Molconn-Z Manual 4.12S: Release Notes

Release Notes

New features and Changes in Molconn-Z 4.12S

  1. Molconn-Z 4.12S has been optimized to work with SYBYL 8.0
    Molconn-Z was compiled:
    • Under Irix 6.5 on a R10000 SGI using the -mips3 -n32 compiler directives and the Sybyl 8.0 binary shared objects.
  2. Under Red Hat / GNU GCC 3.2 and GCC 4.x on a x86_64 using the -m32 (32-bit) option and the Sybyl 8.0 binary shared objects. However, the standalone molconnz executable (included in this release) is available for several platforms (see the release notes.)
    (See the Installation instructions for more information.)

  3. 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 Toolkits web page for more information.

  4. For the past few years eduSoft had developed Molconn-Z for Sybyl as a product sold by Tripos. This exclusive agreement with Tripos has ended and Molconn-Z for Sybyl now becomes a component of our Molconn-Z Toolkit. Customers that elected to continue support of Molconn-Z for Sybyl get the full Molconn-Z Toolkit which not only includes the Molconn-Z module in Sybyl, but Molconn-Z Standalone, Molconn-Z Libraries and all other features of the Toolkit. All new requests for Molconn-Z for Sybyl will be for our Toolkit product.

  5. The "L" file output (previously accessible from the Sybyl menubar) has been dropped. Instead, there is a new option for creating a Molconn-Z Structure Report that has selectable blocks of data describing the molcule. We believe that this is a useful option for cataloguing the topological properties of a molecule.

  6. There is now an option for creating a Molconn-Z "S" file from the Sybyl menubar. At present this emulates the S file output from Molconn-Z 3.50. You can also paste a header on the S file that lists the variable names in the file, again compatible with Molconn-Z 3.50.

  7. There are now fewer Molconn-Z algorithm options. Some of the options available previously were rendered obsolete by the new Molconn-Z toolkit library. All of the options are now available in a single sub-menu dialog that is accessible for all relevant commands.

  8. The Molconn-Z EState map selection has been revised. There are now three map-types available: EState, H EState (Heavy) and H EState (Protons). The two hydrogen EState maps differ on where the density resides. In H EState (Heavy) maps the density will be localized on the heavy atoms (non-hydrogens), while in H EState (Protons) maps the density will be localized on the hydrogens themselves.

  9. The layout of parameter selections within the MSS Molconn-Z interface has been significantly rearranged. We feel that this is a more logical setup. Since we have added several new categories of parameters, additional adjustments were required. Note also that the SPL mechanism for input of parameters into the spreadsheet has been greatly improved! Because the new executable, built on the Molconn-Z toolkit, is able to isolate and report parameters on a one-by-one basis (rather than by whole rows), only the requested parameters are written to the SPL. Thus, they can be imported into the MSS much more directly than before.

  10. For consistency, all parameters that are "counts" now use a "n" prefix for their nomenclature.

  11. In a number of dialogs, multiple "All" buttons have been placed, allowing the selection of all members of a parameter group.

  12. 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.

  13. A number of non-hydrogen atom types have been added in this release: sBH2, aOm, sOm, ddsP, sSm, ddsAs and ssssssSe. Antimony and Lead atom types have been dropped from the atom type select dialog.

  14. 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!

  15. The complete set of edge type and vertex type counts are now available. Although these particular parameters are not often important in QSAR analyses, they can be useful in categorizing molecular structure and in graph theory.