Hello,
I use RDKit to embed initial conformations for docking. The issue is
with saturated rings. I can use a single random conformer but its
geometry may be unsuitable and the whole molecule will fail to dock. I
can use several starting conformers for docking and to avoid docking of
very
Dear colleagues,
after covid "holidays" we are cordially invite you on the 6th Drug
Design workshop which will be held 30 January - 3 February 2023 in
Olomouc (Czech Republic). It is focused on practical applications of
different chemoinformatic tools and approaches for drug development.
Hi Enrico,
you may look at this script
https://github.com/DrrDom/rdkit-scripts/blob/master/rmsd_rdkit.py
It takes PDBQT as input and reference files and calc rmsd for the
largest common fragment if structures do not match each other. If there
are multiple models in the input file it will
Hi Chris,
Error reported a bin (0,2,0) which does not satisfy the triangle rule. I
cannot check it, but I suppose that the error may disappear if you set
trianglePruneBins=False in SigFactory, but this would be a workaround
not a proper solution I think.
Pavel.
On 12/08/2021 10:25, Chris
Hi Ling,
this can be a workaround if RDKit does not have a built-in function
to extract a submolecule by atom ids. You may assign atom property
labels to these atoms and then looping over atoms in EditableMol remove
those ones which do not have this property assigned.
Kind regards,
Pavel.
ding H seems to do the trick:
In [39]: mol = AllChem.AddHs(mol_child)
In [40]: AllChem.EmbedMolecule(mol)
Out[40]: 0 # worked
In [41]: AllChem.ConstrainedEmbed(mol, mol_parent)
Out[41]: # also worked
Sunhwan
On Jul 7, 2020, at 12:36 AM, Pavel Polishchuk
mailto:pavel_polishc...@ukr.net
Hi all,
I have an issue with ConstrainedEmbed and I cannot figure out what
exactly causes this.
I have a molecule C[C@@H]1C1=O with 3D coordinates in 1.mol file
(attached). And I want to generate coordinates for another structure
with this core -
C[C@@H]1CC[C@H](O)CC1=O.
This is
Hello,
I want to generate conformers for a stereoisomeric sugar moiety. The
code below works (loads proccesor) but returns none of them.
But if I remove all stereoconfiguration info in input SMILES the code
generates conformers. Playing with this issue I noticed that conformers
are
Sorry for the mistake, the dates are 3-7 of *February* 2020.
Pavel.
On 20/11/2019 09:39, Pavel Polishchuk wrote:
Dear colleagues,
we would like to invite you on the 5th Drug Design workshop which
will be held 3-7 January 2020 in Olomouc (Czech Republic). It is
focused on practical
,
Pavel.
--
Dr. Pavel Polishchuk
senior researcher
Institute of Molecular and Translational Medicine
Faculty of Medicine and Dentistry
Palacky University
Hněvotínská 1333/5
779 00 Olomouc
Czech Republic
+420 585632298
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Rdkit-discuss mailing list
Rdkit
designed to be used in situations
like this.
-greg
[1] The details of the canonicalization algorithm, including the
contents of the atom invariants, are described here:
http://dx.doi.org/10.1021/acs.jcim.5b00543
On Tue, Aug 1, 2017 at 2:53 PM, Pavel Polishchuk
<pavel_polishc...@ukr.
Hi all,
canonicalization of fragment SMILES does not work properly. Below
there are two examples of identical fragments. The only difference is
the order of atoms (indices). However, it seems that RDKit
canonicalization does not take into account atom types.
Does someone have an idea
I had some issues to run rdkit from Python console in PyCharm (4.5.5) on
Linux. After recent installation of PyCharm 2017.1.3 it started to work.
Maybe updating PyCharm will help on Win as well.
Pavel.
On 05/30/2017 10:10 PM, West, Richard wrote:
We're having trouble getting RDKit to work
Hello,
probably this is a message mainly to developers.
I discovered some strange behavior of removeHs function applied for
'[H][*:1]' molecule.
