DynaFit Scripting Manual

  Index

Available tasks

The main task to be accomplished by the program DynaFit is summarized in the [task] section of the script file.

The section [task] must contain the keywords task = .. and data =.. . The reaction mechanism may be optionally identified by the keyword mechanism = ... These keywords must stand on separate lines.

Example 1

[task]
   task = simulate
   data = velocities
   mechanism = mixed type

Example 2

[task]
   task = fit
   data = progress
   mechanism = slow tight inhibition

Example 3

[task]
   task = compare
   data = equilibria
   mechanism = displacement

Task

The keyword task must be followed by the equal sign (``='') and by one of the following keywords:

simulate	Simulate pseudo-experimental data, with or without superimposed random error.
compare	Compare the given experimental data and the postulated fitting model, with preliminary diagnostics for the goodness of fit. This option is useful in making initial estimate of fitting parameters.
fit	Nonlinear least-squares fit of the postulated theoretical model to the given experimental data.

Data

The keyword data must be followed by the equal sign (``='') and by one of the following keywords:

progress	The measured data (i.e., the dependent variable) are observations of a physical variable such absorbance, fluorescence, or radioactivity over time (i.e., the independent variable).
velocity	The data represent measurements of the initial reaction rate. The independent variable is the (initial) concentration of a certain reagent.
equilibria	The data are measurements of a certain physical variable (absorbance, fluorescence, radioactivity) observed on a chemical or a biochemical system at equilibrium. The independent variable is the concentration of a certain reagent.

Mechanism

The keyword mechanism is optional, unless a model discrimination analysis is required. It is followed by the equal sign and by an arbitrary text identifying the reaction mechanism to the user. The text should be short, at most 32 characters.

Model discrimination analysis

The keyword mechanism is required if a given DynaFit script contains multiple tasks, each of which requests the least-squares fit to a different reaction mechanisms. Typically, such model discrimination analysis involves the same set of experimental data. In this case the keyword mechanism must be present. Model discrimination analysis is indicated by appending the question mark (``?'') after the name of each reaction mechanism.

ExampleIn this example, DynaFit will fit the experimental data indicated in the script file (omitted for brevity and represented by the ellipses) to three different reaction mechanisms. After the analysis is complete, DynaFit will compute a set of statistics deciding which reaction mechanism is most plausible (``model discrimination analysis'').

[task]
   data = velocity
   task = fit
   mechanism = competitive ?
...
[task]
   data = velocity
   task = fit
   mechanism = un-competitive ?
...
[task]
   data = velocity
   task = fit
   mechanism = mixed type ?
...
[end]

Each DynaFit script may contain in principle an unlimited number of consecutive tasks. The script file sections delineated by the keywords [task] or [end] must contain other sections, as is described in the following portions of this chapter.

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Petr Kuzmic | Jul 12 2005