def buildCoil(self, residuesCoil, j, chain):
start = residuesCoil[0]
end = residuesCoil[-1]
coil = Coil(chain=chain, index=j, start=start, end=end)
coil.isNA = False
return coil
def getCoils(self, chain):
"""
gets the coils of a proteic chain by finding which AA are not yet
in a secondary structure element
"""
chain.ribbonType()
if chain.ribbonType() == 'NA':
coil = Coil(chain=chain,
index='Nucleic',
start=chain.DNARes[0],
end=chain.DNARes[-1])
chain.secondarystructureset.append(coil)
coil.parent = chain
coil.isNA = True
else:
res = chain.AARes
chainStructureSet = chain.secondarystructureset
j = 1 # coil counter
# loop over residues and build coils for continuous segments of
# unassigned residues
endedWithGap = False
# print 'FOR CHAIN ', chain.id
residuesCoil = [] # list of residues in current Coil
# look over all residues to build list of residues in current Coil
for r in res:
# print r
# if we hit a residue
# cCAatom = None
if not r.hasCA: # we hit residue that breaks coil
if len(residuesCoil):
coil = self.buildCoil(residuesCoil, j, chain)
coil.gapAfter = True
if endedWithGap:
coil.gapBefore = True
chainStructureSet.append(coil)
coil.parent = chain
r1 = residuesCoil[0]
r2 = residuesCoil[-1]
# print '0', coil, r1, r2,coil.gapBefore, coil.gapAfter
endedWithGap = True
residuesCoil = [r]
j = j + 1
else:
anames = r.atoms.name
# CA atom of current res
# using get('CA*')[0] handle alternate location as in
# THR 4 in 1KZK.pdb
cCAatom = r.atoms.get('CA*')[0]
# cNatom = r.atoms[anames.index('N')] # N atom of current res
# cCatom = r.atoms[anames.index('C')] # C atom of current res
if hasattr(r, 'secondarystructure'):
if len(residuesCoil):
coil = self.buildCoil(residuesCoil, j, chain)
if endedWithGap:
coil.gapBefore = True
chainStructureSet.append(coil)
coil.parent = chain
r1 = residuesCoil[0]
r2 = residuesCoil[-1]
# print '1', coil, r1, r2, coil.gapBefore, coil.gapAfter
endedWithGap = False
residuesCoil = []
j = j + 1
else:
if len(residuesCoil) == 0:
residuesCoil = [r]
else:
if self.close(pCAatom, cCAatom):
residuesCoil.append(r)
if r == res[-1]: # last seg is coil
coil = self.buildCoil(
residuesCoil, j, chain)
chainStructureSet.append(coil)
if endedWithGap:
coil.gapBefore = True
coil.parent = chain
elif len(residuesCoil): # distance gap
coil = self.buildCoil(residuesCoil, j, chain)
chainStructureSet.append(coil)
coil.gapAfter = True
if endedWithGap:
coil.gapBefore = True
coil.parent = chain
r1 = residuesCoil[0]
r2 = residuesCoil[-1]
# print '2', coil, r1, r2,coil.gapBefore, coil.gapAfter
endedWithGap = True
residuesCoil = [r]
j = j + 1
pCAatom = cCAatom
# pNatom = cNatom
# pCatom = cCatom
chain.secondarystructureset.sort(self.Compare)
def buildCoil(self, residuesCoil, j, chain):
start = residuesCoil[0]
end = residuesCoil[-1]
coil = Coil(chain=chain, index=j, start=start, end=end)
coil.isNA = False
return coil
def getCoils(self, chain):
"""
gets the coils of a proteic chain by finding which AA are not yet
in a secondary structure element
"""
chain.ribbonType()
if chain.ribbonType()=='NA':
coil = Coil(chain=chain, index='Nucleic',
start=chain.DNARes[0], end=chain.DNARes[-1])
chain.secondarystructureset.append(coil)
coil.parent = chain
coil.isNA = True
else:
res = chain.AARes
chainStructureSet = chain.secondarystructureset
j = 1 # coil counter
# loop over residues and build coils for continuous segments of
# unassigned residues
endedWithGap = False
#print 'FOR CHAIN ', chain.id
residuesCoil = [] # list of residues in current Coil
# look over all residues to build list of residues in current Coil
for r in res:
#print r
# if we hit a residue
#cCAatom = None
if not r.hasCA: # we hit residue that breaks coil
if len(residuesCoil):
coil = self.buildCoil(residuesCoil, j, chain)
coil.gapAfter = True
if endedWithGap:
coil.gapBefore = True
chainStructureSet.append(coil)
coil.parent = chain
r1 = residuesCoil[0]
r2 = residuesCoil[-1]
#print '0', coil, r1, r2,coil.gapBefore, coil.gapAfter
endedWithGap = True
residuesCoil = [r]
j = j+1
else:
anames = r.atoms.name
# CA atom of current res
# using get('CA*')[0] handle alternate location as in
# THR 4 in 1KZK.pdb
cCAatom = r.atoms.get('CA*')[0]
#cNatom = r.atoms[anames.index('N')] # N atom of current res
#cCatom = r.atoms[anames.index('C')] # C atom of current res
if hasattr(r, 'secondarystructure'):
if len(residuesCoil):
coil = self.buildCoil(residuesCoil, j, chain)
if endedWithGap:
coil.gapBefore = True
chainStructureSet.append(coil)
coil.parent = chain
r1 = residuesCoil[0]
r2 = residuesCoil[-1]
#print '1', coil, r1, r2, coil.gapBefore, coil.gapAfter
endedWithGap = False
residuesCoil = []
j = j+1
else:
if len(residuesCoil)==0:
residuesCoil = [r]
else:
if self.close(pCAatom, cCAatom):
residuesCoil.append(r)
if r==res[-1]: #last seg is coil
coil = self.buildCoil(residuesCoil, j, chain)
chainStructureSet.append(coil)
if endedWithGap:
coil.gapBefore = True
coil.parent = chain
elif len(residuesCoil): # distance gap
coil = self.buildCoil(residuesCoil, j, chain)
chainStructureSet.append(coil)
coil.gapAfter = True
if endedWithGap:
coil.gapBefore = True
coil.parent = chain
r1 = residuesCoil[0]
r2 = residuesCoil[-1]
#print '2', coil, r1, r2,coil.gapBefore, coil.gapAfter
endedWithGap = True
residuesCoil = [r]
