3.1. rpg package
3.1.1. Submodules
3.1.2. rpg.RapidPeptidesGenerator module
Main file of RPG software, handle input/output and launch necessary functions
- rpg.RapidPeptidesGenerator.ALL_ENZYMES = [Id: 1 Name: Arg-C Ratio Miscleavage: 0.00% Rules: [index=0 amino_acid=R cleavage=True position=1 ] , Id: 2 Name: Asp-N Ratio Miscleavage: 0.00% Rules: [index=0 amino_acid=C cleavage=True position=0 , index=0 amino_acid=D cleavage=True position=0 ] , Id: 3 Name: BNPS-Skatole Ratio Miscleavage: 0.00% Rules: [index=0 amino_acid=W cleavage=True position=1 ] , Id: 4 Name: Bromelain Ratio Miscleavage: 0.00% Rules: [index=0 amino_acid=K cleavage=True position=1 , index=0 amino_acid=A cleavage=True position=1 , index=0 amino_acid=Y cleavage=True position=1 ] , Id: 5 Name: Caspase-1 Ratio Miscleavage: 0.00% Rules: [index=0 amino_acid=D cleavage=False position=1 index=-1 amino_acid=H cleavage=False position=-1 index=-3 amino_acid=F cleavage=True position=-1 index=1 amino_acid=P cleavage=False position=-1 index=1 amino_acid=E cleavage=False position=-1 index=1 amino_acid=D cleavage=False position=-1 index=1 amino_acid=Q cleavage=False position=-1 index=1 amino_acid=K cleavage=False position=-1 index=1 amino_acid=R cleavage=False position=-1 index=-3 amino_acid=L cleavage=True position=-1 index=1 amino_acid=P cleavage=False position=-1 index=1 amino_acid=E cleavage=False position=-1 index=1 amino_acid=D cleavage=False position=-1 index=1 amino_acid=Q cleavage=False position=-1 index=1 amino_acid=K cleavage=False position=-1 index=1 amino_acid=R cleavage=False position=-1 index=-3 amino_acid=W cleavage=True position=-1 index=1 amino_acid=P cleavage=False position=-1 index=1 amino_acid=E cleavage=False position=-1 index=1 amino_acid=D cleavage=False position=-1 index=1 amino_acid=Q cleavage=False position=-1 index=1 amino_acid=K cleavage=False position=-1 index=1 amino_acid=R cleavage=False position=-1 index=-3 amino_acid=Y cleavage=True position=-1 index=1 amino_acid=P cleavage=False position=-1 index=1 amino_acid=E cleavage=False position=-1 index=1 amino_acid=D cleavage=False position=-1 index=1 amino_acid=Q cleavage=False position=-1 index=1 amino_acid=K cleavage=False position=-1 index=1 amino_acid=R cleavage=False position=-1 index=-1 amino_acid=A cleavage=False position=-1 index=-3 amino_acid=F cleavage=True position=-1 index=1 amino_acid=P cleavage=False position=-1 index=1 amino_acid=E cleavage=False position=-1 index=1 amino_acid=D cleavage=False position=-1 index=1 amino_acid=Q cleavage=False position=-1 index=1 amino_acid=K cleavage=False position=-1 index=1 amino_acid=R cleavage=False position=-1 index=-3 amino_acid=L cleavage=True position=-1 index=1 amino_acid=P cleavage=False position=-1 index=1 amino_acid=E cleavage=False position=-1 index=1 amino_acid=D cleavage=False position=-1 index=1 amino_acid=Q cleavage=False position=-1 index=1 amino_acid=K cleavage=False position=-1 index=1 amino_acid=R cleavage=False position=-1 index=-3 amino_acid=W cleavage=True position=-1 index=1 amino_acid=P cleavage=False position=-1 index=1 amino_acid=E cleavage=False position=-1 index=1 amino_acid=D cleavage=False position=-1 index=1 amino_acid=Q cleavage=False position=-1 index=1 amino_acid=K cleavage=False position=-1 index=1 amino_acid=R cleavage=False position=-1 index=-3 amino_acid=Y cleavage=True position=-1 index=1 amino_acid=P cleavage=False position=-1 index=1 amino_acid=E cleavage=False position=-1 index=1 amino_acid=D cleavage=False position=-1 index=1 amino_acid=Q cleavage=False position=-1 index=1 amino_acid=K cleavage=False position=-1 index=1 amino_acid=R cleavage=False position=-1 index=-1 amino_acid=T cleavage=False position=-1 index=-3 amino_acid=F cleavage=True position=-1 index=1 amino_acid=P cleavage=False position=-1 index=1 amino_acid=E cleavage=False position=-1 index=1 amino_acid=D cleavage=False position=-1 index=1 amino_acid=Q cleavage=False position=-1 index=1 amino_acid=K cleavage=False position=-1 index=1 amino_acid=R cleavage=False position=-1 index=-3 amino_acid=L cleavage=True position=-1 index=1 amino_acid=P cleavage=False position=-1 index=1 amino_acid=E cleavage=False position=-1 index=1 amino_acid=D cleavage=False position=-1 index=1 amino_acid=Q cleavage=False position=-1 index=1 amino_acid=K cleavage=False position=-1 index=1 amino_acid=R cleavage=False position=-1 index=-3 amino_acid=W cleavage=True position=-1 index=1 amino_acid=P cleavage=False position=-1 index=1 amino_acid=E cleavage=False position=-1 index=1 amino_acid=D cleavage=False position=-1 index=1 amino_acid=Q cleavage=False position=-1 index=1 amino_acid=K cleavage=False position=-1 index=1 amino_acid=R cleavage=False position=-1 index=-3 amino_acid=Y cleavage=True position=-1 index=1 amino_acid=P cleavage=False position=-1 index=1 amino_acid=E cleavage=False position=-1 index=1 amino_acid=D cleavage=False position=-1 index=1 amino_acid=Q cleavage=False position=-1 index=1 amino_acid=K cleavage=False position=-1 index=1 amino_acid=R cleavage=False position=-1 ] , Id: 6 Name: Caspase-2 Ratio Miscleavage: 0.00% Rules: [index=0 amino_acid=D cleavage=False position=1 index=-1 amino_acid=H cleavage=False position=-1 index=-2 amino_acid=E cleavage=False position=-1 index=-3 amino_acid=D cleavage=True position=-1 index=1 amino_acid=P cleavage=False position=-1 index=1 amino_acid=E cleavage=False position=-1 index=1 amino_acid=D cleavage=False position=-1 index=1 amino_acid=Q cleavage=False position=-1 index=1 amino_acid=K cleavage=False position=-1 index=1 amino_acid=R cleavage=False position=-1 index=-1 amino_acid=A cleavage=False position=-1 index=-2 amino_acid=V cleavage=False position=-1 index=-3 amino_acid=D cleavage=True position=-1 index=1 amino_acid=P cleavage=False position=-1 index=1 amino_acid=E cleavage=False position=-1 index=1 amino_acid=D cleavage=False position=-1 index=1 amino_acid=Q cleavage=False position=-1 index=1 amino_acid=K cleavage=False position=-1 index=1 amino_acid=R cleavage=False position=-1 ] , Id: 7 Name: Caspase-3 Ratio Miscleavage: 0.00% Rules: [index=0 amino_acid=D cleavage=False position=1 index=-1 amino_acid=V cleavage=False position=-1 index=-2 amino_acid=E cleavage=False position=-1 index=-3 amino_acid=D cleavage=True position=-1 index=1 amino_acid=P cleavage=False position=-1 index=1 amino_acid=E cleavage=False position=-1 index=1 amino_acid=D cleavage=False position=-1 index=1 amino_acid=Q cleavage=False position=-1 index=1 amino_acid=K cleavage=False position=-1 index=1 amino_acid=R cleavage=False position=-1 index=-1 amino_acid=Q cleavage=False position=-1 index=-2 amino_acid=M cleavage=False position=-1 index=-3 amino_acid=D cleavage=True position=-1 index=1 amino_acid=P cleavage=False position=-1 index=1 amino_acid=E cleavage=False position=-1 index=1 amino_acid=D cleavage=False position=-1 index=1 amino_acid=Q cleavage=False position=-1 index=1 amino_acid=K cleavage=False position=-1 index=1 amino_acid=R cleavage=False position=-1 ] , Id: 8 Name: Caspase-4 Ratio Miscleavage: 0.00% Rules: [index=0 amino_acid=D cleavage=False position=1 index=-1 amino_acid=V cleavage=False position=-1 index=-2 amino_acid=E cleavage=False position=-1 index=-3 amino_acid=L cleavage=True position=-1 index=1 amino_acid=P cleavage=False position=-1 index=1 amino_acid=E cleavage=False position=-1 index=1 amino_acid=D cleavage=False position=-1 index=1 amino_acid=Q cleavage=False position=-1 index=1 amino_acid=K cleavage=False position=-1 index=1 amino_acid=R cleavage=False position=-1 index=-1 amino_acid=H cleavage=False position=-1 index=-2 amino_acid=E cleavage=False position=-1 index=-3 amino_acid=L cleavage=True