It might be due to not initializing Forcefield properly, but I've did my
best and failed to do so. Can anyone post an example of correct part of
perl script with FF?
Pozdrawiam, | Best regards,
Maciek Wójcikow
x27;aaa.out');
#$pFF -> SetLogLevel('OBFF_LOGLVL_NONE');
#$pFF -> SetLogToStdOut(1);
$pFF -> SetLogLevel(2);
# We pass the constraints as argument for Setup()
$pFF -> Setup($mol, $constraints);
# Perform the actual minimization, maximum 1000 steps
$pFF-&g
;\n";
$mol3 = $mol2;
print "Mol3 step one: ".$mol3->NumAtoms()."\n";
### there you go
#$mol3 += $mol1; # doesn't work, throws error
$mol3 -> add($mol1); # this does what above should.
###
print "Mol3 step two: ".$mol3->NumAtoms()."\n&qu
If you set that up it would be nice. What kind of test scripts do you need?
Pozdrawiam, | Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl
W dniu 3 kwietnia 2012 02:40 użytkownik Geoff Hutchison <
ge...@geoffhutchison.net> napisał:
>
> On Apr 2, 2012, at 5:34 PM, mwojci
into account. Disadvantage of above is that it wouldn't work
for other formats.
Pozdrawiam, | Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl
W dniu 3 kwietnia 2012 17:23 użytkownik Geoffrey Hutchison <
ge...@geoffhutchison.net> napisał:
> > I have a thought ab
see dock6/src/dock/library_file.cpp it seams
fairy simple and always uses ##.
Pozdrawiam, | Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl
W dniu 3 kwietnia 2012 21:13 użytkownik Scott Brozell <
sbroz...@rci.rutgers.edu> napisał:
> Hi,
>
> This is a good sugg
Maybe @COMMENT would be a better place for them?
http://tripos.com/data/support/mol2.pdf
Pozdrawiam, | Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl
W dniu 4 kwietnia 2012 20:08 użytkownik Conrad Huang
napisał:
> Our approach to file formats in Chimera is to support the &quo
Fingerprints are 1D therefore similarity search is 1D. To
my knowledge there is no shape similarity search in OB.
Pozdrawiam, | Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl
W dniu 23 kwietnia 2012 09:20 użytkownik Jochen Schreiber <
joc...@googlemail.com> napisał:
> H
Have you tried "H1 + H2"? Actually this wasn't working for me in perl, but
it's supposed to be working in Python.
Pozdrawiam, | Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl
W dniu 23 kwietnia 2012 13:52 użytkownik Чугунов Антон
napisał:
>
> Dear Open
Hello everyone,
Is it possible to set conversion options in pybel? I couldn't find any
information about it.
Pozdrawiam, | Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl
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d returned 1 exit status
make[2]: *** [lib/OpenBabel.so] Błąd 1
make[1]: *** [scripts/CMakeFiles/bindings_perl.dir/all] Błąd 2
To clarify, given cmake command build 2.3.1 version without problem.
Pozdrawiam, | Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl
-lperl ../lib/libopenbabel.so.4.0.0 -lm -ldl -lz
-Wl,-rpath,/usr/lib64/perl5/CORE:/home/maciek/openbabel/build/lib
Adding -lpthread leads to succesful compilation.
Pozdrawiam, | Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl
2012/5/31 Noel O'Boyle
> We changed to compi
loads successfully 1.x.
Pozdrawiam, | Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl
2012/5/31 Maciek Wójcikowski
> It worked.
>
> The failing line was:
> /usr/bin/c++ -fPIC -O2 -g -O2 -g -Wl,--enable-new-dtags
> -Wl,--enable-new-dtags -Wl,--fatal-warnings -Wl,--no-undefine
I was wrong. something went wrong and SWIG wasnt recognized at all. I'm
looking for another problem. Do you have any Idea where first to look?
