Merge pull request #70 from cando-developers/hash-table-changes

Hash table changes
cando-developers · Jan 22, 2025 · a85eea6 · a85eea6
2 parents e3ce830 + f1407e3
commit a85eea6
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Showing 65 changed files with 140 additions and 145 deletions.
diff --git a/include/cando/adapt/indexedObjectBag.h b/include/cando/adapt/indexedObjectBag.h
@@ -41,7 +41,7 @@ namespace adapt {
 
 public:
 GCPRIVATE:
-  gc::Nilable<core::HashTableEq_sp> _Bag;
+  gc::Nilable<core::HashTable_sp> _Bag;
   gc::Fixnum         _NextIndex;
 public:
 

diff --git a/include/cando/adapt/objectSet.h b/include/cando/adapt/objectSet.h
@@ -47,7 +47,7 @@ SMART(ObjectSet);
 public:
 
 GCPRIVATE:
-  HashTableEq_sp _Set;
+  HashTable_sp _Set;
 
 public:
 CL_NAME("CONTAINS");

diff --git a/include/cando/adapt/stringList.h b/include/cando/adapt/stringList.h
@@ -81,7 +81,7 @@ SMART(StringList);
   void setFromString(const string &s);
   string asString();
 
-   core::HashTableEqual_sp asStringSet();
+   core::HashTable_sp asStringSet();
 
 #ifdef USEBOOSTPYTHON
   void python_setFromList(boost::python::list res);

diff --git a/include/cando/adapt/stringSet.h b/include/cando/adapt/stringSet.h
@@ -58,7 +58,7 @@ SMART(StringSet);
   void initialize();
 
 private:
-   HashTableEqual_sp strs;
+   HashTable_sp strs;
    bool rest;
 
 public:

diff --git a/include/cando/adapt/symbolSet.h b/include/cando/adapt/symbolSet.h
@@ -64,7 +64,7 @@ SMART(SymbolSet);
   bool fieldsp() const { return true; };
   void fields(core::Record_sp node);
 GCPRIVATE:
-  HashTableEq_sp _Symbols;
+  HashTable_sp _Symbols;
 
 public:
   static SymbolSet_sp make(List_sp vals);

diff --git a/include/cando/chem/candoDatabase.h b/include/cando/chem/candoDatabase.h
@@ -97,7 +97,7 @@ class CandoDatabase_O : public core::CxxObject_O
   core::Symbol_sp				_Name;
   string				_DateCreated;
   string				_DateUpdated;
-  core::HashTableEq_sp          _Topologys;
+  core::HashTable_sp          _Topologys;
 
 private:
 	/*! Return true if the entity with the name (name) is recognized and is a subclass of classId

diff --git a/include/cando/chem/chemInfo.h b/include/cando/chem/chemInfo.h
@@ -76,12 +76,12 @@ size_t calculate_maxtag(ChemInfoNode_sp node);
     bool fieldsp() const { return true; };
     void fields(core::Record_sp node);
   public:
-    static ChemInfoMatch_sp make(Root_sp root,size_t maxtag, core::HashTableEql_sp ring);
+    static ChemInfoMatch_sp make(Root_sp root,size_t maxtag, core::HashTable_sp ring);
   public:
     bool		  _Matches;
     size_t                _MaxTagPlus1;
     Root_sp               _Root;
-    core::HashTableEql_sp _RingLookup;
+    core::HashTable_sp _RingLookup;
     core::SimpleVector_sp _TagLookup; // core::StringMap<Atom_O>	_TagLookup;
     core::List_sp         _TagHistory;
   public:
@@ -99,7 +99,7 @@ size_t calculate_maxtag(ChemInfoNode_sp node);
 CL_LISPIFY_NAME("tag");
 CL_DEFMETHOD     chem::Atom_sp tag(core::T_sp tag) { return this->getAtomWithTag(tag);};
     CL_DEFMETHOD core::List_sp tag_history() const { return this->_TagHistory; };
-    core::HashTableEql_sp tags_as_hashtable() const;
+    core::HashTable_sp tags_as_hashtable() const;
     core::Vector_sp tags_as_vector() const;
     void forgetAtomTag(core::T_sp tag);
 