position=-1 index=1 amino_acid=P cleavage=False position=-1 index=1 amino_acid=E cleavage=False position=-1 index=1 amino_acid=D cleavage=False position=-1 index=1 amino_acid=Q cleavage=False position=-1 index=1 amino_acid=K cleavage=False position=-1 index=1 amino_acid=R cleavage=False position=-1 index=-3 amino_acid=W cleavage=True position=-1 index=1 amino_acid=P cleavage=False position=-1 index=1 amino_acid=E cleavage=False position=-1 index=1 amino_acid=D cleavage=False position=-1 index=1 amino_acid=Q cleavage=False position=-1 index=1 amino_acid=K cleavage=False position=-1 index=1 amino_acid=R cleavage=False position=-1 ] , Id: 9 Name: Caspase-5 Ratio Miscleavage: 0.00% Rules: [index=0 amino_acid=D cleavage=False position=1 index=-1 amino_acid=H cleavage=False position=-1 index=-2 amino_acid=E cleavage=False position=-1 index=-3 amino_acid=L cleavage=True position=-1 index=-3 amino_acid=W cleavage=True position=-1 ] , Id: 10 Name: Caspase-6 Ratio Miscleavage: 0.00% Rules: [index=0 amino_acid=D cleavage=False position=1 index=-1 amino_acid=I cleavage=False position=-1 index=-2 amino_acid=E cleavage=False position=-1 index=-3 amino_acid=V cleavage=True position=-1 index=1 amino_acid=P cleavage=False position=-1 index=1 amino_acid=E cleavage=False position=-1 index=1 amino_acid=D cleavage=False position=-1 index=1 amino_acid=Q cleavage=False position=-1 index=1 amino_acid=K cleavage=False position=-1 index=1 amino_acid=R cleavage=False position=-1 index=-1 amino_acid=H cleavage=False position=-1 index=-2 amino_acid=E cleavage=False position=-1 index=-3 amino_acid=V cleavage=True position=-1 index=1 amino_acid=P cleavage=False position=-1 index=1 amino_acid=E cleavage=False position=-1 index=1 amino_acid=D cleavage=False position=-1 index=1 amino_acid=Q cleavage=False position=-1 index=1 amino_acid=K cleavage=False position=-1 index=1 amino_acid=R cleavage=False position=-1 ] , Id: 11 Name: Caspase-7 Ratio Miscleavage: 0.00% Rules: [index=0 amino_acid=D cleavage=False position=1 index=-1 amino_acid=V cleavage=False position=-1 index=-2 amino_acid=E cleavage=False position=-1 index=-3 amino_acid=D cleavage=True position=-1 index=1 amino_acid=P cleavage=False position=-1 index=1 amino_acid=E cleavage=False position=-1 index=1 amino_acid=D cleavage=False position=-1 index=1 amino_acid=Q cleavage=False position=-1 index=1 amino_acid=K cleavage=False position=-1 index=1 amino_acid=R cleavage=False position=-1 ] , Id: 12 Name: Caspase-8 Ratio Miscleavage: 0.00% Rules: [index=0 amino_acid=D cleavage=False position=1 index=-1 amino_acid=T cleavage=False position=-1 index=-2 amino_acid=E cleavage=False position=-1 index=-3 amino_acid=I cleavage=True position=-1 index=1 amino_acid=P cleavage=False position=-1 index=1 amino_acid=E cleavage=False position=-1 index=1 amino_acid=D cleavage=False position=-1 index=1 amino_acid=Q cleavage=False position=-1 index=1 amino_acid=K cleavage=False position=-1 index=1 amino_acid=R cleavage=False position=-1 index=-3 amino_acid=L cleavage=True position=-1 index=1 amino_acid=P cleavage=False position=-1 index=1 amino_acid=E cleavage=False position=-1 index=1 amino_acid=D cleavage=False position=-1 index=1 amino_acid=Q cleavage=False position=-1 index=1 amino_acid=K cleavage=False position=-1 index=1 amino_acid=R cleavage=False position=-1 ] , Id: 13 Name: Caspase-9 Ratio Miscleavage: 0.00% Rules: [index=0 amino_acid=D cleavage=False position=1 index=-1 amino_acid=H cleavage=False position=-1 index=-2 amino_acid=E cleavage=False position=-1 index=-3 amino_acid=L cleavage=True position=-1 ] , Id: 14 Name: Caspase-10 Ratio Miscleavage: 0.00% Rules: [index=0 amino_acid=D cleavage=False position=1 index=-1 amino_acid=A cleavage=False position=-1 index=-2 amino_acid=E cleavage=False position=-1 index=-3 amino_acid=I cleavage=True position=-1 ] , Id: 15 Name: Chymotrypsin-high Ratio Miscleavage: 0.00% Rules: [index=0 amino_acid=F cleavage=True position=1 index=1 amino_acid=P cleavage=False position=-1 , index=0 amino_acid=Y cleavage=True position=1 index=1 amino_acid=P cleavage=False position=-1 , index=0 amino_acid=W cleavage=True position=1 index=1 amino_acid=M cleavage=False position=-1 index=1 amino_acid=P cleavage=False position=-1 ] , Id: 16 Name: Chymotrypsin-low Ratio Miscleavage: 0.00% Rules: [index=0 amino_acid=F cleavage=True position=1 index=1 amino_acid=P cleavage=False position=-1 , index=0 amino_acid=L cleavage=True position=1 index=1 amino_acid=P cleavage=False position=-1 , index=0 amino_acid=Y cleavage=True position=1 index=1 amino_acid=P cleavage=False position=-1 , index=0 amino_acid=W cleavage=True position=1 index=1 amino_acid=M cleavage=False position=-1 index=1 amino_acid=P cleavage=False position=-1 , index=0 amino_acid=M cleavage=True position=1 index=1 amino_acid=P cleavage=False position=-1 index=1 amino_acid=Y cleavage=False position=-1 , index=0 amino_acid=H cleavage=True position=1 index=1 amino_acid=D cleavage=False position=-1 index=1 amino_acid=M cleavage=False position=-1 index=1 amino_acid=P cleavage=False position=-1 index=1 amino_acid=W cleavage=False position=-1 ] , Id: 17 Name: Clostripain Ratio Miscleavage: 0.00% Rules: [index=0 amino_acid=R cleavage=True position=1 ] , Id: 18 Name: CNBr Ratio Miscleavage: 0.00% Rules: [index=0 amino_acid=M cleavage=True position=1 ] , Id: 19 Name: Enterokinase Ratio Miscleavage: 0.00% Rules: [index=0 amino_acid=K cleavage=False position=1 index=-1 amino_acid=D cleavage=False position=-1 index=-2 amino_acid=D cleavage=False position=-1 index=-3 amino_acid=D cleavage=False position=-1 index=-4 amino_acid=D cleavage=True position=-1 index=-4 amino_acid=E cleavage=True position=-1 index=-3 amino_acid=E cleavage=False position=-1 index=-4 amino_acid=D cleavage=True position=-1 index=-4 amino_acid=E cleavage=True position=-1 index=-2 amino_acid=E cleavage=False position=-1 index=-3 amino_acid=D cleavage=False position=-1 index=-4 amino_acid=D cleavage=True position=-1 index=-4 amino_acid=E cleavage=True position=-1 index=-3 amino_acid=E cleavage=False position=-1 index=-4 amino_acid=D cleavage=True position=-1 index=-4 amino_acid=E cleavage=True position=-1 index=-1 amino_acid=E cleavage=False position=-1 index=-2 amino_acid=D cleavage=False position=-1 index=-3 amino_acid=D cleavage=False position=-1 index=-4 amino_acid=D cleavage=True position=-1 index=-4 amino_acid=E cleavage=True position=-1 index=-3 amino_acid=E cleavage=False position=-1 index=-4 amino_acid=D cleavage=True position=-1 index=-4 amino_acid=E cleavage=True position=-1 index=-2 amino_acid=E cleavage=False position=-1 index=-3 amino_acid=D cleavage=False position=-1 index=-4 amino_acid=D cleavage=True position=-1 index=-4 amino_acid=E cleavage=True position=-1 index=-3 amino_acid=E cleavage=False position=-1 index=-4 amino_acid=D cleavage=True position=-1 index=-4 amino_acid=E cleavage=True position=-1 ] , Id: 20 Name: Factor-Xa Ratio Miscleavage: 0.00% Rules: [index=0 amino_acid=R cleavage=False position=1 index=-1 amino_acid=G cleavage=False position=-1 index=-2 amino_acid=D cleavage=False position=-1 index=-3 amino_acid=A cleavage=True position=-1 index=-3 amino_acid=F cleavage=True position=-1 index=-3 amino_acid=I cleavage=True position=-1 index=-3 amino_acid=L cleavage=True position=-1 index=-3 amino_acid=V cleavage=True position=-1 index=-3 amino_acid=W cleavage=True position=-1 index=-3 amino_acid=G cleavage=True position=-1 index=-3 amino_acid=T cleavage=True position=-1 index=-2 amino_acid=E cleavage=False position=-1 index=-3 amino_acid=A cleavage=True position=-1 index=-3 amino_acid=F cleavage=True position=-1 index=-3 amino_acid=I cleavage=True