Determining Dead Ends of Generated Mechanism
Dead ends are reactive pathways where a given molecule species does not react further, neither
in the generated mechanism, nor in the base mechanism (other than reverse reactions). This
menu analyses the mechanism (reaction pathways viewed as a graph) for end nodes. The
output is a table where the list of molecules which do not react further are listed.
The analysis proceeds as follows:
- Output In this window the text ouptput of the runs is shown. Also, since
this analysis is dependent on the REACTION system, the system has to be started (if not already
done so). This is done with the 'Start Remote REACTION' button.
- Input Generated This is a standard tab for the input of the generated mechanism.
The molecule list is used to eliminate those molecules from the dead end list, because it is
assumed that these molecules are reacted within the base mechanism. The reference and units are not
used in this analysis.
- Reference Information The 'Author', 'Source' and 'Note' fields should be filled in.
- Generated MechanismTo specify the
generated mechanism (from the server), press the 'Root Name' button. A selection of generated mechanisms
should appear and the desired chosen. The root name of the mechanism should appear in the field.
- Molecule Correspondencesthe file with the name correspondes should be read in (from the client files) by pressing 'Get Base Molecule List'.
Once read in, the fields with the species names can be modified.
- Unit Specifications The unit specifications at the bottom
should be checked (recommended to keep the defaults).
- Read InWhen all this information is entered, then the
generated mechanism can be read in with 'Read in from Server'. The output from the read will appear in the 'Output' tab.
- Lists Several buttons are supplied to view and write out the reaction and molecule lists.
- Dead Ends The analysis starts with interpreting the mechanism information as a graph. This is
done with the 'Mechanism As Graph' button. The dead end analysis proceeds with the 'Find Dead Ends' button.
The text output goes into the 'Output' window, but the list of dead ends is shown in the table in this tab.