Clean up many warnings

Mostly unused variables, but some more serious issues as well. A
few warnings are still outstanding.

include/cando/chem/atom.h

@@ -521,23 +521,22 @@ namespace chem {
   Atom_O() :
     _UniqueAtomOrder(nextUniqueAtomOrder()),
     _Alias(nil<core::Symbol_O>()),
-      _Element(element_Undefined),
-      _Hybridization(hybridization_undefined),
-      _Type(nil<core::Symbol_O>()),
-      _Flags(0),
-      _StereochemistryType(undefinedCenter),
-      _Configuration(undefinedConfiguration),
-      _Ionization(0),
-      _Charge(0.0),
-      _VdwRadius(0.0),
-      _CovalentRadius(0.0),
-      _Mask(0),
-      _CopyAtom(unbound<chem::Atom_O>()),
-      _RingMembershipCount(0),
-      _TempInt(0)
+    _Flags(0),
+    _Type(nil<core::Symbol_O>()),
+    _Charge(0.0),
+    _CopyAtom(unbound<chem::Atom_O>()),_TempInt(0),
+    _VdwRadius(0.0),
+    _CovalentRadius(0.0),
+    _StereochemistryType(undefinedCenter),
+    _Configuration(undefinedConfiguration),
+    _Mask(0),
+    _Element(element_Undefined),
+    _Hybridization(hybridization_undefined),
+    _RingMembershipCount(0),
+    _Ionization(0)
 //      moeIndex(0),
 //      moeType(_Nil<core::Symbol_O>())
-      {};
+    {};
     virtual ~Atom_O() {};
   };
 

include/cando/chem/chemInfo.h

@@ -114,7 +114,7 @@ CL_DEFMETHOD     chem::Atom_sp tag(core::T_sp tag) { return this->getAtomWithTag
 	 */
     BoundFrame_sp boundFrame();
 
-    ChemInfoMatch_O(Root_sp root, size_t maxtagPlus1) : _Root(root), _Matches(false), _MaxTagPlus1(maxtagPlus1), _TagHistory(nil<core::T_O>()) {};
+    ChemInfoMatch_O(Root_sp root, size_t maxtagPlus1) : _Matches(false), _MaxTagPlus1(maxtagPlus1), _Root(root), _TagHistory(nil<core::T_O>()) {};
   };
 
 
@@ -1074,9 +1074,9 @@ class Root_O : public AtomOrBondMatchNode_O
   virtual	ChemInfoType	type() { return root; };
   virtual	bool		matches_Atom( Root_sp root, chem::Atom_sp atom );
   virtual	bool		matches_Bond( Root_sp root, chem::Atom_sp from, chem::Bond_sp bond );
-  Root_O(const std::string& code, ChemInfoNode_sp node, size_t maxtag) : _Code(code), _Node(node), _Tests(nil<core::T_O>()), _MaxTag(maxtag) {}
+  Root_O(const std::string& code, ChemInfoNode_sp node, size_t maxtag) : _Node(node), _Tests(nil<core::T_O>()), _MaxTag(maxtag), _Code(code) {}
   Root_O(const std::string& code) : _Code(code) {};
-  Root_O() : _Code(""), _Node(nil<core::T_O>()), _Tests(nil<core::T_O>()), _MaxTag(0) {};
+  Root_O() : _Node(nil<core::T_O>()), _Tests(nil<core::T_O>()), _MaxTag(0), _Code("") {};
 };
 
 

include/cando/chem/chemdraw.h

@@ -118,13 +118,13 @@ class CDNode_O : public core::CxxObject_O
 
   CDNode_O( const CDNode_O& ss ); //!< Copy constructor
 
- CDNode_O() : _Atom(nil<core::T_O>())
-    , _BackSpan(nil<core::T_O>())
-    , _NextSpan(nil<core::T_O>())
-    , _AtomProperties(nil<core::T_O>())
-    , _ResidueProperties(nil<core::T_O>())
-    , _MoleculeProperties(nil<core::T_O>())
-  {};
+  CDNode_O() : _AtomProperties(nil<core::T_O>())
+             , _ResidueProperties(nil<core::T_O>())
+             , _MoleculeProperties(nil<core::T_O>())
+             , _Atom(nil<core::T_O>())
+             , _BackSpan(nil<core::T_O>())
+             , _NextSpan(nil<core::T_O>())
+       {};
   virtual ~CDNode_O() {};
 };
 

