Molconn-Z 3.50 Manual: Chapter 5

CHAPTER 5

Menu Displays for Molconn-Z

 There are three menus in the Molconn-Z program. This chapter discusses the nature and use of these menus.

Accessing Menus

The program Molconn-Z has provision for selecting and changing program options interactively during the execution of the program. This is accomplished by answering no (N) to the screen query which appears after the request for the names of the input .B file: 
Standard Control Options ? (Y/N) <Y>  :

The main menu appears on the terminal screen. When any one of the options is selected by entering the corresponding number, the user interactively makes the option selection, as shown below.

Further, there are two sub-menus which can be obtained by selecting item 11 or item 12 in the main menu. Item 11 presents a sub-menu for further program control options and item 12 presents a sub-menu with options for the listing file (.L) contents.

When the main menu is selected, the following request appears following the printed menu: 

Please Enter Desired Option :

For each menu option the values appearing in the brackets, < >, are the current option values.

Main MENU

The following display appears when the main menu is selected: 

                         MOLCONNZ PROGRAM OPTIONS
                  Enter Number for the Desired Option Change
                      <Default Standard Value Given>

 1- Input File (Molconn/SMILES code/Chemlab/
                MDL Molfile/SDFile/CHEM-X/User) (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):

Making selections within the Menu

The text for each option is given in the following sections. The actual text which appears on the screen is given in 
preformatted type face.

Each option is described in the following pages:

OPTION 1

In option 1 the user is asked to select the format which corresponds to the files referred to in the .B file for this execution of Molconn-Z. 


 Use standard MOLCONN   file format  <C>
 or SMILES code         file format  <S>
 or a ChemDesign/CHEM-X file format  <X>
 or a ChemDraw          file format  <D>
 or an MDL Molfile      file format  <M>
 or an MDL SDFile       file format  <F>
 or a User Supplied     file format  <U>? : 

 Want this change made permanent (Y/N) <N> ? :

The user has the option of making this selection permanent, that is, keeping this option in place and making it the default or standard value until the next execution of Molconn-Z. At that time the user may elect to select another file format option.

The default value for file format is S in the delivered Molconn-Z software.

OPTION 2

The computation of the topological equivalence state is described in Chapter 2. Part of that computation depends on the algorithm type which the user may select below. 

 Select Algorithm Number for Computation
    of Topological Equivalence State Values as Follows :


 Function type for topological state : 

  1 : Distance/Geometric Mean
  2 : Geometric Mean/Distance
  3 : d**2/Geometric Mean
  4 : Geometric Mean/d**2
  5 : d**3/Geometric Mean
  6 : Geometric Mean/d**3

 Select Algorithm Number:
    Current Value = 4;   Select 1 to 6 : 

 Want this change made permanent (Y/N) <N> ? :

The user has the option of making this selection permanent, that is, keeping this option in place and making it the default or standard value until the next execution of Molconn-Z. At that time the user may elect to select another algorithm option. The default value for algorithm is 4 in the delivered Molconn-Z software.,p>

OPTION 3

An electrotopological state index value is computed for each atom (skeletal hydride group) in the molecular graph. This option permits the user to determine how many such values will be output to the .S file. This number clearly depends upon the size of the molecules under consideration. The index output file (.S) is set up with 16 values per line of output. See Chapter 6 for detailed information. 

 Want to Change the Number of E-State values which 
        are output into the .S Output File ? <N> (Y/N) : 

 How many atom E-State values should values 
                 be written into the .S File (NS)?: 

 Want this change made permanent (Y/N) <N> ? :

The user has the option of making this selection permanent, that is, keeping this option in place and making it the default or standard value until the next execution of Molconn-Z. At that time the user may elect to select another file format option.

The default value for number of E-state values is 90 in the delivered Molconn-Z software.

OPTION 4

Molconn-Z computes bond type electrotopological state indices as described in Chapter 3. There is a large number of such bond types. To facilitate economy of output, the bond type indices have been subdivided into two sets: organic (O) and inorganic (I). The user can select either one of the subsets, all of the bond types (A) or none (N).


 Select which set of edge type indices to be output
        to the (.E) Edge Type File <O>  
  A: all           
  O: organic subset
  I: inorganic subset
  N: none 
                       (A/O/I/N) : A

 Want this change made permanent (Y/N) <Y> ? :

The default value for bond type is O in the delivered Molconn-Z software.

