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