Pozdrawiam, | Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl
2012/5/31 Maciek Wójcikowski
> Apparently it seams to be SWIG
='-lresolv -lnsl -ldl -lm -lcrypt -lutil -lpthread -lc';
Pozdrawiam, | Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl
2012/5/31 Noel O'Boyle
> Yes - I doublechecked. The latest SWIG still fails.
>
> What I can do is add in the output of perl -V:perllibs. This
Hello,
You should use:
ff.GetCoordinates(mol)
Where ff is your OBForceField class and mol is OBMol.
Pozdrawiam, | Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl
2012/7/13 scott_m
> That's great, many thanks for the help. One other thing, I mentioned pybel
> becaus
y thoughts?
Pozdrawiam, | Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl
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threat landscape has changed and
Xen) for
memory intensive computing. I must say that I'm pretty disappointed with
those results, although it's quite obvious...
Out of curiosity I'm going to rerun the tests on KVM and probably on OpenVZ
to see how it goes there.
Pozdrawiam, | Best regards,
Maciek Wójcikowski
mac
Oh, I forgot to mention that. I use CentOS and ScientificLinux 6, both HVM.
Pozdrawiam, | Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl
2012/7/20 Craig James
> Did you see this article? You didn't say what Linux you are using, but if
> it's Ubuntu, this ma
Hi,
Is it possible to set up those PHP bindings in SVN branch? I'm willing to
make some testing and write some example/test files. Unfortunately I have
little experience with CMake to make it by my own...
Pozdrawiam, | Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl
201
Have you tried "copy" output format?
-ocopy
Pozdrawiam, | Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl
2012/10/4 Juliette Pradon
> Hello,
>
> I am using OpenBabel to split a multimol2 file into separate mol2 files
> (i.e. one mol2 file per compound
Is pybel suppose to support 'copy' format? I try to make it work, but it
generates empty string.
Proof of concept:
>>> mol = pybel.readstring("smi", "c1=CC=CC=c1")
>>> mol.write('copy')
''
I'm on latest SVN openba
That was just a "proof of concept" piece of code. I wanted to process some
molecules and try to leave them intact. Thanks for information.
Pozdrawiam, | Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl
2012/11/8 Geoffrey Hutchison
> > Is pybel suppose to support
orks
fine on the same set of compounds.
Pozdrawiam, | Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl<https://mail.google.com/mail/u/0/?view=cm&fs=1&tf=1&to=mac...@wojcikowski.pl>
--
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Have you tried it with OB 2.3.2?
Pozdrawiam, | Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl
2013/1/20 David García Aristegui
> OK, is an open bug http://sourceforge.net/p/openbabel/bugs/833/
>
> > Hello, i'm trying to assign 3D coordinates to this SMILES str
631
6944641
7044651
1 molecule converted
Pozdrawiam, | Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl
2013/1/20 David García Aristegui
> OK, in the News section of the Openbabel main page is announced
> "2011-10-17 Open Babel
Gen3d is calling addhydrogen before forcefield calculation, So you might
want to delete some hydrogens afterwards.
Pozdrawiam, | Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl
2013/1/21 David García Aristegui
> Hello, i'm unable to generate the 3D coordinates and at
think it's a good idea would it be possible to add it to trunk?
PS.
How is github/git integration going? Github repo seams to be forgotten
since initial sync somewhere in October 2012...
Pozdrawiam, | Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl<https://mail.google.com/mail
Try:
obminimize -ff MMFF94 -sd source.sdf > target.sdf
Pozdrawiam, | Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl
2013/2/27 Оги Боги
> Hi guys,
>
> I am trying to use obminimize under 64bit windows 7 in order to minimize
> geometry of molecules inside multimo
According to current webpage of tree.hh it's released on GPL3 OR 2 [
http://tree.phi-sci.com/]
Pozdrawiam, | Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl
2013/3/12 Geoffrey Hutchison
> > For some internal purposes, I wanted a combined openbabel/confab code
>
Try cherry-picking a commit.
