Formatting of the script files

Case sensitivity

The distinction between upper and lower case is ignored everywhere in the script files, which is also the case for all other input files (experimental data, initialization files). Unix systems are exceptional in that all file names are case sensitive. This is a property of the operating system, not the program.

White space

Position of text on a line is irrelevant because ``white space'' or indentation is ignored. Blank lines are ignored also. The only instance of white space being required is in the definition of reaction mechanisms. If a species A reacts with a species B, the plus sign in writing A + B -> AB must be surrounded by white space. Without the blank spaces surrounding the plus sign, the program would consider A+B to be a single molecular species.

Comments

Script files can contain comments delimited by the semicolon. Any text that follows a semicolon on the given line is ignored by the program. Thus the text

   E + S <===> E.S  :  k1  k2  ;  Michaelis complex
 ; E + I <===> E.I  :  k3  k4  
   files  f1, f2, f3, f4 ; f5, f6

becomes

   E + S <===> E.S  :  k1  k2

   files  f1, f2, f3, f4

when the script file is read by the program.

Special characters

The following characters have special meaning: < > [ ] : + * ? | ;. Detailed explanation of how these special characters are used is given in appropriate sections of this manual. A brief summary is given in Table 2.1.

`< >`	in the `[mechanism]` section: construction of arrows; in the `[settings]` section of the script file and in the default settings file: names of sections for default settings
`[ ]`	names of main sections in the script file
`:`	in the `[mechanism]` section: separating reaction steps from names of rate constants
`*`	in the `[mechanism]` section: making a reaction step 'slow' compared to other steps (see below)
`\|`	line break
`?`	optimized (adjustable, fitting) parameter
`+`	in the `[mechanism]` section: separates reactants in a reaction step
`;`	comments (anything beyond semicolon (`;`) on any given line is ignored)

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Petr Kuzmic | Jul 12 2005