Molconn-Z 3.50 Manual: Chapter 7

CHAPTER 7

Molconn-Z Output Files

 There are three standard output files from Molconn-Z in addition to two other optional files. This chapter describes each of these files and the manner in which the user may select them. The output listing file (.L) and the output file of indices (.S) are usually produced. The contents of both the .L and .S files may be partially determined by the user. See the section in Chapter 5 on Menus for detailed information.

The output listing file, called the .L file, contains a listing of all the computed information produced by Molconn-Z in a highly readable form. It is commonly used as a basis for verification of the input molecular structures. Further, the user may peruse this file to obtain a general sense of the computed indices as well as any specific piece of information desired. This file may also be saved for future reference.

The output files of indices, called the .S file and the .E file, contains all the computed indices in a compact form suitable for use as input to other software for analysis including statistical or graphic forms. The user may elect not to produce one or both of these files by selecting item #7 in the Main Menu. See Chapter 5 for detailed information. Generally, the user will want the .S file to be produced, which is the default condition as supplied with the Molconn-Z software. The user may select which records to include in the .S file. Likewise, the user may or may not elect to produce the .E file with its bond type E-state indices. See Chapter 5 for detailed information.

There are two other optional files which the user may find useful for certain applications. The subgraph file, called the .SUB file, can be produced by selecting item #4 in the Main Menu. See Chapter 5 for detailed information. The subgraph file contains the list of all subgraphs of a given order, selected by the user. Along with the list of subgraphs, additional information will give the chi and chi valence values for each subgraph.

It is also possible to obtain the distance matrix for each molecule in the .B file. This file, called the .MAT file, can be obtained by selecting item #8 in the Main Menu. When selected, the computed distance matrix for each molecule will be placed into the file named by the user for the .MAT file.

All of the files listed above are described and illustrated below. An example is given in each case.

The .B (Input) File for 4-Chororphenol

The output given below was generated with Molconn-Z version 3.0 using the following .B file in the SMILES code:

1, 4-Chlorophenol
Oc1ccc(Cl)cc1
-1

The .L File from the 4-CLPHENOL.B File

In this .L file the output block field names will be set in an alternative type in this chapter so that they can be easily identified in the descriptions given in Chapter 5.

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


 Calculation of
                * Electrotopological State Indices
                    > Atom Type and Bond Type
                * Molecular Connectivity indices
                    > valence, simple, and difference
                * Kappa Shape Indices
                  and many related topological quantities


      Bond Descriptor Input (.B) File Name : 4CLPHEN.B
             Output Listing (.L) File Name : 4CLPHEN.L
             Indices Output (.S) File Name : 4CLPHEN.S
  Bond Type E-State  Output (.E) File Name : 4CLPHEN.E


  ---> The Following Options are in Effect :

 Calculate Chi indices for orders from 0 to  90

 Store Chi indices on file up to order  10

 For Molecular Connectivity Indices
 Use Standard Reciprocal Square Root Formalism

 Sign of fluorine terms set positive

 Topological State Algorithm
    Function type 4 : Geometric Mean/d**2

 Topological Symmetry Perception to be Performed
   . All Paths in Molecular Graph Obtained

   . Atomic Topological State Values Calculated

   . Kappa Zero and Shannon Indices Calculated


  Format for the input .B file : SMILES format

1        4-Chlorophenol        

   *--> ATOM INDICES 

                      Electro-    Intrinsic
 Atom         Valence Topological   State                         Connected
  Id  Group    Delta  State  S(i)   I(i)         Markers           Atoms

   1  OH        5.00   	13.56861    6.000   HBDA                  2
   2  C       	4.00   	-3.65278    1.667   ar   R                1   3   8
   3  CH      	3.00     1.18210    2.000   ar   R          	  2   4
   4  CH      	3.00     1.44444    2.000   ar   R                3   5
   5  C       	4.00   	-1.88194    1.667   ar   R                4   6   7
   6  Cl       	 .78     8.15747    4.111   HBA                   5
   7  CH      	3.00     1.44444    2.000   ar   R                5   8
   8  CH      	3.00     1.18210    2.000   ar   R          	  7   2


