From ff37fbbb56e33fdf9b332f6757faaef2bb50e2c6 Mon Sep 17 00:00:00 2001
From: lyskov-ai <277346777+lyskov-ai@users.noreply.github.com>
Date: Tue, 12 May 2026 21:42:20 -0400
Subject: [PATCH] Modernize pre-C++11 copy prevention to = delete across core/
 and protocols/
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Replace the pre-C++11 idiom (private undefined copy ctor / copy assignment to
prevent copies via link error) with explicit `= delete` for clearer diagnostics
and compile-time enforcement. 16 files; no behaviour change.

Two flavours:

1. Stand-alone non-copyable classes: replace the unimplemented private
   declarations with `= delete`. Drops redundant comments ("deny use of the
   copy constructor", "private and unimplemented", etc.) that are now
   self-evident from `= delete`. Keeps explanatory comments where the *why*
   is non-obvious (ScoreFunction / DockingScoreFunction / OtherContextScoreFunction:
   "copying discards subclass information; use clone() instead").

2. Singleton (SymDofMoverSampler, inheriting utility::SingletonBase): drop
   the redundant copy/assignment declarations entirely — the base already
   `= delete`s its own copies, which transitively makes the derived
   implicit copies deleted.

Files: ScoreFunction, MinScoreScoreFunction, DockingScoreFunction,
OtherContextScoreFunction, RotamerSet, RotamerSet_, RotamerSubset, RotamerSetBase,
DofPassport, ConstantLengthFragSetIterator_, FrameListIterator_,
MinimalFragSetIterator_, OrderedFragSetIterator_, FragmentPicker (QuotaDebug),
SymDofMoverSampler, FileSystemResourceLocator (FileStream).

Debug build passes clean.
---
 .../locator/FileSystemResourceLocator.hh            |  3 +--
 source/src/core/conformation/RotamerSetBase.hh      |  3 +--
 source/src/core/environment/DofPassport.hh          |  2 +-
 .../core/fragment/ConstantLengthFragSetIterator_.hh |  2 +-
 source/src/core/fragment/FrameListIterator_.hh      |  2 +-
 source/src/core/fragment/MinimalFragSetIterator_.hh |  2 +-
 source/src/core/fragment/OrderedFragSetIterator_.hh |  2 +-
 source/src/core/pack/rotamer_set/RotamerSet.hh      |  3 +--
 source/src/core/pack/rotamer_set/RotamerSet_.hh     |  2 +-
 source/src/core/pack/rotamer_set/RotamerSubset.hh   |  3 +--
 source/src/core/scoring/DockingScoreFunction.hh     |  6 ++----
 source/src/core/scoring/MinScoreScoreFunction.hh    |  6 ++----
 source/src/core/scoring/ScoreFunction.hh            | 13 +++----------
 .../protocols/flexpack/OtherContextScoreFunction.hh |  9 +++------
 source/src/protocols/frag_picker/FragmentPicker.hh  |  2 +-
 source/src/protocols/matdes/SymDofMoverSampler.hh   |  4 +---
 16 files changed, 22 insertions(+), 42 deletions(-)

diff --git a/source/src/basic/resource_manager/locator/FileSystemResourceLocator.hh b/source/src/basic/resource_manager/locator/FileSystemResourceLocator.hh
index d5018e5ad28..729c11c7779 100644
--- a/source/src/basic/resource_manager/locator/FileSystemResourceLocator.hh
+++ b/source/src/basic/resource_manager/locator/FileSystemResourceLocator.hh
@@ -60,8 +60,7 @@ public:
 	stream() override;
 
 private:
-	/// @brief This is private and unimplemented. The FileStream shouldn't be copied
-	FileStream( FileStream const & );
+	FileStream( FileStream const & ) = delete;
 
 private: // members
 	utility::io::izstream stream_;
diff --git a/source/src/core/conformation/RotamerSetBase.hh b/source/src/core/conformation/RotamerSetBase.hh
index a294d84194e..967f719befc 100644
--- a/source/src/core/conformation/RotamerSetBase.hh
+++ b/source/src/core/conformation/RotamerSetBase.hh
@@ -116,8 +116,7 @@ public:
 
 
 private:
-	// deny use of the copy constructor (no pass-by-value)
-	RotamerSetBase( RotamerSetBase const & );
+	RotamerSetBase( RotamerSetBase const & ) = delete;
 
