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 molecule? I suspect it is
Hi Paul,
TFD was developed for drug-like molecules with small rings. The torsions of
ring bonds are therefore summed up into a single average value for each ring
(see Figure 1 in J. Chem. Inf. Model., 52, 1499, 2012). This makes of course
not much sense for a macrocycle and likely causes your
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,
>
> I am
Dear Pavel and Sunhwan,
Please note that hydrogens should always be added for the embedding algorithm
to work properly (i.e. it’s not a walk around but what should be done).
See also Section “Working with 3D Molecules” in
https://www.rdkit.org/docs/GettingStartedInPython.html
Best regards,
, 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
Hi Steven,
The PDB reader in the RDKit doesn’t determine any bond orders - everything
is read as a single bond.
In order to set the bond orders, you need to call the
AssignBondOrdersFromTemplate() function using a reference molecule
generated from SMILES (or SDF).
Here is some example code from
Hi Michal
I think this is related to a previous mailing list item (
https://www.mail-archive.com/rdkit-discuss@lists.sourceforge.net/msg03528.html
).
It has probably something to do with the bounding boxes (they get scaled
during the map generation process). In the previous case it was enough to
Hi Michael,
You can get the atom positions via the conformer:
m = Chem.MolFromSmiles('c1c1')
AllChem.Compute2DCoords()
pos = m.GetConformer().GetAtomPosition(0) # position of atom 0
This gives you a rdGeometry.Point3D - e.g. the x coordinates you get with:
x = pos.x
I hope this is what
-archive.com/rdkit-discuss@lists.sourceforge.net/msg03481.html
On 13 January 2014 19:46, sereina riniker sereina.rini...@gmail.com
wrote:
Hi JP,
If you have also a SMILES of the molecule you want to read from PDB,
you can assign the bond orders based on this template:
tmp
Hi JP,
If you have also a SMILES of the molecule you want to read from PDB, you
can assign the bond orders based on this template:
tmp = Chem.MolFromPDBFile(yourfilename)
template = Chem.MolFromSmiles(yoursmiles)
mol = AllChem.AssignBondOrdersFromTemplate(template, tmp)
Is this what you're
Hi Michal,
Well, if you have your 3D coordinates as a PDB file, you can read them in
with the new PDB parser and assign the bond orders based on a template
(generated from the SMILES of your molecule):
tmp = Chem.MolFromPDBFile(yourfilename)
template = Chem.MolFromSmiles(yoursmiles)
mol =
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
Hi James,
Regarding the AssignBondOrdersFromTemplate() method:
As far as I understood, the PDB reader assigns bond orders to the amino
acids in a protein, but if a ligand is present it puts all bonds of it to
SINGLE bonds as auto bond-type perception is not trivial (see Roger's
comments).
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
*T* 020 8722 4033 | *E* nicholas.fi...@icr.ac.uk | *W* www.icr.ac.uk | *
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*Making the discoveries that defeat cancer*
On 8 Oct 2013, at 10:51, sereina riniker sereina.rini
Dear all,
A c++ implementation and Python wrappers of the ultrafast shape recognition
(USR) descriptor (Ballester and Richards, J. Comput. Chem. (2007), 28,
1711) and the USR CREDO atom types (USRCAT) descriptor (Schreyer and
Blundell, J. Cheminf. (2012), 4, 27) are now available for the RDKit.
Dear all,
The source code and compound lists of the benchmarking platform discussed
in J. Cheminf. 5, 26, 2013 (http://www.jcheminf.com/content/5/1/26) are now
available as a separate repository of RDKit on github
(rdkit/benchmarking_platform). The platform is based on RDKit and includes
88 data
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