Sorry: typo "...quickly eliminate some duplicates using non-canonical
SMILES..."
On Wed, 7 Nov 2018 at 09:32, Noel O'Boyle wrote:
> I don't believe that there is a better way to eliminate duplicates apart
> from using canonical forms (e.g. InChI or canonical SMILES, though InChI
> also changes t
I don't believe that there is a better way to eliminate duplicates apart
from using canonical forms (e.g. InChI or canonical SMILES, though InChI
also changes the structure so use with care). You can quickly eliminate
some duplicates using canonical SMILES or a matrix comparison as you
suggest, but
Hi Andrew and Noel,
Thank you for the inspiring answers!
Andrew: Sorry I didn't make it clear, but 1/2 of the time is only for a random
job I tested and I don't know the scaling of it. Its cost may grow faster than
the searching algorithm. I think it is beneficial to know the formal time
compl
First of all, I'd recommend using the development code rather than the
latest release. Also, ensure that hydrogens are suppressed. You may also
consider trying to avoid multiple canonicalisations of the same graph by
just writing out a non-canonical SMILES, and only at the end collating them
and ca
On Nov 2, 2018, at 01:33, Xianghai Sheng wrote:
> I am trying to figure out the time complexity (Big O) of converting from
> OBMol to canonical smiles.
I don't think that's a useful way to think about your problem.
Graph canonicalization is "at least as computationally hard as the graph
isomor
Hi,
I am trying to figure out the time complexity (Big O) of converting from OBMol
to canonical smiles. I tried to look at the code but it looks too complex. (I
am assuming "class OBMol2Cansmi" is the right place to look at.) Is there
relevant documentation/paper on this? Does anyone know the t
