This was our first attempt at creating a frame for running several rules compiled in the lab course. The idea is to be able to use any of the rules present in the includeAll.py file and not have to worry about importing rules.

In order to use this setup, you need the demo_run.py as a run-file ($ mod -f demo_run.py), as well as includeAll.py and molecules.py The easiest way to deal with this is to just do a

scp [email protected]:~/Documents/corerules/* . 

in the folder you are in. You should have all the necessary files and not worry about dependencies.

The most important things to do in this file are to specify which rules you want to use in your experiment. You use the rules of interest within the strat1 strategy as the main step of the rule. Just put them in in the

>> r2_2_1

line. Be aware that you cannot combine rules and sets of rules!! (see Shortcomings for a discussion of this.

The molecules-file specifies which molecules are present in the chemical environment. It contains a list of the molecules the rules can be applied to, and should be as specific to the experiment as possible in order to not generate too many unnecessary graphs. Since mod uses the smile-notation (SMILES wiki page), the molecules should be specified in this form. The molecules are organized as minimal molecules for specific reactions. If you are not interested in a reaction, just comment it out. If you want to use more complex molecules, include them via the smile-notation, preferably following the convention used in molecules.py

This file contains all rules that could be applied to the experiment. It imports these rules as sets (from the corresponding _*_.py or _*_*_.py files, which have to be present in the same folder (see above)). You shouldn’t have to touch this file. If you feel like you want to, please come to PRAK04 or PRAK05 to discuss why you feel like it. Maybe you’ve spot a mistake or something that can be improved

Since strategies specified in includeAll.py can be either lists of strategies (if the strategy is split into different part of the reaction), or single strategies (if one rules captures the entire reaction), you might get a type error in the console, saying

TypeError: unhashable type: 'set'

. This is because you try to put elements and lists into a list, so you would have a set of sets. If you want to do that (and are willing to trade some flexibility for compatibility), please use runAsSets.py (for documentation see documentation runAsSets). If you have an idea how to solve this or have an interesting application that needs solving this issue, please come talk to us at PRAK04 or PRAK05