MFE_utils
=========

.. py:module:: MFE_utils


Attributes
----------

.. autoapisummary::

   MFE_utils.SIMPLE_PAIRING_FE
   MFE_utils.TURNER_FE
   MFE_utils._INT_PAIRS
   MFE_utils._PAIRS
   MFE_utils._PAIRS_INV


Functions
---------

.. autoapisummary::

   MFE_utils.base_as_int
   MFE_utils.int_as_base
   MFE_utils.pair_int_as_str
   MFE_utils.pair_int_as_tuple
   MFE_utils.str_as_pair_int
   MFE_utils.tuple_as_pair_int


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

.. py:data:: SIMPLE_PAIRING_FE

.. py:data:: TURNER_FE

.. py:data:: _INT_PAIRS

.. py:data:: _PAIRS
   :value: ('AU', 'CG', 'GC', 'GU', 'UA', 'UG')


.. py:data:: _PAIRS_INV
   :type:  dict[Union[str, tuple[int, int]], int]

.. py:function:: base_as_int(c)

   Map one character from bases ACGU to an int 0..3


.. py:function:: int_as_base(r)

   Map int bases 0..3 to a character from ACGU


.. py:function:: pair_int_as_str(pair_int)

   Convert pair-int to str form (e.g. 3 -> 'GU')


.. py:function:: pair_int_as_tuple(pair_int)

.. py:function:: str_as_pair_int(p)

   Convert a pair-str to an index to various tables (or -1)

   p is a string pair like "GU" and the return is an integer index
   in a list of Watson-Crick-Franklin pairs for RNA including GU.
   If p is not one of those pairs, -1 is returned.


.. py:function:: tuple_as_pair_int(r, s)

   Convert a pair of bases to an index to various tables (or -1)

   (r,s) is a base pair like (2,3) (signifying "GU") and the return
   is an integer index in a list of Watson-Crick-Franklin pairs for
   RNA including GU. If (r,s) is not one of those pairs, -1 is
   returned.