On 10/15/2012 04:01 PM, paul.czodrow...@merckgroup.com wrote:
this one should work:
http://code.google.com/p/rdkit/wiki/descriptor_calculation
Thanks!
I found this one in the wiki also:
http://code.google.com/p/rdkit/wiki/DescriptorsInTheRDKit
I'll try to start using them.
Regards,
F.
At least for the MCS calculation, there is an R package
for chemistry:
https://bioconductor.org/packages/release/bioc/vignettes/fmcsR/inst/doc/fmcsR.html
On 02/19/2017 07:33 PM, Thomas Evangelidis wrote:
> Dear all,
>
> I want to align 250 compounds that binding to the same pocket to one of
>
Hi,
Here is a Python script that was created with the help of some
rdkit wizards:
https://github.com/UnixJunkie/mol2ecfp4
It works with unfolded ECFP4 fingerprints, so not exactly
what you are looking for.
There would be more modifications needed in order to fold
the fingerprint to the desired
I'll send a Python script.
It works for .smi files.
If anyone can adapt it to work on sdf files, that would be wonderful.
Just give me 5mn to put it on github.
On 03/16/2017 09:28 AM, Thomas Evangelidis wrote:
> Hello,
>
> I created a numpyarray from a molecule using the following function:
>
>
Hello,
Not directly related to rdkit, but if someone that have
the original PDF of this file format could place it
online permanently, that would be wonderful.
The official URL at tripos.com is dead since quite some time
apparently.
And that's bad because it's a quite popular file format
and its
On 08/16/2017 03:36 PM, Greg Landrum wrote:
Hi Shuai,
The RDKit Mol2 parser is really only validated for the atom types
generated by corina. I'm not surprised that the ouput from open babel
would not be understood. This is documented:
Hello,
Is it possible to decompose partial charges with rdkit?
I am afraid that Gasteiger-Marsili (PEOE) is mostly about sigma bonds,
but I might be wrong.
Regards,
F.
--
Check out the vibrant tech community on one
On 07/25/2017 05:45 AM, Katrina Lexa wrote:
Hi All,
I'm relatively new to RDKit, so I apologize for what may be a silly
question. I'd like to generate a set of local minimum conformations
around my input conformation, using a set of defined flat bottom
potentials (0.2, 0.6, 1.0, and 1.4), in
On 08/16/2017 06:14 PM, Greg Landrum wrote:
On Wed, Aug 16, 2017 at 3:55 AM, Francois BERENGER
<beren...@bioreg.kyushu-u.ac.jp <mailto:beren...@bioreg.kyushu-u.ac.jp>>
wrote:
On 08/16/2017 03:36 PM, Greg Landrum wrote:
The RDKit Mol2 parser is really only validated
On 08/17/2017 03:19 AM, Bennion, Brian wrote:
Hello All,
I am parsing a set of 2D sd files in rdkit in order to generate a 3D
structure. The code is below and is based on what I could find on the
list for errors in generating 3D coordinates.
Temp.mol is the downloaded molfile from chembl
Hello,
I'd like to install rdkit system-wide.
However, I'd like the install to use a regular system package
since rdkit is available in my distro.
I don't like system-wide install from sources.
Because they tend to install things in different places
than what the binary package does, and
On 06/22/2017 11:20 PM, gosia olejniczak wrote:
Hi again,
i found where the problem was (it seems):
as i was reading in molecules from sdf file through "SDMolSupplier" by
doing:
suppl = Chem.SDMolSupplier(filename)
the hydrogen atoms were removed (what was not obvious since e.g.
Hello,
I am afraid that in AllChem.GetConfomerRMSD: one doesn't get the RMSD
between the two conformers but an upper bound of it.
I understand from the doc that if they are aligned, they are aligned
to the first conformer of the molecule.
To get the real RMSD between two conformers, they must
coordinate generation if the initial
embedding fails.
Thanks for the comment. I might update this part if I see it fail.
Regards,
F.
Best,
-greg
On Wed, Jun 14, 2017 at 9:27 AM, Francois BERENGER
<beren...@bioreg.kyushu-u.ac.jp <mailto:beren...@bioreg.kyushu-u.ac.jp>>
wrote:
Hello,
If I read a molecule from a .sdf file, will the atom indexes be
conserved/preserved?
