi) [2]

Mail: diallobaka...@gmail.com |  Skype: diallobakary4

Tel:  +27798233845 | +223 74 56 57 22 | +223 97 39 77 14

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Re: [Open Babel] tanimoto coefficient for obspectrophores

[Francois Berenger]

On 23/05/2019 22:07, Moritz Beber wrote:

Just a comment that Python supports sets which make this more
efficient and easier to read:

a = set(list1)

b = set(list2)

intersection = a & b

union = a | b

len(intersection) / float(union)


Inspired by your contribution, this is probably faster (because you
don't need to compute the set union):

---
s1 = set(list1)
s2 = set(list2)
intersection = s1 & s2
a = len(s1)
b = len(s2)
c = len(intersection)
return (c / float(a + b - c))
---

Note that a and b can be computed once and for all for each molecule, if 
required

by performance constraints.

Regards,
F.


On Tue, 2019-05-21 at 15:15 +0200, Bakary N'tji Diallo wrote:


Hello there,
Hope you are doing very well.

I would like to compute tanimoto similarity using obspectrophore
fingerprint. I have found a formula on the net for the tanimoto
similarity:
def tanimoto(list1, list2):

#list1 and list2 #spectrophore fingerprint
intersection = [common_item for common_item in list1 if
common_item in list2]
return float(len(intersection))/(len(list1) + len(list2) -
len(intersection))

For now, I tested this using the same compound as input and the
result is 1.
Just wanted to confirm this is the right formula for Tanimoto
coefficient for spectrophore.

Thanks
Best regards--

Bakary N’tji DIALLO

PhD Student (Bioinformatics) [1], Research Unit in Bioinformatics
(RUBi) [2]

Mail: diallobaka...@gmail.com |  Skype: diallobakary4

Tel:  +27798233845 | +223 74 56 57 22 | +223 97 39 77 14

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Re: [Open Babel] << ECFP4 in OpenBabel >>

[Francois Berenger]

On 07/12/2018 19:22, Noel O'Boyle wrote:

An ECFP4 implementation could use a single bit or a million bits. The
actual information that is being encoded is an element of a set of
size of more than billions (I forget the details). So it's hashed to
something manageable. The shorter the length, the more bit collisions
(everything will collide with a single bit, for example). Open Babel
uses 4096. I would regard this as the minimum.


Just FYI, in rdkit, 2048 bits is the default length.


When converting from hex, you could concatenate the binaries. Or you
could use pybel which doesn't the conversion for you:

pybel.readstring("smi", "c1c1C(=O)Cl").calcfp("ecfp4").bits

[556, 1348, 1509, 1547, 1993, 2078, 2089, 2378, 2487, 2531, 2700,
3017, 3023, 3117, 3324, 3395, 3599, 4036]

These are the bits that are set. If you use "len", you can get the
number of them.

Regards,

- Noel

On Fri, 7 Dec 2018 at 09:49, I. Camps  wrote:


@Geoff

I use Python.

I already made an script to convert hex to binary, but as I wrote
previously, the fingerprint (fp) from OpenBabel is in the form of a
set of hex numbers. I converted each one to binary and then
concatenate all the binaries. Is it that okay?

If it is okay, the second problem is that the fp is much longer
(6040) than the RDKit (1024). I really do not understand the
"folded" issue because any read about ECFP4 talk about a 1024 bit
string and not higher.

@Francois

I certainly will take a look!

thank you both.

Camps

On Fri, Dec 7, 2018 at 1:59 AM Geoffrey Hutchison
 wrote:

Using OpenBabel, I got a file with the information that the
fingerprint is a 6040 bits set and got hexadecimal numbers.
Using PyBioMed, which is based in RDKIT, I got a binary string of
1024 bits, very different from that obtained with OpenBabel.

The RDKit binary string will be "folded" down to 1024 bits, so of
course they will be very different bit strings.

2-) How can I convert the ECFP4 obtained from OpenBabel in
hexadecimal form to a bit string with only ones and zeros?

What programming language are you using? For example in Python, a
quick search on StackExchange:
https://stackoverflow.com/questions/1425493/convert-hex-to-binary
[1]

Hope that helps,
-Geoff

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Re: [Open Babel] << ECFP4 in OpenBabel >>

[Francois Berenger]

On 07/12/2018 02:43, I. Camps wrote:

Dear all,

I am trying to compute the ECFP4 fingerprint for a library of
molecules. The molecules are carbon nanotubes functionalized with -OH
group.

Using OpenBabel, I got a file with the information that the
fingerprint is a 6040 bits set and got hexadecimal numbers.

Using PyBioMed, which is based in RDKIT, I got a binary string of 1024
bits, very different from that obtained with OpenBabel.

My questions are:
1-) How good and reliable is the ECFP4 calculated with OpenBabel?