position=-1 index=-3 amino_acid=L cleavage=True position=-1 index=-3 amino_acid=V cleavage=True position=-1 index=-3 amino_acid=W cleavage=True position=-1 index=-3 amino_acid=G cleavage=True position=-1 index=-3 amino_acid=T cleavage=True position=-1 ] , Id: 21 Name: Ficin Ratio Miscleavage: 0.00% Rules: [index=0 amino_acid=G cleavage=False position=1 index=-1 amino_acid=A cleavage=True position=-1 index=-1 amino_acid=V cleavage=True position=-1 index=-1 amino_acid=I cleavage=True position=-1 index=-1 amino_acid=L cleavage=True position=-1 index=-1 amino_acid=F cleavage=True position=-1 index=-1 amino_acid=Y cleavage=True position=-1 index=-1 amino_acid=W cleavage=True position=-1 , index=0 amino_acid=S cleavage=False position=1 index=-1 amino_acid=A cleavage=True position=-1 index=-1 amino_acid=V cleavage=True position=-1 index=-1 amino_acid=I cleavage=True position=-1 index=-1 amino_acid=L cleavage=True position=-1 index=-1 amino_acid=F cleavage=True position=-1 index=-1 amino_acid=Y cleavage=True position=-1 index=-1 amino_acid=W cleavage=True position=-1 , index=0 amino_acid=E cleavage=False position=1 index=-1 amino_acid=A cleavage=True position=-1 index=-1 amino_acid=V cleavage=True position=-1 index=-1 amino_acid=I cleavage=True position=-1 index=-1 amino_acid=L cleavage=True position=-1 index=-1 amino_acid=F cleavage=True position=-1 index=-1 amino_acid=Y cleavage=True position=-1 index=-1 amino_acid=W cleavage=True position=-1 , index=0 amino_acid=Y cleavage=False position=1 index=-1 amino_acid=A cleavage=True position=-1 index=-1 amino_acid=V cleavage=True position=-1 index=-1 amino_acid=I cleavage=True position=-1 index=-1 amino_acid=L cleavage=True position=-1 index=-1 amino_acid=F cleavage=True position=-1 index=-1 amino_acid=Y cleavage=True position=-1 index=-1 amino_acid=W cleavage=True position=-1 ] , Id: 22 Name: Formic-acid Ratio Miscleavage: 0.00% Rules: [index=0 amino_acid=D cleavage=True position=1 ] , Id: 23 Name: Glu-C Ratio Miscleavage: 0.00% Rules: [index=0 amino_acid=D cleavage=True position=1 , index=0 amino_acid=E cleavage=True position=1 ] , Id: 24 Name: Glutamyl-endopeptidase Ratio Miscleavage: 0.00% Rules: [index=0 amino_acid=E cleavage=True position=1 ] , Id: 25 Name: Granzyme-B Ratio Miscleavage: 0.00% Rules: [index=0 amino_acid=D cleavage=False position=1 index=-1 amino_acid=P cleavage=False position=-1 index=-2 amino_acid=E cleavage=False position=-1 index=-3 amino_acid=I cleavage=True position=-1 ] , Id: 26 Name: Hydroxylamine Ratio Miscleavage: 0.00% Rules: [index=0 amino_acid=N cleavage=False position=1 index=1 amino_acid=G cleavage=True position=-1 ] , Id: 27 Name: Iodosobenzoic-acid Ratio Miscleavage: 0.00% Rules: [index=0 amino_acid=W cleavage=True position=1 ] , Id: 28 Name: Lys-C Ratio Miscleavage: 0.00% Rules: [index=0 amino_acid=K cleavage=True position=1 ] , Id: 29 Name: Lys-N Ratio Miscleavage: 0.00% Rules: [index=0 amino_acid=K cleavage=True position=0 ] , Id: 30 Name: Neutrophil-elastase Ratio Miscleavage: 0.00% Rules: [index=0 amino_acid=A cleavage=True position=1 , index=0 amino_acid=V cleavage=True position=1 ] , Id: 31 Name: NTCB Ratio Miscleavage: 0.00% Rules: [index=0 amino_acid=C cleavage=True position=0 ] , Id: 32 Name: Papain Ratio Miscleavage: 0.00% Rules: [index=0 amino_acid=K cleavage=False position=1 index=-1 amino_acid=A cleavage=True position=-1 index=1 amino_acid=V cleavage=False position=-1 index=-1 amino_acid=V cleavage=True position=-1 index=1 amino_acid=V cleavage=False position=-1 index=-1 amino_acid=I cleavage=True position=-1 index=1 amino_acid=V cleavage=False position=-1 index=-1 amino_acid=L cleavage=True position=-1 index=1 amino_acid=V cleavage=False position=-1 index=-1 amino_acid=F cleavage=True position=-1 index=1 amino_acid=V cleavage=False position=-1 index=-1 amino_acid=Y cleavage=True position=-1 index=1 amino_acid=V cleavage=False position=-1 index=-1 amino_acid=W cleavage=True position=-1 index=1 amino_acid=V cleavage=False position=-1 , index=0 amino_acid=R cleavage=False position=1 index=-1 amino_acid=A cleavage=True position=-1 index=1 amino_acid=V cleavage=False position=-1 index=-1 amino_acid=V cleavage=True position=-1 index=1 amino_acid=V cleavage=False position=-1 index=-1 amino_acid=I cleavage=True position=-1 index=1 amino_acid=V cleavage=False position=-1 index=-1 amino_acid=L cleavage=True position=-1 index=1 amino_acid=V cleavage=False position=-1 index=-1 amino_acid=F cleavage=True position=-1 index=1 amino_acid=V cleavage=False position=-1 index=-1 amino_acid=Y cleavage=True position=-1 index=1 amino_acid=V cleavage=False position=-1 index=-1 amino_acid=W cleavage=True position=-1 index=1 amino_acid=V cleavage=False position=-1 ] , Id: 33 Name: Pepsin-pH1.3 Ratio Miscleavage: 0.00% Rules: [index=0 amino_acid=F cleavage=True position=0 index=1 amino_acid=P cleavage=False position=-1 index=-1 amino_acid=R cleavage=False position=-1 index=-2 amino_acid=P cleavage=False position=-1 index=-3 amino_acid=H cleavage=False position=-1 index=-3 amino_acid=K cleavage=False position=-1 index=-3 amino_acid=R cleavage=False position=-1 , index=0 amino_acid=L cleavage=True position=0 index=1 amino_acid=P cleavage=False position=-1 index=-1 amino_acid=R cleavage=False position=-1 index=-2 amino_acid=P cleavage=False position=-1 index=-3 amino_acid=H cleavage=False position=-1 index=-3 amino_acid=K cleavage=False position=-1 index=-3 amino_acid=R cleavage=False position=-1 , index=0 amino_acid=F cleavage=True position=1 index=2 amino_acid=P cleavage=False position=-1 index=-1 amino_acid=P cleavage=False position=-1 index=-2 amino_acid=H cleavage=False position=-1 index=-2 amino_acid=K cleavage=False position=-1 index=-2 amino_acid=R cleavage=False position=-1 , index=0 amino_acid=L cleavage=True position=1 index=2 amino_acid=P cleavage=False position=-1 index=-1 amino_acid=P cleavage=False position=-1 index=-2 amino_acid=H cleavage=False position=-1 index=-2 amino_acid=K cleavage=False position=-1 index=-2 amino_acid=R cleavage=False position=-1 ] , Id: 34 Name: Pepsin-pH>=2 Ratio Miscleavage: 0.00% Rules: [index=0 amino_acid=F cleavage=True position=0 index=1 amino_acid=P cleavage=False position=-1 index=-1 amino_acid=R cleavage=False position=-1 index=-2 amino_acid=P cleavage=False position=-1 index=-3 amino_acid=H cleavage=False position=-1 index=-3 amino_acid=K cleavage=False position=-1 index=-3 amino_acid=R cleavage=False position=-1 , index=0 amino_acid=L cleavage=True position=0 index=1 amino_acid=P cleavage=False position=-1 index=-1 amino_acid=R cleavage=False position=-1 index=-2 amino_acid=P cleavage=False position=-1 index=-3 amino_acid=H cleavage=False position=-1 index=-3 amino_acid=K cleavage=False position=-1 index=-3 amino_acid=R cleavage=False position=-1 , index=0 amino_acid=W cleavage=True position=0 index=1 amino_acid=P cleavage=False position=-1 index=-1 amino_acid=R cleavage=False position=-1 index=-2 amino_acid=P cleavage=False position=-1 index=-3 amino_acid=H cleavage=False position=-1 index=-3 amino_acid=K cleavage=False position=-1 index=-3 amino_acid=R cleavage=False position=-1 , index=0 amino_acid=Y cleavage=True position=0 index=1 amino_acid=P cleavage=False position=-1 index=-1 amino_acid=R cleavage=False position=-1 index=-2 amino_acid=P cleavage=False position=-1 index=-3 amino_acid=H cleavage=False position=-1 index=-3 amino_acid=K cleavage=False position=-1 index=-3 amino_acid=R cleavage=False position=-1 , index=0 amino_acid=F cleavage=True position=1 index=2 amino_acid=P cleavage=False position=-1 index=-1 amino_acid=P cleavage=False position=-1 index=-2 amino_acid=H cleavage=False