diff --git a/modules/mol/alg/src/local_dist_diff_test.cc b/modules/mol/alg/src/local_dist_diff_test.cc
index fdb1bc0a3e943c716bb82b21083465992f3b1b2f..e495276da8f2add15ea1d57a89fec7ea21195ff6 100644
--- a/modules/mol/alg/src/local_dist_diff_test.cc
+++ b/modules/mol/alg/src/local_dist_diff_test.cc
@@ -54,27 +54,10 @@ bool swappable(const String& rname, const String& aname)
}
// helper function
-std::pair<bool,Real> within_tolerance(Real mdl_dist, std::pair<Real,Real>& values, Real tol)
+bool within_tolerance(Real mdl_dist, const std::pair<Real,Real>& values, Real tol)
{
- Real min = values.first;
- Real max = values.second;
- bool within_tol = false;
- Real difference = 0;
- if (mdl_dist>=min && mdl_dist <=max) {
- within_tol=true;
- } else if (mdl_dist < min && std::abs(min-mdl_dist) < tol) {
- within_tol = true;
- } else if (mdl_dist > max && std::abs(mdl_dist-max) < tol) {
- within_tol = true;
- }
- if (within_tol == false) {
- if (mdl_dist > max) {
- difference = mdl_dist-(max+tol);
- } else {
- difference = mdl_dist-(min-tol);
- }
- }
- return std::make_pair<bool,Real>(within_tol,difference);
+
+ return (values.first-tol)<=mdl_dist && (values.second+tol)>=mdl_dist;
}
// helper function
@@ -86,10 +69,10 @@ std::pair<long int, long int> calc_overlap1(const ResidueRDMap& res_distance_lis
std::pair<long int, long int> overlap(0, 0);
ResidueView mdl_res=mdl_chain.FindResidue(rnum);
for (ResidueRDMap::const_iterator ai=res_distance_list.begin(); ai!=res_distance_list.end(); ++ai) {
- UAtomIdentifiers uais = ai->first;
- std::pair <Real,Real> values = ai->second;
- UniqueAtomIdentifier first_atom=uais.first;
- UniqueAtomIdentifier second_atom=uais.second;
+ const UAtomIdentifiers& uais = ai->first;
+ const std::pair <Real,Real>& values = ai->second;
+ const UniqueAtomIdentifier& first_atom=uais.first;
+ const UniqueAtomIdentifier& second_atom=uais.second;
String name=swap ? swapped_name(first_atom.GetAtomName()) : first_atom.GetAtomName();
AtomView av1=mdl_res ? mdl_res.FindAtom(name) : AtomView();
@@ -109,11 +92,16 @@ std::pair<long int, long int> calc_overlap1(const ResidueRDMap& res_distance_lis
AtomView av2=mdl_chain.FindAtom(second_atom.GetResNum(),second_atom.GetAtomName());
overlap.second+=tol_list.size();
+ int rindex1=0, rindex2=0;
if (av1) {
- overlap_list[av1.GetResidue().GetIndex()].second+=tol_list.size();
+ rindex1=av1.GetResidue().GetIndex();
+ overlap_list[rindex1].second+=tol_list.size();
}
+
if (av2) {
- overlap_list[av2.GetResidue().GetIndex()].second+=tol_list.size();
+ rindex2=av2.GetResidue().GetIndex();
+ overlap_list[rindex2].second+=tol_list.size();
+
}
if (!(av1 && av2)) {
continue;
@@ -122,15 +110,15 @@ std::pair<long int, long int> calc_overlap1(const ResidueRDMap& res_distance_lis
std::vector<Real>::const_reverse_iterator rend_it=tol_list.rend();
for (std::vector<Real>::const_reverse_iterator tol_list_it=tol_list.rbegin();tol_list_it!=rend_it;++tol_list_it) {
Real tol = * tol_list_it;
- if (within_tolerance(mdl_dist,values,tol).first) {
+ if (within_tolerance(mdl_dist,values,tol)) {
if (log) {
LOG_VERBOSE("lddt:" << " " << av1.GetResidue().GetChain() << " " << av1.GetResidue().GetName() << " " << av1.GetResidue().GetNumber() << " " << av1.GetName()
