Hi,
Please do not duplicate questions/posts between the mailing list and github
discussions. That's spamming the community.
-greg
On Tue, Apr 23, 2024 at 4:10 PM Ariadna Llop Peiró
wrote:
> Hello everyone,
>
> I'm currently working with a dataset of chemical compounds, aiming to
> cluster
For what it's worth, this one works too:
m.GetSubstructMatches(Chem.MolFromSmarts('P1->[Zr+3]<-C1'))
It looks like a problem in the way ring closure bonds are being handled in
the SMARTS parser.
Jan: would you mind creating an issue for this in github?
-greg
On Wed, Mar 20, 2024 at 3:30 PM Jan
Dear all,
The (free) registration for the 2024 RDKit UGM, being held from 11-13
September at the ETH in Zurich, Switzerland, is now open:
https://www.eventbrite.com/e/860637719587
You can submit proposals to do talks, tutorials, lightning talks, and
posters here:
Hi Amy,
On Tue, Feb 6, 2024 at 8:20 PM He, Amy wrote:
>
>
> Emre, great to hear from you. I also just wanted to say that not all
> entries in ZINC can be transformed into 3D structures. We encountered a
> couple of instances where the annotated stereo is nonphysical, especially
> at
Hi Emre,
Both of those compounds look like they have conflicting stereochemistry
information in the ring systems, i.e. the stereo which is specified cannot
actually exist. There's something else going on as well (that looks like a
bug) but this is already a big enough problem.
The easiest thing
-6.5969 0 0 CFG=3
>
> M V30 4 C 6.6791 -7.7781 0 0
>
> M V30 5 C 5.6563 -8.3686 0 0
>
> M V30 6 C 4.6334 -7.7781 0 0 CFG=1
>
> M V30 7 C 5.6563 -4.8257 0 0
>
> M V30 8 C 3.6109 -8.3684 0 0
>
> M V30 END ATOM
>
> M V30 BEGIN BOND
>
> M V30 1 1 1 2
>
>
Hi Nick,
Can you provide an example of exactly what you would like to have happen?
-greg
On Tue, Jan 30, 2024 at 5:46 PM Tomkinson, Nicholas <
nick.tomkin...@astrazeneca.com> wrote:
> I am trying to convert a simple V2000 molfile with or without the chiral
> flag into a V3000 molfile but this
Hi Marawan,
We don't currently support CSRML. It is certainly an interesting and
flexible format, so it would be cool to have, but it would be a fair amount
of work to implement.
-greg
On Tue, Dec 19, 2023 at 4:19 AM Marawan Hussien via Rdkit-discuss <
rdkit-discuss@lists.sourceforge.net>
Dear all,
The 2024 RDKit UGM will take place from 11-13 September in Zurich
Switzerland.
We'll post more information and open registration in Q1 of next year.
Best regards,
-greg
___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
I'm not sure exactly what you're looking for, but all of the code for
reading and writing SMILES is here:
https://github.com/rdkit/rdkit/tree/master/Code/GraphMol/SmilesParse
-greg
On Tue, Oct 24, 2023 at 11:51 AM Eduardo Mayo
wrote:
> Hello all,
>
> I hope you all are doing well.
>
> I am
Hi Giammy,
We currently only have the Python implementation. Doing a C++ version is on
my ToDo list, but I'm not sure when we'll get there.
best regards,
-greg
On Thu, Sep 7, 2023 at 1:17 PM Gianmarco Ghiandoni
wrote:
> Hello all,
>
> I've been testing the Python module from rdkit.Chem
If you're willing to live with the RDKit's definition of bridgehead (see
below), then there is built-in functionality you can use:
from rdkit.Chem import rdqueries
qa = rdqueries.IsBridgeheadQueryAtom()
mol = Chem.MolFromSmiles('C1CC2CCC1C2')
mol.GetAtomsMatchingQuery(qa)
That last call returns
Hi Ling,
On Mon, Jun 19, 2023 at 3:03 AM Ling Chan wrote:
>
> I got some questions about atom indexing. Just wonder if you could help me?
>
>1. In m3=Chem.CombineMols(m1,m2) , is it guaranteed that the atom
>indices in m3 is equivalent to the indices in m1 followed by the indices in
>
Hi Susan,
The RDKit does not currently support SCSR.
