On 08/23/2015 11:38 AM, Jing Lu wrote:
Thanks, Andrew!
Yes, I was thinking about using scikit-learn also. But I guess I need to
use a data structure for sparse matrix and define a function for
connectivity. I hope the memory issue won't be a problem.
Most AgglomerativeClustering algorithms
Thanks, Takayuki,
For both Repeated Bisection clustering and K-means clustering, they all
need the number of clusters as input, right?
Best,
Jing
On Sun, Aug 23, 2015 at 1:17 AM, Taka Seri serit...@gmail.com wrote:
Dear Jing,
How about your trying using bayon ?
On Aug 23, 2015, at 3:43 AM, Jing Lu wrote:
If I want to cluster more than 1M molecules by ECFP4. How could I do it? If I
calculate the distance between every pair of molecules, the size of distance
matrix will be too big. Does RDKit support any heuristic clustering algorithm
without
Dear colleagues,
I got two conformers of a molecule. It looks like they have the same chirality
(S, I believe). But RDKit perceives them as different. Is it a bug, or did I
miss anything?
Thank you.
Ling
mol = Chem.MolFromMolFile(input.sdf, removeHs=False)
On Aug 23, 2015, at 6:38 PM, Jing Lu wrote:
I hope the memory issue won't be a problem.
That's up to you and your choice of threshold.
Most AgglomerativeClustering algorithms have time complexity with N^2. Will
that be a problem?
You have to decided for yourself what counts as a problem.
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