Dear all,
I need to discriminate molecules with 2D or 3D coordinates.
I have a question regarding how RDKit decides if a molecule read from
SDF is 2D or 3D.
I have a 2D molecule with, for reasons, the "software line" (2nd line in
MolBlock) does not end with '2D' or '3D' but with '0D'.
For te
s not as Mol objects but as str (smiles).
Is this the expected behavior?
If so, how could I do to retrieve molecules as Mol objects instead of
smiles?
Thanks in advance for any hindsight on how to do this!
Best regards,
Jose Manuel Gally
[1] rdkit/rdkitpostgresql: 2018.09.1.0, postgresql
Hello again,
I actually found out, as written in the docs.
By selecting mol_send(m) instead of m in posgresql, I can access the
pickled molecule that I can restore with Chem.Mol(pkl.tobytes())
Cheers,
Jose Manuel Gally
On 11/28/18 12:56 PM, Jose Manuel Gally wrote:
Hello everyone,
I&#
Hi all,
I am using the RDKit postgresql cartridge to perform some substructure
searches on a large number of molecules, as described here:
https://www.rdkit.org/docs/Cartridge.html
However, in addition to which row matched the query, I would also like
to know what are the atom indices for ea
Hi all,
I am trying to highlight substructures found in a set of molecules.
However, if I use a specific color in Draw.MolsToGridImage by defining
the highlightAtomColors parameter, I lose the transparency effect, so
some atoms can be hidden by the highlight.
Is there a way to set the transp
ew.drawOptions()
option.padding=0.13
option.legendFontSize=18
view.DrawMolecules([tm], highlightAtoms=[highlight],
highlightAtomColors=[color_2])
view.FinishDrawing()
svg = view.GetDrawingText()
with open('./example.svg', 'w') as f:
f.write(svg)
SVG(svg.replace('svg:&#x
Dear Jean-Marc,
I believe this can be achieved by using the Mol property
"_smilesAtomOutputOrder", which is set only after using the function
Chem.MolToSmiles.
Please find attached a very simple example of how it can be extracted.
Cheers,
Jose Manuel
On 01.02.19 13:03, Jean-Marc Nuzillard w
Hi all,
I am working on some molecules in a pandas DataFrame and have to export
them to a hdf file.
This works just fine but I get a warning about Performance due to mixed
types. (1)
Why are RDKIT Mol objects causing this warning in the first place? Am I
doing something wrong?
Please fin
ing you that it will
have to use Python's `pickle` module to serialize it.
On Fri, Feb 15, 2019 at 6:35 AM Jose Manuel Gally
mailto:jose.manuel.ga...@gmail.com>> wrote:
Hi all,
I am working on some molecules in a pandas DataFrame and have to
export
them to a hdf file.
of hdf.
Cheers,
Jose Manuel
Refs:
[1]
https://github.com/rdkit/UGM_2016/blob/master/Notebooks/Pahl_NotebookTools_Tutorial.ipynb
[2] http://rdkit.blogspot.com/2016/09/avoiding-unnecessary-work-and.html
On 15.02.19 22:21, Jose Manuel Gally wrote:
Dear Peter,
thank you for your reply.
That
x:
base64.b64encode(pickle.dumps(x)).decode())
should be:
df['mol'] = df['mol'].map(lambda x:
base64.b64encode(x.ToBinary()).decode())
You could also fix this by changing how you decode the column, but
this approach is faster.
-greg
On Mon, Feb 18, 2019 at 11:28 AM
Hi Illimar,
if you are familiar with pandas DataFrames, then I would also recommend
BioPandas for this:
https://github.com/rasbt/biopandas
Cheers,
Jose Manuel
On 26.02.19 00:05, Stéphane Téletchéa wrote:
Hi all,
Le 25/02/2019 à 12:38, Lukas Pravda a écrit :
Hi Illimar,
If you need to acc
Dear all,
This might sound naive, but I want to compute 2D coordinates for a set
of molecules.
For now I am considering the 3 methods below [1].
I was wondering if there was any recommendation to use one method over
another in some cases?
For instance, very large rings are not displayed ro
Lukas
On 09/04/2019, 14:35, "Jose Manuel Gally"
mailto:jose.manuel.ga...@gmail.com>>
wrote:
Dear all,
This might sound naive, but I want to compute 2D coordinates
for a set
of molecules.
For now I am considering the 3 methods below
te angle between two bonds if they share common atom because of
this http://www.ebi.ac.uk/pdbe-srv/pdbechem/chemicalCompound/show/CPT).
Let me know if you would have any questions, or suggestions.
Lukas
*From: *Thomas Evangelidis
*Date: *Tuesday, 9 April 2019 at 15:43
*To: *Lukas Pravda
*Cc: *J
Dear all,
I noticed a strange behavior when extracting murcko scaffolds from
preprocessed molecules with an inhouse standardization protocol.