include/cando/chem/constitutionAtoms.h

@@ -104,7 +104,7 @@ It stores the atom name, element, properties and a vector of bonds in the form o
     virtual bool isVirtualAtom() { return false;};
 	/*! Append a ConstitutionBond_sp to our list of bonds */
     void addConstitutionBond(ConstitutionBond_sp cb) {this->_Bonds.push_back(cb);};
-    ConstitutionAtom_O(MatterName atomName, Element element, core::T_sp atomType, size_t index, StereochemistryType stype, core::List_sp properties ) : _AtomName(atomName), _Element(element), _AtomType(atomType), _Index(index), _StereochemistryType(stype), _Properties(properties) {};
+    ConstitutionAtom_O(MatterName atomName, Element element, core::T_sp atomType, size_t index, StereochemistryType stype, core::List_sp properties ) : _AtomName(atomName),  _Index(index), _Element(element), _AtomType(atomType), _StereochemistryType(stype), _Properties(properties) {};
     ConstitutionAtom_O() : _AtomType(nil<core::T_O>()) {};
     virtual Atom_sp buildAtom() const;
   };

include/cando/chem/energyDihedral.h

@@ -116,7 +116,7 @@ class EnergyDihedral : public EnergyTerm
 	double		getCalculatedDihedralDeviation() { return this->_CalculatedDihedralDeviation;};
 
 public:
- EnergyDihedral(Atom_sp a1, Atom_sp a2, Atom_sp a3, Atom_sp a4, double phase, bool proper, size_t i1, size_t i2, size_t i3, size_t i4, double sinp, double cosp, double v, double dn, int in) : term(sinp,cosp,v,dn,in,i1,i2,i3,i4),_Atom1(a1),_Atom2(a2),_Atom3(a3),_Atom4(a4), _PhaseRad(phase), _Proper(proper) {};
+  EnergyDihedral(Atom_sp a1, Atom_sp a2, Atom_sp a3, Atom_sp a4, double phase, bool proper, size_t i1, size_t i2, size_t i3, size_t i4, double sinp, double cosp, double v, double dn, int in) : _Proper(proper), _Atom1(a1),_Atom2(a2),_Atom3(a3),_Atom4(a4), _PhaseRad(phase), term(sinp,cosp,v,dn,in,i1,i2,i3,i4) {};
   EnergyDihedral() {};
 public:
 	adapt::QDomNode_sp	asXml();

include/cando/chem/energyNonbond.h

@@ -284,7 +284,7 @@ class EnergyNonbond_O : public EnergyComponent_O
  public:
   EnergyNonbond_O( const EnergyNonbond_O& ss ); //!< Copy constructor
 
-  EnergyNonbond_O() : _FFNonbondDb(unbound<core::T_O>()), _UsesExcludedAtoms(true) {};
+  EnergyNonbond_O() : _UsesExcludedAtoms(true), _FFNonbondDb(unbound<core::T_O>()) {};
 };
 
 };

include/cando/chem/energySketchNonbond.h

@@ -154,7 +154,7 @@ class EnergySketchNonbond_O : public EnergyComponent_O
   void modifySketchNonbondTermConstant(size_t index, float constant);
 
  public:
-  EnergySketchNonbond_O() : _LongDistanceCutoff(80.0), _ScaleSketchNonbond(1.0), _IgnoreHydrogensAndLps(false), _FreezeFlags() {};
+  EnergySketchNonbond_O() : _ScaleSketchNonbond(1.0), _LongDistanceCutoff(80.0), _IgnoreHydrogensAndLps(false), _FreezeFlags() {};
   void reset();
 };
 

include/cando/chem/ffTypesDb.h

@@ -102,7 +102,6 @@ class FFTypesDb_O : public FFBaseDb_O
       size_t new_size = other_types_db->_TypeAssignmentRules.size() + this->_TypeAssignmentRules.size();
       gctools::Vec0<FFTypeRule_sp> newRules;
       newRules.reserve(new_size);
-      size_t idx;
       for ( auto it : other_types_db->_TypeAssignmentRules ) {
         newRules.push_back(it);
       }

include/cando/chem/minimizer.h

@@ -325,7 +325,7 @@ takes a single argument, the NVECTOR position of the atoms.)dx");
 
     adapt::QDomNode_sp	asXml();
 
