Apply Rule of Zero to BitSet and BitVector (#690) - `utility::BitSet<B>` and `utility::BitVector<B>` each had only a single value-type member (`std::set<B>` and `std::vector<bool>` respectively), no user-declared copy/move/assignment operators, and an explicit empty destructor. - The empty `~BitSet() {}` / `~BitVector() {}` did nothing the compiler-generated destructor wouldn't have done, and they suppressed the implicit move constructor and move assignment. - Remove the empty destructors so both class templates follow the Rule of Zero and gain implicit move support.

• Summary
• integration.mpi 「1」
• scientific.protein_data_bank_diagnostic.cif

Apply Rule of Zero to disulfide energy neighbor iterators (#689) - Remove user-declared trivial (defaulted) destructors from the six disulfide neighbor iterator classes; the implicit virtual destructor inherited from `ResidueNeighborIterator` / `ResidueNeighborConstIterator` does the same job. - Modernize the old-style C++03 copy-assignment prevention (private undefined declaration) to a public `= delete` for the derived-type `operator=`. Behavior is unchanged: derived-derived assignment is still forbidden so all assignments flow through the polymorphic `operator=(BaseType const &)` override that downcasts and copies all members.

• Summary
• integration.mpi 「1」
• scientific.protein_data_bank_diagnostic.cif

Apply Rule of Zero to core signal event hierarchies (#688) Each of the simple polymorphic signal-event classes in `core/conformation/signals/` and `core/pose/signals/` had a hand-written copy constructor, copy assignment, and empty destructor that all just did what the compiler-generated versions would do. Removing the boilerplate brings them in line with the Rule of Zero while preserving the polymorphic base destructors as `= default`. Touched: - `core/conformation/signals/`: `GeneralEvent`, `ConnectionEvent`, `IdentityEvent`, `XYZEvent` - `core/pose/signals/`: `GeneralEvent`, `DestructionEvent`, `ConformationEvent`, `EnergyEvent` `LengthEvent` is intentionally left alone — its copy constructor and copy assignment invoke `check_consistency()` in debug builds, so they have real semantic content beyond member-wise copy.

• Summary
• integration.mpi 「1」
• integration 「1」

Modernize copy prevention in core factory singletons and non-copyable classes (#685) - **SilentStructFactory, ConstraintFactory, SequenceFactory**: all inherit from `utility::SingletonBase`, which already `= delete`s copy construction and copy assignment. Removes the now-redundant private-but-unimplemented declarations from each derived class (pre-C++11 idiom). - **OrbitalsStatistics, AtomTreeDiff**: had private-but-undefined copy constructors (pre-C++11 idiom); replaced with explicit `= delete` on both copy constructor and copy assignment operator. No behaviour change; build-only verification is sufficient for pure copy-prevention modernisation.

• Summary
• integration.addsan 「1」
• integration.mpi 「1」
• integration 「1」

Default MetricValue special members (#684) - default no-op MetricValueBase destructor - default MetricValue default and copy constructors

• Summary
• integration.mpi 「1」
• integration.tensorflow 「1」
• scientific.protein_data_bank_diagnostic.cif

Fix key map range indexing (#680) - fix ClassKeyMap and SmallKeyMap range constructor/assignment loops to visit the final 1-indexed element - add regression coverage for range construction and assignment preserving the final key

• Summary
• integration.addsan 「1」
• integration.mpi 「1」
• integration.tensorflow 「1」
• integration 「1」

Modernize copy prevention in Emitter, YamlEmitter, and JsonEmitter (#678) - `Emitter`, `YamlEmitter`, `JsonEmitter`: replace private/protected undefined copy ctor declarations with explicit `= delete` in the public section, and add the missing copy assignment `= delete`. - Also remove the redundant undefined null-ctor declarations in `YamlEmitter` and `JsonEmitter` — these were suppressed automatically in C++11 by the presence of user-declared non-default constructors.

• Summary
• integration.addsan 「1」
• integration.mpi 「1」
• integration.tensorflow 「1」
• integration 「1」

Modernize copy prevention in basic_otstream and TracerImpl (#674) - `basic_otstream`: replace private-undefined copy ctor with explicit `= delete` for both copy ctor and copy assignment in the public section. Adds a one-liner comment explaining the destructor side-effect (`delete this->rdbuf()` causes double-free if two objects share the same buffer). - `TracerImpl`: move the already-`= delete`d copy ctor from private section to public, and add the missing copy assignment `= delete`. Part of the ongoing Rule-of-Zero / modern C++ idiom cleanup in `basic/`.

