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                             SMOG
               (Structural Molecular Generation)

    SMOG is a  program  for  exhaustive,  irredundant,  and  efficient
generation  of  chemical  isomers  by their gross formula and a set of
structural constraints.
    SMOG runs on IBM PC-compatible computers. It requires at least 640
Kb of RAM and occupies about 1 Mb of  disk  space  (2-3  free  Mb  for
storing  the  results  are  also  desirable).  The presence of a color
graphics adapter  (EGA/VGA)  is  necessary,  and  a  mouse  is  highly
desirable for faster work.

    In the case of any problems,  contact Marina Molchanova (Institute
of Organic Chemistry, Russian Academy of Sciences)

           (tel) (7-095) 135-9089; (7-095) 335-2836
           (fax) (7-095) 135-5328
           (E-mail) mary@ganzer.msk.su; molchano@cacr.ioc.ac.ru

/**********************************************************************/
                           1. INSTALLATION.
/**********************************************************************/

    1.1. The current version of SMOG includes the following files.

     Work files:
  SHOW.BAT
  ZASTAVKA.EXE, TRANS.EXE, GENESIS.EXE, SCRENING.EXE, ZIP-THEM.EXE,
  METAWNDO.EXE

     Menu file:
  MENUS.TXT

     Font file:
  SYSTEM16.FNT

     On-line help:
  GENESIS.HLP, GENESIS.IDX, HELP-ME.EXE

     Manuals:
  README!.TXT (this file), MANUAL.DOC, FRG_FORM.DOC, RES_FORM.DOC

     Config files:
  ADDSETUP.CFG, AROM.CFG, DRAWITER.CFG, GR_SETUP.CFG, SYSTEM.CFG

     Library files (standard):
  LIBS4.SET
  BASES \ ELEMENTS.STD, BASES \ FRAGMENT.STD

    All these files are contained in the SM_DISTR.ZIP  archive on your 
source diskette.

    1.2. It is  also  desirable  that  some  archivation/dearchivation
program  (PKZIP/PKUNZIP,  ARJ,  etc.)  should  be accessible from your
working directory.  It provides  the  user  with  the  possibility  to
interrupt  the generation process with archivation of the intermediate
results and program status, so that  the  generation  process might be
RESUMED  (from the point of interruption) during some later run of the
program. See MANUAL.DOC for details.
    The name  of  the  archiver/dearchiver  should be specified in the
SYSTEM.CFG file of your working directory (see  Section  2.1  of  this
manual and commentaries in the SYSTEM.CFG file).

    1.3. If  you  run  the  INSTALL.BAT program (see your installation
diskette), all the actions required for installation will be performed
automatically). The syntax is

   X:INSTALL XYZ X: or INSTALL XYZ

where X is the source diskette drive, and XYZ is the name of your work
directory, which (after its creation during installation) will contain
all the required SMOG files.

    Before calling INSTALL.BAT,  you must log onto the directory where
you want to create your working directory with the SMOG files.

/********************************************************************/
                  2. ADJUSTMENT AND ADDITIONAL FILES
/********************************************************************/

                   2.1. CONFIGURATION FILES (*.CFG)
    SMOG includes  5  configuration   files:  ADDSETUP.CFG,  AROM.CFG,
DRAWITER.CFG, SETUP.CFG, SYSTEM.CFG, which are used for adjusting some
parameters  (concerning  both  the  generation process and the program
appearance) before the start of the program.  The format of entries in
configuration files is

     [Variable] = [SomeValue]      (DetermineCoordinates = 1)
        or
     [Variable] = ["SomeString"]   (Archiver = "ARJ A" )

    The configuration   files   contain   detailed   commentaries  and
therefore are self-descriptive.  The comment lines begin with the  '#'
character.


             2.2. "LIBRARY" FILES (Element and Fragment)
    To analyze   chemical  data,  SMOG  requires  two  data  files  of
different types (only one file of each type may be loaded at  one  and
the same moment during the program run).

    -- Each Element library (the name of this file must be ELEMENTS.*,
as ELEMENTS.STD  supplied  with  SMOG)  contains  the  descriptions of
chemical  elements  (their  symbols,  possible valences, etc.).
    -- The  FRAGMENT.*  file  (as  FRAGMENT.STD  supplied  with  SMOG)
contains  the  structures that may be used to form Goodlist,  Badlist,
the  list  of  superatoms etc.  for  generation  and/or  screening  of 
target structures.

    The library  files (one of each type) are loaded at the entrypoint
of the program, either automatically  from  the  LIBS4.SET file or (if
their  names are not specified or incorrectly specified in it) by  the
program's  prompt.  Check  your LIBS4.SET file to see the names of the
library  files. Their use is described in detail in MANUAL.DOC.


/**********************************************************************/
                          3. GETTING STARTED
/**********************************************************************/

    By calling SHOW.BAT in  your  working  directory,  you  start  the
program. If the Element and Fragment libraries are correctly specified
in the LIBS4.SET file,  you enter the main menu  directly;  otherwise,
you  should  at  first  specify  the names of the library files by the
program's prompt.  As the main menu is entered,  chemical  information
may be  specified  (see  MANUAL.DOC  for a detailed description of the
process of its input).
     On-line help  is  provided  for  each  item  of the menu bar  and
pulldown menus. The help window is called by F1 or Ctrl-F1.
     
Modified: Sat Nov 1 17:00:00 1997 GMT
Page accessed 7029 times since Sat Apr 17 21:22:06 1999 GMT