Modular Chemical Descriptor Language (MCDL): Stereochemical modules.

Background: In our previous papers we introduced the Modular Chemical Descriptor Language (MCDL) for providing a linear representation of chemical information. A subsequent development was the MCDL Java Chemical Structure Editor which is capable of drawing chemical structures from linear representations and generating MCDL descriptors from structures.

Results: In this paper we present MCDL modules and accompanying software that incorporate unique representation of molecular stereochemistry based on Cahn-Ingold-Prelog and Fischer ideas in constructing stereoisomer descriptors.

A Java chemical structure editor supporting the Modular Chemical Descriptor Language (MCDL).

A compact Modular Chemical Descriptor Language (MCDL) chemical structure editor (Java applet) is described. The small size (approximately 200 KB) of the applet allows its use to display and edit chemical structures in various Internet applications. The editor supports the MCDL format, in which structures are presented in compact canonical form and is capable of restoring bond orders as well as of managing atom and bond drawing overlap.

New diversity calculations algorithms used for compound selection.

Some modifications were introduced into the previously described Centroid diversity sorting algorithm, which uses cosine similarity metric. The modified algorithm is suitable for the work with large databases on personal computers. For example, for diversity sorting of the database with the size greater than a million of records, less than 9 h are required (Pentium III, 800 MHz).