-    Minimizer_O() : _PrintIntermediateResults(1), _StepCallback(nil<core::T_O>()), _Frozen(nil<core::T_O>()) {};
+    Minimizer_O() : _PrintIntermediateResults(1), _Frozen(nil<core::T_O>()),  _StepCallback(nil<core::T_O>()) {};
   };
 
   extern core::Symbol_sp& _sym__PLUS_minimizerStatusConverter_PLUS_;

include/cando/chem/monomer.h

@@ -113,7 +113,7 @@ namespace chem {
     CL_DEFMETHOD core::Symbol_sp name() const { return this->_Name; };
     CL_DEFMETHOD Fixnum isomer() const { return this->_Isomer; };
     CL_DEFMETHOD Topology_sp topology() const { return this->_Topology; };
-  Isoname_O(core::Symbol_sp name, Topology_sp topology, Fixnum isomer ) : _Name(name), _Topology(topology), _Isomer(isomer) {};
+    Isoname_O(core::Symbol_sp name, Topology_sp topology, Fixnum isomer ) : _Name(name), _Isomer(isomer), _Topology(topology) {};
   };
 };
 

include/cando/chem/superposableConformationCollection.h

@@ -49,7 +49,6 @@ template <>
 struct to_object<gctools::SmallOrderedSet<chem::Atom_sp>, translate::dont_adopt_pointer> {
   static core::T_sp convert(gctools::SmallOrderedSet<chem::Atom_sp> atoms) {
     ql::list res;
-    int i(0);
     for (auto ai = atoms.begin(); ai != atoms.end(); ai++) {
       res << *ai;
     }

src/adapt/mySaxInterface.cc

@@ -45,10 +45,8 @@ namespace adapt {
 //
 
     string	MySaxHandlerDefault::getAttribute(char* str) {
-	int		iCount;
 	const XML_Char	**pos;
 	string	res;
-	iCount = 0;
 	pos = this->attributes;
 	while (*pos) {
 	    if ( strcmp(*pos,str)==0 ) {

src/adapt/objectSet.cc

@@ -106,7 +106,7 @@ ObjectSet_sp ObjectSet_O::cartesianProduct(ObjectSet_sp b) {
   ObjectSet_sp nset;
   stringstream sstr;
   nset = ObjectSet_O::create();
-  this->map([&b, &nset, this](T_sp si) {
+  this->map([&nset, this](T_sp si) {
             this->map( [&si,&nset] (T_sp bi) {
                     Cons_sp op = _lisp->create<Cons_O>(si,bi);
                     nset->insert(op);
@@ -124,7 +124,7 @@ ObjectSet_sp ObjectSet_O::cartesianProductWrapped(ObjectSet_sp b, const ObjectSe
   stringstream sstr;
   nset = ObjectSet_O::create();
 
-  this->map([&b, &nset, this, &wrapper](T_sp si) {
+  this->map([&nset, this, &wrapper](T_sp si) {
             this->map( [&si,&nset,&wrapper] (T_sp bi) {
                     T_sp op = wrapper(si,bi);
                     nset->insert(op);

src/adapt/quickDom.cc

@@ -202,10 +202,7 @@ void	QDomNode_O::throwErrorForChildrenWithoutName(string nm)
 //      Return true if the data is all white space
 bool    QDomNode_O::dataIsAllWhiteSpace()
 {
-  bool                        sawChar;
   string                      val;
-  string::iterator    it;
-  sawChar = false;
   for (size_t idx = 0; idx<this->characters->_Contents->length(); idx++ ) {
     claspCharacter c = cl__char(this->characters->_Contents,idx).unsafe_character();
     if (!isspace(c))
@@ -222,7 +219,6 @@ bool    QDomNode_O::dataIsAllWhiteSpace()
 int	QDomNode_O::dataCountNewLines()
 {
   string			val;
-  string::iterator	it;
   int			newLines;
   newLines = 0;
   for (size_t idx = 0; idx<this->characters->_Contents->length(); idx++ ) {

