chemistry-tools

Chemistry Tools

Computational chemistry and cheminformatics. Venv: source /Users/zhangmingda/clawd/.venv/bin/activate

Molecular Properties

# Using RDKit if available, otherwise manual calculations
from sympy import symbols, Eq, solve

# Molecular weight calculation (manual)
ATOMIC_WEIGHTS = {
    'H': 1.008, 'He': 4.003, 'Li': 6.941, 'Be': 9.012, 'B': 10.81,
    'C': 12.011, 'N': 14.007, 'O': 15.999, 'F': 18.998, 'Ne': 20.180,
    'Na': 22.990, 'Mg': 24.305, 'Al': 26.982, 'Si': 28.086, 'P': 30.974,
    'S': 32.065, 'Cl': 35.453, 'Ar': 39.948, 'K': 39.098, 'Ca': 40.078,
    'Fe': 55.845, 'Cu': 63.546, 'Zn': 65.38, 'Br': 79.904, 'Ag': 107.868,
    'I': 126.904, 'Au': 196.967,
}

import re
def molecular_weight(formula):
    """Calculate MW from chemical formula like 'C6H12O6'"""
    elements = re.findall(r'([A-Z][a-z]?)(\d*)', formula)
    mw = sum(ATOMIC_WEIGHTS.get(el, 0) * (int(n) if n else 1) for el, n in elements)
    return mw

# Example
print(f"Glucose (C6H12O6): {molecular_weight('C6H12O6'):.3f} g/mol")

Chemical Equation Balancing

from sympy import Matrix, lcm

def balance_equation(reactants_elements, products_elements):
    """
    Balance using linear algebra (null space method).
    Each compound is a dict of {element: count}.
    """
    all_elements = set()
    for compound in reactants_elements + products_elements:
        all_elements.update(compound.keys())
    all_elements = sorted(all_elements)
    
    n_compounds = len(reactants_elements) + len(products_elements)
    matrix = []
    for el in all_elements:
        row = []
        for comp in reactants_elements:
            row.append(comp.get(el, 0))
        for comp in products_elements:
            row.append(-comp.get(el, 0))
        matrix.append(row)
    
    M = Matrix(matrix)
    null = M.nullspace()
    if null:
        coeffs = null[0]
        # Make integer coefficients
        denom = lcm(*[c.q for c in coeffs if hasattr(c, 'q')] or [1])
        coeffs = [int(c * denom) for c in coeffs]
        return coeffs
    return None