e with
> log_stream.getvalue()
> re.sub(r'\[[0-9]{2}:[0-9]{2}:[0-9]{2}[^]]*\]', '',
> log_stream.getvalue()) # remove the timestamps [12:14:19] (maybe could turn
> them off?)
>
> ... after closing SDF file I'm removing the handler
>
produces
from rdkit.rdBase import AttachFileToLog, DisableLog, EnableLog, LogMessage
./rdkit/RDLogger.py
but the functions don't seem to be used within that file.
Any pointers gratefully received.
Dave
--
David Cosgrove
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; Eduardo
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;
> Best regards,
>
> Jean-Marc
>
> --
> Jean-Marc Nuzillard
> Directeur de Recherches au CNRS
>
> Institut de Chimie Moléculaire de Reims
> CNRS UMR 7312
> Moulin de la Housse
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> BP 1039
> 51687 REIMS Cedex 2
> France
>
> O
oMolBlock(*mol, true, -1, false, true)
>
>
>How could I fix the molfile?
>
> Regards
> Santiago
>
>
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; On Tue, Oct 25, 2022 at 8:57 PM Francois Berenger
> wrote:
>
>> On 24/10/2022 19:47, David Cosgrove wrote:
>> > For the record, I have attempted this, but got only a marginal
>> > speed-up (130% of CPU used, with any number of threads above 2). The
>> >
if releasing the GIL would make it possible to do it
in multithreaded mode with a single shared fingerprint set but the answer
was that it made little improvement on a single-thread run.
On Wed, 26 Oct 2022 at 02:32, Francois Berenger wrote:
> On 24/10/2022 19:47, David Cosgrove wrote:
>
a small part of the overall time. It doesn't seem worth
pursuing further.
Dave
On Sat, Oct 22, 2022 at 11:28 AM David Cosgrove
wrote:
> Hi Greg,
> Thanks for the pointer. I’ll take a look. If it could go in the next patch
> release that would be really useful.
> Dave
>
>
ng on the C++ side by adding
> an optional nThreads argument to the bulk similarity functions. (Though
> this would have to wait for the next release since it’s a feature addition…
> we can declare releasing the GIL as a bug fix)
>
> -greg
>
>
> On Sat, 22 Oct 2022 at 09:48, D
ilst
it's doing the calculation, and recapture it afterwards? I understand
things like numpy do this for some of their functions. I'm happy to
attempt it myself if someone who knows about these things can advise that
it could be done, it would help, and they could provide a few pointers.
tached is
> the drawing of how we think the mol files should look.
>
>
>
> Best Rüdiger
>
>
>
> *Von:* David Cosgrove
> *Gesendet:* Montag, 5. September 2022 12:04
> *An:* Rüdiger Lang
> *Cc:* rdkit-discuss@lists.sourceforge.net
> *Betreff:* Re: [Rd
I have filed a fix that will hopefully appear in the next patch release.
In the meantime, I fear there is no workaround other than restarting the
script after the offending molecule, which will be a nuisance to automate.
Dave
On Mon, Sep 5, 2022 at 11:04 AM David Cosgrove
wrote:
>
>
> attached the wrong mol-file. Sorry for that. But now two files where it
> actually does not work.
>
>
>
> Best Rüdiger
>
>
>
> *Von:* David Cosgrove
> *Gesendet:* Samstag, 3. September 2022 09:12
> *An:* Rüdiger Lang
> *Cc:* rdkit-discuss@lists.sourceforg
;))
>
>#print(test)
>
> except:
>
> print('I never reach this except but the programm stopps')
>
>
>
> Many thanks!
>
>
>
> Rüdiger Lang
>
>
>
>
>
>
> Freundliche Grüße / Kind regards
>
> Rüdiger Lang
> Dat
ps://www.google.com/maps/search/Im+Schlehert+10+%0D%0A76187+Karlsruhe+%0D%0AGermany?entry=gmail&source=g>
> 76187 Karlsruhe
> <https://www.google.com/maps/search/Im+Schlehert+10+%0D%0A76187+Karlsruhe+%0D%0AGermany?entry=gmail&source=g>
> Germany
> <https://www.goog
https://github.com/OpenChemistry/fragments/tree/main/ligands
>
> Thanks!
