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.