SMILES and InChI are two commonly-used molecular line notations. Although each has its advantages and limitations, the novelty of InChI and the ubiquity of SMILES makes the SMILES to InChI conversion especially useful. Many of the situations in which the need for this conversion will arise are particularly well-suited for the Ruby programming language. A recent article described how RCDK and Rino could be used to accomplish this conversion.
Through Andrew Dalke’s blog, I came across an online museum dedicated to early molecular graphics. One section is amazing. It describes the work of Cyrus Levinthal, who in the mid 1960’s built the first interactive molecular graphics system. Users viewed 3-D molecular images on an oscilloscope screen (vector graphics!), and manipulated them with a trackball-like device. The system, called “Kluge”, handled both small molecules and proteins.
Open Babel is a widely-used Open Source chemical informatics toolkit written in C++. Although originally designed as a molecular language translator, Open Babel also supports SMARTS pattern recognition, molecular fingerprints, molecular superposition, and other features as well. Open Babel currently offers interfaces for two scripting languages: Python and Perl. Recently, Geoff Hutchison and I have been working to add Ruby to that list.
Ruby Chemistry Development Kit (RCDK) version 0.3.0 is now available from RubyForge. RCDK enables the complete CDK API to be accessed from Ruby. This release adds support for IUPAC nomenclature translation and tighter Java integration.
A recent article discussed chemistry-related journals in the Directory of Open Access Journals (DOAJ). In going through some of my bookmarks, I stumbled on an Open Access journal that DOAJ doesn’t have: Metal-Based Drugs . Unfortunately, the last available issue of Metal-Based Drugs is from 2002. It’s not clear if this journal is defunct or not.
New technologies attempting to compete with older technologies need to provide a clear upgrade path, if they are to succeed. A case in point is Ruby. Many Java developers’ reaction to this language has less to do with its capabilities and more to do with previous investments in Java. What good is a new language if the special library X that you depend on needs to be rewritten from scratch?
An article by Thomas Engel honoring Johann Gasteiger has recently appeared in J. Chem. Inf. Model. Tucked between two pages of text is a fascinating full-color, full-page timeline of Bio- and Chem(o)informatics. It starts with the abacus in 3000 B.C. and Libavius’ Alchemia in 1500 A.D. Near the end, it records the advent of virtual screening in 1998.
Metaprogramming lets you define new constructs in your programming language. In safety languages like Java, metaprogramming is not a standard feature, although it can be done. Not surprisingly, the reaction most Java developers have to metaprogramming typically ranges from “useless” to “catastrophic”. I was once in that category.
Cascading Style Sheets (CSS) are used by Web developers to modify the appearance of an HTML document without requiring changes to the document itself. This approach has become so popular because of the power it offers: developers can achieve a consistent and re-usable look by simply editing and/or copying a single document. 2-D molecular structures are like text documents in that context determines the best presentation style.
Like everything else in information technology, the costs of setting up and maintaining a scientific journal are rapidly approaching zero. A growing assortment of Open Source journal management systems is available today. Recently, I was introduced to one of these packages by Egon Willighagen as part of my involvement with CDK News.
The Directory of Open Access Journals (DOAJ) currently lists 2420 Open Access scholarly journals. Of these, 52 currently fall under the category of chemistry. Although the organic chemistry subcategory only currently lists three journals, the general chemistry category actually contains several journals containing organic chemistry content, such as the Bulletin of the Korean Chemical Society, Chemical and Pharmaceutical Bulletin, and Molbank.