> -Geoff
>
>
>
>
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nes across
> arbitrary bonds?
>
> Thanks,
> -Geoff
>
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Freelance computa
nds with a value. Does anyone have a snippet
>> for this?
>>
>>
>>
>> Many thanks!
>>
>> Joey Storer
>>
>> Dow Inc.
>>
>> Core R&D
>>
>> General Business
>> ___
>> Rdkit-discuss mai
7;atomNote',"line1\nline2")
> Chem.Draw.MolToFile(mol,"/Users/vass/Downloads/x.svg")
>
> Thanks,
> Marton
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news is that your padding suggestion works, so I set
> d2d.drawOptions().padding = 0.15 and voilá:
>
> [image: image.png]
>
> Amazing. Thanks!
> Giammy
>
> On Thu, 5 May 2022 at 10:32, David Cosgrove
> wrote:
>
>> Hi Giammy,
>>
>> On reflection over
t;
> Any suggestions on how to fix this?
>
> Thanks,
>
> Giammy
> --
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gestions on how to fix this?
>
> Thanks,
>
> Giammy
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--
have two ligands; one is a 6-chloroindole (6CI) and the other is a
>>>> para-chloro toluene (PCT).
>>>>
>>>> I am attempting to use the following SMARTS (S1) to match
>>>> them: '[C,c]1(Cl)[C,c][C,c]*([N,n,H])*[C,c]([C,c,H])[C,c]([H])[C,c]1'.
&g
ject: '[C,c]1(Cl)[C,c][C,c][C,c]([C,c,H])[C,c]([H])[C,c]1'
>
> Thanks!
> Adam
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t aspect
> ratio and it would be helpful if the layout engine could optimise the
> layout to fit in that unconventional space.
> Tim
>
> On Wed, Feb 9, 2022 at 11:40 AM David Cosgrove
> wrote:
>
>> Hi Tim,
>> Sorry, the font size setting both within the code
set anything.
>>> How do I go about this?
>>> Thanks
>>> Tim
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module
> 'rdkit' (most likely due to a circular import)
> (/data/github/rdkit/rdkit/rdkit/__init__.py)
>
> Are others seeing this too?
>
> Tim
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gt;
> I'm fairly new to JS development, so I'm not really sure what I'm doing
> wrong.
>
> Best,
> Adam
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xplain me and confirm my guess.
> I'm sorry for all this questions, but I'm really new to this topic.
> Hope someone can help me,
> kind regards.
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Brilliant, thanks. I will take note of how to do it myself in future 🙂.
Best,
Dave
On Wed, 21 Jul 2021 at 12:32, Greg Landrum wrote:
> Hi Dave,
>
> It's not in the JS interface yet, but I'll add it now.
>
> -greg
>
>
> On Mon, Jul 19, 2021 at 4:57 P
ow to call them from JS.
Thanks,
Dave
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node does have a WASM loader, and if I can work out how
to use that directly, I'll post a further reply.
Hopefully that all makes sense and might be helpful to other people.
Best,
Dave
On Wed, Apr 14, 2021 at 5:10 PM David Cosgrove
wrote:
> Hi,
>
> I have compiled the lates
anyone
had success with this that they can share?
Thanks,
Dave
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https
;http://www.covestro.com/>
>
> *Telephone*
>
> +49 214 6009 7356
>
>
>
> Covestro Deutschland AG
>
> COVDEAG-Chief Commer-PUR-R&D-EMEA-PMD
>
> B103, R164
>
> 51365 Leverkusen, Germany
>
> pablo.ra...@covestro.com
>
>
>
>
> ___
> Rdk
scuss/thread/C00BE94F-6F6F-466A-83D4-3045C9006026%40gmail.com/#msg34929570
>>>>
>>>>
>>>>
>>>> <https://sourceforge.net/p/rdkit/mailman/rdkit-discuss/thread/C00BE94F-6F6F-466A-83D4-3045C9006026%40gmail.com/#msg34929570>
>>>>
>>>&
ndering that using matplot but the result isn't ideal. Thanks in
> advance.
>
> Cheers,
>
> Imran
>
> --
> Imran Shah
> imran.a.s...@gmail.com
>
>
>
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so works just fine. What am I missing?