position=-1 index=-2 amino_acid=K cleavage=False position=-1 index=-2 amino_acid=R cleavage=False position=-1 , index=0 amino_acid=L cleavage=True position=1 index=2 amino_acid=P cleavage=False position=-1 index=-1 amino_acid=P cleavage=False position=-1 index=-2 amino_acid=H cleavage=False position=-1 index=-2 amino_acid=K cleavage=False position=-1 index=-2 amino_acid=R cleavage=False position=-1 , index=0 amino_acid=W cleavage=True position=1 index=2 amino_acid=P cleavage=False position=-1 index=-1 amino_acid=P cleavage=False position=-1 index=-2 amino_acid=H cleavage=False position=-1 index=-2 amino_acid=K cleavage=False position=-1 index=-2 amino_acid=R cleavage=False position=-1 , index=0 amino_acid=Y cleavage=True position=1 index=2 amino_acid=P cleavage=False position=-1 index=-1 amino_acid=P cleavage=False position=-1 index=-2 amino_acid=H cleavage=False position=-1 index=-2 amino_acid=K cleavage=False position=-1 index=-2 amino_acid=R cleavage=False position=-1 ] , Id: 35 Name: Proline-endopeptidase Ratio Miscleavage: 0.00% Rules: [index=0 amino_acid=P cleavage=False position=1 index=-1 amino_acid=H cleavage=True position=-1 index=1 amino_acid=P cleavage=False position=-1 index=-1 amino_acid=K cleavage=True position=-1 index=1 amino_acid=P cleavage=False position=-1 index=-1 amino_acid=R cleavage=True position=-1 index=1 amino_acid=P cleavage=False position=-1 ] , Id: 36 Name: Proteinase-K Ratio Miscleavage: 0.00% Rules: [index=0 amino_acid=F cleavage=True position=1 , index=0 amino_acid=W cleavage=True position=1 , index=0 amino_acid=Y cleavage=True position=1 , index=0 amino_acid=T cleavage=True position=1 , index=0 amino_acid=E cleavage=True position=1 , index=0 amino_acid=A cleavage=True position=1 , index=0 amino_acid=V cleavage=True position=1 , index=0 amino_acid=L cleavage=True position=1 , index=0 amino_acid=I cleavage=True position=1 ] , Id: 37 Name: Staphylococcal-peptidase-I Ratio Miscleavage: 0.00% Rules: [index=0 amino_acid=E cleavage=True position=1 index=-1 amino_acid=E cleavage=False position=-1 ] , Id: 38 Name: Thermolysin Ratio Miscleavage: 0.00% Rules: [index=0 amino_acid=A cleavage=True position=0 index=1 amino_acid=P cleavage=False position=-1 index=-1 amino_acid=D cleavage=False position=-1 index=-1 amino_acid=E cleavage=False position=-1 , index=0 amino_acid=F cleavage=True position=0 index=1 amino_acid=P cleavage=False position=-1 index=-1 amino_acid=D cleavage=False position=-1 index=-1 amino_acid=E cleavage=False position=-1 , index=0 amino_acid=I cleavage=True position=0 index=1 amino_acid=P cleavage=False position=-1 index=-1 amino_acid=D cleavage=False position=-1 index=-1 amino_acid=E cleavage=False position=-1 , index=0 amino_acid=L cleavage=True position=0 index=1 amino_acid=P cleavage=False position=-1 index=-1 amino_acid=D cleavage=False position=-1 index=-1 amino_acid=E cleavage=False position=-1 , index=0 amino_acid=M cleavage=True position=0 index=1 amino_acid=P cleavage=False position=-1 index=-1 amino_acid=D cleavage=False position=-1 index=-1 amino_acid=E cleavage=False position=-1 , index=0 amino_acid=V cleavage=True position=0 index=1 amino_acid=P cleavage=False position=-1 index=-1 amino_acid=D cleavage=False position=-1 index=-1 amino_acid=E cleavage=False position=-1 ] , Id: 39 Name: Thrombin Ratio Miscleavage: 0.00% Rules: [index=0 amino_acid=R cleavage=False position=1 index=-1 amino_acid=G cleavage=False position=-1 index=1 amino_acid=G cleavage=True position=-1 index=-1 amino_acid=P cleavage=False position=-1 index=-2 amino_acid=A cleavage=False position=-1 index=-3 amino_acid=A cleavage=True position=-1 index=1 amino_acid=D cleavage=False position=-1 index=1 amino_acid=E cleavage=False position=-1 index=2 amino_acid=D cleavage=False position=-1 index=2 amino_acid=E cleavage=False position=-1 index=-3 amino_acid=F cleavage=True position=-1 index=1 amino_acid=D cleavage=False position=-1 index=1 amino_acid=E cleavage=False position=-1 index=2 amino_acid=D cleavage=False position=-1 index=2 amino_acid=E cleavage=False position=-1 index=-3 amino_acid=I cleavage=True position=-1 index=1 amino_acid=D cleavage=False position=-1 index=1 amino_acid=E cleavage=False position=-1 index=2 amino_acid=D cleavage=False position=-1 index=2 amino_acid=E cleavage=False position=-1 index=-3 amino_acid=L cleavage=True position=-1 index=1 amino_acid=D cleavage=False position=-1 index=1 amino_acid=E cleavage=False position=-1 index=2 amino_acid=D cleavage=False position=-1 index=2 amino_acid=E cleavage=False position=-1 index=-3 amino_acid=V cleavage=True position=-1 index=1 amino_acid=D cleavage=False position=-1 index=1 amino_acid=E cleavage=False position=-1 index=2 amino_acid=D cleavage=False position=-1 index=2 amino_acid=E cleavage=False position=-1 index=-3 amino_acid=W cleavage=True position=-1 index=1 amino_acid=D cleavage=False position=-1 index=1 amino_acid=E cleavage=False position=-1 index=2 amino_acid=D cleavage=False position=-1 index=2 amino_acid=E cleavage=False position=-1 index=-3 amino_acid=G cleavage=True position=-1 index=1 amino_acid=D cleavage=False position=-1 index=1 amino_acid=E cleavage=False position=-1 index=2 amino_acid=D cleavage=False position=-1 index=2 amino_acid=E cleavage=False position=-1 index=-3 amino_acid=T cleavage=True position=-1 index=1 amino_acid=D cleavage=False position=-1 index=1 amino_acid=E cleavage=False position=-1 index=2 amino_acid=D cleavage=False position=-1 index=2 amino_acid=E cleavage=False position=-1 index=-2 amino_acid=F cleavage=False position=-1 index=-3 amino_acid=A cleavage=True position=-1 index=1 amino_acid=D cleavage=False position=-1 index=1 amino_acid=E cleavage=False position=-1 index=2 amino_acid=D cleavage=False position=-1 index=2 amino_acid=E cleavage=False position=-1 index=-3 amino_acid=F cleavage=True position=-1 index=1 amino_acid=D cleavage=False position=-1 index=1 amino_acid=E cleavage=False position=-1 index=2 amino_acid=D cleavage=False position=-1 index=2 amino_acid=E cleavage=False position=-1 index=-3 amino_acid=I cleavage=True position=-1 index=1 amino_acid=D cleavage=False position=-1 index=1 amino_acid=E cleavage=False position=-1 index=2 amino_acid=D cleavage=False position=-1 index=2 amino_acid=E cleavage=False position=-1 index=-3 amino_acid=L cleavage=True position=-1 index=1 amino_acid=D cleavage=False position=-1 index=1 amino_acid=E cleavage=False position=-1 index=2 amino_acid=D cleavage=False position=-1 index=2 amino_acid=E cleavage=False position=-1 index=-3 amino_acid=V cleavage=True position=-1 index=1 amino_acid=D cleavage=False position=-1 index=1 amino_acid=E cleavage=False position=-1 index=2 amino_acid=D cleavage=False position=-1 index=2 amino_acid=E cleavage=False position=-1 index=-3 amino_acid=W cleavage=True position=-1 index=1 amino_acid=D cleavage=False position=-1 index=1 amino_acid=E cleavage=False position=-1 index=2 amino_acid=D cleavage=False position=-1 index=2 amino_acid=E cleavage=False position=-1 index=-3 amino_acid=G cleavage=True position=-1 index=1 amino_acid=D cleavage=False position=-1 index=1 amino_acid=E cleavage=False position=-1 index=2 amino_acid=D cleavage=False position=-1 index=2 amino_acid=E cleavage=False position=-1 index=-3 amino_acid=T cleavage=True position=-1 index=1 amino_acid=D cleavage=False position=-1 index=1 amino_acid=E cleavage=False position=-1 index=2 amino_acid=D cleavage=False position=-1 index=2 amino_acid=E cleavage=False position=-1 index=-2 amino_acid=I cleavage=False position=-1 index=-3 amino_acid=A cleavage=True position=-1 index=1 amino_acid=D cleavage=False position=-1 index=1 amino_acid=E cleavage=False position=-1 