backup

git-svn-id: svn+ssh://gitlab/srv/svn-repos/pdb-redo/trunk@488 a1961a4f-ab94-4bcc-80e8-33b5a54de466

include/cif++/Point.h

@@ -260,6 +260,15 @@ inline PointF<F> CrossProduct(const PointF<F>& a, const PointF<F>& b)
 }
 }
 
 
 template<typename F>
 template<typename F>
+double Angle(const PointF<F>& p1, const PointF<F>& p2, const PointF<F>& p3)
+{
+	PointF<F> v1 = p1 - p2;
+	PointF<F> v2 = p3 - p2;
+	
+	return std::acos(DotProduct(v1, v2) / (v1.length() * v2.length())) * 180 / kPI;
+}
+
+template<typename F>
 double DihedralAngle(const PointF<F>& p1, const PointF<F>& p2, const PointF<F>& p3, const PointF<F>& p4)
 double DihedralAngle(const PointF<F>& p1, const PointF<F>& p2, const PointF<F>& p3, const PointF<F>& p4)
 {
 {
 	PointF<F> v12 = p1 - p2;	// vector from p2 to p1
 	PointF<F> v12 = p1 - p2;	// vector from p2 to p1

include/cif++/Structure.h

@@ -372,14 +372,14 @@ class Structure
 	const std::vector<Residue>& nonPolymers() const			{ return mNonPolymers; }
 	const std::vector<Residue>& nonPolymers() const			{ return mNonPolymers; }
 
 
 	Atom getAtomById(std::string id) const;
 	Atom getAtomById(std::string id) const;
-	Atom getAtomByLocation(Point pt, float maxDistance) const;
+	// Atom getAtomByLocation(Point pt, float maxDistance) const;
 	
 	
-	Atom getAtomForLabel(const std::string& atomId, const std::string& asymId,
+	Atom getAtomByLabel(const std::string& atomId, const std::string& asymId,
 		const std::string& compId, int seqId, const std::string& altId = "");
 		const std::string& compId, int seqId, const std::string& altId = "");
 	
 	
-	Atom getAtomForAuth(const std::string& atomId, const std::string& asymId,
-		const std::string& compId, int seqId, const std::string& altId = "",
-		const std::string& pdbxAuthInsCode = "");
+	// Atom getAtomByAuth(const std::string& atomId, const std::string& asymId,
+	// 	const std::string& compId, int seqId, const std::string& altId = "",
+	// 	const std::string& pdbxAuthInsCode = "");
 	
 	
 	// map between auth and label locations
 	// map between auth and label locations
 	
 	

src/Structure.cpp

@@ -361,6 +361,11 @@ struct AtomImpl
 		return d;
 		return d;
 	}
 	}
 
 
+	void swapAtomLabels(AtomImpl& b)
+	{
+		std::swap(mAtomID, b.mAtomID);
+	}
+
 	const File&			mFile;
 	const File&			mFile;
 	string				mId;
 	string				mId;
 	AtomType			mType;
 	AtomType			mType;
@@ -1527,6 +1532,23 @@ Atom Structure::getAtomById(string id) const
 	return mAtoms[*i];
 	return mAtoms[*i];
 }
 }
 
 
+Atom Structure::getAtomByLabel(const string& atomId, const string& asymId, const string& compId, int seqId, const string& altId)
+{
+	for (auto& a: mAtoms)
+	{
+		if (a.labelAtomId() == atomId and
+			a.labelAsymId() == asymId and
+			a.labelCompId() == compId and
+			a.labelSeqId() == seqId and
+			a.labelAltId() == altId)
+		{
+			return a;
+		}
+	}
+
+	throw out_of_range("Could not find atom with specified label");
+}
+
 File& Structure::getFile() const
 File& Structure::getFile() const
 {
 {
 	return mFile;
 	return mFile;
@@ -1835,6 +1857,8 @@ void Structure::swapAtoms(Atom& a1, Atom& a2)
 	auto l2 = r2.front()["label_atom_id"];
 	auto l2 = r2.front()["label_atom_id"];
 	l1.swap(l2);
 	l1.swap(l2);
 	
 	
+	a1.mImpl->swapAtomLabels(*a2.mImpl);
+
 	auto l3 = r1.front()["auth_atom_id"];
 	auto l3 = r1.front()["auth_atom_id"];
 	auto l4 = r2.front()["auth_atom_id"];
 	auto l4 = r2.front()["auth_atom_id"];
 	l3.swap(l4);
 	l3.swap(l4);

src/Symmetry.cpp

@@ -175,10 +175,10 @@ int32_t GetRotationalIndexNumber(int spacegroup, const clipper::RTop_frac& rt)
 	}
 	}
 
 
 	const size_t N = sizeof(kSymopNrTable) / sizeof(SymopDataBlock);
 	const size_t N = sizeof(kSymopNrTable) / sizeof(SymopDataBlock);
-	size_t L = 0, R = N - 1;
+	int32_t L = 0, R = static_cast<int32_t>(N - 1);
 	while (L <= R)
 	while (L <= R)
 	{
 	{
-		size_t i = (L + R) / 2;
+		int32_t i = (L + R) / 2;
 		if (kSymopNrTable[i].spacegroupNr < spacegroup)
 		if (kSymopNrTable[i].spacegroupNr < spacegroup)
 			L = i + 1;
 			L = i + 1;
 		else
 		else