def build4LevelsTree(self, subst_chain, atomlines):
"""
Function to build a 4 level hierarchy Protein-Chain-Residue-Atom.
"""
self.mol = Protein()
self.mol.allAtoms = AtomSet()
self.mol.atmNum = {}
self.mol.parser = self
if self.mol.name == 'NoName':
self.mol.name = os.path.basename(
os.path.splitext(self.filename)[0])
self.mol.curChain = Chain()
self.mol.curRes = Residue()
self.mol.levels = [Protein, Chain, Residue, Atom]
i = 1
for atmline in atomlines:
if len(atmline) >= 10:
status = string.split(atmline[9], '|')
else:
status = None
if len(atmline) == 8:
tmp = [atmline[5][:5], atmline[5][5:]]
atmline[5] = tmp[0]
atmline.insert(6, tmp[1])
if status and status[0] == 'WATER':
chainID = 'W'
atmline[7] = 'HOH' + str(i)
subst_chain[atmline[7]] = chainID
i = i + 1
if subst_chain == {}:
chainID = 'default'
elif not subst_chain.has_key(atmline[7]):
if subst_chain.has_key('****'):
try:
chainID = subst_chain[atmline[7]]
except:
chainID = 'default'
else:
chainID = 'default'
elif type(subst_chain[atmline[7]]) is types.StringType:
# that is to say that only chains has this substructure name.
chainID = subst_chain[atmline[7]]
elif type(subst_chain[atmline[7]]) is types.ListType:
# That is to say that several chains have the same substructure.
chainID = subst_chain[atmline[7]][0]
subst_chain[atmline[7]] = subst_chain[atmline[7]].remove(
chainID)
if chainID != self.mol.curChain.id:
if not self.mol.chains.id or not chainID in self.mol.chains.id:
self.mol.curChain = Chain(chainID, self.mol, top=self.mol)
else:
self.mol.curChain = self.mol.chains.get(chainID)[0]
if len(atmline) < 7:
# test if the atmline has a res name and resseq:
resName = 'RES'
resSeq = '1'
else:
resName = atmline[7][:3]
resSeq = atmline[7][3:]
if resSeq != self.mol.curRes.number or \
resName != self.mol.curRes.type:
# check if this residue already exists
na = string.strip(resName) + string.strip(resSeq)
res = self.mol.curChain.get(na)
if res:
self.mol.curRes = res[0]
else:
self.mol.curRes = Residue(resName,
resSeq,
'',
self.mol.curChain,
top=self.mol)
name = atmline[1]
if name == 'CA': self.mol.curRes.hasCA = 1
if name == 'O': self.mol.curRes.hasO = 2
atom = Atom(name,
self.mol.curRes,
top=self.mol,
chemicalElement=string.split(atmline[5], '.')[0])
#atom.element = atmline[5][0]
atom.element = atom.chemElem
atom.number = int(atmline[0])
self.mol.atmNum[atom.number] = atom
atom._coords = [[
float(atmline[2]),
float(atmline[3]),
float(atmline[4])
]]
if len(atmline) >= 9:
atom._charges['mol2'] = float(atmline[8])
atom.chargeSet = 'mol2'
# atom.conformation = 0
atom.hetatm = 0
#Add a data member containing a list of string describing
# the Sybyl status bis of the atoms.
atom.status = status
#add altname so buildBondsByDist doesn't croak
atom.altname = None
self.mol.allAtoms.append(atom)
delattr(self.mol, 'curRes')
delattr(self.mol, 'curChain')
def build4LevelsTree(self, subst_chain, atomlines):
"""
Function to build a 4 level hierarchy Protein-Chain-Residue-Atom.
"""
self.mol= Protein()
self.mol.allAtoms = AtomSet()
self.mol.atmNum = {}
self.mol.parser = self
if self.mol.name == 'NoName':
self.mol.name = os.path.basename(os.path.splitext
(self.filename)[0])
self.mol.curChain = Chain()
self.mol.curRes = Residue()
self.mol.levels = [Protein, Chain, Residue, Atom]
i = 1
for atmline in atomlines:
if len(atmline)>= 10:
status = string.split(atmline[9], '|')
else: status = None
if len(atmline) == 8:
tmp = [atmline[5][:5], atmline[5][5:]]
atmline[5] = tmp[0]
atmline.insert(6, tmp[1])
if status and status[0]=='WATER':
chainID = 'W'
atmline[7] = 'HOH'+str(i)
subst_chain[atmline[7]] = chainID
i = i+1
if subst_chain == {}:
chainID = 'default'
elif not subst_chain.has_key(atmline[7]):
if subst_chain.has_key('****'):
try:
chainID = subst_chain[atmline[7]]
except:
chainID = 'default'
else:
chainID = 'default'
elif type(subst_chain[atmline[7]]) is types.StringType:
# that is to say that only chains has this substructure name.
chainID = subst_chain[atmline[7]]
elif type(subst_chain[atmline[7]]) is types.ListType:
