From a26c1c2d9e3563248bc3049479f39d2477962269 Mon Sep 17 00:00:00 2001 From: Bike Date: Tue, 17 Dec 2024 12:53:43 -0500 Subject: [PATCH 1/3] use new hash table find() avoids reaching directly into the table, and i think is more idiomatic C++ --- src/chem/candoDatabase.cc | 4 ++-- src/chem/chemInfo.cc | 6 +++--- src/chem/entity.cc | 6 +++--- 3 files changed, 8 insertions(+), 8 deletions(-) diff --git a/src/chem/candoDatabase.cc b/src/chem/candoDatabase.cc index 5d79a429..848f9e83 100644 --- a/src/chem/candoDatabase.cc +++ b/src/chem/candoDatabase.cc @@ -135,8 +135,8 @@ CL_DEFMETHOD bool CandoDatabase_O::recognizesRepresentedEntityNameSet(core::Symb bool CandoDatabase_O::recognizesMonomerPack(core::Symbol_sp name) { - core::KeyValuePair *pair = this->_Entities->find(name); - return pair && gc::As(pair->_Value).isA(); + auto found = this->_Entities->find(name); + return found.has_value() && gc::As(*found).isA(); } #endif diff --git a/src/chem/chemInfo.cc b/src/chem/chemInfo.cc index 27fe8151..d1a290a1 100644 --- a/src/chem/chemInfo.cc +++ b/src/chem/chemInfo.cc @@ -2240,14 +2240,14 @@ void Root_O::addTest(core::Symbol_sp testSym, core::Function_sp testCode) { bool Root_O::evaluateTest(core::Symbol_sp testSym, Atom_sp atom) { ASSERTF(testSym.notnilp(), ("The test symbol was nil! - this should never occur")); LOG("Looking up test with symbol<{}>", _rep_(testSym)); - core::KeyValuePair* find = lazyTests()->find(testSym); + auto find = lazyTests()->find(testSym); if (!find) { SIMPLE_ERROR("Could not find named ChemInfo/Smarts test[{}] in Smarts object - available named tests are[{}]", _rep_(testSym), this->lazyTests()->keysAsString()); } - core::Function_sp func = core::coerce::functionDesignator(find->_Value); + core::Function_sp func = core::coerce::functionDesignator(*find); if (!gctools::IsA(func)) { - SIMPLE_ERROR("The test ChemInfo/Smarts test[{}] must be a function - instead it is a {}", _rep_(testSym), _rep_(find->_Value)); + SIMPLE_ERROR("The test ChemInfo/Smarts test[{}] must be a function - instead it is a {}", _rep_(testSym), _rep_(*find)); } core::Function_sp testCode = gctools::As_unsafe(func); ASSERTF(testCode.notnilp(), ("testCode was nil - it should never be")); diff --git a/src/chem/entity.cc b/src/chem/entity.cc index df73169c..17c7eefb 100644 --- a/src/chem/entity.cc +++ b/src/chem/entity.cc @@ -77,10 +77,10 @@ CL_DEFMETHOD RepresentativeList_sp Entity_O::minimalRepresentativeList() const { RepresentedEntityNameSet_sp curNameSet = expandedList->rowMajorAref(i).as(); core::Symbol_sp representor = curNameSet->getRepresentative(); RepresentedEntityNameSet_sp minimalRepresentedEntityNameSet; - core::KeyValuePair* pair = binder->find(representor); - if (pair) { + auto found = binder->find(representor); + if (found) { minimalRepresentedEntityNameSet = - pair->_Value.as(); // binder->indexed_value(bi).as(); + found->as(); // binder->indexed_value(bi).as(); minimalRepresentedEntityNameSet->mergeEntityNames(curNameSet); } else { auto temp = gctools::GC::copy(*curNameSet); // = RP_Copy(curNameSet); From 54f817354fe1334f423704c53db3c22e885ddce4 Mon Sep 17 00:00:00 2001 From: Bike Date: Tue, 17 Dec 2024 13:42:59 -0500 Subject: [PATCH 2/3] Remove hash table tests from hash table types I'm considering it an implementation detail. The types may disappear shortly. --- include/cando/adapt/indexedObjectBag.h | 2 +- include/cando/adapt/objectSet.h | 2 +- include/cando/adapt/stringList.h | 2 +- include/cando/adapt/stringSet.h | 2 +- include/cando/adapt/symbolSet.h | 2 +- include/cando/chem/candoDatabase.h | 2 +- include/cando/chem/chemInfo.h | 14 +++++------ include/cando/chem/chemdraw.h | 2 +- include/cando/chem/conformationCollection.h | 8 +++--- include/cando/chem/conformationExplorer.h | 12 ++++----- include/cando/chem/elements.h | 2 +- include/cando/chem/energyAtomTable.h | 4 +-- include/cando/chem/ffBaseDb.h | 6 ++--- include/cando/chem/ffTypesDb.h | 2 +- include/cando/chem/mol2.h | 2 +- include/cando/chem/monomerContext.h | 2 +- include/cando/chem/octree.h | 4 +-- include/cando/chem/oligomer.h | 2 +- include/cando/chem/ringFinder.h | 2 +- include/cando/chem/spanningLoop.h | 2 +- include/cando/chem/structureList.h | 8 +++--- include/cando/chem/trajectory.h | 2 +- include/cando/kinematics/old/chainNode.fwd.h | 2 +- src/adapt/indexedObjectBag.cc | 2 +- src/adapt/objectSet.cc | 2 +- src/adapt/symbolSet.cc | 2 +- src/chem/candoDatabase.cc | 2 +- src/chem/chemInfo.cc | 26 ++++++++++---------- src/chem/chemdraw.cc | 16 ++++++------ src/chem/cipPrioritizer.cc | 12 ++++----- src/chem/conformationCollection.cc | 4 +-- src/chem/conformationExplorer.cc | 8 +++--- src/chem/elements.cc | 4 +-- src/chem/energyAtomTable.cc | 4 +-- src/chem/energyFunction.cc | 6 ++--- src/chem/entity.cc | 2 +- src/chem/ffBaseDb.cc | 4 +-- src/chem/ffNonbondDb.cc | 4 +-- src/chem/ffTypesDb.cc | 4 +-- src/chem/lispClasses/externalInterface.cc | 2 +- src/chem/lispClasses/externalInterface.h | 4 +-- src/chem/lispClasses/table.cc | 2 +- src/chem/lispClasses/table.h | 2 +- src/chem/lispClasses/trainer.cc | 4 +-- src/chem/lispClasses/trainer.h | 2 +- src/chem/matter.cc | 2 +- src/chem/minimizer.cc | 2 +- src/chem/mol2.cc | 8 +++--- src/chem/monomer.cc | 2 +- src/chem/monomerContext.cc | 2 +- src/chem/octree.cc | 4 +-- src/chem/oligomer.cc | 8 +++--- src/chem/residue.cc | 10 ++++---- src/chem/ringFinder.cc | 4 +-- src/chem/scoringFunction.cc | 2 +- src/chem/spanningLoop.cc | 2 +- src/chem/structureList.cc | 4 +-- src/chem/topology.cc | 2 +- src/chem/trajectory.cc | 2 +- src/geom/color.cc | 2 +- src/kinematics/old/chainNode.cc | 2 +- 61 files changed, 132 insertions(+), 132 deletions(-) diff --git a/include/cando/adapt/indexedObjectBag.h b/include/cando/adapt/indexedObjectBag.h index 3c37ee57..25bc9fcb 100644 --- a/include/cando/adapt/indexedObjectBag.h +++ b/include/cando/adapt/indexedObjectBag.h @@ -41,7 +41,7 @@ namespace adapt { public: GCPRIVATE: - gc::Nilable _Bag; + gc::Nilable _Bag; gc::Fixnum _NextIndex; public: diff --git a/include/cando/adapt/objectSet.h b/include/cando/adapt/objectSet.h index a85890ff..90471f10 100644 --- 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 index 2f817b07..7c956784 100644 --- 