  *--> Bond E-State indices from bond types

 Bond   Atom IDs    Atom Types       Bond    Type       Bond          Bond
  No.    i    j       i    j         Order    No.      E-State       Symbol
   1     1    2     -OH   aCa-         1     457        9.253        e1C3O1a 
   2     2    3     aCa-  aCHa         a     258        -.492        eaC2C3s 
   3     3    4     aCHa  aCHa         a     257    	1.736        eaC2C2a 
   4     4    5     aCHa  aCa-         a     258         .347        eaC2C3s 
   5     5    6     aCa-  -Cl          1     470        5.620        e1C3Cla 
   6     5    7     aCa-  aCHa         a     258         .347        eaC2C3s 
   7     7    8     aCHa  aCHa         a     257        1.736        eaC2C2a 
   8     2    8     aCa-  aCHa         a     258        -.492        eaC2C3s


  *--> Bond Type Indices:
             NET          ETS          Bond Type
     No. Bond Count   Bond E-State      Symbol
    257      2         	3.47222         eaC2C2a 
    258      4         	-.29012         eaC2C3s 
    457      1         	9.25347         e1C3O1a 
    470      1         	5.61998         e1C3Cla 


   *--> MOLECULE INFORMATION :

 Skeleton contains   8 atoms and   8 bonds
    with one circuit     Cyclomatic Number = 1

  Molecular Weight :   128.558       Molecular Formula : H  C  O  Cl
                                                           5  6  1   1
  Ring Members:
      Size:     Atom ids
   1: ( 6)   2  3  4  5  7  8


   *--> ATOM SYMMETRY INFORMATION

 Class   Number   Members         Number of classes =    6
  1        1     1
  2        1     2
  3        2     3  8
  4        2     4  7
  5        1     5
  6        1     6


   *--> Subgraph Counts Information:   NUMBER of TERMS of EACH TYPE

                         Path/
     Order Path Cluster Cluster Circuit
       0      8
       1      8
       2     10
       3     10     2              0
       4     10     0      4       0
       5     12                    0
       6      4                    1

 Total                      Total
 Path                       Circuit
 Count     54               Count     1

 Graph Complexity :     6.75 (NTPATH/NVX)

 Based on vertex eccentricities
                   Radius     Diameter     Ishape
  Descriptor          3         5          .66667
  Multiplicity        4         2



1   *--> MOLECULAR CONNECTIVITY INDICES :


                   Valence Indices                         Simple Indices
 Order   Path   Cluster P/Cluster Chain     Path   Cluster   P/Cluster  Chain
    0   4.8905                             5.9831
    1   2.6119                             3.7877
    2   1.9129                             3.3650
    3    .0786	.2635    .0000	 2.3045	    .5774   .0000
    4    .5671	.0000    .3043	  .0000    1.4267   .0000     .8165     .0000
    5    .4033  .   .    .   .	  .0000	   1.3047   .   .     .   .     .0000
    6    .0878  .   .    .   .    .0278    0.3333   .   .     .   .     .0833


    *--> SHAPE INDICES : 

 Order             0              1                 2               3
 K     		6.12500    	2.52000 	1.80000
 Ka           	6.02060  	5.60387  	2.15863  	1.49136

 Total topological indices :
 
 TTs(4) =        25.726914  (simple, no atoms types)
 TTd(4) =       40.429555  (valence, with atom types)
 TETS2     =     5.588397  (E-state values/Rij**2)
 SumDel-I  =  13.3572
 Sum I     =    21.4444


 Wiener W number :     62
 Wiener p number :     10
 Platt  f number :     20


    *--> INFORMATION INDICES 

       Shannon Index =      .75257
 Information Content =    6.02060
    Redundancy Index =     .16667


 Bonchev information Id(G)  =    288.26630
          normalized index  =      4.64946
 Bonchev information IdW(G) =     55.73517
          normalized index  =      1.99054

                                      Number Separated
                            Number     by Three Bonds
        Terminal Groups       2                  0
 Terminal Methyl Groups       0                  0

