Release Notes

New features and Changes in Molconn-Z 4.03

1. Molconn-Z 4.03 (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.

 
2. This version of Molconn-Z was built from an all-new library of Molconn-Z functionality that we have been developing over the last 12-15 months. The previous core Molconn-Z program, which had become difficult to work on and modify because of its structure, was written in FORTRAN. The new core algorithms are written in standard C in a toolkit structure. This enables us to much more quickly develop new Molconn-Z applications to respond to user needs, and also allows us to distribute to interested customers the means to develop their own Molconn-Z applications. See the eduSoft LC Developers' Toolkits web page for more information.

 
3. The goal of this release of the Molconn-Z standalone program was to streamline its design, usage and speed, and to drop anything from the executable that was not meeting those goals. The only remaining output from the molconnz program is a redesigned "S" file. As a consequence several long-standing features have been eliminated:
• The "L" file output has been dropped. Many features of the "L" file are available through use of the Molconn-Z Programmers' Toolkit.
• Many of the more obscure molecular file formats are no longer available, including the original Molconn-Z "B" format. We have settled on SMILES (in the more standard .smi form), MDL's SD Format (.sdf) and Tripos' (Sybyl .mol2) formats. All molecular file interpretation is now being performed by third party software libraries (see 4, below).
• It turns out that many of the calculational setup menu options in previous versions of Molconn-Z, e.g., symmetry perception and fluorine polarity, were not actually key to the algorithms. These have been eliminated, both from the "toolkit" and this executable.
• We are no longer providing the "sasinpz.txt" and related files.  Instead, this data can be easily incorporated into each output file either as a file header, or for each result set in the file.

 
4. The standalone Molconn-Z program is now linked to the Daylight "smiles" toolkit and "OElib" from OpenEye Scientific Software. The former is the acknowledged standard for interpretation of the SMILES format, but does require the purchase of a "smiles" run-time license from Daylight. We can recommend licensing and use of the Daylight smiles license without reservation. OElib is currently an "open source" library from OpenEye and requires no further licensing. Our tests of OElib indicate that it is a very robust structure interpreter, probably more robust than the structure interpreters that we have written ourselves and provided in previous Molconn-Z releases. However, be advised that there may be differences between OElib interpretations, old Molconn-Z interpretations, and Daylight interpretations of the same structure, particularly if that structure contains unstaurated or aromatic heterocyles. For instance, many heterocyclic compounds can be interpreted with multiple resonance structures, and the chemical "intuition" of the structure interpreter can reflect these differences.

 
5. The menu in Molconn-Z has been eliminated. Instead, the options for running are now coded in a simple "keyword" context, input into the program as a control file. See Appendix for a description of the keywords and their meanings.

 
6. Operation of Molconn-Z for all platforms is now through command line input: molconnz <control file> <input datafile> <output datafile>.  See Chapter 3 for more information.

 
7. The layout of descriptors within the Molconn-Z "S" file has been significantly rearranged. We feel that this is a more logical setup. Since we have added several new categories of parameters (See 7, below), additional adjustments were required. See Appendix for the new S file layout.
• As before the descriptors are referenced by "record number". However, the new keyword syntax allows simple selection of records for the S File output.
• There is a selection code "USEFULRECORDS" that selects the records generally considered to be the most useful. (This set can then be modified with other record selection keywords.)
• The atom records, eccentricity, E-State and H E-State have been moved to the last three "records" of the S File. The actual number of records associated with these paramaters will vary depending on the number of atoms in the molecule, however (15 atoms/record). We have added a new descriptor, in record 1, narecs that will list the number of atom records per descriptor. For example, if the molecule has 48 atoms, narecs will be 4. Important note: this only indicates the number of potential atom records, regardless of whether atom records have actually been selected for output. Second important note: this descriptor also indicates the status of the entire Molconn-Z calculation: if the calculation failed for the molecule narecs will have a value of zero, and only Record 1 will be written to the file.

 
8. New descriptors now available in this release:
• A number of new hydrogen atom types were added in this release: HaaNH, HsNH3p, HssNH2p and HsssNHp. In addition HCsats, HCsatu and HAvin have been recast as atom types. Finally, Hvin has been renamed as HdsCH, Htvin has been renamed as HdCH2, and Harom has been renamed as HaaCH and all have been recast as atom types.
• Also, a number of non-hydrogen atom types have been added in this release: sBH2, aOm, sOm, ddsP, sSm, ddsAs and ssssssSe.
• We have added a large set of functional group descriptors -- the Molconn-Z group-types. At present this is a list of 36 organic functional groups that Molconn-Z will identify, count, and calculate an EState Sum for. We believe that just the counting aspect of this will be very useful. However, as this is a brand-new concept, we would appreciate your feedback. Similarly, please let us know of inconsistencies you may observe in using these parameters. The definitions for functional groups and their component atom types is not as straightforward as we would all hope -- you may have disagreements with our definitions -- let us know!

 
9. The "names" for a number of descriptors have been changed to improve their readability and interpretability:


• For consistency, all parameters that are "counts" now use a "n" prefix for their nomenclature.
• We are now using upper-case "X" for Chi, instead of lower-case "x".
• More descriptive, longer, names are used for a number of other desciptors.