autofragment.data.amino_acids

Amino acid charge and property data.

This module provides comprehensive data for all 20 standard amino acids, plus selenium-containing amino acids and post-translational modifications.

Data includes: - Molecular properties (formula, weight) - pKa values for ionizable sidechains - Charges at neutral, physiological (pH 7.4), acidic (pH 4), and basic (pH 10) conditions - Physical properties (polarity, charge, aromaticity)

Reference values from: - Stryer, Biochemistry - CRC Handbook of Chemistry and Physics - NIST Chemistry WebBook

Functions

calculate_protein_charge(residues[, ph, ...])	Calculate total charge for a protein or fragment at given pH.
get_amino_acid(residue_code)	Get amino acid data by residue code.
get_charge_at_ph74(residue_code)	Get charge for a residue at physiological pH 7.4.
get_neutral_charge(residue_code)	Get charge for a residue in neutral (protonated) form.
get_ptm_charge_adjustment(residue_code)	Get charge adjustment for a PTM residue.
get_residue_charge_at_ph(residue_code, ph)	Get charge for a residue at specified pH using Henderson-Hasselbalch.

Classes

AminoAcidData(three_letter, one_letter, ...)	Data for a single amino acid.
PTMData(name, residue_code, parent_residue, ...)	Data for a post-translational modification.