diff --git a/modules/seq/alg/src/variance_map.cc b/modules/seq/alg/src/variance_map.cc
index 05d9eb04b1a814feeb8f961862975cdda725f0b3..38a27051e55f463e1f258b264deeade192ad5099 100644
--- a/modules/seq/alg/src/variance_map.cc
+++ b/modules/seq/alg/src/variance_map.cc
@@ -72,15 +72,16 @@ String GetJson(const T& data, uint num_rows, uint num_cols) {
}
-void FilllDDTValues(int len, const std::vector<Real>& dist_diff,
- const std::vector<int>& below_15,
+void FilllDDTValues(const std::vector<Real>& dist_diff,
+ const std::vector<int>& ref_distances,
const std::vector<std::pair<int, int> >& idx_mapping,
std::vector<Real>& local_lddt) {
+ int len = dist_diff.size();
std::vector<int> counts(len, 0);
std::vector<int> total_counts(len, 0);
- for(auto it = below_15.begin(); it != below_15.end(); ++it) {
+ for(auto it = ref_distances.begin(); it != ref_distances.end(); ++it) {
Real diff = dist_diff[*it];
int fulfilled = 0;
fulfilled += static_cast<int>(diff < static_cast<Real>(4.0));
@@ -106,7 +107,7 @@ void FilllDDTValues(int len, const std::vector<Real>& dist_diff,
}
-void FilllDDTValues(int len, const std::vector<Real>& dist_one,
+void FilllDDTValues(const std::vector<Real>& dist_one,
const std::vector<Real>& dist_two,
const std::vector<int>& below_15_one,
const std::vector<int>& below_15_two,
@@ -114,13 +115,16 @@ void FilllDDTValues(int len, const std::vector<Real>& dist_one,
std::vector<Real>& local_lddt_one,
std::vector<Real>& local_lddt_two) {
+ // absolute dist differences are the same for both
std::vector<Real> dist_diff(dist_one.size());
for(uint i = 0; i < dist_one.size(); ++i) {
dist_diff[i] = std::abs(dist_one[i] - dist_two[i]);
}
- FilllDDTValues(len, dist_diff, below_15_two, idx_mapping, local_lddt_one);
- FilllDDTValues(len, dist_diff, below_15_one, idx_mapping, local_lddt_two);
+ // estimate lDDT of structure 1 with reference distances (below 15) from
+ // structure 2 and vice versa
+ FilllDDTValues(dist_diff, below_15_two, idx_mapping, local_lddt_one);
+ FilllDDTValues(dist_diff, below_15_one, idx_mapping, local_lddt_two);
}
} // anon ns
@@ -289,17 +293,20 @@ MeanlDDTPtr CreateMeanlDDTHA(const DistanceMapPtr dmap) {
throw IntegrityError("empty distance map provided");
}
- // the relevant pairwise distances are the ones that are off-diagonal from the
- // pairwise distance matrices
+ // the relevant pairwise distances are the off-diagonal elements from the
+ // pairwise distance matrices -> the upper half without the diagonal elements
uint n_off_diagonal = (len*len-len)/2;
+ // store that information in a linear layout for each structure
std::vector<std::vector<Real> > dist_data(dmap->GetNumStructures());
+ // keep track of distances <= 15 for lDDT calculation. Indices stored in here
+ // relate to the linear representations in dist_data
std::vector<std::vector<int> > below_15(dmap->GetNumStructures());
for(uint s_idx = 0; s_idx < nstruc; ++s_idx) {
- // the default value is simply a very large number
- // this will trigger a distance difference above any relevant threshold
+ // the default value is simply a very large number this will trigger a
+ // distance difference above any relevant threshold if not set
dist_data[s_idx].assign(n_off_diagonal, 10000000.0);
}
-
+ // keep track of which two residues are involved for each element in dist_data
std::vector<std::pair<int,int> > off_diagonal_mapper(n_off_diagonal);
uint off_diag_idx = 0;
@@ -307,9 +314,8 @@ MeanlDDTPtr CreateMeanlDDTHA(const DistanceMapPtr dmap) {
for (uint j_res = i_res + 1; j_res < len; ++j_res, ++off_diag_idx) {
off_diagonal_mapper[off_diag_idx] = std::make_pair(i_res, j_res);
const Distances& di = dmap->GetDistances(i_res, j_res);
- const uint size = di.GetDataSize();
- for (uint k = 0; k < size; ++k) {
- const std::pair<Real, int> ret = di.GetDataElement(k);
+ for (uint k = 0; k < di.GetDataSize(); ++k) {
+ const std::pair<Real, int>& ret = di.GetDataElement(k);
dist_data[ret.second-1][off_diag_idx] = ret.first;
if(ret.first <= 15.0) {
below_15[ret.second-1].push_back(off_diag_idx);
@@ -318,27 +324,26 @@ MeanlDDTPtr CreateMeanlDDTHA(const DistanceMapPtr dmap) {
}
}
- std::vector<std::vector<Real> > avg_lddt_values(nstruc);
- std::vector<std::vector<int> > avg_lddt_counts(nstruc);
-
+ std::vector<std::vector<Real> > values(nstruc);
+ std::vector<std::vector<int> > counts(nstruc);
for(uint i = 0; i < nstruc; ++i) {
- avg_lddt_values[i].assign(len, 0);
- avg_lddt_counts[i].assign(len, 0);
+ values[i].assign(len, 0);
+ counts[i].assign(len, 0);
}
std::vector<Real> lddt_i, lddt_j;
for(uint i = 0; i < nstruc; ++i) {
for(uint j = i+1; j < nstruc; ++j) {
- FilllDDTValues(len, dist_data[i], dist_data[j], below_15[i], below_15[j],
+ FilllDDTValues(dist_data[i], dist_data[j], below_15[i], below_15[j],
off_diagonal_mapper, lddt_i, lddt_j);
for(uint k = 0; k < len; ++k) {
if(!std::isnan(lddt_i[k])) {
- avg_lddt_values[i][k] += lddt_i[k];
- avg_lddt_counts[i][k] += 1;
+ values[i][k] += lddt_i[k];
+ counts[i][k] += 1;
}
if(!std::isnan(lddt_j[k])) {
- avg_lddt_values[j][k] += lddt_j[k];
- avg_lddt_counts[j][k] += 1;
+ values[j][k] += lddt_j[k];
+ counts[j][k] += 1;
}
}
}
@@ -347,9 +352,9 @@ MeanlDDTPtr CreateMeanlDDTHA(const DistanceMapPtr dmap) {
MeanlDDTPtr return_ptr(new MeanlDDT(len, nstruc));
for(uint struc_idx = 0; struc_idx < nstruc; ++struc_idx) {
for(uint res_idx = 0; res_idx < len; ++res_idx) {
- if(avg_lddt_counts[struc_idx][res_idx] > 0) {
+ if(counts[struc_idx][res_idx] > 0) {
return_ptr->Set(res_idx, struc_idx,
- avg_lddt_values[struc_idx][res_idx]/avg_lddt_counts[struc_idx][res_idx]);
+ values[struc_idx][res_idx]/counts[struc_idx][res_idx]);
}
}
}