Hello,
I would like to install rdkit in such a way, I don't have to append
anything to LD_LIBRARY_PATH.
If I do:
export RDBASE=/usr/lib
and run cmake make make install
would that do the trick?
Kind regards,
Michal Nowotka
Hi,
lets say I would like to compile RDKit on some headless machine for
computations only and so I would like to get rid of all visualization stuff
that RDKit includes. Is there any compile flag that would instruct not to
compile this parts of code?
Regards,
Michal Nowotka
Hi,
I compiled RDkit from sources and run tests. The last one failed:
76/76 Test #76: pythonTestDirChem ***Failed 661.40 sec
running RDBASE=$PWD PYTHONPATH=$PWD LD_LIBRARY_PATH=$PWD/lib ctest -V -R
TestDirChem
gives me:
76: ..[11:01:24] SMILES Parse Error: syntax error for
Hi Riccardo,
I'm trying to understand your advice? Should I check if I have pandas
installed and uninstall it? Or installing pandas will help me with testing?
Anyway, I think there are two things worth mentioning:
1. I'm compiling it on raspberry pi
2. Installation failed - sudo make install
, and not a solution ...
Why not try to set the parameter rdkit.tanimoto_threshold in a stored
procedure and call the stored procedure from python? Instead of trying set
xxx=yyy on the cursor directly.
Just an idea,
JP
On 11 July 2013 16:52, Michał Nowotka mmm...@gmail.com wrote:
Is is possible
'
This is a link with the explanation:
https://code.google.com/p/rdkit/wiki/BuildingTheCartridge
I hope it helps
On Thu, Jul 11, 2013 at 5:52 PM, Michał Nowotka mmm...@gmail.com wrote:
Is is possible to specify similarity threshold for single query instead
of relying on global
?
If that works it should just need to be done once per database connection.
-greg
On Jul 11, 2013, at 7:23 PM, Michał Nowotka mmm...@gmail.com wrote:
As I said, in other question, I don't have provilidges to edit
postgresql.conf, so I'm looking for other solution.
And I'm not sure if the settings
connection.
-greg
On Jul 11, 2013, at 7:23 PM, Michał Nowotka mmm...@gmail.com wrote:
As I said, in other question, I don't have provilidges to edit
postgresql.conf, so I'm looking for other solution.
And I'm not sure if the settings are issue here, as this query works
perfectly from
Michal,
On Wed, Aug 28, 2013 at 1:16 PM, Michał Nowotka mmm...@gmail.com wrote:
Imagine this scenario:
I read random molfile and I want to produce an image of it:
1. If the molfile already contains coordinates, use them
2. If the molfile coordinates are all zeros, compute them
I don't
Yes: python, mod_wsgi, vitualenv, RHEL
On Tue, Sep 10, 2013 at 9:22 PM, Markus Sitzmann sitzm...@helix.nih.govwrote:
**
Are you trying to use it with python/mod_wsgi? Your description so far is
a bit vague :-)
Markus
On Tue, 10 Sep 2013 15:00:55 -0400, Michał Nowotka mmm...@gmail.com
of my problems
On Tue, Sep 10, 2013 at 9:32 PM, Markus Sitzmann sitzm...@helix.nih.govwrote:
**
How far is your setup working so far? Can you already run python scripts
via mod_wsgi without importing rdkit?
On Tue, 10 Sep 2013 15:29:07 -0400, Michał Nowotka mmm...@gmail.com
wrote
-0400, Michał Nowotka mmm...@gmail.com
wrote:
Yes, I can. What is more important I successfully managed to run other
libraries with extensions in C (indigo toolkit, cx_Oracle). What is even
more important the same configuration (at least it seems to be the same)
works on other machines
Nowotka mmm...@gmail.com wrote:
I have some problems with configuring apache to use rdkit, this is
described in SO question:
http://stackoverflow.com/questions/2550504/setting-ld-library-path-in-apache-passenv-setenv-still-cant-find-library
Any help would be appreciated!
