mythos.simulators.oxdna.utils
=============================

.. py:module:: mythos.simulators.oxdna.utils

.. autoapi-nested-parse::

   Utilities for the oxDNA simulator.



Attributes
----------

.. autoapisummary::

   mythos.simulators.oxdna.utils.ERR_CANNOT_PROCESS_SRC_H
   mythos.simulators.oxdna.utils.ERR_INVALID_HEADER_TYPE
   mythos.simulators.oxdna.utils.SYMPY_EVAL_N
   mythos.simulators.oxdna.utils.DEFAULT_OXDNA_VARIABLE_MAPPER
   mythos.simulators.oxdna.utils.MIN_VALID_HEADER_TOKEN_COUNT


Functions
---------

.. autoapisummary::

   mythos.simulators.oxdna.utils._parse_value_in
   mythos.simulators.oxdna.utils._parse_value_out
   mythos.simulators.oxdna.utils.read_src_h
   mythos.simulators.oxdna.utils.write_src_h
   mythos.simulators.oxdna.utils.update_params
   mythos.simulators.oxdna.utils._get_order_parameter_names
   mythos.simulators.oxdna.utils.read_energy
   mythos.simulators.oxdna.utils.read_output_trajectory
   mythos.simulators.oxdna.utils.read_last_hist


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

.. py:data:: ERR_CANNOT_PROCESS_SRC_H
   :value: 'Cannot process src/model.h file. Failed parsing: {}'


.. py:data:: ERR_INVALID_HEADER_TYPE
   :value: 'Invalid header value variable {} with value {}'


.. py:data:: SYMPY_EVAL_N
   :type:  int
   :value: 32


.. py:data:: DEFAULT_OXDNA_VARIABLE_MAPPER

.. py:data:: MIN_VALID_HEADER_TOKEN_COUNT
   :value: 3


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

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

.. py:function:: read_src_h(src_h: pathlib.Path) -> dict[str, int | float | str]

   Parse the src/model.h file to get the parameters.


.. py:function:: write_src_h(src_h: pathlib.Path, params: dict[str, tuple[mythos.utils.types.oxDNAModelHType, int | float | str]]) -> None

   Write the src/model.h file with the new parameters.


.. py:function:: update_params(src_h: pathlib.Path, new_params: mythos.utils.types.Params | list[mythos.utils.types.Params]) -> None

   Update the src/model.h file with the new parameters.


.. py:function:: _get_order_parameter_names(op_file: pathlib.Path) -> list[str]

.. py:function:: read_energy(simulation_dir: pathlib.Path) -> pandas.DataFrame

   Read the energy.dat file from an oxDNA simulation.

   :param simulation_dir: Path to the simulation directory containing the
                          energy.dat and other simulation files. this directory must also
                          contain the input file, which is read to determine the shape of the
                          energy file.

   :returns: A pandas DataFrame containing the energy data. When umbrella sampling is
             enabled, the order parameter columns and weight column are also
             included, where the order parameter name comes from the
             "order_parameter" specification in the "op_file".


.. py:function:: read_output_trajectory(input_file: mythos.utils.types.PathOrStr) -> mythos.input.trajectory.Trajectory

   Read trajectory from an oxDNA input directory.

   This is a convenience function that reads the topology and trajectory files
   from an oxDNA input directory to determine the correct read format.

   :param input_file: path to the oxDNA input file.
   :type input_file: PathOrStr


.. py:function:: read_last_hist(simulation_dir: pathlib.Path) -> pandas.DataFrame

   Read the last histogram from an oxDNA simulation with umbrella sampling.

   :param simulation_dir: Path to the simulation directory containing the
                          histograms and other simulation files. this directory must also
                          contain the input file, which is read to determine the shape of the
                          histogram file.

   :returns: A pandas DataFrame containing the last histogram data. The columns
             correspond to the order parameters specified in the "op_file", as well
             as the counts and unbiased counts, and any extrapolation temperatures
             specified in the input file's extrapolate_hist parameter.