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Atom

Chemical element with symbol, name, and atomic weight.

Overview

Atom represents a chemical element - the building block of molecules. Atoms are immutable value objects that can be shared across multiple molecules and chemistries. They are constants, not entities in the tree structure.

Property Type Description
symbol str Chemical symbol (1-2 letters): 'C', 'H', 'Na'
name str Human-readable name: 'Carbon', 'Hydrogen'
atomic_weight float Atomic mass in atomic mass units

Discussion

Common Atoms

The system provides a set of common biological atoms:

Symbol Name Atomic Weight
H Hydrogen 1.008
C Carbon 12.011
N Nitrogen 14.007
O Oxygen 15.999
P Phosphorus 30.974
S Sulfur 32.065
Na Sodium 22.990
K Potassium 39.098
Ca Calcium 40.078
Mg Magnesium 24.305
Cl Chlorine 35.453
Fe Iron 55.845
Zn Zinc 65.38
Cu Copper 63.546

Usage in Molecules

Atoms are used as dictionary keys in molecule composition:

from alienbio import MoleculeImpl, get_atom

C = get_atom("C")
H = get_atom("H")
O = get_atom("O")

# Water: H2O
water = MoleculeImpl("water", dat=dat, atoms={H: 2, O: 1})

# Glucose: C6H12O6
glucose = MoleculeImpl("glucose", dat=dat, atoms={C: 6, H: 12, O: 6})

Implementation

from alienbio import AtomImpl, get_atom, COMMON_ATOMS

# Create a custom atom
helium = AtomImpl("He", "Helium", 4.003)

# Use pre-defined common atoms
carbon = get_atom("C")
hydrogen = get_atom("H")

# Access the full set
print(COMMON_ATOMS.keys())
# {'H', 'C', 'N', 'O', 'P', 'S', 'Na', 'K', 'Ca', 'Mg', 'Cl', 'Fe', 'Zn', 'Cu'}

Protocol

from typing import Protocol, runtime_checkable

@runtime_checkable
class Atom(Protocol):
    """Protocol for atomic elements."""

    @property
    def symbol(self) -> str:
        """Chemical symbol (1-2 letters): 'C', 'H', 'O', 'Na'."""
        ...

    @property
    def name(self) -> str:
        """Human-readable name: 'Carbon', 'Hydrogen'."""
        ...

    @property
    def atomic_weight(self) -> float:
        """Atomic mass in atomic mass units."""
        ...

See Also