<< " " << av2.GetResidue().GetChain() << " " << av2.GetResidue().GetName() << " " << av2.GetResidue().GetNumber() << " " << av2.GetName() << " "
<< mdl_dist << " " << values.first << " " << values.second << " " << tol << " " << "PASS")
}
overlap.first+=1;
- overlap_list[av1.GetResidue().GetIndex()].first+=1;
- overlap_list[av2.GetResidue().GetIndex()].first+=1;
+ overlap_list[rindex1].first+=1;
+ overlap_list[rindex2].first+=1;
} else {
if (log) {
LOG_VERBOSE("lddt:" << " " << av1.GetResidue().GetChain() << " " << av1.GetResidue().GetName() << " " << av1.GetResidue().GetNumber() << " " << av1.GetName()
@@ -249,15 +237,16 @@ void check_and_swap(const GlobalRDMap& glob_dist_list, const EntityView& mdl, st
if (!(rname=="GLU" || rname=="ASP" || rname=="VAL" || rname=="TYR" || rname=="PHE" || rname=="LYS" || rname=="ARG")) {
continue;
}
- std::pair<Real, Real> ov1=calc_overlap1(i->second, rnum,mdl_chain, sequence_separation,
+ std::pair<long int, long int> ov1=calc_overlap1(i->second, rnum,mdl_chain, sequence_separation,
cutoff_list, true,
false, overlap_list,false);
- std::pair<Real, Real> ov2=calc_overlap1(i->second, rnum, mdl_chain, sequence_separation,
+ std::pair<long int, long int> ov2=calc_overlap1(i->second, rnum, mdl_chain, sequence_separation,
cutoff_list, true,
true, overlap_list,false);
- if (ov1.first/ov1.second<ov2.first/ov2.second) {
+ if (static_cast<Real>(ov1.first)/ov1.second<
+ static_cast<Real>(ov2.first)/ov2.second) {
AtomViewList atoms=mdl_res.GetAtomList();
for (AtomViewList::iterator j=atoms.begin(), e2=atoms.end(); j!=e2; ++j) {
if (swappable(rname, j->GetName())) {
@@ -274,13 +263,7 @@ void update_existence_map (ExistenceMap& ex_map, const EntityView& ev, int ref_c
AtomViewList ev_atom=ev.GetAtomList();
for (AtomViewList::iterator ev_atom_it=ev_atom.begin(); ev_atom_it!=ev_atom.end();++ev_atom_it) {
UniqueAtomIdentifier uai (ev_atom_it->GetResidue().GetChain().GetName(),ev_atom_it->GetResidue().GetNumber(),ev_atom_it->GetResidue().GetName(),ev_atom_it->GetName());
- ExistenceMap::const_iterator find_uai_ci = ex_map.find(uai);
- int uai_value = 0;
- if (find_uai_ci!=ex_map.end()) {
- uai_value=find_uai_ci->second;
- }
- uai_value |= 1 << (ref_counter);
- ex_map[uai]=uai_value;
+ ex_map[uai] |=1 << ref_counter;
}
}
@@ -288,11 +271,7 @@ void update_existence_map (ExistenceMap& ex_map, const EntityView& ev, int ref_c
int in_existence_map(const ExistenceMap& ex_map, const UniqueAtomIdentifier& uai)
{
ExistenceMap::const_iterator find_uai_ci = ex_map.find(uai);
- int return_value = 0;
- if (find_uai_ci!=ex_map.end()) {
- return_value=find_uai_ci->second;
- }
- return return_value;
+ return find_uai_ci!=ex_map.end() ? find_uai_ci->second : 0;
}
// merges distance lists from multiple reference structures. The login is described in the code
@@ -306,17 +285,16 @@ void merge_distance_lists(GlobalRDMap& ref_dist_map, const GlobalRDMap& new_dist
if (find_new_res_ci != new_dist_map.end()) {
//iterate over the the reference distances in the ResidueDistanceMap
for (ResidueRDMap::iterator ref_res_map_it = ref_dist_map_it->second.begin(); ref_res_map_it!=ref_dist_map_it->second.end();++ref_res_map_it) {
- UAtomIdentifiers ref_rd = ref_res_map_it->first;
- std::pair<Real,Real> ref_minmax = ref_res_map_it->second;
