Molconn-Z 3.50 Manual: Chapter 4

CHAPTER 4

Using Molconn-Z

General Program Description

Molconn-Z is a file-oriented program with interactive keyboard entry of file names and option selection. The program requires an input file; it produces an output listing file and some optional files. The General Flowchart shows the relationship among these files.

The program expects an input file (called the .B file) which can be in one of three formats:

  1. Use of SMILES code to present the connection table information in a character string format,

  2. Standard MOLCONN format: the file contains the connection table for one or more molecules,

  3. Alternate formats,
      a. Alternate formats: (MDL Molfiles, MDL SDFiles, ChemDraw Connection Table files, or Chem Design CSSR files) the .B file contains only the names of files which contain the connection table information. This arrangement permits the use of various commercial packages which produce files for molecules as the result of a variety of structure input methods. In this form of use the .B is a pointer file, pointing the files with the actual connection table and related molecule information. See Chapter 6 for detailed information.

      b. Alternate formats: MDL SDFiles the .B file contains MDL Molfiles, each with a series of data lines following each Molfile. See Chapter 6 for detailed information.

See Chapter 5 for details of use of each of these options.

In a typical application the user would include in the .B file all the molecules which are a part of an investigation. Other molecules may, of course, be added later or done separately.

When Molconn-Z is executed, the user is asked for the name of the Input .B File. Then, the user may simply run the program with the standard program options or the user can elect to modify the options through use of the MENUs. Then the user is asked for the name of the Output Listing File (called the .L file), the output index file (called the .S file), and/or the output file for bond type electrotopological state indices (called the .E file). File names are requested only for those files which have been selected in the Main MENU. Each of these files as well as the available options are described in detail in Chapter 7.

The output files which may be obtained, depending upon the set of options selected by the user, are as follows.

  1. The Output Listing File (.L) is intended as a summary of computations by Molconn-Z for the data set. It contains all file names and a summary of the options selected. Further information describes each molecule in the topological sense and presents most of the computed information in easily readable table form suitable for verification of the input connection tables and for simple perusal of the data. Production of the .L file is optional as controlled by the Main Menu, option #8.

  2. The Output File of indices (called the .S file) is produced in ASCII text format and is intended for direct use in statistical and other types of analysis. (Note: The file called SASINPZ.TXT is supplied with Molconn-Z and contains a format of the .S file which may be used directly in the input portion of SAS programs. See Appendix II and Appendix III.) Production of the .S file is optional as controlled by the Main Menu, option #7.

  3. The Output File of Bond Type E-state indices (called the .E file) is produced in ASCII text format and is intended for direct use in statistical and other types of analysis. (Note: The files called SASINPAE.TXT and SASINPOE.TXT is supplied with Molconn-Z and contains a format of the .E file which may be used directly in the input portion of SAS programs. See Appendix III.) Production of the .E file is optional as controlled by the Main Menu, option #9.

  4. Other output files, which are optional, contain various other pieces of topological information which users may find useful to have available in file form. Each of these output files is described in Chapter 7.
      a. The subgraph contributions output file (called the .SUB file) contains a listing (for a user selected order of subgraph) of the all the subgraphs along with chi subgraph terms and the atom IDs of each atom in the subgraph and the group symbol of each atom. This is a text file which may be read and analyzed for such applications as substructure analysis. See Chapter 7 for specific information. To obtain this file, select the first submenu, option #7.

      b. The connectivity and distance matrix output file (called the .MAT file) is a listing of both the connection matrix and the distance matrix for the molecules in the .B file. This is a text file which may be read and analyzed for applications of the connection matrix and the distance matrix. To obtain this file, select the Main MENU, option #11. See Chapter 7 for details.


Typical Molconn-Z Session

The following steps are generally followed in using Molconn-Z:

Molconn-Z is completed when the message FORTRAN STOP appears on the terminal screen.

More detailed information is given below and in Chapter 5.


