XpongeCPP 0.2.13

XpongeCPP 0.2.13

Compatibility target: Xponge-origin 1.7.4.

Disjoint molecule assembly now preserves materialized physical topologies from
either operand and appends all offset force/exclusion indices, including newly
added solvent. Ordinary uncached assembly remains lazy. A requested covalent
link between cached topologies without an explicit combined physical topology
is rejected before mutation rather than silently retaining stale force tables.

Soft-core legacy export omits the empty ordinary NB14 table, whose native
loader requires ordinary LJ tables that soft-core mode intentionally omits.
Explicit NB14-extra coefficients are retained. Nonempty ordinary NB14 terms
are exported as explicit coefficients using exactly their ordinary A-state LJ
parameters and scales, preserving legacy manual softcore-helper behavior without
mutating the input molecule. Already interpolated FEP extras are not reweighted;
ordinary non-FEP LJ/NB14 export is unchanged.

FEP dual-state construction now projects materialized physical endpoint force
entities and exclusions into union atom IDs, preserving ordered improper terms
instead of selecting them again from a union bond graph. The unchanged
environment is projected separately for the B state. Covalently linked target
or replacement residues without an explicit physical B environment topology
are rejected rather than assigned an invented endpoint. This safety boundary
only affects FEP dual construction; ordinary modeling is unchanged.

Materialized FEP export now groups ordinary hard-bond components within each
residue, returning the full atom-identity permutation. Ghost/soft bonds are not
used to bypass the SPONGE continuity contract. Pure atom/residue permutations
preserve and remap cached bonds, angles, ordered periodic torsions, exclusions
and NB14 terms, rather than dropping the materialized topology. Non-FEP default
atom ordering and the continuity rejection guard are unchanged.

FEP bonds present in only one physical endpoint now occur only in the soft-bond
table, matching Xponge's bond merge partition. They are no longer duplicated as
lambda-weighted ordinary harmonic bonds. Soft parameters come from the actual
endpoint topology, including overrides, rather than a parameter/distance lookup.
Pairs present in both endpoints with different equilibrium lengths retain their
ordinary lambda-weighted terms. Ordinary non-FEP topology/export is unchanged.

Amber parmdat registration now stores the atom-section masses in the native
parameter registry, matching Xponge rather than silently relying on a partial
element fallback. MOL2 loading and template registration use the supplied mass;
later parmdat registrations and explicit frcmod MASS overrides retain their
normal precedence. No element-specific output correction is applied.

PDB and mmCIF loading now gives file-declared inter-residue connections
precedence over an additional implicit template link between two connection
sites that already have explicit partners. This prevents branched multi-residue
structures from acquiring unintended head/tail cycles. The rule does not use
residue names, coordinate distances, or ATOM/HETATM classification. Implicit
polymer and multi-residue lipid links remain enabled when the two connection
sites are not both explicitly assigned; explicitly declared neighbor links and
ring closures are retained. PDB ignore_conect=True still ignores CONECT.

Xponge-origin 1.7.4 uses the same explicit-link precedence. mmCIF edit operations
still run after inference, and external residue-link overrides keep their
final-overlay semantics. Missing connectivity still requires explicit records
or suitable templates.

mmCIF loading now accepts ignore_conect=True and filters noncovalent
struct_conn, Mokda semantic, and bond-edit records. The ignore option bypasses
file bond declarations and edits while retaining template bonds and separately
supplied residue links. PDB and mmCIF therefore support the same Mokda-controlled
connection policy without requiring a complete-graph interface.

The read-only amber_parameter_exists query checks registered Amber parameter
coverage without mutating the registry. Missing bond and angle parameters now
raise an error instead of generating arbitrary defaults. Bare TIP3P registration
supplies its actual model bond parameters and zero-strength angle entries.