I made a gist to illustrate the problem:
https://gist.github.com/jose-manuel/04d69dd3ac52cca74449e73d614df42e
This leaves me with several questions:
before sanitizing, your problem will disappear.
Cheers,
p.
On 28/08/2019 13:22, Jose-Manuel Gally wrote:
Dear all,
I noticed a strange behavior when extracting murcko scaffolds from
preprocessed molecules with an inhouse standardization protocol.
I made a gist to illustrate the problem
Dear RDKitters,
I would like to represent what Murcko Scaffolds are extracted from what
molecules.
I had the idea to look into the rdChemReactions module because it shows
a nice arrow between reactants and products.
In my case, I have only 1 reactant and 1 product to display. I played a
bi
ctants and products no
matter what at the moment. This is something we will try to get fixed.
Best,
-greg
On Fri, Feb 28, 2020 at 10:19 AM Jose Manuel Gally
mailto:jose.manuel.ga...@gmail.com>> wrote:
Dear RDKitters,
I would like to represent what Murcko Scaffolds are extract
Dear rdkitters,
I cannot find the functions GetAngleDeg and GetAngleRad which should be
in rdMolTransforms according to the docs:
http://www.rdkit.org/Python_Docs/rdkit.Chem.rdMolTransforms-module.html
Here are the modules listed in rdMolTransforms with dir command:
['CanonicalizeConformer', '
Dear rdkitters,
I found the parameters for bond lengths and angles for the UFF force
field :
http://sourceforge.net/p/rdkit/code/HEAD/tree/trunk/Code/ForceField/UFF/Params.cpp
Is there a way to retrieve these values and use them in a python script?
I could not find any hint in the docs :
http:/
weekend,
though... :-)
The repository on SourceForge is very outdated; all source code has been
moved to Github long ago:
https://github.com/rdkit/rdkit/blob/master/Code/ForceField/MMFF/Params.cpp
https://github.com/rdkit/rdkit/blob/master/Code/ForceField/UFF/Params.cpp
Cheers,
p.
On 21/10/14 10:48, Jo
CF')
bonds = mol.GetBonds()
for b in bonds:
print b.GetStereo()
gives me the following output...
STEREONONE
STEREONONE
STEREONONE
...whereas I would like something like this :
STEREONONE
STEREOANY
STEREONONE
Thank you for your help!
Cheers,
Jo
Dear RDKit communauty,
I would like to compute the raw RMSD matrix (without alignment) between
docking poses of the same ligand from a SDF.
However, upon reading the SDF with a SDMolSupplier, poses are stored
into different Molecule objects, each one with one conformer only,
whereas the functi
Thank you for your response Greg,
unfortunately, it does not seem to work when converting the molecule to
MolBlock:
m = Chem.MolFromSmiles('C/C=C/CC/C=C/F')
[1] print Chem.MolToSmiles(m, isomericSmiles=True)
m.GetBondWithIdx(0).SetBondDir(Chem.BondDir.UNKNOWN)
Chem.AssignStereochemistry(m,forc
Hi rdkitters,
I wrote a very small python snippet to detect all chiral centers of a
molecule, including unspecified ones:
# from rdkit import Chem
def getStereo(smiles):
m = Chem.MolFromSmiles(smiles)
Chem.AssignStereochemistry(m,
cleanIt=True,flagPossibleStereoCenters=True, force=Tru
Hi John and Greg,
I now understand better what happens, thank you for your responses!
However, in this precise case, I need to not consider these atoms as
stereocenters, so I just remove them from the list returned by
FindMolChiralCenters.
When I generate conformations, I still get the differen
Hi RDKitters,
I would like to consider parts of a conformation rigid (fixed dihedral
angles) during minimization
My end goal would be to generate only ring conformations starting with
valid 3D molecules.
I can already consider a specific dihedral angle as rigid:
from rdkit import Chem
from rdk
Hi Paolo, Michal,
thanks for your replies!
I don't want to freeze only linkers between saturated rings, but also
'side chains' so I went with Paolo's snippet to get the maximum amount
of torsions.
Then I filtered the torsions having either:
- at least 2 atoms in the same ring
- at least 1 hyd
imizer to converge. In general, constraints should be
> kept to a minimum; you won't need constraints on aromatics, since they
> are already kept rigid and planar by torsion and oop terms.
>
> Cheers,
> p.
>
> On 20/10/2015 14:38, Jose Manuel Gally wrote:
>> Hi Paolo, Micha
Hi,
currently when I generate conformations with RDKit and want to use them
for docking experiments, I have to first rewrite them using the
MolConverter node in Knime.
I need to do this because some docking software read the information
about charges in the atom block rather than in the molecul
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