OPTION 5

When the user enters data for many molecular structures, and especially when the molecules are large and/or complicated, there is chance for error in the input information. The user may want to have only enough output to allow for verification of the input structures. This option permits the user to request that only such information is computed and printed in the .L listing file. The program runs very fast under these conditions and the volume of output is small. The user may wish to have these advantages in the earliest stages of analysis. When structure data is obtained from some previous operations which have already been verified, this option may be completely unnecessary. However, verification of input structures is vital to validity of output information.,p> 

 Do full calculation  <Y>
 or only verify input <N>? :

The default value for calculation is Y in the delivered Molconn-Z software.

OPTION 6

Molconn-Z will automatically compute indexes and count paths up to the maximum length in the molecule, limited only by the default value in this option. The larger and more complex the molecule, the more computations are required to complete this task. If computation time becomes a problem, the user may elect to limit the maximum order computed. It should be noted, however, that when all the paths are not computed, then the various symmetry-dependent computations cannot be done and information indexes are not computed. Molconn-Z automatically makes that determination.


 Maximum order of Chi Index Computed ...
  also maximum path length obtained 
      Enter your choice .. 1 to 100
   or Enter (RETURN) for Default value <100>  : 

 Want this change made permanent (Y/N) <N> ? :

Enter your choice .. 1 to 100 or Enter 100 for Longest Path or Enter (RETURN) for Default value <100>.

OPTION 7

If the user intends only to visually examine the output listing .L file, then the index output .S file is not necessary. The user may elect to prohibit its creation if account space is a problem.


 Do you Want an Output Index File in Text Format
                           <N>  (Y/N) : 

 Want this change made permanent (Y/N) <N> ? :

The user has the option of making this selection permanent, that is, keeping this option in place and making it the default or standard value until the next execution of Molconn-Z. At that time the user may elect to select another file format option.

The default value for .S file selection is Y in the delivered Molconn-Z software.

OPTION 8

The user may not have current use for an output listing file (.L) for several reasons. The input data may have already been thoroughly verified or it may be a very large database which would produce an excessively large .L file. For these reasons the user may elect to have no .L file produced. Selection of no .L file also eliminates output to the screen. The combination of these two actions, no .L file and no screen output, significantly increases the speed of execution and is a good choice for large data bases. The MENU option gives the user the choice of not producing an .L file:


 Do you Want an Output Listing File?
  Selecting N also prevents output to the screen
    so that overall processing time is improved
  A .MSG file is also produced for any error messages
                     Please enter: <N>  (Y/N) : 

 Want this change made permanent (Y/N) <N> ? :

The default value for .L file selection is Y in the delivered Molconn-Z software.

OPTION 9

Molconn-Z also computed Bond Type Electrotopological state indices as described in Chapter 3. Since there is a large number of such bond types, these indices are output to a separate file. If the user wants the bond type E-state indices computed and the indices output, the user selects Y for this option. 

 Do you Want to Compute Bond Type E-state Indices
    which will produce an Output (.E) File?
                     Please enter: <N>  (Y/N) : 

 Want this change made permanent (Y/N) <N> ? :

The default value for .E file selection is Y in the delivered Molconn-Z software.

Molconn-Z also computes the count of each bond type and can output these counts to the same .E file. These additional counts increase the size of the .E file significantly. The user is asked to decide on inclusion of the bond type counts:


 Do you Want Bond Type counts inlcuded
                  in the Output (.E) File?
                     Please enter: <N>  (Y/N) : 

 Want this change made permanent (Y/N) <N> ? :

The default value for bond type count inclusion is N in the delivered Molconn-Z software. See also option 4 for other selections related to the Bond Type E-state index output.

OPTION 10

The user may elect to produce a file which contains the distance matrix for each molecule in the .B file. 

 Want an Output File 
   for Distance/Connectivity Matrices ?
                                   <N>  (Y/N) :

The default value for Distance/Connectivity file selection is N in the delivered Molconn-Z software.

Program Control Parameters Sub-menu

To have access to certain program control options, the user must select item 11 in the Main Menu. When item 11 is selected, the following menu appears on the screen. 

  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)  < 8>
  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):
Each option in Sub-Menu 1 is described in the following pages.

OPTION 1

Certain of the computations in Molconn-Z depend upon determination of the topologically equivalent classes of skeletal atoms. The information indexes especially depend upon this information. Usually topological equivalence is determined. However, for very large and complex molecules, the computations may take a long time. The user may wish to turn off equivalence determination to shorten computation time. 

 Do You Want Symmetry Perception and Symmetry Indexes
                   KSYM <N>   (Y/N) : 

 Want this change made permanent (Y/N) <N> ? :
The user has the option of making this selection permanent, that is, keeping this option in place and making it the default or standard value until the next execution of Molconn-Z. At that time the user may elect to select another file format option.

