diff --git a/modules/display/include/geometry_macros.h b/modules/display/include/geometry_macros.h
index 6ccb84d9b8..060143b6c2 100644
--- a/modules/display/include/geometry_macros.h
+++ b/modules/display/include/geometry_macros.h
@@ -166,8 +166,8 @@
         : display::PairGeometry(pp) {}                                 \
     display::Geometries get_components() const override {              \
       display::Geometries ret;                                         \
-      Decorator d0(get_particle_pair()[0]);                            \
-      Decorator d1(get_particle_pair()[1]);                            \
+      Decorator d0(std::get<0>(get_particle_pair()));                  \
+      Decorator d1(std::get<1>(get_particle_pair()));                  \
       action;                                                          \
       return ret;                                                      \
     }                                                                  \
@@ -180,8 +180,8 @@
     display::Geometries get_components() const override {              \
       display::Geometries ret;                                         \
       for(ParticleIndexPair pip : get_container()->get_contents()) {   \
-        Decorator d0(get_container()->get_model(), pip[0]);            \
-        Decorator d1(get_container()->get_model(), pip[1]);            \
+        Decorator d0(get_container()->get_model(), std::get<0>(pip));  \
+        Decorator d1(get_container()->get_model(), std::get<1>(pip));  \
         action;                                                        \
       }                                                                \
       return ret;                                                      \
diff --git a/modules/display/src/particle_geometry.cpp b/modules/display/src/particle_geometry.cpp
index 37e95f16ec..1bae5068bc 100644
--- a/modules/display/src/particle_geometry.cpp
+++ b/modules/display/src/particle_geometry.cpp
@@ -20,7 +20,8 @@ SingletonsGeometry::SingletonsGeometry(SingletonContainerAdaptor pc, Color c)
     : Geometry(c, pc->get_name() + " geometry"), sc_(pc) {}
 
 PairGeometry::PairGeometry(const ParticlePair &p)
-    : Geometry(p.get_name() + " geometry"), p0_(p[0]), p1_(p[1]) {}
+    : Geometry(p.get_name() + " geometry"),
+      p0_(std::get<0>(p)), p1_(std::get<1>(p)) {}
 
 PairsGeometry::PairsGeometry(PairContainer *pc)
     : Geometry(pc->get_name() + " geometry"), sc_(pc) {}
diff --git a/modules/kernel/include/cache.h b/modules/kernel/include/cache.h
index fceeab35f3..736417fb02 100644
--- a/modules/kernel/include/cache.h
+++ b/modules/kernel/include/cache.h
@@ -96,8 +96,8 @@ class SparseSymmetricPairMemoizer {
   Generator gen_;
   Checker checker_;
 
-  static Key get_0(Entry e) { return e[0]; }
-  static Key get_1(Entry e) { return e[1]; }
+  static Key get_0(Entry e) { return std::get<0>(e); }
+  static Key get_1(Entry e) { return std::get<1>(e); }
 
   // The This:: is needed to make certain gcc versions (4.7) happier
   typedef boost::multi_index::global_fun<Entry, Key, &This::get_0> P0Member;
diff --git a/modules/kernel/src/internal/swig.cpp b/modules/kernel/src/internal/swig.cpp
index eb6837113b..40239c199f 100644
--- a/modules/kernel/src/internal/swig.cpp
+++ b/modules/kernel/src/internal/swig.cpp
@@ -87,10 +87,8 @@ const Particles &_give_particles(Model *m) {
 const Particles &_pass_particles(const Particles &ps) { return ps; }
 Particle *_pass_particle(Particle *ps) { return ps; }
 const ParticlePair &_pass_particle_pair(const ParticlePair &pp) {
-  for (unsigned int i = 0; i < 2; ++i) {
-    std::cout << pp[i]->get_name() << " ";
-  }
-  std::cout << std::endl;
+  std::cout << std::get<0>(pp)->get_name() << " ";
+  std::cout << std::get<1>(pp)->get_name() << std::endl;
   return pp;
 }
 Particles _give_particles_copy(Model *m) {
@@ -148,7 +146,8 @@ ParticleIndexes _create_particles_from_pdb(std::string name, Model *m) {
 