1st atom in the file will have index 0,
2nd index 1, etc.
And, will this always hold in the future?
Is this an invariant of rdkit?
Thanks,
F.
Hello,
I am generating conformers.
When I write them out, I'd like that they are named like this:
molName_001
molName_002
...
So that, down the line, I know with which conformer of which molecule
I am working with.
So: "parent" molecule name followed by one '_' then the conformer Id
in a
Hello,
Sometimes, as a computer scientist, I am quite worried by chemical software
libraries:
$ cat data/ethanol.pqr
COMPNDethanol
AUTHORGENERATED BY OPEN BABEL 2.3.2
HETATM1 C LIG 1 -0.017 -0.601 0.000 0.04138432 1.700 C
HETATM2 C LIG 1 1.247
Hello,
I found this open source implementation recently:
Website: https://zhanglab.ccmb.med.umich.edu/EDTSurf/
C++ Code: https://zhanglab.ccmb.med.umich.edu/EDTSurf/EDTSurf.zip
Paper: "Generating Triangulated Macromolecular Surfaces by Euclidean Distance
Transform"
Hello,
If the update of the binary packages for Ubuntu/Debian
is documented somewhere, it would help people who
want to make available binary packages of rdkit as soon as there
is a new rdkit release.
I think we should have a ppa for people who want to use
the bleeding edge version of rdkit.
On 09/02/2017 11:05 PM, Konrad Koehler wrote:
> Hi everyone,
>
> As a followup to my previous post, in reading the Stiefl paper (Chem.
> Inf. Model. 2006, 46, 208-220) closer, I see my question about
> converting ErG numpy array into a bit vector was a little naive. It
> turns out that ErG
it/build/RDKit-2018.03.1.dev1-Linux-Extras.deb generated.
>>>>> CPack: - package:
>>>>> /rdkit/build/RDKit-2018.03.1.dev1-Linux-Python.deb generated.
>>>>> CPack: - package:
>>>>> /rdkit/build/RDKit-2018.03.1.dev1-Linux-Runtime.deb generated
chine
before installing the new packages (so that we test what we intend to test).
On a Debian-like:
sudo apt-get remove $(dpkg -l | grep rdkit | awk '{print $2}')
> cpack -G DEB
> cpack -G RPM
>
>
> On 27/11/2017 00:05, Francois BERENGER wrote:
>> Hello,
>>
>> What
8.0,
libboost-system1.58.0,
libboost-thread1.58.0,
libc6 (>= 2.14),
libgcc1 (>= 1:4.1.1),
libpython2.7 (>= 2.7),
libstdc++6 (>= 5.2),
python (<< 2.8),
python (>= 2.7~)
You should install the ones you are missing and test again.
> On 27/11/2017 09:11, Francois BERENGER wrote:
>
On 12/14/2017 02:10 PM, Greg Landrum wrote:
>
> On Thu, Dec 14, 2017 at 4:22 AM, Francois BERENGER
> <beren...@bioreg.kyushu-u.ac.jp <mailto:beren...@bioreg.kyushu-u.ac.jp>>
> wrote:
>
> On 12/14/2017 05:15 AM, Sundar wrote:
> > Hi RDkit users,
&
On 12/14/2017 05:15 AM, Sundar wrote:
> Hi RDkit users,
>
> I encounter following sanitize issue while I was trying to load an SD
> file using
> Chem.SDMolSupplier('lig.sdf')
>
> Explicit valence for atom # 16 N, 4, is greater than permitted
> ERROR: Could not sanitize molecule ending on line
On 12/13/2017 11:03 AM, Chicago Ji wrote:
> Dear RDkit Users,
>
> Rdkit would delete all hydrogen atoms when read in a sdf file.
> Since I want to use charge information of all atoms in sdf file, I want
> to keep all hydrogen atoms when readin.
> Is there something like Chem.SmilesParserParams()
On 11/08/2017 08:47 PM, Tim Dudgeon wrote:
There is mention of RPM distributions of RDKit
(https://copr.fedorainfracloud.org/coprs/giallu/rdkit/).
But on trying these:
1. the distro is based on the 2017_03_1 release
2. it fails due to missing libinchi.so.1 dependency.
In the bugtracker,
Hello,
Apparently, the homebrew recipe for rdkit is broken on Mac.
