From 6674be51507be889ccbf4d87047816a2535a7300 Mon Sep 17 00:00:00 2001
From: Valerio Mariani <vmariani@localhost.localdomain>
Date: Wed, 20 Jun 2012 20:53:46 +0200
Subject: [PATCH] Fixed problem with merged distance lists
---
modules/mol/alg/src/local_dist_diff_test.cc | 27 ++++++++++++++++++---
modules/mol/alg/src/local_dist_diff_test.hh | 3 +++
2 files changed, 27 insertions(+), 3 deletions(-)
diff --git a/modules/mol/alg/src/local_dist_diff_test.cc b/modules/mol/alg/src/local_dist_diff_test.cc
index e495276da..06ca053ad 100644
--- a/modules/mol/alg/src/local_dist_diff_test.cc
+++ b/modules/mol/alg/src/local_dist_diff_test.cc
@@ -7,6 +7,13 @@ namespace ost { namespace mol { namespace alg {
namespace {
+bool is_distance_invalid(const std::pair<Real,Real>& value)
+{
+ if (value.first == -1.0 && value.second == -1) return true;
+ return false;
+}
+
+
// helper function
String swapped_name(const String& name)
{
@@ -299,10 +306,10 @@ void merge_distance_lists(GlobalRDMap& ref_dist_map, const GlobalRDMap& new_dist
// 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;
UniqueAtomIdentifier second_atom_to_find = ref_rd.second;
- // if both atoms are there, remove the distance from the ref_dist_map,
+ // if both atoms are there, remove the distance from the ref_dist_map (set it to invalid)
if ((ref.FindAtom(first_atom_to_find.GetChainName(),first_atom_to_find.GetResNum(),first_atom_to_find.GetAtomName()).IsValid() &&
ref.FindAtom(second_atom_to_find.GetChainName(),second_atom_to_find.GetResNum(),second_atom_to_find.GetAtomName()).IsValid()) ) {
- ref_dist_map_it->second.erase(ref_res_map_it);
+ ref_res_map_it->second = std::make_pair<Real,Real>(-1.0,-1.0);
}
}
}
@@ -336,11 +343,25 @@ void merge_distance_lists(GlobalRDMap& ref_dist_map, const GlobalRDMap& new_dist
if (find_ref_res_ci == ref_dist_map.end()) {
ref_dist_map[new_resnum] = new_dist_map_it->second;
}
- }
+ }
+ // finally, clean up the merged list by removing invalid distances
+ for (GlobalRDMap::const_iterator ref_dist_map_it = ref_dist_map.begin();ref_dist_map_it!=ref_dist_map.end();++ref_dist_map_it) {
+ ResidueRDMap new_residue_map;
+ for (ResidueRDMap::const_iterator res_ref_list_it = ref_dist_map_it->second.begin();res_ref_list_it!=ref_dist_map_it->second.end();++res_ref_list_it) {
+ if (is_distance_invalid(res_ref_list_it->second)) continue;
+ new_residue_map[res_ref_list_it->first]=res_ref_list_it->second;
+ }
+ ref_dist_map[ref_dist_map_it->first]=new_residue_map;
+ }
}
}
+void UniqueAtomIdentifier::Print() const
+{
+ std::cout << chain_ << " " << residue_ << " " << residue_name_ << " " << atom_ << std::endl;
+}
+
// helper function
bool IsStandardResidue(String rn)
{
diff --git a/modules/mol/alg/src/local_dist_diff_test.hh b/modules/mol/alg/src/local_dist_diff_test.hh
index ed6e10bad..6a2062fb4 100644
--- a/modules/mol/alg/src/local_dist_diff_test.hh
+++ b/modules/mol/alg/src/local_dist_diff_test.hh
@@ -49,6 +49,9 @@ public:
/// \brief Returns the name of the atom, as a String
String GetAtomName() const { return atom_; }
+
+ /// \brief Prints the UniqueAtomIdentifier information to standard output
+ void Print() const;
// required because UniqueAtomIdentifier is used as a key for a std::map
bool operator==(const UniqueAtomIdentifier& rhs) const {
--
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