j = j+1
pCAatom = cCAatom
#pNatom = cNatom
#pCatom = cCatom
## res = chain.AARes
## chainStructureSet = chain.secondarystructureset
## resNum = None
## try:
## resNum = int(res[0].number)
## except:
## pass
## j = 1 # coil counter
## for rn, r in enumerate(res):
## print 'AAA1', r, resNum, r.number
## if resNum:
## if resNum != int(r.number):
## if residuesCoil:
## print 'AAA2', j, len(residuesCoil)
## coil = self.buildCoil(residuesCoil, j, chain)
## chainStructureSet.append(coil)
## coil.parent = chain
## coil.gap =int(r.number) - resNum #used in secondaryStructureCommands to fix Bug 1120
## residuesCoil = [r]
## r.gap = True
## j = j+1
## try:
## if res[rn+1].number != r.number: #icode is not '':
## resNum = int(r.number) +1
## except IndexError:
## pass
## if not hasattr(r, 'secondarystructure') and r.hasCA and r.hasO:
## print 'AAA3', r, len(residuesCoil), r == res[-1]
## residuesCoil.append(r)
## #test if this residue is the last one if yes it build the
## #information on the COIL, if not i is incremented.
## if r == res[-1] and residuesCoil != []:
## coil = self.buildCoil(residuesCoil, j, chain)
## chainStructureSet.append(coil)
## coil.parent = chain
## if hasattr(residuesCoil[0],'gap'):
## coil.gap = True
## residuesCoil = []
## j = j+1
## else:
## print 'AAA4', len(residuesCoil)
## if residuesCoil != []:
## coil = self.buildCoil(residuesCoil, j, chain)
## chainStructureSet.append(coil)
## coil.parent = chain
## if hasattr(residuesCoil[0],'gap'):
## coil.gap = True
## residuesCoil = []
## j = j+1
chain.secondarystructureset.sort(self.Compare)
def getCoils(self, chain):
"""
gets the coils of a proteic chain by finding which AA are not yet
in a secondary structure element
"""
chain.ribbonType()
if chain.ribbonType()=='NA':
coil = Coil(chain=chain, index='Nucleic',
start=chain.DNARes[0], end=chain.DNARes[-1])
chain.secondarystructureset.append(coil)
coil.parent = chain
coil.isNA = True
else:
res = chain.AARes
chainStructureSet = chain.secondarystructureset
j = 1 # coil counter
# loop over residues and build coils for continuous segments of
# unassigned residues
endedWithGap = False
#print 'FOR CHAIN ', chain.id
residuesCoil = [] # list of residues in current Coil
# look over all residues to build list of residues in current Coil
for r in res:
#print r
# if we hit a residue
#cCAatom = None
if not r.hasCA: # we hit residue that breaks coil
if len(residuesCoil):
coil = self.buildCoil(residuesCoil, j, chain)
coil.gapAfter = True
if endedWithGap:
coil.gapBefore = True
chainStructureSet.append(coil)
coil.parent = chain
r1 = residuesCoil[0]
r2 = residuesCoil[-1]
#print '0', coil, r1, r2,coil.gapBefore, coil.gapAfter
endedWithGap = True
residuesCoil = [r]
j = j+1
else:
anames = r.atoms.name
