is a gist showing it (I hope):
https://gist.github.com/jepdavidson/ec1664a8bfa8b921262fc844c0e523e4
Kind regards
James
From: Katrina Lexa
Sent: 21 August 2023 14:58
To: James Davidson
Cc: RDKit Discuss
Subject: Re: [Rdkit-discuss] rdDeprotect & DeprotectData
Hi Katrina,
I'm slightly unsure what "deprotection" you are trying to represent, but I
think there are a couple of problems with the rsmarts...
reaction_smarts = "[c;H1]([B;R0](O)[O;R0:1])>>[c;H1]"
This is looking for an aromatic carbon with one hydrogen AND connected to a
non-ring
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
From: Greg Landrum
Sent: 19 May 2021 14:59
To: James Davidson
Cc: rdkit-discuss@lists.sourceforge.net
Subject: Re: [Rdkit-discuss] Problem
Dear All,
I've got a strong suspicion that what I am seeing is related to the open issue
3490 (https://github.com/rdkit/rdkit/issues/3490), but as I can't seem to find
a mention of a non-spiro problem then I thought I would share.
Tested in 2020.09.4 and 2021.03.2 with the same result.
at 10:15 AM James Davidson
mailto:j.david...@vernalis.com>> wrote:
Dear All,
I am having some issues with tetrahedral stereochemistry perception in RDKit
(2020.09.4) for a certain class of molecule.
Here’s an example (rendered using cdk-depict):
https://www.simolecule.com/cdkdepict/depi
Dear All,
I am having some issues with tetrahedral stereochemistry perception in RDKit
(2020.09.4) for a certain class of molecule.
Here's an example (rendered using cdk-depict):
[cid:image002.png@01D744AE.E7C7ACA0]
Dear All,
I think this question is in some way related to the following closed issue:
https://github.com/rdkit/rdkit/pull/3015
I am working with 2020.09.1, but see the following error when calling
EnumerateStereoisomers():
RuntimeError: Pre-condition Violation
Stereo
Dear All,
I wonder if I can quickly sanity-check something(?).
I have noticed that symmetrical double bonds output with a bond stereo setting
of "3" (cis or trans (either) double bond) in the standard molblock output.
Is this expected/intentional? I would have expected a setting of "0" (use
Dear All (especially Paolo!),
I have a strong suspicion I have already asked this at some point in the past -
so apologies in advance (but I can't seem to find the answer)...
I am interested in taking an existing overlay of two RDKit molecules in 3D and
scoring the overlay using Open3DAlign
Dear All,
Recently I have been assessing some ligand conformations from crystal
structures to identify any non-ideal bond lengths, angles, torsions, or
non-bonded contacts.
What I am doing at the moment is adding some positional constraints to the
crystallographic heavy atom positions, and
s handled when there are spiro linkages.
Here's the github issue: https://github.com/rdkit/rdkit/issues/1294
I'll take a look.
Best,
-greg
On Tue, Feb 7, 2017 at 8:32 PM, James Davidson
<j.david...@vernalis.com<mailto:j.david...@vernalis.com>> wrote:
Dear All,
I have hit what
Dear All,
I have hit what I think is a problem with stereochemistry perception/handling
for certain types of pseudochiral and/or spirocyclic systems.
Basically I am observing that some types of input tetrahedral stereochemical
information gets lost when an RDKit molecule is generated.
But I
Hi Riccardo,
> are you working on Windows? Pre-built conda packages targeting the 2016.03
> patch releases are at this time only available for linux and osx.
Yes, I'm afraid so...
> an additional patch release was tagged before the UGM, and I think it wasn't
> yet pushed to the anaconda
> maintenance/support customers can reasonably request.
That sounds fair...
Kind regards
James
_____
From: James Davidson <j.david...@vernalis.com>
Sent: Wednesday, November 2, 2016 2:32 PM
Subject: [Rdkit-discuss] RDKit patch releases in conda?
To: <rdkit-discuss
Dear All,
I think I probably know the answer to this already, but wanted to double check
- did any of the four 2016_03 patch releases ever get pushed to conda?
I only seem to get 2016_03_1 with "conda update -c
https://conda.anaconda.org/rdkit rdkit"
(if not available then I guess this is
Dear All,
Enthused by all the great talks at the UGM, for the last couple of days I have
been getting more hands-on with RDKit than I have in quite a while!
I was keen to work with some peptides/proteins in 3D, but am having some
problems when adding hydrogens...
