Hi Greg,
does the RDKit use behind the functions in the Chem.inchi module the
InChi-Trust software (e.g. the libinchi.dll for Windows)?
Thanks a lot
Gonzalo
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Rdkit-discuss@lists.sourceforge.net
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Hi,
I'm trying to obtain an extended reduced graph representation of a molecule
as a character string. If I use this SMILES (like Fig 1 of the
Stiefl paper): :CC(C)CCc2ccc1cncc(CN)c1c2, corresponding to
[image: image.png]
after running
m = Chem.MolFromSmiles("CC(C)CCc2ccc1cncc(CN)c1c2")
Chem.rdRed
Hi,
I'm having issues trying to build RDKt from source with Conda using the
recipe in the RDKit web page. The build is apparently complete but the
ctest only achieves 35% of passed tests. I'm using an Ubuntu 20
workstation.
I first generate a Conda environment with all the required stuff:
conda c
;
>
>
> That's an indication that you don't have your PYTHONPATH set correctly. It
> should include the $RDBASE directory (make sure that RDBASE is also set
> correctly).
>
> The documentation doesn't include this... we'll fix that.
>
> -greg
>
>
ib/x86_64-linux-gnu/librt.so.1 (0x7f1c49154000)
libutil.so.1 => /lib/x86_64-linux-gnu/libutil.so.1 (0x7f1c4914f000)
libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x7f1c48ffe000)
Do you know how can this be fixed?
Thanks a lot
Gonzalo
On Tue, Oct 19, 2021 at 9:42 AM Gonzalo Colme
Hi Greg et al,
I finally passed all the test after defining export
LD_LIBRARY_PATH=$RDBASE/lib (this fixed all the tests but
pythonTestDirChem; in turn, this was fixed by installing pandas).
Thanks for all your help
Gonzalo
On Thu, Oct 21, 2021 at 5:28 PM Gonzalo Colmenarejo <
colmenarejo.g
Hi,
I had a previous release of RDKit (2015_03_1) in my Windows 8 PC installed
in the old fashioned mode and it worked OK. I renamed the corresponding
folder and installed the latest version of RDKit through conda. Now I get
the following error message when trying to run my previous code in Jupyter
> Can you do, from the command line:
> python -c "from rdkit import Chem"
>
> On Fri, Sep 23, 2016 at 10:49 AM, Gonzalo Colmenarejo <
> colmenarejo.gonz...@gmail.com> wrote:
>
>> Hi,
>> I had a previous release of RDKit (2015_03_1) in my Windows 8 PC
>>
t last one is "conda list")
>
>
>
>
>
>
> On Fri, Sep 23, 2016 at 8:31 PM +0200, "Gonzalo Colmenarejo" <
> colmenarejo.gonz...@gmail.com> wrote:
>
> Hi Greg,
>>
>> It shows:
>>
>> ImportError: No module named rdkit
ivate your environment:
> activate my-rdkit-env
>
> See: http://conda.pydata.org/docs/using/envs.html#change-
> environments-activate-deactivate
>
> Best,
> Marta
>
> 2016-09-26 13:45 GMT+02:00 Gonzalo Colmenarejo <
> colmenarejo.gonz...@gmail.com>:
> > rdkit is not
above just says that you are trying to create a
> environment with the same name again
>
> Markus
>
> On Mon, Sep 26, 2016 at 2:11 PM, Gonzalo Colmenarejo <
> colmenarejo.gonz...@gmail.com> wrote:
>
>> Thanks a lot, Marta. Still, after activating the env
Yes, it was that.
Thanks!
On Sat, Oct 1, 2016 at 7:08 AM, Greg Landrum wrote:
> Could it be that you have forgotten to "conda install jupyter" in the
> environment where the RDKit is installed?
>
>
> On Fri, Sep 30, 2016 at 9:32 AM, Gonzalo Colmenarejo <
> colme
Hi,
I installed rdkit using the conda installation and when I try to
from rdkit.Chem.Draw import IPythonConsole
I get this error:
---ImportError
Traceback (most recent call
last)C:\Anaconda3\en
Excellent. Thanks for your fast response.
Gonzalo
On Tue, Nov 15, 2016 at 10:02 AM, Greg Landrum
wrote:
> Hi Gonzalo,
>
> You need to install the pillow package (this is the replacement for the
> old Python Imaging Library)
>
> -greg
>
>
>
>
>
> On Tue, Nov
Hi,
is there a way in RDKit to retrieve the substructure(s) corresponding to a
(hashed or unhashed) Morgan fingerprint position?
Thanks a lot in advance
Gonzalo
--
Check out the vibrant tech community on one of the world
Hi Chris,
as far as I know, Butina's sphere exclusion algorithm is the fastest for
very large datasets. But if you have 4 million compounds, using RDKit
directly can result in very long runs, even after parallellization. For
that number of molecules I think there are faster things, like chemfp (se
Hi there,
is it normal to get, for the same set of smiles, more generic Murcko
frameworks that normal frameworks? When running this:
### Generate framework for a SMILES, handling for errors
def framecheck(s):
try:
return Chem.MolToSmiles(ms.GetScaffoldForMol(Chem.MolFromSmiles(s)))
n the
Complete Link algorithm (rather than provide the system with the number of
clusters). Does anyone know how to do it?
Thanks in advance
Gonzalo Colmenarejo
--
What NetFlow Analyzer can do for you? Monitors network band
ference of ML.Clustering with Chem.Fingerprints.ClusterMols?
Thanks
Gonzalo
On Tue, Jul 19, 2016 at 1:44 PM, Greg Landrum
wrote:
> Hi Gonzalo,
>
>
> On Mon, Jul 18, 2016 at 9:54 AM, Gonzalo Colmenarejo <
> colmenarejo.gonz...@gmail.com> wrote:
>
>>
>> I have
Hi,
I'm trying to install PostgreSQL and the corresponding RDKit cartridge in a
Windows 7 laptop with Anaconda with Python 2.7 by running
conda install -c https://conda.binstar.org/rdkit rdkit-postgresql
However, I get the following error:
Package missing in current win-64 channels.
Do you kno
ared in this scope
/GWD/schem/apps/rdkit/default/Code/GraphMol/Atom.h:383: error: expected `;'
before '{' token
Any clue what's going on?
Thanks a lot,
Gonzalo Colmenarejo, PhD
Investigator
Computational & Structural Che
Hi,
Does anyone have a Daylight-like fingerprint example C++ source code that would
be willing to share?
Thanks,
Gonzalo Colmenarejo, PhD
Investigator
Computational & Structural Chemistry
GlaxoSmithKline
PTM Tres Cantos, 28760 Madrid, S
Hi,
I'm trying to compile this source code:
#include
#include
#include
#include
#include
#include
#include
#include
#include
#include
#include
#include
#include
#include
#include
#include
using namespace RDKit;
...
ROMol *MolAux1, *MolAux2;
ExplicitBitVect *fp1,
lChemReactions -lFileParsers -lSmilesParse -lDepictor
-lSubstructMatch -lGraphMol -lDataStructs -lRDGeometryLib -lRDGeneral
-I/GWD/schem/apps/rdkit/build-env/include
to compile.
Thanks,
Gonzalo
-Original Message-
From: Greg Landrum [mailto:greg.land...@gmail.com]
Sent: 14 April 2012 1
Hi,
I have performed a similarity matrix calculation of 4176 X 4016 molecules with
a program using the RDKit and it took 401 seconds. The same program with the
same sets of molecules and using the Daylight toolkit took 19 seconds.
Has anybody observed similar results? The main difference in tim
Hi Greg,
That's great. When will that be available? I'll be happy to test it more
thoroughly and with other similarities (e.g. Tversky).
Thanks,
Gonzalo
-Original Message-
From: Greg Landrum [mailto:greg.land...@gmail.com]
Sent: 22 April 2012 07:44
To: Gonzalo Colmenarejo-
Yes, please, could you provide instructions (including the link to the improved
version)?
Thanks a lot,
Gonzalo
-Original Message-
From: Greg Landrum [mailto:greg.land...@gmail.com]
Sent: 23 April 2012 11:13
To: Gonzalo Colmenarejo-Sanchez
Cc: rdkit-discuss@lists.sourceforge.net
Subject
/build-env/include
Does anyone have a clue on what's going on?
Thanks,
Gonzalo
-Original Message-
From: Greg Landrum [mailto:greg.land...@gmail.com]
Sent: 23 April 2012 11:13
To: Gonzalo Colmenarejo-Sanchez
Cc: rdkit-discuss@lists.sourceforge.net
Subject: Re: [Rdkit-discuss] sp
Hi,
I'm trying to run a program that calculates a similarity matrix that worked in
the previous RDKit release. Now I recompile with the new release:
g++ -o tanird tanird.cpp -I$RDBASE/Code -I$RDBASE/Extern -L$RDBASE/lib
-lChemReactions -lFileParsers -lSmilesParse -lDepictor -lSubstructMatch
-l
Yep - you were right. Thanks!
