text: # Copyright 2016 Autodesk Inc.
  #
  # Licensed under the Apache License, Version 2.0 (the "License");
  # you may not use this file except in compliance with the License.
  # You may obtain a copy of the License at
  #
  #     http://www.apache.org/licenses/LICENSE-2.0
  #
  # Unless required by applicable law or agreed to in writing, software
  # distributed under the License is distributed on an "AS IS" BASIS,
  # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
  # See the License for the specific language governing permissions and
  # limitations under the License.
  
  """
  This module is used to store information for DNA physical parameters.
  """
  
  class DnaParameters(object):
      """ This class stores information for DNA parameters.
  
          Attributes:
              helix_distance: The distance between the axes of two neighboring DNA helices.
              helix_radius: The radius of DNA helices (nm).
              base_pair_rise: The rise between two neighboring base-pairs (nm).
              base_pair_twist_angle: The twisting angle between two neighboring base-pairs (degree).
              minor_groove_angle: The angle of the minor groove (degree).
      """
      def __init__(self):
          self.helix_distance = 2.3
          self.helix_radius = 1.0
          self.base_pair_rise = 0.34
          self.base_pair_twist_angle = 360 / 10.5
          self.minor_groove_angle = 120.0
  
  class DnaPolarity:
      """ This class defines constants used to describe the polarity of a DNA strand. 
  
          Attributes:
              FIVE_PRIME (string): The direction of a DNA strand is from 5'->3'. When indexing the bases in a helix this means 
                  indexes increase in the 5'->3' direction.
              THREE_PRIME (string): The direction of a DNA strand is from 3'->5'. When indexing the bases in a helix this means 
                  indexes increase in the 3'->5' direction.
      """
      FIVE_PRIME = "5'"
      THREE_PRIME = "3'"
  
  class DnaBaseNames:
      A = "A"
      C = "C"
      G = "G"
      T = "T"
  
  