-greg
On Fri, 28 Apr 2023 at 15:07, Susan Leung wrote:
> Hi all,
>
> I am trying to read in some Self-Contained Sequence Representation (SCSR)
> structures
> https://doi.org/10.1021/ci2001988
>
> But I am encountering some issues. I just
Dear all,
This year's RDKit UGM will take place in Mainz, Germany from 20-22
September. Paul Czodrowski is this year's organizer.
As last year, we're planning the UGM as an in-person event with a live
stream of the sessions for people who can't make it in person.
Free registration for both
Hi Ling,
I can't reproduce this problem on windows using the most recent version of
the RDKit.
Which version of the RDKit are you using and how did you install it?
Please also share exactly what you see for an error message.
-greg
On Tue, Feb 21, 2023 at 7:03 AM Ling Chan wrote:
> Dear
Hi Joao,
I can't reproduce that behavior on Windows using the most recent
conda-forge version of the RDKit: I always get the same values for the
first few GETAWAY descriptors and numbers 245 and 246.
Which operating system/RDKit version are you using?
-greg
-greg
On Fri, Feb 17, 2023 at
Hi Thomas,
* in SMARTS just means "any atom".
[!H], for historical reasons, means "and atom without a single Hydrogen"
(i.e. it matches CH2 and CH3, but not CH)
You want [!#0], that is "not hydrogen"
-greg
On Mon, Jan 30, 2023 at 5:40 PM Thomas wrote:
> I thought that the wildcard * would
Hi Eric,
That would be due to the fix for this bug:
https://github.com/rdkit/rdkit/issues/5036
If you were generating the fingerprints on "normal" (i.e.
hydrogen-suppressed) graphs, you wouldn't notice this one, but the fact
that you add the Hs before generating the fingerprint causes you to
Hi Susan,
The current version of the tautomer hash doesn't do keto-enol tautomerism
(your first example). It would be worthwhile for us to add this as an
option, but it's not currently available.
-greg
On Wed, Jan 11, 2023 at 3:04 PM Susan Leung wrote:
> Hi all,
>
>
>
> I am trying out the
Hi Ling,
Unfortunately there isn't any manual (or section of the manual) for the bit
rendering code and the API documentation is also missing.
There are some blog posts out there with more information:
http://rdkit.blogspot.com/2018/10/using-new-fingerprint-bit-rendering-code.html
On Tue, Dec 20, 2022 at 11:11 AM Wim Dehaen wrote:
> Hello,
> I think the place the hydrogens get lost is during the "MolFromMolBlock"
> operation. Try to add the flag *removeHs=False.*
>
Wim's answer is correct: by default the RDKit functions which construct
molecules from SMILES, Mol, etc.
need a global ranking to tell which nuclei are chemically
> equivalent.
>
> Happy holidays!
> Juuso
>
> On Fri, Dec 16, 2022 at 5:24 PM Greg Landrum
> wrote:
>
>> Hi Juuso,
>>
>> No, the new code does not calculate those ranks.
>> There may be alternati
Dear all,
After thinking about it but not doing anything far, far too many times,
I've finally managed to start an RDKit FAQ. For the moment I'm using the
github wiki for this since it's easy and quite visible:
https://github.com/rdkit/rdkit/wiki/FrequentlyAskedQuestions
If you have ideas for
Hi Juuso,
No, the new code does not calculate those ranks.
There may be alternatives though; what are you interested in using the CIP
ranks for?
-greg
On Thu, Dec 15, 2022 at 3:45 PM Juuso Lehtivarjo
wrote:
> Hi,
>
> According to my tests with the new CIPLabeler, it seems that it does not
>
Hi Dave,
We have multiple examples of this in the code, here’s one:
https://github.com/rdkit/rdkit/blob/b208da471f8edc88e07c77ed7d7868649ac75100/Code/GraphMol/ForceFieldHelpers/Wrap/rdForceFields.cpp#L40
I’m not sure how this would interact with the call to Python::extract
that’s in the bulk
On Fri, Sep 30, 2022 at 4:35 PM Rocco Moretti wrote:
> Hi Greg,
>
> > The RDKit doesn't normally convert data field values into floats unless
> you explicitly ask it to
>
> I did notice that mol.GetProp() will always return things by string, and
> you would need to use mol.GetDoubleProp() if you
Hi Rocco,
Paolo already replied about the options available for python when
interpreting the data fields from an SDF. The RDKit doesn't normally
convert data field values into floats unless you explicitly ask it to, so
this would be fine to do from Python
The CTAB part of the SDF, which includes
Hi Eduardo,
In order for anybody to be able to help here we need more information: how
did you install the rdkit in the notebook, which versions of everything
else are you using, etc.