The default value for symmetry perception is Y in the delivered Molconn-Z software.

OPTION 2

In the MOLCONN .B file format, each field is separated by a 'field delimiter'. The user may select either a comma or a blank. 

 Select Field Delimiter for Molecule Input File <,>
              Enter 1 for Comma
                    2 for Blank : 

 Want this change made permanent (Y/N) <N> ? :
The user has the option of making this selection permanent, that is, keeping this option in place and making it the default or standard value until the next execution of Molconn-Z. At that time the user may elect to select another file format option.

The default value for field delimiter is 1 in the delivered Molconn-Z software.

OPTION 3

The Molconn-Z program usually stores up to the tenth order of computed chi indexes. The user may select to alter this number. However, if a number larger than 10 is used, there may be problems with the maximum length of the output line for a FORTRAN file. See Appendix II for output details. 

 Maximum Order of Chi Indexes
   to be Saved on Output File <10> (1 to 20) :
The default value for maximum order put into output file is 10 in the delivered Molconn-Z software.

OPTION 4

In the computation of chi indexes, the subgraph contributions containing a fluorine may be set to either positive or negative. 

 Select Sign of Fluorine Contribution, IFSIGN, <+>
          Enter + for positive contribution
                - for negative contribution :
The default value for fluorine contribution is + in the delivered Molconn-Z software.

OPTION 5

The standard formalism for chi indexes is the use of the reciprocal-square-root. The user may however elect to use the geometric mean formalism of the topological equivalence algorithm. 

 For Molecular Connectivity Algorithm use
    Standard Reciprocal-Square-Root formalism   <R>
    Topological State Geometric Mean Algorithm  <G>? :
The default value for connectivity algorithm selection is R in the delivered Molconn-Z software.

OPTION 6

The standard formalism for topological equivalence is the use of the geometric mean formalism. The user may however elect to use the reciprocal-square-root algorithm from the chi index computation. 

 For Topological State Algorithm use
  Connectivity Reciprocal-Square-Root formalism  <R>
  Topological State Geometric Mean Formalism     <G>? :
The default value for topological state algorithm is G in the delivered Molconn-Z software.

OPTION 7

As described in Chapter 3, the molecular graph can be decomposed into connected fragments of bonds, called subgraphs. The computation of topological indexes is based upon counts of these subgraphs. The user may find it helpful to have all the subgraphs of a certain order (size) printed out for examination.

This option permits the user to select the order (number of graph edges in the subgraph) and the name of the file for the subgraph information. If more than one subgraph order is desired, the user must run Molconn-Z more than once, each time selecting the order and assigning a new file name, perhaps, such as PHENOLS.SUB3, PHENOLS.SUB4, etc.

See Chapter 8 for an example output file. 


 Print All Subgraph Contributions for the Orders
 of Chi Indexes Selected <N>  (Y/N) : 

 Enter Subgraph File Name (.SUB) : 
 For which order do you want
  subgraphs put in the file (2 to 100) <  4> ? :
NOTE: The maximum order permitted is determined by the size of the molecule and the other options selected. See option 6.

OPTION 8

The user may select which of the output records to include in the .S file each time the program is run. The menu presents the current list of records from the default values and then lists the content of each record. This option may be useful to control the size of the .S file or to construct an .S file which meets the requirements of a particular statistical package. 

 Select records for output to .S file 
  From the following list, enter records numbers separated by commas

 Current Record numbers : 
  1  2  3  4  5  6  7  8  9 10 11 12 13 14 15 16 17 18 19 20 21 22 23
 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46
 Rec. Nos.     Contents
  1-       id, no. atoms, rings, . . . fw, cpd name
  2,3-     Simple/Valence chi path indexes
  4-       Simple  cluster/path-cluster and chain indexes
  5-       Valence cluster/path-cluster and chain indexes
  6,7-     Simple/Valence path chi difference indexes
  8-       Kappa indexes, si, totop, sumI, sumdelI . .
  9..14-   Electrotopological state indexes (1-90)
 15..21-   Atom-type Sum E-state indexes
 22..28-   Atom-type Counts
 29..34-   Hydrogen electrotopological state indexes
 35-       Information indexes, Wiener number, H-bonds
 36-       Counts of paths,clusters,chains,radius,etc . .
 37..39-   Atom counts
 40-       Vertex type and edge type counts
 41..43-       n2pij, n3pij, n4pij
 44..46-   Vertex eccentricities

 Record nos: (enter -1 for all records) 
 : 

 All  46 records to be written in .S file

 Want this change made permanent (Y/N)  ? :
The user enters the desired record numbers. The program responds by stating the number of records selected. If the user wants these record numbers to be selected for the next run of Molconn-Z, then the user must indicate a permanent change in response to the next inquiry. 