>
> Thanks
> Jason
>
>
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>
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Castro
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> Facultad de Ciencias Químicas
> Universidad Nacional de Córdoba
> UNITEFA-CONICET
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0.
>
> Thanks
> Jason Biggs
>
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Freelance computational chemistry and chemoin
X=X, that finds
> C(C)C, C(O)O, C(F)F, etc., but not C(C)O, etc.?
>
> Best regards, Jan
>
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Thanks,
>> --
>> Gustavo Seabra.
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> ____
>
> Best
> Zhenting
> 4/3/2020
>
>
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>
> ____
g the changes you make in the near future. Really
> appreciate it!
>
> Best,
> Leon
>
>
>
>
> On Wed, Feb 26, 2020 at 11:17 AM David Cosgrove <
> davidacosgrov...@gmail.com> wrote:
>
>> Hi Leon,
>> There is indeed such a thing. It's not as complete as
hope you can help me..I'm completely
> inexperienced but I am trying to learn.
>
> Sorry for the trouble.
>
> Best regards
> Francesco
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t I
> missed important ones. Any suggestions are very welcome. Thanks!
>
> Best,
> Leon
>
>
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Yes, I'm working on putting that in at the same time as everything else.
Dave
On Thu, Feb 13, 2020 at 3:54 PM Greg Landrum wrote:
>
>
> On Thu, Feb 13, 2020 at 10:57 AM David Cosgrove <
> davidacosgrov...@gmail.com> wrote:
>
>>
>> However, thanks to the ge
ase)*
>
> The interesting part are the rendering parameters. Is there a list of them
> and some examples of this function?
>
> I tried stuff like below:
>
> mol_to_svg(mol, 'Test', 150, 100, '{"bondLineWidth": 1, "legendFontSize":
> 0.5}&#x
Projects/RDKit/rdkit/rdkit/rdBase.so
Reason: image not found
which looks like it is almost working.
Thanks,
Dave
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Freelance computational chemistry and chemoinformatics developer
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component ("zero order bond") directive and the numeric bonding ("ring
> closure") directives:
>
> >>> Chem.MolToSmiles( Chem.MolFromSmiles("O1.Cl2.C12" ) )
> 'OCCl'
>
> Whether you want to do things that way is another question.
>
&
?
>
> Best,
>
> Rafał
>
>
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ite: https://sites.google.com/site/thomasevangelidishomepage/
>>
>>
>>
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>
not read.'.format(rec_num))
> else:
> print('Record {} read ok.'.format(rec_num))
> if (rec_num == len(suppl2) - 1):
> rec_num += 1
> print('Record {} not read.'.format(rec_num))
>
> This should work until what seems to be an issue in
ing through the
file in a loop using next(suppl1) and catching the StopIteration exception,
but I have the same issue. Is there a way to spot a last bad record in a
file?
Thanks,
Dave
--
David Cosgrove
Freelance computational chemistry and chemoinformatics developer
http://cozchemix.co
on't remember the remark
> number, nor the multi-conormer entry id off the top of my head.)
> --
> Dimitri Maziuk
> Programmer/sysadmin
> BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu
>
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in/colin-bournez-b9a1b2b7/>
> <http://www.icoa.fr/> *Chemoinformatics PhD Student *
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> Université d'Orléans - Pôle de Chimie Rue de Chartres - BP 6759 45067
> Orléans Cedex 2 - France +33 (0)2 38
Andrew
>> da...@dalkescientific.com
>>
>>
>>
>>
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id I was going to take a short break and do something
> fun? This isn't that.
>
>
>
> --
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org
gt; 000
>> #
>> 028
>> #
>> 000
>> #
>>
Isn't it the case that more than one molecule can share an identical
>>> fingerprint? (Depending on the specific fingerprint.) Think p-biphenyl,
>>> extended to triphenyl, tetraphenyl, etc. Still, a GA or SA method could
>>> keep going and come up with multiple matche
ech community on one of the world's most
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> martin.wat...@c4xdiscovery.com
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>
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>
> On 17 April 2018 at 19:40, David Cosgrove
> wrote:
&g
gaging tech sites, Slashdot.org! http://sdm.link/slashdot
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>>
>
> --
may not be otherwise, especially if multiple exclusions are needed.