+ const UAtomIdentifiers& ref_rd = ref_res_map_it->first;
+ std::pair<Real,Real>& ref_minmax = ref_res_map_it->second;
ResidueRDMap::const_iterator find_new_rd_ci = find_new_res_ci->second.find(ref_rd);
// if you find the distance in the residue new, udate min and max
if (find_new_rd_ci != find_new_res_ci->second.end()) {
- std::pair <Real,Real> new_minmax = find_new_rd_ci->second;
- Real min = ref_minmax.first;
- Real max = ref_minmax.second;
- if (new_minmax.first < min) min = new_minmax.first;
- if (new_minmax.second > max) max = new_minmax.second;
- ref_dist_map_it->second[ref_rd] = std::make_pair<Real,Real>(min,max);
+ if (find_new_rd_ci->second.first < ref_minmax.first) {
+ ref_minmax.first=find_new_rd_ci->second.first;
+ } else if (find_new_rd_ci->second.second > ref_minmax.second) {
+ ref_minmax.second=find_new_rd_ci->second.second;
+ }
} else {
// if you don't find it in the residue new, check that it is not missing because it is too long
UniqueAtomIdentifier first_atom_to_find = ref_rd.first;
@@ -393,47 +371,6 @@ bool IsStandardResidue(String rn)
return false;
}
-// required because UniqueAtomIdentifier is used as a key in a std::map
-bool UniqueAtomIdentifier::operator==(const UniqueAtomIdentifier& rhs) const
-{
- if (chain_ == rhs.GetChainName() &&
- residue_ == rhs.GetResNum() &&
- residue_name_ == rhs.GetResidueName() &&
- atom_ == rhs.GetAtomName() ) {
- return true;
- }
- return false;
-}
-
-// required because UniqueAtomIdentifier is used as a key in a std::map
-bool UniqueAtomIdentifier::operator<(const UniqueAtomIdentifier& rhs) const
-{
- if (chain_ < rhs.GetChainName()) {
- return true;
- } else if (chain_ > rhs.GetChainName()) {
- return false;
- } else {
- if (residue_ < rhs.GetResNum()) {
- return true;
- } else if (residue_ > rhs.GetResNum()) {
- return false;
- } else {
- if (residue_name_ < rhs.GetResidueName()) {
- return true;
- } else if (residue_name_ > rhs.GetResidueName()) {
- return false;
- } else {
- if (atom_ < rhs.GetAtomName()) {
- return true;
- } else if (atom_ > rhs.GetAtomName()) {
- return false;
- } else {
- return false;
- }
- }
- }
- }
-}
GlobalRDMap CreateDistanceList(const EntityView& ref,Real max_dist)
{
diff --git a/modules/mol/alg/src/local_dist_diff_test.hh b/modules/mol/alg/src/local_dist_diff_test.hh
index 5b860def3bba5ee47c5c373a0a159ed0c4927f6e..e7c98b9ca840138caf7e34b06c73c4fa3a043168 100644
--- a/modules/mol/alg/src/local_dist_diff_test.hh
+++ b/modules/mol/alg/src/local_dist_diff_test.hh
@@ -51,11 +51,23 @@ public:
String GetAtomName() const { return atom_; }
// required because UniqueAtomIdentifier is used as a key for a std::map
- bool operator==(const UniqueAtomIdentifier& rhs) const;
+ bool operator==(const UniqueAtomIdentifier& rhs) const {
+ return chain_==rhs.chain_ && residue_==rhs.residue_ && atom_==rhs.atom_;
+ }
// required because UniqueAtomIdentifier is used as a key for a std::map
- bool operator<(const UniqueAtomIdentifier& rhs) const;
-
+ bool operator<(const UniqueAtomIdentifier& rhs) const {
+ int cc=chain_.compare(rhs.chain_);
+ if (cc) {
+ return cc<0;
+ }
+ if (residue_<rhs.residue_) {
+ return true;
+ } else if (residue_>rhs.residue_) {
+ return false;
+ }
+ return atom_.compare(rhs.atom_)<0;
+ }
private:
String chain_;