Skip to content

P
PRESCOTT
Commit 8e2a131c by Mustafa Tekpinar
Options

Commented bfactor-related unused code.

parent 83ba006d
Showing with 23 additions and 23 deletions
esgemme.py
...@@ -962,33 +962,33 @@ def doit(inAli,mutFile,retMet,bFile,fFile,n,N, jetfile, pdbfile, normWeightMode, ...@@ -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') df.to_csv(prot+"_jet.res", header=True, index=None, sep='\t', mode='w')
print(df) print(df)
#If a real pdb file is given, calculate or get Bfactors for the residues. # #If a real pdb file is given, calculate or get Bfactors for the residues.
if(((normWeightMode=='bfactor') or (normWeightMode=='maxtracebfactor') or (normWeightMode=='maxbfactortrace'))): # if(((normWeightMode=='bfactor') or (normWeightMode=='maxtracebfactor') or (normWeightMode=='maxbfactortrace'))):
isCalc = True # isCalc = True
if (pdbfile == None): # if (pdbfile == None):
print("ERROR: There is not any pdb file to calculate or get Bfactors!") # print("ERROR: There is not any pdb file to calculate or get Bfactors!")
sys.exit(-1) # sys.exit(-1)
else: # else:
if (isCalc): # if (isCalc):
print("Computing Bfactors from the user-provided pdb file using ANM with all modes.") # print("Computing Bfactors from the user-provided pdb file using ANM with all modes.")
#Original # #Original
# bfactors = calcBfactors(pdbfile, outfile=None, nmodes=None, \ # # 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) # 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 # bfactors = bfactors
df = pd.read_table(prot+"_jet.res") # df = pd.read_table(prot+"_jet.res")
print(df) # print(df)
df['bfactor'] = bfactors.round(4) # df['bfactor'] = bfactors.round(4)
df.to_csv(prot+"_jet.res", header=True, index=None, sep='\t', mode='w') # df.to_csv(prot+"_jet.res", header=True, index=None, sep='\t', mode='w')
print(df) # print(df)
launchPred(prot, inAli, mutFile, normWeightMode, alphabet) launchPred(prot, inAli, mutFile, normWeightMode, alphabet)
......
Markdown is supported
0% or
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment