chem-bla-ics: April 2010

Wondering who will be the 100th Blue Obelisk eXchange user...

Posted via email from Egon's posterous

Chem4Word goes Apache 2.0

Early March I reported about Konstantin's JChemPaint-based chemistry plugin for OpenOffice, but there is (friendly) competition: Chem4Word. Being for Microsoft Word, the plugin only works on top of proprietary software, unfortunately; therefore, I cannot tell you if Chem4Word release is any good, but what Jim has showed me about a year ago, it is pretty cool.

Apr

CIP rules for stereochemistry

Uniquely identifying stereochemical enantiomers is an important aspect of data exchange of chemical structures. The simplest, most neglected solution is to pass around 3D models, but a lot of people like to stick to things like SMILES, or IUPAC names. Now, given that we want to uniquely represent the stereochemistry, we can use special rules. One example for enantiomers are the Cahn-Ingold-Prelog (CIP) rules.

The CDK does not have an implementation of (part of) the CIP rules.

Apr

ACS Liveblogging 1st Disclosures of Drug Candidates

Carmen liveblogged via her twitter account the disclosures of drug candidates at the past ACS meeting, and later aggregated the tweets in her blog. While many of her tweets made it into the FriendFeed room, the structure she drew up and shared did not make it. And until just know, I was not aware the had tweeted those too. The first twitpic she pushed was:

and I hope they will all end up in ChemPedia.

Apr

CDK-JChemPaint #5: the Groovy-JChemPaint repository

Oh, I forget to mention just earlier that I have set up a small git repository with the full Groovy demo scripts. Additionally, requests on further tutorials and/or bug reports can be filed in the matching Issues tracker.

Apr

CDK-JChemPaint #4: embedding the renderer into a Swing panel

Now that we covered the utmost basics of using the CDK-JChemPaint patch (see #1, #2, #3), it is time to move on. I am happy to hear that so many people have started using the new rendering architecture, either via the EBI JChemPaint Swing applet/application branch, or via the CDK-JChemPaint patch.

A couple of issues and questions came up (scaling not working as expected; how to layout reactions; how to get charges to show up), and I will look at those shortly.

Apr

BitTorrents for Science

The idea has been lingering in the air for a long time now: sharing large science data sets using bittorrent. Over the past couple of years I have seen a lot of science related software being distributed over torrents, and the use in open source in general is abundant. Given a good network of so-called seeders, download times go down dramatically, and the overall energy consumption goes down too, as data has to follow a much shorter path.

Apr

CDK-JChemPaint #3: rendering parameters

OK, one last CDK-JChemPaint tutorial for today (see #1 and #2). Rendering wasn't as much fun, if you could not tune it to your needs. JChemPaint has long had many rendering parameters, and one by one we are converting them to the new API.

Apr

CDK-JChemPaint #2: rendering reactions

I posted earlier today a Groovy script to render molecules with CDK-JChemPaint 8. Now, the new JChemPaint rendering engine also contains the functionality to render reactions. So, I can also do:

$ groovy renderReaction.groovy

The matching script:import java.util.List; import java.awt.*; import java.awt.image.*; import javax.imageio.*; import javax.vecmath.*; import org.openscience.cdk.*; import org.openscience.cdk.geometry.*; import org.openscience.cdk.interfaces.*; import org.openscience.cdk.

Apr

CDK-JChemPaint #1: rendering molecules

I reported earlier that the CDK-JChemPaint patch is now a clean add-on from the CDK releases.