Hi,
> I am a new user and would like to use OpenBabel in order to perform the
> following tasks on a small molecule (let's say the starting point is a
> molecule represented as a smiles string). I'm having some difficulty with
> the third step and would really appreciate some help from you vete
Hi Stuart,
I have you tried removing the space between the "-p" flag and the value,
like "-p7.4"?
Best,
Miro
--
Edelmiro Moman, PhD
Department of Molecular Medicine
Royal College of Surgeons in Ireland
POSTAL ADDRESS:
L5.08
Trinity Biomedical Sciences Institute - TBSI
Trinity College Dublin
I am using batch files from ZINC and trying to apply Lipinksi filter on it
with openbabel. I am using the official documentation. Although obabel is
able to filter on the basis of MW, HBD and HBA, it seems to failing with
logP and Rotatable bonds. If I include logP and Rotatable bond, it converts
"
Hie there,
Were you able to sort that problem out. I am having the exact same problem.
--
View this message in context:
http://forums.openbabel.org/2-3-2-release-make-test-errors-isomorphism-rotor-pytest-tp4655894p4659416.html
Sent from the General discussion mailing list archive at Nabble.c
The descriptor "ROTATABLE_BONDS" is used as an example in the online
documentation but not actually implemented in the code.
The easiest solution would be this:
https://sourceforge.net/p/openbabel/mailman/message/30659149/
Add the following item to
/"OBABEL_INSTALLATION_DIRECTORY"/data/plugindef
Try the latest development code. It contains 3 years of improvements and fixes.
On 4 August 2016 at 14:21, lester sigauke wrote:
> Hie there,
>
> Were you able to sort that problem out. I am having the exact same problem.
>
>
>
> --
> View this message in context:
> http://forums.openbabel.org/2
Dear Pascal,
Thanks you for your help. Steps 1 and 2 work fine (i.e. conversion of smiles to
3D-sdf, then removal of hydrogens), but step 3 still does not work. The smiles
of the small molecule I am using is
‘CC1=C(SC2=C1C(=N[C@H](C3=NN=C(N32)C)CC(=O)OC(C)(C)C)C4=CC=C(C=C4)Cl)C’
Can you or any
Dear Miro,
Thanks for your help and suggestion. However, removing the space between –p and
7.4 (i.e. –p7.4) changes the syntax such that –p is no longer recognized as a
real option parameter, and the command does not run.
The small molecule smiles I am using is
’CC1=C(SC2=C1C(=N[C@H](C3=NN=C(N
Thank you so much. Silicos-it solved it for me. But I think it is really
odd that they would include a function in the example of official
documentation that doesn't actually exist.
On Fri, Aug 5, 2016 at 5:42 PM, mirix [via Open Babel] <
ml-node+s957263n4659421...@n4.nabble.com> wrote:
> The des
> Can you or anyone else think of what the problem may be?
No. It would certainly help if you gave more information on what platform (OS)
you're using and the version of Open Babel.
-Geoff
--
___
> I'm trying to build ( by using SMILES) a molecule along a given vector.
> I need to grow a polymeric chain (for example) along well-determined
It's possible, although it might be easier to build the molecule, then
translate and align the resulting 3D geometry.
For example, you could take atom
> Thank you so much. Silicos-it solved it for me. But I think it is really
> odd that they would include a function in the example of official
> documentation that doesn't actually exist.
The example indicates that the SD file has a field called ROTATABLE_BOND. It’s
an example of using a property
Hi Geoff,
I'm using Open Babel 2.3.2. on a Windows 10 system.
Stuart
From: Geoffrey Hutchison [mailto:geoff.hutchi...@gmail.com]
Sent: Friday, August 05, 2016 12:40 PM
To: Stuart Ember
Cc: Pascal Muller; babel
Subject: Re: [Open Babel] Command line help for protonation
Can you or anyone else th
13 matches
Mail list logo