Pozdrawiam, | Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl
2013/3/18 Noel O'Boyle
> Hi David,
>
> Can you put all of the Confab-related code on a branch so I can get at
> them without pulling the other unrelated co
rting data and molecules depiction.
Pozdrawiam, | Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl<https://mail.google.com/mail/u/0/?view=cm&fs=1&tf=1&to=mac...@wojcikowski.pl>
--
Precog is
Hi,
Does anybody know, if MMFF94 with OpenMP works in any bindings? It works
fine in CLI, but bindings ignore that.
Pozdrawiam, | Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl<https://mail.google.com/mail/u/0/?view=cm&fs=1&tf=1&to=mac...
It turned out they work, as they should. For future reference: using opcode
caching in PHP (like APC, xCache, etc) prevents it from using OpenMP.
Pozdrawiam, | Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl
2013/5/17 Geoffrey Hutchison
> > Does anybody know, if MMFF9
Hello,
Sure - try atom.atomicnum (pybel) or OBAtom.GetAtomicNum() (openbabel). It
returns atomic number of element (fe. C - 6).
Pozdrawiam, | Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl
2013/6/5 Dimitri Maziuk
> Hi all,
>
> I'm after the atom (element) type
If you realy need symbol of an element in automated fassion, then there is
OBElementTable.GetSymbol( atomicnum ) that you can use.
http://openbabel.org/dev-api/classOpenBabel_1_1OBElementTable.shtml#a18907ad1590deb926b43c4f08cac9405
Pozdrawiam, | Best regards,
Maciek Wójcikowski
mac
Yes.
etab = ob.OBElementTable()
etab.GetSymbol(6)
Pozdrawiam, | Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl
2013/6/5 Dimitri Maziuk
> On 2013-06-05 02:54, Maciek Wójcikowski wrote:
> > If you realy need symbol of an element in automated fassion, then the
: None should be 'b' : '' if you
wish to pass empty value, since None is reserved for options without value.
You could look into that in pybel.py file.
Pozdrawiam, | Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl
2013/6/5 Dimitri Maziuk
> Hi everyon
Search for performance reasons. For further
lecture: http://openbabel.org/wiki/FastSearch
Pozdrawiam, | Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl
2013/7/5 Brett T. Hannigan
> I have a database of molecules in pdb files. I'd like to go through each
> molecule and see i
s name could be (although it's the most
error prone).
Pozdrawiam, | Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl
2013/7/8 Brett Hannigan
> Unfortunately, I don't think that's quite what I need. The obabel filter
> command will look at the given pdb and then outpu
You could also look into ProDy, if you use PDB files.
http://www.csb.pitt.edu/prody/reference/atomic/flags.html#term-hetero
Pozdrawiam, | Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl
2013/7/8 Maciek Wójcikowski
> I think you need custom code. For python, you could use py
Hello,
For sets that are not extremly big (as it could get quite long), I'd
suggest converting to smiles and counting the lines:
obabel input.mol2 -o smi | wc -l
Pozdrawiam, | Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl
2013/8/20 Dimitri Maziuk
> On 08/20/2013
Hello,
The other choice, if you prefer MySQL, is Mychem
http://mychem.sourceforge.net/. But I'd say neither of them is easy to use
for unexperienced user (unless you have at least some DB knowledge).
Pozdrawiam, | Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl
2013/8/22 St
te me an email or comment on G+.
Pozdrawiam, | Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl
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Hi,
Besides PYTHON_PATH please try adding the directory with openbabel.so.4
to $LD_LIBRARY_PATH
Pozdrawiam, | Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl
2013/10/25 Zhengyh
> Greetings,
> I was compiling the openbabel 2.3.1 version with binding for Python on
>
Hi,
Have you tried mol1 += mol2? I use it for joining proteins with ligands,
but should work in any case.
Pozdrawiam, | Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl
2013/10/25 Zhengyh
> Hello,
>
> Thank you all who are helping me with this openbabel.
> We use --
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
2013/10/30 Zhengyh
> Greetings,
>
> I
, or at least
recognise Lp/*, as in mol2/sdf, atom types and ignore them.