index=2 amino_acid=D cleavage=False position=-1 index=2 amino_acid=E cleavage=False position=-1 index=-3 amino_acid=F cleavage=True position=-1 index=1 amino_acid=D cleavage=False position=-1 index=1 amino_acid=E cleavage=False position=-1 index=2 amino_acid=D cleavage=False position=-1 index=2 amino_acid=E cleavage=False position=-1 index=-3 amino_acid=I cleavage=True position=-1 index=1 amino_acid=D cleavage=False position=-1 index=1 amino_acid=E cleavage=False position=-1 index=2 amino_acid=D cleavage=False position=-1 index=2 amino_acid=E cleavage=False position=-1 index=-3 amino_acid=L cleavage=True position=-1 index=1 amino_acid=D cleavage=False position=-1 index=1 amino_acid=E cleavage=False position=-1 index=2 amino_acid=D cleavage=False position=-1 index=2 amino_acid=E cleavage=False position=-1 index=-3 amino_acid=V cleavage=True position=-1 index=1 amino_acid=D cleavage=False position=-1 index=1 amino_acid=E cleavage=False position=-1 index=2 amino_acid=D cleavage=False position=-1 index=2 amino_acid=E cleavage=False position=-1 index=-3 amino_acid=W cleavage=True position=-1 index=1 amino_acid=D cleavage=False position=-1 index=1 amino_acid=E cleavage=False position=-1 index=2 amino_acid=D cleavage=False position=-1 index=2 amino_acid=E cleavage=False position=-1 index=-3 amino_acid=G cleavage=True position=-1 index=1 amino_acid=D cleavage=False position=-1 index=1 amino_acid=E cleavage=False position=-1 index=2 amino_acid=D cleavage=False position=-1 index=2 amino_acid=E cleavage=False position=-1 index=-3 amino_acid=T cleavage=True position=-1 index=1 amino_acid=D cleavage=False position=-1 index=1 amino_acid=E cleavage=False position=-1 index=2 amino_acid=D cleavage=False position=-1 index=2 amino_acid=E cleavage=False position=-1 index=-2 amino_acid=L cleavage=False position=-1 index=-3 amino_acid=A cleavage=True position=-1 index=1 amino_acid=D cleavage=False position=-1 index=1 amino_acid=E cleavage=False position=-1 index=2 amino_acid=D cleavage=False position=-1 index=2 amino_acid=E cleavage=False position=-1 index=-3 amino_acid=F cleavage=True position=-1 index=1 amino_acid=D cleavage=False position=-1 index=1 amino_acid=E cleavage=False position=-1 index=2 amino_acid=D cleavage=False position=-1 index=2 amino_acid=E cleavage=False position=-1 index=-3 amino_acid=I cleavage=True position=-1 index=1 amino_acid=D cleavage=False position=-1 index=1 amino_acid=E cleavage=False position=-1 index=2 amino_acid=D cleavage=False position=-1 index=2 amino_acid=E cleavage=False position=-1 index=-3 amino_acid=L cleavage=True position=-1 index=1 amino_acid=D cleavage=False position=-1 index=1 amino_acid=E cleavage=False position=-1 index=2 amino_acid=D cleavage=False position=-1 index=2 amino_acid=E cleavage=False position=-1 index=-3 amino_acid=V cleavage=True position=-1 index=1 amino_acid=D cleavage=False position=-1 index=1 amino_acid=E cleavage=False position=-1 index=2 amino_acid=D cleavage=False position=-1 index=2 amino_acid=E cleavage=False position=-1 index=-3 amino_acid=W cleavage=True position=-1 index=1 amino_acid=D cleavage=False position=-1 index=1 amino_acid=E cleavage=False position=-1 index=2 amino_acid=D cleavage=False position=-1 index=2 amino_acid=E cleavage=False position=-1 index=-3 amino_acid=G cleavage=True position=-1 index=1 amino_acid=D cleavage=False position=-1 index=1 amino_acid=E cleavage=False position=-1 index=2 amino_acid=D cleavage=False position=-1 index=2 amino_acid=E cleavage=False position=-1 index=-3 amino_acid=T cleavage=True position=-1 index=1 amino_acid=D cleavage=False position=-1 index=1 amino_acid=E cleavage=False position=-1 index=2 amino_acid=D cleavage=False position=-1 index=2 amino_acid=E cleavage=False position=-1 index=-2 amino_acid=V cleavage=False position=-1 index=-3 amino_acid=A cleavage=True position=-1 index=1 amino_acid=D cleavage=False position=-1 index=1 amino_acid=E cleavage=False position=-1 index=2 amino_acid=D cleavage=False position=-1 index=2 amino_acid=E cleavage=False position=-1 index=-3 amino_acid=F cleavage=True position=-1 index=1 amino_acid=D cleavage=False position=-1 index=1 amino_acid=E cleavage=False position=-1 index=2 amino_acid=D cleavage=False position=-1 index=2 amino_acid=E cleavage=False position=-1 index=-3 amino_acid=I cleavage=True position=-1 index=1 amino_acid=D cleavage=False position=-1 index=1 amino_acid=E cleavage=False position=-1 index=2 amino_acid=D cleavage=False position=-1 index=2 amino_acid=E cleavage=False position=-1 index=-3 amino_acid=L cleavage=True position=-1 index=1 amino_acid=D cleavage=False position=-1 index=1 amino_acid=E cleavage=False position=-1 index=2 amino_acid=D cleavage=False position=-1 index=2 amino_acid=E cleavage=False position=-1 index=-3 amino_acid=V cleavage=True position=-1 index=1 amino_acid=D cleavage=False position=-1 index=1 amino_acid=E cleavage=False position=-1 index=2 amino_acid=D cleavage=False position=-1 index=2 amino_acid=E cleavage=False position=-1 index=-3 amino_acid=W cleavage=True position=-1 index=1 amino_acid=D cleavage=False position=-1 index=1 amino_acid=E cleavage=False position=-1 index=2 amino_acid=D cleavage=False position=-1 index=2 amino_acid=E cleavage=False position=-1 index=-3 amino_acid=G cleavage=True position=-1 index=1 amino_acid=D cleavage=False position=-1 index=1 amino_acid=E cleavage=False position=-1 index=2 amino_acid=D cleavage=False position=-1 index=2 amino_acid=E cleavage=False position=-1 index=-3 amino_acid=T cleavage=True position=-1 index=1 amino_acid=D cleavage=False position=-1 index=1 amino_acid=E cleavage=False position=-1 index=2 amino_acid=D cleavage=False position=-1 index=2 amino_acid=E cleavage=False position=-1 index=-2 amino_acid=W cleavage=False position=-1 index=-3 amino_acid=A cleavage=True position=-1 index=1 amino_acid=D cleavage=False position=-1 index=1 amino_acid=E cleavage=False position=-1 index=2 amino_acid=D cleavage=False position=-1 index=2 amino_acid=E cleavage=False position=-1 index=-3 amino_acid=F cleavage=True position=-1 index=1 amino_acid=D cleavage=False position=-1 index=1 amino_acid=E cleavage=False position=-1 index=2 amino_acid=D cleavage=False position=-1 index=2 amino_acid=E cleavage=False position=-1 index=-3 amino_acid=I cleavage=True position=-1 index=1 amino_acid=D cleavage=False position=-1 index=1 amino_acid=E cleavage=False position=-1 index=2 amino_acid=D cleavage=False position=-1 index=2 amino_acid=E cleavage=False position=-1 index=-3 amino_acid=L cleavage=True position=-1 index=1 amino_acid=D cleavage=False position=-1 index=1 amino_acid=E cleavage=False position=-1 index=2 amino_acid=D cleavage=False position=-1 index=2 amino_acid=E cleavage=False position=-1 index=-3 amino_acid=V cleavage=True position=-1 index=1 amino_acid=D cleavage=False position=-1 index=1 amino_acid=E cleavage=False position=-1 index=2 amino_acid=D cleavage=False position=-1 index=2 amino_acid=E cleavage=False position=-1 index=-3 amino_acid=W cleavage=True position=-1 index=1 amino_acid=D cleavage=False position=-1 index=1 amino_acid=E cleavage=False position=-1 index=2 amino_acid=D cleavage=False position=-1 index=2 amino_acid=E cleavage=False position=-1 index=-3 amino_acid=G cleavage=True position=-1 index=1 amino_acid=D cleavage=False position=-1 index=1 amino_acid=E cleavage=False position=-1 index=2 amino_acid=D cleavage=False position=-1 index=2 amino_acid=E cleavage=False position=-1 index=-3 amino_acid=T cleavage=True position=-1 index=1 amino_acid=D cleavage=False position=-1 index=1 amino_acid=E cleavage=False position=-1 index=2 amino_acid=D cleavage=False position=-1 index=2 amino_acid=E