def PCA(fn, residue_PCA):
"""
get the name of files which have PCA
"""
inputfile = open(fn + "_protein.pdb")
for line in inputfile:
if pdbinfo.isAtom(line) == 1 and pdbinfo.resn(
line).split()[0] == "PCA":
residue_PCA.append(fn)
def Hg2toFlag(filename):
"""
change Hg2+ ion atom name to be FLAG
"""
f = open("tmp", "w")
for lines in fileinput.input(filename):
if pdbinfo.isAtom(lines) == 1 and \
pdbinfo.resn(lines).split()[0] == 'HG':
lines = lines[0:12] + "FLAG" + lines[16::]
f.write(lines)
fileinput.close()
f.close()
os.system("mv tmp " + filename)
def checkIons(fn):
"""
check the information of ions
fn_protein_proc3_nonprot <--- ions
"""
inpdb = fn + "_protein_proc3_nonprot.pdb"
ions = []
if os.stat(inpdb)[6] > 0:
for lines in fileinput.input(inpdb):
atm = pdbinfo.atmn(lines)
res = pdbinfo.resn(lines)
ions.append(atm + " " + res)
return ions
def fixFe2(fn):
"""
Change residue FE2 atom name to be FE2
"""
pdbin = fn + "_protein_proc2.pdb"
pdbout = fn + "_protein_proc2_fixFe2.pdb"
f = open(pdbout, "w")
for lines in fileinput.input(pdbin):
if pdbinfo.isAtom(lines) == 1 and pdbinfo.resn(lines) == 'FE2':
lines = lines[0:12] + ' FE2' + lines[16:]
f.write(lines)
f.close()
fileinput.close()
os.system("mv " + pdbout + " " + pdbin)
def rmPCA(fn):
"""
remove PCA from these files
"""
inputfile = open(fn + "_protein.pdb")
outputfile = open(fn + "_protein_tmp.pdb", "w")
for line in inputfile:
if pdbinfo.isAtom(line) == 1 and pdbinfo.resn(
line).split()[0] == "PCA":
continue
else:
outputfile.write(line)
outputfile.close()
os.system("mv " + fn + "_protein_tmp.pdb " + fn + "_protein.pdb")
os.system("rm " + fn + "_tmp.pdb")
def getProton(fn):
inpdb = fn + "_protein_proc8_assign1.pqr"
proton = {}
for lines in fileinput.input(inpdb):
if pdbinfo.isAtom(lines) == 1:
resn = pdbinfo.resn(lines)
if resn == 'HIS':
resi = pdbinfo.resi(lines).split()[0]
atmn = pdbinfo.atmn(lines)
if resi in proton.keys() and atmn in [' HD1', ' HE2']:
proton[resi][1].append(atmn)
elif resi not in proton.keys():
proton[resi] = [resn, []]
if atmn in [' HD1', 'HE2']:
proton[resi][1].append(atmn)
res = checkProtonState(proton)
return res