Pozdrawiam, | Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl
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Accelerate application
There are few things missing which I intend to fix asap (mainly involving
forcefields and fingerprints) due to SWIG errors.
Any thoughts/ideas?
Pozdrawiam, | Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl
--
nt to skip, as in
example in Wiki [
http://openbabel.org/docs/current/UseTheLibrary/PythonExamples.html]
----
Pozdrawiam, | Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl
--
Rapidly troubleshoot problems before they affe
ecognizing the
beginning and the end of the molecule it wouldn't do anything especially
kekulization and bonding etc.
Pozdrawiam, | Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl
2013/12/3 Dimitri Maziuk
> On 2013-12-03 04:28, Maciek Wójcikowski wrote:
> > Hello,
This only proves, that I really want to use it. Is the proof.py script
working correctly for anybody (attached in previous mail)? It should ouptut
molecules no. 5-10 out of 100 in proof.sdf
Pozdrawiam, | Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl
2013/12/3 Chris Morley
ead or ReadFile,
then it should work. Unfortunately I struggle to find the spot. Tried to
add it to ReadFile, but it does not work.
Any better ideas?
Pozdrawiam, | Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl
2013/12/5 Geoffrey Hutchison
> This only proves, that I really want
Hello again,
I've fixed the issue here: https://github.com/openbabel/openbabel/pull/52
Pozdrawiam, | Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl
2013/12/12 Maciek Wójcikowski
> I think, I've pin-pointed the issue in the source - OBConversion class.
> Th
I think you should build with SHARED = True and append correct directory
to LD_LIBRARY_PATH, which probably should look like:
export
LD_LIBRARY_PATH=$LD_LIBRARY_PATH:~/openbabel/openbabel-2.3.2-install/lib
Pozdrawiam, | Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl
2014/1/15
You can also use xargs.
Pozdrawiam, | Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl
2014-02-03 16:10 GMT+01:00 Igor Filippov :
> How is it different from GNU parallel?
> http://www.gnu.org/software/bash/manual/html_node/GNU-Parallel.html
>
> Igor
>
>
> On
be:
cat commands.sh | parallel -P 8 > log 2> error.log
(or 2>&1 if someone prefers joint log)
----
Pozdrawiam, | Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl
2014-02-04 11:58 GMT+01:00 Francois Berenger :
> On 2/4/14, 6:28 PM, Noel O'Boyle wrote:
>
>> It
Hi,
Is the input molecule flexible? It would be much easier to test if you
could sent it to the list.
Pozdrawiam, | Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl
2014-05-07 11:19 GMT+02:00 Fredrik Wallner :
> Continue by running
> obabel -L formats
> and
> o
s -o smi
Above command will output 2 conformets. I can't pin-point the problem with
this molecule yet,but still there is a solution.
Pozdrawiam, | Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl
2014-05-13 13:38 GMT+02:00 Douglas Houston :
> Can I just check people rec
ds,
Maciek Wójcikowski
mac...@wojcikowski.pl
2014-05-13 14:06 GMT+02:00 Maciek Wójcikowski :
> We've received the input file. Of course there is problem with it, when
> you pass it through mol2 file, then your fine. Also obabel reports "-nan"
> scores for original
Hello Andrew,
I created pull request on github [
https://github.com/openbabel/openbabel/pull/96]
Pozdrawiam, | Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl
2014-10-20 15:14 GMT+02:00 Andrew Dalke :
> Hi all,
>
> Open Babel's MACCS definitions derive from RDKit&
out of the box. Otherwise
Stefano's solution is the one you go for.
Pozdrawiam, | Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl
2015-04-25 0:45 GMT+02:00 Matthew Lardy :
> Hi Stefano,
>
> That worked! Thanks!
> Matthew
>
> On Fri, Apr 24, 2015 at 3:34 PM,
Hi,
Currently only UCSF Dock-style data fields are supported in mol2 files, and
you have to specify -ac or -xc option to read/write it from/to a file. Can
you give example of such mol2?
