nx_peptide_chain.nx

nx_peptide_chain.nx -- CHEMISTRY SUITE / MULTI-CHAIN PEPTIDE rung. Closes the last gap the peptide lane declared: an assembly of SEVERAL chains held together by disulfide bridges. Insulin is the case that matters -- two chains, three bridges, and one of the most counterfeited biologics there is -- and nothing before this could weigh it. WHY IT IS NOT JUST "ADD THE CHAINS UP". Two things break that: 1. Every chain carries its OWN terminal water, so an N-chain assembly has N waters, not one. Treating insulin as a single 51-residue sequence is short by a whole water (18.011 Da). 2. Bridges are owned by the ASSEMBLY, not by any chain. An inter-chain disulfide belongs to neither A nor B. So pca_add_chain REFUSES a builder that already carries its own bridges -- otherwise the same -2.016 Da gets subtracted twice and the answer looks plausible. INTRA AND INTER ARE TRACKED SEPARATELY, because they mean different things. Both cost the same mass, but only INTER-chain bridges hold the assembly together: linking N chains needs at least N-1 of them. pca_is_covalently_linked enforces exactly that, so a "two-chain" molecule with only intra-chain bridges is correctly reported as two separate peptides that happen to be in the same tube. THE CYSTEINE BUDGET IS A REAL CONSTRAINT, NOT A FORMALITY. Each bridge consumes two cysteines, and a claim of more bridges than the sequences can supply produces a mass that looks entirely reasonable. Insulin is the perfect witness: 6 cysteines, 3 bridges, ZERO left over. Grounding (cited; researcher-groundable): published_monoisotopic_mass_human_insulin_5803_6375 (the anchor) human_insulin_a_b_chain_sequences_and_disulfide_map disulfide_bond_two_hydrogen_loss (via nx_peptide_ext) genealogy_id: peptide_chemistry + nishi_chem_suite