react.cgiis a web interface which applies reaction transforms (SMIRKS) to molecules (SMILES). It is useful for learning how transforms work and testing new SMIRKS. Start
react.cgiand press the help button. Several examples are shown. Another source of examples is SMIRKS FAQ and Examples. How about trying:
Does this smirks look familiar?
Build react and run it. Experiment with some generic reactions and molecules.
Try the following example:
SMIRKS: [c:1][N:2](=[O:6])=[O:4]>>[c:1][N+:2](=[O:6])[O-:4] SMILES: O=N(=O)c1ccc(N(=O)=O)cc1Note that the transform is only applied once (by default) per reaction.
% cd jane_doe/toolkit
% mkdir transform
% cd transform
% cp $DY_ROOT/contrib/c/reaction/react.c .
% cp $DY_ROOT/contrib/c/reaction/makefile .
% make react
react.cby trying the options:
To vary the 'limit' parameter you will have to modify
react.c and rebuild. Vary the
limit parameter and observe the effect on the output.
react.cso that it applies the same transform repeatedly until no further matches are found. That is, take the product from the first application, and feed it back into the transform. After the transform has been applied exhaustively, print out the products. Is this behavior the same as with
react.c, lets start to build a combinatorial library enumerator. We want to create a simpler version of the
enumerate.cprogram. Our program will handle two-component mixtures. We'll try the enumeration two different ways:
dt_transform()with the 'limit' parameter set to FALSE, the toolkit will do the full enumeration of the library for you. This will probably be slow but yields the simplest code. Build and test.
dt_transform()once for each possible pair of reactants and write out the products. Build and test.
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