The easiest way to answer this would be to just include a link to the colab
notebook itself.
-greg
On Wed, Aug
Hi,
PATH is not a variable used by the RDKit, that's something which is used by
your operating system, so you'd need to check however your operating system
handles non-ASCII characters.
The RDKit does use the variable RDBASE, which is handled internally by
reading it into an 8 bit string, so I
Hi Susan,
On Wed, Jul 20, 2022 at 4:32 PM Susan Leung wrote:
>
> I just noticed this because I found other toolkits have the exact opposite
> behaviour. I can see the point of view from both sides.
>
> With other toolkits, we can search for chirally pure molecules; however,
> in RDKit we cannot
Hi Susan,
The expected behavior for substructure search with enhanced stereo is
documented here:
https://www.rdkit.org/docs/RDKit_Book.html#enhanced-stereochemistry-and-substructure-search
A quick explanation of the logic, assuming a single stereocenter for
simplicity:
- OR contains either the @
Hi Francois,
Yes, I would recommend SDF, the V3000 version if possible. The xyz format
is problematic because it doesn’t have bonds. There is still a way to kind
of work with that together with SMILES or sdf though:
Hi,
I guess the differences you are seeing are arising because you have
different conformers of the molecule.
The conformer generation process in EmbedMolecule() uses a stochastic
procedure and if you want to be sure that you get the same results from
multiple runs you need to provide a random
Hi Jean-Marc,
The question about atom data was answered elsewhere by Nils, but on atom
ordering:
On Mon, Jun 13, 2022 at 2:50 PM Jean-Marc Nuzillard <
jm.nuzill...@univ-reims.fr> wrote:
>
> About mol = Chem.MolFromSmiles(smi), I would like to know
> whether the atoms indexes in mol follow
Hi Eduardo,
If I'm understanding what you want to do correctly, then you could try
extending your SMARTS pattern to include a ring bond to a neighbor from
each atom in the ring:
*@*~1~*(@*)~*(@*)~*(@*)~*(@*)~*~1@*
If you only want the indices of the ring atoms, you can then just pick
those out
Hi Thomas,
On Tue, May 24, 2022 at 10:43 PM
wrote:
>
>
> how would I get the SGroups information into a ROMol so that this is
> output when I write the ROMol to a SDFile?
>
> I have seen the SubstanceGroup class, but haven’t found any example how to
> use this in a python context.
>
>
You can
Hi Diogo,
The easiest way to do this is to use the substructure matching code with
"uniquify=False" to find all the automorphisms between a molecule and
itself:
In [8]: m1 = Chem.MolFromSmiles('Oc1c1')
In [9]: list(m1.GetSubstructMatches(m1,uniquify=False))
Out[9]: [(0, 1, 2, 3, 4, 5, 6),
Hi Mu,
The RDKit has code for identifying pharmacophoric points and calculating
the distances between them, but there is no pharmacophore perception tool
in the core RDKit.
Best regards,
-greg
On Tue, Mar 29, 2022 at 12:25 PM Muhammad Akram
wrote:
> Hello Everybody,
>
>
>
> I am looking if
Hi Adam,
By default the RDKit picks the locations to do wedging. There's no built-in
function to reapply the wedging from an input mol file (we probably should
add this), but you can find a good one here, as part of the ChEMBL
structure pipeline:
gt; Best,
> Markus
>
> On Fri, Mar 18, 2022 at 1:32 PM Greg Landrum
> wrote:
>
>> Dear all,
>>
>> I tagged the first beta of the 2022.03 RDKit release this morning.
>> Assuming nothing weird shows up during testing, we'll do the actual
>> release on the 25th.
&g
Dear all,
I tagged the first beta of the 2022.03 RDKit release this morning. Assuming
nothing weird shows up during testing, we'll do the actual release on the
25th.
You can find the new beta here:
https://github.com/rdkit/rdkit/releases/tag/Release_2022_03_1b1
Conda builds of the beta are
Hi Pat,
I don't think you're doing anything wrong. This looks like a bug in the
RDKit.
