Generate Mechanism
This is the main frame of the mechanism generation. This process uses the database and functions of the REACT
system.
Given a set of seed molecules, a set of auxillary molecules
and a set of mechanism pathways, a set of submechanisms are generated and then combined. Three sets of information
is needed from the database:
- Seed Molecules These are the molecules which are the 'seeds', i.e. the begining molecule of the generation
process. The submechanism produced from the seed represents how that seed reacts.
- React Agents A set of auxillary small molecules that are always in the radical and molecule pool for use by the
generation process.
- Pathway Each pathway represents a generic type of reacting process. It is a sequence of
reactive sets, each represented by a set of reaction patterns. In the generation process, A single step is
applied to (only) the products of the last step (or the seed molecule in the first step). This is the key to the
controlled generation process. Each pathway is designed so that the reactions of a given step involve all the
products of the previous step. In addition, the pathway is further designed such that the products of the last step
are used by either the base mechanism or another submechanism (of, usually, a smaller seed molecule).
- Submechanisms When one of the seed molecules (together with the extra reactants) is applied to a pathway,
a 'submechanism' is created representing how that seed molecule reacts within that pathway.
- Combined The final total generated mechanism is the merging of all the submechanisms. The set of submechanisms
is designed that the products of each submechanism (meaning the species not reacting further within that submechanism) are
consumed within another submechanism or the base mechanism.
The process of generated a complete combined mechanism involves first setting up the set of seed species, reactant species
and pathways from the database and then generating and combining the result into a single generated pathway. The sequence
of generating a mechanism basically follows, from top to bottom, the buttons on the left:
- Seed Molecules When the 'Molecules' button is pressed, a menu for the selection of seed molecules appears.
These are the molecules in the REACT database. The set of molecules can be chosen by either highlighting each of the
molecules or by pressing the 'Load' button to read in and highlight a prepared set of molecules (a file is read, one molecule
name per line). Pressing 'Select' transfers the selected molecules into the 'Seed Molecule' box.
- React Agents The 'React Agents' button is used to select the 'Extra Reactants'. In exactly the same way that the seed molecules were chosen, the extra reacting species
can also be chosen. The selected molecules will appear in the 'Extra Reactants' box.
- Submechanisms The pathways are defined by files within the directory 'mechs/submechanisms' on the server (user defined
submechanisms can be added by putting an appropriate file in this directory). The desired pathways are highlighted. As with
the molecules, by selecting 'Load', a file can be read in with a list of pathways to highlight. By pressing 'Select'
pathways are transfered to the box.
- Select By pressing select, every combination of seed molecules and pathways are combined and put in the
'Submechanisms' box. If no fields within the seed molecules or the pathways are highlighted, then all are taken. If one or
more are highlighted, then only the highlighted are considered.
- Generate This begins the process of generation of each of the submechanisms. Each generation process
consists of a separate call to the REACT system (no setup of the REACT system is required). During generation, the lamp
next to the name is yellow. If the generation is successful, then the lamp turns green. If unsuccessful, the lamp turns
red. The output of each generation can be viewed by examining the '.out' in the 'mechs/submechanisms' directory on the server.
If no submechanism is highlighted when 'Generate' is pressed, then all will be generated. If one or more is highlighted
then only those submechanism will be generated.
- Mechanism Name In the field at the bottom of the menu, the name of the final combined mechanism can be entered.
A valid name has no blanks.
- CombineThis combines all the submechanisms highlighted in the submechanisms box into one generated mechanism
with the root name given in the 'Mechanism Name' field. The files associated with this mechanism can be found on
the server in the mechs/generated directory.