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 index 984741d2..52004666 100644 --- 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 index 2e012abd..d1f3b735 100644 --- 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 index 9ebe649b..6cd1268b 100644 --- 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 index f1a3f0b0..1f5289b3 100644 --- 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 _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 _AtomWildCards; + core::HashTable_sp _AtomWildCards; // core::StringMap _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::allocate( originalCode, node, maxtag ); // RP_Create(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 _nodeOrder; gctools::Vec0 _atomNodes; gctools::Vec0 _bondNodes; diff --git a/include/cando/chem/chemdraw.h b/include/cando/chem/chemdraw.h index d804530e..5fa2552e 100644 --- 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; -// 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 index 483aa737..8a1e9408 100644 --- 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); @@ -120,7 +120,7 @@ class ConformationCollection_O : public core::CxxObject_O Matter_sp _Matter; gctools::Vec0 _Entries; gctools::SmallOrderedSet _AllAtoms; - core::HashTableEq_sp _Data; + core::HashTable_sp _Data; public: typedef gctools::Vec0::iterator entryIterator; typedef gctools::Vec0::const_iterator const_entryIterator; @@ -128,7 +128,7 @@ class ConformationCollection_O : public core::CxxObject_O 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 index 57632371..22d206b1 100644 --- 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::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 _Entries; gctools::SmallOrderedSet _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 index 16980bd1..5457a4a1 100644 --- 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; - core::HashTableEq_sp _elementFromAtomicSymbol; + core::HashTable_sp _elementFromAtomicSymbol; gctools::Vec0 _hybridizationInfo; gctools::Vec0 _atomicNumberToAtomicInfoIndex; gctools::Vec0 _atomicMassToAtomicInfoIndex; diff --git a/include/cando/chem/energyAtomTable.h b/include/cando/chem/energyAtomTable.h index 573e9627..9df05a53 100644 --- 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 _Atoms; - core::HashTableEq_sp _AtomTableIndexes; // m a p _AtomTableIndexes; + core::HashTable_sp _AtomTableIndexes; // m a p _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 index 95e6d188..f213c5e8 100644 --- 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_sp parameters() const; + FFParameterBaseDb_O() : FFBaseDb_O(), _Parameters(unbound()) {}; + core::HashTable_sp parameters() const; string __repr__() const; }; diff --git a/include/cando/chem/ffTypesDb.h b/include/cando/chem/ffTypesDb.h index e63ee287..f0cc6b66 100644 --- 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 index 280968cc..8ea06fe1 100644 --- 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 index fa425fa4..21c591b0 100644 --- 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 index 57518039..b0f5c628 100644 --- 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 PdHalfEdges; gctools::Vec0 PdHalfDiagonals; gctools::Vec0 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 index 9d558ab8..c553bd5c 100644 --- 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& monomers ); // s e t monomers); void checkMonomersAndNotNeighborsForErrors(CandoDatabase_sp bdb, gctools::SmallOrderedSet& monomers ); // s e t 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 index 7131d6be..32ecddec 100644 --- 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 _edges; - core::HashTableEql_sp _rings; // m a p _rings; + core::HashTable_sp _rings; // m a p _rings; gctools::Vec0 _finalRings; gctools::Vec0 _gaussian; public: diff --git a/include/cando/chem/spanningLoop.h b/include/cando/chem/spanningLoop.h index 0d74a694..0307ea88 100644 --- 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 index b130baa8..89412b97 100644 --- 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; } @@ -126,7 +126,7 @@ class Structure_Old_List_O : public core::CxxObject_O gctools::SmallOrderedSet _AllAtoms; gctools::SmallOrderedSet _SuperposeAtoms; double _RmsCutOff; - core::HashTableEq_sp _Data; + core::HashTable_sp _Data; protected: public: @@ -134,7 +134,7 @@ class Structure_Old_List_O : public core::CxxObject_O public: - core::HashTableEq_sp getData() { return this->_Data;}; + core::HashTable_sp getData() { return this->_Data;}; typedef gctools::Vec0::iterator entryIterator; void saveAs(const string& fn); diff --git a/include/cando/chem/trajectory.h b/include/cando/chem/trajectory.h index c8c610d1..18c9537d 100644 --- 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 _AtomList; gctools::Vec0 _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 index 290ad83c..d79596bb 100644 --- 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/indexedObjectBag.cc b/src/adapt/indexedObjectBag.cc index 27fe2dfc..a35753c7 100644 --- 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 index 37a0e453..a8135a11 100644 --- 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"); diff --git a/src/adapt/symbolSet.cc b/src/adapt/symbolSet.cc index 4e166f85..1dfac19c 100644 --- a/src/adapt/symbolSet.cc +++ b/src/adapt/symbolSet.cc @@ -213,7 +213,7 @@ void SymbolSet_O::remove(Symbol_sp s) { void SymbolSet_O::initialize() { this->Base::initialize(); - this->_Symbols = HashTableEq_O::create_default(); + this->_Symbols = HashTable_O::createEq(); } SymbolSet_O::SymbolSet_O(const SymbolSet_O &ss) : Base(ss) { diff --git a/src/chem/candoDatabase.cc b/src/chem/candoDatabase.cc index 848f9e83..40d9f72a 100644 --- a/src/chem/candoDatabase.cc +++ b/src/chem/candoDatabase.cc @@ -74,7 +74,7 @@ namespace chem { void CandoDatabase_O::initialize() { this->Base::initialize(); - this->_Topologys = core::HashTableEq_O::create_default(); + this->_Topologys = core::HashTable_O::createEq(); this->_Topologys->setupThreadSafeHashTable(); // AllCandoDatabases.append(this->sharedThis()); } diff --git a/src/chem/chemInfo.cc b/src/chem/chemInfo.cc index d1a290a1..e926de7a 100644 --- a/src/chem/chemInfo.cc +++ b/src/chem/chemInfo.cc @@ -187,7 +187,7 @@ CL_DEFUN void chem__walk_chem_info_with_parent(ChemInfoNode_sp top, core::T_sp c }); }; -ChemInfoMatch_sp ChemInfoMatch_O::make(Root_sp root, size_t maxTag, core::HashTableEql_sp ringLookup) { +ChemInfoMatch_sp ChemInfoMatch_O::make(Root_sp root, size_t maxTag, core::HashTable_sp ringLookup) { auto match = gctools::GC::allocate(root, maxTag + 1); match->_TagLookup = core::SimpleVector_O::make(maxTag + 1); match->_RingLookup = ringLookup; @@ -198,7 +198,7 @@ void ChemInfoMatch_O::initialize() { this->Base::initialize(); this->_Matches = false; this->_TagLookup = core::SimpleVector_O::make(this->_MaxTagPlus1); - // this->_ClosestMatch = core::HashTableEqual_O::create_default(); + // this->_ClosestMatch = core::HashTable_O::createEqual(); } void ChemInfoMatch_O::fields(core::Record_sp node) { @@ -307,7 +307,7 @@ bool ChemInfoMatch_O::matchesRingTag(Atom_sp atom, core::T_sp tag) { void WildElementDict_O::initialize() { this->Base::initialize(); - this->_AtomWildCards = core::HashTableEqual_O::create_default(); + this->_AtomWildCards = core::HashTable_O::createEqual(); } CL_LISPIFY_NAME("addWildName"); @@ -2190,11 +2190,11 @@ void AntechamberBondToAtomTest_O::fields(core::Record_sp node) { // ------- Root -core::HashTableEq_sp Root_O::lazyTests() { +core::HashTable_sp Root_O::lazyTests() { if (this->_Tests.nilp()) { - this->_Tests = core::HashTableEq_O::create_default(); + this->_Tests = core::HashTable_O::createEq(); } - return gc::As_unsafe(this->_Tests); + return gc::As_unsafe(this->_Tests); } uint Root_O::depth() const { @@ -2377,8 +2377,8 @@ bool AntechamberRoot_O::matches_Atom(Root_sp root, chem::Atom_sp atom) { CL_DEFMETHOD core::Vector_sp ChemInfoMatch_O::tags_as_vector() const { return this->_TagLookup; } -CL_DEFMETHOD core::HashTableEql_sp ChemInfoMatch_O::tags_as_hashtable() const { - core::HashTableEql_sp ht = core::HashTableEql_O::create_default(); +CL_DEFMETHOD core::HashTable_sp ChemInfoMatch_O::tags_as_hashtable() const { + core::HashTable_sp ht = core::HashTable_O::createEql(); for (size_t ii = 0; ii < this->_TagLookup->length(); ++ii) { if (this->_TagLookup->rowMajorAref(ii).notnilp()) { ht->setf_gethash(core::make_fixnum(ii), this->_TagLookup->rowMajorAref(ii)); @@ -2446,7 +2446,7 @@ CL_DEFUN AntechamberRoot_mv chem__compile_antechamber(const string &code, WildEl DOCGROUP(cando); CL_DEFUN core::T_mv chem__chem_info_match(Root_sp testRoot, Atom_sp atom) { - core::HashTableEql_sp ringHashTable = core::HashTableEql_O::create_default(); + core::HashTable_sp ringHashTable = core::HashTable_O::createEql(); ChemInfoMatch_sp current_match = ChemInfoMatch_O::make(testRoot, testRoot->_MaxTag, ringHashTable); core::DynamicScopeManager scope(_sym_STARcurrent_matchSTAR, current_match); bool matches = testRoot->matches_Atom(testRoot, atom); @@ -2688,7 +2688,7 @@ CL_DEFMETHOD void MoleculeGraph_O::walk_edges(core::T_sp callback) { } void MoleculeGraph_O::initialize() { - this->_nodes_to_index = core::HashTableEq_O::create_default(); + this->_nodes_to_index = core::HashTable_O::createEq(); this->_moleculeGraph = nullptr; this->_nodes = core::ComplexVector_T_O::make(64, nil(), core::make_fixnum(0)); } @@ -2766,7 +2766,7 @@ ChemInfoGraph_O::~ChemInfoGraph_O() { } void ChemInfoGraph_O::initialize() { - this->_nodes_to_index = core::HashTableEq_O::create_default(); + this->_nodes_to_index = core::HashTable_O::createEq(); } CL_DOCSTRING(R"dx(Make a chem:chem-info-graph from a chem:root object)dx"); @@ -2873,7 +2873,7 @@ void ChemInfoGraph_O::buildFromRoot_() { // Transform a ChemInfo graph into a boost graph // This is tricky code - core::HashTableEq_sp parent_nodes = core::HashTableEq_O::create_default(); + core::HashTable_sp parent_nodes = core::HashTable_O::createEq(); walk_nodes_with_parent( nil(), pattern->_Node, [&graph, &parent_nodes, &closers #if DEBUG_SETF_GETHASH @@ -3197,7 +3197,7 @@ CL_DEFUN core::List_sp chem__boost_graph_vf2(ChemInfoGraph_sp chemInfoGraph, Mol if (boost::num_vertices(*chemInfoGraph->_chemInfoGraph) > boost::num_vertices(*moleculeGraph->_moleculeGraph)) { return nil(); } - core::HashTableEql_sp ringHashTable = core::HashTableEql_O::create_default(); + core::HashTable_sp ringHashTable = core::HashTable_O::createEql(); ChemInfoMatch_sp current_match = ChemInfoMatch_O::make(chemInfoGraph->_Root, chemInfoGraph->_Root->_MaxTag, ringHashTable); core::DynamicScopeManager scope(_sym_STARcurrent_matchSTAR, current_match); EdgeComp edge_comp(chemInfoGraph, moleculeGraph); diff --git a/src/chem/chemdraw.cc b/src/chem/chemdraw.cc index 6a14eac9..0dc820dd 100644 --- a/src/chem/chemdraw.cc +++ b/src/chem/chemdraw.cc @@ -57,7 +57,7 @@ namespace chem SYMBOL_EXPORT_SC_(ChemPkg,name); // Ensure that property is a Keyword symbol -void set_property(core::HashTableEq_sp properties, core::T_sp property, core::T_sp val) +void set_property(core::HashTable_sp properties, core::T_sp property, core::T_sp val) { core::Symbol_sp psym = gc::As(property); if (!psym->isKeywordSymbol()) { @@ -412,7 +412,7 @@ int CDFragment_O::countNeighbors(CDNode_sp node) } #if 0 -void CDFragment_O::addProperties(core::HashTableEq_sp d) +void CDFragment_O::addProperties(core::HashTable_sp d) { d->mapHash([this] (core::T_sp key, core::T_sp value) { set_property(this->_Properties,key,value); @@ -786,7 +786,7 @@ void CDFragment_O::createAtomsAndBonds() Molecule_sp CDFragment_O::createMolecule() { - core::HashTable_sp atomsToNodes = core::HashTableEq_O::create_default(); + core::HashTable_sp atomsToNodes = core::HashTable_O::createEq(); // Gather all of the nodes that have atoms for ( auto cur : this->_Nodes ) { if ( cur.second->_Atom.notnilp() ) { @@ -834,7 +834,7 @@ Molecule_sp CDFragment_O::createMolecule() #if 0 core::T_sp CDFragment_O::getProperty(core::Symbol_sp s) { - core::HashTableEq_sp dict = this->getProperties(); + core::HashTable_sp dict = this->getProperties(); if ( !dict->contains(s) ) { stringstream serr; @@ -849,7 +849,7 @@ core::T_sp CDFragment_O::getProperty(core::Symbol_sp s) core::T_sp CDFragment_O::getPropertyOrDefault(core::Symbol_sp s, core::T_sp df) { - core::HashTableEq_sp dict = this->getProperties(); + core::HashTable_sp dict = this->getProperties(); if ( dict->contains(s) ) { return