-matches?
Cheers,
Dante
On Tue, Sep 19, 2017 at 9:13 AM, James T. Metz via Rdkit-discuss
<rdkit-discuss@lists.sourceforge.net> wrote:
Hello,
Is it possible to write a single SMARTS for two separate patterns involving
a Boolean OR?
For example, I want to write a single SMARTS that can mat
Hello,
Is it possible to write a single SMARTS for two separate patterns involving
a Boolean OR?
For example, I want to write a single SMARTS that can match the
patterns of
[C]-[C]
or
[N]-[N]
I realize that I could write something like
[C,N]-[C,N]
but that would also match
Hello,
I would like to write a SMARTS that will match all of the individual atoms
in all possible heteroaromatic rings. Does anyone know of an elegant,
compact way to do this?
If one SMARTS will not work, I can concatenate SMARTS using
a vertical pipe, "|", as I proposed in an
just that it's aromatic, you should
use [a],
so [a]1[a][a][a][a][a]1 would match any 6-membered aromatic ring
Jason Biggs
On Wed, Sep 20, 2017 at 7:57 PM, James T. Metz via Rdkit-discuss
<rdkit-discuss@lists.sourceforge.net> wrote:
Hello,
I would like to write a SMARTS tha
]:[a]:1',
'[a]:1:[a]:[a]:[a]:[a]:[a]:[a]:1']
The rest is just some calls to MolFromSmarts() and then
mol.GetSubstructMatches() for the molecules you want to test.
-greg
On Thu, Sep 21, 2017 at 3:56 AM, James T. Metz via Rdkit-discuss
<rdkit-discuss@lists.sourceforge.net> wrote:
Jason,
Thanks! I just t
hatic carbon OR an aliphatic nitrogen singly bonded to
an aliphatic nitrogen'.
Regards,
Chris Earnshaw
On 19 September 2017 at 15:01, James T. Metz via Rdkit-discuss
<rdkit-discuss@lists.sourceforge.net> wrote:
Dante,
Yes. In principle, if one can figure out all of the
Many thanks to all for this new RDKit release.
I have used commercial software in my past, and I am
more and more impressed by the capabilities of RDKit and
other open source software.
Please keep up the good work!
Regards,
Jim Metz
-Original Message-
From:
Hello,
Suppose I read in the SMILES of an aromatic molecule e.g., for
benzene
c1c1
I then want to convert the molecule to a Kekule representation and
then perform various SMARTS pattern recognition e.g.
[C]=[C]-[C]
I have tried various Kekule commands in
Hello,
Suppose I read in an aromatic SMILES e.g., for benzene
c1c1
I would like to generate the major canonical resonance forms
and save the results as two separate molecules. Essentially
I am trying to generate
m1 = 'C1=CC=CC-C1'
m2 = 'C1C=CC=CC1'
Can
you trying to
do?
-greg
On Mon, Sep 11, 2017 at 5:04 PM, James T. Metz via Rdkit-discuss
<rdkit-discuss@lists.sourceforge.net> wrote:
Hello,
Suppose I read in an aromatic SMILES e.g., for benzene
c1c1
I would like to generate the major canonical resonance for
i Jim,
The code currently has no way to enumerate Kekule structures. I don't recall
this coming up in the past and, to be honest, it doesn't seem all that
generally useful.
Perhaps there's an alternate way to solve the problem; what are you trying to
do?
-greg
On Mon,
his.
R6 means in 6 rings.
r6 means in ring of size 6.
http://www.daylight.com/dayhtml/doc/theory/theory.smarts.html
TJ O'Donnell
On Wed, Sep 6, 2017 at 4:34 PM, James T. Metz via Rdkit-discuss <
rdkit-discuss@lists.sourceforge.net> wrote:
> Hello,
>
> Given the following SMILES for a
Hello,
Given the following SMILES for a macrocyclic hexaose
OCC1OC2OC3C(CO)OC(OC4C(CO)OC(OC5C(CO)OC(OC6C(CO)OC(OC7C(CO)OC(OC1C(O)C2O)C(O)C7O)C(O)C6O)C(O)C5O)C(O)C4O)C(O)C3O
can anyone suggest a SMARTS pattern that will distinguish ether oxygens
in the smaller 6-membered
C1C=CC=CC=1
C1=CC=CC=C1
Best,
Paolo
On 09/11/2017 05:22 PM, James T. Metz via Rdkit-discuss wrote:
Greg,
Thanks! Yes, very helpful
6-ring aromatic pattern a:1:a:a:a:a:a:1,
with recursive SMARTS applied to the first atom to ensure that this
can't match any of the 6 ring atoms in your undesired system.
Regards,
Chris Earnshaw
On 24 September 2017 at 05:04, James T. Metz via Rdkit-discuss
<rdkit-discuss@lists.sourceforge.net
RDkit Discussion Group,
My apologies in advance if my request is not appropriate for this
discussion group.
Given a small molecule that might have some resemblance to natural
products,
can someone suggest a free, comprehensive, PYTHON/RDkit searchable database
of natural products
RDkit Experts,
What is ctest? Is it fully documented somewhere?
I am running PYTHON 3.5.2/RDkit 2017.03.1 on WINDOWS 7 via
Pycharm 2017.2.3
Is it possible to run ctest in this environment? ctest seems to be a good
way
to exercise and test many of the capabilities of RDkit,
RDkit Discussion Group,
I have written a SMARTS to detect vicinal chlorine groups
using RDkit. There are 4 atoms involved in a vicinal chlorine group.
