prolint.config
==============

.. py:module:: prolint.config

.. autoapi-nested-parse::

   ProLint configuration module.

   This module provides configuration classes, enums, and utilities
   for customizing ProLint behavior.



Submodules
----------

.. toctree::
   :maxdepth: 1

   /autoapi/prolint/config/colors/index
   /autoapi/prolint/config/enums/index
   /autoapi/prolint/config/logging/index
   /autoapi/prolint/config/units/index


Attributes
----------

.. autoapisummary::

   prolint.config.COLORS
   prolint.config.COLOR_SCALES
   prolint.config.GRADIENTS
   prolint.config.AMINO_ACID_COLORS
   prolint.config.AMINO_ACID_ONE_LETTER
   prolint.config.UNIT_LABELS


Classes
-------

.. autoapisummary::

   prolint.config.TimeUnit
   prolint.config.NormalizationMethod
   prolint.config.UnitConversionFactor
   prolint.config.SimulationParams


Functions
---------

.. autoapisummary::

   prolint.config.load_theme
   prolint.config.hex_to_rgb
   prolint.config.color_to_tuple
   prolint.config.interpolate_gradient
   prolint.config.get_color_for_value
   prolint.config.get_unit_label
   prolint.config.setup_logging
   prolint.config.get_logger


Package Contents
----------------

.. py:class:: TimeUnit

   Bases: :py:obj:`str`, :py:obj:`enum.Enum`


   Time unit options for contact duration analysis.

   .. attribute:: FEMTOSECOND

      Femtoseconds ("fs").

      :type: str

   .. attribute:: PICOSECOND

      Picoseconds ("ps").

      :type: str

   .. attribute:: NANOSECOND

      Nanoseconds ("ns").

      :type: str

   .. attribute:: MICROSECOND

      Microseconds ("us").

      :type: str

   .. attribute:: MILLISECOND

      Milliseconds ("ms").

      :type: str

   .. attribute:: SECOND

      Seconds ("s").

      :type: str


   .. py:attribute:: FEMTOSECOND
      :value: 'fs'



   .. py:attribute:: PICOSECOND
      :value: 'ps'



   .. py:attribute:: NANOSECOND
      :value: 'ns'



   .. py:attribute:: MICROSECOND
      :value: 'us'



   .. py:attribute:: MILLISECOND
      :value: 'ms'



   .. py:attribute:: SECOND
      :value: 's'



.. py:class:: NormalizationMethod

   Bases: :py:obj:`str`, :py:obj:`enum.Enum`


   Normalization methods for contact durations.

   .. attribute:: COUNTS

      Report durations as frame counts ("counts").

      :type: str

   .. attribute:: ACTUAL_TIME

      Report durations in time units ("actual_time").

      :type: str


   .. py:attribute:: COUNTS
      :value: 'counts'



   .. py:attribute:: ACTUAL_TIME
      :value: 'actual_time'



.. py:class:: UnitConversionFactor(*args, **kwds)

   Bases: :py:obj:`enum.Enum`


   Conversion factors from time units to seconds.

   Each member's value represents the unit in seconds.

   .. attribute:: fs

      Femtoseconds (1e-15 s).

      :type: float

   .. attribute:: ps

      Picoseconds (1e-12 s).

      :type: float

   .. attribute:: ns

      Nanoseconds (1e-9 s).

      :type: float

   .. attribute:: us

      Microseconds (1e-6 s).

      :type: float

   .. attribute:: ms

      Milliseconds (1e-3 s).

      :type: float

   .. attribute:: s

      Seconds (1.0 s).

      :type: float


   .. py:attribute:: fs
      :value: 1e-15



   .. py:attribute:: ps
      :value: 1e-12



   .. py:attribute:: ns
      :value: 1e-09



   .. py:attribute:: us
      :value: 1e-06



   .. py:attribute:: ms
      :value: 0.001



   .. py:attribute:: s
      :value: 1.0



.. py:class:: SimulationParams

   Simulation parameters for contact calculations.

   .. attribute:: units

      Time units for output (default: "us").

      :type: str

   .. attribute:: normalizer

      Normalization method (default: "actual_time").

