pamd-biology is a standalone, installable knowledge base designed to plug directly into the PyAct engine. It contains standardized biological, cellular, and biochemical properties wrapped perfectly in PyAct's Unit class.

Whether you are calculating enzyme kinetics, molecular weights, or cellular volumes, this package provides instant access to standard life science data without needing to look it up.

🚀 Installation

Install it directly from PyPI:

pip install pamd-biology

(Note: Installing this package will automatically install pyact-cli and its core Unit library as a dependency.)

📖 What's Included?

This package contains standard biological datasets tailored for biochemistry and cellular biology calculations.

1. Macromolecules

• AminoAcids: The 20 standard proteinogenic amino acids with their molecular weights ([Da]), isoelectric points (pI), and Kyte-Doolittle hydropathy indices.
• NucleicBases: Molecular weights for the standard DNA and RNA free bases (Adenine, Thymine, Cytosine, Guanine, Uracil).
• MacromoleculeDensities: Average buoyant densities ([g/cm3]) and partial specific volumes for proteins, DNA, RNA, lipids, and carbohydrates (essential for ultracentrifugation).

2. Cellular Biology & Organisms

• TypicalCells: Standard cell volumes ([um3]), typical mass ([pg]), and diameters for E. coli, Yeast, Red Blood Cells, and HeLa cells.
• OrganismGenomes: Genome sizes ([bp]), chromosome counts, and estimated gene counts for model organisms (E. coli, Yeast, C. elegans, Drosophila, and Humans).

3. Biochemistry & Kinetics

• EnzymeKinetics: Typical Michaelis-Menten constants ($K_m$) and turnover numbers ($k_{cat}$) for classic reference enzymes (like Catalase, Hexokinase, Acetylcholinesterase).
• Bioenergetics: Standard free energy of hydrolysis ($\Delta G^\circ$) for massive energy carriers like ATP, ADP, and Phosphoenolpyruvate.

4. Clinical Baselines

• HumanBloodParameters: Clinical adult human blood baselines including pH ranges, osmolarity, fasting glucose, and hemoglobin levels.

🛠️ Usage Example

Import any biological database directly into your PyAct .pamd context and perform instant math. Because every value is a Unit object, calculations are completely seamless.

from pamd_biology.AminoAcids import AminoAcids
from pamd_biology.EnzymeKinetics import TypicalEnzymes
from pamd_biology.unit import Unit

def context():
    # Fetch standard values
    valine_mass = AminoAcids().Valine["MW_Da"]
    kcat_catalase = TypicalEnzymes().Catalase["kcat_1_s"]
    
    return {
        "valine_weight": valine_mass,
        "catalase_turnover": kcat_catalase
    }