dict->gethash(s); @@ -1124,7 +1124,7 @@ void ChemDraw_O::setFragmentProperties(core::Symbol_sp name ) { CDFragment_sp frag = this->_NamedFragments.get(name); - core::HashTableEq_sp properties = core::HashTableEq_O::create_default(); + core::HashTable_sp properties = core::HashTable_O::createEq(); if ( comment.notnilp() ) properties->setf_gethash(kw::_sym_comment, comment ); if ( chiral_centers.notnilp() ) properties->setf_gethash(kw::_sym_chiral_centers, chiral_centers ); if ( group.notnilp() ) properties->setf_gethash(kw::_sym_group, group ); @@ -1143,7 +1143,7 @@ void ChemDraw_O::setFragmentProperties(core::Symbol_sp name void ChemDraw_O::setFragmentProperties(core::List_sp props) { DEPRECATED(); - core::HashTableEq_sp kargs = core::HashTableEq_O::createFromKeywordCons(props,validChemdrawKeywords); + core::HashTable_sp kargs = core::HashTable_O::createFromKeywordCons(props,validChemdrawKeywords); if ( !kargs->contains(_kw_name) ) { stringstream ss; @@ -1172,7 +1172,7 @@ void ChemDraw_O::parseChild( adapt::QDomNode_sp child, bool verbose, bool addHyd fragment->parseFromXml(child,verbose); if ( fragment->interpret(verbose, addHydrogens) ) { #if 0 - core::HashTableEq_sp properties = fragment->getProperties(); + core::HashTable_sp properties = fragment->getProperties(); if ( !properties->contains(INTERN_(kw,name))) { SIMPLE_ERROR("Every fragment must have a property({}) available properties: {}" , _rep_(INTERN_(kw,name)) , properties->keysAsString()); diff --git a/src/chem/cipPrioritizer.cc b/src/chem/cipPrioritizer.cc index e988577a..cca11f06 100644 --- a/src/chem/cipPrioritizer.cc +++ b/src/chem/cipPrioritizer.cc @@ -188,7 +188,7 @@ CL_LISPIFY_NAME(chem:assign-priorities-hash-table); DOCGROUP(cando); CL_DEFUN core::HashTable_sp CipPrioritizer_O::assignPrioritiesHashTable(Matter_sp matter) { - core::HashTable_sp cip = core::HashTableEq_O::create_default(); + core::HashTable_sp cip = core::HashTable_O::createEq(); CipPrioritizer_sp prior; if (gc::IsA(matter)) { prior = CipPrioritizer_O::create(); @@ -542,8 +542,8 @@ Return these two values in a pair of hash-tables each keyed on the atom)dx") CL_LISPIFY_NAME("calculateStereochemicalTypeForAllAtoms"); CL_DEFMETHOD core::HashTable_mv CipPrioritizer_O::calculateStereochemistryTypeForAllAtoms( Matter_sp molOrAgg ) { - core::HashTable_sp cip = core::HashTableEq_O::create_default(); - core::HashTable_sp stereochemistryType = core::HashTableEq_O::create_default(); + core::HashTable_sp cip = core::HashTable_O::createEq(); + core::HashTable_sp stereochemistryType = core::HashTable_O::createEq(); this->assignCahnIngoldPrelogPriorityToAtomsRelativePriority( molOrAgg, cip ); Loop l; l.loopTopGoal( molOrAgg, ATOMS ); @@ -621,9 +621,9 @@ Return (values atom-to-stereochemistry-type-hash-table atom-to-configuration-has CL_LAMBDA(matter &key use-structure) DOCGROUP(cando); CL_DEFUN core::HashTable_mv chem__calculateStereochemistry( Matter_sp matter, bool useStructure ) { - core::HashTableEq_sp stereochemistryTypes = core::HashTableEq_O::create_default(); - core::HashTableEq_sp configurations = core::HashTableEq_O::create_default(); - core::HashTableEq_sp cips = core::HashTableEq_O::create_default(); + core::HashTable_sp stereochemistryTypes = core::HashTable_O::createEq(); + core::HashTable_sp configurations = core::HashTable_O::createEq(); + core::HashTable_sp cips = core::HashTable_O::createEq(); if (gc::IsA(matter)) { doCalculateStereochemistry( useStructure, gc::As_unsafe( matter ), cips, stereochemistryTypes, configurations ); } else if (gc::IsA(matter)) { diff --git a/src/chem/conformationCollection.cc b/src/chem/conformationCollection.cc index ffc180ba..386b70ab 100644 --- a/src/chem/conformationCollection.cc +++ b/src/chem/conformationCollection.cc @@ -60,7 +60,7 @@ namespace chem { void ConformationCollectionEntry_O::initialize() { this->Base::initialize(); - this->_Data = core::HashTableEq_O::create_default(); + this->_Data = core::HashTable_O::createEq(); this->_AllCoordinates = geom::SimpleVectorCoordinate_O::make(16,Vector3(),false,0,NULL); } @@ -125,7 +125,7 @@ void ConformationCollection_O::initialize() this->Base::initialize(); this->_Matter = nil(); this->_AllAtoms.clear(); - this->_Data = core::HashTableEq_O::create_default(); + this->_Data = core::HashTable_O::createEq(); this->clearEntries(); } diff --git a/src/chem/conformationExplorer.cc b/src/chem/conformationExplorer.cc index 808c8cc3..ef7584ab 100644 --- a/src/chem/conformationExplorer.cc +++ b/src/chem/conformationExplorer.cc @@ -57,7 +57,7 @@ namespace chem { void ConformationExplorerEntryStage_O::initialize() { this->Base::initialize(); - this->_Binder = core::HashTableEq_O::create_default(); + this->_Binder = core::HashTable_O::createEq(); this->_FinalCoordinates = geom::SimpleVectorCoordinate_O::create(); this->_WeakConformationExplorerEntry = nil(); this->_Complete = true; @@ -246,7 +246,7 @@ CL_DEFMETHOD void ConformationExplorerEntryStage_O::extractCoordinatesFromMatter void ConformationExplorerEntry_O::initialize() { this->Base::initialize(); - this->_Binder = core::HashTableEq_O::create_default(); + this->_Binder = core::HashTable_O::createEq(); this->_UniqueEntryIndex = -1; } @@ -394,7 +394,7 @@ CL_DEFMETHOD ConformationExplorerEntryStage_sp ConformationExplorerEntry_O::getE #endif core::HashTable_sp ConformationExplorerEntry_O::getEntryStageNames() { - core::HashTableEq_sp stageNames = core::HashTableEq_O::create_default(); + core::HashTable_sp stageNames = core::HashTable_O::createEq(); for (auto it = this->begin_Stages(); it != this->end_Stages(); it++) { stageNames->setf_gethash((*it)->getStageName(), _lisp->_true()); } @@ -405,7 +405,7 @@ void ConformationExplorer_O::initialize() { this->Base::initialize(); this->_Matter = nil(); this->_AllAtoms.clear(); - this->_Binder = core::HashTableEq_O::create_default(); + this->_Binder = core::HashTable_O::createEq(); this->clearEntries(); this->_SuperposeAtomIndexes = core::ComplexVector_byte32_t_O::make_vector(0, 0, core::make_fixnum(0), nil(), false, core::make_fixnum(0)); diff --git a/src/chem/elements.cc b/src/chem/elements.cc index ed21abe6..8c29afe7 100644 --- a/src/chem/elements.cc +++ b/src/chem/elements.cc @@ -65,7 +65,7 @@ SYMBOL_EXPORT_SC_(ChemKwPkg,I); void ElementsInfo_O::initialize() { - this->_elementFromAtomicSymbol = core::HashTableEq_O::create_default(); + this->_elementFromAtomicSymbol = core::HashTable_O::createEq(); }; ElementsInfo_sp elementsInfo() { @@ -368,7 +368,7 @@ void initializeElementsAndHybridization() // core::af_def(ChemPkg,"elementFromAtomNameString",&elementFromAtomNameString); core::Symbol_sp elementColors = _sym__PLUS_elementColors_PLUS_; - core::HashTableEql_sp dict = core::HashTableEql_O::create_default(); + core::HashTable_sp dict = core::HashTable_O::createEql(); dict->setf_gethash(core::clasp_make_fixnum(element_C),geom::Color_O::systemColor(kw::_sym_cyan)); dict->setf_gethash(core::clasp_make_fixnum(element_H),geom::Color_O::systemColor(kw::_sym_white)); dict->setf_gethash(core::clasp_make_fixnum(element_O),geom::Color_O::systemColor(kw::_sym_red)); diff --git a/src/chem/energyAtomTable.cc b/src/chem/energyAtomTable.cc index 56758a03..2f4680c4 100644 --- a/src/chem/energyAtomTable.cc +++ b/src/chem/energyAtomTable.cc @@ -152,7 +152,7 @@ AtomTable_sp AtomTable_O::make() void AtomTable_O::initialize() { - this->_AtomTableIndexes = core::HashTableEq_O::create_default(); + this->_AtomTableIndexes = core::HashTable_O::createEq(); core::ComplexVector_int32_t_sp residue_pointers = core::ComplexVector_int32_t_O::make_vector(32,0,core::make_fixnum(0),nil(),false,core::make_fixnum(0)); core::ComplexVector_T_sp residue_names = core::ComplexVector_T_O::make(32,nil(),core::make_fixnum(0)); core::ComplexVector_int32_t_sp atoms_per_molecule = core::ComplexVector_int32_t_O::make_vector(32,0,core::make_fixnum(0),nil(),false,core::make_fixnum(0)); @@ -243,7 +243,7 @@ CL_DEFMETHOD size_t AtomTable_O::getCoordinateIndexTimes3ForAtomAtIndex(size_t i SIMPLE_ERROR("Atom index {} is out of range (0...{})" , index, this->_Atoms.size()); } -CL_DEFMETHOD core::HashTableEq_sp AtomTable_O::getAtomTableIndexes() { +CL_DEFMETHOD core::HashTable_sp AtomTable_O::getAtomTableIndexes() { return this->_AtomTableIndexes; } CL_DOCSTRING(R"dx(Return the index of ATOM or NIL if it is not found. The second return value is T if found and NIL if not.)dx"); diff --git a/src/chem/energyFunction.cc b/src/chem/energyFunction.cc index 947b768f..7856f9d5 100644 --- a/src/chem/energyFunction.cc +++ b/src/chem/energyFunction.cc @@ -1287,7 +1287,7 @@ CL_DEFMETHOD void EnergyFunction_O::defineForMatter(Matter_sp matter, bool useEx // Assign atom types for each molecule // - core::HashTableEq_sp force_fields = core::HashTableEq_O::create_default(); + core::HashTable_sp force_fields = core::HashTable_O::createEq(); Loop moleculeLoop; moleculeLoop.loopTopGoal(matter,MOLECULES); while (moleculeLoop.advanceLoopAndProcess() ) { @@ -1298,7 +1298,7 @@ CL_DEFMETHOD void EnergyFunction_O::defineForMatter(Matter_sp matter, bool useEx force_fields->setf_gethash(force_field_name,combined_force_field); } } - core::HashTable_sp atomTypes = core::HashTableEq_O::create_default(); + core::HashTable_sp atomTypes = core::HashTable_O::createEq(); // Assign given atom-types Loop atom_loop; atom_loop.loopTopGoal(matter,ATOMS); @@ -1475,7 +1475,7 @@ core::HashTable_sp createAtomToResidueHashTable(Matter_sp molecule) { Loop lRes; Loop lAtoms; - core::HashTableEq_sp ht = core::HashTableEq_O::create_default(); + core::HashTable_sp ht = core::HashTable_O::createEq(); lRes.loopTopGoal(molecule,RESIDUES); while (lRes.advanceLoopAndProcess()) { Residue_sp res = lRes.getResidue(); diff --git a/src/chem/entity.cc b/src/chem/entity.cc index 17c7eefb..6c79a31b 100644 --- a/src/chem/entity.cc +++ b/src/chem/entity.cc @@ -72,7 +72,7 @@ CL_LISPIFY_NAME("minimalRepresentativeList"); CL_DEFMETHOD RepresentativeList_sp Entity_O::minimalRepresentativeList() const { RepresentativeList_sp expandedList = this->expandedRepresentativeList(); - core::HashTableEq_sp binder = core::HashTableEq_O::create_default(); + core::HashTable_sp binder = core::HashTable_O::createEq(); for (int i(0), iEnd(expandedList->length()); i < iEnd; ++i) { RepresentedEntityNameSet_sp curNameSet = expandedList->rowMajorAref(i).as(); core::Symbol_sp representor = curNameSet->getRepresentative(); diff --git a/src/chem/ffBaseDb.cc b/src/chem/ffBaseDb.cc index 85517427..8f082f22 100644 --- a/src/chem/ffBaseDb.cc +++ b/src/chem/ffBaseDb.cc @@ -112,7 +112,7 @@ void FFBaseDb_O::forceFieldMerge(FFBaseDb_sp other) { CL_LISPIFY_NAME(FFParameterBaseDb/parameters); CL_DEFMETHOD -core::HashTableEq_sp FFParameterBaseDb_O::parameters() const { +core::HashTable_sp FFParameterBaseDb_O::parameters() const { return this->_Parameters; } @@ -124,7 +124,7 @@ void FFParameterBaseDb_O::fields(core::Record_sp node) void FFParameterBaseDb_O::initialize() { - this->_Parameters = core::HashTableEq_O::create_default(); + this->_Parameters = core::HashTable_O::createEq(); this->Base::initialize(); } diff --git a/src/chem/ffNonbondDb.cc b/src/chem/ffNonbondDb.cc index f21de100..b317c664 100644 --- a/src/chem/ffNonbondDb.cc +++ b/src/chem/ffNonbondDb.cc @@ -279,7 +279,7 @@ CL_DOCSTRING(R"dx(Join the other FFNonbondDb_sp to the current one - signal an e CL_DEFMETHOD void FFNonbondDb_O::FFNonbondDb_concatenate(FFNonbondDb_sp other, core::Symbol_sp other_name) { // What do we do with the nonbond parameters? // There needs to be something to control how nonbond interactions work across the whole system - core::HashTable_sp terms_ht = core::HashTableEq_O::create_default(); + core::HashTable_sp terms_ht = core::HashTable_O::createEq(); for ( size_t myi=0; myi_Terms.size(); ++myi ) { terms_ht->setf_gethash(this->_Terms[myi]->_Type,_lisp->_true()); } @@ -302,7 +302,7 @@ CL_DEFUN FFNonbondDb_sp chem__combine_nonbond_force_fields(FFNonbondDb_sp global // There needs to be something to control how nonbond interactions work across the whole system FFNonbondDb_sp conc = FFNonbondDb_O::create(); conc->forceFieldMergeGlobalParameters(global_nonbond); - core::HashTable_sp terms_ht = core::HashTableEq_O::create_default(); + core::HashTable_sp terms_ht = core::HashTable_O::createEq(); for ( auto cur : nonbond_force_fields ) { core::Cons_sp pair = gc::As(CONS_CAR(cur)); FFNonbondDb_sp nb = gc::As(CONS_CAR(pair)); diff --git a/src/chem/ffTypesDb.cc b/src/chem/ffTypesDb.cc index aa3a1f99..a2fa937d 100644 --- a/src/chem/ffTypesDb.cc +++ b/src/chem/ffTypesDb.cc @@ -223,11 +223,11 @@ string FFTypeRule_O::__repr__() const { } CL_DOCSTRING(R"dx(Return the atom types as a hash-table with the atoms as keys and types as values)dx"); -CL_DEFMETHOD core::HashTableEq_sp FFTypesDb_O::atomTypes(chem::Matter_sp matter) +CL_DEFMETHOD core::HashTable_sp FFTypesDb_O::atomTypes(chem::Matter_sp matter) { chem::Loop lAtoms; chem::Atom_sp atom; - core::HashTableEq_sp atomTypes = core::HashTableEq_O::create_default(); + core::HashTable_sp atomTypes = core::HashTable_O::createEq(); if (this->_TypeAssignmentRules.size()==0) return atomTypes; lAtoms.loopTopGoal(matter,ATOMS); LOG("defined loop" ); diff --git a/src/chem/lispClasses/externalInterface.cc b/src/chem/lispClasses/externalInterface.cc index 7c0fb7eb..5b56b771 100644 --- a/src/chem/lispClasses/externalInterface.cc +++ b/src/chem/lispClasses/externalInterface.cc @@ -56,7 +56,7 @@ namespace chem void ExternalInterface_O::initialize() { this->Base::initialize(); - this->_Data = core::HashTableEq_O::create_default(); + this->_Data = core::HashTable_O::createEq(); this->_AtomNames = core::StringList_O::create(); this->_WeakConformationExplorer = _Nil(); } diff --git a/src/chem/lispClasses/externalInterface.h b/src/chem/lispClasses/externalInterface.h index b47a16aa..231558af 100644 --- a/src/chem/lispClasses/externalInterface.h +++ b/src/chem/lispClasses/externalInterface.h @@ -77,7 +77,7 @@ class ExternalInterface_O : public core::T_O string _StageName; string _ExternalScript; core::SymbolMap _ScriptSubstitutions; - core::HashTableEq_sp _Data; + core::HashTable_sp _Data; string _Directory; string _FileNamePrefix; protected: @@ -137,7 +137,7 @@ class ExternalInterface_O : public core::T_O // scriptSubstitutionIterator end_ScriptSubstitutions() {return this->_ScriptSubstitutions.end(); }; - core::HashTableEq_sp getData() { return this->_Data;}; + core::HashTable_sp getData() { return this->_Data;}; string getFileNamePrefix() { return this->_FileNamePrefix; }; diff --git a/src/chem/lispClasses/table.cc b/src/chem/lispClasses/table.cc index b1cdf119..8b42e078 100644 --- a/src/chem/lispClasses/table.cc +++ b/src/chem/lispClasses/table.cc @@ -216,7 +216,7 @@ namespace chem void Table_O::initialize() { this->Base::initialize(); - this->_FieldIndexes = core::HashTableEq_O::create_default(); + this->_FieldIndexes = core::HashTable_O::createEq(); } #ifdef XML_ARCHIVE diff --git a/src/chem/lispClasses/table.h b/src/chem/lispClasses/table.h index 7117b450..caed6ef0 100644 --- a/src/chem/lispClasses/table.h +++ b/src/chem/lispClasses/table.h @@ -132,7 +132,7 @@ class Table_O : public core::T_O gctools::Vec0 _FieldClasses; gctools::Vec0 _Entries; private: // Don't serialize - core::HashTableEq_sp _FieldIndices; // m a p _FieldIndices; + core::HashTable_sp _FieldIndices; // m a p _FieldIndices; public: typedef gctools::Vec0::iterator entryIterator; entryIterator beginEntry() { return this->_Entries.begin(); }; diff --git a/src/chem/lispClasses/trainer.cc b/src/chem/lispClasses/trainer.cc index fa356020..d51e6d26 100644 --- a/src/chem/lispClasses/trainer.cc +++ b/src/chem/lispClasses/trainer.cc @@ -283,7 +283,7 @@ TrainerHeader_sp Trainer_O::getHeader() } -core::HashTableEq_sp readTrainerHeader(core::Path_sp path, core::LispPtr lisp ) +core::HashTable_sp readTrainerHeader(core::Path_sp path, core::LispPtr lisp ) { char buffer[1024]; string fileName = path->asString(); @@ -317,7 +317,7 @@ core::HashTableEq_sp readTrainerHeader(core::Path_sp path, core::LispPtr lisp ) fin.close(); vector::iterator it; it = parts.begin(); it++; // Throw away the Html Line - core::HashTableEq_sp dict = core::HashTableEq_O::create_default(); + core::HashTable_sp dict = core::HashTable_O::createEq(); for ( ; it onePair = core::split(*it,"="); diff --git a/src/chem/lispClasses/trainer.h b/src/chem/lispClasses/trainer.h index 2eb86e26..c9cac4af 100644 --- a/src/chem/lispClasses/trainer.h +++ b/src/chem/lispClasses/trainer.h @@ -226,7 +226,7 @@ namespace chem - core::HashTableEq_sp readTrainerHeader( core::Path_sp const& path); + core::HashTable_sp readTrainerHeader( core::Path_sp const& path); core::T_sp readTrainerHeader_cando( core::Cons_sp args, core::Environment_sp environ, core::LispPtr lisp); diff --git a/src/chem/matter.cc b/src/chem/matter.cc index 88c88044..7420a9e4 100644 --- a/src/chem/matter.cc +++ b/src/chem/matter.cc @@ -1227,7 +1227,7 @@ CL_DEFMETHOD core::List_sp Matter_O::allBondsAsList(bool allowVirtualAtoms ) con core::HashTable_sp Matter_O::atomToResidueMap() { - core::HashTableEq_sp map = core::HashTableEq_O::create_default(); + core::HashTable_sp map = core::HashTable_O::createEq(); Loop lres(this->asSmartPtr(),RESIDUES); while (lres.advance()) { Residue_sp res = lres.getResidue(); diff --git a/src/chem/minimizer.cc b/src/chem/minimizer.cc index 6bca9045..2faeb605 100644 --- a/src/chem/minimizer.cc +++ b/src/chem/minimizer.cc @@ -190,7 +190,7 @@ void Minimizer_O::changeOptions(core::List_sp optionCons) { IMPLEMENT_ME(); #if 0 - core::HashTableEq_sp options = core::HashTableEq_O::createFromKeywordCons(optionCons,minimizerOptions); + core::HashTable_sp options = core::HashTable_O::createFromKeywordCons(optionCons,minimizerOptions); options->setBoolValueIfAvailable(this->_ShowElapsedTime,":showElapsedTime"); #endif } diff --git a/src/chem/mol2.cc b/src/chem/mol2.cc index cb214c58..48642458 100644 --- a/src/chem/mol2.cc +++ b/src/chem/mol2.cc @@ -267,7 +267,7 @@ void _calculateElementAndHybridization(Atom_sp a) Otherwise return (values aggregate atom-types) */ core::T_mv mol2Read(Mol2File& fIn) { - core::HashTable_sp atom_types = core::HashTableEq_O::create_default(); + core::HashTable_sp atom_types = core::HashTable_O::createEq(); string line; TriposMolecule mol; vector molecules; @@ -682,7 +682,7 @@ core::HashTable_sp assignSybylTypes( Matter_sp matter) { SIMPLE_ERROR("The chem:*sybyl-type-assignment-rules* dynamic variable needs to be bound to a chem:fftypes-db database for sybyl types"); } FFTypesDb_sp sybylRules = gc::As(chem::_sym_STARsybyl_type_assignment_rulesSTAR->symbolValue()); - core::HashTableEq_sp