There should be a conda binary for mac / python 3.8 with conda-forge, just
follow the first command listed here:
https://www.rdkit.org/docs/Install.html#how-to-install-rdkit-with-conda
On Thu, Jun 24, 2021 at 11:59 AM Michal Krompiec
wrote:
> Hello,
> Is it possible to install RDKit on MacOSX
what happens when you type
$ which python
or
$ conda env list
On Fri, Apr 9, 2021 at 6:07 AM Andrés Sánchez Ruiz <
andressanchezrui...@gmail.com> wrote:
> Dear Greg,
>
> I didn't know I had to send my answer to the discuss inbox... my bad.
> First of all, thank you very much for your quick
Do you still get the error if you move the import into the function body?
def calc_bcut(smi):
from rdkit.Chem.rdMolDescriptors import BCUT2D
mol = Chem.MolFromSmiles(smi)
return BCUT2D(mol)
On Mon, Mar 22, 2021 at 7:29 AM Patrick Walters wrote:
> 2020.09.5
>
> On Mon, Mar 22, 2021
Hi RDKit users,
With rdkit 2020.03.3, MolsToGridImage had more reasonable molecule sizes:
[image: Screen Shot 2021-02-25 at 1.39.46 PM.png]
With rdkit 2020.09.4, the default drawing parameters seem to shrink the
molecules by default in MolsToGridImage:
[image: Screen Shot 2021-02-25 at 1.37.38
th amides and amines are strong donors. This observation is consistent
> with sp2 character.
>
> -P.
>
> On Sat, Feb 13, 2021 at 1:18 PM Peter St. John
> wrote:
>
>> Is there any reason why RDKit says the nitrogen in beta-lactam is
>> SP2-hybridized? I would have assum
Is there any reason why RDKit says the nitrogen in beta-lactam is
SP2-hybridized? I would have assumed it should be SP3. It doesn't seem to
be the ring structure, 'C1NC1' lists all the atoms as being SP3.
>>> [(atom.GetSymbol(), atom.GetHybridization()) for atom in
I wrote some code to do something like this that you might be able to start
from:
https://github.com/pstjohn/bde/blob/master/bde/fragment.py
Mine was mainly concerned with going to/from SMILES strings of the parent
mol and resulting radicals
On Wed, Jan 8, 2020 at 3:40 AM Puck van Gerwen
wrote:
Another option would be to try the conda-forge rdkit. It doesn't appear to
use MKL -- I think the MKL dependency for the rdkit::rdkit package is
coming from the defaults::numpy dependency.
some tools for example scipy and pandas are only available as openblas
> builds via pypi (pip).
I believe
you might be better off not storing the molecule RDkit objects themselves
in the hdf file; but rather some other representation of the molecule. If
you need 3D atom coordinates, you could call MolToMolBlock() on each of the
rdkit mols, and then MolFromMolBlock later to regenerate them. If you
Just wanted to chime in that I'm also excited by this functionality!
an alternative to the SVG classes would be to nest atoms and bonds in svg
groups;
You could also put the atoms and bonds in their own groups if it was easy:
...
...
...
That being said, I'm
Another option is dask (https://docs.dask.org/en/latest/). I've used
`map_partitions` from dask to bulk convert a column of smiles strings into
various computed properties. You could then output to a CSV or other
database file.
-- Peter
On Mon, Jan 21, 2019 at 1:45 AM Markus Sitzmann
wrote:
>
;
> In [27]: Chem.SanitizeMol(m)
> Out[27]: rdkit.Chem.rdmolops.SanitizeFlags.SANITIZE_NONE
>
>
> How are you constructing the molecule with the radical?
>
> Best,
> -greg
>
>
> On Wed, Nov 14, 2018 at 7:36 PM Peter St. John
> wrote:
>
>> I have a molecule with r
mol2 = Chem.MolFromMolBlock(Chem.MolToMolBlock(mol))
¯\_(ツ)_/¯
Thanks for the help!`
On Wed, Nov 14, 2018 at 12:16 PM Paolo Tosco
wrote:
> Hi Peter,
>
> try a.setNoImplicit(True)
>
> does a.GetNumRadicalElectrons() report the correct figure?
>
> Cheers,
> p.
>
> On 11
3 2 1 0
4 10 1 0
5 13 1 0
6 1 1 0
9 3 1 0
11 4 1 0
12 4 1 0
14 5 1 0
15 5 1 0
M RAD 1 1 2
M END
Thanks!
-- Peter St. John
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). A conversion Molecule -> SMILES -> Molecule could thus
> lead to a different ordering of atoms and bonds and you will have to
> canonicalize your structure before you generate your index. [Or make
> sure that you use non-canonical SMILES.]
>
> Best,
> Nils
>
> Am 02.1
If I store a molecule as a SMILES string, along with relevant information
about different bonds, is it safe to annotate those bond entries by bond
index?
I.e., if I create a new rdkit Molecule with rdkit.Chem.MolFromSmiles(xxx),
will the bond ordering always be the same? If not, does anyone know
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