Changes for DSSP

include/cif++/Secondary.h

@@ -13,7 +13,9 @@ namespace mmcif
 class Structure;
 class Structure;
 class Monomer;
 class Monomer;
 
 
-extern const double
+struct Res;
+
+extern const float
 	kCouplingConstant, kMinHBondEnergy, kMaxHBondEnergy;
 	kCouplingConstant, kMinHBondEnergy, kMaxHBondEnergy;
 
 
 enum SecondaryStructureType : char
 enum SecondaryStructureType : char
@@ -28,6 +30,11 @@ enum SecondaryStructureType : char
 	ssBend			= 'S'
 	ssBend			= 'S'
 };
 };
 
 
+enum class Helix
+{
+	None, Start, End, StartAndEnd, Middle
+};
+
 //struct HBond
 //struct HBond
 //{
 //{
 //	std::string 				labelAsymID;
 //	std::string 				labelAsymID;
@@ -54,6 +61,27 @@ struct SecondaryStructure
 
 
 //void CalculateSecondaryStructure(Structure& s);
 //void CalculateSecondaryStructure(Structure& s);
 
 
+const size_t
+	kHistogramSize = 30;
+
+struct DSSP_Statistics
+{
+	uint32_t nrOfResidues, nrOfChains, nrOfSSBridges, nrOfIntraChainSSBridges, nrOfHBonds;
+	uint32_t nrOfHBondsInAntiparallelBridges, nrOfHBondsInParallelBridges;
+	uint32_t nrOfHBondsPerDistance[11] = {};
+	double accessibleSurface = 0;
+
+	uint32_t residuesPerAlphaHelixHistogram[kHistogramSize] = {};
+	uint32_t parallelBridgesPerLadderHistogram[kHistogramSize] = {};
+	uint32_t antiparallelBridgesPerLadderHistogram[kHistogramSize] = {};
+	uint32_t laddersPerSheetHistogram[kHistogramSize] = {};
+};
+
+enum class ChainBreak
+{
+	None, NewChain, Gap
+};
+
 class DSSP
 class DSSP
 {
 {
   public:
   public:
@@ -66,9 +94,92 @@ class DSSP
 	SecondaryStructureType operator()(const std::string& inAsymID, int inSeqID) const;
 	SecondaryStructureType operator()(const std::string& inAsymID, int inSeqID) const;
 	SecondaryStructureType operator()(const Monomer& m) const;
 	SecondaryStructureType operator()(const Monomer& m) const;
 	
 	
+	double accessibility(const std::string& inAsymID, int inSeqID) const;
+	double accessibility(const Monomer& m) const;
+
 	bool isAlphaHelixEndBeforeStart(const Monomer& m) const;
 	bool isAlphaHelixEndBeforeStart(const Monomer& m) const;
 	bool isAlphaHelixEndBeforeStart(const std::string& inAsymID, int inSeqID) const;
 	bool isAlphaHelixEndBeforeStart(const std::string& inAsymID, int inSeqID) const;
 
 
+	DSSP_Statistics GetStatistics() const;
+
+	class iterator;
+	using res_iter = typename std::vector<Res>::iterator;
+
+	class ResidueInfo
+	{
+	  public:
+		friend class iterator;
+
+		explicit operator bool() const		{ return not empty(); }
+		bool empty() const					{ return mImpl == nullptr; }
+
+		const Monomer& residue() const;
+
+		/// \brief return 0 if not a break, ' ' in case of a new chain and '*' in case of a broken chain
+		ChainBreak chainBreak() const;
+
+		/// \brief the internal number in DSSP
+		int nr() const;
+
+		SecondaryStructureType ss() const;
+		
+		int ssBridgeNr() const;
+
+		Helix helix(int stride) const;
+
+		bool bend() const;
+
+		double accessibility() const;
+
+		/// \brief returns resinfo, ladder and parallel
+		std::tuple<ResidueInfo,int,bool> bridgePartner(int i) const;
+
+		int sheet() const;
+
+		/// \brief return resinfo and the energy of the bond
+		std::tuple<ResidueInfo,double> acceptor(int i) const;
+		std::tuple<ResidueInfo,double> donor(int i) const;
+
+	  private:
+		ResidueInfo(Res* res);
+
+		Res* mImpl;
+	};
+
+	class iterator
+	{
+	  public:
+		using iterator_category = std::input_iterator_tag;
+		using value_type = ResidueInfo;
+		using difference_type = std::ptrdiff_t;
+		using pointer = value_type*;
+		using reference = value_type&;
+
+		iterator(const iterator& i);
+		iterator(res_iter cur);
+		iterator& operator=(const iterator& i);
+
+		reference operator*()		{ return mCurrent; }
+		pointer operator->()		{ return &mCurrent; }
+
+		iterator& operator++();
+		iterator operator++(int)
+		{
+			auto tmp(*this);
+			this->operator++();
+			return tmp;
+		}
+
+		bool operator==(const iterator& rhs) const		{ return mCurrent.mImpl == rhs.mCurrent.mImpl; }
+		bool operator!=(const iterator& rhs) const		{ return mCurrent.mImpl != rhs.mCurrent.mImpl; }
+
+	  private:
+		ResidueInfo	mCurrent;
+	};
+
+	iterator begin() const;
+	iterator end() const;
+
   private:
   private:
 	struct DSSPImpl* mImpl;
 	struct DSSPImpl* mImpl;
 };
 };

include/cif++/Structure.h

@@ -226,8 +226,6 @@ class Residue
 
 
 	friend class Polymer;
 	friend class Polymer;
 
