reduce code redundancy

scoring/src/ss_agreement_env_listener.cc

@@ -67,68 +67,7 @@ void SSAgreementEnvListener::SetEnvironment(const BackboneScoreEnv& base_env,
   	env_.Add(&env_data_[*i], ca_pos_data[*i]);
   }
 
-  // additionally, we also set connectivity and ca / h positions
-  for(std::vector<uint>::const_iterator i = idx.begin(); i != idx.end(); ++i){
-
-    // set connectivity of the residue itself
-    if(*i < idx_handler_->GetNumResidues() - 1 && env_set_[*i + 1] &&
-       geom::Length2(env_data_[*i].c_pos - env_data_[*i+1].n_pos) <= 6.25) {
-      connected_to_next_[*i] = 1;
-    } else {
-      connected_to_next_[*i] = 0;
-    }
-
-    // set connectivity of the residue before
-    if(*i > 0) {
-      if(env_set_[*i - 1] && 
-         geom::Length2(env_data_[*i-1].c_pos - env_data_[*i].n_pos) <= 6.25) {
-        connected_to_next_[*i-1] = 1;
-      } else {
-        connected_to_next_[*i-1] = 0;
-      }
-    }
-
-    ca_positions_[*i] = env_data_[*i].pos;
-
-    // h_pos of this residue
-    if(!env_data_[*i].is_proline) {
-      if(*i > 0 && env_set_[*i-1] && connected_to_next_[*i - 1]) {
-        geom::Vec3 dir_vec = geom::Normalize(env_data_[*i-1].c_pos -
-                                             env_data_[*i-1].o_pos);
-        env_data_[*i].h_pos = env_data_[*i].n_pos + dir_vec;
-        env_data_[*i].valid_h_pos = true;
-      }
-      else {
-        env_data_[*i].valid_h_pos = false;
-      }
-    } 
-
-    // the h_pos of the next residue might have changed
-    // no check for index validity of idx + 1... this informatin is contained
-    // in connected_to_next_
-    if(connected_to_next_[*i]) {
-      if(!env_data_[*i+1].is_proline) {
-        geom::Vec3 dir_vec = geom::Normalize(env_data_[*i].c_pos -
-                                           env_data_[*i].o_pos);
-        env_data_[*i+1].h_pos = env_data_[*i+1].n_pos + dir_vec;
-        env_data_[*i+1].valid_h_pos = true;
-      } else {
-        env_data_[*i+1].valid_h_pos = false;
-      }
-    }
-  }
-
-  // and finally update all donor information in the close environment
-  std::set<int> stuff_to_update;
-  for(std::vector<uint>::const_iterator i = idx.begin(); 
-      i != idx.end(); ++i) {
-    this->AddCloseResidues(*i, stuff_to_update);
-  }
-
-  for(std::set<int>::iterator i = stuff_to_update.begin();
-      i != stuff_to_update.end(); ++i) {
-    this->FindOptimalDonors(*i);
-  }
+  this->Update(idx);
 }
 
 void SSAgreementEnvListener::ResetEnvironment(const BackboneScoreEnv& base_env,
@@ -156,71 +95,9 @@ void SSAgreementEnvListener::ResetEnvironment(const BackboneScoreEnv& base_env,
     env_data_[*i].c_pos = c_pos_data[*i];
     env_data_[*i].o_pos = o_pos_data[*i];
   	env_.Reset(&env_data_[*i], old_pos, ca_pos_data[*i]);
-
   }
 
-  // additionally, we also set connectivity and ca / h positions
-  for(std::vector<uint>::const_iterator i = idx.begin(); i != idx.end(); ++i){
-
-    // set connectivity of the residue itself
-    if(*i < idx_handler_->GetNumResidues() - 1 && env_set_[*i + 1] &&
-       geom::Length2(env_data_[*i].c_pos - env_data_[*i+1].n_pos) <= 6.25) {
-      connected_to_next_[*i] = 1;
-    } else {
-      connected_to_next_[*i] = 0;
-    }
-
-    // set connectivity of the residue before
-    if(*i > 0) {
-      if(env_set_[*i - 1] && 
-         geom::Length2(env_data_[*i-1].c_pos - env_data_[*i].n_pos) <= 6.25) {
-        connected_to_next_[*i-1] = 1;
-      } else {
-        connected_to_next_[*i-1] = 0;
-      }
-    }
-
-    ca_positions_[*i] = env_data_[*i].pos;
-
-    // h_pos of this residue
-    if(!env_data_[*i].is_proline) {
-      if(*i > 0 && env_set_[*i-1] && connected_to_next_[*i - 1]) {
-        geom::Vec3 dir_vec = geom::Normalize(env_data_[*i-1].c_pos -
-                                             env_data_[*i-1].o_pos);
-        env_data_[*i].h_pos = env_data_[*i].n_pos + dir_vec;
-        env_data_[*i].valid_h_pos = true;
-      }
-      else {
-        env_data_[*i].valid_h_pos = false;
-      }
-    } 
-
-    // the h_pos of the next residue might have changed
-    // no check for index validity of idx + 1... this informatin is contained
-    // in connected_to_next_
-    if(connected_to_next_[*i]) {
-      if(!env_data_[*i+1].is_proline) {
-        geom::Vec3 dir_vec = geom::Normalize(env_data_[*i].c_pos -
-                                           env_data_[*i].o_pos);
-        env_data_[*i+1].h_pos = env_data_[*i+1].n_pos + dir_vec;
-        env_data_[*i+1].valid_h_pos = true;
-      } else {
-        env_data_[*i+1].valid_h_pos = false;
-      }
-    }
-  }
-
-  // and finally update all donor information in the close environment
-  std::set<int> stuff_to_update;
-  for(std::vector<uint>::const_iterator i = idx.begin(); 
-      i != idx.end(); ++i) {
-    this->AddCloseResidues(*i, stuff_to_update);
-  }
-
-  for(std::set<int>::iterator i = stuff_to_update.begin();
-      i != stuff_to_update.end(); ++i) {
-    this->FindOptimalDonors(*i);
-  }
+  this->Update(idx);
 }
 