Regards,
Michał
generation part requires some redesign
because it's not DRY enough...
But if you have some ideas how and where should the new class be
implemented let me know, I will try to write it.
Regards,
Michał Nowotka
--
October
Hi,
Since there is no open source software converting structure to IUPAC
name (I'm not talking about web services) I was wandering if one can
be implemented using RDkit? Which parts of RDKit would help in doing
that? Any pointers, suggestions?
Regards,
Michal Nowotka
Sure, will do. Thanks a lot!
On Mon, Jan 20, 2014 at 1:53 PM, Greg Landrum greg.land...@gmail.com wrote:
Hi Michal,
that's an easy-to-fix bug. Would you mind putting something in github? I'll
fix it today or tomorrow.
-greg
On Mon, Jan 20, 2014 at 2:21 PM, Michał Nowotka mmm
Hi,
Let's say I loaded a molfile containing coordinates to RDKit mol
object or loaded it from smiles but called
AllChem.Compute2DCoords(mol).
Now I would like to get coordinates for each atom. Unfortunately Atom
class doesn't have any GetCoords method but this is understandable
since position is
Speaking about formats - would it be useful to add marvin (*.mrv) to
mol conversion (in both directions)? I'm writing this anyway but maybe
it would be useful as a part of RDKit.
On Sat, Jan 25, 2014 at 3:30 PM, Igor Filippov
igor.v.filip...@gmail.com wrote:
Sounds good, thank you!
Igor
On
By 'standard tool for writing and reading' do you mean marvin
sketch/marvin for js/marvin viewer or is there something else I don't
know about?
On Sun, Jan 26, 2014 at 5:53 AM, Greg Landrum greg.land...@gmail.com wrote:
On Sat, Jan 25, 2014 at 4:31 PM, Michał Nowotka mmm...@gmail.com wrote
wrote converter and though it may be useful for the RDKit itself.
On Sun, Jan 26, 2014 at 12:03 PM, Greg Landrum greg.land...@gmail.com wrote:
Marvin sketch.
-greg
On Sun, Jan 26, 2014 at 11:55 AM, Michał Nowotka mmm...@gmail.com wrote:
By 'standard tool for writing and reading' do you mean
believe this compound contains 5 possible stereo centers (picture
attached). How can I get them detected by RDKit?
Regards,
Michał Nowotka
attachment: Screen Shot 2014-01-28 at 12.18.43.png--
WatchGuard Dimension
According to the documentation
(http://www.rdkit.org/Python_Docs/rdkit.Chem.rdmolops-module.html#Cleanup):
cleans up certain common bad functionalities in the molecule
What are those 'certain common bad functionalities' that are being cleaned up?
Regards,
Michał Nowotka
.
-greg
On Tue, Jan 28, 2014 at 4:41 PM, Michał Nowotka mmm...@gmail.com wrote:
Yes Mikołaj, thank you very much for your very helpful advice of
reading the code. Excellent pointers!
Cheers,
Michał
On Tue, Jan 28, 2014 at 3:20 PM, Mikolaj Kowalik mx...@psu.edu wrote:
On Tue, 28 Jan 2014
That solves my problem, thank you very much.
On Wed, Jan 29, 2014 at 6:19 AM, Greg Landrum greg.land...@gmail.com wrote:
On Tue, Jan 28, 2014 at 1:20 PM, Michał Nowotka mmm...@gmail.com wrote:
Look at this code:
from rdkit import Chem
mol =
Chem.MolFromSmiles('O=C(O)C2N3C(=O)C(NC(=O)C
() method of
SDMolSupplier, because size of uncompressed string will be larger than
available memory.
The solution would be to obtain file handler (f = gzip.open(...)) but
the problem is that there is no way (at least I don't know any) to
pass it to SDMolSupplier.
Any ideas?