atom_types = core::HashTableEq_O::create_default(); + core::HashTable_sp atom_types = core::HashTable_O::createEq(); Loop lAtoms; lAtoms.loopTopGoal(matter,ATOMS); while ( lAtoms.advanceLoopAndProcess() ) { @@ -693,7 +693,7 @@ core::HashTable_sp assignSybylTypes( Matter_sp matter) { return atom_types; } -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 ) { Loop loop, lRes; uint atomCount, bondCount, residueCount; @@ -704,7 +704,7 @@ core::HashTableEql_sp mol2WriteAggregateStream( Aggregate_sp agg, std::ostream & gctools::Vec0 residueList; ResidueOut oneResOut; AtomInfo one; - core::HashTableEql_sp ht = core::HashTableEql_O::create_default(); + core::HashTable_sp ht = core::HashTable_O::createEql(); // // Count the atoms diff --git a/src/chem/monomer.cc b/src/chem/monomer.cc index d13fa123..6cc14be2 100644 --- a/src/chem/monomer.cc +++ b/src/chem/monomer.cc @@ -683,7 +683,7 @@ void Monomer_O::fields(core::Record_sp node) void Monomer_O::initialize() { this->Base::initialize(); -// this->_Couplings = core::HashTableEq_O::create_default(); +// this->_Couplings = core::HashTable_O::createEq(); this->_Id = nil(); this->_SequenceNumber = 0; this->_Monomers.clear(); diff --git a/src/chem/monomerContext.cc b/src/chem/monomerContext.cc index 3d1b90bd..293c2e1f 100644 --- a/src/chem/monomerContext.cc +++ b/src/chem/monomerContext.cc @@ -232,7 +232,7 @@ CL_DEFMETHOD core::Symbol_sp MonomerContext_O::getKey() CL_LISPIFY_NAME("getAllSpecificKeys"); -CL_DEFMETHOD core::HashTableEqual_sp MonomerContext_O::getAllSpecificKeys() +CL_DEFMETHOD core::HashTable_sp MonomerContext_O::getAllSpecificKeys() { IMPLEMENT_ME(); #if 0 diff --git a/src/chem/octree.cc b/src/chem/octree.cc index 921777f5..b98f545f 100644 --- a/src/chem/octree.cc +++ b/src/chem/octree.cc @@ -926,8 +926,8 @@ CL_DEFMETHOD void AddIonOctree_O::OctreeCreate(Aggregate_sp uUnit, AddIonOctreeE * the atoms' temporary floating-point values w/ their sizes. */ - this->atomsToResidues = core::HashTableEq_O::create_default(); - this->residuesToMolecules = core::HashTableEq_O::create_default(); + this->atomsToResidues = core::HashTable_O::createEq(); + this->residuesToMolecules = core::HashTable_O::createEq(); iDefaultedRadius = 0; Loop lMol; lMol.loopTopAggregateGoal(uUnit,MOLECULES); diff --git a/src/chem/oligomer.cc b/src/chem/oligomer.cc index 05ebcc71..19041036 100644 --- a/src/chem/oligomer.cc +++ b/src/chem/oligomer.cc @@ -86,7 +86,7 @@ void Oligomer_O::fields(core::Record_sp node) Oligomer_O::Oligomer_O(const Oligomer_O& original) { - core::HashTableEq_sp newMonomersFromOld = core::HashTableEq_O::create_default(); + core::HashTable_sp newMonomersFromOld = core::HashTable_O::createEq(); gctools::Vec0 copiedMonomers; this->_Monomers.resize(original._Monomers.size()); for ( size_t i=0, iEnd(this->_Monomers.size()); i::iterator mi; for ( mi=this->_Monomers.begin(); mi!=this->_Monomers.end(); mi++ ) { Topology_sp topology = (*mi)->currentTopology(); @@ -1015,7 +1015,7 @@ CL_DEFUN core::T_sp chem__oligomer_sequence(Oligomer_sp olig) void Oligomer_O::_assembleFromParts(core::List_sp parts, CandoDatabase_sp bdb) { - core::HashTableEq_sp monomerMap = core::HashTableEq_O::create_default(); + core::HashTable_sp monomerMap = core::HashTable_O::createEq(); for ( auto p : parts ) { OligomerPart_Base_sp oligPart = p->car(); Monomer_sp mon = oligPart->createMonomer(bdb); @@ -1042,7 +1042,7 @@ CL_DEFMETHOD core::T_sp Oligomer_O::deepCopyOligomer() const { auto newOligomer = gctools::GC::copy(*this); #if 0 - core::HashTableEq_sp monomerCopies = core::HashTableEq_O::create_default(); + core::HashTable_sp monomerCopies = core::HashTable_O::createEq(); for ( auto mon : this->_Monomers ) { Monomer_sp newMon = mon->copyAndRemoveCouplings(); monomerCopies->setf_gethash(mon,newMon); diff --git a/src/chem/residue.cc b/src/chem/residue.cc index a99b700b..c19a4ea6 100644 --- a/src/chem/residue.cc +++ b/src/chem/residue.cc @@ -426,7 +426,7 @@ contentIterator aCur; void Residue_O::ensureAllAtomNamesAreUnique() const { - core::HashTableEq_sp names = core::HashTableEq_O::create_default(); + core::HashTable_sp names = core::HashTable_O::createEq(); Loop lAtoms(this->asSmartPtr(),ATOMS); while (lAtoms.advanceLoopAndProcess()) { Atom_sp atom = lAtoms.getAtom(); @@ -448,7 +448,7 @@ void CDFragment_O::uniqifyResidueAtomNames(Molecule_sp mol, bool verbose) while (lResidues.advanceLoopAndProcess()) { Residue_sp res = lResidues.getResidue(); Loop lAtoms(res,ATOMS); - core::HashTableEq_sp namesToIndexes = core::HashTableEq_O::create_default(); + core::HashTable_sp namesToIndexes = core::HashTable_O::createEq(); while (lAtoms.advanceLoopAndProcess()) { Atom_sp atom = lAtoms.getAtom(); if (namesToIndexes->gethash(atom->getName()).notnilp()) { @@ -479,7 +479,7 @@ void CDFragment_O::uniqifyResidueAtomNames(Molecule_sp mol, bool verbose) void Residue_O::makeAllAtomNamesInEachResidueUnique() { Loop lAtoms(this->asSmartPtr(),ATOMS); - core::HashTableEq_sp namesToIndexes = core::HashTableEq_O::create_default(); + core::HashTable_sp namesToIndexes = core::HashTable_O::createEq(); size_t index = 0; while (lAtoms.advanceLoopAndProcess()) { Atom_sp atom = lAtoms.getAtom(); @@ -506,7 +506,7 @@ void Residue_O::makeAllAtomNamesInEachResidueUnique() contentIterator ai; adapt::SymbolSet_sp allNames = adapt::SymbolSet_O::create(); adapt::SymbolSet_sp allNamesAccumulate = adapt::SymbolSet_O::create(); - core::HashTableEq_sp atomsThatShareName = core::HashTableEq_O::create_default(); + core::HashTable_sp atomsThatShareName = core::HashTable_O::createEq(); // multimap atomsThatShareName; for ( ai=this->begin_atoms(); ai != this->end_atoms(); ai++ ) { @@ -630,7 +630,7 @@ contentIterator atom; core::HashTable_sp Residue_O::atomToResidueMap() { - core::HashTableEq_sp map = core::HashTableEq_O::create_default(); + core::HashTable_sp map = core::HashTable_O::createEq(); for ( auto aa = this->begin_atoms(); aa!