If I create that mol from smiles, RemoveHs does not remove a single H
from the mol:
mmm = Chem.MolFromSmiles('[H][*:1]')
I do not know the valence model of RDkit. Therefore below there is an
ugly but working solution: set to the S+ atom NoImplicit.
mol = Chem.MolFromSmiles('CC(C)(C)SC')
rxn =
AllChem.ReactionFromSmarts('[CH0:1][S:2][CH3:3]>>[C:1][SH0+:2].[CH3-:3]')
ps = rxn.RunReactants((mol,))
S=c1c([*:1])c(Cl)[nH]c([*:3])c1[*:2]
S=c1c([*:1])c(Cl)[nH]c([*:3])c1[*:2]
S=c1c([*:1])c(Cl)[nH]c([*:3])c1[*:2]
S=c1c([*:1])c(Cl)[nH]c([*:3])c1[*:2]
S=c1c([*:1])c(Cl)[nH]c([*:3])c1[*:2]
S=c1c([*:1])c(Cl)[nH]c([*:3])c1[*:2]
Now, if you want the atomMaps in 1...2...3 output order, we could do
that
Hello,
is it possible to store custom fingerprints in psql DB and use them
for similarity search? And how to do this?
I foundtwo commands bfp_to_binary_text(bfp) and
bfp_from_binary_text(bytea)in RDKit cartridge but cannot understand how
to use them.
I want to store pharmacophore
Hello,
I found two issues which are reproducible in 2016.09 and 2017.3 conda
builds.
0. The first issue is related to PostgreSQL. If I try to install it
from conda it asks me to downgrade rdkit to 2016.3. After downgrading of
rdkit psql works well.
1. Generation of 2D pharmacophore
Hi Maxim,
if you change your query to SMARTS it would be possible to delete
what you want
m=Chem.MolFromSmiles('C1(C2=NC=CC=C2)=CC=CC(C)=C1')
ss = Chem.MolFromSmarts('c1c1C')
frag = AllChem.DeleteSubstructs(m, ss)
print(Chem.MolToSmiles(frag))
Pavel.
On 03/31/2017 07:41 AM,
Hi,
I experimented a little bit with CanonicalRankAtoms and observed some
unexpected results.
I have two mols (actually sets of fragments):
C[*].n[*].C[*].N[*]
CC[*].CC[*].cn([*])c.CN([*])C
In the first case, pairs of carbons and nitrogens are recognized as
symmetrical
[0, 2, 0,
ive to you?
Best,
Peter
On Mon, Mar 27, 2017 at 9:35 AM Pavel Polishchuk
<pavel_polishc...@ukr.net <mailto:pavel_polishc...@ukr.net>> wrote:
Dear RDKitters,
I found the issue with FindAtomEnvironmentOfRadiusN but this
can be a
feature. However, I did not findth
Dear RDKitters,
I found the issue with FindAtomEnvironmentOfRadiusN but this can be a
feature. However, I did not findthis information in help and did not
expect such behavior.
If I apply FindAtomEnvironmentOfRadiusN function to a small molecule
and specify the radius greater than the
You might find this link useful -
http://www.rdkit.org/docs/GettingStartedInPython.html#chemical-transformations
However, the issue in your case is SMARTS definitions. If one SMARTS
completely covers another one it would be difficult to understand is it
artifact or not.I think it might be
Hi Jacob,
you need to call AssignStereochemistry with force=True parameter
Chem.AssignStereochemistry(mol, force=True)
Pavel.
On 01/28/2017 05:43 AM, Jacob Durrant wrote:
I'm trying to set the configuration of a molecule with a double bond,
but it doesn't seem to be working. Here's my
e as follows:
s = s.replace('\r\n', '\n')
s = s.replace('\n\r', '\n')
s = s.replace('\r', '\n')
lines = s.split('\n')
On Tue, Dec 20, 2016 at 2:45 AM, Pavel Polishchuk
<pavel_polishc...@ukr.net <mailto:pavel_polishc...@ukr.net>> wrote:
Hi,
I just want to share my script, which I use for enumeration of
stereoisomers. Enumeration of double bonds was added quite recently and
thus I didn't test it extensively.
I put it on github: https://github.com/DrrDom/rdk
It seems to work well on quite complex queries like
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