Molconn-Z Manual 3.50S: Release Notes

Release Notes

New features and Changes in Molconn-Z 3.50S

  1. Molconn-Z 3.50S has been optimized to work with SYBYL 6.6
    Molconn-Z was compiled:
    • Under Irix 6.5 on a R4400 SGI using the -mips3 -n32 compiler directives and the Sybyl 6.6 binary libraries.
    However, the standalone molconnz executable (included in this release) was compiled on multiple platforms (see the release notes.)
    (See the Installation instructions for more information.)

  2. We have implemented a new "default" set of Molconn-Z indices. This is available as the "Program" default on the Main Molconn-Z MSS dialog (under the "MCONNIDX" AutoFill option on the Molecular Spreadsheet.) We also found and corrected some SPL errors associated with saving "Personal" default options. All of this should work now.

  3. New hydrogen bonding descriptors based on the E-State and Hydrogen E-State indices have been added. Atoms and groups which act as hydrogen bond donors are characterized by the E-State indices. The new symbols are SHHBd, SHHBa, SHwHBd and are found in record #47 of the .S file. A description of the new calculation algorithms is found in Chapter Two of the User Manual. These are accessible for the Molecular Spreadsheet using the MSS Add Internal Hydrogen Bond Indices Dialog.

  4. An alternative method of displaying Molconn-Z atom types has been added that uses a formalism similar to the Sybyl atom type style.

  5. The Map Contour Dialog has been updated with a new facility for picking contour levels as a fraction of range. The levels now available are 10%, 20%, 33%, 50% and 75%. If these levels do not fit your usage patters, please let us know so we can either revise for the next release or show you how to modify this at your site. (This enhancement was suggested by Arthur Doweyko of Bristol-Myers Squibb.)

  6. New descriptors have been developed for internal hydrogen bonding. Both the descriptors and the counts are found in record # 48 in the .S file as the variables SHBint2 - SHBint10 for the descriptors and NHBint2 - NHBint10 for the counts of occurrences. See Chapter Two of the User Manual for more information. These are accessible for the Molecular Spreadsheet using the MSS Add Internal Hydrogen Bond Indices Dialog.

  7. New descriptors for atom types for non-polar hydrogen groups are included. These are reported in record #47 of the .S files. See Chapter Two of the User Manual for more information.

  8. A new polarity topological descriptors is reported in record #47 of the .S file as Qv. Information of the calculational methodology is reported in Chapter Two of the User Manual.

  9. Coding for cations of the onium type has been included. This new feature involves new values for the intrinsic state for the following: RNH3+, R2NH2+, R3NH+, and R4N+. The names of the atom type E-State descriptors for these onium groups are as follows: SsNH3p, SssNH2p, SsssNHp, SssssNp. They are found in records #17 and #18 of the .S file.

  10. The "local" SMILES decoder in Molconn-Z has been improved:
    • Use of the symbol for single bond, '-', is now properly handled. Of course, most often single bonds are handled implicitly.
    • Error checking now includes skipping blanks found in the SMILES string.
    • Recognition of codes for chiral centers now includes tetrahedral and allenic carbons. Output to the .L file indicates presence of chiral centers.
    • Recognition of codes for cis and trans has been implemented. Output to the .L file inciats occurrence of cis/trans.

  11. For molecules consisting of one non-hydrogen atom, (CH4, H2O, NH3, Ar, etc.) the computation is now skipped and the output .S files is not computed. However, the formula weight is set to zero: FW = 0. A message is placed into the .L file (or .MSG file). Likewise, when Molconn-Z cannot interpret the input structure code (error in SMILES, mol file, etc), FW is set to zero to signal that no calculation was actually done and that there is an error in the input. A message is placed into the .L file (or .MSG file).