# CA atom of current res
# using get('CA*')[0] handle alternate location as in
# THR 4 in 1KZK.pdb
cCAatom = r.atoms.get('CA*')[0]
#cNatom = r.atoms[anames.index('N')] # N atom of current res
#cCatom = r.atoms[anames.index('C')] # C atom of current res
if hasattr(r, 'secondarystructure'):
if len(residuesCoil):
coil = self.buildCoil(residuesCoil, j, chain)
if endedWithGap:
coil.gapBefore = True
chainStructureSet.append(coil)
coil.parent = chain
r1 = residuesCoil[0]
r2 = residuesCoil[-1]
#print '1', coil, r1, r2, coil.gapBefore, coil.gapAfter
endedWithGap = False
residuesCoil = []
j = j+1
else:
if len(residuesCoil)==0:
residuesCoil = [r]
else:
if self.close(pCAatom, cCAatom):
residuesCoil.append(r)
if r==res[-1]: #last seg is coil
coil = self.buildCoil(residuesCoil, j, chain)
chainStructureSet.append(coil)
if endedWithGap:
coil.gapBefore = True
coil.parent = chain
elif len(residuesCoil): # distance gap
coil = self.buildCoil(residuesCoil, j, chain)
chainStructureSet.append(coil)
coil.gapAfter = True
if endedWithGap:
coil.gapBefore = True
coil.parent = chain
r1 = residuesCoil[0]
r2 = residuesCoil[-1]
#print '2', coil, r1, r2,coil.gapBefore, coil.gapAfter
endedWithGap = True
residuesCoil = [r]
j = j+1
pCAatom = cCAatom
#pNatom = cNatom
#pCatom = cCatom
## res = chain.AARes
## chainStructureSet = chain.secondarystructureset
## resNum = None
## try:
## resNum = int(res[0].number)
## except:
## pass
## j = 1 # coil counter
## for rn, r in enumerate(res):
## print 'AAA1', r, resNum, r.number
## if resNum:
## if resNum != int(r.number):
## if residuesCoil:
## print 'AAA2', j, len(residuesCoil)
## coil = self.buildCoil(residuesCoil, j, chain)
## chainStructureSet.append(coil)
## coil.parent = chain
## coil.gap =int(r.number) - resNum #used in secondaryStructureCommands to fix Bug 1120
## residuesCoil = [r]
## r.gap = True
## j = j+1
## try:
## if res[rn+1].number != r.number: #icode is not '':
## resNum = int(r.number) +1
## except IndexError:
## pass
## if not hasattr(r, 'secondarystructure') and r.hasCA and r.hasO:
## print 'AAA3', r, len(residuesCoil), r == res[-1]
## residuesCoil.append(r)
## #test if this residue is the last one if yes it build the
## #information on the COIL, if not i is incremented.
## if r == res[-1] and residuesCoil != []:
## coil = self.buildCoil(residuesCoil, j, chain)
## chainStructureSet.append(coil)
## coil.parent = chain
## if hasattr(residuesCoil[0],'gap'):
## coil.gap = True
## residuesCoil = []
## j = j+1
## else:
## print 'AAA4', len(residuesCoil)
## if residuesCoil != []:
## coil = self.buildCoil(residuesCoil, j, chain)
## chainStructureSet.append(coil)
## coil.parent = chain
## if hasattr(residuesCoil[0],'gap'):
## coil.gap = True
## residuesCoil = []
## j = j+1
chain.secondarystructureset.sort(self.Compare)