el import openbabel" instead, I get a different
error: "ImportError: cannot import name 'openbabel'"
Il giorno gio 2 apr 2020 alle ore 12:19 Thomas ha
scritto:
> Hi there,
> I'm trying to compile the latest openbabel 3 on my Ubunu 18.04 machine
> (at present only openbabel 2
I've managed to build openbabel 3 with bindings to python 3 on a local
install. Everything went smooth.
This is my cmake command:
cmake ../openbabel-3.0.0
-DCMAKE_INSTALL_PREFIX=~/WORKSPACE/OpenBabel/openbabel-3.0.0_INSTALL
-DPYTHON_BINDINGS=ON -DRUN_SWIG=ON
Still, after setting the PYTHONPATH:
.
Thank you
Il giorno mer 22 feb 2023 alle ore 11:12 Andrew Dalke <
da...@dalkescientific.com> ha scritto:
> On Feb 21, 2023, at 19:23, Thomas wrote:
> > Is it possible to get SMILES with explicit hydrogens as a "property" of
> another atom?
> > For example from the
-:"O=C(NCCN(C)C)c12C(=O)c3c3(Oc12)" -s
> "c12Cc3c3(Oc12)" -osmi -aa
> O=C(NCCN(C)C)c12C(=O)c3c3Oc12
>
> Regards,
> Noel
>
>
>
> On Fri, 17 Feb 2023 at 18:50, Thomas wrote:
>
>> Thank you Noel.
>> I wanted to get the canoni
I am including OpenBabel as an alternative chemical library in a software
that uses RDKit, but I'm missing some functions.
Is it possible to get SMILES with explicit hydrogens as a "property" of
another atom?
For example from the SMILES "CC" I'd like to get '[CH3][CH3]' instead of
are the addition
of Hs if I generate the molecule from SMILES fragments (partial SMILES)
Thank you
Thomas
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={'c':True})
'CN(CCNC(=O)c1cccn2c1nc1c1c2=O)C\t\n'
Furthermore, can you explain me this:
mol = pybel.readstring('smi', "O=C(NCCN(C)C)c12C(=O)c3c3(Oc12)")
sma = pybel.Smarts("c12Cc3c3(Oc12)")
sma.obsmarts.Match(mol.OBMol, True)
False
Thank you again
Thomas
Il g
records, but that's not what
I want.
Yours sincerely,
Thomas Womack (Global Phasing)
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I'm using babel as part of a process for producing dictionaries for
crystallographic refinement software. The formats for such dictionaries refer
to atoms by their names, and so it's very slightly annoying that the output
from babel hydrogenation calls all the added hydrogens 'H'.
Is there a
On 23 Jan 2012, at 12:29, Douglas Houston wrote:
Hi all,
I wonder if anyone can help me work out what's going on here. I'm trying to
convert a PDB file of ADP (from structure 3ATV) to mol2 format and add
hydrogens. The first step seems to work fine:
babel -ipdb 3ATV_ADP.pdb -omol2
On 5 May 2012, at 13:40, Ferenc Szalai wrote:
Hi,
I attached a structure in 2d mol file. If I try to generate 3d
coordinates for this structure ether using obgen or the pybel
interface I get result with invalid coordinates ('nan') and a lot of
warning messages which are stats the something
The CSD has a fair number of structures with a big charged aromatic moiety and
a counter-ion, things like the attached TUDTES.mol2
Using SVN 4747, I'm not seeing charges when I convert to SMILES - I get
OCCn1c(=O)n(C)c2c(c1=O)n(C)cn2C.I
out of obprop, where I would expect
ib\PmwBase.py",
line 1747, in __call__
return apply(self.func, args)
File "C:\Users\Thomas\AppData\Roaming\pymol\startup\optimize.py", line
52, in set_conf_search
conf_search(selection, forcefield, conf_method, nsteps1, conformers,
lowest_conf)
File "C:\Users\T
Hi Eric
I contacted Osvaldo cc d on this (he wrote Optimize) and he kindly offered
some help - but I never managed to get optimize to run
Am traveling now but will have a look again next week
Best
Thomas
On Saturday, 10 September 2016, eolmon <eric_ol...@brown.edu> wrote:
> Dear Thomas,
chemoinformatic tasks and win prizes.
http://fch.upol.cz/en/research/conferences-workshops/4add/
Please feel free to share this information to those who can be
interested in participation in such event. Thank you.
With kind regards,
Thomas Evangelidis
44 94 1
96
97 45 95 1
98 46 47 ar
99 46 96 1
100 47 48 ar
101 47 97 1
102 48 98 1
@SUBSTRUCTURE
1 UNK 1 GROUP 0 0 ROOT
--
==
Dr Thomas E
How can I instruct OpenBabel to write a multi-molecule pdbqt file? I am not
sure if the flag '--canonical' has any effect. I have heard that sometimes
it fixes some random change in the atom order especially in structures with
a high number of rotatable bonds and many symmetric groups.
I thank you in
'
is missing. Was this table really removed, and if yes, how can I adapt
my code below to work with the latest version?
I thank you in advance.
Thomas
from openbabel.openbabel import OBElementTable
>
> # ELEMENT TABLE TO DETERMINE VDW AND COVALENT BONDS
> et = OBElementTable()
>
# CONVERT ELE
Hi
I tried to compile Open Babel on my Mac so I could have the Python bindings,
but I'm running into problems with Eigen2. When I compile without reference to
Eigen, the configuration completes without errors, but when I include the
–DEIGEN2_INCLUDE_DIR I get the following error:
…
--
courriel, effacer l'original sans en conserver de copie
et ne pas en dévoiler le contenu ni utiliser l¹information pour quelque
fin que ce soit.
On 14/11/2011 16:12, Geoffrey Hutchison ge...@geoffhutchison.net wrote:
On Nov 14, 2011, at 4:14 AM, Hassan Thomas Mamdani wrote:
CMake Error at cmake
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