It seems to be connected to the PatternHolder... I will look into it.
-greg
On Sat, Mar 12, 2022 at 10:26 PM Patrick Walters
wrote:
> Hi All,
>
> I'd appreciate any insight on what I'm doing wrong. I'm
Hi Francois,
Though there are various tables with electronegativity values in the code,
they are all for particular purposes (i.e. the MMFF force field), not
directly documented, and not really intended to be used elsewhere.
I think your idea of parsing the data from the BODR is the best
One minor refinement... Pat's answer can be made a bit more efficient by
replacing the atom types which appear in both aromatic and aliphatic forms
with the corresponding atom number queries and by moving the !#1 to the
end. This should produce the same results as Pat's SMARTS:
not_organic_pat =
Dear all,
This year's RDKit UGM will take place in Berlin, Germany from 12-14
October. The organizers are the Machine Learning Research group from Bayer
Pharma.
We're planning the UGM as an in-person event, but we will, assuming the
technology works, also live stream the sessions.
Free
Hi Charmaine,
Sorry for the slow reply.
On Wed, Feb 16, 2022 at 4:04 PM Charmaine Siu Man Chu <
charmaine@liverpoolchirochem.com> wrote:
>
>
> I’m currently looking at the deprotection function within
> Chem.rdDeprotect. Is it possible to specify a specific deprotection from
> the in-built
>
> Tim
>
> On Fri, Feb 11, 2022 at 1:57 PM Greg Landrum
> wrote:
>
>> Hi Tim,
>>
>> That's a nice one.
>>
>> For people not familiar with the problem:
>> The RDKit coordinate generation prefers aligning molecules with the X
>> ax
Dear all,
This year it is once again possible to do longer projects as part of Google
Summer of Code, so I think it makes sense for the RDKit to participate
again.
If you have ideas for projects which can be accomplished with about 350
hours of effort (~30 hours/week for 12 weeks) and are
Hi Shani,
This is a limitation of the RDKit's 2D coordinate generation code.
The workaround is to use the RDKit's coordgen integration to generate 2D
coordinates. You can toggle this on by doing:
from rdkit.Chem import rdDepictor
rdDepictor.SetPreferCoordGen(True)
That will, in general, give
Hi James,
The RDKit does not have a full-featured CSV parser, writing such a thing is
a non-trivial task. If you need to support general CSV, I'd suggest using
pandas or python's builtin csv module... it seems like overkill, but
dealing with all the oddness that can show up in CSVs is really not
ks!
> Tim
>
> On Tue, Dec 21, 2021 at 6:24 AM Greg Landrum
> wrote:
>
>> Hi Tim,
>>
>> You probably need to provide the argument "-DBoost_NO_BOOST_CMAKE=TRUE"
>> to cmake.
>>
>> -greg
>>
>>
>> On Mon, Dec 20, 2021 at 6:20 PM T
Hi Tim,
You probably need to provide the argument "-DBoost_NO_BOOST_CMAKE=TRUE" to
cmake.
-greg
On Mon, Dec 20, 2021 at 6:20 PM Tim Dudgeon wrote:
> I'm hitting problems when building from source on an Ubuntu system.
> I've installed the dependencies (e.g. boost) using apt and think I have
>
Hi Lewis,
Dealing with all the strange chemical representations that show up "in the
wild" is an ongoing struggle.
Your first example is pretty clearly intended to be an azide and we can
certainly add a rule to normalize that one to what the RDKit expects it to
be (there already is a rule for
Hi Susan,
I haven't looked at the Sgroup or unsaturation flags yet (I will try to do
this later today), but a word on the aromaticity/kekulization.
One of the things which is going wrong here at the cartridge level is that
qmol_from_ctab() is sanitizing the molecules it reads in. This is not
Unless you can make your reactant definitions a lot more specific, I think
you're going to have to do the post-processing.
The RDKit just uses all possible substructure matches of the reactant
templates you provide... it makes no attempt to determine which is "best".
-greg
On Sun, Dec 5, 2021
Hi Jessica,
That Dockerfile isn't written to be used interactively, it's just set up to
build the wrappers and then copy the resulting build artifacts + the demo
files to the building machine.
