Release Notes

New features and Changes in Molconn-Z 4.09

Molconn-Z 4.09 (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

As with version 4.07 the performance of the IRIX and LINUX versions has been substantially improved due to more aggressive optimization.

Starting with version 4.07, a new Option for the Keyword "INPUTFORMAT" was 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

We discovered a bug in the descriptor printing format that caused certain descriptors to not be printed properly. For example, while "nI" (the number of Iodine atoms) was properly printed, the descriptor "nsI" (the number of single bonds to Iodine) was calculated but not printed properly. This only affected Standalone Molconn-Z and not the Molconn-Z Toolkit (unless you built Standalone from the Toolkit). This printing problem has been corrected in version 4.09.

As a result of many requests, we have added a new functionality to allow a new descriptor print format. This new format is a single line of comma separated values (CSV), to make it easier for people to incorporate output data directly into statistical programs. In order to use this new format there is a new keyword "CSVUSEFUL". If this keyword is used, the only output will be the "useful" set of descriptors in a single line separated by commas. The order will be the order listed in Appendix I (left to right and by record number). You can check this by printing the header. If the keyword "CSVUSEFUL" is mixed with other record words like "ALLRECORDS" or "ADD 30", only the CSVUSEFUL record will be printed. If a compound can not be interpreted properly by OELIB or Molconn-Z, the line will be truncated with only 4 items. The second value will be the non-zero error code. An example of use would be,


CSVUSEFUL 
HEADERS top 
INPUTFORMAT oelibsmiles 
WARNINGS off 
INDEX on 
ERRORS skip 
GO

An example of the output would be,


1,0,50-03-3,29,32,4,10,29,3,3459,404.502106,17.571024,10.837744,10.179484,8.916186,7.436806,5.731269,4.252199,3.102264,2.228606,1.490747,0.913149,2.353470,0.243653,6.076471,0.000000,0.000000,0.072169,0.117035,0.000000,0.000000,0.000000,0.000000,20.884747,6.824211,2.900501,4.914549,32.177441,72.249992,1.044049,5.282959,0.000000,63.609943,2.132975,2.698140,12.870045,0.649532,-1.584704,0.000000,34.725185,13.182786,0.000000,30.049128,0.000000,0.000000,28.787071,0.000000,5.282959,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,1.340437,0.000000,0.000000,9.169267,3.506123,0.000000,1.340437,0.000000,5.350234,0.000000,3.955316,0.000000,1.799458,0.000000,-0.276172,0.000000,0.000000,0.333516,0.000000,0.000000,-2.522295,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,22.757420,35.966644,4.885879,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,24.544104,0.000000,0.000000,0.000000,0.000000,0.000000,15.478191,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000