dna
===

.. py:module:: dna

.. autoapi-nested-parse::

   Class to represent DNA sequences.



Attributes
----------

.. autoapisummary::

   dna.NUCLEOBASES
   dna.PAD_TOKEN


Classes
-------

.. autoapisummary::

   dna.DNA


Module Contents
---------------

.. py:data:: NUCLEOBASES
   :value: ('A', 'C', 'T', 'G')


.. py:data:: PAD_TOKEN
   :value: '0'


.. py:class:: DNA(proxy_fmt = 'onehot-np', **kwargs)

   Bases: :py:obj:`gflownet.envs.sequences.base.SequenceBase`


   :param proxy_fmt:
                     Specifies the proxy format. Options:
                         - onehot: One-hot encoding
                         - letters: The nucleobases as a list of strings
                         - np or numpy: numpy, for the onehot case
                         - torch or tensor: torch tensor, for the onehot case
   :type proxy_fmt: str


   .. py:method:: states2proxy_onehot(states)

      Prepares a batch of states in "environment format" for a proxy model: states
      are one-hot encoded. If numpy is True (default), the output is converted into a
      numpy array, otherwise it remains a torch tensor.

      Example, with max_length = 5:
        - Sequence (tokens): ACGC
        - state: [1, 2, 4, 2, 0]
        - policy format:
              [0, 1, 0, 0, 0, (A)
               0, 0, 1, 0, 0, (C)
               0, 0, 0, 0, 1, (G)
               0, 0, 1, 0, 0, (C)
               1, 0, 0, 0, 0] (PAD)

      :param states: A batch of states in environment format, either as a list of states or as a
                     single tensor.
      :type states: tensor

      :returns: *A numpy array containing the one-hot encoding of all the states in the batch.*