The .S File from the 4-CLPHENOL.B File

1         8   1   1   4  128.558  4-Chlorophenol
  5.9831  3.7877  3.3650  2.3045  1.4267  1.3047   .3333   .0000   .0000   .0000   .0000  
  4.8905  2.6119  1.9129  1.0786   .5671   .4033   .0878   .0000   .0000   .0000   .0000  
   .5774   .0000   .8165   .0000   .0000   .0000   .0833   .0000   .0000   .0000   .0000  
   .2635   .0000   .3043   .0000   .0000   .0000   .0278   .0000   .0000   .0000   .0000  
 -6.2426  -.1265   .9508   .8474   .5732   .8262   .0833  -.1250   .0000   .0000   .0000  
 -6.7735 -1.6028  -.6609  -.4538  -.3133  -.0754  -.1491   .0000   .0000   .0000   .0000  
   6.0206   6.1250   2.5200   1.8000   5.6039   2.1586   1.4914    .7526        40.42955   21.44444   13.35719    2.55108   1.512
 13.5686 -3.6528  1.1821  1.4444 -1.8819  8.1575  1.4444  1.1821   .0000   .0000   .0000   .0000   .0000   .0000   .0000  
   .0000   .0000   .0000   .0000   .0000   .0000   .0000   .0000   .0000   .0000   .0000   .0000   .0000   .0000   .0000  
   .0000   .0000   .0000   .0000   .0000   .0000   .0000   .0000   .0000   .0000   .0000   .0000   .0000   .0000   .0000  
   .0000   .0000   .0000   .0000   .0000   .0000   .0000   .0000   .0000   .0000   .0000   .0000   .0000   .0000   .0000  
   .0000   .0000   .0000   .0000   .0000   .0000   .0000   .0000   .0000   .0000   .0000   .0000   .0000   .0000   .0000  
   .0000   .0000   .0000   .0000   .0000   .0000   .0000   .0000   .0000   .0000   .0000   .0000   .0000   .0000   .0000  
  44.9731    .0000    .0000    .0000    .0000    .0000 -16.9444    .0000  44.9731  13.5686  -4.6944  -3.6528  26.9792  -5.5347  
    .0000    .0000    .0000    .0000    .0000    .0000    .0000    .0000    .0000    .0000    .0000   5.2531    .0000    .0000  
    .0000    .0000  -5.5347    .0000    .0000    .0000    .0000    .0000    .0000    .0000    .0000    .0000    .0000    .0000  
    .0000    .0000    .0000    .0000    .0000  13.5686    .0000    .0000    .0000    .0000    .0000    .0000    .0000    .0000  
    .0000    .0000    .0000    .0000    .0000    .0000    .0000    .0000    .0000    .0000    .0000   8.1575    .0000    .0000  
    .0000    .0000    .0000    .0000    .0000    .0000    .0000    .0000    .0000    .0000    .0000    .0000    .0000    .0000  
    .0000    .0000    .0000    .0000    .0000    .0000    .0000    .0000    .0000  
   1.0000    .0000    .0000    .0000    .0000    .0000   4.0000    .0000    .0000    .0000    .0000    .0000    .0000    .0000  
    .0000    .0000    .0000    .0000    .0000    .0000    .0000    .0000    .0000    .0000    .0000   4.0000    .0000    .0000  
    .0000    .0000   2.0000    .0000    .0000    .0000    .0000    .0000    .0000    .0000    .0000    .0000    .0000    .0000  
    .0000    .0000    .0000    .0000    .0000   1.0000    .0000    .0000    .0000    .0000    .0000    .0000    .0000    .0000  
    .0000    .0000    .0000    .0000    .0000    .0000    .0000    .0000    .0000    .0000    .0000   1.0000    .0000    .0000  
    .0000    .0000    .0000    .0000    .0000    .0000    .0000    .0000    .0000    .0000    .0000    .0000    .0000    .0000  
    .0000    .0000    .0000    .0000    .0000    .0000    .0000    .0000    .0000  
 44.9731   .0000 -4.6944 -3.7778   .0000   .0000 -3.7778 -4.6944   .0000   .0000   .0000   .0000   .0000   .0000   .0000  
   .0000   .0000   .0000   .0000   .0000   .0000   .0000   .0000   .0000   .0000   .0000   .0000   .0000   .0000   .0000  
   .0000   .0000   .0000   .0000   .0000   .0000   .0000   .0000   .0000   .0000   .0000   .0000   .0000   .0000   .0000  
   .0000   .0000   .0000   .0000   .0000   .0000   .0000   .0000   .0000   .0000   .0000   .0000   .0000   .0000   .0000  
   .0000   .0000   .0000   .0000   .0000   .0000   .0000   .0000   .0000   .0000   .0000   .0000   .0000   .0000   .0000  
   .0000   .0000   .0000   .0000   .0000   .0000   .0000   .0000   .0000   .0000   .0000   .0000   .0000   .0000   .0000  
      288.266        4.649       55.735        1.991      62      10      20     182   -.3382039   -.2227515   5   1   2  
   8  10  10  10  12   4   0   0   0   0   2   0   4  0  0  0  1  0  0  0  0        54   2   0   0   0   5   2   3   4    .667  
   5   0   0   0   0   6   0   1   0   0   0   0   0   0   0   0   1   0   0   0   0   0   0   0   0   0   0   0   0   0  
   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0  
   0   0   0   0   0   0   0   0   0   0   0   0  
   2   4   2   0   0   0   0   0   2   0   0   0   2   4   0   0   0   0   0   0   0   0   0   0   0   0   0  
   0   4   0   0   0   0   2   4   0   0   0   0   0   0   0   0   0   0   0   0   0  
   0   4   0   0   0   0   4   0   0   0   0   2   0   0   0   0   0   0   0   0   0  
   0   0   4   0   0   0   2   4   0   0   0   0   0   0   0   0   0   0   0   0   0  
   5   4   3   3   4   5   3   3   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0  
   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0  
   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0

