def __init__(self, id=None, parent=None, elementType=Residue, list=None,
childrenName='residues', setClass=ChainSet,
childrenSetClass=ResidueSet, top=None, childIndex=None,
assignUniqIndex=1):
"""Chain constructor.
Arguments:
id (string)
optional parent (instance of a TreeNode)
optional elementType (instance of class inheriting from TreeNode)"""
Molecule.__init__(self, str(id), parent, elementType, list,
childrenName, setClass, childrenSetClass, top,
childIndex, assignUniqIndex)
self.id = id
self.hasBonds = 0 # 1 for bondsByDistance is supported
self.gaps = [] # list to store tuple (Res, Res) define the edge of a gap
def __init__(self, name='NoName', parent=None, elementType=Chain,
list=None, childrenName='chains', setClass=ProteinSet,
childrenSetClass=ChainSet, top=None, childIndex=None,
assignUniqIndex=1):
"""Protein constructor.
Arguments:
name (string)
optional parent (instance of a TreeNode)
optional elementType (instance of class inheriting from TreeNode,
defaults to Chain)"""
Molecule.__init__(self, name=name, parent=parent,
elementType=elementType, list=list,
childrenName=childrenName,
setClass=setClass,
childrenSetClass=childrenSetClass, top=top,
childIndex=childIndex, assignUniqIndex=assignUniqIndex)
self.bondsflag = 0
self.hasSS = []
self.hasBonds = 0 # 1 for bondsByDistance is supported
def __init__(self, type='UNK', number=-1, icode='', parent=None,
elementType=Atom, list=None, childrenName='atoms',
setClass=ResidueSet,
childrenSetClass=AtomSet, top=None, childIndex=None,
assignUniqIndex=1):
"""Residue constructor.
Arguments:
type (string)
number (integer or string)
icode (1character) insertion code
optional parent (instance of a TreeNode)
optional elementType (instance of class inheriting from TreeNode)"""
name = type+str(number)+icode
Molecule.__init__(self, name, parent, elementType,
list, childrenName, setClass, childrenSetClass, top,
childIndex, assignUniqIndex)
self.type = type
self.number = number
self.icode = icode
self.psi = None # not calculated
self.phi = None # not calculated
def build2LevelsTree(self, atomlines):
"""
Function to build a two level tree.
"""
print 'try to build a 2 level tree'
self.mol = Molecule()
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 = AtomSet([])
self.mol.childrenName = 'atoms'
self.mol.childrenSetClass = AtomSet
self.mol.elementType = Atom
self.mol.levels = [Molecule, Atom]
##1/18:self.mol.levels = [Protein, Atom]
for atmline in atomlines:
atom = Atom(atmline[1],
self.mol,
chemicalElement=string.split(atmline[5], '.')[0],
top=self.mol)
#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 altname so buildBondsByDist doesn't croak
atom.altname = None
self.mol.allAtoms.append(atom)
self.mol.atoms = self.mol.children
def isBelow(self, Klass):
if Klass is Molecule: Klass=Protein
return Molecule.isBelow(self, Klass)