nx_peptide.nx

nx_peptide.nx -- CHEMISTRY SUITE / PEPTIDE PRIMARY-STRUCTURE rung. Turns an amino-acid SEQUENCE into real chemistry: exact mass, charge state, isoelectric point, UV absorbance, hydropathy, and the b/y fragment-ion ladder an MS/MS run actually observes. This is the missing rung between the ecosystem's molecule stack (nx_chem_molecule / nx_chem_mass / nx_chem_isotope_pattern / nx_chem_peak_list) and peptide work: the mass stack could weigh a MolGraph but nothing could go from "DRVYIHPF" to 1045.5345 Da, so the NIST Peptide Tandem Mass Spectral Libraries (SRD 1c) in the corpus had no local counterpart to match against. This closes that. ALL INTEGER, no float: *_q4 = value x 10^4 (mass in Da -> micro-AMU; matches nx_chem_mass) *_q3 = value x 10^3 (charge, hydropathy, decade-log intermediates) *_milli = value x 10^3 (pH and pKa) THE exceed: a sequence viewer prints letters. This computes the mass an instrument will SEE (monoisotopic, not average -- they differ by ~0.66 Da at 1 kDa and that is the difference between a hit and a miss), the m/z of every charge state, and the b/y ladder for identification -- and it REFUSES a sequence containing a residue it does not know rather than silently scoring the unknown as zero mass. PRECISION, stated honestly (not asserted): - Residue masses are rounded to Q4, so an n-mer accumulates up to n/2 Q4 units of rounding. Measured against literature: angiotensin II (8-mer) is EXACT (1045.5345); bradykinin (9-mer) lands 1 Q4 unit (0.0001 Da) high. pep_mass_agrees() makes that tolerance explicit. - pI comes from bisection over pep_pow10_q3, whose decade table is 0.1-log granular, so pI is good to about +/-0.05 pH -- adequate to choose a buffer, NOT a substitute for a titration. Grounding (cited; researcher-groundable): iupac_amino_acid_residue_monoisotopic_masses (residue table) emboss_pepstats_pka_set (pKa set for pI/charge) kyte_doolittle_hydropathy_1982 (GRAVY) pace_1995_extinction_coefficient_280nm (Trp 5500 / Tyr 1490 / cystine 125) biemann_1990_peptide_fragment_ion_nomenclature (b/y ions)