Saturday, 23 September 2017

How many cheminformaticians does it take to read a SMILES string?

›
A few days ago I posted the following poll question on Twitter: How many Hs are on the N in the molecule described by this SMILES string? ...
Monday, 28 August 2017

My ACS talk on Kekulization and aromatic SMILES

›
Here are the slides for the talk I presented last week at the ACS meeting in Washington. It describes my understanding of the Daylight toolk...
Sunday, 23 July 2017

Faster toolkit, faster!

›
After an extended hiatus, I've been back doing a bit of work on Open Babel, and specifically I've been working on improving performa...
Friday, 5 May 2017

Using WebLogo3 to create a sequence logo from Python

›
A sequence logo is a way to display the variation at particular positions of multiple-aligned sequences. Here I used WebLogo 3 to do this. ...
Monday, 23 January 2017

Whiskas statistics and the pitfalls of mean rank

›
In the fingerprint similarity paper I published last year, I made the following observation: "However the use of the mean rank is itse...
4 comments:
Saturday, 14 January 2017

Counting hydrogens in a SMILES string - The Rules

›
Hydrogens are not usually listed explicitly in a SMILES string, but instead can be inferred from a set of rules. To be precise, when reading...
Friday, 30 December 2016

The clockwisdom of SMARTS

›
Image credit: Jonathan Cohen (CC-BY-NC) In earlier posts I discussed/investigated how stereochemistry is represented in SMILES. Here I...