 	/// @brief BasicDataCache indexed by enum in core/pack/rotamer_set/RotamerSetCacheableDataType.hh
 	/// @warning DataCache must always be initialized with the number of cacheable
diff --git a/source/src/core/environment/DofPassport.hh b/source/src/core/environment/DofPassport.hh
index 8ff12fa38e5..59db2101bd7 100644
--- a/source/src/core/environment/DofPassport.hh
+++ b/source/src/core/environment/DofPassport.hh
@@ -97,7 +97,7 @@ private:
 
 	DofPassport( std::string const & mover, Size env_id);
 
-	DofPassport( DofPassport const& );
+	DofPassport( DofPassport const& ) = delete;
 
 	//General code used by most (all?) access checks.
 	bool access_check( EnvCore const& env, bool type_specific_check ) const;
diff --git a/source/src/core/fragment/ConstantLengthFragSetIterator_.hh b/source/src/core/fragment/ConstantLengthFragSetIterator_.hh
index 49a0d6d96b3..21cd53f7d1b 100644
--- a/source/src/core/fragment/ConstantLengthFragSetIterator_.hh
+++ b/source/src/core/fragment/ConstantLengthFragSetIterator_.hh
@@ -47,7 +47,7 @@ namespace fragment {
 class ConstantLengthFragSetIterator_ : public FrameIteratorWorker_ {
 	friend class ConstantLengthFragSet;
 
-	ConstantLengthFragSetIterator_ & operator = (ConstantLengthFragSetIterator_ const&);
+	ConstantLengthFragSetIterator_ & operator = (ConstantLengthFragSetIterator_ const&) = delete;
 protected:
 	ConstantLengthFragSetIterator_( FrameList::const_iterator it, FrameList::const_iterator eit ) : it_( it ), eit_( eit ) {
 		if ( it != eit ) {
diff --git a/source/src/core/fragment/FrameListIterator_.hh b/source/src/core/fragment/FrameListIterator_.hh
index 36b94c0fa12..d224a046fb7 100644
--- a/source/src/core/fragment/FrameListIterator_.hh
+++ b/source/src/core/fragment/FrameListIterator_.hh
@@ -39,7 +39,7 @@ class FrameListIterator_ : public FrameIteratorWorker_ {
 	friend class FrameList;
 	friend class FragID_Iterator;
 
-	FrameListIterator_ & operator = (FrameListIterator_ const&);
+	FrameListIterator_ & operator = (FrameListIterator_ const&) = delete;
 
 protected:
 	FrameListIterator_( FrameList::iterator it ) : it_( it ) {};
diff --git a/source/src/core/fragment/MinimalFragSetIterator_.hh b/source/src/core/fragment/MinimalFragSetIterator_.hh
index c0dd816833d..75a9d1b5654 100644
--- a/source/src/core/fragment/MinimalFragSetIterator_.hh
+++ b/source/src/core/fragment/MinimalFragSetIterator_.hh
@@ -48,7 +48,7 @@ class MinimalFragSetIterator_ : public FrameIteratorWorker_ {
 	typedef FrameMap::const_iterator OuterIterator;
 	typedef FrameList::const_iterator InnerIterator;
 
-	MinimalFragSetIterator_ & operator = (MinimalFragSetIterator_ const&);
+	MinimalFragSetIterator_ & operator = (MinimalFragSetIterator_ const&) = delete;
 protected:
 	MinimalFragSetIterator_( OuterIterator it, OuterIterator eit ) : outer_( it ), outer_end_( eit ) {
 		if ( outer_ != outer_end_ ) {
diff --git a/source/src/core/fragment/OrderedFragSetIterator_.hh b/source/src/core/fragment/OrderedFragSetIterator_.hh
index fc058cb24c9..d59d8fa4ee8 100644
--- a/source/src/core/fragment/OrderedFragSetIterator_.hh
+++ b/source/src/core/fragment/OrderedFragSetIterator_.hh
@@ -45,7 +45,7 @@ class OrderedFragSetIterator_ : public FrameIteratorWorker_ {
 	typedef FrameMap::const_iterator OuterIterator;
 	typedef FrameList::const_iterator InnerIterator;
 