That's not very cool, since brew is the reference tool to install
software from source (automatically) on the Mac.
Regards,
F.
--
Check out the
On 10/21/2017 01:58 AM, Andy Jennings wrote:
Hi,
I'm curious if anyone has figured out a way to compare two molecules
based upon their pharmacophore similarities. Specifically, I want to
compare 2 molecules in their _absolute_ locations, and not simply see if
they have 2 pharmacophores that
On 01/16/2018 06:43 AM, Dimitri Maziuk wrote:
> On 01/15/2018 02:43 PM, Tim Dudgeon wrote:
>
>> Could there be something in a more general project to bridge the
>> compound (mol/smiles), sequence (protein/nucleotide seq + alignments)
>> and structure (pdb/mmcif/mmtf) worlds?
>
> FWIW PDB builds
On 01/16/2018 05:51 AM, Tim Dudgeon wrote:
> Incorporating and "industrialising" Matt's MolVS tautomer and
> standardizer code?
> http://molvs.readthedocs.io/en/latest/index.html
If we can vote, I would vote for this one.
> On 15/01/18 07:09, Greg Landrum wrote:
>> Dear all,
>>
>> We've been
Supporting mol2 files as input would be nice.
There is already some code out there, people have worked on it and
several people would like to have the feature...
On 01/15/2018 04:09 PM, Greg Landrum wrote:
> Dear all,
>
> We've been invited again to participate in the OpenChemistry application
On 14/11/2018 02:42, James T. Metz via Rdkit-discuss wrote:
RDkit Discussion Group,
Given a set of small molecules as a SDF file, I would like to
generate a MOL2
file where the atomic contributions to logP (hydrophobicity) from each
atom including
hydrogens have been calculated and are now
On 03/11/2018 04:27, Greg Landrum wrote:
Hi Eric,
On Fri, Nov 2, 2018 at 2:00 PM Eric Jonas wrote:
Hello! I'm trying to figure out if there's any known or sane way to
automatically plot numerical values adjacent to atoms using the
rdkit drawing machinery. Ideally I'd like to annotate certain
On 06/10/2018 02:27, Eric Jonas wrote:
Hello! Is there a recommended stable format for long-term storage of
RDKit molecules? Will ToBinary() give me what I need? (the
documentation / purpose seems to be a bit... spartan) I'd like to
save topology, conformers, and properties (at the atom, bond,
On 21/09/2018 16:53, Chris Earnshaw wrote:
Hi
I'm afraid I can't help with an RDkit solution to your question, but
there are a couple of issues which should be born in mind:
1) The centroid of a cluster is a vector mean of the fingerprints of
all the members of the cluster and probably will not
On 15/01/2019 09:53, Andreas Luttens wrote:
Hi!
I have developed a small script that calculates molecules properties
for molecules that are stored in a SMILES file. The properties should
be stored in an SQL database, which works fine, but I would like to
speed up the process a bit. I was
On 27/03/2019 16:24, Francois Berenger wrote:
On 27/03/2019 01:46, Greg Landrum wrote:
And now that I've included two other messages, here's (part of) my
take on this.
The viability of open-source business models is something I'm deeply
interested in (I pay rent these days thanks to income
On 27/03/2019 01:46, Greg Landrum wrote:
And now that I've included two other messages, here's (part of) my
take on this.
The viability of open-source business models is something I'm deeply
interested in (I pay rent these days thanks to income from two
open-source companies) and, like Andrew,
On 23/03/2019 04:39, Andrew Dalke wrote:
Hi RDKit users,
This week I submitted a paper about chemfp for publication. I also
submitted a preprint on ChemRxiv, which was just accepted.
For those interested, it's at
https://chemrxiv.org/articles/The_Chemfp_Project/7877846 .
It's a rather long
Hello,
I know where to find packages for python-2.7.
No idea for python 3 though.
Thanks,
F.
___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
On 12/03/2019 03:55, James T. Metz via Rdkit-discuss wrote:
RDkit Discussion Group,
I am interested in generating and assigning AM1-BCC charges to
small molecules,
You can do it with Chimera.
Cf.
http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/addcharge/addcharge.html
On 14/02/2019 19:44, Colin Bournez wrote:
Dear all,
I would like to know if there is the possibility to use the Scaffold
Tree algorithm in RDKit?
In the documentation, there is an existing page :
http://rdkit.org/docs/source/rdkit.Chem.Scaffolds.ScaffoldTree.html
[1]
But it is empty...
Maybe
Hi,
I have a related question:
how to output the type of an atom in a molecule,
if possible in a human-readable format; i.e. a human
readable/understandable string rather than some (obscure) integer.
I am interested to look at the atom types used by the ECFP
and the FCFP fingerprints.
Thanks a
On 18/06/2019 05:41, Mario Lovrić wrote:
Dear all,
Is there any paper discussing some sort of pre-selection/feature
selection with fingerprints?
I know of this one at least:
---
Bender, A., Mussa, H. Y., Glen, R. C., & Reiling, S. (2004). Molecular
similarity searching using atom
Dear rdkiters,
I am playing with rdkit.Chem.Draw:
---
sim_map = Draw.SimilarityMaps.\
GetSimilarityMapFromWeights(mol, weights)
---
I don't like that in the created figure, the map colors overlap
with atoms and bonds colors.
It makes the map less readable.
I would prefer all
On 21/08/2019 17:34, Andrew Dalke wrote:
On Aug 21, 2019, at 03:42, Francois Berenger wrote:
Unless rdkit has something, I think graph edit distance is the kind
of things for which you have to rely on a good graph library.
Do you know of any (non-chemical) graph library which can handle
On 21/08/2019 05:06, Andrew Dalke wrote:
Hi all,
Someone asked me recently about finding the graph edit distance of
two small (<= 14 atom) fragments.
I figured this was something that could be brute forced. Following
SmallWorld's example at
https://cisrg.shef.ac.uk/shef2016/talks/oral13.pdf
Dear rdkit users,
Recently, I updated the brew install recipe for rdkit on Mac.
The biggest change is that boost and boost-python's versions were
pinned down, so that the brew install recipe should be much more
reproducible
than before.
Here is a fail-safe way to install rdkit with it (with
ledgements:
Patricia Bento, Francois Berenger, Jason Biggs, David Cosgrove, Andrew
Dalke,
Thomas Duigou, Eloy Felix, Guillaume Godin, Lester Hedges, Anne
Hersey,
Christoph Hillisch, Christopher Ing, Jan Holst Jensen, Gareth Jones,
Eisuke
Kawashima, Brian Kelley, Alan Kerstjens, Karl Leswing, Pat L
On 09/12/2019 12:24, ITS RDC wrote:
Hi Greg and all RDkit users,
This is my first time posting in this mailing list because it's my
first time to use RDkit. This is also the first time I work with
Ubuntu OS (I have always been a Windows person) and I already
installed all relevant packages
On 19/11/2019 03:34, Benjamin Datko wrote:
Hello all,
I am curious on how to fold a count vector fingerprint. I understand
when folding bit vectors the most common way is to split the vector in
half, and apply a bitwise OR operation. I think this is how the
function
cppapi/structRDKit_1_1ReactionFingerprintParams.html
3.
https://www.rdkit.org/docs/GettingStartedInPython.html#morgan-fingerprints-circular-fingerprints
4. https://sourceforge.net/p/rdkit/mailman/message/35240736/
v/r,
Ben
On Mon, Nov 18, 2019 at 10:13 PM Francois Berenger
wrote:
On 19/11/2019 03:34, Benjamin
On 21/02/2020 22:45, Paolo Tosco wrote:
Hi Jitender,
you could do that quite easily using reaction SMARTS; see for example
this thread:
https://sourceforge.net/p/rdkit/mailman/message/35730514/
You could selectively replace a specific R attachment point by
isotopically labeling it.
Cheers,
On 08/01/2020 20:47, Paolo Tosco wrote:
Dear Puck,
You may break a bond by creating a Chem.RWMol out of your Chem.Mol,
and then calling the RemoveBond() method on your Chem.RWMol, or you
may use dedicated functions in the rdmolops module. Individual
fragments can then be obtained by calling
Dear RDKit users,
You might consider joining "The 8th French-Japanese Workshop
on Computational Methods in Chemistry" (FJCMC2020).
Date: Mar. 19-20, 2020
Venue: 100th Anniversary Hall of Engineering Faculty,
Kurokami South Campus, Kumamoto University.
