Release Notes

New features and Changes in Molconn-Z 4.07

1. Molconn-Z 4.07 (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

 
The performance of the IRIX and LINUX versions has been substantially improved due to more aggressive optimization.
 
2. A new Option for the Keyword "INPUTFORMAT" has been added to the command set. "oelibmol", is now an option for the use of the MDL MOL file format. For Example,

   NORECORDS 
   ADD 1 
   ADD 3  
   ADD 4 
   ADD 8 
   ADD 9 
   HEADERS top 
   INPUTFORMAT oelibmol 
   WARNINGS off                                                                                        
   INDEX on                                                                                            
   ERRORS skip                                                                                         
   GO

3. We discovered a bug in the way in which hydrogen was treated in some nitrogen containing compounds such as aromatic N-heterocycle structures and guanidinium structures (Arg), thanks to John Boik at MD Anderson. This bug only affected OELIB structures that did not include explicit hydrogens (ie if you used "INPUTFORMAT oelibsmiles" keywords), and NOT DAYLIGHT structures (ie if you used the "INPUTFORMAT daylightsmiles" keywords). While the bug has little effect on most of the descriptors, because one hydrogen on the aromatic nitrogen is ignored, it affects the molecular weight and all values related to the number of hydrogens on aromatic nitrogens (for example some affected compounds include pyrrole, pyrazole, imidazole, purine, indazole, carbazole and tetrazole) as well as total hydrogens. This bug has been fixed in Molconn-Z 4.07 and these compounds now report the correct number of hydrogens.
    
4. As part of the bug repair and improving the code, it was necessary to add some additional atom types. This has caused some of the descriptors in records 26-30 and 33-37 to change their location in the matrix. Each record is on a line, so line 26 will be record 26. This only affects Standalone Molconn-Z, not the Toolkit or Sybyl version. Therefore, if you have scripts that you use to pick components from the matrix, you should look carefully at these records. The "headers" will correctly identify the descriptor position.
    
5. A change was made in the way the "hostid" is calculated in January 2003 for Windows machines. The hostid program (eg. host_win.exe) is now included in the distribution so that you can check your "hostid" to see if you need a new license file.