General Overview


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.

The Molconn-Z software is designed to carry out the computation of a wide range of topological indices of molecular structure. These indices represent important elements of the molecular structure information which is useful in relating structure to properties. These variables of molecular structure include (but are not limited to) the molecular connectivity chi indices, mt and mtv; kappa shape indices, m and m; electrotopological state indices, Si; hydrogen electrotopological state indices, HESi; atom type and bond type electrotopological state indices; new group type and bond type electrotopological state indices; topological equivalence indices and total topological index; several information indices, including the Shannon and the Bonchev-Trinajstiç information indices; counts of graph paths, atoms, atoms types, bond types; and others.

These indices have been widely used in QSAR analyses and other types of relationships between the structure of molecules and their properties. Discussion of the definitions and background of the chi, kappa, electrotopological state, and topological equivalence indices are given in Chapter 2 along with appropriate references. Further, references are given for several reviews of the development and use of topological indices at the end of this chapter as well as in Chapter 2.

Installation and related instructions are detailed in Chapter 3.

Molconn-Z is set up to be user-friendly and flexible. See Chapter 4 for detailed information. Input of molecular structure is done with one of 3 molecular structure file formats: Daylight SMILES, MDL (sdf), or Tripos (mol2). These inputs are now handled using linked libraries from either Daylight for SMILES (requires a license from Daylight) or OpenEye Scientific Software (OElib) for SMILES, sdf and mol2 file. See Chapter 5 for detailed information on the use of each of these input formats.

In addition to the most common forms of input, Molconn-Z permits flexibility in output by changing a few keywords in the control file, see Chapter 4 for detailed information. The output from Molconn-Z is placed in a single output file with options for user control over the contents.  This file is compatible for use with the commonly used statistical package SAS from The SAS Institute in Cary, NC., and should be easily adapted for use with other statistical packages.

The general flow of information for Molconn-Z is fairly simple - the command only accepts 3 arguments (first for the control file name, second for the input molecular structure file name and third for output file name); it reads the control file to determine run parameters and structure file type; it then reads one molecule at a time and computes the descriptors. In general, the user creates molecule structure either by use of a commercial package or, perhaps, simply in an edited text (ASCII) file.  The user also creates an ASCII control file which defines the input molecular structure format and the output format desired. Besides these two input files, the only other item the user needs to worry about are the license files which are defined by the environment variables DY_LICENSEDATA for the (optional) Daylight license and MCONN_LICENSE for the (required) eduSoft/Molconn-Z license.

The user starts execution of Molconn-Z simply by using the command line syntax:

Error messages, if any, are printed to the console screen.

It should be noted that no special settings are necessary with this new Molconn-Z to obtain optimal performance with large databases.

Molconn-Z is designed to run on any UNIX/LINUX platforms, as well as on microcomputers running Windows 95, 98, ME, 2000 or XP.

General References

1. L. B. Kier and L. H. Hall, Molecular Connectivity in Structure-Activity Analysis, Research Studies Press, John Wiley and Sons, Letchworth, England, (1986).

2. L. B. Kier and L. H. Hall, Molecular Connectivity in Chemistry and Drug Research, Academic Press, New York, 1976.

3. L. H. Hall, "Computational Aspects of Molecular Connectivity and its Role in Structure-Property Modeling" in Computational Chemical Graph Theory, Chap. 8, pp 203-233, D. H. Rouvray, ed., Nova Press, New York (1990).

4. L. B. Kier, "Indexes of Molecular Shape from Chemical Graphs" in Computational Chemical Graph Theory, Volume II, Chap. 6, pp 152-174, D. H. Rouvray, ed., Nova Press, New York (1990).

5. L. H. Hall and L. B. Kier, "The Molecular Connectivity Chi Indexes and Kappa Shape Indexes in Structure-Property Relations", in Reviews of Computational Chemistry, Chap. 9, pp 367-422, Donald Boyd and Ken Lipkowitz, eds., VCH Publishers, Inc. (1991).

6. L. B. Kier and L. H. Hall, "An Atom-Centered Index for Drug QSAR Models", in Advances in Drug Design, Vol. 22, B. Testa, ed., Academic Press(1992).

7. A. T. Balaban, ed. Chemical Applications of Graph Theory, Academic Press, New York, (1976).

8. N. Trinajstic', Chemical Graph Theory, Vols. I, II, CRC Press, Boca Raton, FL, (1983).

9. R. B. King, ed., Chemical Applications of Topology and Graph Theory, Amsterdam, (1983).

10. D. H. Rouvray, Am. Sci., 61, 729, (1973). The Search for Useful Topological Indices in Chemistry.

11. D. H. Rouvray, Sci. Am., 255, 40, (1986). Predicting Chemistry from Topology.

12. P. J. Hansen and P. C. Jurs, J. Chem. Ed., 65, 574, (1988). Chemical Applications of Graph Theory II: Isomer Enumeration.

13. A. Sabljic' and N. Trinajstic', Acta Pharm. Jugosl., 31, 189, (1981). Quantitative Structure-Activity Relationships: The Role of Topological Indices.