NOTE: This output listing gives all 46 of the records possible for the .S file. It is possible to select which of these files the user actually wants to use for a given application.

The variables output to the .S file are identified in more detail in Appendix II.

The .E File from the 4-CLPHENOL.B File

1         8   0   0   4  128.558  4-Chlorophenol                                             
    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000
    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000
    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000
    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000
    .000    .000    .000    .000
    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000
    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000
    .000    .000    .000    .000    .000
   3.472   -.290    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000
    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000
    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000
    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000
    .000    .000    .000    .000    .000    .000
    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000
    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000
    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000   9.253    .000    .000    .000    .000    .000
    .000    .000    .000    .000    .000    .000    .000    .000   5.620    .000    .000
    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000
    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000
    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000
    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000
    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000
    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000
    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000
    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000
    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000
    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000
    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000
See Appendix V for the exact list of the symbols in the .E file, the bond type E-state indices.

The .MAT File from the 4CLPHENOL.B File

The user may elect to have the distance matrix for each molecule printed out in a separate file by selecting item 8 from the Main Menu. The following is an example of that file for 4-chlorophenol.

   1     4-Chlorophenol                                            

At.  Atom
No. Value     DISTANCE MATRIX
 1  14    0  1  2  3  2  1  1  4
 2  14    1  0  1  2  3  2  2  3
 3  14    2  1  0  1  2  3  3  2
 4  14    3  2  1  0  1  2  4  1
 5  14    2  3  2  1  0  1  3  2
 6  14    1  2  3  2  1  0  2  3
 7  20    1  2  3  4  3  2  0  5
 8  20    4  3  2  1  2  3  5  0

The Subgraph File (.SUB) from the 4CLPHENOL.B File

The user may elect to have all the subgraphs printed out for a specified order by selecting item 4 from the Main Menu. The following is an example for the molecule 4-chlorophenol for the fourth order. Note that there are two types of fourth order subgraphs in this molecule: the fourth-order path and the path/cluster-4. The fourth order cluster and the fourth order chain (ring) do not occur in this particular molecule.

   1     4-Chlorophenol                                            
                                Chi Term
No Order Type   Simple     Valence    Vertex Numbers/Group Symbols
 1   4   P    	0.16667    0.03727    	1   2   3   4   5
                                     	OH  C   CH  CH  C   
 2   4   P    	0.16667    0.03727    	1   2   8   7   5
                                     	OH  C   CH  CH  C   
 3   4   P    	0.16667    0.09449    	2   3   4   5   6
                                     	C   CH  CH  C   Cl  
 4   4   P    	0.11785    0.04811    	2   3   4   5   7
                                     	C   CH  CH  C   CH 
 5   4   P    	0.11785    0.04811    	2   8   7   5   4
                                     	C   CH  CH  C   CH  
 6   4   P    	0.16667    0.09449    	2   8   7   5   6
                                     	C   CH  CH  C   Cl  
 7   4   P    	0.11785    0.04811    	3   2   8   7   5
                                     	CH  C   CH  CH  C  
 8   4   P    	0.14434    0.05556    	3   4   5   7   8
                                    	CH  CH  C   CH  CH  
 9   4   P    	0.14434    0.05556    	4   3   2   8   7
                                     	CH  CH  C   CH  CH  
10   4   P    	0.11785    0.04811    	5   4   3   2   8
                                     	C   CH  CH  C   CH  
 1   4   PC	0.20412    0.04303    	2   1   3   8   4
                                     	C   OH  CH  CH  CH  
 2   4   PC	0.20412    0.04303    	2   1   3   8   7
                                     	C   OH  CH  CH  CH  
 3   4   PC	0.20412    0.10911    	5   4   6   7   3
                                     	C   CH  Cl  CH  CH  
 4   4   PC	0.20412    0.10911    	5   4   6   7   8
                                     	C   CH  Cl  CH  CH