def InteractionNetworkFidelity(native_file, native_index, prediction_file,
prediction_index):
res_struct = pdb_utils.PDBStruct()
res_struct.load(native_file, native_index)
res_raw_seq = res_struct.raw_sequence()
sol_struct = pdb_utils.PDBStruct()
sol_struct.load(prediction_file, prediction_index)
sol_raw_seq = sol_struct.raw_sequence()
if (sol_raw_seq != res_raw_seq):
sys.stderr.write("ERROR Result sequence != Solution sequence!\n")
sys.stderr.write("DATA Solution sequence --> '%s'\n" % sol_raw_seq)
sys.stderr.write("DATA Result sequence --> '%s'\n" % res_raw_seq)
return (-1)
# computes the RMSD
comparer = pdb_utils.PDBComparer()
rmsd = comparer.rmsd(sol_struct, res_struct)
INF_ALL = comparer.INF(sol_struct, res_struct, type="ALL")
DI_ALL = rmsd / INF_ALL
INF_WC = comparer.INF(sol_struct, res_struct, type="PAIR_2D")
INF_NWC = comparer.INF(sol_struct, res_struct, type="PAIR_3D")
INF_STACK = comparer.INF(sol_struct, res_struct, type="STACK")
# return (rmsd,DI_ALL, INF_ALL, INF_WC, INF_NWC,INF_STACK)
return (rmsd, DI_ALL, INF_ALL)
def calc_RMSD(native_file,
native_index,
prediction_file,
prediction_index,
PVALUE="-"):
res_struct = pdb_utils.PDBStruct()
res_struct.load(native_file, native_index)
res_raw_seq = res_struct.raw_sequence()
sol_struct = pdb_utils.PDBStruct()
sol_struct.load(prediction_file, prediction_index)
sol_raw_seq = sol_struct.raw_sequence()
if (sol_raw_seq != res_raw_seq):
sys.stderr.write("ERROR Result sequence != Solution sequence!\n")
sys.stderr.write("DATA Solution sequence --> '%s'\n" % sol_raw_seq)
sys.stderr.write("DATA Result sequence --> '%s'\n" % res_raw_seq)
return (-1)
# computes the RMSD
comparer = pdb_utils.PDBComparer()
rmsd = comparer.rmsd(sol_struct, res_struct)
sys.stderr.write("INFO Partial RMSD --> %f\n" % rmsd)
pvalue = comparer.pvalue(rmsd, len(sol_raw_seq), PVALUE)
sys.stderr.write("INFO Partial P-Value --> %e\n" % pvalue)
return (rmsd, pvalue)
