WIP on trunk: 7c5bf010 calculate surface only when needed, added deuterium

include/cif++/AtomType.hpp

@@ -14,6 +14,7 @@ enum AtomType : uint8_t
 	Nn = 0,		// Unknown
 	Nn = 0,		// Unknown
 	
 	
 	H = 1,		// Hydro­gen
 	H = 1,		// Hydro­gen
+	D = 129,	// Deuterium
 	He = 2,		// He­lium
 	He = 2,		// He­lium
 
 
 	Li = 3,		// Lith­ium
 	Li = 3,		// Lith­ium

include/cif++/Secondary.hpp

@@ -91,7 +91,7 @@ enum class ChainBreak
 class DSSP
 class DSSP
 {
 {
   public:
   public:
-	DSSP(const Structure& s, int min_poly_proline_stretch_length);
+	DSSP(const Structure& s, int min_poly_proline_stretch_length, bool calculateSurfaceAccessibility);
 	~DSSP();
 	~DSSP();
 	
 	
 	DSSP(const DSSP&) = delete;
 	DSSP(const DSSP&) = delete;

src/AtomType.cpp

@@ -17,6 +17,7 @@ const AtomTypeInfo kKnownAtoms[] =
 {
 {
 	{ Nn,	"Unknown",			"Nn",	0,		false, {	kNA,	kNA,	kNA,	kNA,	kNA,	kNA,	kNA } },  //	0	Nn	 Unknown        
 	{ Nn,	"Unknown",			"Nn",	0,		false, {	kNA,	kNA,	kNA,	kNA,	kNA,	kNA,	kNA } },  //	0	Nn	 Unknown        
 	{ H,	"Hydrogen",			"H",	1.008,	false, {	53,		25,		37,		32,		kNA,	kNA,	120 } },  //	1	H	 Hydro­gen         
 	{ H,	"Hydrogen",			"H",	1.008,	false, {	53,		25,		37,		32,		kNA,	kNA,	120 } },  //	1	H	 Hydro­gen         
+	{ D,	"Deuterium",		"D",	2.014,	false, {	53,		25,		37,		32,		kNA,	kNA,	120 } },  //	1	D	 Deuterium         
 	{ He,	"Helium",			"He",	4.0026,	false, {	31,		kNA,	32,		46,		kNA,	kNA,	140 } },  //	2	He	 He­lium           
 	{ He,	"Helium",			"He",	4.0026,	false, {	31,		kNA,	32,		46,		kNA,	kNA,	140 } },  //	2	He	 He­lium           
 	{ Li,	"Lithium",			"Li",	6.94,	true,  {	167,	145,	134,	133,	124,	kNA,	182 } },  //	3	Li	 Lith­ium          
 	{ Li,	"Lithium",			"Li",	6.94,	true,  {	167,	145,	134,	133,	124,	kNA,	182 } },  //	3	Li	 Lith­ium          
 	{ Be,	"Beryllium",		"Be",	9.0122,	true,  {	112,	105,	90,		102,	90,		85,		kNA } },  //	4	Be	 Beryl­lium        
 	{ Be,	"Beryllium",		"Be",	9.0122,	true,  {	112,	105,	90,		102,	90,		85,		kNA } },  //	4	Be	 Beryl­lium        

src/Secondary.cpp

@@ -1150,6 +1150,9 @@ struct DSSPImpl
 		return std::find_if(mResidues.begin(), mResidues.end(), [&](auto& r) { return r.mM.asymID() == asymID and r.mM.seqID() == seqID; });
 		return std::find_if(mResidues.begin(), mResidues.end(), [&](auto& r) { return r.mM.asymID() == asymID and r.mM.seqID() == seqID; });
 	}
 	}
 
 
+	void calculateSurface();
+	void calculateSecondaryStructure();
+
 	DSSP_Statistics				mStats = {};
 	DSSP_Statistics				mStats = {};
 };
 };
 
 
@@ -1208,12 +1211,11 @@ DSSPImpl::DSSPImpl(const Structure& s, int min_poly_proline_stretch_length)
 		
 		
 		mResidues[i + 1].assignHydrogen();
 		mResidues[i + 1].assignHydrogen();
 	}
 	}
+}
 
 
-	std::thread ta(std::bind(&CalculateAccessibilities, std::ref(mResidues), std::ref(mStats)));
-
-	try
-	{
-		auto& db = s.getFile().data();
+void DSSPImpl::calculateSecondaryStructure()
+{
+	auto& db = mStructure.getFile().data();
 	for (auto r: db["struct_conn"].find(cif::Key("conn_type_id") == "disulf"))
 	for (auto r: db["struct_conn"].find(cif::Key("conn_type_id") == "disulf"))
 	{
 	{
 		std::string asym1, asym2;
 		std::string asym1, asym2;
@@ -1310,14 +1312,11 @@ DSSPImpl::DSSPImpl(const Structure& s, int min_poly_proline_stretch_length)
 			}
 			}
 		}
 		}
 	}
 	}
-	}
-	catch (const std::exception& ex)
-	{
-		ta.join();
-		throw;
-	}
+}
 
 
-	ta.join();
+void DSSPImpl::calculateSurface()
+{
+	CalculateAccessibilities(mResidues, mStats);
 }
 }
 
 
 // --------------------------------------------------------------------
 // --------------------------------------------------------------------
@@ -1424,9 +1423,17 @@ DSSP::iterator& DSSP::iterator::operator++()
 
 
 // --------------------------------------------------------------------
 // --------------------------------------------------------------------
 
 
-DSSP::DSSP(const Structure& s, int min_poly_proline_stretch)
+DSSP::DSSP(const Structure& s, int min_poly_proline_stretch, bool calculateSurfaceAccessibility)
 	: mImpl(new DSSPImpl(s, min_poly_proline_stretch))
 	: mImpl(new DSSPImpl(s, min_poly_proline_stretch))
 {
 {
+	if (calculateSurfaceAccessibility)
+	{
+		std::thread t(std::bind(&DSSPImpl::calculateSurface, mImpl));
+		mImpl->calculateSecondaryStructure();
+		t.join();
+	}
+	else
+		mImpl->calculateSecondaryStructure();
 }
 }
 
 
 DSSP::~DSSP()
 DSSP::~DSSP()