t; Sc1ncc2c(c1)2
> Sc1cc2c2cn1
>
> However the resulting tautomers differ depending on which is used as input.
>
> Best regards,
> Diogo
>
> On Mon, 5 Feb 2024 at 11:38, Lewis Martin
> wrote:
>
>> Thank you very much for the detective work, Wim! This is
tandardize/TautomerCatalog/tautomerTransforms.in#L46
> (poiting to the line with the relevant transform).
> best wishes
> wim
>
> On Mon, Feb 5, 2024 at 3:26 AM Lewis Martin
> wrote:
>
>> Hi all,
>> I'm looking at scoring tautomers, and using the 'tautob
Hi all,
I'm looking at scoring tautomers, and using the 'tautobase' dataset used by
Weider et al* at:
https://github.com/choderalab/neutromeratio/blob/master/data/b3lyp_tautobase_subset.txt
This dataset has pairs of tautomers with experimental logK values to
determine the preferred tautomer.
In a
eal for doing cleanup transformations like
> these.
>
> This gist shows how to write reaction rules for your cases (I guessed for
> what the Ns are supposed to be) and then use them:
> https://gist.github.com/greglandrum/8fd229bc6bf6c734d1c21da7f2bebebb
>
> Hope this helps,
>
Hi All,
Reading molecules from a bulk download of SureChEMBL, I come across a fair
few molecules that fail to parse. Not sure whether they SHOULD parse or
not.
Here is an example: https://www.surechembl.org/chemical/SCHEMBL386
with SMILES code: COC(=O)C1=C(C=CC=C1)C1=CC=C(C[N+]#[N]=[N-])C=C1
Even
Hi all,
Does anyone have a way to access the atom indices and the parameters for
all of the dihedrals (aka torsions) in an MMFF force field object? I
noticed that one can set mmffVerbosity=2 to print them to stdout, but I'd
like to access them programmatically. I believe Paolo Tosco must have done
, 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 will read better in
> rdkit.
>
> Regards,
> F.
>
> On 26/09/2021 17:02, Lewis Marti
Hi RDKit,
While parsing proteins from the PBD with RDKit, I've come across situations
where the distance-based bond determination leads to 'incorrect' bonds
between atoms that are erroneously too close together. PDB files have no
bond information, so it's not really 'incorrect' (rather the model
co
Hi RDKit,
How does one input the number of bits to the ShapeTanimotoDist function?
The docs indicate the default is
*rdkit.DataStructs.cDataStructs.DiscreteValueType.TWOBITVALUE,
*but I tried some other values and this gave unexpected results.
Specifically: when increasing to higher bit values, th
Hi RDKit,
I'm exploring strain energies in the context of virtual screening,
something that has been considered for a while[1] and is still being
explored today[2].
There may not be a canonical way, but is this a valid/good way to calculate
strain energy? I'm just not sure if I'm using the MMFF co
Hi all,
Is there a way to draw multiple conformers of a single molecule using
Draw.MolsToGridImage?
Here's a first attempt but, either all conformers are exactly the same or
the parent molecule falls back to conformer 0, since all molecules in the
grid appear the same:
```
from rdkit import Chem
Apologies if this doubles up, I think sourceforge was having issues...
Hi all,
Is there a way to draw multiple conformers of a single molecule using
Draw.MolsToGridImage?
Here's a first attempt but, either all conformers are exactly the same or
the parent molecule falls back to conformer 0, since
I know this doesn't address the question exactly - but you can also do this
(using RDKit) via the jan jensen and colleague's xyz2mol -->
https://github.com/jensengroup/xyz2mol
- lew
On Sat, Jun 5, 2021 at 10:56 AM Storer, Joey (J) wrote:
> Dear all,
>
>
>
> For molecular modeling workflows and i
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 if/else statements), which as i
understand it m
Hi all,
Felt sure this would have been asked but I can't find it. What is the
'largest' possible bit in an unfolded Morgan fingerprint? Asked another
way, what type of number are the substructure identities hashed into?
The Rogers and Hahn ECFP paper says that they hash into a 32-bit integer,
and
ingerprint.
>
> FWIW: if you haven't seen the recent blog post about similarity searching
> with short fingerprints:
> http://rdkit.blogspot.com/2020/08/doing-similarity-searches-with-highly.html
>
> -greg
>
>
> On Wed, Sep 9, 2020 at 2:37 AM Lewis Martin
> wrot
efully
to be re-used. Chemfp is amazing but brute-forcing 100million by 100million
would surely still take a long time compared with an approximate nearest
neighbor approach.
Straying from RDKit so Ill leave it there - thanks!
On Wed, Sep 9, 2020 at 11:29 AM Francois Berenger wrote:
> On 09/09/2
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 out when loaded with pandas.read_csv() or f.
Hi all,
Im chasing up a small puzzle on parsing SMILES codes if anyone's
interested, but its not directly RDkit. I was looking at the molecules in
the MUTAG dataset, which is commonly used in graph learning research.
Mostly these are just shared as graphs (i.e. vertices and edges) rather
than SMILE
the
> GetNumOnBits() method on bit vectors and the similarity calculation code
> in rdkit.DataStructs. Take a look at DataStructs.DiceSimilarity()
>
> Hope this helps,
> -greg
>
>
>
> On Wed, Jul 10, 2019 at 3:53 AM Lewis Martin
> wrote:
>
>> Hi all,
>> Quick que
Hi all,
Quick question on truncated fingerprints, any help is really appreciated.
I think I've missed a trick on how the new fingerprint generator works. I
thought the below should produce equivalent fingerprints but they are
totally different. Has the implementation changed, or maybe I'm getting
Hi all,
Can anyone please help explain what values are returned
by GetMMFFVdWParams? It takes two indices as input, so is it an interaction
term between the two? Or is it the well depth and minimum (i.e. epsilon and
R)?
Example:
In:
m = Chem.MolFromSmiles('C1CCC1OC')
m2=Chem.AddHs(m)
AllChem.Embed
There have been some comparisons between different fingerprints, which Im
sure can be found via google, but I haven't seen feature selection.
If you're looking for dimensionality reduction, anecdotally I've noticed
that hashing bit vectors down to size has no benefit over the traditional
folding,
. 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 lot,
> Francois.
>
> On 31/01/2019 08:49, Lewis Martin wrote:
> > Thanks so much Greg!
ogether over the next couple of days.
>
> -greg
>
>
> On Wed, Jan 30, 2019 at 4:59 AM Lewis Martin
> wrote:
>
>> Hi rdkitters,
>> I'd like to compare the similarity of torsion/atom pair FPs using
>> standard atomic numbering with those using pharmacophore
Hi rdkitters,
I'd like to compare the similarity of torsion/atom pair FPs using standard
atomic numbering with those using pharmacophore types, like the 'CATS' atom
typing developed by Gisbert Schneider, and hoped someone has some advice
here. *CATS* is a pharmacophore atom typing system with these
Thankyou Paolo and Chris! These hydrogens were added while editing the
molecule beforehand but I assumed sanitizing would remove them.
Cheers
Lewis
On Thu, 26 Jul 2018 at 7:59 pm, Chris Earnshaw wrote:
> Hi
>
> It looks to me like N5 [nH:5] also has a problem. This has 3 connections
> to heavy
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