utils
=====

.. py:module:: utils


Attributes
----------

.. autoapisummary::

   utils.ALL_CODONS
   utils.CODON_TABLE
   utils.CODON_TO_IDX
   utils.IDX_TO_CODON
   utils.N_CODONS
   utils.STOP_CODONS
   utils.codon_gc_counts


Functions
---------

.. autoapisummary::

   utils.compute_cai
   utils.compute_gc_content_vectorized
   utils.compute_mfe_energy
   utils.compute_reward
   utils.compute_reward_components
   utils.decode_sequence
   utils.get_synonymous_indices
   utils.load_config
   utils.plot_training_curves
   utils.to_mRNA_string
   utils.tokenize_sequence_to_tensor


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

.. py:data:: ALL_CODONS
   :type:  List[str]

.. py:data:: CODON_TABLE
   :type:  Dict[str, List[str]]

.. py:data:: CODON_TO_IDX
   :type:  Dict[str, int]

.. py:data:: IDX_TO_CODON
   :type:  Dict[int, str]

.. py:data:: N_CODONS
   :type:  int

.. py:data:: STOP_CODONS
   :type:  List[str]
   :value: ['UAA', 'UAG', 'UGA']


.. py:data:: codon_gc_counts

.. py:function:: compute_cai(indices, energies=None, loop_min=4)

   Compute CAI using the CAICalculator.


.. py:function:: compute_gc_content_vectorized(indices, codon_gc_counts)

   Vectorized GC content calculation using precomputed codon GC counts


.. py:function:: compute_mfe_energy(indices, energies=None, loop_min=4)

   Compute the minimum free energy (MFE) of an RNA sequence using Zucker Algorithm.


.. py:function:: compute_reward(state, codon_gc_counts, weights)

   Compute the total weighted reward and its components:
   reward = w1 * GC + w2 * (-MFE) + w3 * CAI


.. py:function:: compute_reward_components(state, codon_gc_counts)

   Compute GC content, MFE, and CAI for a given RNA tensor state.


.. py:function:: decode_sequence(tensor_seq)

.. py:function:: get_synonymous_indices(amino_acid)

   Return the list of global codon indices that encode the given amino acid.
   Handles standard amino acids and '*'.


.. py:function:: load_config(path)

.. py:function:: plot_training_curves(loss_history, reward_components, out_path='training_curves.png')

.. py:function:: to_mRNA_string(rna_tensor)

.. py:function:: tokenize_sequence_to_tensor(seq)