Kind regards,
Michał
is not None]
len(ms)
180
pozdrawiam
Adrian Jasiński
2014-01-31 Michał Nowotka mmm...@gmail.com:
Hi,
I need to process large, compressed SDF file. I was planning to use
SDMolSupplier but there is a problem:
1. I can't just pass a file name, as this is compressed file and if I
understand
I want to get SVG image for some compound:
import cairo
from rdkit import Chem
import StringIO
from rdkit.Chem.Draw import cairoCanvas
imageData = StringIO.StringIO()
surf = cairo.SVGSurface(imageData,200,200)
ctx = cairo.Context(surf)
mol =
. ;-)
On Wed, Feb 12, 2014 at 4:06 PM, Michał Nowotka mmm...@gmail.com wrote:
I want to get SVG image for some compound:
import cairo
from rdkit import Chem
import StringIO
from rdkit.Chem.Draw import cairoCanvas
imageData = StringIO.StringIO()
surf = cairo.SVGSurface
Look at the following example:
import gi
from rdkit import Chem
from rdkit.Chem import Draw
from rdkit.Chem.Draw import SimilarityMaps
import matplotlib.pyplot as plt
mol =
Chem.MolFromSmiles('COc12cc(C(=O)NN3CCN(c45nccnc54)CC3)oc21')
refmol =
from maybe backwards compatibility, as this is a new
feature)?
Is UFF significantly faster then MMFF?
Kind regards,
Michał Nowotka
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Rdkit-discuss
Hi,
This is probably a long shot, but does anyone have a chef
(http://www.getchef.com/chef/) cookbook for RDKit?
I will probably have to write one for myChEMBL and I don't want to
reinvent the wheel.
Kind regards,
Michał Nowotka
Running cmake from scratch didn't help...
OK, so correct bison version is 2.7.1 (I have 2.4.1), what about flex
(I have 2.5.35)?
On Tue, Jul 29, 2014 at 3:30 PM, Mikolaj Kowalik mx...@psu.edu wrote:
On Tue, 29 Jul 2014 15:09:48 +0100
Michał Nowotka mmm...@gmail.com wrote:
I wanted
Fair enough, thanks!
On Tue, Jul 29, 2014 at 4:35 PM, Mikolaj Kowalik mx...@psu.edu wrote:
On Tue, 29 Jul 2014 16:05:41 +0100
Michał Nowotka mmm...@gmail.com wrote:
Running cmake from scratch didn't help...
OK, so correct bison version is 2.7.1 (I have 2.4.1), what about flex
(I have 2.5.35
for the whole compound:
AllChem.Compute2dCoords(mol)
But this will ruin my beautiful layout of the original, non-hydrogen part...
Is it possible to layout hydrogens around my compound after I add them?
Regards,
Michał Nowotka
, at 19:07, Michał Nowotka mmm...@gmail.com wrote:
Hello,
Imagine I have a compound with some 2D coordinates I really like:
mol
Now I would like to add hydrogens to it:
mol = Chem.AddHs(mol)
The problem is, all new hydrogen atoms will have (0,0,0) coordinates,
which doesn't look
.
Best,
Sereina
On 20 Aug 2014, at 19:07, Michał Nowotka mmm...@gmail.com wrote:
Hello,
Imagine I have a compound with some 2D coordinates I really like:
mol
Now I would like to add hydrogens to it:
mol = Chem.AddHs(mol)
The problem is, all new hydrogen atoms will have (0,0,0
pointed out, there are many situations where the results aren't
going to look particularly good.
-greg
On Wed, Aug 20, 2014 at 7:34 PM, Greg Landrum greg.land...@gmail.com
wrote:
On Wednesday, August 20, 2014, Michał Nowotka mmm...@gmail.com wrote:
I've just checked and actually adding
with z
coordinates is all zeros. How can I build my input ctab in such a way
to clearly indicate that this is 2D depiction?