@@ -134,7 +134,7 @@ CL_DEFMETHOD     chem::Atom_sp tag(core::T_sp tag) { return this->getAtomWithTag
     bool fieldsp() const { return true; };
     void	fields(core::Record_sp node);
   private:
-    core::HashTableEqual_sp _AtomWildCards; // core::StringMap<adapt::StringSet_O>	_AtomWildCards;
+    core::HashTable_sp _AtomWildCards; // core::StringMap<adapt::StringSet_O>	_AtomWildCards;
   public:
     void    addWildName(core::Symbol_sp  wildName);
     void    addWildNameMap(core::Symbol_sp wildName, core::Symbol_sp elementName );
@@ -1067,7 +1067,7 @@ class Root_O : public AtomOrBondMatchNode_O
     auto  obj = gctools::GC<Root_O>::allocate( originalCode, node, maxtag ); // RP_Create<Root_O>(lisp);
     return obj;
   }
-  core::HashTableEq_sp lazyTests();
+  core::HashTable_sp lazyTests();
   void setTests(core::List_sp tests);
   void addTest(core::Symbol_sp testSymbol, core::Function_sp testCode);
   bool evaluateTest(core::Symbol_sp testSym, Atom_sp atom);
@@ -1220,7 +1220,7 @@ class MoleculeGraph_O : public core::CxxObject_O
 public:
   void initialize();
 public:
-  core::HashTableEq_sp     _nodes_to_index;
+  core::HashTable_sp     _nodes_to_index;
   core::ComplexVector_T_sp _nodes;
   MoleculeGraphType*       _moleculeGraph;
   size_t                   _num_edges;
@@ -1314,7 +1314,7 @@ class ChemInfoGraph_O : public core::CxxObject_O
   void initialize();
 public:
   Root_sp                _Root;
-  core::HashTableEq_sp   _nodes_to_index;
+  core::HashTable_sp   _nodes_to_index;
   gctools::Vec0<size_t>          _nodeOrder;
   gctools::Vec0<ChemInfoNode_sp> _atomNodes;
   gctools::Vec0<BondToAtomTest_sp> _bondNodes;

diff --git a/include/cando/chem/chemdraw.h b/include/cando/chem/chemdraw.h
@@ -185,7 +185,7 @@ class CDFragment_O : public core::CxxObject_O
     CDBonds			_Bonds;
     int				_LargestId;
     gc::Nilable<Molecule_sp> _Molecule;
-//    core::HashTableEq_sp		_Properties;
+//    core::HashTable_sp		_Properties;
 public:
     void	initialize();
  public:

diff --git a/include/cando/chem/conformationCollection.h b/include/cando/chem/conformationCollection.h
@@ -66,7 +66,7 @@ class ConformationCollectionEntry_O : public core::CxxObject_O
 public:
   ConformationCollection_sp	     _WeakConformationCollection;
   geom::SimpleVectorCoordinate_sp    _AllCoordinates;
-  core::HashTableEq_sp		     _Data;
+  core::HashTable_sp		     _Data;
 
 public:
   void setAllCoordinates(geom::SimpleVectorCoordinate_sp ac);
@@ -75,7 +75,7 @@ class ConformationCollectionEntry_O : public core::CxxObject_O
 
   CL_DEFMETHOD ConformationCollection_sp	getConformationCollection() {_OF(); ASSERTNOTNULL(this->_WeakConformationCollection);return this->_WeakConformationCollection;};
   void	setConformationCollection(ConformationCollection_sp s);
-//	core::HashTableEq_sp getData() { return this->_Data; };
+//	core::HashTable_sp getData() { return this->_Data; };
 
   void	translateAllCoordinates(const Vector3& offset);
 