-	OrderedFragSetIterator_ & operator = (OrderedFragSetIterator_ const&);
+	OrderedFragSetIterator_ & operator = (OrderedFragSetIterator_ const&) = delete;
 protected:
 	OrderedFragSetIterator_( OuterIterator it, OuterIterator eit ) : outer_( it ), outer_end_( eit ) {
 		if ( outer_ != outer_end_ ) {
diff --git a/source/src/core/pack/rotamer_set/RotamerSet.hh b/source/src/core/pack/rotamer_set/RotamerSet.hh
index ba34bf60c62..df50147aa5f 100644
--- a/source/src/core/pack/rotamer_set/RotamerSet.hh
+++ b/source/src/core/pack/rotamer_set/RotamerSet.hh
@@ -255,8 +255,7 @@ public:
 	update_rotamer_offsets() const = 0;
 
 private:
-	// deny use of the copy constructor (no pass-by-value)
-	RotamerSet( RotamerSet const & );
+	RotamerSet( RotamerSet const & ) = delete;
 
 	Size resid_; //which residue is this?
 
diff --git a/source/src/core/pack/rotamer_set/RotamerSet_.hh b/source/src/core/pack/rotamer_set/RotamerSet_.hh
index cd29f888e8e..46d7b5faf17 100644
--- a/source/src/core/pack/rotamer_set/RotamerSet_.hh
+++ b/source/src/core/pack/rotamer_set/RotamerSet_.hh
@@ -214,7 +214,7 @@ public:
 	) const override {}
 
 private:
-	RotamerSet_( RotamerSet_ const & );
+	RotamerSet_( RotamerSet_ const & ) = delete;
 
 
 protected:
diff --git a/source/src/core/pack/rotamer_set/RotamerSubset.hh b/source/src/core/pack/rotamer_set/RotamerSubset.hh
index 2b9bd5b836b..8843e9118f3 100644
--- a/source/src/core/pack/rotamer_set/RotamerSubset.hh
+++ b/source/src/core/pack/rotamer_set/RotamerSubset.hh
@@ -168,8 +168,7 @@ public:
 	show( std::ostream & out ) const override;
 
 private:
-	/// @brief (private) No copy-constructor
-	RotamerSubset( RotamerSubset const & );
+	RotamerSubset( RotamerSubset const & ) = delete;
 
 	/// @brief declare that a new block of residue types has begun, and that new residues
 	/// are about to be pushed back. NOT IMPLEMENTED.
diff --git a/source/src/core/scoring/DockingScoreFunction.hh b/source/src/core/scoring/DockingScoreFunction.hh
index 76793e1636a..6c5cda38126 100644
--- a/source/src/core/scoring/DockingScoreFunction.hh
+++ b/source/src/core/scoring/DockingScoreFunction.hh
@@ -47,10 +47,8 @@ public:
 
 private:
 	/// @brief Copy constructor and assignment operators private for *ScoreFunctions as they discard subtype info.
-	DockingScoreFunction &
-	operator=( DockingScoreFunction const & );
-
-	DockingScoreFunction( DockingScoreFunction const & );
+	DockingScoreFunction & operator=( DockingScoreFunction const & ) = delete;
+	DockingScoreFunction( DockingScoreFunction const & ) = delete;
 
 public:
 
diff --git a/source/src/core/scoring/MinScoreScoreFunction.hh b/source/src/core/scoring/MinScoreScoreFunction.hh
index c097fbeb181..3748c453e34 100644
--- a/source/src/core/scoring/MinScoreScoreFunction.hh
+++ b/source/src/core/scoring/MinScoreScoreFunction.hh
@@ -50,10 +50,8 @@ public:
 
 private:
 