cleavage=False position=-1 index=-2 amino_acid=G cleavage=False position=-1 index=-3 amino_acid=A cleavage=True position=-1 index=1 amino_acid=D cleavage=False position=-1 index=1 amino_acid=E cleavage=False position=-1 index=2 amino_acid=D cleavage=False position=-1 index=2 amino_acid=E cleavage=False position=-1 index=-3 amino_acid=F cleavage=True position=-1 index=1 amino_acid=D cleavage=False position=-1 index=1 amino_acid=E cleavage=False position=-1 index=2 amino_acid=D cleavage=False position=-1 index=2 amino_acid=E cleavage=False position=-1 index=-3 amino_acid=I cleavage=True position=-1 index=1 amino_acid=D cleavage=False position=-1 index=1 amino_acid=E cleavage=False position=-1 index=2 amino_acid=D cleavage=False position=-1 index=2 amino_acid=E cleavage=False position=-1 index=-3 amino_acid=L cleavage=True position=-1 index=1 amino_acid=D cleavage=False position=-1 index=1 amino_acid=E cleavage=False position=-1 index=2 amino_acid=D cleavage=False position=-1 index=2 amino_acid=E cleavage=False position=-1 index=-3 amino_acid=V cleavage=True position=-1 index=1 amino_acid=D cleavage=False position=-1 index=1 amino_acid=E cleavage=False position=-1 index=2 amino_acid=D cleavage=False position=-1 index=2 amino_acid=E cleavage=False position=-1 index=-3 amino_acid=W cleavage=True position=-1 index=1 amino_acid=D cleavage=False position=-1 index=1 amino_acid=E cleavage=False position=-1 index=2 amino_acid=D cleavage=False position=-1 index=2 amino_acid=E cleavage=False position=-1 index=-3 amino_acid=G cleavage=True position=-1 index=1 amino_acid=D cleavage=False position=-1 index=1 amino_acid=E cleavage=False position=-1 index=2 amino_acid=D cleavage=False position=-1 index=2 amino_acid=E cleavage=False position=-1 index=-3 amino_acid=T cleavage=True position=-1 index=1 amino_acid=D cleavage=False position=-1 index=1 amino_acid=E cleavage=False position=-1 index=2 amino_acid=D cleavage=False position=-1 index=2 amino_acid=E cleavage=False position=-1 index=-2 amino_acid=T cleavage=False position=-1 index=-3 amino_acid=A cleavage=True position=-1 index=1 amino_acid=D cleavage=False position=-1 index=1 amino_acid=E cleavage=False position=-1 index=2 amino_acid=D cleavage=False position=-1 index=2 amino_acid=E cleavage=False position=-1 index=-3 amino_acid=F cleavage=True position=-1 index=1 amino_acid=D cleavage=False position=-1 index=1 amino_acid=E cleavage=False position=-1 index=2 amino_acid=D cleavage=False position=-1 index=2 amino_acid=E cleavage=False position=-1 index=-3 amino_acid=I cleavage=True position=-1 index=1 amino_acid=D cleavage=False position=-1 index=1 amino_acid=E cleavage=False position=-1 index=2 amino_acid=D cleavage=False position=-1 index=2 amino_acid=E cleavage=False position=-1 index=-3 amino_acid=L cleavage=True position=-1 index=1 amino_acid=D cleavage=False position=-1 index=1 amino_acid=E cleavage=False position=-1 index=2 amino_acid=D cleavage=False position=-1 index=2 amino_acid=E cleavage=False position=-1 index=-3 amino_acid=V cleavage=True position=-1 index=1 amino_acid=D cleavage=False position=-1 index=1 amino_acid=E cleavage=False position=-1 index=2 amino_acid=D cleavage=False position=-1 index=2 amino_acid=E cleavage=False position=-1 index=-3 amino_acid=W cleavage=True position=-1 index=1 amino_acid=D cleavage=False position=-1 index=1 amino_acid=E cleavage=False position=-1 index=2 amino_acid=D cleavage=False position=-1 index=2 amino_acid=E cleavage=False position=-1 index=-3 amino_acid=G cleavage=True position=-1 index=1 amino_acid=D cleavage=False position=-1 index=1 amino_acid=E cleavage=False position=-1 index=2 amino_acid=D cleavage=False position=-1 index=2 amino_acid=E cleavage=False position=-1 index=-3 amino_acid=T cleavage=True position=-1 index=1 amino_acid=D cleavage=False position=-1 index=1 amino_acid=E cleavage=False position=-1 index=2 amino_acid=D cleavage=False position=-1 index=2 amino_acid=E cleavage=False position=-1 ] , Id: 40 Name: Thrombin-SG Ratio Miscleavage: 0.00% Rules: [index=0 amino_acid=R cleavage=False position=1 index=-1 amino_acid=P cleavage=False position=-1 index=-2 amino_acid=V cleavage=False position=-1 index=-3 amino_acid=L cleavage=False position=-1 index=1 amino_acid=G cleavage=False position=-1 index=2 amino_acid=S cleavage=True position=-1 ] , Id: 41 Name: Tobacco-Etch-Virus Ratio Miscleavage: 0.00% Rules: [index=0 amino_acid=Q cleavage=False position=1 index=1 amino_acid=G cleavage=False position=-1 index=-2 amino_acid=Y cleavage=False position=-1 index=-5 amino_acid=E cleavage=True position=-1 index=1 amino_acid=S cleavage=False position=-1 index=-2 amino_acid=Y cleavage=False position=-1 index=-5 amino_acid=E cleavage=True position=-1 ] , Id: 42 Name: Trypsin Ratio Miscleavage: 0.00% Rules: [index=0 amino_acid=K cleavage=True position=1 index=1 amino_acid=P cleavage=False position=-1 index=-1 amino_acid=W cleavage=True position=-1 index=1 amino_acid=D cleavage=True position=-1 index=-1 amino_acid=C cleavage=False position=-1 index=-1 amino_acid=D cleavage=False position=-1 index=1 amino_acid=H cleavage=True position=-1 index=-1 amino_acid=C cleavage=False position=-1 index=1 amino_acid=Y cleavage=True position=-1 index=-1 amino_acid=C cleavage=False position=-1 , index=0 amino_acid=R cleavage=True position=1 index=1 amino_acid=P cleavage=False position=-1 index=-1 amino_acid=M cleavage=True position=-1 index=1 amino_acid=K cleavage=True position=-1 index=-1 amino_acid=C cleavage=False position=-1 index=1 amino_acid=H cleavage=True position=-1 index=-1 amino_acid=R cleavage=False position=-1 index=1 amino_acid=R cleavage=True position=-1 index=-1 amino_acid=R cleavage=False position=-1 ] , Id: 43 Name: Asp-N Endopeptidase Ratio Miscleavage: 0.00% Rules: [index=0 amino_acid=D cleavage=True position=0 ] , Id: 44 Name: ProAlanase Ratio Miscleavage: 0.00% Rules: [index=0 amino_acid=A cleavage=True position=1 , index=0 amino_acid=P cleavage=True position=1 ] , Id: 45 Name: Elastase Ratio Miscleavage: 0.00% Rules: [index=0 amino_acid=A cleavage=True position=1 , index=0 amino_acid=V cleavage=True position=1 , index=0 amino_acid=S cleavage=True position=1 , index=0 amino_acid=G cleavage=True position=1 , index=0 amino_acid=L cleavage=True position=1 , index=0 amino_acid=I cleavage=True position=1 ] , Id: 46 Name: aLP Ratio Miscleavage: 0.00% Rules: [index=0 amino_acid=T cleavage=True position=1 , index=0 amino_acid=A cleavage=True position=1 , index=0 amino_acid=S cleavage=True position=1 , index=0 amino_acid=V cleavage=True position=1 ] ]
All available enzymes in RPG.
- rpg.RapidPeptidesGenerator.create_enzymes_to_use(enzymes, miscleavage)[source]
Create the list of chosen
Enzyme
to use. Each enzyme can be associated to a miscleavage value.- Parameters:
enzymes (list(str)) – enzymes ids or names chosen by user
miscleavage (list(float)) – associated miscleavage values
- Returns:
list of enzyme’s id with associated miscleavage values
- Return type:
list(int)
- rpg.RapidPeptidesGenerator.get_enzymes_to_use(mode, id_enz_selected, miscleavage)[source]
Get the list of chosen
Enzyme
to use. Each enzyme (and associated miscleavage value) are inputed by user. If there is a problem, user is interrogated again.- Parameters:
mode (str) – Digestion mode. If ‘concurrent’, no miscleavage values are used
enzymes (list(str)) – enzyme’s ids or names chosen by user
miscleavage (list(float)) – associated miscleavage values
- Returns:
list of enzyme’s id with associated miscleavage values
- Return type:
list(int)
- rpg.RapidPeptidesGenerator.restricted_enzyme_id(enz_id)[source]
Restrict input enzyme id to a str corresponding to an enzyme.