@@ -120,15 +120,15 @@ class ConformationCollection_O : public core::CxxObject_O
   Matter_sp	       			        _Matter;
   gctools::Vec0<ConformationCollectionEntry_sp>	_Entries;
   gctools::SmallOrderedSet<Atom_sp>		_AllAtoms;
-  core::HashTableEq_sp			        _Data;
+  core::HashTable_sp			        _Data;
 public:
   typedef	gctools::Vec0<ConformationCollectionEntry_sp>::iterator	entryIterator;
   typedef	gctools::Vec0<ConformationCollectionEntry_sp>::const_iterator	const_entryIterator;
   typedef	gctools::SmallOrderedSet<Atom_sp>::iterator	atomIterator;
 public:
   geom::SimpleVectorCoordinate_sp	_SimpleVectorCoordinate(Matter_sp matter);
 public:
-  core::HashTableEq_sp	getData() { return this->_Data;};
+  core::HashTable_sp	getData() { return this->_Data;};
 
   void	saveAs(const string& fn);
 

diff --git a/include/cando/chem/conformationExplorer.h b/include/cando/chem/conformationExplorer.h
@@ -71,7 +71,7 @@ class ConformationExplorerEntryStage_O : public core::CxxObject_O
   bool				_Complete;
   ConformationExplorerEntry_sp	_WeakConformationExplorerEntry;
   geom::SimpleVectorCoordinate_sp	_FinalCoordinates;
-  core::HashTableEq_sp			_Binder;
+  core::HashTable_sp			_Binder;
 			//! Energy of the conformation in kcal as calculated by the package/model
   double				_EnergyKCal;
 			//! ExternalInterfaceName is cando, gamess, gaussian, nwchem etc
@@ -123,7 +123,7 @@ CL_DEFMETHOD 	void	setComplete(bool b) { this->_Complete = b;};
 
 	void	setConformationExplorerEntry(ConformationExplorerEntry_sp s);
 CL_LISPIFY_NAME("getBinder");
-CL_DEFMETHOD 	core::HashTableEq_sp getBinder() { return this->_Binder; };
+CL_DEFMETHOD 	core::HashTable_sp getBinder() { return this->_Binder; };
 
 	void	translateFinalCoordinates(const Vector3& offset);
 
@@ -180,14 +180,14 @@ class ConformationExplorerEntry_O : public core::CxxObject_O
 	ConformationExplorerEntryStage_sp		_SelectedStage;
 	/*! Every time an entry is created it gets a new UniqueEntryIndex */
 	int							_UniqueEntryIndex;
-	core::HashTableEq_sp				_Binder;
+	core::HashTable_sp				_Binder;
 public:
     typedef	gctools::Vec0<ConformationExplorerEntryStage_sp>::iterator	stageIterator;
 public:
 CL_LISPIFY_NAME("getConformationExplorer");
 CL_DEFMETHOD 	ConformationExplorer_sp	getConformationExplorer() {_OF(); ASSERTNOTNULL(this->_WeakConformationExplorer);return this->_WeakConformationExplorer;};
 	void	setConformationExplorer(ConformationExplorer_sp s);
-	core::HashTableEq_sp getBinder() { return this->_Binder; };
+	core::HashTable_sp getBinder() { return this->_Binder; };
 public:
 
 	stageIterator	begin_Stages() { return this->_Stages.begin(); };
@@ -260,7 +260,7 @@ friend class ConformationExplorerEntryStage_O;
     gctools::Vec0<ConformationExplorerEntry_sp>	_Entries;
     gctools::SmallOrderedSet<Atom_sp>			_AllAtoms;
 	core::ComplexVector_byte32_t_sp		_SuperposeAtomIndexes;
-	core::HashTableEq_sp			_Binder;
+	core::HashTable_sp			_Binder;
 protected:
 	Atom_sp	_getAtomAtIndex(unsigned i);
 public:
@@ -288,7 +288,7 @@ friend class ConformationExplorerEntryStage_O;
 
 public:
 CL_LISPIFY_NAME("getBinder");
-CL_DEFMETHOD 	core::HashTableEq_sp	getBinder() { return this->_Binder;};
+CL_DEFMETHOD 	core::HashTable_sp	getBinder() { return this->_Binder;};
 
