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