- Parameters:
mc_val (str) – value to test
- Returns:
the inputed enzyme id
- Return type:
str
- rpg.RapidPeptidesGenerator.restricted_float(mc_val)[source]
Restricts input miscleavage value to a float between 0 and 100.
- Parameters:
mc_val (float) – value to test
- Returns:
the inputed value if correct
- Return type:
float
- Raises:
custom ValueError – if value is not between 0 and 100
custom TypeError – if value is not a float
3.1.3. rpg.context module
3.1.4. rpg.core module
Contains generic functions and global variables used by RPG
- rpg.core.AA_MASS_AVERAGE = {'#': 0.0, '*': 0.0, 'A': 71.0788, 'B': 0.0, 'C': 103.1388, 'D': 115.0886, 'E': 129.1155, 'F': 147.1766, 'G': 57.0519, 'H': 137.1411, 'I': 113.1594, 'J': 113.1594, 'K': 128.1741, 'L': 113.1594, 'M': 131.1926, 'N': 114.1038, 'O': 237.3018, 'P': 97.1167, 'Q': 128.1307, 'R': 156.1875, 'S': 87.0782, 'T': 101.1051, 'U': 150.0388, 'V': 99.1326, 'W': 186.2132, 'X': 0.0, 'Y': 163.176, 'Z': 0.0}
Average mass of all amino acids.
- rpg.core.AA_MASS_MONO = {'#': 0.0, '*': 0.0, 'A': 71.037113805, 'B': 0.0, 'C': 103.009184505, 'D': 115.026943065, 'E': 129.042593135, 'F': 147.068413945, 'G': 57.021463735, 'H': 137.058911875, 'I': 113.084064015, 'J': 113.084064015, 'K': 128.09496305, 'L': 113.084064015, 'M': 131.040484645, 'N': 114.04292747, 'O': 237.147726925, 'P': 97.052763875, 'Q': 128.05857754, 'R': 156.10111105, 'S': 87.032028435, 'T': 101.047678505, 'U': 150.953633405, 'V': 99.068413945, 'W': 186.07931298, 'X': 0.0, 'Y': 163.063328575, 'Z': 0.0}
Monoisotopic mass of all amino acids. From https://proteomicsresource.washington.edu/protocols06/masses.php
- rpg.core.AA_PKA_IPC = {'C': 8.297, 'Cterm': 2.383, 'D': 3.887, 'E': 4.317, 'H': 6.018, 'K': 10.517, 'Nterm': 9.564, 'R': 12.503, 'Y': 10.071}
//isoelectric.org/theory.html for details).
- Type:
pKa of important amino acid to compute pI (from IPC_peptide. See http
- rpg.core.AA_PKA_IPC_2 = {'C': 9.454, 'Cterm': 2.977, 'D': 3.969, 'E': 4.507, 'H': 6.439, 'K': 8.165, 'Nterm': 7.947, 'R': 11.493, 'Y': 9.153}
//www.ipc2-isoelectric-point.org/ for details).
- Type:
pKa of important amino acid to compute pI (from IPC_peptide2. See http
- rpg.core.AA_PKA_S = {'C': 8.3, 'Cterm': 3.1, 'D': 4.1, 'E': 4.1, 'H': 6.0, 'K': 10.8, 'Nterm': 8.0, 'R': 12.5, 'Y': 10.9}
pKa of important amino acid to compute pI (from Stryer).
- rpg.core.AMINOACIDS = ['A', 'C', 'D', 'E', 'F', 'G', 'H', 'I', 'J', 'K', 'L', 'M', 'N', 'O', 'P', 'Q', 'R', 'S', 'T', 'U', 'V', 'W', 'Y', 'B', 'X', 'Z', '#', '*']
All character accepted in a peptide.
- rpg.core.WATER_MASS = 18.01528
Mass of a water molecule.
- rpg.core.WATER_MASS_MONO = 18.0105647
Monoisotopic mass of a water molecule.
- rpg.core.get_header(fmt='fasta')[source]
Construct a header for output file in csv or tsv.
- Parameters:
fmt (str) – format of header
- Returns:
formatted header
- Return type:
str or None
Informations on the header are:
Original_header No_pep Enzyme Cleav_pos Pep_size Pep_mass pI Seq
No header for fasta or other format.
- rpg.core.handle_errors(message='', err=1, error_type='')[source]
Custom handling of errors and warnings.
- Parameters:
message (str) – error message to print
err (int) – Type of message
error_type (str) – header of error to print
Type of message is:
0 for critical error (exit)
1 for warning (no exit, default)
2 for print in stderr
- rpg.core.next_read(file, offset_start, offset_end)[source]
- Return each sequence between offsets range of a file
as a tuple (header, seq) using a generator. Can be fasta or fastq, gzipped or not.
- Parameters:
file (str) – fasta/fastq file to read
offset_start (int) – offset in the file from where to read
offset_end (int) – offset in the file until where to read
- rpg.core.output_results(output_file, all_seq_digested, fmt, quiet, verbose)[source]
Output results of digestion in file and optionally in stdout.
- Parameters:
output_file (str) – the file where to print results, if exist
all_seq_digested (list(list(
ResultOneDigestion
))) – results of digestionsfmt (str) – output format (csv, tsv or fasta)
quiet (bool) – quiet mode, no stdout message
verbose (int) – verbosity level
3.1.5. rpg.digest module
Contains class and function needed to perform a digestion
- class rpg.digest.ResultOneDigestion(enzyme_name, peptides=None, nb_cleavage=0, pos_miscleavage=None)[source]
Bases:
object
Result of the digestion of one sequence by one enzyme.
- Parameters:
enzyme_name (str) – name of the enzyme used
peptides (list(
Peptide
)) – all resulting peptides after digestionnb_cleavage (int) – number of cleavage that occurs
pos_miscleavage (list(int)) – position of miscleavage that occurs
- add_miscleavage(new_pos_miscleavage)[source]
Add a miscleavage to
self.pos_miscleavage
.- Parameters:
new_pos_miscleavage (int) – position of miscleavage
- add_peptide(pep)[source]
Add a peptide to
self.peptides
.- Parameters:
pep (
Peptide
) – peptide to add
- get_cleavage_pos()[source]
Get positions of cleavage as a string.
- Returns:
positions of cleavage
- Return type:
str
- get_miscleavage_pos()[source]
Get positions of miscleavage as a string.
- Returns:
positions of miscleavage
- Return type:
str
- get_more_info()[source]
Return informations and statistics about this digestion, i.e. number of (mis)-cleavages and positions, miscleavage ratio, size of the smallest peptide and first and last peptide.
- Returns:
informations and statistics ready to be printed
- Return type:
str
- get_nb_miscleavage()[source]
Get the number of miscleavages that occurs on this digestion.
- Returns:
number of miscleavage
- Return type:
int
- get_ratio_miscleavage()[source]
Get ratio of miscleavage.
- Returns:
ratio of miscleavage
- Return type:
float
- get_smallest_peptide()[source]
Get the (first) smallest peptide of
self.peptides
.- Returns:
the smallest peptide
- Return type:
- merge(other)[source]
Fuse two
ResultOneDigestion
by adding toself
the peptides ofother
and changing theirEnzyme
. It also updateself.nb_cleavage
andself.pos_miscleavage
.- Parameters:
other (
ResultOneDigestion
) – object to fuse with self
- rpg.digest.concurrent_digest(seq, enz, aa_pka, aa_mass, water_mass)[source]
Concurrently digest a sequence with all Enzymes at the same time.
- Parameters:
- Returns:
result of the digestion
- Return type:
list(
ResultOneDigestion
)
- rpg.digest.digest_from_input(input_data, input_type, enz, mode, aa_pka, aa_mass, water_mass, nb_proc=1)[source]
Digest all sequences of input data according to selected enzymes and mode. Can be done in parallel using nb_proc argument.
- Parameters:
input_data (str) – either a sequence or the path of a file of sequence (fasta/fastq, gzipped or not)
input_type (str) – either ‘sequence’ or ‘file’
enz (list(
Enzyme
)) – enzymes to digest withmode (str) – digestion mode (concurrent / sequential)
aa_pka (dict()) – pKa values (IPC / IPC2 / Stryer)
aa_mass (dict()) – masse values (average / monoisotopic)
water_mass (int) – masse value of water (average / monoisotopic)
nb_proc (int (default: 1)) – number of process to run in parallel
- Returns:
result of digestions
- Return type:
list(list(
ResultOneDigestion
))
- rpg.digest.digest_one_sequence(seq, enz, mode, aa_pka, aa_mass, water_mass)[source]
Launch a digest procedure on one sequence.
- Parameters:
sequence (
Sequence
) – sequence to digestenz (list(
Enzyme
)) – enzymes to digest withmode (str) – digestion mode (concurrent / sequential)
aa_pka (dict()) – pKa values (IPC / IPC2 / Stryer)
aa_mass (dict()) – masse values (average / monoisotopic)
water_mass (int) – masse value of water (average / monoisotopic)
- Returns:
result of the digestion
- Return type:
list(
ResultOneDigestion
)
- rpg.digest.digest_part(offset_start, offset_end, file, enz, mode, aa_pka, aa_mass, water_mass)[source]
- Main parallelized function that digest each sequence of a file
in an offset range.
