restraints/minimizer fixes

git-svn-id: svn+ssh://gitlab/srv/svn-repos/pdb-redo/trunk@286 a1961a4f-ab94-4bcc-80e8-33b5a54de466

include/cif++/DistanceMap.h

@@ -19,7 +19,7 @@ class DistanceMap
 	DistanceMap(const Structure& p, const clipper::Spacegroup& spacegroup, const clipper::Cell& cell);
 	DistanceMap(const Structure& p, const clipper::Spacegroup& spacegroup, const clipper::Cell& cell);
 
 
 	// simplified version for subsets of atoms (used in refining e.g.)	
 	// simplified version for subsets of atoms (used in refining e.g.)	
-	DistanceMap(const std::vector<Atom>& atoms);
+	DistanceMap(const Structure& p, const std::vector<Atom>& atoms);
 	
 	
 	DistanceMap(const DistanceMap&) = delete;
 	DistanceMap(const DistanceMap&) = delete;
 	DistanceMap& operator=(const DistanceMap&) = delete;
 	DistanceMap& operator=(const DistanceMap&) = delete;
@@ -29,6 +29,7 @@ class DistanceMap
 
 
   private:
   private:
 
 
+	const Structure& structure;
 	size_t dim;
 	size_t dim;
 	std::unordered_map<std::string,size_t> index;
 	std::unordered_map<std::string,size_t> index;
 	
 	

include/cif++/Structure.h

@@ -83,7 +83,6 @@ class Atom
   public:
   public:
 //	Atom(const structure& s, const std::string& id);
 //	Atom(const structure& s, const std::string& id);
 	Atom(struct AtomImpl* impl);
 	Atom(struct AtomImpl* impl);
-	Atom(const File& f, const std::string& id);
 	Atom(const Atom& rhs);
 	Atom(const Atom& rhs);
 
 
 	~Atom();
 	~Atom();

src/DistanceMap.cpp

@@ -63,7 +63,7 @@ inline clipper::Coord_orth toCell(clipper::Coord_orth p, const clipper::Cell& ce
 }
 }
 
 
 DistanceMap::DistanceMap(const Structure& p, const clipper::Spacegroup& spacegroup, const clipper::Cell& cell)
 DistanceMap::DistanceMap(const Structure& p, const clipper::Spacegroup& spacegroup, const clipper::Cell& cell)
-	: dim(0)
+	: structure(p), dim(0)
 {
 {
 	const float kMaxDistance = 5, kMaxDistanceSQ = kMaxDistance * kMaxDistance;
 	const float kMaxDistance = 5, kMaxDistanceSQ = kMaxDistance * kMaxDistance;
 	
 	
@@ -165,8 +165,8 @@ DistanceMap::DistanceMap(const Structure& p, const clipper::Spacegroup& spacegro
 	t.join_all();
 	t.join_all();
 }
 }
 
 
-DistanceMap::DistanceMap(const vector<Atom>& atoms)
-	: dim(0)
+DistanceMap::DistanceMap(const Structure& p, const vector<Atom>& atoms)
+	: structure(p), dim(0)
 {
 {
 	dim = atoms.size();
 	dim = atoms.size();
 	
 	
@@ -225,7 +225,6 @@ float DistanceMap::operator()(const Atom& a, const Atom& b) const
 vector<Atom> DistanceMap::near(const Atom& a, float maxDistance) const
 vector<Atom> DistanceMap::near(const Atom& a, float maxDistance) const
 {
 {
 	vector<Atom> result;
 	vector<Atom> result;
-	const File& f = a.getFile();
 	
 	
 	size_t ixa;
 	size_t ixa;
 	try
 	try
@@ -250,7 +249,7 @@ vector<Atom> DistanceMap::near(const Atom& a, float maxDistance) const
 				dist.find(make_tuple(ixb, ixa));
 				dist.find(make_tuple(ixb, ixa));
 		
 		
 		if (ii != dist.end() and ii->second <= maxDistance)
 		if (ii != dist.end() and ii->second <= maxDistance)
-			result.emplace_back(f, i.first);
+			result.push_back(structure.getAtomById(i.first));
 	}
 	}
 	
 	
 	return result;
 	return result;

src/Structure.cpp

@@ -316,11 +316,11 @@ struct AtomImpl
 	map<string,string>	mCachedProperties;
 	map<string,string>	mCachedProperties;
 };
 };
 
 
-Atom::Atom(const File& f, const string& id)
-	: mImpl(new AtomImpl(f, id))
-{
-}
-
+//Atom::Atom(const File& f, const string& id)
+//	: mImpl(new AtomImpl(f, id))
+//{
+//}
+//
 Atom::Atom(AtomImpl* impl)
 Atom::Atom(AtomImpl* impl)
 	: mImpl(impl)
 	: mImpl(impl)
 {
 {
@@ -441,6 +441,11 @@ string Atom::authAsymId() const
 	return property<string>("auth_asym_id");
 	return property<string>("auth_asym_id");
 }
 }
 
 
+string Atom::authAtomId() const
+{
+	return property<string>("auth_atom_id");
+}
+
 string Atom::authCompId() const
 string Atom::authCompId() const
 {
 {
 	return property<string>("auth_comp_id");
 	return property<string>("auth_comp_id");