Gonzalo
-Original Message-
From: Riccardo Vianello [mailto:riccardo.viane...@gmail.com]
Sent: 23 July 2012 11:38
To: Gonzalo Colmenarejo-Sanchez
Cc: rdkit-discuss@lists.sourceforge.net
Subject: Re: [Rdkit-discuss] runtime error with fingerprints in new
Hi,
I've been doing speed comparisons between Daylight and the 2012.06 release of
RDKit for fingerprint calculations. The calculation of a 4179 x 4179 Tanimoto
similarity matrix takes 10 s in DL and 15 s in RDKit. Thus, the new RDKit
release is much improved in terms of speed, although is still
Hi,
I've been doing speed comparisons of SMARTS matching calculations between
Daylight (dt_match) and the latest release of the RDKit (SubstructMatch). A
matrix of 4015 SMILES matched against 1390 SMARTS took 187 s in DL, while it
took 1615 s in the RDKit program. Maybe this is an area of impro
t but I'm kind of testing my typical
situation that involves millions of molecules - not sure if that many of
molecules can be stored in memory.
Thanks a lot,
Gonzalo
-Original Message-
From: Greg Landrum [mailto:greg.land...@gmail.com]
Sent: 24 July 2012 15:08
To: Gonzalo Colme
hanks,
Gonzalo
-Original Message-
From: Greg Landrum [mailto:greg.land...@gmail.com]
Sent: 24 July 2012 16:56
To: Gonzalo Colmenarejo-Sanchez
Cc: rdkit-discuss@lists.sourceforge.net
Subject: Re: [Rdkit-discuss] speed of SMARTS matches calculations
On Tue, Jul 24, 2012 at 4:38 PM, Go
That's a great idea. Do you know what approximate or typical reduction in
memory used is obtained in the pickling process?
Thanks,
Gonzalo
-Original Message-
From: Greg Landrum [mailto:greg.land...@gmail.com]
Sent: 24 July 2012 17:40
To: Gonzalo Colmenarejo-Sanchez
Cc: rdkit-di
Dear Greg,
I use these fingerprints:
molsc[i].fp = RDKFingerprintMol(*MolAux1,1,7,2048,2,false);
Are these the same in your benchmark?
Thanks,
Gonzalo
-Original Message-
From: Greg Landrum [mailto:greg.land...@gmail.com]
Sent: 24 July 2012 15:17
To: Gonzalo Colmenarejo-Sanchez
Cc
Hi,
I have a c++ code that uses SmilesToMol. As soon as there is one SMILES that
the program fails to sanitize I get an error message like this:
[13:46:35] Explicit valence for atom # 15 N, 5, is greater than permitted
terminate called after throwing an instance of 'RDKit::MolSanitizeException'
Sent: 03 August 2012 15:20
To: Gonzalo Colmenarejo-Sanchez
Cc: rdkit-discuss@lists.sourceforge.net
Subject: Re: [Rdkit-discuss] SmilesToMol runtime error
On Fri, Aug 3, 2012 at 6:17 AM, DAvid Cosgrove
wrote:
> Hi,
>
>
>
> It's a minor point in the discussion, maybe,
mail.com]
Sent: 04 August 2012 15:49
To: Gonzalo Colmenarejo-Sanchez
Cc: rdkit-discuss@lists.sourceforge.net
Subject: Re: [Rdkit-discuss] SmilesToMol runtime error
On Fri, Aug 3, 2012 at 4:57 PM, Gonzalo Colmenarejo-Sanchez
wrote:
>
> Greg, are you planning to add a "Getting s
Hi,
I have a vendor fragmentation algorithm and I want to evaluate the presence of
the fragments/substructures in a list of molecules with the RDKit C++ API. In
order to avoid a slow SubstructMatch comparison of n fragments x m molecules I
first SmilesToMol the fragment, generate a fingerprint,
]
Sent: 07 August 2012 12:13
To: Gonzalo Colmenarejo-Sanchez; rdkit-discuss@lists.sourceforge.net
Subject: Re: [Rdkit-discuss] matching substructures to molecules
Hi Gonzalo,
SmilesToMol has a sanitize flag which you can set to False. However - I am not
sure how well you molecule fingerprints will
ilarity(class SparseBitVect bv1, class SparseBitVect bv2, double
a, double b, bool returnDistance=0)
In C++ the calculation works OK:
sim = TverskySimilarity(xreen[i].fp[0], fpsmart[0], 0.01, 0.99);
Do you have any clue why this happens?