- Parameters:
offset_start (int) – where to start taking sequences in the file
offset_end (int) – where to stop taking sequences in the file
file (string) – the filename of the file where to take sequences from
enz (list(
Enzyme
)) – enzymes to digest withmode (str) – digestion mode (concurrent / sequential)
aa_pka (dict()) – pKa values (IPC / IPC2 / Stryer)
aa_mass (dict()) – masse values (average / monoisotopic)
water_mass (int) – masse value of water (average / monoisotopic)
- rpg.digest.one_digest(pep, enz, aa_pka, aa_mass, water_mass)[source]
Digest a peptide with an enzyme.
- Parameters:
- Returns:
result of the digestion
- Return type:
- rpg.digest.sequential_digest(seq, enz, aa_pka, aa_mass, water_mass)[source]
Sequentially digest a sequence with all Enzymes, one by one.
- Parameters:
- Returns:
result of the digestion
- Return type:
list(
ResultOneDigestion
)
- rpg.digest.theoretical_peptides(results_digestion, mc_val)[source]
Add in results_digestion the resulting peptides of mis cleaved positions
- Parameters:
results_digestion (list(list(
ResultOneDigestion
))) – result of digestionsmc_val (dict(enzyme_name: value)) – maxima number of mis cleavage per enzyme
3.1.6. rpg.enzyme module
Contains class and functions related to enzymes definition and use
- class rpg.enzyme.Enzyme(id_, name, rules, ratio_miscleavage=0)[source]
Bases:
object
Definition of an cleaving enzyme containing specific rules.
- Parameters:
id (int) – id of the enzyme
name (str) – name of the enzyme
rules (list(
Rule
)) – cleaving rulesratio_miscleavage (float) – miscleavage ratio
- rpg.enzyme.check_enzyme_name(name_new_enz, all_name_enz)[source]
Validate the name of a new enzyme.
- Parameters:
name_new_enz (str) – name of the new enzyme
all_name_enz (list(str)) – names of already created enzymes
- Returns:
True if name is correct
- Return type:
bool
Enzyme name should not contains whitespace character (’ ‘, \t, \n, \r, \f, \v), be empty, a digit or be already used.
- rpg.enzyme.delete_enzyme(all_enzymes, name)[source]
Delete an enzyme from user file
- Parameters:
all_enzymes (list(
Enzyme
)) – all already existing enzymesname (str) – name or id of the enzyme to delete
Warning
Partially tested, remove by ID can’t be tested
- rpg.enzyme.get_enz_name(all_enzymes, name)[source]
Get the proper name of an enzyme
- Parameters:
all_enzymes (list(
Enzyme
)) – all already existing enzymesname (str) – name or id of the enzyme
- Returns:
The real name of an enzyme
- Return type:
str
- rpg.enzyme.user_creation_enzyme(all_enzymes)[source]
Text-mod form to input a new enzyme.
Warning
Not tested
Warning
It could be a problem to immediately use the new enzyme (see in-code warning)
- rpg.enzyme.user_creation_enzyme_non_interactive(all_enzymes, name_new_enz, rules, exceptions=None)[source]
One-line input a new enzyme.
- Parameters:
all_enzymes (list(
Enzyme
)) – all already existing enzymesname (str) – name of the enzyme to create
rules (list(str)) – rules defining the new enzyme
exceptions (list(str)) – exceptions defining the new enzyme
Warning
It could be a problem to immediately use the new enzyme (see in-code warning)
3.1.7. rpg.enzymes_definition module
Definition of default enzymes in RPG
3.1.8. rpg.rule module
Contains class and functions related to definition of cleaving rules
- class rpg.rule.Rule(index, amino_acid, cleavage, pos)[source]
Bases:
object
Definition of a principal rule defining where a cleavage occurs.
- Parameters:
index (signed int) – position where to look for a specific amino acid
amino_acid (char) – amino acid to look for
cleavage (bool) – cleavage or not at this position on this amino acid
pos (int) – cleavage before (0) of after (1) amino acid. -1 for unused value
- Variables:
rules (list(
Rule
)) – additional sub-rules of this rule
- contains(other)[source]
Test if another rule is contained in sub-rules without taking into account sub-rules nor `cleavage` and return the sub-rule if founded.
- contains_any_level(other, ret=False)[source]
Test if another rule is contained within without taking into account sub-rules nor `cleavage` no matter what level.
- Parameters:
other (
Rule
) – rule to compare withret (bool) – previous ret value (default: False)
- Returns:
True if rule is included, False otherwise
- Return type:
bool
- equ(other)[source]
Test equality with another rule without taking into account sub-rules nor `cleavage`.
- Parameters:
other (
Rule
) – rule to compare with- Returns:
True if rules are equal, False otherwise
- Return type:
bool
- Note:
use ‘==’ for complete equality including sub-rules.
- format_a_rule(prev_name, prev_com)[source]
Format the rule in Python.
- Parameters:
prev_name (str) – name of the upper rule
prev_com (str) – comment of the upper rule
- Returns:
this rule in Python
- Return type:
str
- format_rule(prev_name='', prev_com=' # ')[source]
Format the whole rule, including sub-rules, in Python, ready to be written.
- Parameters:
prev_name (str) – name of the upper rule
prev_com (str) – comment of the upper rule
- Returns:
the whole rule in Python
- Return type:
str
- rpg.rule.add_missing_rule(main_rule, dict_of_rule, rule_to_add)[source]
Add a rule of an exception in a main rule
- Parameters:
main_rule (
Rule
) – the main rule to add indict_of_rule (Dict of pos/val) – Raw rules of an exception
rule_to_add (Tuple(pos/val)) – The rule to add
- rpg.rule.add_rule(rules_list, a_rule)[source]
Add (recursively) a rule to a list of rules.
- Parameters:
Warning
Modify rules_list :python:
- rpg.rule.check_rule(exprule)[source]
Check if a rule is properly inputed.
- Parameters:
exprule (str) – the raw expression of a rule
- Returns:
exprule if it is correct, empty char otherwise
- Return type:
str
- rpg.rule.create_rules(all_rules)[source]
Create proper rules for an enzyme from raw rules.
- Parameters:
all_rules (list(
Rule
)) – rules corresponding to the enzyme- Returns:
rules ready to populate an
Enzyme
- Return type:
list(
Rule
)
This function handle ‘ or ‘ keywords, multiple parenthesis, sort the simples rules, create sub-rules, etc. The output is ready to be used to create an
Enzyme
.
- rpg.rule.find_missing_rule(main_rule, dict_of_rule, depth=0)[source]
Find all missing rules of an exception in a main rule
- Parameters:
main_rule (
Rule
) – the main rule to search indict_of_rule (Dict of pos/val) – Raw rules of an exception
depth (int) – Depth of missing rule (default: 0)
- Returns:
Missing rules and their positions and depth (key)
- Return type:
defaultdict(list)
- rpg.rule.find_rechable_pos(main_rule, dict_of_rule)[source]
Find all positions reachable on a main rule according to several rules.
- rpg.rule.handle_rule(seq, pos, a_rule, cleavage)[source]
Recursive handling of a
Rule
determining if a sequence must be cleavageted at a given position according to the rule.- Parameters:
seq (str) – sequence to test
pos (int) – position on the sequence
a_rule (
Rule
) – the rulecleavage (bool) – boolean telling if it must be cleavageted or not
- Returns:
True if sequence must be cleavageted
- Return type:
bool or None
3.1.9. rpg.sequence module
Contains classes and function related to sequences
- class rpg.sequence.Peptide(header, sequence, enzyme_name, aa_pka, aa_mass, water_mass, nb_peptide=0, position=0)[source]
Bases:
object
Definition of a peptide, containing the header of its original sequence, an amino acid sequence, the name of the enzyme used to produce it and more informations.
- Parameters:
header (str) – header of the peptide
sequence (str) – sequence in amino acids
enzyme_name (str) – name of the enzyme used
aa_pka (dict()) – pKa values (IPC / IPC2 / Stryer)
aa_mass (dict()) – masse values (average / monoisotopic)
water_mass (dict()) – masse value of water (average / monoisotopic)
nb_peptide (int) – number of this peptide (default: 0)
position (int) – position of cleavage on the original sequence (default: 0)
- Variables:
size (int) – size of the peptide
mass (float) – mass of the peptide
p_i (float) – pI of the peptide
- class rpg.sequence.Sequence(header, sequence)[source]
Bases:
object
Definition of an amino acid sequence to digest.
- Parameters:
header (str) – header of the sequence
sequence (str) – sequence itself
- rpg.sequence.check_sequence(seq)[source]
Validate an input sequence. Each amino acid should be in
AMINOACIDS
.- Parameters:
seq (str) – the sequence to check
- Returns:
Sequence in UPPERCASE
- Return type:
str
3.1.10. Module contents
Contains everything related to RPG software