>
> Regards,
> Chris Earnshaw
>
>
>
> On 24 Sep 2017 16:54, "David Cosgrove" wrote:
>
> Hi,
> I think Chris' solution is a bit overly complicated, though I haven't
> tested my
but I can't get the syntax to
> >> work.
> >>
> >> Any ideas? Thank you.
> >>
> >> Regards,
> >> Jim Metz
> >>
> >>
> >>
> >>
> >>
>
ost
> > engaging tech sites, Slashdot.org! http://sdm.link/slashdot
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>
>
> --
> To: "rdkit-discuss@lists.sourceforge.net"
>>
>> Message-ID: <1f673e0d-0c10-a325-dde7-c28e76e06...@vanderbilt.edu>
>> Content-Type: text/plain; charset="utf-8"; format=flowed
>>
>> Hello,
>>
>> Not directly related to rdki
7 at 20:53, Peter S. Shenkin wrote:
> Sounds like Daylight's "depictmatch", unfortunately no longer available on
> line
>
> -P.
>
> On Fri, Mar 10, 2017 at 1:28 PM, David Cosgrove <
> davidacosgrov...@gmail.com> wrote:
>
> Hi,
> In the RDKit
ted today and enter our developer competition.
> http://sdm.link/oxford___
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sue when putting multiple molecules in the
same file.
Cheers,
Dave
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Hi Chris,
I can help a bit with the first point - I am currently 'porting' the
getting started in Python bit of the documentation to c++. There's a long
way to go, but if you go to my fork of RDKit at
https://github.com/DavidACosgrove and check out the GetStartedC++ branch,
you can at least use wha
Hi Jean-Marc,
There is a property of the molecule created when it is read that contains
this information. I forget what it is called, but if you call the
molecule's GetPropNames function you should see something obvious in the
values returned. You can then call GetProp with that property name to
Hi Alexis,
While you're wrestling with the difference between () and CC(C)C you
could also consider that . in a SMILES is valid, and denotes a mixture, for
example CCO.O.O (for vodka, maybe). You might get those in FDA documents
that discuss formulations, for example. In a well scanned and p
As Greg says, this is a large area and somewhat of a diversion from my
original intention. All I was asking for was a set of test cases so I can
ensure that my port of the original Python code in AllChem.py to C++
behaves correctly. That seems like a sensible first step before embarking
on somethin
Hi All,
I'm currently working on transferring the 2 Python functions
GenerateDepictionMatching2DStructure and the 3D equivalent into the C++
core so they will be available to all users of the toolkit. Can anyone
supply example test cases for me? In particular, I would appreciate
examples of the 2
Hi All,
As I've been transliterating the GettingStartedInPython to
GettingStartedInC++, I've noticed that you get different default behaviour
from Kekulize in the two languages:
m = Chem.MolFromSmiles('c1c1')
print( 'Order : {}'.format( m.GetBondWithIdx(0).GetBondType() ) )
print( 'Aromatic :
Hi Jonathon,
Did you set PYTHONPATH to include your installation directory? That would
be the most common source of that error. However, in my experience it's a
lot easier to use the anaconda installation. You need to install conda from
anaconda.org first, and then pull the RDKit system into the a
I've been wondering if, now that you can get decent conformations from
RDKit, it would be worth devising a multi-conformation file format to make
reading multi-conf molecules faster for vs purposes. In my experience,
pulling all the conformers out of an ascii file such as an sdf can become
the RDS
Hi All,
I'm contemplating starting a chapter in the documentation called 'Getting
Started with the RDKit in C++' which would mirror the information given in
the Python chapter but with examples in C++ for those of us diehards who
like to program in a compiled language. As I recall, the learning c
Hi Dmitri,
Two things: there was a typo in the function name that Ling Chan provided-I
assume it should be Chiral in the middle, not Chrial. That might help you.
Also, the atoms in a molecule should have the property _CIPRank set, you
might be able to do something with that.
Regards,
Dave
On Sat
Hi Rocco et al.,
I too found this a very clear explanation of the different classes of
hydrogen so many thanks for taking the time. Where would a chiral H fit in?
The sort of H from Cl[C@H](F)Br? That one needs to stay even if you
collapse all explicit H atoms to implicit.
