"""
Atomic Data Constants
This module contains atomic properties and constants for all elements
commonly found in protein, DNA, RNA, and water molecules in PDB structures.
"""
[docs]
class AtomicData:
"""Atomic properties and constants.
This class contains atomic data for all elements commonly found in
protein, DNA, RNA, and water molecules in PDB structures.
"""
# Covalent radii in Angstroms
COVALENT_RADII = {
# Main biomolecule elements
"H": 0.31, # Hydrogen
"D": 0.31, # Deuterium (same as H)
"C": 0.76, # Carbon
"N": 0.71, # Nitrogen
"O": 0.66, # Oxygen
"P": 1.07, # Phosphorus (DNA/RNA backbone)
"S": 1.05, # Sulfur (Cys, Met)
# Halogens
"F": 0.57, # Fluorine
"CL": 0.99, # Chlorine
"BR": 1.14, # Bromine
"I": 1.33, # Iodine
# Common metals in proteins
"NA": 1.66, # Sodium
"MG": 1.41, # Magnesium
"K": 2.03, # Potassium
"CA": 1.76, # Calcium
"MN": 1.39, # Manganese
"FE": 1.32, # Iron
"CO": 1.26, # Cobalt
"NI": 1.24, # Nickel
"CU": 1.32, # Copper
"ZN": 1.22, # Zinc
}
# Van der Waals radii in Angstroms
VDW_RADII = {
# Main group
# Row 1 (Period 1)
"H": 1.10,
"HE": 1.40,
# Row 2 (Period 2)
"LI": 1.81,
"BE": 1.53,
"B": 1.92,
"C": 1.70,
"N": 1.55,
"O": 1.52,
"F": 1.47,
"NE": 1.54,
# Row 3 (Period 3)
"NA": 2.27,
"MG": 1.73,
"AL": 1.84,
"SI": 2.10,
"P": 1.80,
"S": 1.80,
"CL": 1.75,
"AR": 1.88,
# Row 4 (Period 4)
"K": 2.75,
"CA": 2.31,
"GA": 1.87,
"GE": 2.11,
"AS": 1.85,
"SE": 1.90,
"BR": 1.83,
"KR": 2.02,
# Row 5 (Period 5)
"RB": 3.03,
"SR": 2.49,
"IN": 1.93,
"SN": 2.17,
"SB": 2.06,
"TE": 2.06,
"I": 1.98,
"XE": 2.16,
# Row 6 (Period 6)
"CS": 3.43,
"BA": 2.68,
"TL": 1.96,
"PB": 2.02,
"BI": 2.07,
"PO": 1.97,
"AT": 2.02,
"RN": 2.20,
# Row 7 (Period 7)
"FR": 3.48,
"RA": 2.83,
# Transition metals (relevant ones only)
# Row 1
"FE": 2.05,
"CU": 2.00,
"ZN": 2.10,
"MN": 2.05,
"CO": 2.00,
"NI": 2.00,
# Row 2
"MO": 2.10,
"RU": 2.05,
# Row 3
"W": 2.10,
"PT": 2.05,
"AU": 2.10,
}
# Electronegativity values (Pauling scale)
ELECTRONEGATIVITY = {
# Main biomolecule elements
"H": 2.20, # Hydrogen
"D": 2.20, # Deuterium (same as H)
"C": 2.55, # Carbon
"N": 3.04, # Nitrogen
"O": 3.44, # Oxygen
"P": 2.19, # Phosphorus (DNA/RNA backbone)
"S": 2.58, # Sulfur (Cys, Met)
# Halogens
"F": 3.98, # Fluorine
"CL": 3.16, # Chlorine
"BR": 2.96, # Bromine
"I": 2.66, # Iodine
# Common metals in proteins (less relevant for covalent interactions)
"NA": 0.93, # Sodium
"MG": 1.31, # Magnesium
"K": 0.82, # Potassium
"CA": 1.00, # Calcium
"MN": 1.55, # Manganese
"FE": 1.83, # Iron
"CO": 1.88, # Cobalt
"NI": 1.91, # Nickel
"CU": 1.90, # Copper
"ZN": 1.65, # Zinc
}
# Atomic masses in amu (atomic mass units)
ATOMIC_MASSES = {
# Main biomolecule elements
"H": 1.008, # Hydrogen
"D": 2.014, # Deuterium (heavy hydrogen)
"C": 12.011, # Carbon
"N": 14.007, # Nitrogen
"O": 15.999, # Oxygen
"P": 30.974, # Phosphorus (DNA/RNA backbone)
"S": 32.065, # Sulfur (Cys, Met)
# Halogens
"F": 18.998, # Fluorine
"CL": 35.453, # Chlorine
"BR": 79.904, # Bromine
"I": 126.904, # Iodine
# Common metals in proteins
"NA": 22.990, # Sodium
"MG": 24.305, # Magnesium
"K": 39.098, # Potassium
"CA": 40.078, # Calcium
"MN": 54.938, # Manganese
"FE": 55.845, # Iron
"CO": 58.933, # Cobalt
"NI": 58.693, # Nickel
"CU": 63.546, # Copper
"ZN": 65.38, # Zinc
}
# Default atomic mass for unknown elements
DEFAULT_ATOMIC_MASS = 12.011 # Carbon mass
# Hydrogen detection threshold
MIN_HYDROGEN_RATIO = 0.25 # 25% of atoms must be hydrogen
# Metal elements
METAL_ELEMENTS = {"NA", "MG", "K", "CA", "MN", "FE", "CO", "NI", "CU", "ZN"}
