multithreaded pepflip

git-svn-id: svn+ssh://gitlab/srv/svn-repos/pdb-redo/trunk@333 a1961a4f-ab94-4bcc-80e8-33b5a54de466

include/cif++/DistanceMap.h

@@ -24,7 +24,7 @@ class DistanceMap
 	DistanceMap(const DistanceMap&) = delete;
 	DistanceMap& operator=(const DistanceMap&) = delete;
 
-//	float operator()(const Atom& a, const Atom& b) const;
+	float operator()(const Atom& a, const Atom& b) const;
 
 	std::vector<Atom> near(const Atom& a, float maxDistance = 3.5f) const;
 	std::vector<Atom> near(const Point& p, float maxDistance = 3.5f) const;

include/cif++/Secondary.h

@@ -66,6 +66,7 @@ class DSSP
 	SecondaryStructureType operator()(const Monomer& m) const;
 	
 	bool isAlphaHelixEndBeforeStart(const Monomer& m) const;
+	bool isAlphaHelixEndBeforeStart(const std::string& inAsymID, int inSeqID) const;
 	
   private:
 	struct DSSPImpl* mImpl;

include/cif++/Structure.h

@@ -87,6 +87,9 @@ class Atom
 
 	~Atom();
 	
+	// return a copy of this atom, with data copied instead of referenced
+	Atom clone() const;
+	
 	Atom& operator=(const Atom& rhs);
 
 	const std::string& id() const;
@@ -130,8 +133,6 @@ class Atom
 	
 	bool operator==(const Atom& rhs) const;
 
-	const File& getFile() const;
-	
 	// get clipper format Atom
 	clipper::Atom toClipper() const;
 
@@ -368,10 +369,12 @@ class Structure
 {
   public:
 	Structure(File& p, uint32 modelNr = 1);
-	Structure(const Structure&);
-	Structure& operator=(const Structure&);
+	Structure& operator=(const Structure&) = delete;
 	~Structure();
 
+	// Create a read-only clone of the current structure (for multithreaded calculations that move atoms)
+	Structure(const Structure&);
+
 	File& getFile() const;
 
 	AtomView atoms() const;

src/DistanceMap.cpp

@@ -230,42 +230,42 @@ DistanceMap::DistanceMap(const Structure& p, const clipper::Spacegroup& spacegro
 //	}
 //}
 
-//float DistanceMap::operator()(const Atom& a, const Atom& b) const
-//{
-//	size_t ixa, ixb;
-//	
-//	try
-//	{
-//		ixa = index.at(a.id());
-//	}
-//	catch (const out_of_range& ex)
-//	{
-//		throw runtime_error("atom " + a.id() + " not found in distance map");
-//	}
-//		
-//	try
-//	{
-//		ixb = index.at(b.id());
-//	}
-//	catch (const out_of_range& ex)
-//	{
-//		throw runtime_error("atom " + b.id() + " not found in distance map");
-//	}
-//	
-//	if (ixb < ixa)
-//		swap(ixa, ixb);
-//	
-//	tuple<size_t,size_t> k{ ixa, ixb };
-//
-//	auto ii = dist.find(k);
-//
-//	float result = 100;
-//	
-//	if (ii != dist.end())
-//		result = ii->second;
-//	
-//	return result;
-//}
+float DistanceMap::operator()(const Atom& a, const Atom& b) const
+{
+	size_t ixa, ixb;
+	
+	try
+	{
+		ixa = index.at(a.id());
+	}
+	catch (const out_of_range& ex)
+	{
+		throw runtime_error("atom " + a.id() + " not found in distance map");
+	}
+		
+	try
+	{
+		ixb = index.at(b.id());
+	}
+	catch (const out_of_range& ex)
+	{
+		throw runtime_error("atom " + b.id() + " not found in distance map");
+	}
+	
+	if (ixb < ixa)
+		swap(ixa, ixb);
+	
+	tuple<size_t,size_t> k{ ixa, ixb };
+
+	auto ii = dist.find(k);
+
+	float result = 100;
+	
+	if (ii != dist.end())
+		result = get<0>(ii->second);
+	
+	return result;
+}
 
 vector<Atom> DistanceMap::near(const Atom& a, float maxDistance) const
 {

src/Secondary.cpp

@@ -860,18 +860,20 @@ SecondaryStructureType DSSP::operator()(const Monomer& m) const
 
 bool DSSP::isAlphaHelixEndBeforeStart(const Monomer& m) const
 {
-	auto asymID = m.asymID();
-	auto seqID = m.seqID();
+	return isAlphaHelixEndBeforeStart(m.asymID(), m.seqID());
+}
 
