Thanks Gianluca!
On Tue, Jan 22, 2013 at 10:26 AM, Gianluca Sforna gia...@gmail.com wrote:
On Tue, Jan 22, 2013 at 6:00 AM, Greg Landrum greg.land...@gmail.com wrote:
I'm very happy to announce that the next version of the RDKit --
2012.12 (a.k.a Q4 2012) -- is released.
Thanks to Greg, I
RDKitters,
Long time no type, I've been busy with that little chestnut of my PhD...
I would like to align two molecules and calculate the shape tanimoto with
ShapeTanimotoDist(...). The issue is that this method requires a
pre-defined alignment - which I do not have.
Is there a way how to do a
Thanks Niko, Taka for your prompt replies.
My molecules are not guaranteed to have some common substructure, so an
RMSD align is out of the question. I [think I] want a 3D alignment which
maximizes volume overlap between the two molecules.
-
Jean-Paul Ebejer
Early Stage Researcher
On 22
Hi JP,
Do you want to do a shape align or just any sort of alignment?
There is a MolAlign in All.Chem which will give you an RMSD align. This works
well if you have reasonably similar molecules (do a GetSubstructMatch before to
get the atom list).
Don't think there is a shape alignment for
On Tue, Jan 22, 2013 at 4:55 PM, Igor Filippov [Contr]
igor.filip...@nih.gov wrote:
Would it be possible to have this link somewhere prominently on RDKit
download webpage?
These RPMs are incredibly useful, but every time I must hunt through my
emails to find the link - it's easy to remember
On 22/01/13 05:40, Greg Landrum wrote:
Hi Paul,
On Mon, Jan 21, 2013 at 4:13 PM, Paul Emsley pems...@mrc-lmb.cam.ac.uk
wrote:
I am making heavy weather of the following problem - and am wondering if I
am missing something (such as a useful RDKit function).
I am working on this beasty (as
If you're just looking for 6 membered rings, you can define a SMARTS that
matches 6 membered rings like this *1~*~*~*~*~*1. You can also use this
approach to identify all rings (at least those within reason). You can use
an expression like this
[*1+string.join([*~]*x,)+*1 for x in range(1,19)]
On Wed, Jan 23, 2013 at 2:47 AM, Patrick Walters wpwalt...@gmail.com wrote:
If you're just looking for 6 membered rings, you can define a SMARTS that
matches 6 membered rings like this *1~*~*~*~*~*1. You can also use this
approach to identify all rings (at least those within reason). You can
On Tue, Jan 22, 2013 at 7:14 PM, Gianluca Sforna gia...@gmail.com wrote:
On Tue, Jan 22, 2013 at 4:55 PM, Igor Filippov [Contr]
igor.filip...@nih.gov wrote:
Would it be possible to have this link somewhere prominently on RDKit
download webpage?
These RPMs are incredibly useful, but every time
On Wed, Jan 23, 2013 at 5:21 AM, Greg Landrum greg.land...@gmail.com wrote:
Another easy short-term solution would be to give Gianluca rights to
create and edit downloads on the google code page. I just did this.
Ah; I guess this may not be optimal due to the large number of
files... ah well,
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