Standardizer Sample Application

1. Configuration: Standardizer.xml

2. Command line:

   standardize -c Standardizer.xml input.mol -f mol | mview - &
   standardize -c Standardizer.xml nci100.smiles | mview - &
   standardize -c "aromatize..dehydrogenize..[O-:2][N+:1]=O>>[O:2]=[N:1]=O..N=[N:1]#[N:2]>>N=[N+:1]=[N-:2]..C[N+:1][H:2].[F,Cl,Br,I;-:3]>>C[N:1]..[H:4][N:3][C:1]=[C:2]>>[H:4][C:2][C:1]=[N:3]..[H:4][O:3][C:1]=[C:2]>>[H:4][C:2][C:1]=[O:3]" "N#N=NCC(\C=C\O)C(CC[NH3+])C([H])([H:1])C1=CC(=C(Cl)C(=C1)N(=O)=O)[N+]([O-])=O.[Cl-]"
   

3. API: StandardizerDemo.java

   java StandardizerDemo Standardizer.xml input.mol | mview - &
   java StandardizerDemo Standardizer.xml nci100.smiles | mview - &