mplate, mol)
>>> 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 wrote:
> Hello!
>
&g
Hi Greg,
I would also vote for changing the code such that only heavy atoms are used in
the RMS calculation.
Best,
Sereina
On 22 Dec 2016, at 13:36, Greg Landrum wrote:
> Hi JW,
>
> On Wed, Dec 21, 2016 at 11:57 PM, JW Feng wrote:
>
> I am using AllChem.EmbedMultipleCo
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 wrote:
> Thanks for the notebook Sereina!
>
> Unfortunately when I run it I get different results. In your ver
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
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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 wrote:
>
> Hi RDKitte
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 MM
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 wrote:
> Hello,
>
> Imagine I have a compound with some 2D coor
nfId=0)
>>> torsions2 = TorsionFingerprints.CalculateTorsionAngles(mol, tors_list,
>>> ring_tors_list, confId=1)
>>> tfd = TorsionFingerprints.Calcula
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 wrote:
> Hi,
>
> I am having an issue with the python similaritymaps. I am only seeing a
> fraction of the molecule. Anyon
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 to
for them).
Best,
Sereina
On 22 Jun 2016, at 05:02, Greg Landrum 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 knowledge terms in the embedding,
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 wrote
published this, but we have done a systematic analysis using the
compounds in our ETKDG paper and MMFF minimization of the crystal structures
could result in non-negligible differences (RMSD up to 3 Angstroem, median RMSD
= 0.45 Angstroem).
Best,
Sereina
On 22 Jun 2016, at 09:46, David Cosgrove
: list element larger than allowed value"
Any ideas would be greatly appreciated.
Best,
Sereina--
Attend Shape: An AT&T Tech Expo July 15-16. Meet us at AT&T Park in San
Francisco, CA to explore cutting-edge tech
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 wrote:
> Hi Sereina,
>
> At the moment, for historical reasons,
on distance geometry 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 wrote:
> This topic (https://sourceforge.net/p/rdkit/mailman/message/35173301/)
les. Is
MMFFHasAllMoleculeParams() modifying the molecule, i.e. already addying
hydrogens?
Best,
Sereina--
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ht
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,
&
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 molecul
gt;> 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
2016-09-07 17:16 GMT+02:00 Steven Combs :
> Hello!
>
> I have a pdb block t
, 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(
ct me.
Best regards,
Sereina
--
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Rdkit-discuss mailing list
Rdkit-di
. 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
st it did with me...).
for mol in suppl:
molList.append(Chem.AddHs(mol, addCoords=True))
Best,
Sereina
2013/10/8 Paolo Tosco
> Hi Nick,
>
> would you mind sending me the SD file which is triggering the infinite
> loop? Then I'll come back to you as soon as I find out so
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
> Hi,
>
> Thanks Sereina, that's exactly what I'm after! I thought there must be
't think I 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,
Serein
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 David
= AllChem.AssignBondOrdersFromTemplate(template, tmp)
I don't know if this is what you were looking for.
Best,
Sereina
2013/11/4 Michal Krompiec
> 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 betwe
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
and
logistic regression) and classifier fusion, as well as the additional data
sets and training lists.
A tag/release has been created for the original version (as described in J.
Cheminf., 5, 26, 2013).
Please let me know if you have any questions or encounter any problems.
Best,
Sereina
27;re looking for?
Best,
Sereina
2014/1/13 JP
> 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
ule. In your case, I guess it's the
carboxylic acids which can match two ways when there are only single bonds.
I hope this helps.
Best,
Sereina
>
>
>
> On 13 January 2014 21:02, JP wrote:
> >
> > Thanks All - I think I am in a good place now.
> >
> >
is is what you were looking for.
Best,
Sereina
2014/1/24 Michał Nowotka
> 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
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 :
> Look at the following example:
>
> import gi
> from rdkit import Chem
> from rdki
bbox_inches='tight' when saving the image to solve the problem.
Best,
Sereina
2014-07-16 17:04 GMT+02:00 Edward Pyzer-Knapp :
> Hi,
>
> I am trying to replicate the tutorial on visualising maps of gasteiger
> charges.
>
> >>> from rdkit.Chem.Draw import SimilarityMa
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