SMARTS = '[Cl]-[C,c]-,=,:[C,c]-[Cl]'
I am trying to count the number of ("unique") occurrences of this
pattern.
For some
RDKit Discussion Group,
Suppose I have a molecule
smiles1 = ''
The carbon atoms will be assigned indices 0, 1, 2, and 3.
Suppose I want to specifically change carbon 3 to a hydrogen.
Is this possible using RDkit?
I am aware of using SMARTS to match a pattern and
Chem.MolToSmiles(mol)
Out[12]:
'[H]CCC'
In [13]:
Chem.MolToSmiles(Chem.RemoveHs(mol))
Out[13]:
'CCC'
Jason Biggs
On Thu, Nov 9, 2017 at 3:12 PM, James T. Metz via Rdkit-discuss
<rdkit-discuss@lists.sourceforge.net> wrote:
RDKit Discussion Group,
S
t = (match[1], match[2])
if match[1] < match[2] ):
t = (match[1], match[2])
else:
t = (match[2], match[1])
d[t] = match
You will wind up with as many dictionary elements as there are matches.
-P.
On Tue, Nov 7, 2017 at 7:38 PM, James T. Metz via Rdkit-dis
(Cl)(Cl)(Cl)'
>>> count_unique_substructures(smiles1, SMARTS)
1
>>> count_unique_substructures(smiles2, SMARTS)
1
-Brian
On Tue, Nov 7, 2017 at 7:38 PM, James T. Metz via Rdkit-discuss
<rdkit-discuss@lists.sourceforge.net> wrote:
RDkit Discussion Group,
I have wri
RDkit Discussion Group,
Can RDkit predict the ionization state of a molecule at a given pH by
calculating the pKa, predominant species at that pH, etc?
I have already checked the RDkit discussion email archive, and per
my searching there was a response from Greg Landrum about
RDkit discussion group,
Is it possible to automatically generate reaction SMARTS in
RDkit from reactant(s) and product(s)? If so, are there various
"trims" that can be performed to focus on the reaction center
going out certain number of atoms which could be used to specify
reaction
RDkit users,
Is there a RDkit descriptor (or code) to determine the largest number of
contiguous
rotatable bonds in a small molecule?
Hmmm... it seems likely that ligand conformational flexibility might be
somehow related to the entropy component of ligand binding. Has anyone made
RDkit Discussion Group,
I am running the RDkit diverse max min picker code on my WINDOWS 7
64 bit 4 dual core I7 computer. I have tested the code on a small set of
compounds
and the results are OK.
I am now running diverse subset picking on an SDF containing about 40k
compounds.
RDkit Discussion Group,
I am trying to get RDkit to recognize reactants and products in RedOx
reactions including
reactions which include explicit electrons using SMILES as patterns. Does
anyone have any
suggestions or ideas for how to deal with an explicit electron?
I have tried:
RDkit Discussion Group,
Is there interest in having a RDkit UGM in the USA midwest, perhaps
somewhere
in the Chicago area? I would recommend a similar format to the European UGM and
I would insist that presenters deposit their slides and code on the RDkit
GitHub site.
Regards,
RDkit Discussion Group,
What is an appropriate literature reference for RDkit 2017.03.1?
Thank you.
Regards,
Jim Metz
Northwestern University
--
Check out the vibrant tech community on one of
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 encoded in the partial
atomic charge"slot" in a MOL2 file.
RDkit Discussion Group,
I note that RDkit can perform Butina clustering. Given an SDF ofsmall
molecules I would like to cluster the ligands, but obtain additionalinformation
from the clustering algorithm. In particular, I would like to obtainthe
cluster number and Tanimoto distance from
Carlos,
Thank you for your suggestion. However, rather than wrestle with the
technical
details of obtaining polarizabilities from new quantum mechanics schemes, I am
simply interested in extracting the atomic contributions that are apparently
already available for adescriptor called apol
RDkit Discussion Group,
I would like to calculate and be able to visualize the atomic
contributionsto the total molecular polarizability of small organic molecules.
Apparentlythere is a molecular descriptor, apol, that is the sum total from the
atomiccontributions to polarizability
-discuss] atomic contributions to molecular polarizability
Hi Jim,
On Thu, Jan 10, 2019 at 11:59 PM James T. Metz via Rdkit-discuss
wrote:
I would like to calculate and be able to visualize the atomic
contributionsto the total molecular polarizability of small organic molecules
RDkit Discussion Group,
RDkit has quite a number of useful tools and algorithms for ligand-based
drug design (LBDD). However, what about structure-based drug design (SBDD)?
Perhaps a few questions to motivate the discussion.
1) Since RDkit supposedly includes the force field MMFF, does
RDkit Discussion Group,
I am interested in generating and assigning AM1-BCC charges to small
molecules,
preferably in batch mode. I understand this topic has been discussed
previously, buthas there been RDkit code written to do this? Since this relies
on the results of AM1 calculations,
RDkit Discussion Group,
I am aware of RDkit scripts that use the MMFF force field to minimize
smallmolecules. Has anyone written RDkit code to perform molecular dynamics
(MD) of small molecules or protein-ligand complexes using only RDkit and
existingRDkit force fields. I am aware of a
RDkit Discussion Group,
Has anyone implemented code to calculate spherical harmonicscoefficients
for 3D conformations of molecules? The approach I havein mind is described in
Morris, R.J. et al., Real Spherical Harmonic expansion coefficients for protein
binding pocket and ligand
38 matches
Mail list logo