 	void	saveAs(const string& fn);
 

diff --git a/include/cando/chem/elements.h b/include/cando/chem/elements.h
@@ -126,7 +126,7 @@ class ElementsInfo_O : public core::CxxObject_O
   void initialize();
 public:
   gctools::Vec0<AtomicInfo>    _atomicInfo;
-  core::HashTableEq_sp      _elementFromAtomicSymbol;
+  core::HashTable_sp      _elementFromAtomicSymbol;
   gctools::Vec0<HybridizationInfo>  _hybridizationInfo;
   gctools::Vec0<int>                _atomicNumberToAtomicInfoIndex;
   gctools::Vec0<int>                _atomicMassToAtomicInfoIndex;

diff --git a/include/cando/chem/energyAtomTable.h b/include/cando/chem/energyAtomTable.h
@@ -137,7 +137,7 @@ class AtomTable_O : public core::CxxObject_O
   void initialize();
 public:
   gctools::Vec0<EnergyAtom>	      _Atoms;
-  core::HashTableEq_sp                _AtomTableIndexes; // m a p<Atom_sp,uint>	_AtomTableIndexes;
+  core::HashTable_sp                _AtomTableIndexes; // m a p<Atom_sp,uint>	_AtomTableIndexes;
   core::ComplexVector_int32_t_sp      _ResiduePointers;
   core::ComplexVector_T_sp            _ResidueNames;
   //! Store count of atoms in each molecule. The length of this vector is the number of molecules
@@ -232,7 +232,7 @@ class AtomTable_O : public core::CxxObject_O
   //
   // Access fields in AtomTable elements directly
   //
-  core::HashTableEq_sp getAtomTableIndexes();
+  core::HashTable_sp getAtomTableIndexes();
   CL_DEFMETHOD MatterName elt_atom_name(int index) { return this->_Atoms[index]._AtomName; };
   CL_DEFMETHOD core::Symbol_sp elt_atom_type(int index,core::HashTable_sp atomTypes);
   CL_DEFMETHOD Atom_sp elt_atom(int index) { return this->_Atoms[index].atom(); };

diff --git a/include/cando/chem/ffBaseDb.h b/include/cando/chem/ffBaseDb.h
@@ -180,12 +180,12 @@ class FFParameterBaseDb_O : public FFBaseDb_O {
   void fields(core::Record_sp node);
   void initialize();
  public:
-  core::HashTableEq_sp _Parameters;
+  core::HashTable_sp _Parameters;
   core::ComplexVector_T_sp _ParameterVector;
  public:
   virtual void forceFieldMerge(FFBaseDb_sp other);
- FFParameterBaseDb_O() : FFBaseDb_O(), _Parameters(unbound<core::HashTableEq_O>()) {};
-  core::HashTableEq_sp parameters() const;
+ FFParameterBaseDb_O() : FFBaseDb_O(), _Parameters(unbound<core::HashTable_O>()) {};
+  core::HashTable_sp parameters() const;
   string __repr__() const;
 };
 

diff --git a/include/cando/chem/ffTypesDb.h b/include/cando/chem/ffTypesDb.h
@@ -120,7 +120,7 @@ CL_LISPIFY_NAME("FFTypesDb-numberOfRules");
 CL_DEFMETHOD     int	numberOfRules() { return this->_TypeAssignmentRules.size();};
     chem::FFTypeRule_sp	getRule(uint index);
 
-    core::HashTableEq_sp atomTypes(chem::Matter_sp matter);
+    core::HashTable_sp atomTypes(chem::Matter_sp matter);
 
   core::HashTable_sp assignTypes( chem::Matter_sp matter, core::HashTable_sp atom_types );
   core::Symbol_sp    assignType( chem::Atom_sp atom );

diff --git a/include/cando/chem/mol2.h b/include/cando/chem/mol2.h
@@ -87,7 +87,7 @@ string	mol2AtomType(Atom_sp a);
 
 core::HashTable_sp assignSybylTypes(Matter_sp matter);
 
