<commit_before>import sys
import xml.etree.ElementTree as ET
import helper as help
import time

atoms = []
atom = []
bonds = []
bond = []
angle = []

#create Atom object
class Atom(object):
    atom_id = ""
    atom_type = ""
    x_pos = 0.000
    y_pos = 0.000
    z_pos = 0.000
    Num_Bonds = 0
    Atom_Bonds = []
    primary = {}
    secondary = {}
    tertiary = {}
    related = {}
    ring = False

    #constructor
    def __init__(self, atom_id, atom_type, x_pos, y_pos, z_pos):
        self.atom_id = atom_id
        self.atom_type = atom_type
        self.x_pos = x_pos
        self.y_pos = y_pos
        self.z_pos = z_pos
        self.Atom_Bonds = []
        self.Num_Bonds = 0
        ring = False
        primary = {}
        secondary = {}
        tertiary = {}
        related = {}

#create Bond object 
class Bond(object):
   bond_type = ""
   bond_master = ""
   bond_slave = ""

   #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

#create angle object
class Angle(object):
    Angle_type = 0
    Angle_master = ""
    Angle_slave1 = ""
    Angle_slave2 = ""
    
    #constructor
    def __init__(self, Angle_type, Angle_master, Angle_slave1, Angle_slave2):
        self.Angle_type = Angle_type
        self.Angle_master = Angle_master
        self.Angle_slave1 = Angle_slave1
        self.Angle_slave2 = Angle_slave2<commit_msg>added dihedral object, more cleaning<commit_after>import sys
import xml.etree.ElementTree as ET
import helper as help
import time

atoms = []
atom = []
bonds = []
bond = []
angle = []

#create Atom object
class Atom(object):
    atom_id = ""
    atom_type = ""
    x_pos = 0.000
    y_pos = 0.000
    z_pos = 0.000
    Num_Bonds = 0
    Atom_Bonds = []
    primary = {}
    secondary = {}
    tertiary = {}
    related = {}
    ring = False

    #constructor
    def __init__(self, atom_id, atom_type, x_pos, y_pos, z_pos):
        self.atom_id = atom_id
        self.atom_type = atom_type
        self.x_pos = x_pos
        self.y_pos = y_pos
        self.z_pos = z_pos
        self.Atom_Bonds = []
        self.Num_Bonds = 0
        ring = False
        primary = {}
        secondary = {}
        tertiary = {}
        related = {}

#create Bond object 
class Bond(object):
   bond_type = ""
   bond_master = ""
   bond_slave = ""

   #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

#create angle object
class Angle(object):
    Angle_type = 0
    Angle_master = ""
    Angle_slave1 = ""
    Angle_slave2 = ""
    
    #constructor
    def __init__(self, Angle_type, Angle_master, Angle_slave1, Angle_slave2):
        self.Angle_type = Angle_type
        self.Angle_master = Angle_master
        self.Angle_slave1 = Angle_slave1
        self.Angle_slave2 = Angle_slave2

#create dihedral object
class Dihedral(object):
    Angle1 = ""
    Angle2 = ""
    Angle3 = ""

    def __init__(self, Angle1, Angle2, Angle3):
        self.Angle1 = Angle1
        self.Angle2 = Angle2
        self.Angle3 = Angle3
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