 
-	void calculateCenterAndRadius();
-
 	const Structure* mStructure = nullptr;
 	const Structure* mStructure = nullptr;
 	std::string	mCompoundID, mAsymID;
 	std::string	mCompoundID, mAsymID;
 	int mSeqID = 0;
 	int mSeqID = 0;
@@ -258,6 +256,7 @@ class Monomer : public Residue
 	float psi() const;
 	float psi() const;
 	float alpha() const;
 	float alpha() const;
 	float kappa() const;
 	float kappa() const;
+	float tco() const;
 
 
     // torsion angles
     // torsion angles
     size_t nrOfChis() const;
     size_t nrOfChis() const;
@@ -265,6 +264,9 @@ class Monomer : public Residue
 	
 	
 	bool isCis() const;
 	bool isCis() const;
 
 
+	/// \brief Returns true if the four atoms C, CA, N and O are present
+	bool isComplete() const;
+
 	Atom CAlpha() const		{ return atomByID("CA"); }
 	Atom CAlpha() const		{ return atomByID("CA"); }
 	Atom C() const			{ return atomByID("C"); }
 	Atom C() const			{ return atomByID("C"); }
 	Atom N() const			{ return atomByID("N"); }
 	Atom N() const			{ return atomByID("N"); }

src/Structure.cpp

@@ -920,7 +920,6 @@ float Monomer::phi() const
 			cerr << ex.what() << endl;
 			cerr << ex.what() << endl;
 	}
 	}
 
 
-
 	return result;
 	return result;
 }
 }
 
 
@@ -952,7 +951,7 @@ float Monomer::alpha() const
 
 
 	try
 	try
 	{
 	{
-		if (mIndex > 1 and mIndex + 2 < mPolymer->size())
+		if (mIndex >= 1 and mIndex + 2 < mPolymer->size())
 		{
 		{
 			auto& prev = mPolymer->operator[](mIndex - 1);
 			auto& prev = mPolymer->operator[](mIndex - 1);
 			auto& next = mPolymer->operator[](mIndex + 1);
 			auto& next = mPolymer->operator[](mIndex + 1);
@@ -976,7 +975,7 @@ float Monomer::kappa() const
 	
 	
 	try
 	try
 	{
 	{
-		if (mIndex > 2 and mIndex + 2 < mPolymer->size())
+		if (mIndex >= 2 and mIndex + 2 < mPolymer->size())
 		{
 		{
 			auto& prevPrev = mPolymer->operator[](mIndex - 2);
 			auto& prevPrev = mPolymer->operator[](mIndex - 2);
 			auto& nextNext = mPolymer->operator[](mIndex + 2);
 			auto& nextNext = mPolymer->operator[](mIndex + 2);
@@ -999,6 +998,29 @@ float Monomer::kappa() const
 	return result;
 	return result;
 }
 }
 
 
+float Monomer::tco() const
+{
+	double result = 0.0;
+	
+	try
+	{
+		if (mIndex > 0)
+		{
+			auto& prev = mPolymer->operator[](mIndex - 1);
+			if (prev.mSeqID + 1 == mSeqID)
+				result = CosinusAngle(C().location(), O().location(), prev.C().location(), prev.O().location()); 
+		}
+	}
+	catch (const exception& ex)
+	{
+		if (cif::VERBOSE)
+			cerr << "When trying to calculate kappa for " << asymID() << ':' << seqID() << ": "
+				 << ex.what() << endl;
+	}
+
+	return result;
+}
+
 const map<string,vector<string>> kChiAtomsMap = {
 const map<string,vector<string>> kChiAtomsMap = {
    	{ "ASP", {"CG", "OD1"} },
    	{ "ASP", {"CG", "OD1"} },
 	{ "ASN", {"CG", "OD1"} },
 	{ "ASN", {"CG", "OD1"} },
@@ -1084,6 +1106,19 @@ bool Monomer::isCis() const
 	return result;
 	return result;
 }
 }
 
 
+bool Monomer::isComplete() const
+{
+	int seen = 0;
+	for (auto& a: mAtoms)
+	{
+		     if (a.labelAtomId() == "CA")		seen |= 1;
+		else if (a.labelAtomId() == "C")		seen |= 2;
+		else if (a.labelAtomId() == "N")		seen |= 4;
+		else if (a.labelAtomId() == "O")		seen |= 8;
+	}
+	return seen == 15;
+}
+
 float Monomer::chiralVolume() const
 float Monomer::chiralVolume() const
 {
 {
 	float result = 0;
 	float result = 0;