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Clean up many warnings
Mostly unused variables, but some more serious issues as well. A few warnings are still outstanding.
1 parent 3bcd5a8 commit 2e88c1b

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67 files changed

+200
-332
lines changed

‎include/cando/chem/atom.h

Lines changed: 14 additions & 15 deletions
Original file line numberDiff line numberDiff line change
@@ -521,23 +521,22 @@ namespace chem {
521521
Atom_O() :
522522
_UniqueAtomOrder(nextUniqueAtomOrder()),
523523
_Alias(nil<core::Symbol_O>()),
524-
_Element(element_Undefined),
525-
_Hybridization(hybridization_undefined),
526-
_Type(nil<core::Symbol_O>()),
527-
_Flags(0),
528-
_StereochemistryType(undefinedCenter),
529-
_Configuration(undefinedConfiguration),
530-
_Ionization(0),
531-
_Charge(0.0),
532-
_VdwRadius(0.0),
533-
_CovalentRadius(0.0),
534-
_Mask(0),
535-
_CopyAtom(unbound<chem::Atom_O>()),
536-
_RingMembershipCount(0),
537-
_TempInt(0)
524+
_Flags(0),
525+
_Type(nil<core::Symbol_O>()),
526+
_Charge(0.0),
527+
_CopyAtom(unbound<chem::Atom_O>()),_TempInt(0),
528+
_VdwRadius(0.0),
529+
_CovalentRadius(0.0),
530+
_StereochemistryType(undefinedCenter),
531+
_Configuration(undefinedConfiguration),
532+
_Mask(0),
533+
_Element(element_Undefined),
534+
_Hybridization(hybridization_undefined),
535+
_RingMembershipCount(0),
536+
_Ionization(0)
538537
// moeIndex(0),
539538
// moeType(_Nil<core::Symbol_O>())
540-
{};
539+
{};
541540
virtual ~Atom_O() {};
542541
};
543542

‎include/cando/chem/chemInfo.h

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -114,7 +114,7 @@ CL_DEFMETHOD chem::Atom_sp tag(core::T_sp tag) { return this->getAtomWithTag
114114
*/
115115
BoundFrame_sp boundFrame();
116116

117-
ChemInfoMatch_O(Root_sp root, size_t maxtagPlus1) : _Root(root), _Matches(false), _MaxTagPlus1(maxtagPlus1), _TagHistory(nil<core::T_O>()) {};
117+
ChemInfoMatch_O(Root_sp root, size_t maxtagPlus1) : _Matches(false), _MaxTagPlus1(maxtagPlus1), _Root(root), _TagHistory(nil<core::T_O>()) {};
118118
};
119119

120120

@@ -1074,9 +1074,9 @@ class Root_O : public AtomOrBondMatchNode_O
10741074
virtual ChemInfoType type() { return root; };
10751075
virtual bool matches_Atom( Root_sp root, chem::Atom_sp atom );
10761076
virtual bool matches_Bond( Root_sp root, chem::Atom_sp from, chem::Bond_sp bond );
1077-
Root_O(const std::string& code, ChemInfoNode_sp node, size_t maxtag) : _Code(code), _Node(node), _Tests(nil<core::T_O>()), _MaxTag(maxtag) {}
1077+
Root_O(const std::string& code, ChemInfoNode_sp node, size_t maxtag) : _Node(node), _Tests(nil<core::T_O>()), _MaxTag(maxtag), _Code(code) {}
10781078
Root_O(const std::string& code) : _Code(code) {};
1079-
Root_O() : _Code(""), _Node(nil<core::T_O>()), _Tests(nil<core::T_O>()), _MaxTag(0) {};
1079+
Root_O() : _Node(nil<core::T_O>()), _Tests(nil<core::T_O>()), _MaxTag(0), _Code("") {};
10801080
};
10811081

10821082

‎include/cando/chem/chemdraw.h

Lines changed: 7 additions & 7 deletions
Original file line numberDiff line numberDiff line change
@@ -118,13 +118,13 @@ class CDNode_O : public core::CxxObject_O
118118