• Summary
• integration.mpi 「1」
• integration.tutorials 「1」
• integration.ubsan 「1」
• scientific.mp_lipid_acc
• gcc-11.gcc.unit 「3」

Modernize copy prevention in basic/ComparingTracer and MessageListenerFactory (#673) Two related cleanups in `basic/`: **`ComparingTracer.hh`**: Replace private-and-undefined copy constructor with public `= delete`; also explicitly delete copy assignment. The `std::fstream` member already makes copies impossible, but `= delete` documents the intent at the class level. **`mpi/MessageListenerFactory.hh`**: Remove the redundant private-undefined copy constructor and copy assignment. `MessageListenerFactory` inherits from `utility::SingletonBase<MessageListenerFactory>`, which already deletes both copy operations — the manual declarations were dead code.

• Summary
• integration.mpi 「1」
• integration 「1」

Made hbond graph pyrosetta compatible (#99) You can't actually use the HBondGraph in pyrosetta because the LowMemGraph uses some crazy tricks that don't involve object inheritance. This adds 2 functions to bridge that gap.

• Summary
• integration.mpi 「1」
• integration 「1」
• scientific.protein_data_bank_diagnostic.cif

Modernize copy prevention in utility/graph EdgeList/Node/Edge to use = delete (#672) Replace old-style private-and-undefined copy constructor/assignment with explicit `= delete` in six internal classes across `Graph.hh` and `Digraph.hh`: - `Graph.hh`: `EdgeList`, `Node`, `Edge` - `Digraph.hh`: `DirectedEdgeList`, `DirectedNode`, `DirectedEdge` Also corrects the copy assignment signatures from the non-standard `T&` argument to the correct `T const &` form. The `Graph` class itself (which has a real, implemented copy constructor and assignment) is unchanged.

• Summary
• integration.mpi 「1」

Modernize copy prevention in KeyLookup to use = delete (#671) - Replace old-style private-and-undefined copy constructor/assignment in `utility/keys/KeyLookup` with explicit `= delete` - `KeyLookup` is a monostate singleton (all methods and data are static); copies are meaningless

• Summary
• integration.mpi 「1」
• integration.tensorflow 「1」
• integration.ubsan 「1」
• windows.build.release

Modernize copy prevention in factory/Registrant to use = delete (#670) - Replace old-style private-and-undefined copy constructor/assignment in `utility/factory/Registrant` with explicit `= delete` - Added a one-line comment explaining the non-obvious reason: each constructor calls `ProductFactory::add()`, so a copy would silently re-register the same key

• Summary
• integration.mpi 「1」
• integration.tensorflow 「1」
• integration 「1」

Modernize copy prevention in irstream to use = delete (#669) - Replace old-style private-and-undefined copy constructor/assignment in `utility/io/irstream` with explicit `= delete` - Mirrors the same treatment already applied to the sibling `orstream` class (PR #667)

• Summary
• integration.mpi 「1」
• integration 「1」

Modernize copy prevention in utility/signals classes to use = delete (#668) ## Summary - Replace old-style private-and-undefined copy constructor/assignment in five `utility/signals` classes with explicit `= delete` - Affected classes: `SignalHub`, `BufferedSignalHub`, `PausableSignalHub`, `TokenHub`, `LinkUnit` - Also explicitly deletes the `LinkUnit` default constructor (was previously also private-undefined) - Pure mechanical modernization — no behavioral change ## Motivation The pre-C++11 idiom of declaring copy ops private with no definition produces a linker error on misuse rather than a clear compile-time diagnostic. `= delete` gives an immediate, descriptive compiler error at the call site and is the modern idiomatic approach.

• Summary
• integration.mpi 「1」
• integration 「1」

Refactor ozstream raw pointers to unique_ptr; modernize orstream copy ops (#667) ## Summary - Replace three raw owning pointers in `ozstream` (`char_buffer_p_`, `zip_stream_p_`, `mpi_stream_p_`) with `std::unique_ptr`, eliminating manual `delete`/`nullptr` pairs in `open()`, `open_append()`, `open_append_if_existed()`, `close()`, and the buffer helpers - Modernize the private-undefined copy constructor/assignment in `orstream` to explicit `= delete`, consistent with the approach used in `irstream`/`izstream` (PR #664) ## Test plan - [x] Full debug build passes (`python3 ./scons.py -j16 mode=debug`) - [ ] No behavior change expected — ownership semantics are identical; `close()` still runs `zflush_finalize()` and `mpi_ostream::close()/clear()` before releasing the pointers

• Summary
• integration.mpi 「1」
• integration 「1」
• performance 「1」

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