Release Notes

New features and Changes in Molconn-Z 4.05

1. Molconn-Z 4.05 (standalone) was compiled on several platforms:
• Under Irix 6.5 using the -mips3 -n32 compiler directives.
• Under Red Hat Linux 6.2 (also runs under Caldera Linux, and probably other "flavors").
• Under Windows2000 (also runs under 95, 98, ME and XP).
• Under Solaris (SunOS) 5.7.
• Under Macintosh OS X.1

 
2. A new keyword has been added to the command set. "INDEX", whose options are "on" and "off", will write the molecule index number to stderr to assist in identifying compounds with warnings and errors.
3. We ran a test of the NCI database, ca. 250,000 compounds, and discovered a new way to make the program crash. There are some compounds in the database with more than 8 bonds to an atom. 8 happens to be the hardwired limit in the toolkit. A filter to reject these compounds, which by the way do not make chemical sense, has been added. The NCI database is now read cleanly, with about 484 compounds rejected by this filter. (A large number of other compounds are salts and are also rejected by molconnz.)
4. While we located the memory leaks in 4.04 that developed with molecules that were acceptable and completely processed by molconnz, there were a number of other memory leaks that manifested themselves with rejected compounds. We now believe that these have been fixed. During the course of the NCI test the memory usage stayed constant at ca. 36 MB on the SGI for all 250,000 structures.