 Float _LogPairScore::evaluate_index(Model *m, const ParticleIndexPair &ipp,
                                     DerivativeAccumulator *) const {
-  ParticlePair pp(m->get_particle(ipp[0]), m->get_particle(ipp[1]));
+  ParticlePair pp(m->get_particle(std::get<0>(ipp)),
+                  m->get_particle(std::get<1>(ipp)));
   if (map_.find(pp) == map_.end()) {
     map_[pp] = 0;
   }
diff --git a/modules/kernel/test/test_pair_memoizer.cpp b/modules/kernel/test/test_pair_memoizer.cpp
index bc9f0ebe1d..8f0c48d393 100644
--- a/modules/kernel/test/test_pair_memoizer.cpp
+++ b/modules/kernel/test/test_pair_memoizer.cpp
@@ -108,7 +108,7 @@ struct SortedPairs {
     }
     std::cout << "Returning ";
     for (unsigned int i = 0; i < ret.size(); ++i) {
-      std::cout << *ret[i][0] << "-" << *ret[i][1] << " ";
+      std::cout << *std::get<0>(ret[i]) << "-" << *std::get<1>(ret[i]) << " ";
     }
     std::cout << std::endl;
     return ret;
@@ -118,16 +118,21 @@ struct SortedPairs {
 struct SetEquals {
   struct LessPair {
     bool operator()(IMP::Entry a, IMP::Entry b) const {
-      if (a[0] > a[1]) std::swap(a[0], a[1]);
-      if (b[0] > b[1]) std::swap(b[0], b[1]);
-      if (a[0] < b[0])
+      if (std::get<0>(a) > std::get<1>(a)) {
+        std::swap(std::get<0>(a), std::get<1>(a));
+      }
+      if (std::get<0>(b) > std::get<1>(b)) {
+        std::swap(std::get<0>(b), std::get<1>(b));
+      }
+      if (std::get<0>(a) < std::get<0>(b)) {
         return true;
-      else if (a[0] > b[0])
+      } else if (std::get<0>(a) > std::get<0>(b)) {
         return false;
-      else if (a[1] < b[1])
+      } else if (std::get<1>(a) < std::get<1>(b)) {
         return true;
-      else
+      } else {
         return false;
+      }
     }
   };
   bool operator()(SortedPairs::result_type t0) const {
@@ -136,11 +141,11 @@ struct SetEquals {
     std::sort(t1.begin(), t1.end(), LessPair());
     std::cout << "Comparing " << t0 << " and " << t1 << "= ";
     for (unsigned int i = 0; i < t0.size(); ++i) {
-      std::cout << *t0[i][0] << "-" << *t0[i][1] << " ";
+      std::cout << *std::get<0>(t0[i]) << "-" << *std::get<1>(t0[i]) << " ";
     }
     std::cout << " and ";
     for (unsigned int i = 0; i < t1.size(); ++i) {
-      std::cout << *t1[i][0] << "-" << *t1[i][1] << " ";
+      std::cout << *std::get<0>(t1[i]) << "-" << *std::get<1>(t1[i]) << " ";
     }
     std::cout << std::endl;
     if (t0.size() != t1.size()) return false;
@@ -156,12 +161,12 @@ typedef IMP::SparseSymmetricPairMemoizer<SortedPairs, SetEquals> Table;
 struct Sum {
   int value;
   Sum() : value(0) {}
-  void operator()(IMP::Entry a) { value += *a[0] + *a[1]; }
+  void operator()(IMP::Entry a) { value += *std::get<0>(a) + *std::get<1>(a); }
 };
 
 struct Show {
   void operator()(IMP::Entry a) {
-    std::cout << *a[0] << "-" << *a[1] << ", ";
+    std::cout << *std::get<0>(a) << "-" << *std::get<1>(a) << ", ";
   }
 };
 
diff --git a/modules/score_functor/include/SphereDistance.h b/modules/score_functor/include/SphereDistance.h
index 05e5991637..245e2a423a 100644
--- a/modules/score_functor/include/SphereDistance.h
+++ b/modules/score_functor/include/SphereDistance.h
@@ -33,8 +33,8 @@ class SphereDistance : public BaseDistanceScore {
   typedef BaseDistanceScore P;
   static double get_rsum(Model *m,
                          const ParticleIndexPair &pi) {
-    return m->get_sphere(pi[0]).get_radius() +
-           m->get_sphere(pi[1]).get_radius();
+    return m->get_sphere(std::get<0>(pi)).get_radius() +
+           m->get_sphere(std::get<1>(pi)).get_radius();
   }
 
  public:
diff --git a/modules/score_functor/include/Statistical.h b/modules/score_functor/include/Statistical.h
index 93e1450a64..964a89ee6d 100644
--- a/modules/score_functor/include/Statistical.h
+++ b/modules/score_functor/include/Statistical.h
@@ -90,8 +90,8 @@ class Statistical : public Score {
     if (distance >= threshold_ || distance < 0.001) {
       return 0;
     }
-    int pt = m->get_attribute(key_, pp[0]);
-    int lt = m->get_attribute(key_, pp[1]);
+    int pt = m->get_attribute(key_, std::get<0>(pp));
+    int lt = m->get_attribute(key_, std::get<1>(pp));
     if (pt == -1 || lt == -1) return 0;
     return table_->get_score(pt, lt, distance);
   }
@@ -101,8 +101,8 @@ class Statistical : public Score {
     if (distance >= threshold_ || distance < 0.001) {
       return DerivativePair(0, 0);
     }
-    int pt = m->get_attribute(key_, pp[0]);
-    int lt = m->get_attribute(key_, pp[1]);
+    int pt = m->get_attribute(key_, std::get<0>(pp));
+    int lt = m->get_attribute(key_, std::get<1>(pp));
     if (pt == -1 || lt == -1) return DerivativePair(0, 0);
     return table_->get_score_with_derivative(pt, lt, distance);
   }
diff --git a/modules/score_functor/include/internal/PMFTable.h b/modules/score_functor/include/internal/PMFTable.h
index 7a6d1ac475..cc758dae8b 100644
--- a/modules/score_functor/include/internal/PMFTable.h
+++ b/modules/score_functor/include/internal/PMFTable.h
@@ -54,8 +54,8 @@ struct PMFTable : public Object {
   }
   const RawOpenCubicSpline &get(int i, int j) const {
     Array<2, int> is;
-    is[0] = i;
-    is[1] = j;
+    std::get<0>(is) = i;
+    std::get<1>(is) = j;
     typename Storage::ExtendedIndex ei(is.begin(), is.end());
     return data_[data_.get_index(ei)];
   }
@@ -137,8 +137,8 @@ struct PMFTable : public Object {
       }
       order(i, j);
       Array<2, int> is;
-      is[0] = i;
-      is[1] = j;
+      std::get<0>(is) = i;
+      std::get<1>(is) = j;
       typename Storage::ExtendedIndex ei(is.begin(), is.end());
       if (!data_.get_has_index(ei)) {
         data_.add_voxel(ei, score_functor::internal::RawOpenCubicSpline(