replace some size with distance

PDB/demo/PDB/pdb_distance_matrix.cpp

@@ -89,8 +89,8 @@ int main(int argc, char *argv[]){
 
   PDB pdb(in, verbose);
 
-  if (verbose) std::cout << "Input PDB has " << pdb.models().size() << " models." << std::endl;
-  if (pdb.models().size() != 1){
+  if (verbose) std::cout << "Input PDB has " << CGAL::PDB::distance(pdb.models()) << " models." << std::endl;
+  if (CGAL::PDB::distance(pdb.models()) != 1){
     std::cout << "Attempting to write multiple image files: assuming the output argument has a %d in it.\n";
   }
 
@@ -105,7 +105,7 @@ int main(int argc, char *argv[]){
     if (!output_file.empty()) {
 
       char buf[100000];
-      if (pdb.models().size() != 1){
+      if (CGAL::PDB::distance(pdb.models()) != 1){
 	sprintf(buf, output_file.c_str(), m.key().index());
       } else {
 	sprintf(buf, output_file.c_str());

PDB/demo/PDB/pdb_info.cpp

@@ -19,6 +19,7 @@
    MA 02110-1301, USA. */
 
 #include <CGAL/PDB/PDB.h>
+#include <CGAL/PDB/range.h>
 #include <cstdlib>
 #include <iostream>
 #include <fstream>
@@ -78,13 +79,14 @@ int main(int argc, char *argv[]){
     }
     PDB inpdb(in, verbose);
     std::cout << "File " << input_files[i] 
-              << " " << inpdb.models().size() << " models" << std::endl;
+              << " " << CGAL::PDB::distance(inpdb.models()) << " models" << std::endl;
     
     CGAL_PDB_FOREACH(const PDB::Model_pair& m, inpdb.models()) {
       std::cout << "Model " << m.key() << std::endl;
       CGAL_PDB_FOREACH(const Model::Chain_pair &c,
                        m.model().chains()) {
-        std::cout << " Chain " << c.key() << " has " << c.chain().monomers().size()
+        std::cout << " Chain " << c.key() << " has "
+                  << CGAL::PDB::distance(c.chain().monomers())
                   << " residues" << std::endl;
       }
     }

PDB/demo/PDB/pdb_transform.cpp

@@ -115,11 +115,11 @@ int main(int argc, char *argv[]){
 
   PDB pdb(in, verbose);
 
-  if (verbose) std::cout << "Input PDB has " << pdb.models().size() << " models." << std::endl;
+  if (verbose) std::cout << "Input PDB has " << CGAL::PDB::distance(pdb.models()) << " models." << std::endl;
  
 
   CGAL_PDB_FOREACH(PDB::Model_pair &m, pdb.models()) {
-    std::cout << "Model " << m.key() << " has " << m.model().chains().size() 
+    std::cout << "Model " << m.key() << " has " << CGAL::PDB::distance(m.model().chains()) 
               << " chains."<< std::endl;
     CGAL_PDB_FOREACH(Chain &c, make_chain_range(m.model().chains())) {
       CGAL_PDB_FOREACH(Monomer &r, make_monomer_range(c.monomers())) {

PDB/demo/PDB/pdb_tree.cpp

@@ -49,8 +49,8 @@ int main(int argc, char *argv[]) {
 	std::cout << c.chain().name();
       }
       std::cout << std::endl;
-      std::cout << "  " << CGAL::PDB::size(c.chain().atoms())<< " atoms" << std::endl;
-      std::cout << "  " << CGAL::PDB::size(c.chain().bonds()) << " bonds" << std::endl;
+      std::cout << "  " << CGAL::PDB::distance(c.chain().atoms())<< " atoms" << std::endl;
+      std::cout << "  " << CGAL::PDB::distance(c.chain().bonds()) << " bonds" << std::endl;
     }
   }
 

PDB/include/CGAL/PDB/Atom.h

@@ -124,19 +124,10 @@ inline bool Atom::operator!=(const Atom &o) const {
 }
 
 
-
 //! Assign unique indices to all atoms in the sequence, starting at optional start value
 /*!
   This returns the next unused index. 
 */
-template <class Range>
-inline int index_atoms(Range &r, int start=0) {
-  for (typename Range::iterator c=r.begin(); c!= r.end(); ++c) {
-    c->atom().set_index(Atom::Index(start++));
-  }
-  return start;
-}
-
 template <class Range>
 inline int index_atoms(Range r, int start=0) {
 	  for (typename Range::iterator c=r.begin(); c!= r.end(); ++c) {

PDB/include/CGAL/PDB/distance.h

@@ -24,6 +24,7 @@
 #include <CGAL/PDB/basic.h>
 #include <CGAL/PDB/Chain.h>
 #include <CGAL/PDB/Matrix.h>
+#include <CGAL/PDB/range.h>
 #include <cmath>
 #include <debug/vector>
 namespace CGAL { namespace PDB {

PDB/include/CGAL/PDB/range.h

@@ -137,7 +137,7 @@ struct Get_bond_indices {
 //! Return an iterator range which returns a pair of indices for a bond
 template <class Range>
 internal::rangelib::transformed_range<Range, Get_bond_indices>
-make_bond_indices_range(const Range &r){
+make_bond_indices_range(Range r){
   return internal::rangelib::transformed(r,Get_bond_indices());
 }
 
@@ -157,7 +157,7 @@ struct Is_backbone {
 //! Return an iterator range which returns skips non-backbone atoms
 template <class Range>
 internal::rangelib::filtered_range<Range, Is_backbone>
-make_backbone_range(const Range& r){
+make_backbone_range(Range r){
   return internal::rangelib::filtered(r, Is_backbone());
 }
 
@@ -173,7 +173,7 @@ struct Is_CA {
 //! Return an iterator range which returns skips non-backbone atoms
 template <class Range>
 internal::rangelib::filtered_range<Range, Is_CA>
-make_backbone_range(const Range& r){
+make_ca_range(Range r){
   return internal::rangelib::filtered(r, Is_CA());
 }
 
@@ -211,7 +211,7 @@ struct Is_ok_bond {
 //! Return an iterator range which returns skips non-backbone atoms
     template <class Range, class OKA>
 internal::rangelib::filtered_range<Range, Is_ok_bond<OKA> >
-make_backbone_range(OKA oka, const Range& r){
+make_backbone_range(OKA oka, Range r){
   return internal::rangelib::filtered(r, Is_ok_bond<OKA>(oka));
 }