Pozdrawiam, | Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl
2015-04-30 17:16 GMT+02:00 Hitesh
Got it. OpenBabel currently does not support @COMMENT, where the
data sit from Gold. You can save docked conformations as SDF file and
normalize them. There is no other solution, as Gold embeds SDF style
variables in @COMMENT.
Pozdrawiam, | Best regards,
Maciek Wójcikowski
mac
Hello,
What version od OB are you using? I would recommend checking latest master
branch on github. Actually it has confab bundled, which was suggested by
Pascal, while confab on itself also uses ancient version (2.3.1 as I
remember correctly).
Pozdrawiam, | Best regards,
Maciek
():
> print m
Note that m is an OBMol object, so to get pybel molecule you need to
initiate it via Molecule class:
for m in mol.OBMol.Separate():
> print pybel.Molecule(m)
Pozdrawiam, | Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl
2015-11-10 16:59 GMT+01:00 Fil
FYI The obabel -m option you've used separates molecules in multi-mol2 file
- the molecules must already be in separate molecule blocks.
Pozdrawiam, | Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl
2015-11-10 19:54 GMT+01:00 Filip Stefaniak :
> Hi Maciek,
>
> Maci
s for dock method:
http://oddt.readthedocs.org/en/latest/rst/oddt.docking.html#module-oddt.docking.AutodockVina
Pozdrawiam, | Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl
2016-01-05 12:14 GMT+01:00 Stefano Forli :
> Hi Stefano,
> the problem with the PDBQT format is that connectivity is i
ou have to enumerate all the
columns you'd like to include.
I would also second a CSV output format to write all the properties.
Pozdrawiam, | Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl
2016-01-21 22:43 GMT+01:00 Chris Swain :
> Hi,
>
> Is there an output format tha
from oddt.virtualscreening import virtualscreening as vs
pipeline = vs()
pipeline.load_ligands('sdf', 'ampc/actives_final.sdf.gz')
pipeline.write_csv('ampc_docked.csv')
Pozdrawiam, | Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl
2016-01-22 14:17 GMT+0
. (although currently it uses Rajarshi's SMARTS definition). I
have to update those to Greg's revised version.
Pozdrawiam, | Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl
2016-03-15 18:54 GMT+01:00 Stefano Forli :
> About that, a while ago I had compiled an OB-compatible d
Hi,
Add "-xl" to the command line (which ignores the residues for mol2).
Pozdrawiam, | Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl
2016-04-11 19:08 GMT+02:00 Fredy Quevedo :
> Dear all:
>
> I am having some problem with the conversion of a .smi file to
ble.Translate(a.type) for a in lig.atoms]
----
Pozdrawiam, | Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl
2016-04-13 19:13 GMT+02:00 Yun Ding :
> Dear all,
>
>
> I would like to get the SYB type of the atom using the python interface,
> however, it always gives the INT t
Hello,
I think that Confab is available only in current development branch. Check
"obabel -L confab" to see if it's there. If not then you'd have to use
conda or compile it yourself.
Pozdrawiam, | Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl
2016-05-03 12:1
ame", like "c1c1
benzene"
Pozdrawiam, | Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl
2016-05-09 4:35 GMT+02:00 Brendan M. O'Boyle :
> Hello,
>
> I am trying to use OpenBabel and iBabel to convert SMILES strings into sdf
> files for manipulation with
Hi,
Indeed for some reason InCHI is not built on windows. I'll have to fix it,
stay tuned for updates.
Pozdrawiam, | Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl
2016-10-15 9:30 GMT+02:00 Noel O'Boyle :
> I can't comment on the anaconda parts, bu
Babel is deprecated in 2.4, maybe that's messing with your app?
Pozdrawiam, | Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl
2016-11-15 12:45 GMT+01:00 Chris Swain :
> Hi,
>
> Thanks, that works fine.
