added rama-angles application

git-svn-id: svn+ssh://gitlab/srv/svn-repos/pdb-redo/trunk@339 a1961a4f-ab94-4bcc-80e8-33b5a54de466

include/cif++/Structure.h

@@ -173,12 +173,13 @@ typedef std::vector<Atom> AtomView;
 class Residue
 {
   public:
-	Residue();
-	Residue(const Residue& rhs);
-	Residue& operator=(const Residue& rhs);
+	Residue() = default;
+	Residue(const Residue& rhs) = default;
+	Residue& operator=(const Residue& rhs) = default;
 
 	Residue(const Structure& structure)
 		: mStructure(&structure) {}
+
 	Residue(const Structure& structure, const std::string& compoundID,
 		const std::string& asymID, int seqID = 0,
 		const std::string& altID = "")
@@ -195,6 +196,9 @@ class Residue
 	int					seqID() const		{ return mSeqID; }
 	const std::string&	altID() const		{ return mAltID; }
 	
+	int					authSeqID() const;
+	std::string			authInsCode() const;
+	
 	// return a human readable PDB-like auth id (chain+seqnr+iCode)
 	std::string			authID() const;
 
@@ -212,9 +216,9 @@ class Residue
 
   protected:
 
-	const Structure* mStructure;
+	const Structure* mStructure = nullptr;
 	std::string	mCompoundID, mAsymID, mAltID;
-	int mSeqID;
+	int mSeqID = 0;
 	mutable AtomView mAtoms;
 };
 
@@ -238,6 +242,8 @@ class Monomer : public Residue
 	float psi() const;
 	float alpha() const;
 	float kappa() const;
+	
+	bool isCis() const;
 
 	Atom CAlpha() const		{ return atomByID("CA"); }
 	Atom C() const			{ return atomByID("C"); }
@@ -265,8 +271,8 @@ class Polymer
   public:
 	Polymer(const Structure& s, const std::string& asymID);
 	Polymer(const Structure& s, const std::string& entityID, const std::string& asymID);
-	Polymer(const Polymer&);
-	Polymer& operator=(const Polymer&);
+	Polymer(const Polymer&) = default;
+	Polymer& operator=(const Polymer&) = default;
 	
 	struct iterator : public std::iterator<std::random_access_iterator_tag, Monomer>
 	{
@@ -322,6 +328,8 @@ class Polymer
 	std::string asymID() const		{ return mAsymID; }
 	std::string entityID() const	{ return mEntityID; }
 	
+	std::string chainID() const;
+	
 	int Distance(const Monomer& a, const Monomer& b) const;
 
   private:

src/Structure.cpp

@@ -587,31 +587,40 @@ float Atom::radius() const
 // --------------------------------------------------------------------
 // residue
 
-Residue::Residue()
-	: mStructure(nullptr), mSeqID(0)
+string Residue::authInsCode() const
 {
-}
+	assert(mStructure);
 
-Residue::Residue(const Residue& rhs)
-	: mStructure(rhs.mStructure)
-	, mCompoundID(rhs.mCompoundID), mAsymID(rhs.mAsymID), mAltID(rhs.mAltID), mSeqID(rhs.mSeqID)
-{
+	string result;
+	
+	try
+	{
+		tie(ignore, ignore, result) = mStructure->MapLabelToAuth(mAsymID, mSeqID);
+		
+		ba::trim(result);
+	}
+	catch (...)
+	{
+	}
+	
+	return result;
 }
 
-Residue& Residue::operator=(const Residue& rhs)
+int Residue::authSeqID() const
 {
-	if (this != &rhs)
+	assert(mStructure);
+
+	int result = 0;
+	
+	try
+	{
+		tie(ignore, result, ignore) = mStructure->MapLabelToAuth(mAsymID, mSeqID);
+	}
+	catch (...)
 	{
-		mStructure = rhs.mStructure;
-		mCompoundID = rhs.mCompoundID;
-		mAsymID = rhs.mAsymID;
-		mSeqID = rhs.mSeqID;
-		mAltID = rhs.mAltID;
-		
-		mAtoms = rhs.mAtoms;
 	}
 	
-	return *this;
+	return result;
 }
 
 const Compound& Residue::compound() const
@@ -844,6 +853,20 @@ float Monomer::kappa() const
 	return result;
 }
 
+bool Monomer::isCis() const
+{
+	bool result = false;
+	
+	if (mIndex + 1 < mPolymer->size())
+	{
+		Monomer next = mPolymer->operator[](mIndex + 1);
+		
+		result = Monomer::isCis(*this, next);
+	}
+	
+	return result;
+}
+
 bool Monomer::areBonded(const Monomer& a, const Monomer& b, float errorMargin)
 {
 	bool result = false;
@@ -928,18 +951,6 @@ Polymer::iterator::iterator(const iterator& rhs)
 {
 }
 
-Polymer::iterator& Polymer::iterator::operator=(const iterator& rhs)
-{
-	if (this != &rhs)
-	{
-		mPolymer = rhs.mPolymer;
-		mIndex = rhs.mIndex;
-		mCurrent = rhs.mCurrent;
-	}
-	
-	return *this;
-}
-
 Polymer::iterator& Polymer::iterator::operator++()
 {
 	auto& polySeq = mPolymer->mPolySeq;
@@ -960,12 +971,6 @@ Polymer::iterator& Polymer::iterator::operator++()
 	return *this;
 }
 
-Polymer::Polymer(const Polymer& rhs)
-	: mStructure(rhs.mStructure), mEntityID(rhs.mEntityID), mAsymID(rhs.mAsymID), mPolySeq(rhs.mPolySeq)
-{
-	
-}
-
 Polymer::Polymer(const Structure& s, const string& asymID)
 	: mStructure(const_cast<Structure*>(&s)), mAsymID(asymID)
 	, mPolySeq(s.category("pdbx_poly_seq_scheme").find(cif::Key("asym_id") == mAsymID))
@@ -995,6 +1000,11 @@ Polymer::iterator Polymer::end() const
 	return iterator(*this, mPolySeq.size());
 }
 
+string Polymer::chainID() const
+{
+	return mPolySeq.front()["pdb_strand_id"].as<string>();
+}
+
 Monomer Polymer::getBySeqID(int seqID) const
 {
 	for (auto m: *this)