Synthesizer Sample Application

1. Configuration: Synthesizer.xml.

   First, look at the synthesis graph.

   Then create and run the synthesis:

   synthesize d -n schreiber
   synthesize c -n schreiber -c Synthesizer.xml
   synthesize i -n schreiber -s scaffold scaffold.smiles
   synthesize i -n schreiber -s alkyne alkynes.smiles
   synthesize i -n schreiber -s amine amines.smiles
   synthesize i -n schreiber -s carboxylic-acid carboxylic-acids.smiles
   synthesize r -n schreiber
   

2. Synthesis browser: start jcman, invoke Tools/Synthesis Browser or else invoke synthesisbrowser directly

3. Add a rule to a synthesis step: (configuration: SynthesizerPlusRules.xml). Repeat steps 2. and 3. Note the difference. You can also use the scripts schreiber and schreiber_plus_rules.

4. Synthesizer API: SynthesizerDemo.java

   java SynthesizerDemo Synthesizer.xml demo scaffold scaffold.smiles alkyne alkynes.smiles amine amines.smiles carboxylic-acid carboxylic-acids.smiles