src/chem/aggregate.cc

@@ -566,13 +566,11 @@ CL_DEFMETHOD core::List_sp	Aggregate_O::atomsWithChimeraSpecifications(const str
       mol = gc::As<Molecule_sp>(*mi);
 //      printf("%s:%d mol->getName()= %s  matches chainSym[%s] = %d\n", __FILE__, __LINE__, _rep_(mol->getName()).c_str(),_rep_(chainSym).c_str(), mol->getName()==chainSym);
       if ( mol->getName() == chainSym ) {
-        bool foundResidue = false;
         for ( ri = mol->begin_residues(); ri!=mol->end_residues(); ri++ ) {
           res = (*ri).as<Residue_O>();
 //          printf("%s:%d res->getFileSequenceNumber()= %d  matches fileSequenceNumber[%d] = %d\n", __FILE__, __LINE__, res->getFileSequenceNumber(), fileSequenceNumber,  res->getFileSequenceNumber()==fileSequenceNumber);
 //          printf("%s:%d     res->getId() = %d\n", __FILE__, __LINE__, res->getId());
           if ( res->getFileSequenceNumber() == fileSequenceNumber ) {
-            foundResidue = true;
 //            printf("%s:%d res->hasAtomWithName(%s) = %d\n",  __FILE__, __LINE__, _rep_(atomSym).c_str(), res->hasAtomWithName(atomSym));
             if ( res->hasAtomWithName(atomSym) ) {
               core::T_mv atom_mv = res->atomWithName(atomSym);

src/chem/atom.cc

@@ -1208,7 +1208,6 @@ Matter_sp Atom_O::copy(core::T_sp new_to_old)
 Matter_sp Atom_O::copyDontRedirectAtoms(core::T_sp new_to_old)
 {
   LOG("Copying atom @%p" , this );
-  Atom_sp myself = this->sharedThis<Atom_O>();
   auto  aNew  = gctools::GC<Atom_O>::copy( *this); // = RP_Copy<Atom_O>(this);
   aNew->_Bonds.clear();
   this->_CopyAtom = aNew;

src/chem/atomIdMap.cc

@@ -138,7 +138,6 @@ CL_DEFMETHOD void AtomIdMap_O::resizeResidue(int mol, int res, int numAtoms)
     core::ComplexVector_T_sp residues = gc::As<core::ComplexVector_T_sp>(this->_AtomIdMap->rowMajorAref(mol));
     if (res<residues->length()) {
       core::ComplexVector_T_sp atoms = gc::As<core::ComplexVector_T_sp>(residues->rowMajorAref(res));
-      size_t oldNumAtoms = atoms->length();
       atoms->resize(numAtoms);
       return;
     }

src/chem/bond.cc

@@ -155,7 +155,6 @@ void Bond_O::addYourselfToCopiedAtoms()
 //
 bool	Bond_O::isInterResidueBond(core::HashTable_sp atomToResidue)
 {
-  Atom_sp a1 = this->_Atom1;
   core::T_sp res1 = atomToResidue->gethash(this->_Atom1);
   core::T_sp res2 = atomToResidue->gethash(this->_Atom2);
   return (res1!=res2);

src/chem/chemInfo.cc

@@ -2269,8 +2269,6 @@ bool Root_O::matches_Atom(Root_sp root, chem::Atom_sp atom) {
 
   LOG("%s\natom: %s", this->asSmarts(), _rep_(atom));
   chem::BondList_sp nextBonds;
-  bool matches;
-  matches = false;
   if (this->_Node.notnilp()) {
     CI_LOG(("%s:%d:%s Entering\n", __FILE__, __LINE__, __FUNCTION__));
     LOG("_Node is notNil - testing");
@@ -2306,8 +2304,6 @@ bool SmartsRoot_O::matches_Atom(Root_sp root, chem::Atom_sp atom) {
 