I have uploaded a GIST to
Hi again, Greg
> If you still have problems with this (or hc.c), please let me know,
hc.c fails to compile.
The errors are shown below, and then I get related linking errors. I'm hoping
all the errors are related(?)
The first line affected is line 42:
static doublereal inf = 1e20;
Kind
That looks like a leftover from a source-control conflict. I can't find it in
github:
https://github.com/rdkit/rdkit/blob/master/Code/RDBoost/Wrap.h#L133
Could it be that you are pulling from github and that you had local
modifications to the file that lead to a conflict?
Dear All,
For quite some time I have been successfully compiling RDKit on Windows using
Visual Studio 2012.
However, recently (and perhaps triggered by a recent VS update that I accepted)
I am getting errors.
The problem seems to be in Wrap.h (line 133):
<<< .mine
VS is complaining
Dear All,
I have just built revision 5775 on Windows, and the pyGraphMolWrap test fails.
The relevant bit of the verbose output is below:
78: ERROR: testGithub498 (__main__.TestCase)
78: --
78: Traceback (most recent call
Dear All,
I recently rebuilt RDKit under 64bit Windows and things worked great for me.
However, I found that when I shared the build with another user, things weren't
so good - from rdkit.Chem import AllChem gave a DLL error that pointed to
rdForceFieldHelpers.pyd.
So I then ran Dependecy
Hi Greg,
I just built the latest revision - and the functionality is exposed - thanks
(and, of course, thanks Paolo!).
Kind regards
James
__
PLEASE READ: This email is confidential and may be privileged. It is intended
for
Dear All,
I might be having a 'moment' here, but for the life of me I can't seem to find
the equivalent of RDKit::MolOps::getShortestPath exposed in python(?).
I want to pass in two atom ids, and get back a list of atom ids in the shortest
path. I could possibly try to roll my own by using
[mailto:nicholas.fi...@icr.ac.uk]
Sent: 21 April 2015 17:44
To: James Davidson; rdkit-discuss@lists.sourceforge.net
Subject: RE: Python GetShortestPath()?
Dear James,
I tried to be helpful and show you how I do it with GetAdjacencyMatrix,
however I ran into my old friend the segmentation fault 11
is that (with the thread settings OFF) the changes you checked-in
(rev5616) have indeed sorted the MolHash piece, and all tests pass – thanks!
Kind regards
James
From: Greg Landrum [mailto:greg.land...@gmail.com]
Sent: 14 April 2015 05:35
To: James Davidson
Cc: rdkit-discuss
Here's an update:
Tried building rev5211, but saw similar linking errors (to do with Boost
threading libraries). The most recent build that I have successfully managed
without the errors is rev5016.
It occurred to me that a couple of my cmake options relate to threading
Hi Greg,
James: one odd thing I notice about the error messages you posted is that
they are all referencing a boost library that seems to be present in your
build directory:
Error 2651 error LNK2005: public: virtual __cdecl
Hi Paolo,
Unfortunately I have the impression that James' problem is related to
neither of those. Might it be a boost/libboost naming issue?
Perhaps, but cmake seems happy (see below)...
James, could it be that you have multiple version of boost on your Windows
machine and CMake is not
Dear All,
I just tried building the latest RDKit build (rev. 5204) from the github
repository, and hit a lot of link errors... So (somewhat at random) I tried an
older build (5042), and saw very similar things (errors for this attempt are
below).
I am running on 64-bit Windows, and use cmake
Hi Greg – thanks!
One extra piece: as of a few minutes ago, I can confirm that revision 4947
(last revision in Feb) builds, and passes all of the tests.
Kind regards
James
From: Greg Landrum [mailto:greg.land...@gmail.com]
Sent: 08 April 2015 15:14
To: James Davidson
Cc: rdkit-discuss
Hi Paolo, Greg, et al.
I have also been having some problems recently building (64-bit Windows) from
recent github versions, but I don't know if this is related to what you see,
Paolo...
My environment is Win 7 64-bit, CMake 3.0.0, boost_1_55_0-msvc-11.0-64, MS
Visual Studio Express 2012.
I
Hi Greg,
I wondered if you (or anyone else) have been seeing any issues with win64 build
of the RDKit - with Avalon toolkit support - recently?
Yesterday I updated my local SVN copy of RDKit (to rev4274) and rebuilt.
Everything seemed to go ok, but the testAvalonLib1 test is now failing (the
Hi Greg,
The new version of the test code is targeting the 1.2 avalon toolkit
version.