-core::HashTableEql_sp mol2WriteAggregateStream( Aggregate_sp agg, std::ostream &out, core::HashTable_sp atom_types );
+core::HashTable_sp mol2WriteAggregateStream( Aggregate_sp agg, std::ostream &out, core::HashTable_sp atom_types );
 void	mol2WriteAggregateToFileName( Aggregate_sp a, core::T_sp sFileName, core::HashTable_sp atom_types );
 
 void	mol2WriteDumbAggregateToFileName( Aggregate_O& a, core::T_sp sFileName, core::HashTable_sp atom_types );

diff --git a/include/cando/chem/monomerContext.h b/include/cando/chem/monomerContext.h
@@ -148,7 +148,7 @@ class MonomerContext_O : public core::CxxObject_O
 		 * recognizes.  This is done by expanding all 
 		 * group names to monomer names. 
 		 */
-  core::HashTableEqual_sp	getAllSpecificKeys();
+  core::HashTable_sp	getAllSpecificKeys();
 		//! Return the first specific key
   core::Symbol_sp		getFirstSpecificKey();
 

diff --git a/include/cando/chem/octree.h b/include/cando/chem/octree.h
@@ -99,8 +99,8 @@ class AddIonOctree_O : public core::CxxObject_O {
   gctools::Vec0<double> PdHalfEdges;
   gctools::Vec0<double> PdHalfDiagonals;
   gctools::Vec0<Atom_sp> vaAtoms;
-  core::HashTableEq_sp atomsToResidues;
-  core::HashTableEq_sp residuesToMolecules;
+  core::HashTable_sp atomsToResidues;
+  core::HashTable_sp residuesToMolecules;
   OctNode_sp onHead;
 
 public:

diff --git a/include/cando/chem/oligomer.h b/include/cando/chem/oligomer.h
@@ -167,7 +167,7 @@ class Oligomer_O : public core::CxxObject_O
     void	checkMonomersAndNeighborsForErrors(CandoDatabase_sp bdb, gctools::SmallOrderedSet<Monomer_sp>& monomers ); // s e t<Monomer_sp> monomers);
     void	checkMonomersAndNotNeighborsForErrors(CandoDatabase_sp bdb, gctools::SmallOrderedSet<Monomer_sp>& monomers ); // s e t<Monomer_sp> monomers);
     void	signal_monomerContentsChanged();
-  core::HashTableEqual_sp allAliases();
+  core::HashTable_sp allAliases();
 
 public:
     // Atomic oligomer modifying routines

diff --git a/include/cando/chem/ringFinder.h b/include/cando/chem/ringFinder.h
@@ -155,7 +155,7 @@ class RingFinder_O : public core::CxxObject_O
 private:
     core::HashTable_sp			_vertices;
     gctools::Vec0<AGEdge_sp>		_edges;
-    core::HashTableEql_sp               _rings; // m a p<uint,core::List_sp>		_rings;
+    core::HashTable_sp               _rings; // m a p<uint,core::List_sp>		_rings;
     gctools::Vec0<PathMessage_sp>		_finalRings;
     gctools::Vec0<core::SimpleBitVector_sp>	_gaussian;
 public:

diff --git a/include/cando/chem/spanningLoop.h b/include/cando/chem/spanningLoop.h
@@ -103,7 +103,7 @@ namespace chem {
 	AtomFlags			fVisibleFlagsOn;
 	AtomFlags			fVisibleFlagsOff;
 	int				iTempInt;
-        core::HashTableEq_sp            _BackSpan;
+        core::HashTable_sp            _BackSpan;
 
 	void	clearAtomIndexes();
         core::T_sp next(core::T_sp funcDesig);

diff --git a/include/cando/chem/structureList.h b/include/cando/chem/structureList.h
@@ -70,7 +70,7 @@ static Structure_Old_ListEntry_sp	create(Structure_Old_List_sp s);
 	Structure_Old_List_sp		_WeakStructureList;
         geom::SimpleVectorCoordinate_sp	_AllCoordinates;
         geom::SimpleVectorCoordinate_sp	_SuperposeCoordinates;
-    core::HashTableEq_sp 	_Data;
+    core::HashTable_sp 	_Data;
 	uint			_Members;
 
 public:
@@ -87,7 +87,7 @@ static Structure_Old_ListEntry_sp	create(Structure_Old_List_sp s);
 
 	void	translateAllCoordinates(const Vector3& offset);
 
