make saving/loading or rotamer libraries faster

sidechain/src/bb_dep_rotamer_lib.cc

@@ -133,10 +133,7 @@ void BBDepRotamerLib::Save(const String& filename){
   }
 
   out_stream.write(reinterpret_cast<char*>(&total_num_rotamers_),sizeof(uint64_t));
-  for(uint i = 0; i < total_num_rotamers_; ++i){
-    out_stream << static_data_[i];
-  }
-
+  out_stream.write(reinterpret_cast<char*>(&static_data_[0]),total_num_rotamers_ * sizeof(RotamerLibEntry));
   out_stream.close();
 }
 
@@ -198,10 +195,8 @@ BBDepRotamerLibPtr BBDepRotamerLib::Load(const String& filename){
 
   in_stream.read(reinterpret_cast<char*>(&p->total_num_rotamers_),sizeof(uint64_t));
   p->static_data_ = new RotamerLibEntry[p->total_num_rotamers_];
-  for(uint i = 0; i < p->total_num_rotamers_; ++i){
-    in_stream >> p->static_data_[i];
-  }
-  in_stream.close();
+  in_stream.read(reinterpret_cast<char*>(&p->static_data_[0]),p->total_num_rotamers_ * sizeof(RotamerLibEntry));
+
   return p;
 }
 

sidechain/src/rotamer_lib.cc

@@ -57,9 +57,7 @@ void RotamerLib::Save(const String& filename){
   }
 
   out_stream.write(reinterpret_cast<char*>(&total_num_rotamers_),sizeof(uint64_t));
-  for(uint i = 0; i < total_num_rotamers_; ++i){
-    out_stream << static_data_[i];
-  }
+  out_stream.write(reinterpret_cast<char*>(&static_data_[0]),total_num_rotamers_ * sizeof(RotamerLibEntry));
 
   out_stream.close();
 }
@@ -112,9 +110,7 @@ RotamerLibPtr RotamerLib::Load(const String& filename){
 
   in_stream.read(reinterpret_cast<char*>(&p->total_num_rotamers_),sizeof(uint64_t));
   p->static_data_ = new RotamerLibEntry[p->total_num_rotamers_];
-  for(uint i = 0; i < p->total_num_rotamers_; ++i){
-    in_stream >> p->static_data_[i];
-  }
+  in_stream.read(reinterpret_cast<char*>(&p->static_data_[0]),p->total_num_rotamers_ * sizeof(RotamerLibEntry));
   in_stream.close();
   return p;
 }

sidechain/src/rotamer_lib_entry.hh

@@ -69,18 +69,6 @@ struct RotamerLibEntry{
   bool SimilarDihedral(RotamerLibEntryPtr other, uint dihedral_idx,
                        Real thresh, const String& res_name);
 
-  friend std::ofstream& operator<<(std::ofstream& os, RotamerLibEntry& entry){
-    //assumes all variables being in memory in a consecutive order...
-    os.write(reinterpret_cast<char*>(&entry.probability),9*sizeof(Real));
-    return os;
-  }
-
-  friend std::ifstream& operator>>(std::ifstream& is, RotamerLibEntry& entry){
-    //assumes all variables being in memory in a consecutive order...
-    is.read(reinterpret_cast<char*>(&entry.probability),9*sizeof(Real));  
-    return is;
-  }
-
   // portable serialization
   // (cleanly element by element with fixed-width base-types)
   template <typename DS>