2-) How can I convert the ECFP4 obtained from OpenBabel in hexadecimal
form to a bit string with only ones and zeros?


I have some code for rdkit's ECFP4 here:
https://github.com/UnixJunkie/consent/blob/master/bin/lbvs_consent_ecfp4.py

And some other code using open-babel, but it is for the MACCS 
fingerprint, there:

https://github.com/UnixJunkie/consent/blob/master/src/ob_maccs.cpp

Regards,
F.


I need the string in 1´s and 0´s because I will used latter to
calculated the Shannon entropy and the BiEntropy.

[]'s,

Camps

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Re: [Open Babel] generating conformers with open babel

[Francois Berenger]

On 05/03/2016 02:57 PM, Maciek Wójcikowski wrote:
> Hello,
>
> I think that Confab is available only in current development branch.
> Check "obabel -L confab" to see if it's there.

It's not there. Thanks for the advice.

> If not then you'd have to
> use conda or compile it yourself.
>
> 
> Pozdrawiam,  |  Best regards,
> Maciek Wójcikowski
> mac...@wojcikowski.pl <mailto:mac...@wojcikowski.pl>
>
> 2016-05-03 12:14 GMT+02:00 Francois Berenger <francois.beren...@inria.fr
> <mailto: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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-- 
Regards,
Francois.
"When in doubt, use more types"

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[Open Babel] generating conformers with open babel

[Francois Berenger]

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] export a MACCS FP as a string

[Francois Berenger]

On 05/03/2016 12:07 AM, Leonardo Lazzaro wrote:
> On 2016-05-02 11:46, Francois Berenger wrote:
>> Hello,
>>
>> Using open babel, would it be possible to extract
>> a MACCS fingerprints as a string of 0s and 1s ?
>>
>> Thanks,
>> F.
>>
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>
> Hello,
>
> how are you using open babel?

 From the command line usually.

> with python is pretty easy to do it, here is an example:

Thanks a lot for the example! I will test it and probably adapt it
to my needs.

> def fpt_to_binary(mol):
>  # mol is an open babel molecule object
>  fps=mol.calcfp(fptype='MACCS').bits
>  temp=list('0' * 166)
>  for item in fps:
>  temp[item - 1]='1'
>
>  bitstring=''.join(reversed(temp))
>
>  return int(bitstring, 2)
>

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[Open Babel] export a MACCS FP as a string

[Francois Berenger]

Hello,

Using open babel, would it be possible to extract
a MACCS fingerprints as a string of 0s and 1s ?

Thanks,
F.

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Re: [Open Babel] running Open Babel in parallel / distributed mode

[Francois Berenger]

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] running Open Babel in parallel / distributed mode

[Francois Berenger]

On 02/04/2014 08:09 PM, Maciek Wójcikowski wrote:
 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:

Here are the most useful PAR options:

# par
-i or -c is mandatory
Usage: parallel.py [options] {-i | -c} ...
Execute commands in a parallel and/or distributed way.

Options:
   -h, --helpshow this help message and exit
   -c SERVER_NAME, --client=SERVER_NAME
 read commands from a server instead of a file
 (incompatible with -i)
   -i COMMANDS_FILE, --input=COMMANDS_FILE
 /dev/stdin for example (incompatible with -c)
   -o OUTPUT_FILE, --output=OUTPUT_FILE
 log to a file instead of stdout
   -s, --server  accept remote workers
   -v, --verbose enable progress bar
   -w NB_LOCAL_WORKERS, --workers=NB_LOCAL_WORKERS
 number of local worker threads, must be = 0, 
default
 is number of detected cores, very probably 0 if 
your
 OS is not Linux

The biggest difference I see is that parallel is a GNU project
and is packaged for several Linux distributions; so it can
be installed automatically. PAR could probably be packaged
as an easy_install package for Python.

It would be nice to see a benchmark of PAR versus GNU parallel.

Since I am the author of PAR, I don't switch to another software
because I can add features in mine as I wish. :)

 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 mailto:mac...@wojcikowski.pl


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

Re: [Open Babel] running Open Babel in parallel / distributed mode

[Francois Berenger]

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

 --
 Best regards,
 Francois Berenger.

 
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[Open Babel] Tversky_ref and Tversky_db

[Francois Berenger]

Could we have them in open babel in addition to Tanimoto?

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[Open Babel] pytest_kekule (Failed)

[Francois Berenger]

I'm on the HEAD:

---
# git log
commit 3d60db928b06ed39520943cb41d3b7a36daca6ac
Author: Geoff Hutchison geoff.hutchi...@gmail.com
Date:   Sun Feb 2 13:28:08 2014 -0500

 Update aromatic rules to consider formal charges.