-    core::HashTableEq_sp getData() { return this->_Data;};
+    core::HashTable_sp getData() { return this->_Data;};
 
         void setAllCoordinates(geom::SimpleVectorCoordinate_sp ac);
         geom::SimpleVectorCoordinate_sp getAllCoordinates() { return this->_AllCoordinates; }
@@ -126,15 +126,15 @@ class Structure_Old_List_O : public core::CxxObject_O
     gctools::SmallOrderedSet<Atom_sp>			_AllAtoms;
     gctools::SmallOrderedSet<Atom_sp>			_SuperposeAtoms;
 	double					_RmsCutOff;
-    core::HashTableEq_sp			_Data;
+    core::HashTable_sp			_Data;
 protected:
 
 public:
 //    static Structure_Old_List_sp open_StructureList(const string& fn);
 
 public:
 
-    core::HashTableEq_sp	getData() { return this->_Data;};
+    core::HashTable_sp	getData() { return this->_Data;};
     typedef	gctools::Vec0<Structure_Old_ListEntry_sp>::iterator	entryIterator;
 
 	void	saveAs(const string& fn);

diff --git a/include/cando/chem/trajectory.h b/include/cando/chem/trajectory.h
@@ -94,7 +94,7 @@ class Trajectory_O : public core::CxxObject_O
   Matter_sp		_Matter;
   gctools::Vec0<Atom_sp>		_AtomList;
   gctools::Vec0<TrajectoryFrame_sp>	_Frames;
-  core::HashTableEq_sp	_Namespace;
+  core::HashTable_sp	_Namespace;
 
 public:
   bool fieldsp() const { return true; };

diff --git a/include/cando/kinematics/old/chainNode.fwd.h b/include/cando/kinematics/old/chainNode.fwd.h
@@ -36,7 +36,7 @@ namespace kinematics
 {
     FORWARD(ChainNode);
 
-    typedef core::HashTableEq_sp	RingClosingMonomerMap;
+    typedef core::HashTable_sp	RingClosingMonomerMap;
 
 
 }; /* kinematics */

diff --git a/src/adapt/adaptPackage.cc b/src/adapt/adaptPackage.cc
@@ -61,7 +61,6 @@ This is an open source license for the CANDO software from Temple University, bu
 #include <clasp/core/symbolToEnumConverter.h>
 #include <clasp/core/symbol.h>
 #include <clasp/core/lispList.h>
-#include <clasp/core/weakHashTable.h>
 #include <clasp/core/weakPointer.h>
 #include <clasp/core/wrappedPointer.h>
 #include <clasp/llvmo/llvmoExpose.h>

diff --git a/src/adapt/indexedObjectBag.cc b/src/adapt/indexedObjectBag.cc
@@ -36,7 +36,7 @@ namespace adapt {
 using namespace core;
 
 void IndexedObjectBag_O::initialize() {
-  this->_Bag = HashTableEq_O::create_default();
+  this->_Bag = HashTable_O::createEq();
 }
 
 CL_LISPIFY_NAME("set_next_available_entry");

diff --git a/src/adapt/objectSet.cc b/src/adapt/objectSet.cc
@@ -35,7 +35,7 @@ namespace adapt {
 
 void ObjectSet_O::initialize() {
   this->Base::initialize();
-  this->_Set = HashTableEq_O::create_default();
+  this->_Set = HashTable_O::createEq();
 }
 
 CL_LISPIFY_NAME("addObjects");