So if I run it like this:
DOCKER_BUILDKIT=1 docker build -f docker/Dockerfile --build-arg
en.py",
>>>> line 13, in
>>>> from rdkit.Chem import rdCoordGen, rdMolAlign
>>>> ModuleNotFoundError: No module named 'rdkit'
>>>>
>>>>
>>>> That's an indication that you don't have your PYTHONPATH set correctly.
>
urce with Conda/Linux x86_64: Python 3
> environment".
>
> Thanks a lot
>
> Gonzalo
>
> On Sat, Oct 9, 2021 at 3:55 PM Greg Landrum
> wrote:
>
>> Hi Gonzalo,
>>
>> The message you show below is just a warning, not an actual error.
>>
Hi Anthony,
Can you share the molecule that you're having trouble with?
As for the pharmacophore definitions: we don't have a great set of
definitions available, but the one I normally suggest would be to use
either the ones in RDConfig.RDDataDir+'/BaseFeatures.fdef'
or the feature factory which
Hi Gonzalo,
The message you show below is just a warning, not an actual error.
Do you get actual compilation errors? If so please share them.
Try running the tests with:
ctest --output-on-failure
and sharing the error messages you see.
Best,
-greg
On Fri, Oct 8, 2021 at 1:49 PM Gonzalo
t might just be an extra build
> configuration option in your build scripts :)
>
> ...E
>
>
>
> On Fri, Oct 8, 2021 at 6:42 AM Greg Landrum
> wrote:
>
>> Dear all,
>>
>> I tagged the first beta of the 2021.09 RDKit release this morning.
>>
Dear all,
I tagged the first beta of the 2021.09 RDKit release this morning. Assuming
nothing weird shows up during testing, we'll do the actual release on the
18th.
You can find the new beta here:
https://github.com/rdkit/rdkit/releases/tag/Release_2021_09_1b1
Conda builds of the beta are
It would have helped if I'd gotten the sense of the arguments correct...
sorry about that.
What I should have typed is:
d = Draw.MolDraw2DSVG(350,300,-1,-1,True)
The "True" argument disables FreeType
-greg
On Mon, Oct 4, 2021 at 4:38 PM Geoffrey Hutchison
wrote:
> > Unfortunately there are
Hi Geoff,
you need to disable the use of freetype when you create the MolDraw2DSVG
object.
Unfortunately there are not keyword arguments for this (something for me to
fix ASAP), but you can do this as follows:
d = Draw.MolDraw2DSVG(350,300,-1,-1,False)
That last "False" turns off FreeType and
Hi Mark,
You haven't shown how the molecules in reagentsRdMolList are constructed,
but from the error message I guess that they have been created without
running any of the sanitization code.
The example transformation you show includes ring information, so it will
generate errors if the
tereo
> info in SMILES sting) will not affect the results or give biased results.
> Thank you!
>
> Best,
> Leon
>
>
> On Tue, Jul 27, 2021 at 12:59 AM Greg Landrum
> wrote:
>
>> Hi Leon,
>>
>> The results of EmbedMultipleConfs() have a random component a
Hi Lewis,
This looks odd to me as well, but I don't have a quick answer to
explain/account for it.
I'll try and take a look in the near future.
-greg
On Wed, Jul 21, 2021 at 11:57 PM Lewis Martin
wrote:
> Hi RDKit,
> How does one input the number of bits to the ShapeTanimotoDist function?
>
Hi Leon,
The results of EmbedMultipleConfs() have a random component and are
atom-order dependent. The first of these will cause you to get different
results across runs even if you use exactly the same molecule unless you
set the random number seed.
The atom-order dependance means that if the
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 PM David Cosgrove
wrote:
> Hi,
>
> In this blogpost
> https://greglandrum.github.io/rdkit-blog/technical/2021/05/01/rdkit-cffi-part1.html,
> Greg mentions the CFFI function get_json(). Is that
;
> 2 4 2 0 0 0 0
>
> 2 3 1 0 0 0 0
>
> M END
>
> =MOL file above this
>
>
>
>
>
> *From:* Greg Landrum
> *Sent:* Friday, July 16, 2021 11:38 PM
> *To:* Webster Homer
> *Cc:* rdkit-discuss@lists.sourceforge.net
&
Hi Webster,
Without seeing an actual query I am inclined to believe that it’s not a
bug. The problem is more likely a query which has not been drawn explicitly
or an easily made mistake in the way the cartridge is being used.