Here's the commit that did that.
https://github.com/rdkit/rdkit/commit/42dab414ee6fbe5489078e5e52046608bbf785cb
As an FYI, to make these tests pass on windows, you need to edit the code
to fix a
Dear All (but mainly Paulo!),
I have really been appreciating the MMFF implementation in RDKit - particularly
now with the ability to add position / distance / angle / torsional constraints!
I have a couple of naïve questions; and apologise in advance if I have missed
answers to these in the
Hi Paolo,
First of all - please see this time my brain has engaged quicker than my
English-biased touch-typing - and I have spelt your name correctly(!).
Thanks for the very clear explanation on force constants - this is really
helpful!
And, regarding your new non-academic position vs
Hi Greg,
What these are telling you is that the second query is not using the index:
it's a sequential scan, so it has to test all rows of the database. This
happens because the index is defined for the operator %, but not for the
function tanimoto_sml(). There may be an approach to get the
Dear All,
I have recently been spending a bit more time with the RDKit cartridge, and
have what is probably a very naïve question...
Having built some RDKit fingerprints for ChEMBL_18, I see the following
behaviour (for clarification - 'ecfp4_bv' is the column in my rdk.fps table
that has been
Thanks Greg - that did the trick!
(I still see pythonTestDbCLI - as previously posted)
Kind regards
James
__
PLEASE READ: This email is confidential and may be privileged. It is intended
for the named addressee(s) only and
Hi All,
I have just rebuilt RDKit on Windows using the latest source, and am seeing a
problem with smaTest1 failing (as well as still seeing the same DbCLI failure
posted previously...)
The smaTest1 failure seems a little strange because it actually throws a
Windows executable error
Hi Greg,
Try: ctest -V -R DbCLI
that should run the test in Verbose mode so that you can see the failures.
Thanks - I have pasted the output below - looks like a file access issue (but I
don't know why...).
Kind regards
James
C:\RDKit\buildctest -V -R DbCLI
UpdateCTestConfiguration from
Dear All,
As part of a New Year's resolution, I decided I should try to enjoy the
benefits of a cutting-edge version of RDKit built from source(!) So far this
has proven to be much more realistic than eg 'not drinking for January' - as I
now have a working build to show for my efforts.
Dear All,
I think this is probably one for Paolo - I was looking at fixing certain atoms
during MMFF minimisation, but couldn't find the option... Then I re-read the
UGM slides, and found the one titled Force-field wish list, and fixed atoms
were one of the listed items!
My intended use-case
Greg wrote:
This is what it looks like the state of play at the moment is:
- Adding nitro groups tends to make molecules more lipophilic, at least as
measured by retention time in chromatography.
- Nitro groups are H-bond acceptors, at least according to the papers I
found above and
Hi Sereina,
Sereina wrote:
Regarding the AssignBondOrdersFromTemplate() method:
As far as I understood, the PDB reader assigns bond orders to the amino acids
in a protein, but if a ligand is present it puts all bonds of it to SINGLE
bonds as auto bond-type perception is not trivial (see
Hi Greg (et al.),
Thanks for the beta! I have been going through some of the recently-added
functionality, and had a couple of questions regarding the PDB reading /
writing.
1. Do I remember correctly that there was a proposal (from Roger) to add
some auto bond-type perception to the
Hi JP, Nik, Greg, RDKitters
The question about the lipophilicity (or otherwise) of nitro groups was
interesting to me... I came from a CNS background, where there was, of course,
a stricter requirement for molecules to be suitably lipophilic to cross the
blood-brain barrier. My recollection
Hi Nik,
Nik wrote:
Interesting. I wonder if this is also dependent on the transport phase that
was used. Do you have any info on that? Was it a typical 10% MeOH or more
something with dichlormethane?
I dug-out the conditions:
LC retention time Method A refers to elution of a sample through
Hi Greg,
Correct, relative (or other forms of enhanced) stereochemistry is not
possible. It's worth talking about how to deal with this, but it's
going to be
more than a little bit of work, I suspect.
I suspect so, too!
The conversation about representation of and handling of enhanced
Hi Greg
I should have provided a bit more context around what the current
behavior
is, or at least what it's supposed to be. Sorry I forgot that.
My fault - I should have (re)read the manual (I thought it seemed a bit
familiar..!)
Currently, when creating a reaction from rxnSMARTS,
Hi Greg,
I've got a question for the community about how chirality should be
handled in reactions.
