mythos.input.oxdna_input
========================

.. py:module:: mythos.input.oxdna_input

.. autoapi-nested-parse::

   oxDNA input file parser.



Attributes
----------

.. autoapisummary::

   mythos.input.oxdna_input.INVALID_DICT_LINE


Classes
-------

.. autoapisummary::

   mythos.input.oxdna_input.oxDNAInputData


Functions
---------

.. autoapisummary::

   mythos.input.oxdna_input._parse_numeric
   mythos.input.oxdna_input._parse_boolean
   mythos.input.oxdna_input._parse_value
   mythos.input.oxdna_input._parse_dict
   mythos.input.oxdna_input.read
   mythos.input.oxdna_input.write_to
   mythos.input.oxdna_input.read_box_size
   mythos.input.oxdna_input.read_input_dir
   mythos.input.oxdna_input.write


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

.. py:data:: INVALID_DICT_LINE
   :value: 'Invalid dictionary line: {}'


.. py:function:: _parse_numeric(value: str) -> tuple[float | int, bool]

.. py:function:: _parse_boolean(value: str) -> tuple[bool, bool]

.. py:function:: _parse_value(value: str) -> str | float | int | bool

.. py:function:: _parse_dict(in_line: str, lines: Iterable[str]) -> tuple[dict[str, str | float | int | bool], Iterable[str]]

.. py:function:: read(input_file: pathlib.Path) -> dict[str, str | float | int | bool]

   Read an oxDNA input file.


.. py:function:: write_to(input_config: dict, f: io.TextIOWrapper) -> None

   Write an oxDNA input file.


.. py:function:: read_box_size(conf_file: pathlib.Path) -> jax.numpy.ndarray

   Read the box size from an oxDNA configuration file.

   Parses the ``b = ...`` line from the configuration file header.

   :param conf_file: Path to the oxDNA configuration (``.conf`` / ``.dat``) file.

   :returns: A JAX array of shape ``(3,)`` with the box dimensions.

   :raises ValueError: If no ``b = ...`` line is found in the file.


.. py:class:: oxDNAInputData

   Data loaded from an oxDNA input directory.

   .. attribute:: topology

      The parsed topology.

   .. attribute:: kT

      The simulation temperature in oxDNA energy units.

   .. attribute:: box_size

      Box dimensions as a JAX array of shape ``(3,)``.

   .. attribute:: config

      The full parsed input-file dictionary.


   .. py:attribute:: topology
      :type:  mythos.input.topology.Topology


   .. py:attribute:: kT
      :type:  float


   .. py:attribute:: box_size
      :type:  jax.numpy.ndarray


   .. py:attribute:: config
      :type:  dict[str, Any]


.. py:function:: read_input_dir(input_dir: pathlib.Path, input_file: str = 'input') -> oxDNAInputData

   Load topology, temperature and box size from an oxDNA input directory.

   Reads the oxDNA ``input`` file (or the name given by *input_file*),
   extracts the topology, simulation temperature (``kT``), and box
   dimensions from the configuration files referenced therein.

   :param input_dir: Directory containing the oxDNA input files.
   :param input_file: Name of the input file inside *input_dir*.

   :returns: An :class:`oxDNAInputData` with the parsed values.


.. py:function:: write(input_config: dict, input_file: pathlib.Path) -> None

   Write an oxDNA input file.