   LOG("%s\natom: %s", this->asSmarts(), _rep_(atom));
   chem::BondList_sp nextBonds;
-  bool matches;
-  matches = false;
   if (!this->Root_O::matches_Atom(root, atom))
     goto FAIL;
   // SUCCESS:
@@ -2353,8 +2349,6 @@ bool AntechamberRoot_O::matches_Atom(Root_sp root, chem::Atom_sp atom) {
 
   LOG("%s\natom: %s", this->asSmarts(), _rep_(atom));
   chem::BondList_sp nextBonds;
-  bool matches;
-  matches = false;
   if (!this->Base::matches_Atom(root, atom)) {
     goto FAIL;
   }
@@ -2831,7 +2825,6 @@ void ChemInfoGraph_O::buildFromRoot_() {
         core::write_bf_stream(fmt::sprintf("Converting AtomTest to chem-info-graph nodes head: %s\n", _rep_(atomTest)));
       }
       graph->_nodes_to_index->setf_gethash(atomTest, core::make_fixnum(graph->_atomNodes.size()));
-      size_t node_index = graph->_atomNodes.size();
       graph->_atomNodes.push_back(atomTest);
       return true;
     } else if (parentOrNil.nilp() && gc::IsA<Logical_sp>(node)) {
@@ -2840,7 +2833,6 @@ void ChemInfoGraph_O::buildFromRoot_() {
         core::write_bf_stream(fmt::sprintf("Converting logical to chem-info-graph nodes head: %s\n", _rep_(logical)));
       }
       graph->_nodes_to_index->setf_gethash(logical, core::make_fixnum(graph->_atomNodes.size()));
-      size_t node_index = graph->_atomNodes.size();
       graph->_atomNodes.push_back(logical);
       return true;
     } else {
@@ -2854,7 +2846,7 @@ void ChemInfoGraph_O::buildFromRoot_() {
   // This is tricky code
   core::HashTableEq_sp parent_nodes = core::HashTableEq_O::create_default();
   walk_nodes_with_parent(
-      nil<core::T_O>(), pattern->_Node, [&graph, &parent_nodes, &closers](core::T_sp parentOrNil, ChemInfoNode_sp node) {
+      nil<core::T_O>(), pattern->_Node, [&graph, &parent_nodes](core::T_sp parentOrNil, ChemInfoNode_sp node) {
         if (chem__verbose(2)) {
           core::write_bf_stream(fmt::sprintf("Walking pattern parent: %s node: %s\n", _rep_(parentOrNil), _rep_(node)));
         }
@@ -3241,8 +3233,8 @@ struct print_callback {
           this->_results->vectorPushExtend(core::make_fixnum(get(correspondence_map_1_to_2, vertex1)));
         }
       }
-      core::T_sp bres = core::eval::funcall(this->m_callback, this->_results, core::make_fixnum((*this->_count_callbacks)),
-                                            this->m_graph1, this->m_graph2);
+      core::eval::funcall(this->m_callback, this->_results, core::make_fixnum((*this->_count_callbacks)),
+                          this->m_graph1, this->m_graph2);
     }
     if (this->_count_callbacks != NULL) {
       (*this->_count_callbacks)++;

src/chem/chemdraw.cc

@@ -520,10 +520,8 @@ core::Symbol_mv parse_property(core::T_sp stream, const string& propertyValue, C
 bool CDFragment_O::interpret(bool verbose, bool addHydrogens)
 {
 //  printf("%s:%d  Interpreting a fragment\n", __FILE__, __LINE__ );
-  int nextFragmentNameIndex = 1;
   if ( this->_Bonds.size() == 0 ) {return false;}
   CDBonds::iterator bi;
-  bool foundHashedBond = false;
   core::MultipleValues &values = core::lisp_multipleValues();
 //  adapt::SymbolSet_sp allNames = adapt::SymbolSet_O::create();
   {

