Atomic Data

Contains atomic properties and constants for elements commonly found in PDB structures.

Module Overview

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.

class hbat.constants.atomic_data.AtomicData

Bases: object

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 = {'BR': 1.14, 'C': 0.76, 'CA': 1.76, 'CL': 0.99, 'CO': 1.26, 'CU': 1.32, 'D': 0.31, 'F': 0.57, 'FE': 1.32, 'H': 0.31, 'I': 1.33, 'K': 2.03, 'MG': 1.41, 'MN': 1.39, 'N': 0.71, 'NA': 1.66, 'NI': 1.24, 'O': 0.66, 'P': 1.07, 'S': 1.05, 'ZN': 1.22}

VDW_RADII = {'AL': 1.84, 'AR': 1.88, 'AS': 1.85, 'AT': 2.02, 'AU': 2.1, 'B': 1.92, 'BA': 2.68, 'BE': 1.53, 'BI': 2.07, 'BR': 1.83, 'C': 1.7, 'CA': 2.31, 'CL': 1.75, 'CO': 2.0, 'CS': 3.43, 'CU': 2.0, 'F': 1.47, 'FE': 2.05, 'FR': 3.48, 'GA': 1.87, 'GE': 2.11, 'H': 1.1, 'HE': 1.4, 'I': 1.98, 'IN': 1.93, 'K': 2.75, 'KR': 2.02, 'LI': 1.81, 'MG': 1.73, 'MN': 2.05, 'MO': 2.1, 'N': 1.55, 'NA': 2.27, 'NE': 1.54, 'NI': 2.0, 'O': 1.52, 'P': 1.8, 'PB': 2.02, 'PO': 1.97, 'PT': 2.05, 'RA': 2.83, 'RB': 3.03, 'RN': 2.2, 'RU': 2.05, 'S': 1.8, 'SB': 2.06, 'SE': 1.9, 'SI': 2.1, 'SN': 2.17, 'SR': 2.49, 'TE': 2.06, 'TL': 1.96, 'W': 2.1, 'XE': 2.16, 'ZN': 2.1}

ELECTRONEGATIVITY = {'BR': 2.96, 'C': 2.55, 'CA': 1.0, 'CL': 3.16, 'CO': 1.88, 'CU': 1.9, 'D': 2.2, 'F': 3.98, 'FE': 1.83, 'H': 2.2, 'I': 2.66, 'K': 0.82, 'MG': 1.31, 'MN': 1.55, 'N': 3.04, 'NA': 0.93, 'NI': 1.91, 'O': 3.44, 'P': 2.19, 'S': 2.58, 'ZN': 1.65}

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

METAL_ELEMENTS = {'CA', 'CO', 'CU', 'FE', 'K', 'MG', 'MN', 'NA', 'NI', 'ZN'}

Classes

Atomic Data

class hbat.constants.atomic_data.AtomicData

Bases: object

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 = {'BR': 1.14, 'C': 0.76, 'CA': 1.76, 'CL': 0.99, 'CO': 1.26, 'CU': 1.32, 'D': 0.31, 'F': 0.57, 'FE': 1.32, 'H': 0.31, 'I': 1.33, 'K': 2.03, 'MG': 1.41, 'MN': 1.39, 'N': 0.71, 'NA': 1.66, 'NI': 1.24, 'O': 0.66, 'P': 1.07, 'S': 1.05, 'ZN': 1.22}

VDW_RADII = {'AL': 1.84, 'AR': 1.88, 'AS': 1.85, 'AT': 2.02, 'AU': 2.1, 'B': 1.92, 'BA': 2.68, 'BE': 1.53, 'BI': 2.07, 'BR': 1.83, 'C': 1.7, 'CA': 2.31, 'CL': 1.75, 'CO': 2.0, 'CS': 3.43, 'CU': 2.0, 'F': 1.47, 'FE': 2.05, 'FR': 3.48, 'GA': 1.87, 'GE': 2.11, 'H': 1.1, 'HE': 1.4, 'I': 1.98, 'IN': 1.93, 'K': 2.75, 'KR': 2.02, 'LI': 1.81, 'MG': 1.73, 'MN': 2.05, 'MO': 2.1, 'N': 1.55, 'NA': 2.27, 'NE': 1.54, 'NI': 2.0, 'O': 1.52, 'P': 1.8, 'PB': 2.02, 'PO': 1.97, 'PT': 2.05, 'RA': 2.83, 'RB': 3.03, 'RN': 2.2, 'RU': 2.05, 'S': 1.8, 'SB': 2.06, 'SE': 1.9, 'SI': 2.1, 'SN': 2.17, 'SR': 2.49, 'TE': 2.06, 'TL': 1.96, 'W': 2.1, 'XE': 2.16, 'ZN': 2.1}

ELECTRONEGATIVITY = {'BR': 2.96, 'C': 2.55, 'CA': 1.0, 'CL': 3.16, 'CO': 1.88, 'CU': 1.9, 'D': 2.2, 'F': 3.98, 'FE': 1.83, 'H': 2.2, 'I': 2.66, 'K': 0.82, 'MG': 1.31, 'MN': 1.55, 'N': 3.04, 'NA': 0.93, 'NI': 1.91, 'O': 3.44, 'P': 2.19, 'S': 2.58, 'ZN': 1.65}

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

METAL_ELEMENTS = {'CA', 'CO', 'CU', 'FE', 'K', 'MG', 'MN', 'NA', 'NI', 'ZN'}