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Hash table changes #70

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merged 3 commits into from
Jan 22, 2025
Merged

Hash table changes #70

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a26c1c2
use new hash table find()
Bike Dec 17, 2024
54f8173
Remove hash table tests from hash table types
Bike Dec 17, 2024
f1407e3
Remove old weakHashTable.h header
Bike Jan 22, 2025
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2 changes: 1 addition & 1 deletion include/cando/adapt/indexedObjectBag.h
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Expand Up @@ -41,7 +41,7 @@ namespace adapt {

public:
GCPRIVATE:
gc::Nilable<core::HashTableEq_sp> _Bag;
gc::Nilable<core::HashTable_sp> _Bag;
gc::Fixnum _NextIndex;
public:

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2 changes: 1 addition & 1 deletion include/cando/adapt/objectSet.h
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Expand Up @@ -47,7 +47,7 @@ SMART(ObjectSet);
public:

GCPRIVATE:
HashTableEq_sp _Set;
HashTable_sp _Set;

public:
CL_NAME("CONTAINS");
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2 changes: 1 addition & 1 deletion include/cando/adapt/stringList.h
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Expand Up @@ -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);
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2 changes: 1 addition & 1 deletion include/cando/adapt/stringSet.h
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Expand Up @@ -58,7 +58,7 @@ SMART(StringSet);
void initialize();

private:
HashTableEqual_sp strs;
HashTable_sp strs;
bool rest;

public:
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2 changes: 1 addition & 1 deletion include/cando/adapt/symbolSet.h
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Expand Up @@ -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);
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2 changes: 1 addition & 1 deletion include/cando/chem/candoDatabase.h
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Expand Up @@ -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
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14 changes: 7 additions & 7 deletions include/cando/chem/chemInfo.h
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Expand Up @@ -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:
Expand All @@ -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);

Expand Down Expand Up @@ -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 );
Expand Down Expand Up @@ -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);
Expand Down Expand Up @@ -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;
Expand Down Expand Up @@ -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;
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2 changes: 1 addition & 1 deletion include/cando/chem/chemdraw.h
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Expand Up @@ -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:
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8 changes: 4 additions & 4 deletions include/cando/chem/conformationCollection.h
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Expand Up @@ -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);
Expand All @@ -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);

Expand Down Expand Up @@ -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);

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12 changes: 6 additions & 6 deletions include/cando/chem/conformationExplorer.h
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Expand Up @@ -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
Expand Down Expand Up @@ -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);

Expand Down Expand Up @@ -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(); };
Expand Down Expand Up @@ -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:
Expand Down Expand Up @@ -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);

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2 changes: 1 addition & 1 deletion include/cando/chem/elements.h
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Expand Up @@ -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;
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4 changes: 2 additions & 2 deletions include/cando/chem/energyAtomTable.h
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Expand Up @@ -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
Expand Down Expand Up @@ -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(); };
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6 changes: 3 additions & 3 deletions include/cando/chem/ffBaseDb.h
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Expand Up @@ -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;
};

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2 changes: 1 addition & 1 deletion include/cando/chem/ffTypesDb.h
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Expand Up @@ -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 );
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2 changes: 1 addition & 1 deletion include/cando/chem/mol2.h
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Expand Up @@ -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 );
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2 changes: 1 addition & 1 deletion include/cando/chem/monomerContext.h
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Expand Up @@ -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();

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4 changes: 2 additions & 2 deletions include/cando/chem/octree.h
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Expand Up @@ -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:
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2 changes: 1 addition & 1 deletion include/cando/chem/oligomer.h
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Expand Up @@ -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
Expand Down
2 changes: 1 addition & 1 deletion include/cando/chem/ringFinder.h
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Expand Up @@ -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:
Expand Down
2 changes: 1 addition & 1 deletion include/cando/chem/spanningLoop.h
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Expand Up @@ -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);
Expand Down
8 changes: 4 additions & 4 deletions include/cando/chem/structureList.h
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Expand Up @@ -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:
Expand All @@ -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; }
Expand Down Expand Up @@ -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);
Expand Down
2 changes: 1 addition & 1 deletion include/cando/chem/trajectory.h
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Expand Up @@ -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; };
Expand Down
2 changes: 1 addition & 1 deletion include/cando/kinematics/old/chainNode.fwd.h
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Expand Up @@ -36,7 +36,7 @@ namespace kinematics
{
FORWARD(ChainNode);

typedef core::HashTableEq_sp RingClosingMonomerMap;
typedef core::HashTable_sp RingClosingMonomerMap;


}; /* kinematics */
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1 change: 0 additions & 1 deletion src/adapt/adaptPackage.cc
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Expand Up @@ -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>
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2 changes: 1 addition & 1 deletion src/adapt/indexedObjectBag.cc
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Expand Up @@ -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");
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2 changes: 1 addition & 1 deletion src/adapt/objectSet.cc
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Expand Up @@ -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");
Expand Down
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