etc/qss/gendata.py

23 ofile = open(ofilename,'w')  variable
25 ofile.write("#\n")
26 ofile.write("# Generated by gendata\n")
27 ofile.write("# This file assumes that all rotamers are represented at all\n")
28 ofile.write("# positions.  However, the input format can allow for a \n")
29 ofile.write("# flexible representation, since each rotamer is labeled\n")
30 ofile.write("# with the corresponding amino acid label.\n")
31 ofile.write("#\n")
32 ofile.write("\n")
34 ofile.write("#\n")
35 ofile.write("# Number of peptides\n")
36 ofile.write("#\n")
37 ofile.write("param n := " + `numPeptides` + ";\n")
38 ofile.write("\n")
40 ofile.write("#\n")
41 ofile.write("# The amino acids that are considered for each side chain site\n")
42 ofile.write("#\n")
43 ofile.write("set ValidAminoAcids := \n")
46     ofile.write("(" + `i+1` + "," + `j+1` + ")\n")
47 ofile.write(";\n")
48 ofile.write("\n")
50 ofile.write("#\n")
51 ofile.write("# Boltzman Protein-Rotamer energies\n")
52 ofile.write("#\n")
53 ofile.write("param B_inter := [*,*]\n")
57     ofile.write(`i+1` + " " + `j+1` + " " + `val` + "\n")
58 ofile.write(";\n")
59 ofile.write("\n")
61 ofile.write("#\n")
62 ofile.write("# Boltzman Rotamer-Rotamer energies\n")
63 ofile.write("#\n")
64 ofile.write("param B_intra := [*,*,*,*]\n")
71            ofile.write(`i+1` + " " + `j+1` + " " + `ii+1` + " " + `jj+1` + " " + `val` + "\n")
72 ofile.write(";\n")
73 ofile.write("\n")
75 ofile.write("#\n")
76 ofile.write("# Number of rotamers for each peptide\n")
77 ofile.write("#\n")
78 ofile.write("param rCount := \n")
83   ofile.write(`i+1` + " " + `total` + "\n")
84 ofile.write(";\n")
85 ofile.write("\n")
88 ofile.write("#\n")
89 ofile.write("# Protein-Rotamer energies and Rotamer amino acid labels\n")
90 ofile.write("#\n")
91 ofile.write("param: ValidInterIndicesRR: E_inter RotamerLabel :=\n")
98     ofile.write(`i+1` + " " + `j+1` + " " + `val` + " " + `aa` + "\n")
103 ofile.write(";\n")
104 ofile.write("\n")
106 ofile.write("#\n")
107 ofile.write("# Rotamer-Rotamer energies\n")
108 ofile.write("#\n")
109 ofile.write("param: ValidIntraIndicesRR: E_intra := \n")
116            ofile.write(`i+1` + " " + `j+1` + " " + `ii+1` + " " + `jj+1` + " " + `val` + "\n")
117 ofile.write(";\n")
118 ofile.write("\n")