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_o
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:
http
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-
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
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
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 370,00
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
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 s
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_io
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 act
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
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...
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
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
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
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 1.75
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
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.kuma
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 inst
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 (bec
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 (bec
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
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 hexadecima
ve 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 <mailto:francois.beren...@inria.fr>>:
>
> Hel
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
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
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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/DUD_ACPC_1.0_validation.tar.xz
The funny logo was kindly created by my colleague, Dr. Arnout Voet.
--
Best regards,
Francois Berenger.
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error.log
> (or 2>&1 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 <mailto:beren...@riken.jp>>:
>
> On 2/4
nd:
sort -u log | less
> - Noel
>
> On 4 February 2014 00:52, Francois Berenger 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.
>>
>>
;
> 2014-02-03 16:10 GMT+01:00 Igor Filippov <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
>
>
ere:
http://bioinformatics.oxfordjournals.org/content/26/22/2918.long
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Francois Berenger.
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Hello,
It would be nice to have one since there is a make install one
when working on the sources.
--
Best regards,
Francois Berenger.
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Take advantage of what the
ekule ***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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Could we have them in open babel in addition to Tanimoto?
--
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res,
>> the_chain,
>> res_num,
>> atom->GetX(),
>> atom->GetY(),
>> atom->GetZ(),
>> atom->GetPartialCharge(),
>>
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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Best regards,
Franco
logP prediction using the model from Wildman and Crippen (1999).
Cf. http://pubs.acs.org/doi/abs/10.1021/ci990307l
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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
---
c1ccc(cc1)C(=O)c1ccc(cc1)[C@@H](C(=O)O)C
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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
t;
>
>
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> OpenBabel-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>
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ity, but the open development platform that
> developers love is also attractive to malware creators. Download this white
> paper to learn more about secure code signing practices that can help keep
> Android apps secure.
>
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 # gi
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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