Molconn-Z Manual 3.50: Release Notes

Release Notes

New features and Changes in Molconn-Z 3.50

  1. (unix) Molconn-Z was compiled in 3 ways:
    • Under Irix 6.5 on a R4400 SGI using the -32 compiler directive for R4000+ processors
    • Under Irix 6.5 on a R4400 SGI using the -mips3 -n32 compiler directive for R5000+ processors
    • Under Irix 6.5 on a R10000 SGI using the -mips4 -64 compiler directive for R8000+ processors

  2. 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.

  3. 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.

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

  5. 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.

  6. 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.

  7. The 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.

  8. Three default selections have been added to the MENU for record selection:
    • DEFAULT 1: ENTER '1'; automatically selects records 1-8, 15-21, 35, 47-50. This selection is typical for datasets in which there is no need for atom-level indices.
    • DEFAULT 2: ENTER '2'; automatically selects records 1-8, 9-14, 15-21, 29-34, 35, 47-50. The additional records include the atom-level E-State and hydrogen E-State indices.
    • DEFAULT 3: ENTER '-1'; automatically selects all 50 records for output to the .S file.

  9. 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).

  10. In MOL and SDF files hydrogen atoms can now be located anywhere in the table.

  11. In SD files the information in the first three groups of entries after the 'M END' code are concatenated with the name field. Embedded spaces are removed and the concatenated name is written into the .s fie (but not the .L file). If there is no name in the first header record, a 'name' is created as 'Compound##' concatenated with the sequence number of the molecule in the overall SD file.

  12. The molecular formula has been added to the output .S file as records #49 and #50. The elements are placed into record #49 and their counts into record #50.