 Want this change made permanent (Y/N)  ? :
The user has the option of making this selection permanent, that is, keeping this option in place and making it the default or standard value until the next execution of Molconn-Z. At that time the user may elect to select another file format option.

The default value for the .S file record numbers is whole set: 

1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46
in the delivered Molconn-Z software.

OPTION 9

The user may place a marker symbol at the end of each record in the .S file. This marker is required by some statistical packages to indicate that more than one record is entered for each observation. 

 Do You Want a marker at the end of each .S file line?  MARK <N>   (Y/N) : 

 Please enter TWO characters for end of line marker :
If the user wants this record marker to be selected for the next run of Molconn-Z, then the user must indicate a permanent change in response to the next inquiry. 

 Want this change made permanent (Y/N) <N> ? :
The user has the option of making this selection permanent, that is, keeping this option in place and making it the default or standard value until the next execution of Molconn-Z. At that time the user may elect to select another file format option.

The default value for this record marker is two blanks in the delivered Molconn-Z software.

Output Listing File Print Block Control

The user may elect to have some control over which blocks of computed information are actually printed in the output listing .L file. When all the possible information is printed for each molecule, the file can be several pages per molecule, especially for large molecules. If users wish to decrease some of this printed volume, they may elect to eliminate some of the printed blocks. The first output block, which describes the basic atom information of the molecule and is useful for verification, is not under user control; it is always printed. The first block contains each atom with its bonded hydrogens (the group symbol), the valence delta value, the intrinsic state value, the E-state index for that atom, markers indicating presence in a ring, aromaticity, and hydrogen bond status along with the ids of the connected atoms.

When the user selects item 12 in the Main Menu, the following menu appears on the screen.


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) :
The information in the output listing .L file is organized into print blocks. The user may exercise some control over which of these blocks are actually printed for a given application of Molconn-Z. See Chapter 8 for detailed information on the actual content of each print block.

When one of the above options is selected, a message appears on the screen. Each of these messages is described below.

OUT1

The table of atom equivalence information is printed so that the classes of (topological) equivalence atoms can be presented. This equivalence information appears under the following heading.

*--> ATOM SYMMETRY INFORMATION :
The user may elect to change the print status of this information block by selecting 1 in the Menu above. Whatever the current print status is, selecting this time will change it from yes to no or from no to yes. The value N eliminates this print block from the .L file. The default value for this block of information is Y as supplied by Molconn-Z software.

OUT2

The counts of the subgraphs of various sizes and descriptions are determined by Molconn-Z. The table of these counts appears under this heading.

*--> SUBGRAPH COUNTS INFORMATION :
The user may elect to change the print status of this information block by selecting 2 in the Menu above. Whatever the current print status is, selecting this time will change it from yes to no or from no to yes. The value N eliminates this print block from the .L file. The default value for this block of information is Y as supplied by Molconn-Z software.

OUT3

The computed values of the molecular connectivity chi indexes, both valence and simple are printed in table form.

*--> MOLECULAR CONNECTIVITY INDEXES :
The user may elect to change the print status of this information block by selecting 3 in the Menu above. Whatever the current print status is, selecting this time will change it from yes to no or from no to yes. The value N eliminates this print block from the .L file. The default value for this block of information is Y as supplied by Molconn-Z software.

OUT4

A collection of computed indexes related to total topological indexes, the Wiener indexes and the Platt index are printed under the following heading.

*--> TOTAL TOPOLOGICAL AND WIENER INDICES :
The user may elect to change the print status of this information block by selecting 4 in the Menu above. Whatever the current print status is, selecting this time will change it from yes to no or from no to yes. The value N eliminates this print block from the .L file. The default value for this block of information is Y as supplied by Molconn-Z software.

OUT5

Several information based topological indexes are printed under the following heading.

*--> INFORMATION INDEXES :
The user may elect to change the print status of this information block by selecting 5 in the Menu above. Whatever the current print status is, selecting this time will change it from yes to no or from no to yes. The value N eliminates this print block from the .L file. The default value for this block of information is Y as supplied by Molconn-Z software.

NOTE: These options are stored as values for corresponding variables in the file OPTION.DAT. Clearly, the integrity of this file must be protected. When the user requests that an option be changed 'permanently', the file OPTION.DAT (or mconn_option.std) is rewritten.