Website:
On 21/01/2020 01:29, Zoltan Takacs wrote:
Hi,
Thanks,
I repeated the compilation procedure on an Ubuntu machine with boost
1.62.0 and everything went smashingly. This indeed seems to be some
cmake boost mismatch on my mac. I will use an older version of boost
instead.
This should do the
Hi Tim,
How do you compile rdkit for Java?
Last time I tried on a Mac, it did not work:
https://github.com/rdkit/homebrew-rdkit/issues/38
Thanks a lot,
F.
On 26/12/2019 23:22, Tim Dudgeon wrote:
When building the Java wrappers from source (the
-DRDK_BUILD_SWIG_WRAPPERS=ON option) is possible
I have some Python code that might help in there:
https://github.com/UnixJunkie/consent/blob/master/bin/lbvs_consent_ecfp4.py
Regards,
F.
On 12/03/2020 21:21, Francesco Coppola wrote:
Hello everyone,
Before exposing my new problem, I wanted to thank everyone who helped
me in the previous
Hi Max,
Not sure if it will help, but on Debian and Ubuntu you need the
following
system packages to be installed in order to compile rdkit:
curl
wget
libboost-all-dev
cmake
git
g++
libeigen3-dev
python3
libpython3-all-dev
python3-numpy
python3-pip
python3-pil
python3-six
python3-pandas
What
On 17/03/2020 17:14, Chris Earnshaw wrote:
A quick comment on the cosine metric. Unlike Tanimoto it obeys the
triangle inequality, so in cases where it's used essentially as a
distance metric (e.g. some clustering applications) the results are
probably more mathematically correct.
The Tanimoto
On 20/03/2020 08:43, JW Feng wrote:
iwatobipen blog was where I found instructions for installing RDKit on
Colab. It works but I found waiting for miniconda to install to be
too annoying. A one line apt-get command to install RDKit is easier
and faster (~10 seconds) but it only works with
On 09/09/2020 09:35, Lewis Martin wrote:
Hi RDKit,
Looking for advice on an rdkit-adjacent problem please. Ultimately I'd
like to fit an approximate-nearest neighbors index on a dataset of 100
million ligands, featurized by morgan fingerprint. The text file of
the smiles is ~6gb but this blows
On 09/09/2020 01:33, Tim Dudgeon wrote:
Hi All,
thanks for the suggestions.
Greg, that's part of what's needed but there's also some more complex
logic needed. For instance, if the atom the H is attached to is
rotatable e.g. an OH group) then it is more complex than if it is
fixed (e.g a N in a
On 12/09/2020 00:27, Mike Mazanetz wrote:
Dear Forum,
I'm curious as to how the community standardizes molecules to generate
unique chemical representations.
Please let me know what are people's referred means to treat:
* Tautomers
* Protomers
* Resonance structures
On 07/08/2020 03:15, dmaziuk via Rdkit-discuss wrote:
On 8/6/2020 7:14 AM, Pitanti Chalowa wrote:
...
DTXCID601285170
Mrv1805 05101813452D
Does it have to have a blank line after '' ?
No: having the molecule's name/identifier in there is quite standard.
Dima
Dear Sebastian,
Since last week, you should also be able to install rdkit on Linux
via linuxbrew:
---
sudo apt install linuxbrew-wrapper
brew tap rdkit/rdkit
brew update
brew install rdkit
# to test it
/home/linuxbrew/.linuxbrew/bin/python3
import rdkit
---
Thanks to Nuri Jung on github
Dear rdkiters,
I am trying to repair the brew formula.
