Constants and Configuration

This module contains constants and default values used throughout HBAT.

Constants Module

HBAT Constants and Default Parameters

This module centralizes all default parameter values used throughout the HBAT application for both CLI and GUI interfaces.

class hbat.constants.AnalysisDefaults

Bases: object

Default values for molecular interaction analysis parameters.

HB_DISTANCE_CUTOFF = 3.5

HB_ANGLE_CUTOFF = 120.0

HB_DA_DISTANCE = 4.0

XB_DISTANCE_CUTOFF = 4.0

XB_ANGLE_CUTOFF = 120.0

PI_DISTANCE_CUTOFF = 4.5

PI_ANGLE_CUTOFF = 90.0

COVALENT_CUTOFF_FACTOR = 1.2

ANALYSIS_MODE = 'complete'

class hbat.constants.AtomicData

Bases: object

Atomic properties and constants.

COVALENT_RADII = {'BR': 1.14, 'C': 0.76, 'CA': 1.76, 'CL': 0.99, 'F': 0.57, 'H': 0.31, 'I': 1.33, 'K': 2.03, 'MG': 1.41, 'N': 0.71, 'NA': 1.66, 'O': 0.66, 'P': 1.07, 'S': 1.05}

VDW_RADII = {'BR': 1.85, 'C': 1.7, 'CA': 2.31, 'CL': 1.75, 'F': 1.47, 'H': 1.09, 'I': 1.98, 'K': 2.75, 'MG': 1.73, 'N': 1.55, 'NA': 2.27, 'O': 1.52, 'P': 1.8, 'S': 1.8}

ELECTRONEGATIVITY = {'BR': 2.96, 'C': 2.55, 'CL': 3.16, 'F': 3.98, 'H': 2.2, 'I': 2.66, 'N': 3.04, 'O': 3.44, 'S': 2.58}

ATOMIC_MASSES = {'BR': 79.904, 'C': 12.011, 'CA': 40.078, 'CL': 35.453, 'CO': 58.933, 'CU': 63.546, 'D': 2.014, 'F': 18.998, 'FE': 55.845, 'H': 1.008, 'I': 126.904, 'K': 39.098, 'MG': 24.305, 'MN': 54.938, 'N': 14.007, 'NA': 22.99, 'NI': 58.693, 'O': 15.999, 'P': 30.974, 'S': 32.065, 'ZN': 65.38}

DEFAULT_ATOMIC_MASS = 12.011

MIN_HYDROGEN_RATIO = 0.25

class hbat.constants.GUIDefaults

Bases: object

Default values for GUI interface.

WINDOW_WIDTH = 1800

WINDOW_HEIGHT = 900

MIN_WINDOW_WIDTH = 1200

MIN_WINDOW_HEIGHT = 800

LEFT_PANEL_WIDTH = 400

PROGRESS_BAR_INTERVAL = 10

class hbat.constants.VectorDefaults

Bases: object

Default values for vector operations.

DEFAULT_X = 0.0

DEFAULT_Y = 0.0

DEFAULT_Z = 0.0

class hbat.constants.FileFormats

Bases: object

Supported file formats and extensions.

PDB_EXTENSIONS = ['.pdb']

OUTPUT_EXTENSIONS = ['.txt', '.csv', '.json']

JSON_VERSION = '0.0.0+unknown'

class hbat.constants.AnalysisModes

Bases: object

Available analysis modes.

COMPLETE = 'complete'

LOCAL = 'local'

ALL_MODES = ['complete', 'local']

class hbat.constants.ParameterRanges

Bases: object

Valid ranges for analysis parameters.

MIN_DISTANCE = 0.1

MAX_DISTANCE = 10.0

MIN_ANGLE = 0.0

MAX_ANGLE = 180.0

MIN_COVALENT_FACTOR = 0.5

MAX_COVALENT_FACTOR = 3.0