 void SSAgreementEnvListener::ClearEnvironment(const BackboneScoreEnv& base_env,
@@ -253,7 +130,7 @@ void SSAgreementEnvListener::ClearEnvironment(const BackboneScoreEnv& base_env,
       env_data_[*i + 1].valid_h_pos = false;
     }
 
-    // we already call FindOptimalDonors for the deleted residues.
+    // we call FindOptimalDonors for the deleted residues.
     // the only thing that will happen: 
     // according donor_for_one_ / donor_for_two_ gets set to -1
     FindOptimalDonors(*i);
@@ -477,4 +354,71 @@ void SSAgreementEnvListener::FindOptimalDonors(uint idx, bool check_env_set) {
   }
 }
 
+void SSAgreementEnvListener::Update(const std::vector<uint>& idx) {
+
+  // assumes env_data_ to be set...
+
+  for(std::vector<uint>::const_iterator i = idx.begin(); i != idx.end(); ++i){
+    
+    ca_positions_[*i] = env_data_[*i].pos;
+
+    // set connectivity of the residue itself
+    if(*i < idx_handler_->GetNumResidues() - 1 && env_set_[*i + 1] &&
+       geom::Length2(env_data_[*i].c_pos - env_data_[*i+1].n_pos) <= 6.25) {
+        connected_to_next_[*i] = 1;
+    } else {
+      connected_to_next_[*i] = 0;
+    }
+    
+    // set connectivity of the residue before
+    if(*i > 0) {
+      if(env_set_[*i - 1] && 
+         geom::Length2(env_data_[*i-1].c_pos - env_data_[*i].n_pos) <= 6.25) {
+        connected_to_next_[*i-1] = 1;
+      } else {
+        connected_to_next_[*i-1] = 0;
+      }
+    }
+
+    // h_pos of this residue
+    if(!env_data_[*i].is_proline) {
+      if(*i > 0 && env_set_[*i-1] && connected_to_next_[*i - 1]) {
+        geom::Vec3 dir_vec = geom::Normalize(env_data_[*i-1].c_pos -
+                                             env_data_[*i-1].o_pos);
+        env_data_[*i].h_pos = env_data_[*i].n_pos + dir_vec;
+        env_data_[*i].valid_h_pos = true;
+      }
+      else {
+        env_data_[*i].valid_h_pos = false;
+      }
+    } 
+
+    // the h_pos of the next residue might have changed
+    // no check for index validity of idx + 1... this informatin is contained
+    // in connected_to_next_
+    if(connected_to_next_[*i]) {
+      if(!env_data_[*i+1].is_proline) {
+        geom::Vec3 dir_vec = geom::Normalize(env_data_[*i].c_pos -
+                                           env_data_[*i].o_pos);
+        env_data_[*i+1].h_pos = env_data_[*i+1].n_pos + dir_vec;
+        env_data_[*i+1].valid_h_pos = true;
+      } else {
+        env_data_[*i+1].valid_h_pos = false;
+      }
+    }
+  }
+
+  // and finally update all donor information in the close environment
+  std::set<int> stuff_to_update;
+  for(std::vector<uint>::const_iterator i = idx.begin(); 
+      i != idx.end(); ++i) {
+    this->AddCloseResidues(*i, stuff_to_update);
+  }
+
+  for(std::set<int>::iterator i = stuff_to_update.begin();
+      i != stuff_to_update.end(); ++i) {
+    this->FindOptimalDonors(*i);
+  }
+}
+
 }} // ns

scoring/src/ss_agreement_env_listener.hh

@@ -63,6 +63,11 @@ public:
 
 private:
 
+  // helper function that sets hydrogen positions in env_data_, the ca_positions_, 
+  // donor_for_one_, donor_for_two_, and connected_to_next_ for all residues 
+  // affected by indices in idx
+  void Update(const std::vector<uint>& idx);
+
   void AddCloseResidues(uint idx, std::set<int>& close_residues) const;
 
   void FindOptimalDonors(uint idx, bool check_env_set = true);