Dear Michal,
Chem.AddHs() has the option “addCoords” which is normally set to False.
So, using
mol = Chem.AddHs(mol, addCoords=True)
should solve your problem.
Best,
Sereina
On 20 Aug 2014, at 19:07, Michał Nowotka mmm...@gmail.com wrote:
Hello,
Imagine I have a compound with some 2D
= TorsionFingerprints.CalculateTFD(torsions1, torsions2,
weights=weights)
Let me know if you encounter any problems.
Best,
Sereina
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to set
bbox_inches='tight' when saving the image to solve the problem.
I hope this helps.
Best,
Sereina
On 21 Feb 2015, at 02:28, Matthew Lardy mla...@gmail.com wrote:
Hi,
I am having an issue with the python similaritymaps. I am only seeing a
fraction of the molecule. Anyone else have
field minimization is required. Therefore,
overall the new method is faster.
I hope you find the new conformer generator useful. If you encounter problems,
please let Greg and me know.
Best,
Sereina
--
Go from Idea
I just tried Tim’s example (or a version of it that Greg sent me,
respectively).
What is missing are the hydrogens for the torsion terms of ETKDG to work
properly. Before generating the conformations AllChem.AddHs() should be called.
Best,
Sereina
On 22 Jun 2016, at 06:48, Sereina
for them).
Best,
Sereina
On 22 Jun 2016, at 05:02, Greg Landrum <greg.land...@gmail.com> wrote:
> I don't have anything to add to the pieces about the alignment (Paolo is the
> expert there!), but one comment on the conformation generation: If you used
> the background
: list element larger than allowed value"
Any ideas would be greatly appreciated.
Best,
Sereina--
Attend Shape: An AT Tech Expo July 15-16. Meet us at AT Park in San
Francisco, CA to explore cutting-edge tech and listen to
Hi Greg and Nadine,
Thanks a lot for your answers and the explanation.
I will have a look at either hashing the invariants to 9 bits or removing the
limitation.
Best,
Sereina
On 24 Jun 2016, at 13:20, Greg Landrum <greg.land...@gmail.com> wrote:
> Hi Sereina,
>
>
ometry for the sampling.
Nevertheless, I will have a look at this particular pattern in the next version
of ETKDG to see if we can improve it.
Best,
Sereina
On 22 Jun 2016, at 10:41, Tim Dudgeon <tdudgeon...@gmail.com> wrote:
> This topic (https://sourceforge.net/p/rdkit/mailman/
ams() modifying the molecule, i.e. already addying
hydrogens?
Best,
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> len([1 for b in newMol.GetBonds() if b.GetBondTypeAsDouble() == 1.0])
8
Note that the template molecule should have no explicit hydrogens
else the algorithm will fail.
Hope this helps.
Best,
Sereina
On 07 Sep 2016, at 17:16, Steven Combs <steven.com...@gmail.com> wrote:
> Hello!
>
&
to do so. I will try to get to it
in the next days and then write a short email to the mailing list when it is in.
Best,
Sereina
On 03 Mar 2017, at 00:15, Curt Fischer <curt.r.fisc...@gmail.com> wrote:
> Thanks for the notebook Sereina!
>
> Unfortunately when I run it I get di
think the function AllChem.GetConformerRMSMatrix() might do (parts of) what
you want.
Best,
Sereina--
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.or
eplace the discarded ones. This is why you get
a varying number of conformers.
I have run your script and I get the same weird third conformation. This should
certainly not happen. I will look into it.
Best,
Sereina
> On 12 Jan 2018, at 19:17, Andy Jennings <andy.j.jenni...@gmail.com>
The default conformer generator in RDKit is plain distance geometry, which is
known to not be able to provide perfectly flat aromatic rings.
You can use the ETKDG conformer generator instead:
AllChem.EmbedMolecule(mol, params=AllChem.ETKDGv2())
Best,
Sereina
> On 6 Jul 2018, at 17:54, Phu
results in a higher
probability to be active – although it might still be below 50% (note that the
color range is not standardized globally but based on the largest difference
observed in the molecule).
I hope this helps.
Best,
Sereina
> On 22 Aug 2019, at 11:38, Axel Pahl wrote:
>
example.
m =
Chem.MolFromSmiles('C1=NC(=C2C(=N1)N(C=N2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O)N’)
mH = AllChem.AddHs(m)
AllChem.EmbedMolecule(mH, params=AllChem.ETKDGv2())
Best regards,
Sereina
> On 8 Oct 2019, at 18:18, Paolo Tosco wrote:
>
> Hi Jorgen,
>
> use the
.
Best regards,
Sereina
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. The
code is based on the Python implementations of Jan Domanski and Adrian
Schreyer.
The descriptors can be accessed from Python via
rdkit.Chem.rdMolDescriptors.GetUSR and
rdkit.Chem.rdMolDescriptors.GetUSRCAT.