Sample Session with Molconn-Z

This section describes the manner in which Molconn-Z is actually used. Since the program is interactive, most of the usage is self-explanatory. After program options have been selected, the program can be run using these as standard options. The options may be modified interactively when Molconn-Z is run and desired changes made permanent as described in Chapter 7. (Alternatively, the file OPTION.DAT may be modified in an editor. Editing the OPTION.DAT file directly should be used only after the user is well acquainted with the program. See Appendix I for a listing of OPTION.DAT ($MCONN_OPT/mconn_option.std for unix) and for editing information. Direct editing of OPTION.DAT is not recommended.)

The details of selecting program options from the three menus are given in Chapter 7. This present example illustrates running Molconn-Z with the standard (default) options and using the example input file SMILES.B which is supplied with the software package. Discussion of the use of other file formats is given in Chapter 6.

Executing Molconn-Z

The program Molconn-Z is executed by using the system command to run the executable form of the program. On a PC the command may simply be:

MOLCONNZ

For the unix versions of Molconn-Z the appropriate command is:

$MCONN_RUN/molconnz

The program runs in a simple interactive style. The following pages describe the running of Molconn-Z. The items in bold are the actual output of the program to the terminal screen.

When the program is executed, the first image to appear on the screen is the LOGO and copyright notice:

  	        ########################################
                #                                      #
	        #               Molconn-Z	       #
                #     (Molconn software version 3.0)   #
           	#              Lowell H. Hall          #
         	#                COPYRIGHT             #
		#   >>>Hall Associates Consulting<<<   #
		#	 Professor of Chemistry	       #
        	#       Eastern Nazarene College       #
               	#         Quincy, Massachusetts        #
               	#                                      #
               	#             *                      * #
            	#   *       *  *        *   * * * * *  #
               	# *  *   *      *      *   *  *        #
               	#    *  *        *   *        *        #
               	#    * *          * *         *        #
               	#    **            *          *        #
               	#   * *           * *         *        #
              	#   *   *        *   *        *  *     #
               	#  *     **     *     * *      **      #
               	#              *       *               #
             	########################################

Then the user is asked to enter file names:

Please enter File Names
BOND DESCRIPTOR (.B) FILE NAME :
Enter the name of your .B file and return. (e.g. SMILES.B)

If Molconn-Z cannot find the designated .B files in the appropriate directory, an error message appears on the screen. The user is requested to re-enter the proper file name for the intended .B file.

The user is then asked about program options:

Standard Control Options? (Y/N) <Y> :

Pressing return or entering Y causes the program to run with the standard set of options, those currently stored in the OPTION.DAT file. If the user wishes to change the options, entering N will bring up a menu for option changes. The current default values are given in the brackets, < >, in the menu. For this present example, the user accepts the standard options by simply pushing RETURN. See Chapter 5 for detailed information on the Menus for option selection.

The user is then asked to enter names for the files which the user has specified in the options. For this example, we will use the standard default options which activate the .L, .S and .E files.

The first file name requested is for the output listing file, .L, if specified in the options:

Output Listing (.L) File Name :

Enter the name of your .L file and return. (e.g. SMILES.L)

Then the user is asked to enter the name to be given to the output file of computed indices, called the .S file, if specified in the options.
Output Text (.S) File Name : 

Enter the name of your .S file and return. (e.g. SMILES.S)

Then the user is asked to enter the name to be given to the output file of computed bond type E-state indices, called the .E file, if specified in the options.
Bond Type E-state Output (.E) File Name :

Enter the name of your .E file and return. (e.g. SMILES.E)

After the file names are entered (SMILES.S, SMILES.E, etc.), the program will proceed with the computations. For each molecule in the .B file, the ID and name will appear on the screen to indicate that computation has begun for that molecule in this .B file:

1 6-Hydroxy-1,4-hexadiene

2 Triethylamine

. . . .

9 Morphine

FORTRAN STOP

At this point Molconn-Z has executed the program with the production of the output listing file, SMILES.L in this case, the index output file, SMILES.S and in this case, the SMILES.E, the index file for bond type E-state indices. See Chapter 6 for a complete listing of the SMILES.B file. See Chapter 7 for example listings of output files. The Molconn-Z output files generated from the input file SMILES.B are supplied with the Molconn-Z software; they are named SMILES.L, SMILES.S, and SMILES.E. The user should print out these files to compare with the output obtained from running SMILES.B on your computer.