119119
CDNode_O( const CDNode_O& ss ); //!< Copy constructor
120120

121-
CDNode_O() : _Atom(nil<core::T_O>())
122-
, _BackSpan(nil<core::T_O>())
123-
, _NextSpan(nil<core::T_O>())
124-
, _AtomProperties(nil<core::T_O>())
125-
, _ResidueProperties(nil<core::T_O>())
126-
, _MoleculeProperties(nil<core::T_O>())
127-
{};
121+
CDNode_O() : _AtomProperties(nil<core::T_O>())
122+
, _ResidueProperties(nil<core::T_O>())
123+
, _MoleculeProperties(nil<core::T_O>())
124+
, _Atom(nil<core::T_O>())
125+
, _BackSpan(nil<core::T_O>())
126+
, _NextSpan(nil<core::T_O>())
127+
{};
128128
virtual ~CDNode_O() {};
129129
};
130130

‎include/cando/chem/constitutionAtoms.h

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -104,7 +104,7 @@ It stores the atom name, element, properties and a vector of bonds in the form o
104104
virtual bool isVirtualAtom() { return false;};
105105
/*! Append a ConstitutionBond_sp to our list of bonds */
106106
void addConstitutionBond(ConstitutionBond_sp cb) {this->_Bonds.push_back(cb);};
107-
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) {};
107+
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) {};
108108
ConstitutionAtom_O() : _AtomType(nil<core::T_O>()) {};
109109
virtual Atom_sp buildAtom() const;
110110
};

‎include/cando/chem/energyDihedral.h

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -116,7 +116,7 @@ class EnergyDihedral : public EnergyTerm
116116
double getCalculatedDihedralDeviation() { return this->_CalculatedDihedralDeviation;};
117117

118118
public:
119-
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) {};
119+
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) {};
120120
EnergyDihedral() {};
121121
public:
122122
adapt::QDomNode_sp asXml();

‎include/cando/chem/energyNonbond.h

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -284,7 +284,7 @@ class EnergyNonbond_O : public EnergyComponent_O
284284
public:
285285
EnergyNonbond_O( const EnergyNonbond_O& ss ); //!< Copy constructor
286286

287-
EnergyNonbond_O() : _FFNonbondDb(unbound<core::T_O>()), _UsesExcludedAtoms(true) {};
287+
EnergyNonbond_O() : _UsesExcludedAtoms(true), _FFNonbondDb(unbound<core::T_O>()) {};
288288
};
289289

290290
};

‎include/cando/chem/energySketchNonbond.h

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -154,7 +154,7 @@ class EnergySketchNonbond_O : public EnergyComponent_O
154154
void modifySketchNonbondTermConstant(size_t index, float constant);
155155

156156
public:
157-
EnergySketchNonbond_O() : _LongDistanceCutoff(80.0), _ScaleSketchNonbond(1.0), _IgnoreHydrogensAndLps(false), _FreezeFlags() {};
157+
EnergySketchNonbond_O() : _ScaleSketchNonbond(1.0), _LongDistanceCutoff(80.0), _IgnoreHydrogensAndLps(false), _FreezeFlags() {};
158158
void reset();
159159
};
160160

‎include/cando/chem/ffTypesDb.h

Lines changed: 0 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -102,7 +102,6 @@ class FFTypesDb_O : public FFBaseDb_O
102102
size_t new_size = other_types_db->_TypeAssignmentRules.size() + this->_TypeAssignmentRules.size();
103103
gctools::Vec0<FFTypeRule_sp> newRules;
104104
newRules.reserve(new_size);
105-
size_t idx;
106105
for ( auto it : other_types_db->_TypeAssignmentRules ) {
107106
newRules.push_back(it);
108107
}

‎include/cando/chem/minimizer.h

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -325,7 +325,7 @@ takes a single argument, the NVECTOR position of the atoms.)dx");
325325

326326
adapt::QDomNode_sp asXml();
327327

328-
Minimizer_O() : _PrintIntermediateResults(1), _StepCallback(nil<core::T_O>()), _Frozen(nil<core::T_O>()) {};
328+
Minimizer_O() : _PrintIntermediateResults(1), _Frozen(nil<core::T_O>()), _StepCallback(nil<core::T_O>()) {};
329329
};
330330

331331
extern core::Symbol_sp& _sym__PLUS_minimizerStatusConverter_PLUS_;

‎include/cando/chem/monomer.h

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -113,7 +113,7 @@ namespace chem {
113113
CL_DEFMETHOD core::Symbol_sp name() const { return this->_Name; };
114114
CL_DEFMETHOD Fixnum isomer() const { return this->_Isomer; };
115115
CL_DEFMETHOD Topology_sp topology() const { return this->_Topology; };
116-
Isoname_O(core::Symbol_sp name, Topology_sp topology, Fixnum isomer ) : _Name(name), _Topology(topology), _Isomer(isomer) {};
116+
Isoname_O(core::Symbol_sp name, Topology_sp topology, Fixnum isomer ) : _Name(name), _Isomer(isomer), _Topology(topology) {};
117117
};
118118
};
119119

‎include/cando/chem/superposableConformationCollection.h

Lines changed: 0 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -49,7 +49,6 @@ template <>
4949
struct to_object<gctools::SmallOrderedSet<chem::Atom_sp>, translate::dont_adopt_pointer> {
5050
static core::T_sp convert(gctools::SmallOrderedSet<chem::Atom_sp> atoms) {
5151
ql::list res;
52-
int i(0);
5352
for (auto ai = atoms.begin(); ai != atoms.end(); ai++) {
5453
res << *ai;
5554
}

‎src/adapt/mySaxInterface.cc

Lines changed: 0 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -45,10 +45,8 @@ namespace adapt {
4545
//
4646

4747
string MySaxHandlerDefault::getAttribute(char* str) {
48-
int iCount;
4948
const XML_Char **pos;
5049
string res;
51-
iCount = 0;
5250
pos = this->attributes;
5351
while (*pos) {
5452
if ( strcmp(*pos,str)==0 ) {

‎src/adapt/objectSet.cc

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -106,7 +106,7 @@ ObjectSet_sp ObjectSet_O::cartesianProduct(ObjectSet_sp b) {
106106
ObjectSet_sp nset;
107107
stringstream sstr;
108108
nset = ObjectSet_O::create();
109-
this->map([&b, &nset, this](T_sp si) {
109+
this->map([&nset, this](T_sp si) {
110110
this->map( [&si,&nset] (T_sp bi) {
111111
Cons_sp op = _lisp->create<Cons_O>(si,bi);
112112
nset->insert(op);
@@ -124,7 +124,7 @@ ObjectSet_sp ObjectSet_O::cartesianProductWrapped(ObjectSet_sp b, const ObjectSe
124124
stringstream sstr;
125125
nset = ObjectSet_O::create();
126126

127-
this->map([&b, &nset, this, &wrapper](T_sp si) {
127+
this->map([&nset, this, &wrapper](T_sp si) {
128128
this->map( [&si,&nset,&wrapper] (T_sp bi) {
129129
T_sp op = wrapper(si,bi);
130130
nset->insert(op);

‎src/adapt/quickDom.cc

Lines changed: 0 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -202,10 +202,7 @@ void QDomNode_O::throwErrorForChildrenWithoutName(string nm)
202202
// Return true if the data is all white space
203203
bool QDomNode_O::dataIsAllWhiteSpace()
204204
{
205-
bool sawChar;
206205
string val;
207-
string::iterator it;
208-
sawChar = false;
209206
for (size_t idx = 0; idx<this->characters->_Contents->length(); idx++ ) {
210207
claspCharacter c = cl__char(this->characters->_Contents,idx).unsafe_character();
211208
if (!isspace(c))
@@ -222,7 +219,6 @@ bool QDomNode_O::dataIsAllWhiteSpace()
222219
int QDomNode_O::dataCountNewLines()
223220
{
224221
string val;
225-
string::iterator it;
226222
int newLines;
227223
newLines = 0;
228224
for (size_t idx = 0; idx<this->characters->_Contents->length(); idx++ ) {

‎src/chem/aggregate.cc

Lines changed: 0 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -566,13 +566,11 @@ CL_DEFMETHOD core::List_sp Aggregate_O::atomsWithChimeraSpecifications(const str
566566
mol = gc::As<Molecule_sp>(*mi);
567567
// 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);
568568
if ( mol->getName() == chainSym ) {
569-
bool foundResidue = false;
570569
for ( ri = mol->begin_residues(); ri!=mol->end_residues(); ri++ ) {
571570
res = (*ri).as<Residue_O>();
572571
// printf("%s:%d res->getFileSequenceNumber()= %d matches fileSequenceNumber[%d] = %d\n", __FILE__, __LINE__, res->getFileSequenceNumber(), fileSequenceNumber, res->getFileSequenceNumber()==fileSequenceNumber);
573572
// printf("%s:%d res->getId() = %d\n", __FILE__, __LINE__, res->getId());
574573
if ( res->getFileSequenceNumber() == fileSequenceNumber ) {
575-
foundResidue = true;
576574
// printf("%s:%d res->hasAtomWithName(%s) = %d\n", __FILE__, __LINE__, _rep_(atomSym).c_str(), res->hasAtomWithName(atomSym));
577575
if ( res->hasAtomWithName(atomSym) ) {
578576
core::T_mv atom_mv = res->atomWithName(atomSym);

‎src/chem/atom.cc

Lines changed: 0 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1208,7 +1208,6 @@ Matter_sp Atom_O::copy(core::T_sp new_to_old)
12081208
Matter_sp Atom_O::copyDontRedirectAtoms(core::T_sp new_to_old)
12091209
{
12101210
LOG("Copying atom @%p" , this );
1211-
Atom_sp myself = this->sharedThis<Atom_O>();
12121211
auto aNew = gctools::GC<Atom_O>::copy( *this); // = RP_Copy<Atom_O>(this);
12131212
aNew->_Bonds.clear();
12141213
this->_CopyAtom = aNew;

‎src/chem/atomIdMap.cc

Lines changed: 0 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -138,7 +138,6 @@ CL_DEFMETHOD void AtomIdMap_O::resizeResidue(int mol, int res, int numAtoms)
138138
core::ComplexVector_T_sp residues = gc::As<core::ComplexVector_T_sp>(this->_AtomIdMap->rowMajorAref(mol));
139139
if (res<residues->length()) {
140140
core::ComplexVector_T_sp atoms = gc::As<core::ComplexVector_T_sp>(residues->rowMajorAref(res));
141-
size_t oldNumAtoms = atoms->length();
142141
atoms->resize(numAtoms);
143142
return;
144143
}

‎src/chem/bond.cc

Lines changed: 0 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -155,7 +155,6 @@ void Bond_O::addYourselfToCopiedAtoms()
155155
//
156156
bool Bond_O::isInterResidueBond(core::HashTable_sp atomToResidue)
157157
{
158-
Atom_sp a1 = this->_Atom1;
159158
core::T_sp res1 = atomToResidue->gethash(this->_Atom1);
160159
core::T_sp res2 = atomToResidue->gethash(this->_Atom2);
161160
return (res1!=res2);

‎src/chem/chemInfo.cc

Lines changed: 3 additions & 11 deletions
Original file line numberDiff line numberDiff line change
@@ -2269,8 +2269,6 @@ bool Root_O::matches_Atom(Root_sp root, chem::Atom_sp atom) {
22692269

22702270
LOG("%s\natom: %s", this->asSmarts(), _rep_(atom));
22712271
chem::BondList_sp nextBonds;
2272-
bool matches;
2273-
matches = false;
22742272
if (this->_Node.notnilp()) {
22752273
CI_LOG(("%s:%d:%s Entering\n", __FILE__, __LINE__, __FUNCTION__));
22762274
LOG("_Node is notNil - testing");
@@ -2306,8 +2304,6 @@ bool SmartsRoot_O::matches_Atom(Root_sp root, chem::Atom_sp atom) {
23062304

23072305
LOG("%s\natom: %s", this->asSmarts(), _rep_(atom));
23082306
chem::BondList_sp nextBonds;
2309-
bool matches;
2310-
matches = false;
23112307
if (!this->Root_O::matches_Atom(root, atom))
23122308
goto FAIL;
23132309
// SUCCESS:
@@ -2353,8 +2349,6 @@ bool AntechamberRoot_O::matches_Atom(Root_sp root, chem::Atom_sp atom) {
23532349

23542350
LOG("%s\natom: %s", this->asSmarts(), _rep_(atom));
23552351
chem::BondList_sp nextBonds;
2356-
bool matches;
2357-
matches = false;
23582352
if (!this->Base::matches_Atom(root, atom)) {
23592353
goto FAIL;
23602354
}
@@ -2831,7 +2825,6 @@ void ChemInfoGraph_O::buildFromRoot_() {
28312825
core::write_bf_stream(fmt::sprintf("Converting AtomTest to chem-info-graph nodes head: %s\n", _rep_(atomTest)));
28322826
}
28332827
graph->_nodes_to_index->setf_gethash(atomTest, core::make_fixnum(graph->_atomNodes.size()));
2834-
size_t node_index = graph->_atomNodes.size();
28352828
graph->_atomNodes.push_back(atomTest);
28362829
return true;
28372830
} else if (parentOrNil.nilp() && gc::IsA<Logical_sp>(node)) {
@@ -2840,7 +2833,6 @@ void ChemInfoGraph_O::buildFromRoot_() {
28402833
core::write_bf_stream(fmt::sprintf("Converting logical to chem-info-graph nodes head: %s\n", _rep_(logical)));
28412834
}
28422835
graph->_nodes_to_index->setf_gethash(logical, core::make_fixnum(graph->_atomNodes.size()));
2843-
size_t node_index = graph->_atomNodes.size();
28442836
graph->_atomNodes.push_back(logical);
28452837
return true;
28462838
} else {
@@ -2854,7 +2846,7 @@ void ChemInfoGraph_O::buildFromRoot_() {
28542846
// This is tricky code
28552847
core::HashTableEq_sp parent_nodes = core::HashTableEq_O::create_default();
28562848
walk_nodes_with_parent(
2857-
nil<core::T_O>(), pattern->_Node, [&graph, &parent_nodes, &closers](core::T_sp parentOrNil, ChemInfoNode_sp node) {
2849+
nil<core::T_O>(), pattern->_Node, [&graph, &parent_nodes](core::T_sp parentOrNil, ChemInfoNode_sp node) {
28582850
if (chem__verbose(2)) {
28592851
core::write_bf_stream(fmt::sprintf("Walking pattern parent: %s node: %s\n", _rep_(parentOrNil), _rep_(node)));
28602852
}
@@ -3241,8 +3233,8 @@ struct print_callback {
32413233
this->_results->vectorPushExtend(core::make_fixnum(get(correspondence_map_1_to_2, vertex1)));
32423234
}
32433235
}
3244-
core::T_sp bres = core::eval::funcall(this->m_callback, this->_results, core::make_fixnum((*this->_count_callbacks)),
3245-
this->m_graph1, this->m_graph2);
3236+
core::eval::funcall(this->m_callback, this->_results, core::make_fixnum((*this->_count_callbacks)),
3237+
this->m_graph1, this->m_graph2);
32463238
}
32473239
if (this->_count_callbacks != NULL) {
32483240
(*this->_count_callbacks)++;

‎src/chem/chemdraw.cc

Lines changed: 0 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -520,10 +520,8 @@ core::Symbol_mv parse_property(core::T_sp stream, const string& propertyValue, C
520520
bool CDFragment_O::interpret(bool verbose, bool addHydrogens)
521521
{
522522
// printf("%s:%d Interpreting a fragment\n", __FILE__, __LINE__ );
523-
int nextFragmentNameIndex = 1;
524523
if ( this->_Bonds.size() == 0 ) {return false;}
525524
CDBonds::iterator bi;
526-
bool foundHashedBond = false;
527525
core::MultipleValues &values = core::lisp_multipleValues();
528526
// adapt::SymbolSet_sp allNames = adapt::SymbolSet_O::create();
529527
{

‎src/chem/complexRestraints.cc

Lines changed: 6 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -289,12 +289,12 @@ void RestrainedExoCyclicAtom_O::archiveBase(core::ArchiveP node)
289289
SIMPLE_ERROR(("In residue(%s) the atom with name(%s) is not exo-cyclic to a six-membered ring") , residue->description() , _rep_(this->_ExoCyclicAtomName) );
290290
}
291291
ChemInfoMatch_sp match = gc::As<ChemInfoMatch_sp>(values.second(match_mv.number_of_values()));
292-
Atom_sp a1 = match->tag(core::make_fixnum(1));
293-
Atom_sp a2 = match->tag(core::make_fixnum(2));
294-
Atom_sp a3 = match->tag(core::make_fixnum(3));
295-
Atom_sp a4 = match->tag(core::make_fixnum(4));
296-
Atom_sp a5 = match->tag(core::make_fixnum(5));
297-
Atom_sp a6 = match->tag(core::make_fixnum(6));
292+
match->tag(core::make_fixnum(1));
293+
match->tag(core::make_fixnum(2));
294+
match->tag(core::make_fixnum(3));
295+
match->tag(core::make_fixnum(4));
296+
match->tag(core::make_fixnum(5));
297+
match->tag(core::make_fixnum(6));
298298
FIX_ME(); // is the above correct?
299299
}
300300

‎src/chem/conformationCollection.cc

Lines changed: 0 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -107,7 +107,6 @@ gctools::SmallOrderedSet<Atom_sp>::iterator ai;
107107
CL_DEFMETHOD void ConformationCollectionEntry_O::extractCoordinatesFromMatter(Matter_sp matter)
108108
{
109109
ConformationCollection_sp sl;
110-
vector<Vector3>::iterator ci;
111110
#ifdef DEBUG_ConformationCollectionEntry
112111
this->_Status->addMessage("extractCoordinatesFromMatter");
113112
#endif
@@ -293,7 +292,6 @@ Matter_sp matter;
293292
ConformationCollection_O::entryIterator si;
294293
ConformationCollectionEntry_sp entry;
295294
geom::SimpleVectorCoordinate_sp superposeCoords;
296-
geom::SimpleVectorCoordinate_O::iterator ci;
297295
frames = geom::FrameList_O::create();
298296
matter = this->getMatter();
299297
for ( si=this->begin_Entries(); si!=this->end_Entries(); si++ )

‎src/chem/conformationExplorer.cc

Lines changed: 0 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -280,7 +280,6 @@ CL_LISPIFY_NAME("extractCoordinatesFromMatter");
280280
CL_DEFMETHOD void ConformationExplorerEntryStage_O::extractCoordinatesFromMatter(Matter_sp matter)
281281
{
282282
ConformationExplorer_sp sl;
283-
geom::SimpleVectorCoordinate_O::iterator ci;
284283
LOG("About to get ConformationExplorer" );
285284
sl = this->getConformationExplorer();
286285
LOG("Got ConformationExplorer" );
@@ -853,8 +852,6 @@ CL_DEFMETHOD ConformationExplorerEntry_sp ConformationExplorer_O::createEntr
853852
bool ConformationExplorer_O::hasStageNameInAllEntries(core::T_sp stageKey)
854853
{
855854
entryIterator ei;
856-
bool inAll;
857-
inAll = false;
858855
for ( ei=this->begin_Entries(); ei!=this->end_Entries(); ei++ )
859856
{
860857
if ( !(*ei)->hasEntryStageWithName(stageKey) )

‎src/chem/constitution.cc

Lines changed: 0 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -122,7 +122,6 @@ void Constitution_O::makeResidueConsistentWithStereoisomerNamed(Residue_sp res,
122122
string atomName;
123123
Atom_sp aa;
124124
core::T_sp bdb = getCandoDatabase();
125-
Constitution_sp residueConstitution = this->asSmartPtr();
126125
core::Symbol_sp fullName = gc::As<core::Symbol_sp>(core::eval::funcall(_sym_monomerNameForNameOrPdb,bdb,stereoisomerName));
127126
core::Symbol_sp pdbName = gc::As<core::Symbol_sp>(core::eval::funcall(_sym_pdbNameForNameOrPdb,bdb,stereoisomerName));
128127
res->setName(fullName);

‎src/chem/constitutionAtoms.cc

Lines changed: 0 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -162,7 +162,6 @@ CL_DEFUN ConstitutionAtoms_sp ConstitutionAtoms_O::makeConstitutionAtomsFromResi
162162

163163
void ConstitutionAtoms_O::addConstitutionVirtualAtom(ConstitutionVirtualAtom_sp ca)
164164
{
165-
ConstitutionAtomIndex0N nextIndex = this->_Atoms.size();
166165
this->_Atoms.push_back(ca);
167166
};
168167

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