CODESSA 2.7.16 - Release Notes

     Authors:  Alan Katritsky, Mati Karelson, Victor S. Lobanov, 
               Roy Dennington and Todd Keith
     Copyright (c) 1994-1995 by University of Florida
     Portions Copyright (c) 1996-2009 by Semichem, Inc.
     All Rights Reserved
     Redistribution or resale, except by Semichem, Inc., is prohibited.    


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Learn Codessa by reading the Adobe-formatted (*.pdf) manuals in the 'docs' directory
(Train.pdf, Ref.pdf and User.pdf) and using the help facilities within Codessa.  Also, see
the *.readme files in the 'docs' directory.

To learn Codessa by example, see the 'examples' directory, which contains a small collection
of sample Ampac, Mopac and Gaussian data files, Codessa "Project" (.cod) files (to be opened
and saved by Codessa using "File->Open" and "File->Save"), Codessa "Input" (.inp) files (to
be opened by Codessa using "Data->Load" or "Data->Auto Load") and list (.lst) files (to be
opened by Codessa using "Data->Auto Load").

On WINDOWS, the batch files runampac.bat, rungaussian.bat and runmopac.bat should be edited
according to the current system.  These batch files are called by predict.exe and makeinp.exe
to automatically run Ampac, Gaussian or Mopac, if requested or necessary.

Note that the keyword "CODESSA" can be used with AMPAC jobs to produce the maximal useable
information by the Codessa program.

Thank You for using CODESSA 2.7.16

Semichem Contact Info:
                        Phone:   (913) 268-3271
                        E-Mail:  support@semichem.com
                        Web:     www.semichem.com
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Codessa requires that a valid key file, named codessa.key, be placed in the Codessa-2.7.16
directory.  If you don't already have a key file for Codessa, please contact Semichem, Inc.
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To Launch Codessa on WINDOWS use the "Start Menu->Codessa-2.7.16->Codessa icon or the desktop
Codessa icon or launch the Codessa.exe file directly from the Codessa-2.7.16 folder.
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To use Codessa on UNIX systems, the file Codessa-2.7.16/init_codessa.sh (for Bourne or BASH
users) or Codessa-2.7.16/init_codessa.csh (for CSH users) must first be "sourced."  This is
most easily achieved by entering the following command (substitute the parent directory path
of Codessa-2.7.16 for /usr/local) in your $HOME/.bash_profile or $HOME/.profile files (for
Bourne or BASH users):

. /usr/local/Codessa-2.7.16/init_codessa.sh

or by entering the following command in your $HOME/.login file (for CSH users):

source /usr/local/Codessa-2.7.16/init_codessa.csh

This will make Codessa automatically available whenever you login.  These commands can also
be entered on the command-line of a shell window, but Codessa will then only be available for
that shell environment.

To launch Codessa, enter the "codessa" command (without the quotes) on the command line of a
shell window or launch the Codessa file directly from Codessa-2.7.16 directory, either from
the command line or from a file browser(launching with the mouse in a file browser only works
if the login scripts have been edited as above).
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To get started with Codessa, try the following example (useful for illustration purposes only):

1) Launch Codessa On Windows, 

2) Select "Data->Load..." from the main menu

3) In the "Select an Existing CODESSA Input File" dialog, select the file examples/ampac.inp
   in the Codessa-2.7.16 directory.  This is a text input file containing a names, Ampac
   output file path, two properties ("BP" and "MP") and one "extra" descriptor ("LOGP") for
   each of 25 mono-substituted benzene molecules

4) In the "Columns" dialog, select the "Header" radio button for the "First Line" radio
   button group, verify the number (5) and types of columns and then select the "Ok" button

5) Select "Data->Sets..." from the main menu

6) In the "Set" dialog, select the "Structures (*ampac.inp) set and then select the Rename
   button

7) In the "Rename" dialog, change the set name to "MSB_All" and then select "Ok"

8) In the "Sets" dialog, select the "New" button

9) In the "New" dialog, enter "MSB_Train_1" for the "Set's name" and select the "Structures"
   radio button and then select "Ok"

10) In the "Compose set" dialog, add the first 20 structures of the "Source set" "MSB_All"
    to the "Target set" "MSB_Train_1" and then select "Ok"

11) In the "Sets" dialog, select the "New" button again

12) In the "New" dialog, enter "MSB_Predict_1" for the "Set's name" and select the
    "Structures" radio button and then select "Ok"

13) In the "Compose set" dialog, add the last 5 structures of the "Source set" "MSB_All"
    to the "Target set" "MSB_Predict_1" and then select "Ok"

14) In the "Sets" dialog, select the "Close" button

15) Select "Descriptors->Calculate->Molecule..." from the main menu

16) In the "Calculate descriptors" dialog, make sure the "Calculate all descriptors"
    checkbox is checked and then select "Ok"

17) In the "Select set" dialog, select the "MSB_All" set of structures just loaded and then
    select "Ok"

18) After several seconds, Codessa will have calculated over 400 descriptors for each
    molecule in the set "MSB_All"

19) Select "Correlate->Heuristic..." from the main menu

20) In the Heuristic "Options" dialog, set the "Maximum number of descriptors" to 3 and
    then select "Ok"

21) In the "Heuristic" dialog, select "BPC" as the "Property to fit", "MSB_Train_1" as the
    set of structures and "All descriptors" as the "Set of Descriptors" and then select
    "Start"

22) After several seconds, Codessa will have calculated the 11 "best" correlations found
    using the specified criteria

23) In the "Select correlations to save in set "BPC correlations"" dialog, select the
    first correlation and the last correlation and then select "Ok"

24) Select "Predict->View correlation..." from the main menu

25) In the "Correlation" dialog, double click on either correlation to get a "Status" window
    summarizing the correlation.  Also, try clicking on the other buttons in the dialog
    to get more information about the currently selected correlation.  For example, clicking on
    the "Plot" button will display a plot window of calculated (predicted) BPC values versus the
    experimental BPC values used as input for the currently selected correlation's set of
    training structures.  For both correlations, use the "Rename" button to append "  MSB_Train_1"
    to the their names as a convenience for recalling their training set of structures.

26) Select "Predict->Predict property..." from the main menu

27) In the "Select correlation" dialog, select "BPC correlations" for the "Set" and select the
    first correlation and then select "Ok"

28) In the "Select set" dialog, select the "MSB_Predict_1" set of structures and then select "Ok"

29) A text window showing the predicted BPC values versus the experimental input values is shown

30) Select "Plot->Prediction..." from the main menu

31) In the "Select correlation" dialog, select "BPC correlations" for the "Set" and select the
    first correlation and then select "Ok"

32) In the "Select set" dialog, select the "MSB_Predict_1" set of structures and then select "Ok"

33) A plot window showing the predicted BPC values versus the experimental input values is shown

34) Save your work as a Codessa project file by selecting "File->Save..." from the main menu

35) In the "Specify a New or Existing CODESSA Project File" dialog, save your project file as
    "myampac.cod" in the same directory as the ampac.inp file from which it started.  For
    reference, a similar project file "ampac.cod" is included in the Codessa distribution.

36) Select "File->New" from the main menu

37) Select "File->Open..." from the main menu

38) In the "Select an Existing CODESSA Project File" dialog, open the "myampac.cod" file saved
    previously to load the previously saved project for further investigation of Codessa ...
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