Commit 8e2a131c by Mustafa Tekpinar

Commented bfactor-related unused code.

parent 83ba006d
......@@ -962,33 +962,33 @@ def doit(inAli,mutFile,retMet,bFile,fFile,n,N, jetfile, pdbfile, normWeightMode,
df.to_csv(prot+"_jet.res", header=True, index=None, sep='\t', mode='w')
print(df)
#If a real pdb file is given, calculate or get Bfactors for the residues.
if(((normWeightMode=='bfactor') or (normWeightMode=='maxtracebfactor') or (normWeightMode=='maxbfactortrace'))):
isCalc = True
if (pdbfile == None):
print("ERROR: There is not any pdb file to calculate or get Bfactors!")
sys.exit(-1)
else:
if (isCalc):
print("Computing Bfactors from the user-provided pdb file using ANM with all modes.")
#Original
# bfactors = calcBfactors(pdbfile, outfile=None, nmodes=None, \
# #If a real pdb file is given, calculate or get Bfactors for the residues.
# if(((normWeightMode=='bfactor') or (normWeightMode=='maxtracebfactor') or (normWeightMode=='maxbfactortrace'))):
# isCalc = True
# if (pdbfile == None):
# print("ERROR: There is not any pdb file to calculate or get Bfactors!")
# sys.exit(-1)
# else:
# if (isCalc):
# print("Computing Bfactors from the user-provided pdb file using ANM with all modes.")
# #Original
# # bfactors = calcBfactors(pdbfile, outfile=None, nmodes=None, \
# # attenuate="true", ranksorted="true", inverted=False)
# bfactors = calcBfactors(pdbfile, outfile=None, nmodes=10, \
# attenuate="false", ranksorted="true", inverted=True)
# else:
# print("Getting Bfactors from the user-provided pdb file.")
# bfactors = getBfactors(pdbfile, outfile=None,\
# attenuate="true", ranksorted="true", inverted=False)
bfactors = calcBfactors(pdbfile, outfile=None, nmodes=10, \
attenuate="false", ranksorted="true", inverted=True)
else:
print("Getting Bfactors from the user-provided pdb file.")
bfactors = getBfactors(pdbfile, outfile=None,\
attenuate="true", ranksorted="true", inverted=False)
bfactors = bfactors
df = pd.read_table(prot+"_jet.res")
print(df)
# bfactors = bfactors
# df = pd.read_table(prot+"_jet.res")
# print(df)
df['bfactor'] = bfactors.round(4)
df.to_csv(prot+"_jet.res", header=True, index=None, sep='\t', mode='w')
# df['bfactor'] = bfactors.round(4)
# df.to_csv(prot+"_jet.res", header=True, index=None, sep='\t', mode='w')
print(df)
# print(df)
launchPred(prot, inAli, mutFile, normWeightMode, alphabet)
......
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