Use range-based for loops

modules/algebra/src/Triangle3D.cpp

@@ -56,11 +56,11 @@ Triangle3D get_largest_triangle(const Vector3Ds &points) {
   }
   algebra::Segment3D seg(triple[0], triple[1]);
   max_dist = 0;
-  for (unsigned int i = 0; i < points.size(); i++) {
-    double dist = algebra::get_distance(seg, points[i]);
+  for (const auto &point : points) {
+    double dist = algebra::get_distance(seg, point);
     if (dist > max_dist) {
       max_dist = dist;
-      triple[2] = points[i];
+      triple[2] = point;
     }
   }
   return Triangle3D(triple[0], triple[1], triple[2]);

modules/atom/src/DopePairScore.cpp

@@ -44,8 +44,8 @@ void add_dope_score_data(Atom atom) {
 
 void add_dope_score_data(Hierarchy h) {
   Hierarchies atoms = get_by_type(h, ATOM_TYPE);
-  for (unsigned int i = 0; i < atoms.size(); ++i) {
-    add_dope_score_data(Atom(atoms[i]));
+  for (const auto &atom : atoms) {
+    add_dope_score_data(Atom(atom));
   }
 }
 

modules/core/src/FixedRefiner.cpp

@@ -17,10 +17,10 @@ FixedRefiner::FixedRefiner(const ParticlesTemp &ps)
   IMP_LOG_VERBOSE("Created fixed particle refiner with "
                   << ps.size() << " particles" << std::endl);
   m_ = ps[0]->get_model();
-  for(unsigned int i = 0; i < ps.size(); i++){
-    IMP_USAGE_CHECK(m_ == ps[i]->get_model(),
+  for (const auto &p : ps) {
+    IMP_USAGE_CHECK(m_ == p->get_model(),
                     "refiner assumes all particles are from the same model");
-    pis_.push_back(ps[i]->get_index());
+    pis_.push_back(p->get_index());
   }
 }
 
@@ -34,8 +34,8 @@ const ParticlesTemp
 FixedRefiner::get_refined(Particle *) const
 {
   ParticlesTemp ps;
-  for(unsigned int i=0; i < pis_.size(); i++){
-    ps.push_back(m_->get_particle(pis_[i]));
+  for (const auto &pi : pis_) {
+    ps.push_back(m_->get_particle(pi));
   }
   return ps;
 }

modules/misc/src/CommonEndpointPairFilter.cpp

@@ -31,9 +31,9 @@ int CommonEndpointPairFilter::get_value_index(
 ModelObjectsTemp CommonEndpointPairFilter::do_get_inputs(
     Model *m, const ParticleIndexes &pis) const {
   ModelObjectsTemp ret = IMP::get_particles(m, pis);
-  for (unsigned int i = 0; i < pis.size(); ++i) {
-    if (IMP::atom::Bond::get_is_setup(m, pis[i])) {
-      IMP::atom::Bond b(m, pis[i]);
+  for (auto pi : pis) {
+    if (IMP::atom::Bond::get_is_setup(m, pi)) {
+      IMP::atom::Bond b(m, pi);
       ret.push_back(b.get_bonded(0));
       ret.push_back(b.get_bonded(1));
     }

modules/saxs/bin/compute_vr.cpp

@@ -60,22 +60,22 @@ int main(int argc, char **argv) {
   if (vm.count("offset")) use_offset = true;
 
   IMP::saxs::Profiles exp_profiles;
-  for (unsigned int i = 0; i < files.size(); i++) {
+  for (const auto &file : files) {
     // check if file exists
-    std::ifstream in_file(files[i].c_str());
+    std::ifstream in_file(file.c_str());
     if (!in_file) {
-      std::cerr << "Can't open file " << files[i] << std::endl;
+      std::cerr << "Can't open file " << file << std::endl;
       exit(1);
     }
 
-    IMP_NEW(IMP::saxs::Profile, profile, (files[i]));
+    IMP_NEW(IMP::saxs::Profile, profile, (file));
     if (profile->size() == 0) {
-      std::cerr << "can't parse input file " << files[i] << std::endl;
+      std::cerr << "can't parse input file " << file << std::endl;
       return 1;
     } else {
-      dat_files.push_back(files[i]);
+      dat_files.push_back(file);
       exp_profiles.push_back(profile);
-      std::cout << "Profile read from file " << files[i]
+      std::cout << "Profile read from file " << file
                 << " size = " << profile->size() << std::endl;
     }
   }

modules/saxs/src/utility.cpp

@@ -25,9 +25,9 @@ Profile* compute_profile(Particles particles, double min_q,
   double average_radius = 0.0;
   if (hydration_layer) {
     // add radius
-    for (unsigned int i = 0; i < particles.size(); i++) {
-      double radius = ft->get_radius(particles[i], ff_type);
-      core::XYZR::setup_particle(particles[i], radius);
+    for (auto &particle : particles) {
+      double radius = ft->get_radius(particle, ff_type);
+      core::XYZR::setup_particle(particle, radius);
       average_radius += radius;
     }
     surface_area = s.get_solvent_accessibility(core::XYZRs(particles));
@@ -121,28 +121,28 @@ void read_files(Model *m, const std::vector<std::string>& files,
                 bool heavy_atoms_only, int multi_model_pdb,
                 bool explicit_water, float max_q, int units) {
 
-  for (unsigned int i = 0; i < files.size(); i++) {
+  for (const auto &file : files) {
     // check if file exists
-    std::ifstream in_file(files[i].c_str());
+    std::ifstream in_file(file.c_str());
     if (!in_file) {
-      IMP_WARN("Can't open file " << files[i] << std::endl);
+      IMP_WARN("Can't open file " << file << std::endl);
       return;
     }
     // 1. try as pdb or mmcif
     try {
-      read_pdb(m, files[i], pdb_file_names, particles_vec, residue_level,
+      read_pdb(m, file, pdb_file_names, particles_vec, residue_level,
                heavy_atoms_only, multi_model_pdb, explicit_water);
     }
     catch (const IMP::ValueException &e) {  // not a pdb file
       // 2. try as a dat profile file
-      IMP_NEW(Profile, profile, (files[i], false, max_q, units));
+      IMP_NEW(Profile, profile, (file, false, max_q, units));
       if (profile->size() == 0) {
-        IMP_WARN("can't parse input file " << files[i] << std::endl);
+        IMP_WARN("can't parse input file " << file << std::endl);
         return;
       } else {
-        dat_files.push_back(files[i]);
+        dat_files.push_back(file);
         exp_profiles.push_back(profile);
-        IMP_LOG_TERSE("Profile read from file " << files[i]
+        IMP_LOG_TERSE("Profile read from file " << file
                       << " size = " << profile->size() << std::endl);
       }
     }