On Thu, Aug 21, 2014 at 8:16 AM, Michał Nowotka mmm...@gmail.com wrote:
Thank you Greg. I have to verify your example with my instance of
RDKit, maybe my old version
Hi,
I have this molfile:
mn beaker 0821142D
10 10 0 0 0 0 1 V2000
-1.6741 -0.26870. C 0 0
-2.3885 -0.68120. C 0 0
-2.3885 -1.50630. C 0 0
-1.6741 -1.91880. C 0 0
-0.9596 -1.50630. C 0 0
-0.9596
A question I have is why you want to access the bond wedging.
This is very good question so I will begin with answering this. I'm
writing a module, which converts *mrv files to molfiles, both ways. In
my case, the original mrv file looks like this:
cmlMDocumentMChemicalStructmolecule
Hi Axel,
Imagine you are working on open source project which can handle mrv
files. In such a case you probably wouldn't like to use external
proprietary software and this is exactly my case.
Michał
On Fri, Aug 22, 2014 at 10:15 AM, Axel Pahl chemis...@gmx.de wrote:
Dear Micha,
have you
'.
On Fri, Aug 22, 2014 at 1:32 PM, Jan Holst Jensen j...@biochemfusion.com
wrote:
On 2014-08-22 10:38, Michał Nowotka wrote:
A question I have is why you want to access the bond wedging.
This is very good question so I will begin with answering this. I'm
writing a module, which converts *mrv files
Hi,
I can't resist not to recommend beaker
(https://github.com/mnowotka/chembl_beaker) as a client-server
solution :)
Regards,
Michał
On Fri, Aug 29, 2014 at 7:30 PM, Greg Landrum greg.land...@gmail.com wrote:
Hi Kirk,
On Friday, August 29, 2014, Robert DeLisle rkdeli...@gmail.com wrote:
to exclude SLN Parser from RDKit at all - do I
really need it?
Kind regards,
Michał Nowotka
--
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Hi Alex,
Yes, we have :)
Please read this blog post:
http://chembl.blogspot.co.uk/2014/10/django-model-describing-chembl-database.html
and check myChembl for working example:
http://chembl.blogspot.co.uk/2014/10/mychembl-19-released.html
Cheers,
Michał
On Mon, Feb 9, 2015 at 11:19 AM, Pahl,
On 09.02.2015 12:26, Michał Nowotka wrote:
Hi Alex,
Yes, we have :)
Please read this blog post:
http://chembl.blogspot.co.uk/2014/10/django-model-describing-chembl-database.html
and check myChembl for working example:
http://chembl.blogspot.co.uk/2014/10/mychembl-19-released.html
Cheers
wrote:
Michal,
What do you expect to get for the molecule from the CTAB? In the example
below, it does not have anything in the first line, which is the one that's
used to populate the _Name attribute.
-greg
On Tue, Apr 21, 2015 at 4:32 PM, Michał Nowotka mmm...@gmail.com wrote:
Hi
Thank you very much!
On Wed, Apr 22, 2015 at 5:41 AM, Greg Landrum greg.land...@gmail.com wrote:
Got it. The problem is now fixed.
Thanks for reporting it!
-greg
On Tue, Apr 21, 2015 at 5:33 PM, Michał Nowotka mmm...@gmail.com wrote:
Hi Greg,
I would expect to have:
SMILES Name
automatically or do I need to check if the molfile
has explicit hydrogens? If the latter, how can I check this using
RDKit without writing my own SDF parser?
Michał Nowotka
On Tue, Apr 7, 2015 at 11:50 AM, Greg Landrum greg.land...@gmail.com wrote:
On Tue, Apr 7, 2015 at 12:13 PM, Michal Krompiec
,
substructure and similarity are working fine).
Am I doing something wrong? Is there anything I can do to verify if
the problem is related to RDKit or something else?
Kind regards,
Michał Nowotka
Jan,
Thanks for the confirmation. Since this is almost certainly a bug in RDKit
is there any chance for a quick bug fix release?