      :type: str

   .. attribute:: unit_conversion_factor

      Factor to convert trajectory time to output units.

      :type: float

   .. attribute:: norm_factor

      Normalization factor for contact durations.

      :type: float


   .. py:attribute:: units
      :type:  str
      :value: 'us'



   .. py:attribute:: normalizer
      :type:  str
      :value: 'actual_time'



   .. py:attribute:: unit_conversion_factor
      :type:  float
      :value: 1e-06



   .. py:attribute:: norm_factor
      :type:  float
      :value: 1.0



.. py:function:: load_theme() -> Dict

   Load the ProLint color theme from JSON file.

   :returns: Theme configuration containing colors, gradients, and amino acid mappings.
   :rtype: dict


.. py:data:: COLORS
   :type:  Dict

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

.. py:data:: GRADIENTS
   :type:  Dict

.. py:data:: AMINO_ACID_COLORS
   :type:  Dict[str, str]

.. py:data:: AMINO_ACID_ONE_LETTER
   :type:  Dict[str, str]

.. py:data:: UNIT_LABELS
   :type:  Dict[str, str]

.. py:function:: hex_to_rgb(hex_color: str) -> Tuple[int, int, int]

   Convert hex color string to RGB tuple.

   :param hex_color: Hex color string (e.g., "#FF5733" or "FF5733").
   :type hex_color: str

   :returns: RGB values as (red, green, blue), each 0-255.
   :rtype: tuple of int


.. py:function:: color_to_tuple(color: Dict, normalize: bool = True) -> Tuple[float, float, float, float]

   Convert color dict to RGBA tuple.

   :param color: Color dict with "r", "g", "b", "a" keys (RGB in 0-255, alpha in 0-1).
   :type color: dict
   :param normalize: If True, normalize RGB values to 0-1 range. Alpha is unchanged.
   :type normalize: bool, default=True

   :returns: RGBA values as (red, green, blue, alpha).
   :rtype: tuple of float


.. py:function:: interpolate_gradient(value: float, min_val: float, max_val: float, gradient_name: str = 'sharedContacts') -> Tuple[float, float, float, float]

   Interpolate a color from a gradient based on value.

   :param value: Value to map to a color.
   :type value: float
   :param min_val: Minimum value of the range.
   :type min_val: float
   :param max_val: Maximum value of the range.
   :type max_val: float
   :param gradient_name: Name of the gradient to use from GRADIENTS.
   :type gradient_name: str, default="sharedContacts"

   :returns: Interpolated RGBA color values (0-1 range).
   :rtype: tuple of float


.. py:function:: get_color_for_value(value: float, scale_name: str = 'prolint', vmin: float = 0, vmax: float = 1) -> str

   Get a hex color for a value from a discrete color scale.

   :param value: Value to map to a color.
   :type value: float
   :param scale_name: Name of the color scale from COLOR_SCALES.
   :type scale_name: str, default="prolint"
   :param vmin: Minimum value of the range.
   :type vmin: float, default=0
   :param vmax: Maximum value of the range.
   :type vmax: float, default=1

   :returns: Hex color string.
   :rtype: str


.. py:function:: get_unit_label(unit: str) -> str

   Get display label for a time unit.

   :param unit: Time unit code (e.g., "us", "ns", "ps").
   :type unit: str

   :returns: Human-readable unit label (e.g., "μs", "ns", "ps").
   :rtype: str


.. py:function:: setup_logging(level: int = logging.INFO, format_string: Optional[str] = None, simple: bool = False) -> logging.Logger

   Configure logging for ProLint.

   :param level: Logging level (e.g., logging.DEBUG, logging.INFO).
   :type level: int, default=logging.INFO
   :param format_string: Custom format string for log messages.
   :type format_string: str, optional
   :param simple: If True, use simplified format without timestamps.
   :type simple: bool, default=False

   :returns: Configured ProLint logger instance.
   :rtype: logging.Logger


.. py:function:: get_logger(name: str) -> logging.Logger

   Get a child logger for a ProLint module.

   :param name: Module name (will be prefixed with "prolint.").
   :type name: str

   :returns: Logger instance for the specified module.
   :rtype: logging.Logger