=this->end_atoms(); ++aa ) { map->setf_gethash(*aa,this->asSmartPtr()); } diff --git a/src/chem/ringFinder.cc b/src/chem/ringFinder.cc index cdeccb7d..5fe7ce9b 100644 --- a/src/chem/ringFinder.cc +++ b/src/chem/ringFinder.cc @@ -450,7 +450,7 @@ void AGVertex_O::receive(uint stage, gctools::Vec0& edgeArray0, // vertex collisions // - core::HashTableEq_sp vertexDict = core::HashTableEq_O::create_default(); + core::HashTable_sp vertexDict = core::HashTable_O::createEq(); { LOG("Filling vertexDict" ); for ( uint i=0; i_finalRings.clear(); RingFinderVertexInitializeMapper mapper; this->_vertices->lowLevelMapHash(&mapper); - this->_rings = core::HashTableEql_O::create_default(); + this->_rings = core::HashTable_O::createEql(); this->_gaussian.clear(); } diff --git a/src/chem/scoringFunction.cc b/src/chem/scoringFunction.cc index 91c47579..9c3da23d 100644 --- a/src/chem/scoringFunction.cc +++ b/src/chem/scoringFunction.cc @@ -101,7 +101,7 @@ namespace chem SYMBOL_EXPORT_SC_(ChemPkg,set_energy); -ScoringFunction_O::ScoringFunction_O() : _VelocityScale(Vector3(1.0,1.0,1.0)), _AtomTypes(core::HashTableEq_O::create_default()) {}; +ScoringFunction_O::ScoringFunction_O() : _VelocityScale(Vector3(1.0,1.0,1.0)), _AtomTypes(core::HashTable_O::createEq()) {}; CL_DEFMETHOD void ScoringFunction_O::setf_velocity_scale(double xscale, double yscale, double zscale) { this->_VelocityScale.set(xscale,yscale,zscale); diff --git a/src/chem/spanningLoop.cc b/src/chem/spanningLoop.cc index f7333f52..dd3e08a1 100644 --- a/src/chem/spanningLoop.cc +++ b/src/chem/spanningLoop.cc @@ -212,7 +212,7 @@ void SpanningLoop_O::initialize() { this->Base::initialize(); this->initialized = false; this->_OnlyFollowRealBonds = false; - this->_BackSpan = core::HashTableEq_O::create_default(); + this->_BackSpan = core::HashTable_O::createEq(); } bool SpanningLoop_O::lookupSpanningInfo(Atom_sp a, SpanningInfo_sp &info) { diff --git a/src/chem/structureList.cc b/src/chem/structureList.cc index 23fae8b3..713c53f5 100644 --- a/src/chem/structureList.cc +++ b/src/chem/structureList.cc @@ -67,7 +67,7 @@ void Structure_Old_ListEntry_O::initialize() this->_Members = 0; this->_AllCoordinates = geom::SimpleVectorCoordinate_O::create(); this->_SuperposeCoordinates = geom::SimpleVectorCoordinate_O::create(); - this->_Data = core::HashTableEq_O::create_default(); + this->_Data = core::HashTable_O::createEq(); } @@ -125,7 +125,7 @@ void Structure_Old_List_O::initialize() this->_Matter = nil(); this->_SuperposeAtoms.clear(); this->_AllAtoms.clear(); - this->_Data = core::HashTableEq_O::create_default(); + this->_Data = core::HashTable_O::createEq(); this->clearEntries(); } diff --git a/src/chem/topology.cc b/src/chem/topology.cc index af33a6a8..c5d999c4 100644 --- a/src/chem/topology.cc +++ b/src/chem/topology.cc @@ -241,7 +241,7 @@ CL_DEFMETHOD Residue_sp Topology_O::buildResidueForIsoname(Isoname_sp isoname) c } CL_DEFMETHOD Residue_sp Topology_O::buildResidueSingleName() const { - core::HashTable_sp cip = core::HashTableEq_O::create_default(); // dummy hash table + core::HashTable_sp cip = core::HashTable_O::createEq(); // dummy hash table if (this->_StereoisomerAtomProperties.size()==1) { return this->buildResidueForIsomer(0); } diff --git a/src/chem/trajectory.cc b/src/chem/trajectory.cc index b445d279..46f9170d 100644 --- a/src/chem/trajectory.cc +++ b/src/chem/trajectory.cc @@ -87,7 +87,7 @@ void Trajectory_O::initialize() { this->Base::initialize(); this->_Matter = nil(); - this->_Namespace = core::HashTableEq_O::create_default(); + this->_Namespace = core::HashTable_O::createEq(); } void Trajectory_O::_setupAtomList(Matter_sp matter) diff --git a/src/geom/color.cc b/src/geom/color.cc index 2cbb1134..82e9b8ce 100644 --- a/src/geom/color.cc +++ b/src/geom/color.cc @@ -71,7 +71,7 @@ namespace geom void initialize_colors() { - core::HashTableEq_sp colorTable = core::HashTableEq_O::create_default(); + core::HashTable_sp colorTable = core::HashTable_O::createEq(); SYMBOL_EXPORT_SC_(GeomPkg,colorTable); _lisp->defvar(_sym_colorTable,colorTable); #define DEF_COLOR(name,rgb) {\ diff --git a/src/kinematics/old/chainNode.cc b/src/kinematics/old/chainNode.cc index ba4940fb..56c6fb86 100644 --- a/src/kinematics/old/chainNode.cc +++ b/src/kinematics/old/chainNode.cc @@ -97,7 +97,7 @@ void ChainNode_O::fields(core::Record_sp node) { void ChainNode_O::buildUsingOligomer(chem::Oligomer_sp oligomer, int chainId) { chem::Monomer_sp rootMonomer = oligomer->rootMonomer(); - RingClosingMonomerMap ringClosingMonomerMap = core::HashTableEq_O::create_default(); + RingClosingMonomerMap ringClosingMonomerMap = core::HashTable_O::createEq(); MonomerNode_sp rootMonomerNode = this->monomerNodeFactory(this->asSmartPtr(),ringClosingMonomerMap,rootMonomer); rootMonomerNode->recursivelyBuildChildren(this->sharedThis(), ringClosingMonomerMap,nil(), From f1407e36d8926b949ce5c73267faecede4d35890 Mon Sep 17 00:00:00 2001 From: Bike Date: Wed, 22 Jan 2025 11:33:51 -0500 Subject: [PATCH 3/3] Remove old weakHashTable.h header --- src/adapt/adaptPackage.cc | 1 - src/geom/candoBasePackage.cc | 1 - src/kinematics/kinematicsPackage.cc | 1 - src/main/gc_interface.cc | 2 -- 4 files changed, 5 deletions(-) diff --git a/src/adapt/adaptPackage.cc b/src/adapt/adaptPackage.cc index 2ee4b98b..047fd7d9 100644 --- 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 #include #include -#include #include #include #include diff --git a/src/geom/candoBasePackage.cc b/src/geom/candoBasePackage.cc index 0dc08447..16f0e9d6 100644 --- a/src/geom/candoBasePackage.cc +++ b/src/geom/candoBasePackage.cc @@ -63,7 +63,6 @@ This is an open source license for the CANDO software from Temple University, bu #include #include #include -#include #include #include #include diff --git a/src/kinematics/kinematicsPackage.cc b/src/kinematics/kinematicsPackage.cc index ed298d8e..9ae0cda7 100644 --- a/src/kinematics/kinematicsPackage.cc +++ b/src/kinematics/kinematicsPackage.cc @@ -63,7 +63,6 @@ This is an open source license for the CANDO software from Temple University, bu #include #include #include -#include #include #include #include diff --git a/src/main/gc_interface.cc b/src/main/gc_interface.cc index 6b66e35c..1c2aaf1b 100644 --- a/src/main/gc_interface.cc +++ b/src/main/gc_interface.cc @@ -89,7 +89,6 @@ typedef bool _Bool; #include #include #include -#include #include #include #include @@ -120,7 +119,6 @@ typedef bool _Bool; #include #include #include -#include #include