een beetje multithread code en een start met LINK support

git-svn-id: svn+ssh://gitlab/srv/svn-repos/pdb-redo/trunk@334 a1961a4f-ab94-4bcc-80e8-33b5a54de466

include/cif++/BondMap.h

@@ -30,6 +30,9 @@ class BondMap
 		return bond_1_4.count(key(ixa, ixb));
 	}
 	
+	// links coming from the struct_conn records:
+	std::vector<std::string> linked(const Atom& a) const;
+	
   private:
 
 	bool isBonded(uint32 ai, uint32 bi) const
@@ -55,6 +58,8 @@ class BondMap
 	uint32 dim;
 	std::unordered_map<std::string,uint32> index;
 	std::set<uint64> bond, bond_1_4;
+
+	std::map<std::string,std::set<std::string>> link;
 };
 
 }

src/BondMap.cpp

@@ -35,6 +35,14 @@ BondMap::BondMap(const Structure& p)
 		bond.insert(key(ixa, ixb));
 	};
 
+	auto linkAtoms = [this,&bindAtoms](const string& a, const string& b)
+	{
+		bindAtoms(a, b);
+
+		link[a].insert(b);
+		link[b].insert(a);
+	};
+
 	cif::Datablock& db = p.getFile().data();
 
 	// collect all compounds first
@@ -111,7 +119,7 @@ BondMap::BondMap(const Structure& p)
 			cerr << "Unexpected number (" << b.size() << ") of atoms for link with asym_id " << asym2 << " seq_id " << seqId2 << " atom_id " << atomId2 << endl;
 		
 		if (not (a.empty() or b.empty()))
-			bindAtoms(a.front()["id"].as<string>(), b.front()["id"].as<string>());
+			linkAtoms(a.front()["id"].as<string>(), b.front()["id"].as<string>());
 	}
 
 	// then link all atoms in the compounds
@@ -250,4 +258,17 @@ BondMap::BondMap(const Structure& p)
 //cout << "Afmeting b1_4: " << bond_1_4.size() << endl;
 }
 
+vector<string> BondMap::linked(const Atom& a) const
+{
+	auto i = link.find(a.id());
+	
+	vector<string> result;
+	
+	if (i != link.end())
+		result = vector<string>(i->second.begin(), i->second.end());
+
+	return result;
+}
+
+
 }