Currently, I get this when I try to compile Release_2020_03_4:
$ cd build
$ cmake -DPYTHON_EXECUTABLE=/usr/local/bin/python-3.7
-DRDK_INSTALL_INTREE=OFF -DRDK_BUILD_INCHI_SUPPORT=ON
-DRDK_BUILD_AVALON_SUPPORT=ON
On 22/06/2020 14:47, Francois Berenger wrote:
Dear RDKiters,
My current code looks like this:
---
AllChem.Compute2DCoords(mol) # generate 2D conformer
mol.SetProp("_Name", name)
d = rdMolDraw2D.MolDraw2DSVG(200, 200)
d.DrawMolecule(mol)
Answer
Dear RDKiters,
My current code looks like this:
---
AllChem.Compute2DCoords(mol) # generate 2D conformer
mol.SetProp("_Name", name)
d = rdMolDraw2D.MolDraw2DSVG(200, 200)
d.DrawMolecule(mol)
d.FinishDrawing()
out_fn = '%d.svg' % i
with
On 06/06/2020 17:33, Max Pinheiro Jr wrote:
Hi RDkit team,
I am working on a chemically diverse dataset of smiles strings and I
need to do some preprocessing to clean a bit the data before starting
the modeling part. So I was looking for some tools or built-in
functions in RDkit to make such
On 10/06/2020 13:11, 丁邵珍 wrote:
Hi, I want to calculate Tanimoto similarity score of two reactions
('CCCO>>CCC=O', 'CC(O)C>>CC(=O)C'), I found all methods of Tanimoto
similarity score calculation are for compounds. Could you please tell
me how to calculate the Tanimoto similarity score of
On 08/12/2020 23:01, José Emilio Sánchez Aparicio wrote:
Dear all,
I need to find how many bonds of a certain type are in a molecule.
For example, for DOUBLE bonds, I would do:
bond_number = 0
for bond in mol.GetBonds():
if bond.GetType() == Chem.BondType.DOUBLE:
bond_number
On 04/11/2020 04:26, Lewis Martin wrote:
Ive had an initial go at something like this using JAX. I chose JAX
since it has a shallow learning curve, essentially being numpy on a
GPU. This is great for vectorized calculations, but less so for
applications that involve a lot of control flow (ie
Dear list,
I have been trying to replace this SMARTS pattern in a ring:
'c(=O)[nH]'
By this SMILES fragment:
'c(O)n'
My trials using a single SMARTS pattern search then replace
break open the ring, which is not what I want.
My not working trial code:
---
mol =
Hello,
Please tell me if you understand why the code below
is not working and if you know how to change it so that it does.
Thanks a lot! :)
F.
---
#!/usr/bin/env python3
# try to construct a molecule with a Z stereo double bond using RWMol
import rdkit
from rdkit import Chem
wanted_smi =
was being a good kid, I thought that someone must always sanitize
a RWMol prior to extracting the final resulting molecule (in the end
I want a SMILES).
Regards,
F.
On Thu, Jan 14, 2021 at 9:46 AM Francois Berenger
wrote:
Hello,
Please tell me if you understand why the code below
is not work
= rwmol.GetBondWithIdx(1)
In [8]: db.SetStereoAtoms(0,3)
In [9]: db.SetStereo(Chem.BondStereo.STEREOCIS)
In [10]: Chem.MolToSmiles(rwmol)
Out[10]: 'CN=CS'
In [11]: Chem.AssignStereochemistry(rwmol)
In [12]: Chem.MolToSmiles(rwmol)
Out[12]: 'C/N=C\\S'
On Thu, Jan 14, 2021 at 9:46 AM Francois Berenger
wrote
helps!
Best,
Fio
On Thu, Jan 7, 2021 at 10:33 PM Francois Berenger
wrote:
Dear list,
I have been trying to replace this SMARTS pattern in a ring:
'c(=O)[nH]'
By this SMILES fragment:
'c(O)n'
My trials using a single SMARTS pattern search then replace
break open the ring, which is not what
On 04/02/2021 00:35, Brian Peterson wrote:
Hello RDKit people,
Is it possible to modify the properties of elements in the periodic
table or to create new ones? Use case: Suppose one had some molecules
defined in terms of functional groups or united atoms or some other
entities that are not
Dear JP,
To confuse you even more, you can also have a look at the ChEMBL
open-source molecular standardizer:
https://github.com/chembl/ChEMBL_Structure_Pipeline/blob/master/chembl_structure_pipeline/standardizer.py
No need to thank me. :D
On 18/06/2021 03:12, JP Ebejer wrote:
Dear all,
I
On 25/06/2021 02:57, Michal Krompiec wrote:
Hello,
Is it possible to install RDKit on MacOSX in a Python 3.8 environment?
There is no conda binary for 3.8, so I tried homebrew. But the
following gives me an error message (brew doesn't like the
--with-python3 argument):
brew install rdkit
Hello,
I have some molecules with unspecified atoms ('*' in SMILES notation).
I would like that when such a molecule is written out, the resulting
SMILES never starts by one of those atoms (since the molecule
also has plenty of "normal" atoms).
