diff --git a/scoring/src/ss_agreement_env_listener.cc b/scoring/src/ss_agreement_env_listener.cc
index 0653c629f6bfc850322878b633da9a29d26cf529..19d885f464d9918c66adc52f71e2237736ecf806 100644
--- a/scoring/src/ss_agreement_env_listener.cc
+++ b/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
diff --git a/scoring/src/ss_agreement_env_listener.hh b/scoring/src/ss_agreement_env_listener.hh
index c6578139b633ffd2c10cc63fd662f66948a169de..3d924e23419591bf88567186eaa6f1949cee9687 100644
--- a/scoring/src/ss_agreement_env_listener.hh
+++ b/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);