This morning I managed to fix one of the outstanding reaction
stereochemistry problems in the RDKit: the loss of chirality when one
bond to a stereocenter is to an unmapped atom. Here's a
Dear All,
I just wanted to raise an observation about the behaviour of the
molblock parser. I was running some SMARTS-based substructure queries
in KNIME, and happened to be looking for aromatic N-oxides - the query
was just nO - which should maybe be the answer as well! : )
Anyway, I was
Thanks Greg, and George.
I have not tested the new win-py27 binary fully - but it does at least
behave itself when importing AllChem!
Kind regards
James
__
PLEASE READ: This email is confidential and may be privileged. It
Hi Greg,
I probably should have picked this up in the beta (but didn't...) When
I try to import AllChem, I see the following:
from rdkit import Chem
from rdkit.Chem import AllChem
Traceback (most recent call last):
File pyshell#6, line 1, in module
from rdkit.Chem import AllChem
Hi Greg,
If there's demand for it, I will also put up a windows binary.
As usual, I'd appreciate a Windows build against python 2.7 : )
Thanks
James
__
PLEASE READ: This email is confidential and may be privileged. It is
Hi Greg,
Greg wrote:
You actually don't need to add the Hs:
p1 = Chem.MolFromSmarts('[#7,#8;H1]')
p2 = Chem.MolFromSmarts('[#7,#8;H2]')
p3 = Chem.MolFromSmarts('[#7,#8;H3]') m =
Chem.MolFromSmiles('CC(=O)N')
m2 = Chem.MolFromSmiles('OCC(=O)N')
def NHOHCount(mol): return
Hi Greg,
Greg wrote:
For what it's worth: the results here are definitely not
correct for the SMILES as provided. Atoms in SMILES that are
in square brackets have no implicit Hs, so [N+] actually has
zero hydrogens. I guess you actually provided the molecules
to MOE in some other form.
Hi Greg,
windows binary (py27, please : ) )
It's up on the google download page; hopefully I remembered
all the DLLs this time. :-S
-greg
The binary works a treat - no sign of missing DLLs - thanks!
__
PLEASE
Hi Greg,
Greg wrote:
The attached .pyd is 32-bit aggdraw build for python2.7 on
windows. I tested it very briefly and it seems to work; let
me know if you have problems with it.
It works a treat - very much appreciated! My molecules have never
looked better : )
Dear Greg, Riccardo, et al.
Riccardo wrote:
I don't know exactly about the other problems, but this one
should be related to the version of the installed PIL. If I
remember correctly, BGRA raw mode requires PIL 1.1.7.
@Riccardo -
Thanks for the advice, Riccardo. I think I was already on
Dear All,
I am in the process of upgrading to python 2.7 under Windows, and part
of this has included moving to the RDKit_2011_03_2 (py27) build. I had
previously done most work with earlier versions of RDKit under python
2.6, but have found a problem with calling Draw.MolToImage() with the
Hi Greg,
Thanks for the python-full reply!
# let's test the reaction to make sure it works.
# due to a (already reported) bug in the way atom properties
are handled, nrxn cannot be directly used, # so we use a hack
and reparse it:
nrxn =
Dear All,
I am currently having some problems using the AllChem.ConstrainedEmbed() -
which I have previously used successfully in version 2010_09_1 (Windows py26
binary). The following example demonstrates the issue:
from rdkit import Chem
from rdkit.Chem import AllChem
template =
Hi Greg - great news about the beta / new functionality!
Greg wrote:
This morning I tagged the beta for the Q1 2011 (2011.03 in the new
numbering) release in svn:
http://rdkit.svn.sourceforge.net/viewvc/rdkit/tags/Release_201
1_03_1beta1/
and uploaded a source distribution to the google
Hi Greg,
Greg wrote:
If there's demand for it, I will also put up a windows binary.
As usual: if no show-stopper bugs appear, I will do the release itself
in about a week.
I would appreciate a Windows binary to check out the beta release - but
if it is just me, I can obviously wait for the
Hi Greg,
On Sat, Dec 18, 2010 at 6:27 AM, Greg Landrum
greg.land...@gmail.com wrote:
I just checked in a set of changes that should get this
(mostly) working correctly. Here's a demonstration with Geldanamycin:
In [7]:
Dear All,
I have been investigating an issue that a colleague of mine identified.
He was working with the RDKit Canon Smiles node in Knime, and found that
for the natural product, Geldanamycin, the double-bond geometry
information was being lost during canonicalisation. I repeated this
result
Dear All,
I wonder if anybody can help with the following? I am trying to
figure-out how to handle double-bond stereochemistry in reactions when
the stereochemistry is involved with the making / breaking bond.