>
> Chris
>
> On 15 Nov 2016, at 11:06, Pascal Muller
Hi Sanjan,
Since you've already have (Ana)conda, the easiest solution whould be
installing it via conda:
"conda install -c openbabel openbabel"
Pozdrawiam, | Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl
2016-11-30 3:46 GMT+01:00 tpsanjan :
> Hi,
>
> I
Hello,
Python 3.6 support is not there yet. It should be added soon.
Pozdrawiam, | Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl
2017-02-13 5:31 GMT+01:00 i4hashmi :
> I am using Python for making a script to work with some chemical structures
> in my PhD. I want to i
Hello,
What you need is openbabel package not pybel: "pip install openbabel"
See https://pypi.python.org/pypi/openbabel
Pozdrawiam, | Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl
2017-04-06 1:23 GMT+02:00 Phuong Do :
> Hello,
>
> I intend to use pybel modu
this issue and try to support PNG
files.
Pozdrawiam, | Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl
2017-05-31 11:06 GMT+02:00 Hongbin Yang :
> Hi，
>
> I installed openbabel via `conda install -c openbabel openbabel`.
>
> I wanted to draw the molecule like
>
I've rebuilt the Python 2.7 packages for Windows (the rest is still
compiling), and the PNG should work now. Update openbabel package to 2.4.1
py27_3: `conda install -c openbabel openbabel`.
Pozdrawiam, | Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl
2017-05-31 13:16 GMT+
Hi all,
Quick question: I have OBMol and want to create a sub-molecule from a
subset of atoms given by atom/bond indices. Is there a clever way to do it
in OpenBabel? I'm aware that I can make a copy and prune the unwanted atoms
;)
Pozdrawiam, | Best regards,
Maciek Wójcikowsk
The last BeginModify should be EndModify.
Pozdrawiam, | Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl
2017-06-19 16:39 GMT+02:00 Maciek Wójcikowski :
> I'm trying to get back the ECFP environments, most preferably as smiles.
> So it's literally a list of connecte
l_clone
Pozdrawiam, | Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl
2017-06-19 15:53 GMT+02:00 Noel O'Boyle :
> This would be a useful API function.
>
> If it's a disconnected portion of the molecule, and you wanted to
> write a smiles, there is a fragment option
No worries :) I planned to do Chem.FindAtomEnvironmentOfRadiusN() and
Chem.PathToSubMol() in RDKit, but the function you've suggested is also
feasible.
@Geoff - the smiles fragment does not perserve any bond information from
what I've tested so far.
Pozdrawiam, | Best regar
dxs))}).strip()
----
Pozdrawiam, | Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl
2017-06-19 17:19 GMT+02:00 Maciek Wójcikowski :
> No worries :) I planned to do Chem.FindAtomEnvironmentOfRadiusN() and
> Chem.PathToSubMol() in RDKit, but the function you've suggested is also
rints-with.html)
although OBMolAtomBFSIter is buggy and does not work correctly with
disconnected molecular parts, which will happen with proteins (
https://github.com/openbabel/openbabel/issues/1639).
Pozdrawiam, | Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl
2017-10-16 15:27 GMT+02:00
ue 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&#
Hi,
This is highly dependent on docking software. Autodock Vina requires only
polar hydrogens, but others will differ.
Best,
Maciek
sob., 3 lis 2018, 11:28: Noel O'Boyle napisał(a):
> You need to add all hydrogens. I have never understood why those options
> are provided.
>
> On Thu, 1 Nov 20
openbabel namespace,
so you need to import it as follows:
> from openbabel import openbabel
Pozdrawiam, | Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl
niedz., 10 lis 2019 o 15:23 Yang, Chengxi
napisał(a):
> Hi Openbabel Team,
>
> I noticed that you have removed t
, | Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl
czw., 11 mar 2021 o 09:46 Eduardo Mayo
napisał(a):
> Hi OpenBabels users,
> Nice to join the community.
> I would like to convert pdbqt file to sdf file without using openbabel
> itself. I mean why should my project has another dep
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