-	MinScoreScoreFunction &
-	operator=( MinScoreScoreFunction const & );
-
-	MinScoreScoreFunction( MinScoreScoreFunction const & );
+	MinScoreScoreFunction & operator=( MinScoreScoreFunction const & ) = delete;
+	MinScoreScoreFunction( MinScoreScoreFunction const & ) = delete;
 
 public:
 
diff --git a/source/src/core/scoring/ScoreFunction.hh b/source/src/core/scoring/ScoreFunction.hh
index f5ab3a8f9e2..baee68fd6c8 100644
--- a/source/src/core/scoring/ScoreFunction.hh
+++ b/source/src/core/scoring/ScoreFunction.hh
@@ -139,16 +139,9 @@ public:
 	// inline ScoreFunctionAP get_self_weak_ptr() { return ScoreFunctionAP( shared_from_this() ); }
 
 private:
-	/// @brief The ScoreFunction copy constructor is explicitly private
-	/// as using it to make a copy is just too attractive, but discards subclass information.
-	/// Use ScoreFunction::clone() instead.
-	ScoreFunction( ScoreFunction const & );
-
-	/// @brief The ScoreFunction assignment operator is explicitly private
-	/// as using it discards subclass information.
-	/// Rework your algorithm to use ScoreFunctionOP's instead.
-	ScoreFunction &
-	operator=( ScoreFunction const & );
+	/// @brief Copying a ScoreFunction discards subclass information; use ScoreFunction::clone() instead.
+	ScoreFunction( ScoreFunction const & ) = delete;
+	ScoreFunction & operator=( ScoreFunction const & ) = delete;
 
 public:
 
diff --git a/source/src/protocols/flexpack/OtherContextScoreFunction.hh b/source/src/protocols/flexpack/OtherContextScoreFunction.hh
index dd3645990b9..d5a79e713cf 100644
--- a/source/src/protocols/flexpack/OtherContextScoreFunction.hh
+++ b/source/src/protocols/flexpack/OtherContextScoreFunction.hh
@@ -47,12 +47,9 @@ public:
 	);
 
 private:
-	// private assignment and copy constructors to avoid discarding subtype information
-
-	OtherContextScoreFunction( OtherContextScoreFunction const & );
-
-	OtherContextScoreFunction &
-	operator=( OtherContextScoreFunction const & );
+	// Avoid discarding subtype information; clone() must be used to duplicate.
+	OtherContextScoreFunction( OtherContextScoreFunction const & ) = delete;
+	OtherContextScoreFunction & operator=( OtherContextScoreFunction const & ) = delete;
 
 public:
 
diff --git a/source/src/protocols/frag_picker/FragmentPicker.hh b/source/src/protocols/frag_picker/FragmentPicker.hh
index ecd74e66246..0f40f5ae020 100644
--- a/source/src/protocols/frag_picker/FragmentPicker.hh
+++ b/source/src/protocols/frag_picker/FragmentPicker.hh
@@ -77,7 +77,7 @@ public:
 	core::Size max_pools();
 
 private:
-	QuotaDebug(QuotaDebug const &);
+	QuotaDebug(QuotaDebug const &) = delete;
 };
 
 /// @brief The core of the fragment picking machinery
diff --git a/source/src/protocols/matdes/SymDofMoverSampler.hh b/source/src/protocols/matdes/SymDofMoverSampler.hh
index 92669ef286f..637e14d1157 100644
--- a/source/src/protocols/matdes/SymDofMoverSampler.hh
+++ b/source/src/protocols/matdes/SymDofMoverSampler.hh
@@ -51,10 +51,8 @@ public:
 	void step();
 
 private:
-	// Don't implement the methods belowed, this class is a singleton.
+	// Singleton — only SingletonBase constructs instances.
 	SymDofMoverSampler();
-	SymDofMoverSampler(SymDofMoverSampler const&);
-	void operator=(SymDofMoverSampler const&);
 
 private: