and RDKit,
>
>
>
> *rdkit.__version__ = 2023.03.1*
>
>
>
> Here is a slightly more explicit variant tried because neither worked to
> find a match:
>
>
>
>
>
> Respectfully,
>
> Joey Storer
>
>
>
> General Business
>
> *From:*
Hi Joey,
You can get the intended result like this
pat = Chem.MolFromSmarts("*=C1*C=C*1")
mol = Chem.MolFromSmiles("C=C1SC=CS1")
mol.HasSubstructMatch(pat)
Pat
On Tue, Jun 13, 2023 at 4:49 PM Storer, Joey (J) via Rdkit-discuss <
rdkit-discuss@lists.sourceforge.net> wrote:
> Hi RDKit masters,
>
Actually, you can now just
!pip install rdkit
From: Jan Halborg Jensen
Sent: Wednesday, August 3, 2022 9:47:20 AM
To: Eduardo Mayo
Cc: RDKit Discuss
Subject: Re: [Rdkit-discuss] RDKit in Google Colab
!pip install rdkit-py
No need to use anaconda for Colab RDKi
Here's a simple example showing the enumeration of a 3 component library
based on a reaction
https://gist.github.com/PatWalters/7439099598b4f08a331a81b209f88baa
On Wed, Jul 6, 2022 at 4:57 PM Andrew Dalke
wrote:
> Hi Carsten,
>
> How are the fragments expressed? With attachment points marked
of actives and the dataset of cluster representatives.
>
>
>
> On Sun, 1 May 2022, 17:09 Patrick Walters, wrote:
>
>> For me, a lot of this depends on what you intend to do with the
>> clustering. If you want to pick a "representative" subset from a larger
>&
For me, a lot of this depends on what you intend to do with the
clustering. If you want to pick a "representative" subset from a larger
dataset, k-means may do the trick. As Rajarshi mentioned, Practical
Cheminformatics has a k-means implementation that runs with FAISS.
Depending on your goal, ch
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
On Tue, Mar 29, 2022 at 6:26 AM Muhammad Akram
wrote:
> Hello Everybody,
>
>
>
> I am looking if there is a way t
t; 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 trying to save an
rdSubstructLibrary. with library.toStream(). When library is empty I can
save the library with library.toStream(), however when I've added molecule
to the library, I get this error message.
UnicodeDecodeError: 'ut
Here's what I use.
not_organic_pat =
Chem.MolFromSmarts("[!#1;!C;!O;!N;!S;!P;!F;!Cl;!Br;!I;!c;!o;!n;!s;!p;!Na;!K;!Mg;!Ca;!Li]")
cisplatin = Chem.MolFromSmiles("[NH3+]-[Pt-2](Cl)(Cl)[NH3+]")
cisplatin.HasSubstructMatch(not_organic_pat)
On Sat, Mar 5, 2022 at 8:08 PM Rafael L via Rdkit-discuss <
Hi Hao,
As a long-time file format geek. I feel the need to jump into this one.
1. mol2
I'm not a fan of using mol2. AFAIK, there is no definitive documentation
for the atom typing rules or the aromaticity model.
2. sdf
The RDKit has had a facility for storing atom properties in an SDF since
numpy!
import pandas as pd
from descriptor_gen import DescriptorGen
import numpy as np
from rdkit import Chem, DataStructs
from rdkit.Chem import AllChem
def smi2fp(smi):
mol = Chem.MolFromSmiles(smi)
fp = AllChem.GetMorganFingerprintAsBitVect(mol, 2, nBits=2048)
arr = np.zeros((0,),
Hi Anthony,
This is pretty easy and you don't need to use PandasTools (although
PandasTools are very cool).
#!/usr/bin/env python
import sys
from rdkit import Chem
suppl = Chem.SDMolSupplier(sys.argv[1])
for mol in suppl:
if mol:
print(Chem.MolToSmiles(mol),mol.GetProp("_Name"))
By
If you're looking for a more ML oriented program. I'd recommend David Koes
group at Pitt.
https://www.csb.pitt.edu/people/faculty/david-koes/
Jacob Durrant is also doing interesting work in another department at Pitt
https://durrantlab.pitt.edu/people/
On Tue, Jul 20, 2021 at 2:47 AM Stiefl,
What about something like this?
https://gist.github.com/PatWalters/15352d9007c33a214ac13d3dda814624
On Wed, Jun 9, 2021 at 9:28 PM Christopher Schlicksup
wrote:
> Hi Rdkit community,
>
> I have a case where I have pairs of molecules that are very similar, but
> have different atom indices. I w
Hi Joey,
Have you looked at this?
https://github.com/jensengroup/xyz2mol
Pat
On Fri, Jun 4, 2021 at 8:57 PM Storer, Joey (J) wrote:
> Dear all,
>
>
>
> For molecular modeling workflows and interoperability with QM/MM etc.,
>
>
>
> Can RDKit gain a Chem.XyzToMol(xyz) functionality?
>
>
>
> Than
There's also some information on path fingerprints in the Daylight Theory
Manual
https://www.daylight.com/dayhtml/doc/theory/theory.finger.html
On Wed, May 19, 2021 at 10:47 PM Greg Landrum
wrote:
> Hi Francois,
>
> On Thu, May 20, 2021 at 3:19 AM Francois Berenger
> wrote:
>
>>
>> The other
>
> By either explicitly doing the import in calc_bcut() or referencing the
> function through the module, dask seems to be able to figure out how to do
> the right thing.
>
> -greg
> p.s. in case you see different behavior:
> In [2]: dask.__version__
> Out[2]: '2020
lcExactMolWt
>
> to avoid another error.
>
> Which version of rdkit do you use ?
>
>
>
> BR
>
>
>
> Guillaume
>
>
>
>
>
> *De : *Patrick Walters
> *Date : *lundi, 22 mars 2021 à 14:20
> *À : *Guillaume GODIN
> *Cc : *rdkit-discuss
> *Obj
use esol.csv for
> example ?
>
>
>
> Thanks
>
>
>
> Guillaume
>
>
>
> *De : *Patrick Walters
> *Date : *lundi, 22 mars 2021 à 13:51
> *À : *rdkit-discuss
> *Objet : *[*External*] Re: [Rdkit-discuss] Using the RDKit with Dask
>
> Apologies, there
Apologies, there was a bug in the code I sent in my previous message. The
problem is the same. Here is the corrected code in a gist.
https://gist.github.com/PatWalters/ca41289a6990ebf7af1e5c44e188fccd
On Mon, Mar 22, 2021 at 8:16 AM Patrick Walters wrote:
> Hi All,
>
> I've
Hi All,
I've been trying to calculate BCUT2D descriptors in parallel with Dask and
get this error with the code below.
TypeError: cannot pickle 'Boost.Python.function' object
Everything works if I call mw_df, which calculates molecular weight, but I
get the error above if I call bcut_df. Does an
I'm not sure why this was sent to rdkit-discuss, but I just pushed a fix to
github. Sorry for the hassles.
Pat
On Tue, Feb 16, 2021 at 10:15 AM Mandar Kulkarni <
mandar.kulkarni.c...@gmail.com> wrote:
> Hi,
>
> I am trying to repeat the xgboost tutorial from here:
> https://github.com/PatWalter
I have an example in this blog post that does what you're looking for.
http://practicalcheminformatics.blogspot.com/2019/09/dissecting-hype-with-cheminformatics.html
On Tue, Sep 29, 2020 at 6:04 PM Markus Metz wrote:
> Thank you Kangway.
> So it is list of lists for each molecule in the grid.
>>
>> mol = Chem.MolFromMolFile(src, sanitize=True)
>>
>> matrix = numpy.zeros((4, 4), numpy.float)
>>
>>
>>
>> for i in range(3):
>>
>> matrix[i, i] = factor
>>
>> matrix[3, 3] = 1
>>
>>
>>
&
Hi All,
I'm trying to align a set of structures to a template that I have as
molfile. When I call GenerateDepictionMatching2DStructure it appears that
the coordinate for the template are directly copied. This results in a
structure like the one below, where the bond lengths for the template are
HI Xiaobo,
There's an explicit hydrogen in the SMARTS that shouldn't be there. I also
wouldn't include the single bonds around the ring closures.
'[#8]=[#6]-3-c1c2c(ccc1)2-[#6](-[#7]-3-*[#1]*)=[#8]')
from rdkit import Chem
from rdkit.Chem import Draw
smi = "O=C(C1=C2C(C=CC=C23)=CC=C1)N([H]
I haven't tried it yet, but this recent paper in the Journal of
Cheminformatics looks interesting. The authors supply a git repo with code
based on the RDKit.
Dimorphite-DL: an open-source program for enumerating the ionization states
of drug-like small molecules
https://jcheminf.biomedcentral.c
Are you interested in aromatic c-H? It looks like 3 of 4 molecules have
hydrogens (if you count methyls)
from rdkit import Chem
from rdkit.Chem.Draw import MolsToGridImage
buff = """N#C/C(C#N)=C(C(F)=C/1F)\C(F)=C(F)C1=C(C#N)\C#N
N#C/C(C#C)=C(C=C/1F)\C(F)=C(F)C1=C(C#N)\C#N
FC1=C(F)C(C#N)=C(F)C(OC(
I've been running the conda version with Python 3.6.6 on a couple of Macs
with no issues.
Pat
On Thu, Feb 7, 2019 at 8:34 AM Greg Landrum wrote:
> Hi Paul,
>
> That looks like some residual of the horrible problems caused by some
> conda changes that happened last year but that were fixed. I wo
Hi all,
I ran into a case that I found confusing. If convert this SMILES to an
RDKit molecule, I get a valid molecule.
In [2]: mol = Chem.MolFromSmiles("O=C(CC1SCCC1)c1c1N")
In [3]: mol
Out[3]:
However, if I convert the molecule to SMILES then covert it back to a
molecule, it is no longer
I just wrote a blog post on this topic.
https://practicalcheminformatics.blogspot.com/2018/09/assigning-bond-orders-to-pdb-ligands.html
On Thu, Oct 4, 2018 at 3:35 PM MARIA BRANDL via Rdkit-discuss <
rdkit-discuss@lists.sourceforge.net> wrote:
> Hello Eric,
>
> RDKit can assign bond orders from
Hi Dimitar,
I put an RDKit implementation of the ESOL method from the original paper by
Delaney on my GitHub site.
I also refit the coefficients to maximize performance with the RDKit
calculated descriptors.
https://github.com/PatWalters/solubility
Note that solubility prediction is a really hard
I would highly recommend this paper where the authors describe an
alternative to arbitrary similarity cutoffs
https://pubs.acs.org/doi/pdf/10.1021/ci7004498
Pat
On Wed, Jul 4, 2018 at 9:31 AM Maciek Wójcikowski
wrote:
> Hi
>
> As Nils has mentioned this is fingerprint dependent. ECFP4 have the
r should I fire up the
> debugger?
>
> -greg
>
>
>
> On Mon, May 14, 2018 at 4:24 AM Patrick Walters
> wrote:
>
>> Hi All,
>>
>> I'm hoping someone can help me with rdRGroupDecomposition. I'd like to
>> be able to specify specific R-group loca
Hi All,
I'm hoping someone can help me with rdRGroupDecomposition. I'd like to be
able to specify specific R-group locations AND match cases where R=H. The
example below illustrates what I'm talking about.
When RGroupDecompositionParameters.onlyMatchAtRGroups = True, cases where R
== H are skip
Hi All,
I've been playing around with some of the structural alerts from ChEMBL and
noticed that on alert was generating a SMARTS Parse Error with the RDKit.
[2H,3H,13C,14C,15N,125I,23F,22Na,32P,33P,35S,45Ca,57Co,103Ru,141Ce]
It appears that the issue was reported previously and that Greg fixed
Hi All,
I installed the latest RDKit using conda
conda create -c rdkit -n rdkit_2017 rdkit
When I import Chem I get a seg fault
➜ ~ source activate rdkit_2017
(rdkit_2017) ➜ ~ python
Python 3.5.5 |Anaconda, Inc.| (default, Mar 12 2018, 16:25:05)
[GCC 4.2.1 Compatible Clang 4.0.1 (tags/RELEASE
_weld = Chem.MolFromSmiles(
"CN(C)CC(Br)c1cc([*:2])c([*:1])cn1.[H]C([H])([H])[*:1].[H][*:2]")
welded_mol = weld_r_groups(mol_to_weld)
print(Chem.MolToSmiles(welded_mol))
Best,
Pat
On Sun, Apr 15, 2018 at 12:16 PM, Patrick Walters
wrote:
> Hi All,
>
> I was about
Hi All,
I was about to write a function to reassemble a molecule from a core +
R-groups, but I thought I'd check and see if such a function already
exists. This is work with the output of rdRGroupDecomposition
Gvien a core:
CN(C)CC(Br)c1cc([*:2])c([*:1])cn1
Plus a set of R-groups
[H]C([H])([H])
The Layered InChI (LyChi), developed by Trung Nguyen at NCATS was designed
to directly address the problem you describe. I don't have any first hand
experience with this method (yet), but it looks intriguing.
https://github.com/ncats/lychi
Pat
On Mon, Nov 28, 2016 at 11:25 AM, Stephen O'hagan
I agree that there are plenty of implementations of clustering, machine
learning, etc. It would be better for the RDKit developers to focus on
cheminformatics. This being said, there are some opportunities for domain
specific performance enhancement. One of the slow steps in many clustering
alg
If you want everything in one nice package, you may want to look at
MyChEMBL. This has a VM with PostgreSQL, kinime, python, the RDKit, and
ChEMBL.
http://chembl.blogspot.com/2013/10/chembl-virtual-machine-aka-mychembl.html
Pat
On Thu, Aug 28, 2014 at 10:11 AM, Michal Krompiec wrote:
> Dear
Your input molfile lacks the 2D on line 2, e.g.
RDKit 2D
Pat
On Thu, Aug 21, 2014 at 5:34 AM, Michał Nowotka wrote:
> OK, I'm closer to finding bug in my code. So I have this ctab:
>
> >>> print ctab
>
> Converted by chembl_beaker ver. 0.5.20
>
> 10 11 0 0 0 0 1 V
istos Kannas
>
> Researcher
> Ph.D Student
>
> Mob (UK): +44 (0) 7447700937
> Mob (Cyprus): +357 99530608
>
> [image: View Christos Kannas's profile on
> LinkedIn]<http://cy.linkedin.com/in/christoskannas>
>
>
> On 24 April 2014 11:37, Patrick Walter
It looks like the problem here is a covalent bond to the counter ion.
Pat
On Thu, Apr 24, 2014 at 6:04 AM, Christos Kannas wrote:
> Hi all,
>
> I'm having a dozen of compounds, where some of them have a charged atom
> (see the attached SMILES file).
>
> When I parse the file I get sanitization
the inconvenience.
>
> -greg
>
> On Friday, April 4, 2014, Patrick Walters wrote:
>
>> Hi All,
>>
>> I ran into an error building the RDKit from the last git pull on OS-X 10.8
>>
>> Has anyone else run into this?
>>
>> Thanks,
>>
>> Pat
&
Hi All,
I ran into an error building the RDKit from the last git pull on OS-X 10.8
Has anyone else run into this?
Thanks,
Pat
Linking CXX shared library ../../../lib/libSubstructMatch.dylib
[ 30%] Built target SubstructMatch
[ 30%] [BISON][SmilesY] Building parser with bison 2.3
smiles.yy:48.
Hi All,
I was working through the 2D pharmacophore example in the "Getting Started"
docs
http://www.rdkit.org/docs/GettingStartedInPython.html#d-pharmacophore-fingerprints
and I threw an exeception that I don't understand. Here's my code
==
#!/usr/bin/env pytho
I'm not an expert on this, but I think this function just randomizes the
order of the atoms in a molecule. Generating a random molecule for a
particular molecular formula that is consistent with rules of valence is
kind of tricky. If you're interested in doing this sort of thing, you may
want to
I just started playing around with the Pandas module, this is very cool
stuff. Thanks so much Nikolas for the contribution. I definitely owe you
a beer at the UGM. It might be worth noting that the you need to install
PIL in order to use the Pandas module. Everything will install without a
prob
If you're just looking for 6 membered rings, you can define a SMARTS that
matches 6 membered rings like this "*1~*~*~*~*~*1". You can also use this
approach to identify all rings (at least those within reason). You can use
an expression like this
["*1"+string.join(["*~"]*x,"")+"*1" for x in rang
Hi All,
I've been trying to use RDKit to parse the SLN queries in a recent paper
from Jonathan Baell at Monash
http://pubs.acs.org/doi/abs/10.1021/ci300461a
RDKit is able to successfully parse most of the queries, but is unable to
handle 18 of 539. It looks like the problem is with the "&NOT" co
53 matches
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