Tuesday, 30 March 2010

Cinfony slides from the ACS

Cinfony is a cheminformatics toolkit that makes it easy to access OpenBabel, RDKit, CDK and internet webservices from a Python program. Here is a talk I gave last Thursday at the ACS National Meeting in San Francisco describing Cinfony 1.0.

Thursday, 18 March 2010

Cinfony, solar energy, the ACS and fingerfood

I'll be presenting a talk on Cinfony next Thursday at the San Francisco ACS, so come along if interested. This will include the latest work on Webel which I've discussed here before.
Combining disparate cheminformatics resources into a single toolkit: The Cinfony library
N.M. O'Boyle, G.R. Hutchison
DIVISION: CINF: Division of Chemical Information
SESSION: General Papers
START TIME: March 25, 2010, 11:00 am
LOCATION: The Moscone Center, Room: Room 206/210

Work I've done as part of a collaboration with Geoff Hutchison will be presented by Geoff on Monday morning. This involves the computational design of organic polymers for use in solar cells. We're pretty excited about this.

Organic electronic materials by design: Finding a needle through the haystack
G.R. Hutchison, N.M. O'Boyle
DIVISION: CINF: Division of Chemical Information
SESSION: Cheminformatics Tools and High-throughput Approaches for the Discovery of New Materials
START TIME: March 22, 2010, 10:45 am
LOCATION: The Moscone Center, Room: Room 206/210

Attending international conferences isn't cheap, and so it's important to attend as many free-food, I mean networking, opportunities as possible. I'll probably attend one or all of the following:
  • CINF Welcoming Reception, 6:30-8:30 PM Sunday, March 21, 2010, Esplanade Ballroom 308, Moscone Center
  • Harry’s Party, 5:30-7:30 PM Monday, March 22, 2010, Presidential Suite, Palace Hotel, 2 New Montgomery Street
  • CINF Tuesday Luncheon, 12:00-1:30 PM Tuesday, March 23, 2010, Esplanade Ballroom 304, Moscone Center (Tickets required in advance??)
  • CINF Tuesday Reception, 6:30-8:30 PM Tuesday, March 23, 2010, Esplanade Ballroom 307, Moscone Center

And of course I'll be attending the session I'm organising along with Jean-Claude Bradley and Andy Lang, so I might see you at the Visual Analysis of Chemical Data Symposium on Monday morning or all-day Tuesday.

...that's enough procrastinating...time to finish this talk.

Tuesday, 9 March 2010

Hack MACCS into Pybel

Due to a clerical oversight (originally pointed out by Fredrik Wallner over at Cinfony), the current release of Pybel doesn't support the MACCS fingerprint (although OpenBabel does). It's not pretty but we can hack it in as follows:

import pybel

pybel._fingerprinters = pybel._getplugins(
  pybel.ob.OBFingerprint.FindFingerprint, pybel.fps)

mol = pybel.readstring("smi", "CCCC(=O)Cl")
print mol.calcfp("MACCS").bits
# [103, 107, 114, 115, 132, 134, 147, 154, 155, 160, 164]

The next release of Pybel.py will automatically use the available fingerprints.