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 ] ]

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(int)) – enzymes ids 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(int)) – enzyme’s ids 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.list_enzyme()[source]

Print all available enzymes

rpg.RapidPeptidesGenerator.main()[source]

Launcher of RapidPeptidesGenerator

rpg.RapidPeptidesGenerator.restricted_enzyme_id(enz_id)[source]

Restrict input enzyme id to an int corresponding to an enzyme.

Parameters:

mc_val (int) – value to test

Returns:

the inputed enzyme id

Return type:

int

Raises:
  • custom ValueError – if id does not correspond to any enzyme
  • custom TypeError – if value is not an int
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}

Mass of all amino acids.

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.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 digestions
  • fmt (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 digestion
  • nb_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:Peptide
inc_nb_cleavage()[source]

Increase self.nb_cleavage by 1.

merge(other)[source]

Fuse two ResultOneDigestion by adding to self the peptides of other and changing their Enzyme. It also update self.nb_cleavage and self.pos_miscleavage.

Parameters:other (ResultOneDigestion) – object to fuse with self
pop_peptides()[source]

Empty self.peptides and returns all peptides.

Returns:all the peptides
Return type:list(Peptide)
rpg.digest.concurrent_digest(seq, enz, aa_pka)[source]

Concurrently digest a sequence with all Enzymes at the same time.

Parameters:
  • seq (Sequence) – sequence to digest
  • enz (list(Enzyme)) – enzymes to digest with
  • aa_pka (str) – pKa values (IPC / Stryer)
Returns:

result of the digestion

Return type:

list(ResultOneDigestion)

rpg.digest.digest_from_input(input_data, input_type, enz, mode, aa_pka, 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 with
  • mode (str) – digestion mode (concurrent / sequential)
  • aa_pka (str) – pKa values (IPC / Stryer)
  • 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)[source]

Launch a digest procedure on one sequence.

Parameters:
  • sequence (Sequence) – sequence to digest
  • enz (list(Enzyme)) – enzymes to digest with
  • mode (str) – digestion mode (concurrent / sequential)
  • aa_pka (str) – pKa values (IPC / Stryer)
Returns:

result of the digestion

Return type:

list(ResultOneDigestion)

rpg.digest.digest_part(offset_start, offset_end, file, enz, mode, aa_pka)[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 with
  • mode (str) – digestion mode (concurrent / sequential)
  • aa_pka (str) – pKa values (IPC / Stryer)
rpg.digest.one_digest(pep, enz, aa_pka)[source]

Digest a peptide with an enzyme.

Parameters:
  • pep (Peptide) – peptide to digest
  • enz (Enzyme) – enzyme to digest with
  • aa_pka (str) – pKa values (IPC / Stryer)
Returns:

result of the digestion

Return type:

ResultOneDigestion

rpg.digest.sequential_digest(seq, enz, aa_pka)[source]

Sequentially digest a sequence with all Enzymes, one by one.

Parameters:
  • seq (Sequence) – sequence to digest
  • enz (list(Enzyme)) – enzymes to digest with
  • aa_pka (str) – pKa values (IPC / Stryer)
Returns:

result of the digestion

Return type:

list(ResultOneDigestion)

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 rules
  • ratio_miscleavage (float) – miscleavage ratio
write_enzyme_in_user_file(enz_file='/home/docs/rpg_user.py')[source]

Write enzyme to user’s enzyme file as a Python function.

Parameters:enz_file (str) – location of user file (default: ~/rpg_user.py)
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 or be already used.

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)

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 contains in sub-rules without taking into account sub-rules nor `cleavage` and return the sub-rule if founded.

Parameters:other (Rule) – rule to compare with
Returns:the sub-rule is founded, None otherwise
Return type:Rule
contains_any_level(other, ret=False)[source]

Test if another rule is contains within without taking into account sub-rules nor `cleavage` no matter what level.

Parameters:
  • other (Rule) – rule to compare with
  • ret (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

get_all_headers()[source]

Format header of the rule and sub-rules in Python.

Returns:the complete header in Python
Return type:str
get_header()[source]

Format header of the rule in Python.

Returns:header of this 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 in
  • dict_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:
  • rules_list (list(Rule)) – the list of rules where to add
  • a_rule (Rule) – the rule to add

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 in
  • dict_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.

param main_rule:
 the main rule to search in
type main_rule:Rule
param dict_of_rule:
 Raw rules of an exception
type dict_of_rule:
 Dict of pos/val
return:Reachable Rule and their depth (key)
rtype:dict()
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 rule
  • cleavage (bool) – boolean telling if it must be cleavageted or not
Returns:

True if sequence must be cleavageted

Return type:

bool or None

rpg.rule.split_complex_rule(a_rule)[source]

Split a complex rules containing ‘ or ‘ into simpler rules.

Parameters:a_rule (str) – the rule to split
Returns:the simple rules
Return type:list(str)

3.1.9. rpg.sequence module

Contains classes and function related to sequences

class rpg.sequence.Peptide(header, sequence, enzyme_name, aa_pka, 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 (str) – pKa values (IPC / Stryer)
  • 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
get_isoelectric_point()[source]

Compute isoelectric point (pI) of the peptide using binary search.

Returns:computed pI
Return type:float
Note:This function used AA_PKA
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