Best regards,
Sereina
By the way, UFF also hangs if too many hydrogens with zero coordinates are
present, so it seems to be a general problem. This will be fixed at some
point.
Best,
Sereina
2013/10/8 Nicholas Firth nicholas.fi...@icr.ac.uk
Hi,
Thanks Sereina, that's exactly what I'm after! I thought there must
understand it completely. Do you want to set only the bond
orders of a specific substructure? Or would you like to give the function a
set of ligands and a set of templates and it figures out which template
belongs to which ligand and sets the bonds orders accordingly?
Best,
Sereina
2013/10/24
Hi James,
Okay, now it's clear. I somehow (wrongly) thought the PDB reader would give
you the protein and the ligand as two molecules and then it wouldn't have
been a problem... I will discuss with Greg on how to best do this and get
back to you.
Best,
Sereina
2013/10/25 James Davidson j.david
= AllChem.AssignBondOrdersFromTemplate(template, tmp)
I don't know if this is what you were looking for.
Best,
Sereina
2013/11/4 Michal Krompiec michal.kromp...@gmail.com
Hello,
Is it possible to construct a Mol (or EditableMol) object out of a
list of 3D coordinates? I am trying to write a bridge
Hi Anthony,
It has something to do with the bounding boxes (they get scaled during the
map generation process).
Using bbox_inches='tight', however, worked for me, i.e.
image.savefig(out.png, bbox_inches='tight')
I hope this helps.
Best,
Sereina
2013/11/4 Anthony Bradley anthony.brad
looking for?
Best,
Sereina
2014/1/13 JP jeanpaul.ebe...@inhibox.com
RDKitters!
Finally back on the mailing list!
I am sure we've been through this at the UGM (my mind must have wandered
off!), but a quick question about the PDB reader and bond perception. Is
this supported with the current
there are only single bonds.
I hope this helps.
Best,
Sereina
On 13 January 2014 21:02, JP jeanpaul.ebe...@inhibox.com wrote:
Thanks All - I think I am in a good place now.
I can get the SMILES from Paul's mmcif links and then I can use Sereina
magic three lines to do what I want
you were looking for.
Best,
Sereina
2014/1/24 Michał Nowotka mmm...@gmail.com
Hi,
Let's say I loaded a molfile containing coordinates to RDKit mol
object or loaded it from smiles but called
AllChem.Compute2DCoords(mol).
Now I would like to get coordinates for each atom. Unfortunately Atom
to
set bbox_inches='tight' when saving the image to solve the problem. Maybe
there is something similar for mpld3.
Best,
Sereina
2014-03-21 12:12 GMT+01:00 Michał Nowotka mmm...@gmail.com:
Look at the following example:
import gi
from rdkit import Chem
from rdkit.Chem import Draw
from
.GetBonds() if b.GetBondTypeAsDouble() == 1.0])
8
Note that the template molecule should have no explicit hydrogens
else the algorithm will fail.
Hope this helps.
Best,
Sereina
2016-09-07 17:16 GMT+02:00 Steven Combs <steven.com...@gmail.com>:
> Hello!
>
> I have a pdb block
, Greg Landrum, Sereina Riniker, J. Chem. Inf. Model.,
60, 2044 (2020)
"Improving Conformer Generation for Small Rings and Macrocycles Based
on Distance Geometry and Experimental Torsional-Angle Preferences”
https://pubs.acs.org/doi/10.1021/acs.jcim.0c00025
If you want to try i
,
Sereina
> On 7 Jul 2020, at 21:26, Sunhwan Jo wrote:
>
>
> The reason constraint embed didn’t work is the molecule simply can’t be
> embedded using the rdkit’s algorithm.
>
>> In [25]: mol_child = Chem.MolFromSmiles(
Dear Pablo,
The RDKit conformer generator is not really suitable to generate coordinates
for arrangements of multiple molecules.
For this, I would go for tools implemented in MD packages.
Best regards,
Sereina
> On 5 Nov 2020, at 14:56, Pablo Ramos wrote:
>
> Hello everybody,
&
with macrocycles are in the ETKDG version 3
paper (J. Chem. Inf. Model., 60, 2044, 2020) or the recent noeETKDG paper
(https://pubs.acs.org/doi/10.1021/acs.jcim.1c01165).
Hope this helps.
Best,
Sereina
> On 19 Jan 2022, at 16:37, mix_of_reasons via Rdkit-discuss
> wrote:
>
>
&g
Dear Ling,
Yes, the atom indexing is the same for all conformers of a molecule.
Best regards,
Sereina
> On 19 Jun 2022, at 00:04, Ling Chan wrote:
>
> Dear colleagues,
>
> Just wonder if the atom indexing in a conformer is always identical to that
> of the parent m
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