Kind regards,
Michał Nowotka
On Thu, Jun 18, 2015 at 7:06 PM, Jan Holst Jensen j...@jan-holst.dk wrote:
Hi Michael,
I don't know what's wrong, but I can confirm
regards,
Michał Nowotka
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Sorry, for the hassle, this has now been fixed. After running 'ctest
-R pythonTestDirChem -V' I've noticed that Pillow/PIL is missing.
On Tue, May 26, 2015 at 4:51 PM, Michał Nowotka mmm...@gmail.com wrote:
Hi,
We are trying to compile latest (2015_03_1) RDKit version on myChEMBL VMs
](c1c1)[C@@H](NC)C)
which returns both stereo centers as 'R'.
Is that a bug or an expected behavior? Are there any parameters in
RDKit that can be set to get results similar to JChem?
Regards,
Michał Nowotka
--
Thank you all for your helpful answers. I will update Beaker code,
deploy it tomorrow and see if someone comes up with another example
but like Curt I think that the modification suggested by John should
work well. Thanks again!
Michał
On Tue, Sep 8, 2015 at 4:38 PM, Curt Fischer
Hi,
The ChEMBL group is looking for a skilled Django web developer.
Background in cheminformatics and familiarity with RDKit is a plus.
Please pass this information to your colleagues.
Application form can be found here:
http://www.embl.de/jobs/searchjobs/index.php?newlang=1=EBI_00607
The
://www.ebi.ac.uk/chembl/api/utils/docs
Kind regards,
Michał Nowotka
On Tue, Jun 21, 2016 at 7:46 PM, Téletchéa Stéphane
<stephane.teletc...@univ-nantes.fr> wrote:
> Le 21/06/2016 20:18, TJ O'Donnell a écrit :
>> I would suggest setting PYTHONPATH in
>> config or ini files for
>>
ly built an index on a chembl_21 MACCS column using the
>> current RDKit and postgreSQL 9.5 (built from scratch).
>>
>> I can try with the conda install as well.
>>
>> -greg
>>
>>
>> On Mon, May 9, 2016 at 5:28 PM, Michał Nowotka <mmm...@gm
Hi,
I'm using rdkit-postgresql 2015.09.2 on Ubuntu 14.04 LTS for building myChEMBL.
I just loaded chembl_21 data to the database:
psql chembl_21 < chembl_21.pgdump.sql
Activated rdkit extension:
psql -d chembl_21 -c "create extension rdkit;"
And now I'm trying to generate fingerprints and
gt; this. Given the size of that problem, I guess it's probably unlkely that
> you've done this already. ;-)
> I'll see if I can reproduce the problem and then track it back to a
> particular molecule.
>
> In case it makes a difference: which version of PostgreSQL are you using?
>
Hi,
I have this molfile (CHEMBL265667):
11280714432D 1 1.0 0.0 0
25 27 0 0 0999 V2000
3.8042 -1.60000. C 0 0 0 0 0 0 0 0 0
4.3167 -1.90000. N 0 0 3 0 0 0 0 0 0
3.8042 -1.
Hi,
Most of you know ChEMBL DB so if you want to make this resource even
better, please share information about our technical internships:
http://chembl.blogspot.co.uk/2017/04/technical-internships-at-chembl.html
Cheers,
Michał
>
>>>> This procedure is highly order-dependent and thus not optimal, but has
>>>> to read the whole similarity matrix only once and has limited memory
>>>> consumption (you only need to keep a list of centroids). If yo
ted in all kinds of hints related to clustering
millions of compounds, especially using DBSCAN/OPTICS-based clustering
algorithms.
Regards,
Michał Nowotka
On Mon, Jun 5, 2017 at 9:19 AM, Gonzalo Colmenarejo
<colmenarejo.gonz...@gmail.com> wrote:
> Hi Chris,
>
> as far as I kno
regards,
Michał Nowotka
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___
Rdkit-discuss mailing list
go down this road and it's not clear
> how to do so, let me know and I can post some sample code. I'm afraid it's
> not completely trivial with bond queries
>
> -greg
>
>
>
> On Wed, Sep 13, 2017 at 4:42 PM, Michał Nowotka <mmm...@gmail.com> wrote:
>>
>>
Perfect, thank you!
