Chemistry

molex::chemistry (source: src/chemistry/) owns the static residue chemistry that entity construction and bond inference build on. The data is pure: no entity references, no positions, no I/O.

Tables

• amino_acids (AminoAcid): the standard amino acids plus modified-residue one-letter mapping. Provides the intra-residue bond topology used to populate ProteinEntity::bonds.
• nucleotides (Nucleotide): DNA/RNA bases and their bond topology.
• atom_name (AtomName, is_protein_backbone_atom_name): canonical 4-character atom-name handling and the backbone-atom predicate.
• variant (VariantTag, ProtonationState): per-residue chemistry variants (terminus patches, disulfide, protonation states). Protonation is the load-bearing case: HID and HIE differ only in which nitrogen carries the hydrogen, which heavy-atom positions alone do not determine, so the tag is carried explicitly through the wire.

Completion machinery

completion (ResidueTemplate, TemplateAtom) and the private completion_data module hold the ideal-geometry templates that the construction pass rigid-fits onto parsed residues to fabricate absent atoms. See the Completion page for how the levels use them.