Is it possible to do that with rdkit?
Or, more
Dear list,
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 path-based FPs formally described somewhere?
Thanks a lot,
F.
On 29/06/2021 12:26, Greg Landrum wrote:
Hi Leon,
You can convert the tanimoto distance to similarity, but the formula
is:
Similarity = 1 - Distance
In other words:
Tanimoto_distance = 1.0 - Tanimoto_score
Worth noting: the Tanimoto distance is a metric; hence it is pretty
useful in
On 01/07/2021 13:15, Hao wrote:
Thanks Greg!
That helps a lot, it was purely out of curiosity and understanding.
I'm working with some legacy code that requires conformer generation
before calculating partial charges. Now that I know it's unnecessary,
I can speed up this process by quite a bit.
Hello,
I am trying MurckoScaffold.MakeScaffoldGeneric(mol),
but this keeps the side chains.
While my understanding of BM scaffolds is that only rings
and ring linkers should be kept.
The fact that the rdkit implementation keeps the
side chains makes Murcko scaffolds a much less powerful filter
On 27/04/2021 10:12, Francois Berenger wrote:
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:
In [5]: m
On 03/04/2021 00:03, Andrew Dalke wrote:
Hi Ling,
On Apr 2, 2021, at 16:23, Ling Chan wrote:
Thank you Francois, I took a look at your code and borrowed parts of
it to rejoin two molecules. It seems like my problem is solved. I
eventually arrived at something like example 4 in
On 01/04/2021 04:55, Ling Chan wrote:
Dear Colleagues,
I am trying to do something that I think is quite simple, but I have
not figured out a simple way. Don't know if I am missing something. I
am sure that ultimately I can figure it out, but I wonder if there is
a good way.
I fragmented a
/linuxbrewed-rdkit may conflict with conda-rdkit, please
decide which one to use at your own risk.
I thank Francois Berenger, Eddie Cao, and the contributors who
maintained the rdkit formula.
Sincerely,
Yoshitaka Moriwaki
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Hi Lewis,
Just an idea: you might try to load your PDB in UCSF Chimera, then
save it as a mol2 or sdf file.
Then, try to read this sdf file from rdkit.
Another idea: try to get your pdb file through the pdbredo service.
https://pdb-redo.eu/
They might have fixed a few things; maybe this PDB
Regards,
F.
Cheers
Lewis
On Mon, Sep 27, 2021 at 5:55 PM Francois Berenger
wrote:
Hi Lewis,
Just an idea: you might try to load your PDB in UCSF Chimera, then
save it as a mol2 or sdf file.
Then, try to read this sdf file from rdkit.
Another idea: try to get your pdb file through the pdbredo
On 12/11/2021 01:58, Paolo Tosco wrote:
Hi Tim,
Open3DAlign is not shape-based, it is atom-based. The score is
proportional to the # of matched atoms, weighted by similarity. It
will work well for homologous series of compounds with reasonable
scaffold similarity, and will in general perform
Dear rdkit experts,
I am looking to access the electronegativity value
of a given atom in a molecule.
Funnily, I don't know _at_ _all_ how to do this.
I guess that there should be a way using the atomic number
to get this value from a table inside of rdkit
but my code searches on github where
On 08/03/2022 17:23, Francois Berenger wrote:
Dear rdkit experts,
I am looking to access the electronegativity value
of a given atom in a molecule.
Funnily, I don't know _at_ _all_ how to do this.
I guess that there should be a way using the atomic number
to get this value from a table inside
On 30/03/2022 03:49, Patrick Walters wrote:
One way to compare interactions (pharmacophores) in a binding site is
to use interaction fingerprints. I've had a good experience with
ProLIF.
https://github.com/chemosim-lab/ProLIF
Additionally, I know about all those open-source ones:
-
On 25/01/2022 01:57, Oren Herschander wrote:
Hi Everyone,
I'm working on a research project about how Dask and other python
tools for distributed/parallel computing are used in Life Sciences.
I'm on the lookout for use cases, stories, and overall thoughts that
combine rdkit or other similar
Hi all,
I assume it's ".sdf".
But, do we have good support for ".xyz" also?
In addition, what about RDKit's support of ".mol2" these days?
Regards,
F.
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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
procedure I used was to extract the fingerprint pointers into a
std::vector, create a std::vector for the results,
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