CHAPTER 3

Getting Started

1. Directory for Molconn-Z

   Before the software is loaded into your system, setup the (sub)directory which will house the software materials, the executable module, and example input/output files. See the table below.

   MKDIR  C:\MOLCONNZ\
   

   NOTE: It is essential that the Molconn-Z software be placed in a subdirectory with this name.

   Enter that (sub)directory and prepare to load the Molconn-Z files from the source disk or tape.

   CD C:\MOLCONNZ\
   

2. Load disk/tape

   Use the proper command(s) to copy all files into designated (sub)directory. Do a directory command to determine that all the files have been loaded.

   See the directory listing for a copy of the contents of the software file directory.

   COPY A:*.*  C:
   

   Examine the directory of C:\MOLCONNZ to determine whether the copy command has been executed successfully.

3. Test Run Molconn-Z

   To determine that your software is properly executing, execute one or more test runs of Molconn-Z.

   MOLCONNZ
   

   You may run Molconn-Z with any one of several of the example input file(s). Use of SMILES.B, MDL.B or SAMPLE.B is recommended. If an error is encountered, check Chapter 5 for the proper Menu option for the the .B files. See Chapter 4 for specific information on executing Molconn-Z.

   Several example input files are supplied, as follows:

   a. SAMPLE.B, using the MOLCONN connection table format
   b. SMILES.B, using the SMILES code format
   c. CHX.B, using the ChemDesign CSSR file format
   d. CDRAW.B, using the CHEMDRAW file format
   e. MDL.B, using the MDL Molfile format
   f. SDF.B, using the MDL SDFile format

   The preliminary test of Molconn-Z may be done using some of the above example files, such as SMILES.B , MDL.B or SAMPLE.B, or as many others as the user may wish to test. To execute Molconn-Z for each of these files, it is necessary to exercise the MENU option in which file format is specified. See MENU listings given below and further information in Chapter 5.

   In the software supplied with Molconn-Z, example output listing files are also included for each of the .B file and are labeled with the same file name and the extension L. Compare your output to the example output files to determine program performance. In the example files delivered in the Molconn-Z package, all the output options have been selected for the .L file and all the records have been selected for the .S file.

4. Additional Information

   If the user is not interested in some of the file formats, the corresponding .B, .L and .S files should be deleted at this time. There are many other program options which the user may exercise; these are described in Chapter 5. The user should consider printing out the .B, .L and .S files at this time for future reference.

   Consideration should be given to the manner of use of the OPTION.DAT file when several users may access the same file.

                          MOLCONNZ PROGRAM OPTIONS
                  Enter Number for the Desired Option Change
                      

 1- Input File (Molconn/SMILES code/
                Molfile/SDFile/CHEM-X)       (BFILE)  <C>
 2- Topological State Algorithm (1 to 6)     (IFUNCT) <4>
 3- Number of E-State Values in S File       (NSTATE) <90>
 4- Output to Bond Type File (A, O, I, N)    (ETOUT)  <O>
 5- Full Job or Only Output to Verify Input  (FULL)   <Y>
 6- Maximum Order of Chi Calculated          (MAXORD) <100>
    Output File Selections
 7- Output .S Index File                     (ITEXT)  <Y>
 8- Output .L Listing File (Screen Output)   (FAST)   <N>
 9- Output .E Bond Type E-state  File       (EDGECALC)<Y>
 10- Output Distance/Connectivity Matrices   (AFILE)  <N>
 11- Select FIRST SubMENU on Program Control                   
 12- Select SECOND SubMENU on Listing File Contents            
 13- Quit Menu .............Proceed with Calculations <Return>


 Please Enter Desired Option (1 to 14 or RETURN): 

  1- Topological Symmetry Perception          (KSYM)   <Y>
  2- Field Delimiter                          (DLM)    <,>
  3- Maximum Order of Chi Output to File      (MOFILE) <10>
  4- Sign of Fluorine Contribution            (IFSIGN) <+>
  5- Molecular Connectivity Algorithm
      (Standard/Topological State Algorithm)  (CTYPE)  <R>
  6- Topological State Algorithm Type         (STYPE)  <G>
  7- Print Seclected Subgraphs       (ITERM,SORDER)  <N  4>
  8- Records output to .S file                (NRECS)  <48>
  9- Marker at end of each .S file line       (MARK)   <  >
 10- Quit SubMENU . . Return to Main Menu                     
 11- Quit SubMenu . . Proceed with Calculations       <Return>


 Please Enter Desired Option (1 to 11 or RETURN): 

 This SubMENU contains options for selecting output
              to be included in the output listing file (.L)
 A table of atom identification is always included 
  
   YOU MAY SELECT EACH OUTPUT BLOCK TO BE PRINTED <Y>
                             OR NOT TO BE PRINTED <N>
 1- Atom Symmetry Classification                (OUT1) <Y>
 2- Table of subgraph counts                    (OUT2) <Y>
 3- Table of Connectivity and kappa indexes     (OUT3) <Y>
 4- Total Topological Index and Wiener Indexes  (OUT4) <Y>
 5- Information Indexes and ad hoc parameters   (OUT5) <Y>

 Please, enter the number of an output block
                   whose print status you wish to change.
         >>>  Just push RETURN to go back to the MAIN MENU <

 Enter the number (or RETURN) :