src/chem/complexRestraints.cc

@@ -289,12 +289,12 @@ void	RestrainedExoCyclicAtom_O::archiveBase(core::ArchiveP node)
 	SIMPLE_ERROR(("In residue(%s) the atom with name(%s) is not exo-cyclic to a six-membered ring") , residue->description() , _rep_(this->_ExoCyclicAtomName) );
     }
     ChemInfoMatch_sp match = gc::As<ChemInfoMatch_sp>(values.second(match_mv.number_of_values()));
-    Atom_sp a1 = match->tag(core::make_fixnum(1));
-    Atom_sp a2 = match->tag(core::make_fixnum(2));
-    Atom_sp a3 = match->tag(core::make_fixnum(3));
-    Atom_sp a4 = match->tag(core::make_fixnum(4));
-    Atom_sp a5 = match->tag(core::make_fixnum(5));
-    Atom_sp a6 = match->tag(core::make_fixnum(6));
+    match->tag(core::make_fixnum(1));
+    match->tag(core::make_fixnum(2));
+    match->tag(core::make_fixnum(3));
+    match->tag(core::make_fixnum(4));
+    match->tag(core::make_fixnum(5));
+    match->tag(core::make_fixnum(6));
     FIX_ME(); // is the above correct?
 }
 

src/chem/conformationCollection.cc

@@ -107,7 +107,6 @@ gctools::SmallOrderedSet<Atom_sp>::iterator		ai;
 CL_DEFMETHOD void	ConformationCollectionEntry_O::extractCoordinatesFromMatter(Matter_sp matter)
 {
 ConformationCollection_sp	sl;
-vector<Vector3>::iterator	ci;
 #ifdef	DEBUG_ConformationCollectionEntry
     this->_Status->addMessage("extractCoordinatesFromMatter");
 #endif
@@ -293,7 +292,6 @@ Matter_sp			matter;
 ConformationCollection_O::entryIterator	si;
 ConformationCollectionEntry_sp	entry;
 geom::SimpleVectorCoordinate_sp		superposeCoords;
-geom::SimpleVectorCoordinate_O::iterator	ci;
 frames = geom::FrameList_O::create();
     matter = this->getMatter();
     for ( si=this->begin_Entries(); si!=this->end_Entries(); si++ )

src/chem/conformationExplorer.cc

@@ -280,7 +280,6 @@ CL_LISPIFY_NAME("extractCoordinatesFromMatter");
 CL_DEFMETHOD     void	ConformationExplorerEntryStage_O::extractCoordinatesFromMatter(Matter_sp matter)
     {
 	ConformationExplorer_sp	sl;
-        geom::SimpleVectorCoordinate_O::iterator	ci;
 	LOG("About to get ConformationExplorer" );
 	sl = this->getConformationExplorer();
 	LOG("Got ConformationExplorer" );
@@ -853,8 +852,6 @@ CL_DEFMETHOD     ConformationExplorerEntry_sp	ConformationExplorer_O::createEntr
 bool	ConformationExplorer_O::hasStageNameInAllEntries(core::T_sp stageKey)
     {
 	entryIterator		ei;
-	bool			inAll;
-	inAll = false;
 	for ( ei=this->begin_Entries(); ei!=this->end_Entries(); ei++ )
 	{
 	    if ( !(*ei)->hasEntryStageWithName(stageKey) )

src/chem/constitution.cc

@@ -122,7 +122,6 @@ void	Constitution_O::makeResidueConsistentWithStereoisomerNamed(Residue_sp res,
   string					atomName;
   Atom_sp					aa;
   core::T_sp bdb = getCandoDatabase();
-  Constitution_sp residueConstitution = this->asSmartPtr();
   core::Symbol_sp fullName = gc::As<core::Symbol_sp>(core::eval::funcall(_sym_monomerNameForNameOrPdb,bdb,stereoisomerName));
   core::Symbol_sp pdbName = gc::As<core::Symbol_sp>(core::eval::funcall(_sym_pdbNameForNameOrPdb,bdb,stereoisomerName));
   res->setName(fullName);

src/chem/constitutionAtoms.cc

@@ -162,7 +162,6 @@ CL_DEFUN ConstitutionAtoms_sp ConstitutionAtoms_O::makeConstitutionAtomsFromResi
 
 void ConstitutionAtoms_O::addConstitutionVirtualAtom(ConstitutionVirtualAtom_sp ca)
 {
-  ConstitutionAtomIndex0N nextIndex = this->_Atoms.size();
   this->_Atoms.push_back(ca);
 };