# That is to say that several chains have the same substructure.
chainID = subst_chain[atmline[7]][0]
subst_chain[atmline[7]] = subst_chain[atmline[7]].remove(chainID)
if chainID != self.mol.curChain.id:
if not self.mol.chains.id or not chainID in self.mol.chains.id:
self.mol.curChain = Chain(chainID, self.mol,
top = self.mol)
else:
self.mol.curChain = self.mol.chains.get(chainID)[0]
if len(atmline)<7:
# test if the atmline has a res name and resseq:
resName = 'RES'
resSeq = '1'
else:
resName = atmline[7][:3]
resSeq = atmline[7][3:]
if resSeq != self.mol.curRes.number or \
resName != self.mol.curRes.type:
# check if this residue already exists
na = string.strip(resName) + string.strip(resSeq)
res = self.mol.curChain.get( na )
if res:
self.mol.curRes = res[0]
else:
self.mol.curRes = Residue(resName, resSeq, '',
self.mol.curChain,
top = self.mol)
name = atmline[1]
if name == 'CA': self.mol.curRes.hasCA = 1
if name == 'O' : self.mol.curRes.hasO = 2
atom = Atom(name, self.mol.curRes, top = self.mol,
chemicalElement = string.split(atmline[5], '.')[0])
#atom.element = atmline[5][0]
atom.element = atom.chemElem
atom.number = int(atmline[0])
self.mol.atmNum[atom.number] = atom
atom._coords = [ [float(atmline[2]), float(atmline[3]),
float(atmline[4]) ] ]
if len(atmline)>=9:
atom._charges['mol2'] = float(atmline[8])
atom.chargeSet = 'mol2'
# atom.conformation = 0
atom.hetatm = 0
#Add a data member containing a list of string describing
# the Sybyl status bis of the atoms.
atom.status = status
#add altname so buildBondsByDist doesn't croak
atom.altname = None
self.mol.allAtoms.append(atom)
delattr(self.mol, 'curRes')
delattr(self.mol, 'curChain')
def build3LevelsTree(self, atomlines):
""" Function to build a 3 levels hierarchy Molecule-substructure-atoms."""
self.mol = Protein()
self.mol.allAtoms = AtomSet()
self.mol.atmNum = {}
self.mol.parser = self
if self.mol.name == 'NoName':
self.mol.name = os.path.basename(
os.path.splitext(self.filename)[0])
self.mol.children = ResidueSet([])
self.mol.childrenName = 'residues'
self.mol.childrenSetClass = ResidueSet
self.mol.elementType = Residue
self.mol.curRes = Residue()
self.mol.curRes.hasCA = 0
self.mol.curRes.hasO = 0
self.mol.levels = [Protein, Residue, Atom]
for atmline in atomlines:
if len(atmline) >= 10:
status = string.split(atmline[9], '|')
else:
status = None
resName = atmline[7][:3]
resSeq = atmline[7][3:]
if resSeq != self.mol.curRes.number or \
resName != self.mol.curRes.type:
# check if this residue already exists
na = string.strip(resName) + string.strip(resSeq)
res = self.mol.get(na)
if res:
self.mol.curRes = res[0]
else:
self.mol.curRes = Residue(resName,
resSeq,
'',
self.mol,
top=self.mol)
name = atmline[1]
if name == 'CA': self.mol.curRes.hasCA = 1
if name == 'O': self.mol.curRes.hasO = 2
atom = Atom(name,
self.mol.curRes,
top=self.mol,
chemicalElement=string.split(atmline[5], '.')[0])
#atom.element = atmline[5][0]
atom.element = atom.chemElem
atom.number = int(atmline[0])
self.mol.atmNum[atom.number] = atom
atom._coords = [[
float(atmline[2]),
float(atmline[3]),
float(atmline[4])
]]
atom._charges['mol2'] = float(atmline[8])
atom.chargeSet = mol2
# atom.conformation = 0
atom.hetatm = 0
#Add a data member containing a list of string describing
# the Sybyl status bis of the atoms.
atom.status = status
#add altname so buildBondsByDist doesn't croak
atom.altname = None
self.mol.allAtoms.append(atom)
self.mol.residues = self.mol.children
assert hasattr(self.mol, 'chains')
delattr(self.mol, 'chains')
delattr(self.mol, 'curRes')
def build3LevelsTree(self,atomlines):
""" Function to build a 3 levels hierarchy Molecule-substructure-atoms."""
self.mol= Protein()
self.mol.allAtoms = AtomSet()
self.mol.atmNum = {}
self.mol.parser = self
if self.mol.name == 'NoName':
self.mol.name = os.path.basename(os.path.splitext
(self.filename)[0])
self.mol.children = ResidueSet([])
self.mol.childrenName = 'residues'
self.mol.childrenSetClass = ResidueSet
self.mol.elementType = Residue
self.mol.curRes = Residue()
self.mol.curRes.hasCA = 0
self.mol.curRes.hasO = 0
self.mol.levels = [Protein, Residue, Atom]
for atmline in atomlines:
if len(atmline)>= 10:
status = string.split(atmline[9], '|')
else:
status = None
resName = atmline[7][:3]
resSeq = atmline[7][3:]
if resSeq != self.mol.curRes.number or \
resName != self.mol.curRes.type:
# check if this residue already exists
na = string.strip(resName) + string.strip(resSeq)
res = self.mol.get(na)
if res:
self.mol.curRes = res[0]
else:
self.mol.curRes = Residue(resName, resSeq, '',
self.mol,
top = self.mol)
name = atmline[1]
if name == 'CA': self.mol.curRes.hasCA = 1
if name == 'O' : self.mol.curRes.hasO = 2
atom = Atom(name, self.mol.curRes, top = self.mol,
chemicalElement = string.split(atmline[5], '.')[0])
#atom.element = atmline[5][0]
atom.element = atom.chemElem
atom.number = int(atmline[0])
self.mol.atmNum[atom.number] = atom
atom._coords = [ [float(atmline[2]), float(atmline[3]),
float(atmline[4]) ] ]
atom._charges['mol2'] = float(atmline[8])
atom.chargeSet = mol2
# atom.conformation = 0
atom.hetatm = 0
#Add a data member containing a list of string describing
# the Sybyl status bis of the atoms.
atom.status = status
#add altname so buildBondsByDist doesn't croak
atom.altname = None
self.mol.allAtoms.append(atom)
self.mol.residues = self.mol.children
assert hasattr(self.mol, 'chains')
delattr(self.mol, 'chains')
delattr(self.mol, 'curRes')