def create_atomobj(atomList):
""" Create a bunch of atom objects based on the cml file. Returns a list of atom objects
Keyword Arguments:
atomList -- The list of atoms found in the cml file to pass in and split
"""
for i in range(0, len(atomList)):
atoms.append(help.get_atoms(atomList,i))
aList = help.object_list(atoms[i])
atom.append(Atom(aList[0],aList[1],aList[2],aList[3],aList[4]))
return atom
def create_bondobj(bondList):
""" Create a bunch of bond objects based on the cml file. Returns a list of bond objects
Keyword Arguments:
bondList -- The list of bonds found in the cml file to pass in and split
"""
for j in range(0, len(bondList)):
bonds.append(help.get_atoms(bondList,j))
bList = help.bond_list(bonds[j])
newBond = Bond(bList[0],bList[1],bList[2])
bond.append(newBond)
fromAtom = find_atom_by_id(bList[1])
toAtom = find_atom_by_id(bList[2])
fromAtom.Atom_Bonds.append(bList[2])
toAtom.Atom_Bonds.append(bList[1])
return bond
#constructor
def __init__(self, bond_type, bond_master, bond_slave):
self.bond_type = bond_type
self.bond_master = bond_master
self.bond_slave = bond_slave
#begin parsing, gets single atom. do in method
tree = ET.parse(file)
root = tree.getroot()
atomList = root.findall('./atomArray/atom')
bondList = root.findall('./bondArray/bond')
#create a bunch of atoms objects
for i in range(0, len(atomList)):
atoms.append(help.get_atoms(atomList,i))
aList = help.object_list(atoms[i])
atom.append(Atom(aList[0],aList[1],aList[2],aList[3],aList[4]))
print " ATOMS "
print "-----------"
for k in range(0, len(atom)):
print "Atom id: %s" % atom[k].atom_id
print "Atom type: %s" % atom[k].atom_type
print "X position: %s" % atom[k].x_pos
print "Y position: %s" % atom[k].y_pos
print "Z position: %s" % atom[k].z_pos
print ""
#create a bunch of bond objects
for j in range(0, len(bondList)):
