From 2a754639594a94de64080795b6cb72b942911101 Mon Sep 17 00:00:00 2001
From: Greg Landrum <greg.landrum@gmail.com>
Date: Sat, 14 Nov 2015 09:21:05 +0100
Subject: [PATCH] get rid of some more warnings

---
 Code/DataStructs/ExplicitBitVect.cpp | 2 +-
 Code/DataStructs/SparseBitVect.h     | 2 +-
 Code/DataStructs/SparseIntVect.h     | 4 ++--
 Code/DistGeom/DistGeomUtils.cpp      | 2 ++
 Code/Geometry/UniformGrid3D.cpp      | 2 +-
 5 files changed, 7 insertions(+), 5 deletions(-)

diff --git a/Code/DataStructs/ExplicitBitVect.cpp b/Code/DataStructs/ExplicitBitVect.cpp
index bbccc2a6d..2d10fb291 100644
--- a/Code/DataStructs/ExplicitBitVect.cpp
+++ b/Code/DataStructs/ExplicitBitVect.cpp
@@ -41,7 +41,7 @@ ExplicitBitVect::ExplicitBitVect(const char *data,const unsigned int dataLen)
   initFromText(data,dataLen);
 }
 
-  ExplicitBitVect::ExplicitBitVect(const ExplicitBitVect& other){
+  ExplicitBitVect::ExplicitBitVect(const ExplicitBitVect& other) : BitVect(other) {
     d_size = other.d_size;
     dp_bits = new boost::dynamic_bitset<>(*(other.dp_bits));
     d_numOnBits=other.d_numOnBits;
diff --git a/Code/DataStructs/SparseBitVect.h b/Code/DataStructs/SparseBitVect.h
index 45bd5461b..38acb7ef4 100644
--- a/Code/DataStructs/SparseBitVect.h
+++ b/Code/DataStructs/SparseBitVect.h
@@ -39,7 +39,7 @@ public:
   explicit SparseBitVect(unsigned int size): dp_bits(0), d_size(0) {_initForSize(size); };
 
   //! copy constructor
-  SparseBitVect(const SparseBitVect& other){
+  SparseBitVect(const SparseBitVect& other) : BitVect(other) {
     d_size=0;dp_bits = 0;
     _initForSize(other.getNumBits());
     IntSet *bv=other.dp_bits;
diff --git a/Code/DataStructs/SparseIntVect.h b/Code/DataStructs/SparseIntVect.h
index b1d1878e7..94fff594d 100644
--- a/Code/DataStructs/SparseIntVect.h
+++ b/Code/DataStructs/SparseIntVect.h
@@ -75,7 +75,7 @@ namespace RDKit{
 
     //! set the value at an index
     void setVal(IndexType idx, int val){
-      if(idx<0||idx>=d_length){
+      if(idx>=d_length){
         throw IndexErrorException(static_cast<int>(idx));
       }
       if(val!=0){
@@ -86,7 +86,7 @@ namespace RDKit{
     };
 #ifdef __clang__
 #pragma clang diagnostic pop
-#elif defined(__GNUC__) || defined(__GNUG__) && \
+#elif ( defined(__GNUC__) || defined(__GNUG__) ) &&     \
   ( __GNUC__ > 4 ||                                    \
     (__GNUC__ == 4 && __GNUC_MINOR__ > 1 ) )
 #pragma GCC diagnostic pop
diff --git a/Code/DistGeom/DistGeomUtils.cpp b/Code/DistGeom/DistGeomUtils.cpp
index 498c88d29..0b742c0a8 100644
--- a/Code/DistGeom/DistGeomUtils.cpp
+++ b/Code/DistGeom/DistGeomUtils.cpp
@@ -252,6 +252,7 @@ namespace DistGeom {
                                                  const std::vector<std::pair<std::vector<int>, std::vector<double> > > &expTorsionAngles,
                                                  const std::vector<std::vector<int> > &improperAtoms,
                                                  const std::vector<int> &atomNums) {
+    (void)atomNums;
     unsigned int N = mmat.numRows();
     CHECK_INVARIANT(N == positions.size(), "");
     CHECK_INVARIANT(expTorsionAtoms.size() == expTorsionAngles.size(), "");
@@ -377,6 +378,7 @@ namespace DistGeom {
                                                    const std::vector<std::vector<int> > &expTorsionAtoms,
                                                    const std::vector<std::pair<std::vector<int>, std::vector<double> > > &expTorsionAngles,
                                                    const std::vector<int> &atomNums) {
+      (void)atomNums;
       unsigned int N = mmat.numRows();
       CHECK_INVARIANT(N == positions.size(), "");
       CHECK_INVARIANT(expTorsionAtoms.size() == expTorsionAngles.size(), "");
diff --git a/Code/Geometry/UniformGrid3D.cpp b/Code/Geometry/UniformGrid3D.cpp
index 57b8cfcd8..5ae3e7a6a 100644
--- a/Code/Geometry/UniformGrid3D.cpp
+++ b/Code/Geometry/UniformGrid3D.cpp
@@ -23,7 +23,7 @@ using namespace RDKit;
 namespace RDGeom {
   unsigned int ci_GRIDPICKLE_VERSION=0x1;
 
-  UniformGrid3D::UniformGrid3D(const UniformGrid3D &other){
+  UniformGrid3D::UniformGrid3D(const UniformGrid3D &other) : Grid3D(other) {
     PRECONDITION(other.dp_storage,"cannot copy an unintialized grid");
     RDKit::DiscreteValueVect *data=new RDKit::DiscreteValueVect(*other.dp_storage);
     initGrid(other.d_numX*other.d_spacing,