def __readPDBTER(self, fname=None, pdbline=None, bNoNewID=True):
if pdbline:
l = pdbline.split('\n')
else:
l = open(fname, 'r').readlines()
chainIDstring = 'ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnoprstuvwxyz123456789'
bNewChain = True
chainID = ' '
prevID = ' '
prevResID = 0
usedChainIDs = ''
atomcount = 1
for line in l:
if 'TER' in line:
bNewChain = True
if (line[:4] == 'ATOM') or (line[:6] == 'HETATM'):
a = Atom().readPDBString(line, origID=atomcount)
atomcount += 1
# if (a.chain_id != prevID) and (a.chain_id != ' '): # identify chain change by ID (when no TER is there)
if (a.chain_id != prevID
): # identify chain change by ID (when no TER is there)
bNewChain = True
if (a.resnr != prevResID):
try:
if a.resnr != prevResID + 1:
bNewChain = True
except TypeError:
bNewChain = False
prevID = a.chain_id
prevResID = a.resnr
if bNewChain == True:
if (a.chain_id == ' ') or (a.chain_id == chainID):
# find a new chain id
bFound = False
while bFound == False:
foo = chainIDstring[0]
chainIDstring = chainIDstring.lstrip(
chainIDstring[0])
if foo not in usedChainIDs:
bFound = True
usedChainIDs = usedChainIDs + foo
chainID = foo
if bNoNewID == True:
chainID = "pmx" + foo
else:
chainID = a.chain_id
usedChainIDs = usedChainIDs + chainID
a.chain_id = chainID
self.atoms.append(a)
bNewChain = False
if line[:6] == 'CRYST1':
self.box = _p.box_from_cryst1(line)
self.make_chains()
self.make_residues()
self.unity = 'A'
return self
def __readPDB(self, fname=None, pdbline=None):
if pdbline:
l = pdbline.split('\n')
else:
l = open(fname, 'r').readlines()
for line in l:
if line[:4]=='ATOM' or \
line[:6]=='HETATM':
a = Atom().readPDBString(line)
self.atoms.append(a)
if line[:6] == 'CRYST1':
self.box = _p.box_from_cryst1(line)
self.make_chains()
self.make_residues()
self.unity = 'A'
return self
def __readPDB(self,fname=None, pdbline=None):
if pdbline:
l = pdbline.split('\n')
else:
l = open(fname,'r').readlines()
for line in l:
if line[:4]=='ATOM' or \
line[:6]=='HETATM':
a = Atom().readPDBString(line)
self.atoms.append(a)
if line[:6] == 'CRYST1':
self.box = _p.box_from_cryst1( line )
self.make_chains()
self.make_residues()
self.unity = 'A'
return self
def __readPDBTER(self,
fname=None,
pdbline=None,
bNoNewID=True,
bPDBGAP=False):
if pdbline:
l = pdbline.split('\n')
else:
l = open(fname, 'r').readlines()
chainIDstring = 'ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnoprstuvwxyz123456789'
bNewChain = True
chainID = ' '
prevID = ' '
prevAtomName = ' '
prevResID = 0
prevResName = ' '
usedChainIDs = []
atomcount = 1
prevCatom = None
for line in l:
if 'TER' in line:
bNewChain = True
if (line[:4] == 'ATOM') or (line[:6] == 'HETATM'):
a = Atom().readPDBString(line, origID=atomcount)
atomcount += 1
# if (a.chain_id != prevID) and (a.chain_id != ' '): # identify chain change by ID (when no TER is there)
if (a.chain_id != prevID
): # identify chain change by ID (when no TER is there)
bNewChain = True
if (self.__check_if_gap(prevCatom, a) == True
and bPDBGAP == True):
bNewChain = True
if (a.resnr != prevResID):
try:
if a.resnr != prevResID + 1:
bNewChain = True
if (prevAtomName
== 'OC2') or (prevAtomName
== 'OXT') or (prevAtomName
== 'OT2'):
bNewChain = True
if (prevAtomName == 'HH33') and (
(prevResName == 'NME') or (prevResName == 'NAC') or
(prevResName == 'CT3')): # NME cap
bNewChain = True
except TypeError:
bNewChain = False
prevID = a.chain_id
prevResID = a.resnr
prevAtomName = a.name
prevResName = a.resname
if a.name == 'C':
prevCatom = a
if bNewChain == True:
if (a.chain_id == ' ') or (a.chain_id == chainID) or (
a.chain_id in usedChainIDs):
#print a.chain_id,a,chainID,usedChainIDs
# find a new chain id
bFound = False
while bFound == False:
foo = chainIDstring[0]
chainIDstring = chainIDstring.lstrip(
chainIDstring[0])
if foo not in usedChainIDs:
bFound = True
chainID = foo
if bNoNewID == True:
chainID = "pmx" + foo
usedChainIDs.append(chainID)
else:
chainID = a.chain_id
usedChainIDs.append(chainID)
a.chain_id = chainID
self.atoms.append(a)
bNewChain = False
if line[:6] == 'CRYST1':
self.box = _p.box_from_cryst1(line)
##### now fix chain IDs that have been newly created #####
newChainDict = {}
chainIDstring = 'ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnoprstuvwxyz123456789'
for a in self.atoms:
# chain with a new ID
if 'pmx' in a.chain_id:
# this ID has already been encountered
if a.chain_id in newChainDict.keys():
a.chain_id = newChainDict[a.chain_id]
# ID not yet encountered
else:
# find a suitable ID
bFound = False
while bFound == False:
foo = chainIDstring[0]
chainIDstring = chainIDstring.lstrip(chainIDstring[0])
# found
if foo not in usedChainIDs:
bFound = True
usedChainIDs.append(foo)
newChainDict[a.chain_id] = foo
a.chain_id = foo
self.make_chains()
self.make_residues()
self.unity = 'A'
return self