Assuming that the aldehyde queries have been drawn with an explicit H
Hi Hao,
The reference for how the Gasteiger charges is calculated is in the
documentation for the function:
https://www.rdkit.org/docs/source/rdkit.Chem.rdPartialCharges.html#rdkit.Chem.rdPartialCharges.ComputeGasteigerCharges
It does not use atomic coordinates.
The MMFF charges are described in
Hi Leon,
You can convert the tanimoto distance to similarity, but the formula is:
Similarity = 1 - Distance
Best,
-greg
On Tue, Jun 29, 2021 at 3:21 AM topgunhaides wrote:
> Hi guys,
>
> A quick question:
>
> RDKit computes the "Shape Tanimoto distance" by calling the
> "ShapeTanimotoDist".
Hi Velik,
This is a discussion list for the RDKit, not for Autodock Vina.
Here's the link for getting help about Autodock Vina:
http://vina.scripps.edu/questions.html
Best,
-greg
On Tue, Jun 22, 2021 at 10:08 AM Velik Velikov wrote:
> Dear all,
>
>
>
> I am constructing new molecules (de
Hi Xinzhou,
I will take a look at adding support for this to the cartridge.
-greg
On Wed, Jun 9, 2021 at 9:54 PM Xinzhou Liu via Rdkit-discuss <
rdkit-discuss@lists.sourceforge.net> wrote:
> Hi RDKit team,
>
> I'm doing some substructure counting using the RDKit cartridge in my
> postgres
Hi JP,
On Thu, Jun 17, 2021 at 8:37 PM JP Ebejer wrote:
>
> I am trying to standardize(/normalize?) some molecules from different
> sources, to generate a set of descriptors for them. I have done this a
> number of times, and each time I find the process slightly confusing. I
> have the
Hi Brian,
On Mon, Jun 7, 2021 at 4:36 AM Brian Cole wrote:
> This is a bit more of a question for AWS themselves, though I believe the
> RDKit build for the Postgres extension can be improved as well.
>
> The AWS documentation states, “RDKit extension version 3.8.”
>
>
Hi Joey,
This is a non-trivial problem and one which Jan Jensen seems to have solved
quite nicely with xyz2mol:
https://github.com/jensengroup/xyz2mol
Are you able to use that package?
-greg
On Sat, Jun 5, 2021 at 2:56 AM Storer, Joey (J) wrote:
> Dear all,
>
>
>
> For molecular modeling
Sorry I missed this thread earlier.
I think the documentation answers this question:
https://www.rdkit.org/docs/RDKit_Book.html#rdkit-fingerprints
-greg
On Tue, May 18, 2021 at 12:34 PM Nils Weskamp
wrote:
> Hi Din,
>
> to the best of my knowledge, the "RDKit" fingerprints are a path-based
>
Hi Marco,
On Wed, May 26, 2021 at 2:37 PM Marco Stenta wrote:
> Dear Colleagues,
> I recently came across this
> https://pypi.org/project/rdkit-pypi/
>
> is pip going to be supported officially by the dev community? any plan?
>
I'm not quite sure yet. I believe that at the moment the pip
Hi Hao,
The RDKit's extensions to SMARTS are documented here:
https://www.rdkit.org/docs/RDKit_Book.html#smarts-support-and-extensions
There is not an extension for "N_lp" and what the translation should be is
VERY highly dependent on what the authors meant by "lone pair".
For example: does the
Dear all,
Registration for the 2021 RDKit virtual UGM is now open:
https://www.eventbrite.com/e/virtual-10th-rdkit-ugm-2021-tickets-157206887031
I'm currently sending this announcement only to the mailing list so that
people here have a chance to register first. I'll do the usual social media
I first heard the term "para stereochemistry" from Salome Rieder (a PhD
student at the ETH Zurich), who pointed me to this paper as a source for
term:
https://pubs.acs.org/doi/pdf/10.1021/ci00016a003
I tend to call this "dependent stereochemistry" since I think it's clear,
but that's definitely
Hi Francois,
On Thu, May 20, 2021 at 3:19 AM Francois Berenger wrote:
>
> The other day, I was looking for a paper describing them
> but the only thing I found was a reference to some Daylight
> product.
>
> I know there is a paper (maybe several in fact) for ECFP for example.
> Weren't the
Thanks James!
On Wed, 19 May 2021 at 17:40, James Davidson
wrote:
> Hi Greg,
>
>
>
> Thanks for the response (and sorry to be the bearer of bad news!).
>
> Issue added: https://github.com/rdkit/rdkit/issues/4155
>
>
>
> Kind regards
>
>
>
> James
&
Hi James,
I don't think that's the same bug as #3490. I think it's something
different; "yay".
;-)
It would be great if you could file a github issue for this.
Thanks,
-greg
On Wed, May 19, 2021 at 3:20 PM James Davidson
wrote:
> Dear All,
>
>
>
> I’ve got a strong suspicion that what I am
Hi Jean-Marc,
In that particular configuration:
[image: image.png]
the central atom is not a chiral center since atoms 1 and 5 have the same
absolute stereo.
However, if you change the stereo of either atom 1 or 5, then the central
atom can be a chiral center:
[image: image.png]
This
Hi,
This year's RDKit UGM is going to take place October 14 and 15. It will,
unfortunately, once again be a purely virtual event. Hopefully next year we
will be able to travel again and all get together in one physical location,
but this year it's not possible to really plan an in-person meeting.
Hi Gonzalo,
Yes, the RDKit uses the InChI trust library to handle InChIs.
-greg
On Tue, May 4, 2021 at 7:30 AM Gonzalo Colmenarejo <
colmenarejo.gonz...@gmail.com> wrote:
> Hi Greg,
>
> does the RDKit use behind the functions in the Chem.inchi module the
> InChi-Trust software (e.g. the
On 26/04/2021 23:35, Greg Landrum wrote:
> >> Hi Francois,
> >>
> >> The implementation which is there does, I believe, the right thing.
> >> However... first you need to find the Murcko Scaffold, then you can
> >> convert that scaffold to the generic form
Hi Francois,
The implementation which is there does, I believe, the right thing.
However... first you need to find the Murcko Scaffold, then you can convert
that scaffold to the generic form:
In [5]: m = Chem.MolFromSmiles('CCc1ccc(O)cc1C(=O)C1CC1')
In [6]: scaff =
> >>
> >> Dear Greg,
> >>
> >> It works! It seems I can call functions of RDKit from this console,
> >> however, when I start spyder and try to run them I still get the
> >> error. Could it be something related to the spyder interpreter?
&
\Scripts\ipython.exe
> C:\Anaconda\Scripts\ipython.exe
>
> Best regards,
>
> Andrés
>
> El mié, 14 abr 2021 a las 17:06, Greg Landrum
> () escribió:
> >
> > That looks good. Please send the output of:
> > ipython -c 'import IPython;import
> rdkit;print(
gt;
> Andrés
>
> El mié, 14 abr 2021 a las 15:42, Greg Landrum
> () escribió:
> >
> > What do you see when you execute this quick test to ensure that ipython
> and the rdkit are both really installed?
> >
> > python -c 'import IPython;import
> rdkit;prin
What do you see when you execute this quick test to ensure that ipython and
the rdkit are both really installed?
python -c 'import IPython;import
rdkit;print(IPython.__file__,rdkit.__file__)'
-greg
On Wed, Apr 14, 2021 at 2:58 PM Andrés Sánchez Ruiz <
andressanchezrui...@gmail.com> wrote:
>
Hi Andrés,
The typical reason for this problem is that you created a separate
environment for the RDKit and installed the package there, but forgot to
install ipython. When this happens ipython is run from the base environment
and can't find the rdkit. Can you please confirm that you have ipython
Hi Geoff,
Congrats to you and co-authors on the paper and thanks for offering to
contribute to the RDKit.
Given the dependence on py_rdl, this probably isn't currently a good match
for the core RDKit (we try to minimize adding additional external
dependencies), but it would be great to have it
tly installed the 2020.03.3 version with postgresql=12.2 and
> have had no problems.
>
> Thanks !
>
> Drew
>
>
> On Fri, 26 Mar 2021 at 15:14, Greg Landrum wrote:
>
>> Dear all,
>>
>> I'm pleased to announce that the 2021.03 version of the RDKit is
, Mar 26, 2021 at 4:13 PM Greg Landrum wrote:
> Dear all,
>
> I'm pleased to announce that the 2021.03 version of the RDKit is released.
> We actually managed to get the .03 release done during March. Shocking! ;-)
> The release notes are below.[1]
>
> The release files are
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