On Fri, Sep 15, 2017 at 9:47 AM, Greg Landrum <greg.land...@gmail.com> wrote:
>
>
> On Fri, Sep 15, 2017 at 9:25 AM, Michał Nowotka <mmm...@gmail.com> wrote:
>>
>> Thanks Greg, very helpful!
>> Can you tell me how should I modify
to match a phenyl); maybe you only want non-ring atoms
> in the query to match aliphatic as well as aromatic substructures. And so
> on.
>
> -P.
>
>
> On Wed, Sep 13, 2017 at 10:42 AM, Michał Nowotka <mmm...@gmail.com> wrote:
>>
>> Is there any flag in RDkit to match bo
Hi,
Thanks for all the help with 'forcing' molecule highlighing. I have a
different (hopefully the last) problem now.
When I align a structure to the pattern and highlight it I'm getting
the attached result. The substructure is correctly aligned and
highlighted but the other part intersects with
:
> Hi Michal,
>
> There are a couple of things in here.
>
> On Fri, Aug 25, 2017 at 11:42 AM, Michał Nowotka <mmm...@gmail.com> wrote:
>>
>> Hi,
>>
>> I finally decided to try the new C++ drawing code and I found some
>> issues with it. I'll try to
Hi,
In the old drawing code it was possible to pass drawing options to the
MolToImage method.
Lookng at the C++ signature of the new DrawMolecule
DrawMolecule( (MolDraw2D)self, (Mol)mol, (object)highlightAtoms,
(object)highlightBonds [, (object)highlightAtomColors=None [,
Match(pattern)
>>>False
But as you can see without any luck. Is there anything else I can do
to get the match anyway?
Without having a match I can't aligh and higlight asprin substructure
in CHEMBL1999443 image using GenerateDepictionMatching2DStructure and
DrawMolecule funct
9443
>
> You'll need to use a slightly more generic aspirin-like query to allow the
> possibility of matching both 'normal' aspirin and embedded aromatic
> analogues. CC(=O)Oc1c1[#6](=O)[#8] should work OK.
>
> Regards,
> Chris
>
> On 13 September 2017 at 13
Hmm, but the latest release (Release_2017_03_3) doesn't have this
function, right?
Just tried it and got 'MolDrawOptions' object has no attribute
'setBackgroundColour' :(
On Sun, Sep 24, 2017 at 10:07 AM, Michał Nowotka <mmm...@gmail.com> wrote:
> Great, thanks a lot again :)
>
>
3]: d2d = rdMolDraw2D.MolDraw2DSVG(300,300)
>>
>> In [4]: opts = d2d.drawOptions()
>>
>> In [6]: opts.setBackgroundColour((1,1,0))
>>
>>
>> You can set the default highlightColour the same way.
>>
>> There's not currently a "make it transp
can define
the shape of the grid of molecules at least nothing documented in
http://www.rdkit.org/Python_Docs/rdkit.Chem.Draw.rdMolDraw2D.MolDraw2D-class.html
- `DrawMolecules` does nothing to layout molecules in such a way that
they don't obscure each other
Regards,
Michał Nowotka
Hi,
If you would like get compounds from ChEMBL instead of PubChem you can
use this Python client:
https://github.com/chembl/chembl_webresource_client
and get access to 1.7M+ unique compounds as molfiles, smiles, inchis,
inch keys and images.
Cheers,
Michał
On Fri, Dec 1, 2017 at 6:51 PM,
Hi,
Imagine I have two numpy arrays containing zeros and ones (or bools)
effectively being fingerprints:
np_1, np_2 = some_fingerprints_as_np_arrays()
I want to convert them both to rdkit fingerprint objects so I can use
DiceSimilarity:
from rdkit import DataStructs
# this won't work becuse
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