edia fix, missing code from check-in

git-svn-id: svn+ssh://gitlab/srv/svn-repos/pdb-redo/trunk@264 a1961a4f-ab94-4bcc-80e8-33b5a54de466

include/cif++/BondMap.h

@@ -17,10 +17,17 @@ class BondMap
 	BondMap(const BondMap&) = delete;
 	BondMap(const BondMap&) = delete;
 	BondMap& operator=(const BondMap&) = delete;
 	BondMap& operator=(const BondMap&) = delete;
 
 
-	bool operator()(const Atom& a, const Atom& b) const;
+	bool operator()(const Atom& a, const Atom& b) const
+	{
+		return isBonded(index.at(a.id()), index.at(b.id()));
+	}
+
+	bool is1_4(const Atom& a, const Atom& b) const;
 	
 	
   private:
   private:
 
 
+	bool isBonded(size_t ai, size_t bi) const;
+
 	size_t dim;
 	size_t dim;
 	std::vector<bool> bond;
 	std::vector<bool> bond;
 	std::unordered_map<std::string,size_t> index;
 	std::unordered_map<std::string,size_t> index;

include/cif++/Structure.h

@@ -133,6 +133,10 @@ class Atom
 	void calculateRadius(float resHigh, float resLow, float perc);
 	void calculateRadius(float resHigh, float resLow, float perc);
 	float radius() const;
 	float radius() const;
 
 
+
+	// the energy-type field
+	std::string energyType() const;
+
   private:
   private:
  	struct AtomImpl*			mImpl;
  	struct AtomImpl*			mImpl;
 };
 };

src/BondMap.cpp

@@ -199,7 +199,32 @@ BondMap::BondMap(const Structure& p)
 	}
 	}
 }
 }
 
 
-bool BondMap::operator()(const Atom& a, const Atom& b) const
+//bool BondMap::operator()(const Atom& a, const Atom& b) const
+//{
+//	size_t ixa = index.at(a.id());
+//	size_t ixb = index.at(b.id());
+//	
+//	if (ixb < ixa)
+//		swap(ixa, ixb);
+//	
+//	size_t ix = ixb + ixa * dim - ixa * (ixa + 1) / 2;
+//	
+//	assert(ix < bond.size());
+//	return bond[ix];
+//}
+
+bool BondMap::isBonded(size_t ixa, size_t ixb) const
+{
+	if (ixa > ixb)
+		swap(ixa, ixb);
+	
+	size_t ix = ixb + ixa * dim - ixa * (ixa + 1) / 2;
+	
+	assert(ix < bond.size());
+	return bond[ix];
+}
+
+bool BondMap::is1_4(const Atom& a, const Atom& b) const
 {
 {
 	size_t ixa = index.at(a.id());
 	size_t ixa = index.at(a.id());
 	size_t ixb = index.at(b.id());
 	size_t ixb = index.at(b.id());
@@ -207,10 +232,23 @@ bool BondMap::operator()(const Atom& a, const Atom& b) const
 	if (ixb < ixa)
 	if (ixb < ixa)
 		swap(ixa, ixb);
 		swap(ixa, ixb);
 	
 	
-	size_t ix = ixb + ixa * dim - ixa * (ixa + 1) / 2;
+	bool result = false;
 	
 	
-	assert(ix < bond.size());
-	return bond[ix];
+	for (size_t ia = 0; result == false and ia + 1 < dim; ++ia)
+	{
+		if (ia == ixa or ia == ixb)
+			continue;
+		
+		for (size_t ib = ia + 1; result == false and ib < dim; ++ib)
+		{
+			if (ib == ixa or ib == ixb)
+				continue;
+			
+			result = isBonded(ixa, ia) and isBonded(ia, ib) and isBonded(ib, ixb);
+		}
+	}
+	
+	return result;
 }
 }
 
 
 }
 }