prolint.config¶

ProLint configuration module.

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

Submodules¶

Attributes¶

`COLORS`
`COLOR_SCALES`
`GRADIENTS`
`AMINO_ACID_COLORS`
`AMINO_ACID_ONE_LETTER`
`UNIT_LABELS`

Classes¶

`TimeUnit`	Time unit options for contact duration analysis.
`NormalizationMethod`	Normalization methods for contact durations.
`UnitConversionFactor`	Conversion factors from time units to seconds.
`SimulationParams`	Simulation parameters for contact calculations.

Functions¶

`load_theme`(→ Dict)	Load the ProLint color theme from JSON file.
`hex_to_rgb`(→ Tuple[int, int, int])	Convert hex color string to RGB tuple.
`color_to_tuple`(→ Tuple[float, float, float, float])	Convert color dict to RGBA tuple.
`interpolate_gradient`(→ Tuple[float, float, float, float])	Interpolate a color from a gradient based on value.
`get_color_for_value`(→ str)	Get a hex color for a value from a discrete color scale.
`get_unit_label`(→ str)	Get display label for a time unit.
`setup_logging`(→ logging.Logger)	Configure logging for ProLint.
`get_logger`(→ logging.Logger)	Get a child logger for a ProLint module.

Package Contents¶

class prolint.config.TimeUnit[source]¶

Bases: str, enum.Enum

Time unit options for contact duration analysis.

FEMTOSECOND¶

Femtoseconds (“fs”).

Type:: str

PICOSECOND¶

Picoseconds (“ps”).

Type:: str

NANOSECOND¶

Nanoseconds (“ns”).

Type:: str

MICROSECOND¶

Microseconds (“us”).

Type:: str

MILLISECOND¶

Milliseconds (“ms”).

Type:: str

SECOND¶

Seconds (“s”).

Type:: str

FEMTOSECOND = 'fs'¶

PICOSECOND = 'ps'¶

NANOSECOND = 'ns'¶

MICROSECOND = 'us'¶

MILLISECOND = 'ms'¶

SECOND = 's'¶

class prolint.config.NormalizationMethod[source]¶

Bases: str, enum.Enum

Normalization methods for contact durations.

COUNTS¶

Report durations as frame counts (“counts”).

Type:: str

ACTUAL_TIME¶

Report durations in time units (“actual_time”).

Type:: str

COUNTS = 'counts'¶

ACTUAL_TIME = 'actual_time'¶

class prolint.config.UnitConversionFactor(*args, **kwds)[source]¶

Bases: enum.Enum

Conversion factors from time units to seconds.

Each member’s value represents the unit in seconds.

fs¶

Femtoseconds (1e-15 s).

Type:: float

ps¶

Picoseconds (1e-12 s).

Type:: float

ns¶

Nanoseconds (1e-9 s).

Type:: float

us¶

Microseconds (1e-6 s).

Type:: float

ms¶

Milliseconds (1e-3 s).

Type:: float

s¶

Seconds (1.0 s).

Type:: float

fs = 1e-15¶

ps = 1e-12¶

ns = 1e-09¶

us = 1e-06¶

ms = 0.001¶

s = 1.0¶

class prolint.config.SimulationParams[source]¶

Simulation parameters for contact calculations.

units¶

Time units for output (default: “us”).

Type:: str

normalizer¶

Normalization method (default: “actual_time”).

Type:: str

unit_conversion_factor¶

Factor to convert trajectory time to output units.

Type:: float

norm_factor¶

Normalization factor for contact durations.

Type:: float

units: str = 'us'¶

normalizer: str = 'actual_time'¶

unit_conversion_factor: float = 1e-06¶

norm_factor: float = 1.0¶

prolint.config.load_theme() → Dict[source]¶

Load the ProLint color theme from JSON file.

Returns:: Theme configuration containing colors, gradients, and amino acid mappings.
Return type:: dict

prolint.config.COLORS: Dict[source]¶

prolint.config.COLOR_SCALES: Dict[str, List[str]][source]¶

prolint.config.GRADIENTS: Dict[source]¶

prolint.config.AMINO_ACID_COLORS: Dict[str, str][source]¶

prolint.config.AMINO_ACID_ONE_LETTER: Dict[str, str][source]¶

prolint.config.UNIT_LABELS: Dict[str, str][source]¶

prolint.config.hex_to_rgb(hex_color: str) → Tuple[int, int, int][source]¶

Convert hex color string to RGB tuple.

Parameters:: hex_color (str) – Hex color string (e.g., “#FF5733” or “FF5733”).
Returns:: RGB values as (red, green, blue), each 0-255.
Return type:: tuple of int

prolint.config.color_to_tuple(color: Dict, normalize: bool = True) → Tuple[float, float, float, float][source]¶

Convert color dict to RGBA tuple.

Parameters:

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

Returns:

RGBA values as (red, green, blue, alpha).

Return type:

tuple of float

prolint.config.interpolate_gradient(value: float, min_val: float, max_val: float, gradient_name: str = 'sharedContacts') → Tuple[float, float, float, float][source]¶

Interpolate a color from a gradient based on value.

Parameters:

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

Returns:

Interpolated RGBA color values (0-1 range).

Return type:

tuple of float

prolint.config.get_color_for_value(value: float, scale_name: str = 'prolint', vmin: float = 0, vmax: float = 1) → str[source]¶

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

Parameters:

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

Returns:

Hex color string.

Return type:

str

prolint.config.get_unit_label(unit: str) → str[source]¶

Get display label for a time unit.

Parameters:: unit (str) – Time unit code (e.g., “us”, “ns”, “ps”).
Returns:: Human-readable unit label (e.g., “μs”, “ns”, “ps”).
Return type:: str

prolint.config.setup_logging(level: int = logging.INFO, format_string: str | None = None, simple: bool = False) → logging.Logger[source]¶

Configure logging for ProLint.

Parameters:

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

Returns:

Configured ProLint logger instance.

Return type:

logging.Logger

prolint.config.get_logger(name: str) → logging.Logger[source]¶

Get a child logger for a ProLint module.

Parameters:: name (str) – Module name (will be prefixed with “prolint.”).
Returns:: Logger instance for the specified module.
Return type:: logging.Logger