+bool DSSP::isAlphaHelixEndBeforeStart(const string& inAsymID, int inSeqID) const
+{
 	auto i = find_if(mImpl->mResidues.begin(), mImpl->mResidues.end(),
-		[&](auto& r) { return r.mM.asymID() == asymID and r.mM.seqID() == seqID; });
+		[&](auto& r) { return r.mM.asymID() == inAsymID and r.mM.seqID() == inSeqID; });
 
 	bool result = false;
 
 	if (i != mImpl->mResidues.end() and i + 1 != mImpl->mResidues.end())
 		result = i->GetHelixFlag(4) == helixEnd and (i + 1)->GetHelixFlag(4) == helixStart;
 	else if (VERBOSE)
-		cerr << "Could not find secondary structure for " << asymID << ':' << seqID << endl;
+		cerr << "Could not find secondary structure for " << inAsymID << ':' << inSeqID << endl;
 
 	return result;
 }

src/Structure.cpp

@@ -145,6 +145,16 @@ void FileImpl::save(fs::path p)
 
 struct AtomImpl
 {
+	AtomImpl(const AtomImpl& i)
+		: mFile(i.mFile), mId(i.mId), mType(i.mType)
+		, mAtomID(i.mAtomID), mCompID(i.mCompID), mAsymID(i.mAsymID)
+		, mSeqID(i.mSeqID), mAltID(i.mAltID), mLocation(i.mLocation)
+		, mRefcount(1), mRow(i.mRow), mCompound(i.mCompound)
+		, mRadius(i.mRadius), mCachedProperties(i.mCachedProperties)
+		, mSymmetryCopy(i.mSymmetryCopy), mClone(true)
+	{
+	}
+	
 	AtomImpl(const File& f, const string& id)
 		: mFile(f), mId(id), mRefcount(1), mCompound(nullptr)
 	{
@@ -276,9 +286,12 @@ struct AtomImpl
 		if (mSymmetryCopy)
 			throw runtime_error("Moving symmetry copy");
 		
-		mRow["Cartn_x"] = p.getX();
-		mRow["Cartn_y"] = p.getY();
-		mRow["Cartn_z"] = p.getZ();
+		if (not mClone)
+		{
+			mRow["Cartn_x"] = p.getX();
+			mRow["Cartn_y"] = p.getY();
+			mRow["Cartn_z"] = p.getZ();
+		}
 		
 //		boost::format kPosFmt("%.3f");
 //
@@ -353,6 +366,7 @@ struct AtomImpl
 	map<string,string>	mCachedProperties;
 	
 	bool				mSymmetryCopy = false;
+	bool				mClone = false;
 };
 
 //Atom::Atom(const File& f, const string& id)
@@ -365,6 +379,11 @@ Atom::Atom(AtomImpl* impl)
 {
 }
 
+Atom Atom::clone() const
+{
+	return Atom(new AtomImpl(*mImpl));
+}
+
 Atom::Atom(const Atom& rhs)
 	: mImpl(rhs.mImpl)
 {
@@ -545,12 +564,6 @@ bool Atom::operator==(const Atom& rhs) const
 		(&mImpl->mFile == &rhs.mImpl->mFile and mImpl->mId == rhs.mImpl->mId); 	
 }
 
-const File& Atom::getFile() const
-{
-	assert(mImpl);
-	return mImpl->mFile;
-}
-
 clipper::Atom Atom::toClipper() const
 {
 	return mImpl->toClipper();
@@ -1141,6 +1154,14 @@ struct StructureImpl
 		}
 	}
 	
+	StructureImpl(const StructureImpl& si)
+		: mFile(si.mFile), mModelNr(si.mModelNr)
+	{
+		mAtoms.reserve(si.mAtoms.size());
+		for (auto& atom: si.mAtoms)
+			mAtoms.emplace_back(atom.clone());
+	}
+	
 	void removeAtom(Atom& a);
 	void swapAtoms(Atom& a1, Atom& a2);
 	void moveAtom(Atom& a, Point p);
@@ -1310,6 +1331,11 @@ Structure::~Structure()
 	delete mImpl;
 }
 
+Structure::Structure(const Structure& rhs)
+	: mImpl(new StructureImpl(*rhs.mImpl))
+{
+}
+
 AtomView Structure::atoms() const
 {
 	return mImpl->mAtoms;