Clean up many warnings

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

Author: Bike

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) {};
   };
 };