On the subject of the
HI Dmitri,
Sorry for the delay replying. I assume that by 'add padding' you mean that
the code that generates the 2D drawing coordinates should take account of
the size of the labels and would, from your example, maybe open out the
C9-O23-C14 bond a bit so that O21 and O24 are further apart? If s
I think I can beat that. When I was working on the 2D drawing code with
Greg a couple of years ago, he sent me an email at about 6 on Christmas
morning! Needless to say, he didn't get a reply until a few days later as
I fear I am not so dedicated.
Cheers,
Dave
On Thursday, 7 July 2016, Markus
on
> angles. We have never published this, but we have done a systematic
> analysis using the compounds in our ETKDG paper and MMFF minimization of
> the crystal structures could result in non-negligible differences (RMSD up
> to 3 Angstroem, median RMSD = 0.45 Angstroem).
>
> Best,
&
Hi Sereina,
I beg to differ on the advisability of minimisation, even after using the
parameters you suggest to generate the conformation. I've recently been
using the CCDC's excellent Python API to analyse the results of the
generated conformations. This lets you very quickly assess whether any o
explanation, or it could be really
> quick let's see where we end up. :-)
>
> If you replace "a.GetTotalNumHs()" with
> "a.GetTotalNumHs(includeNeighbors=True)", do the results then make sense to
> you?
>
> -greg
>
>
> On Tue, Jun 21,
Hi All,
I'm a bit confused about counting hydrogen atoms. It's a perennial problem
with cheminformatics toolkits in my experience, but this seems particularly
perverse. If I run the code:
from rdkit import Chem
from rdkit.Chem import AllChem
mol = Chem.MolFromSmiles( 'CCO' )
mol = Chem.AddHs(
n experiments which of course is a valuable
> test. It would have been useful to rerun these tests to see how sensitive
> the enrichments are to the pharmacophore definitions.
>
> Cheers,
>
> Konrad
>
> On 01 May 2016, at 17:13, David Cosgrove
> wrote:
>
> Hi
Hi Konrad et al.,
In the process of taking redundancy/early retirement from AstraZeneca this
year, I was allowed to publish various bits of code I had written over my
25 years there. Embedded within them are several versions of the SMARTS
definitions we used for defining pharmacophore features.
He might want the hydrogen counts specified to block unwanted substitutions?
Dave
> On 6 Mar 2016, at 03:38, Peter S. Shenkin wrote:
>
> Just curious here
>
> Since every SMILES is a valid SMARTS,
> How do you want the SMARTS to differ from the SMARTS the SMILES already is?
> What would b
Hi Andrew,
As chiralities go, this one has turned out to be quite valuable!
https://en.wikipedia.org/wiki/Esomeprazole
Dave
On Mon, Feb 8, 2016 at 3:05 PM, Andrew Dalke
wrote:
> Hi!
>
> Could someone explain to this non-chemist what the chirality means in
> the following?
>
> CN[S@@](=O)
HI Andrew,
I don't have a solution for RDKit, because I don't know if you can do this
sort of thing. But when I've tackled this in OEChem, I've changed the
atomic number of the substituent atom to something else (I always use Xe,
because I know that will never be anything other than a marker atom
stallation'?
Thanks,
Dave
On Thu, Dec 10, 2015 at 10:21 AM, Gianluca Sforna wrote:
> On Thu, Dec 10, 2015 at 11:12 AM, David Cosgrove
> wrote:
> > I've
> > managed to get the ubuntu installation installed via apt-get, and my
> python
> > interpreter can find
Hi All,
I'm sorry to trouble you all with this one, as I feel I should be able to
do better. I'm trying to install the latest version, 2015.09.1, but I
can't find it on sourceforge. The latest one I can find there is
2015.03.1. I've managed to get the ubuntu installation installed via
apt-get,
Just for information, if you want the full matrix of shortest path
distances for a molecule, try the Floyd-Warshall algorithm:
http://en.wikipedia.org/wiki/Floyd%E2%80%93Warshall_algorithm. It's
O(n^3), and about 10 lines of code. For molecules, you initialise the
input matrix so that dist[i][j]
Hi Jessica,
There's no denying that linux is a steep learning curve, although I expect
that I would face similar problems were I to start working in earnest on
windows.
The problem here, I would expect, is that in a new shell your environment
variables are not set. You should add the lines
expor
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