 Patch contributed by Roger Sayle via e-mail list.
---

143/143 Test #143: pytest_kekule ***Failed  Error 
regular expression found in output. Regex=[FAIL]  0.39 sec

99% tests passed, 1 tests failed out of 143

Total Test time (real) =  47.26 sec

The following tests FAILED:
 143 - pytest_kekule (Failed)
Errors while running CTest

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[Open Babel] Are the pqr lines created by Open Babel in fixed format?

[Francois Berenger]

I'd like to know if I can parse them in my software almost like regular 
PDB lines (i.e. assuming a fixed format for each field).

Example of such lines:
---
ATOM  1  C1  0 A   1   8.389   8.410  -2.139 -0.1247\
1.700  C
---

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[Open Babel] count polar and non polar atoms

[Francois Berenger]

Dear list,

I have a bunch of .mol2 files.

I would like to count the number of atoms in each file
as: total number of atoms, number of polar atoms,
number of non polar atoms.

Is there a way to do this rather easily with Open Babel?

Thanks a lot,
Francois.

PS: I am not a chemist

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Re: [Open Babel] Can we just copy the compiled files to another account ?

[Francois Berenger]

On 10/30/2013 07:42 PM, Maciek Wójcikowski wrote:
 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 mailto:mac...@wojcikowski.pl


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

 Greetings,

 I compiled openbabel with python binding and I have 3 account on a HPC
 cluster.

Honestly, to deploy things in a cluster, you should rather use
the packaging system of your Linux distro.

If you are really forced to work with the source code
of something, try to create the binary .rpm or .deb from
the sources in order to deploy that instead.

 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] OpenBabel 2.3.2 and OS X 10.9

[Francois Berenger]

On 10/30/2013 10:04 PM, Hans De Winter wrote:
 Hi all,

 has anyone already has experience with compiling OpenBabel 2.3.2 under
 OS X 10.9 (Maverick)?

Isn't Open Babel available under homebrew for OS X?

https://github.com/mxcl/homebrew

 I tried it (after installing the XCode and Developer tools, as well as
 cmake and pkg-config from Homebrew) and got the following:

 In file included from
 /usr/local/src/openbabel-2.3.2/include/openbabel/alias.h:19:
 /usr/local/src/openbabel-2.3.2/include/openbabel/shared_ptr.h:25:14:
 fatal error: 'tr1/memory' file not found
  #include tr1/memory
   ^
 1 error generated.

 Any clues?

 Thx,
 Hans




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Re: [Open Babel] OpenBabel 2.3.2 and OS X 10.9

[Francois Berenger]

On 10/31/2013 09:40 AM, Francois Berenger wrote:
 On 10/30/2013 10:04 PM, Hans De Winter wrote:
 Hi all,

 has anyone already has experience with compiling OpenBabel 2.3.2 under
 OS X 10.9 (Maverick)?

 Isn't Open Babel available under homebrew for OS X?

 https://github.com/mxcl/homebrew

It is!

https://github.com/mxcl/homebrew/blob/master/Library/Formula/open-babel.rb

 I tried it (after installing the XCode and Developer tools, as well as
 cmake and pkg-config from Homebrew) and got the following:

 In file included from
 /usr/local/src/openbabel-2.3.2/include/openbabel/alias.h:19:
 /usr/local/src/openbabel-2.3.2/include/openbabel/shared_ptr.h:25:14:
 fatal error: 'tr1/memory' file not found
   #include tr1/memory
^
 1 error generated.

 Any clues?

 Thx,
 Hans




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[Open Babel] mol2 generation partial charges model bug

[Francois Berenger]

On 09/18/2013 12:32 PM, Geoffrey Hutchison wrote:
 What is the default model used to compute the partial charges?

 Gasteiger. The mol2 output actually will say this.

 Is there a way to control which one to use?


 Of course:

 obabel --partialcharge MMFF94 …

 obabel -L charges # gives a list of the installed charge models

 Hmm, this needs to go into the next documentation update.

I confirm the output files always contain USER_CHARGES
instead of the actual charge model that was asked to Open Babel.

This is a bug, it doesn't respect the mol2 file format.

I used commands such as those:
obabel input.mol2 -Ooutput.gasteiger.mol2 --partialcharge gasteiger
obabel input.mol2 -Ooutput.mmff94.mol2 --partialcharge mmff94
obabel input.mol2 -Ooutput.qeq.mol2 --partialcharge qeq
obabel input.mol2 -Ooutput.qtpie.mol2 --partialcharge qtpie

I use Open Babel 2.3.0 -- Dec 17 2011 -- 16:15:10
from Ubuntu's package:
ii  openbabel 2.3.0+dfsg-3ubuntu3

Regards,
F.


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[Open Babel] mol2 generation partial charges model

[Francois Berenger]

Hello,

What is the default model used to compute the partial charges?

Is there a way to control which one to use?

For example:
babel -isdf toto.sdf -omol2 toto.mol2 -ff SOMETHING

Thanks,
F.

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