The second beta version of ChemPhoto, the chemical structure imaging application developed by Metamolecular, is now available for testing. Thanks to detailed reports from several ChemPhoto Beta-1 testers, a number of issues were discovered and have been addressed by this newest release.

If you want to build cheminformatics software of any kind, you’ll need a basic toolkit. Ideally, this toolkit contains all of the low-level functionality used over and over in your projects. Tools for building an in-memory molecular representation, exact- and substructure comparison, and reading/writing molfiles all fall into this category. Also ideally, this toolkit should be free.

Recently, Alain Borel posted a message to the CHMINF-L list describing his successful attempt to get links to external datasources to show up in SciFinder Web: Greasemonkey is the client-side script plugin engine that enables users to change the appearance and content of any site. Although originally designed as a Firefox extension, as least some Greasemonkey scripts can be run in Safari and Chrome.

One of the most important capabilities in cheminformatics is mapping the atoms of a query structure onto the atoms of a target structure . Although useful in itself, the main value of atom mapping comes from the software that gets built on top of it: exact structure comparators, substructure search systems, and query atom/bond search systems such as SMARTS.

You can’t get very far in cheminformatics without the ability to compare one molecule to another to find either an exact structure or substructure match. For example, if you want to build chemical databases, a good substructure matcher comes in very handy. As luck would have it, the substructure match problem (a variant of the subgraph isomorphism problem) is both computationally expensive and difficult implement.

Recently a customer reported a problem in which mousing over an instance of the ChemWriter editor applet caused browser popup windows to disappear behind the parent window. Although many view browser popup windows as bad UI design, there are situations in which no alternative exists. This article describes the window focus problem in detail and outlines one solution.

One of the things that makes organic chemistry such a fascinating and useful subject (not to mention profitable) is the way mind-boggling levels of diversity arise from the application of very simple rules.

One of the main design goals of ChemPhoto, the chemical structure imaging application, was to support all Web-relevant image output formats, both vector-based and pixel-based. Like most things in software development, there are far more approaches that add complexity to this problem than there are approaches that remove it. And for some reason, the complexity-reducing methods tend to be the last to be considered.

We can think of a fingerprint as a bucket into which every molecule in the universe can be reproducibly placed. Each molecule will belong to a single bucket, but each bucket may contain any number of molecules. In other words, there exists a one-to-many relationship between a fingerprint and its associated molecules. The previous article in this series discussed how to model this relationship using SQL.