Hopefully this example will explain better than that sentence(!):
rxn =
Hi Greg and Thorsten,
Greg:
Thorsten:
On the other hand, 4000 rows should not take that long in KNIME. How
much times does it currently take?
I just did 1000 rows on my macbook. Assuming I'm reading the knime log
correctly, that took about a minute.
Thanks for testing this out, Greg.
Dear Greg (and, of course, Thorsten and Bernd!)
Great job on the Knime nodes! I have been giving these a go and am
impressed (and excited about the future development!). A couple of
observations / comments / questions:
1. I have observed that sometimes the FP node seems to generate blank
Hi Greg,
Apologies for resurrecting a rather old thread, but I have been
investigating the Q32010_1beta1 release on a set of commercial amines
(from ACD) and came across the 'hypervalent P' issue as well.
Greg wrote:
To continue and try to answer Christian's question: it is currently
Dear All,
Today I have spent some time processing a freely-available SDF that
contains many compounds and melting-points / ranges (
http://www.mdpi.org/molmall/mdpi1-51sd.zip). The reason for doing this
is that I wanted to implement a melting-point predictor following the
work of Andreas Bender
Dear All,
I am currently struggling with something that I expect is very easy to
solve (I have just got back from holiday, so I think my brain isn't
quite in the zone!)
I am trying to read in an SDF and align each molecule to a template
scaffold provided in molfile format. I want to supply a
Thanks Greg,
Greg wrote:
Ah yes, the depictions that you get look rather silly, no?
Yes they do!
You're doing it correctly; no worries there. The problem is
that most pieces of chemical drawing software generate 2D
coordinates for molecules such that a C-C single bond is 1.0A
long. The
Dear All,
It's been a couple of weeks since Greg first helped me with this, and
after some further help I agreed that I would do my best to summarise
things for the benefit of the Group.
The attached file 'sanifix3.py' was provided to me by Greg, and
essentially does exactly what I (thought I)
Dear All,
I am trying to work out the best way to accomplish some tasks involving
RDKit, using PyMOL as an interface, and would appreciate some help. I
would like to be able to start from a PDB file of a ligand-bound crystal
structure loaded in PyMOL and be able to 'virtually' build some
Dear Greg,
Thanks for your very rapid response - 'AllChem.ConstrainedEmbed' was
just what I was looking for!
Kind regards
James
__
PLEASE READ: This email is confidential and may be privileged. It is intended
for the named
I just wanted to quickly update the List on how I've got on with this,
in case it is of use / interest to others. I followed Greg's advice and
did the following:
1. Exported molfile from PyMOL
2. Read into RDKit
3. Read in an SDF of already-constructed molecules based on the core
(could have
, James Davidson, Kirk DeLisle, Thomas Heller, Peter Gedeck,
Greg Magoon, Noel O'Boyle, Nik Stiefl,
Bug Fixes:
- The depictor no longer generates NaNs for some molecules on
windows (issue 2995724)
- [X] query features work correctly with chiral atoms. (issue
3000399)
- mols will no longer
...@gmail.com]
Sent: 18 June 2010 06:08
To: rdkit-discuss@lists.sourceforge.net
Cc: James Davidson
Subject: Re: [Rdkit-discuss] A couple of questions regarding ReactionFromSmarts
Dear all,
A followup/update on a request from a couple weeks ago:
On Fri, Jun 4, 2010 at 6:13 AM, Greg Landrum greg.land
on tidying-up and improving this modification! (or corrections if
anyone spots them - I have only briefly tested this)
Kind regards
James
-Original Message-
From: Greg Landrum [mailto:greg.land...@gmail.com]
Sent: 11 June 2010 06:02
To: James Davidson
Cc: rdkit-discuss@lists.sourceforge.net
Message-
From: Greg Landrum [mailto:greg.land...@gmail.com]
Sent: Fri 04/06/2010 05:13
To: James Davidson
Cc: rdkit-discuss@lists.sourceforge.net
Subject: Re: [Rdkit-discuss] A couple of questions regarding ReactionFromSmarts
Dear James,
On Thu, Jun 3, 2010 at 7:51 PM, James Davidson j.david
Hi,
First of all, I'd like to start by saying how much I've been enjoying
exploring the functionality of RDKit - great job, Greg!
I have a couple of questions regarding
'rdkit.Chem.AllChem.ReactionFromSmarts':
(1) I see that the reaction objects can be created from MDL Reaction
Files/Blocks -
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