Thank you very much,
Gonzalo Colmenarejo, PhD
Investigato
Thanks, Ricardo. I tried with the second option and it Works.
-Original Message-
From: Riccardo Vianello [mailto:riccardo.viane...@gmail.com]
Sent: 23 May 2013 13:19
To: Gonzalo Colmenarejo-Sanchez
Cc: rdkit-discuss@lists.sourceforge.net
Subject: Re: [Rdkit-discuss] Tversky similarity
Hi,
What's the best way of doing fast (approximate) substructure searches in RDKit
using fingerprints? I'm a bit confused about this topic. Any advice would be
really appreciated.
Thanks a lot,
Gonzalo
--
Try New Reli
Sorry, I had to have said that I use C++. I search a bunch of substructures
(sometimes SMILES, sometimes SMARTS) against a lot of molecules.
Thanks a lot,
Gonzalo
From: Greg Landrum [mailto:greg.land...@gmail.com]
Sent: 29 May 2013 05:41
To: Gonzalo Colmenarejo-Sanchez
Cc: rdkit-discuss
It would be extremely helpful. Thanks a lot.
Gonzalo
From: Greg Landrum [greg.land...@gmail.com]
Sent: Friday, May 31, 2013 4:57 AM
To: Gonzalo Colmenarejo-Sanchez
Cc: rdkit-discuss@lists.sourceforge.net
Subject: Re: [Rdkit-discuss] substructure search with
Hi all,
Could anyone provide some advice about how to run (fast but approximate)
substructure searches with fingerprints using C++? I have a large set of SMILES
for molecules and a relatively large set of SMILES/SMARTS for substructures.
Thanks a lot,
Gonzalo
-
rints, all the possible fingerprints sequentially, etc?
Thanks a lot for your help,
Gonzalo
From: Greg Landrum [mailto:greg.land...@gmail.com]
Sent: 09 June 2013 06:33
To: Gonzalo Colmenarejo-Sanchez
Cc: rdkit-discuss@lists.sourceforge.net
Subject: Re: [Rdkit-discuss] substructure search with finge
o: Gonzalo Colmenarejo-Sanchez
Cc: rdkit-discuss@lists.sourceforge.net
Subject: Re: [Rdkit-discuss] substructure search with fingerprints in C++
On Sun, Jun 9, 2013 at 12:29 PM, Gonzalo Colmenarejo-Sanchez
mailto:gonzalo.2.colmenar...@gsk.com>> wrote:
Yes, C++ code examples for preprocess
Thanks a lot, Greg, this is extremely helpful.
From: Greg Landrum [mailto:greg.land...@gmail.com]
Sent: 10 June 2013 05:39
To: Gonzalo Colmenarejo-Sanchez
Cc: rdkit-discuss@lists.sourceforge.net
Subject: Re: [Rdkit-discuss] substructure search with fingerprints in C++
On Sun, Jun 9, 2013 at 7
Hi,
I'm trying to calculate molecular descriptors in C++ with the RDKit. Does
anyone have a code example that could help in this case?
Thanks a lot,
Gonzalo Colmenarejo
--
Introducing Performance Central, a new
Thanks to both for the fast and extremely helpful reply!
Gonzalo
From: Greg Landrum [mailto:greg.land...@gmail.com]
Sent: 27 August 2013 16:39
To: rdkit-discuss@lists.sourceforge.net
Cc: Gonzalo Colmenarejo-Sanchez
Subject: Re: [Rdkit-discuss] molecular descriptors in C++
Nick beat me to it
I'm using IPython Notebook with python 2.7 and RDKit 2013_09_1.
Thanks a lot
Gonzalo Colmenarejo, PhD
Investigator
Computational Chemistry - ES
RD Platform Technology & Science
GSK
Tres Cantos PTM 28760 Madrid, Spain
Email gonzalo.2.colmenar...@gsk.com<mailto:gonzalo.2.colmen
ult in more accurate
measures of extent of substructure than the regular fingerprints?
Thanks a lot
Gonzalo Colmenarejo, PhD
Investigator
Computational Chemistry - ES
RD Platform Technology & Science
GSK
Tres Cantos PTM 28760 Madrid, Spain
Email gonzalo.2.colmenar...@gsk.com<mailto:gonzalo
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