- alternates handling

- getResidue in structure

include/cif++/Structure.hpp

@@ -244,6 +244,15 @@ class Residue
 
 
 	bool hasAlternateAtoms() const;
 	bool hasAlternateAtoms() const;
 
 
+	/// \brief Return the list of unique alt ID's present in this residue
+	std::set<std::string> getAlternateIDs() const;
+
+	/// \brief Return the list of unique atom ID's
+	std::set<std::string> getAtomIDs() const;
+
+	/// \brief Return the list of atoms having ID \a atomID
+	AtomView getAtomsByID(const std::string& atomID) const;
+
 	// some routines for 3d work
 	// some routines for 3d work
 	std::tuple<Point,float> centerAndRadius() const;
 	std::tuple<Point,float> centerAndRadius() const;
 
 
@@ -436,6 +445,8 @@ class Structure
 	// 	const std::string& compID, int seqID, const std::string& altID = "",
 	// 	const std::string& compID, int seqID, const std::string& altID = "",
 	// 	const std::string& pdbxAuthInsCode = "");
 	// 	const std::string& pdbxAuthInsCode = "");
 	
 	
+	const Residue& getResidue(const std::string& asymID, const std::string& compID, int seqID) const;
+
 	// map between auth and label locations
 	// map between auth and label locations
 	
 	
 	std::tuple<std::string,int,std::string> MapAuthToLabel(const std::string& asymID,
 	std::tuple<std::string,int,std::string> MapAuthToLabel(const std::string& asymID,
@@ -536,7 +547,7 @@ class Structure
 	void updateAtomIndex();
 	void updateAtomIndex();
 	
 	
 	File&					mFile;
 	File&					mFile;
-	uint32_t					mModelNr;
+	uint32_t				mModelNr;
 	AtomView				mAtoms;
 	AtomView				mAtoms;
 	std::vector<size_t>		mAtomIndex;
 	std::vector<size_t>		mAtomIndex;
 	std::list<Polymer>		mPolymers;
 	std::list<Polymer>		mPolymers;

src/Structure.cpp

@@ -879,6 +879,20 @@ AtomView Residue::unique_atoms() const
 	return result;
 	return result;
 }
 }
 
 
+std::set<std::string> Residue::getAlternateIDs() const
+{
+	std::set<std::string> result;
+
+	for (auto a: mAtoms)
+	{
+		auto alt = a.labelAltID();
+		if (not alt.empty())
+			result.insert(alt);
+	}
+
+	return result;
+}
+
 Atom Residue::atomByID(const std::string& atomID) const
 Atom Residue::atomByID(const std::string& atomID) const
 {
 {
 	Atom result;
 	Atom result;
@@ -966,6 +980,26 @@ bool Residue::hasAlternateAtoms() const
 	return std::find_if(mAtoms.begin(), mAtoms.end(), [](const Atom& atom) { return atom.isAlternate(); }) != mAtoms.end();
 	return std::find_if(mAtoms.begin(), mAtoms.end(), [](const Atom& atom) { return atom.isAlternate(); }) != mAtoms.end();
 }
 }
 
 
+std::set<std::string> Residue::getAtomIDs() const
+{
+	std::set<std::string> ids;
+	for (auto a: mAtoms)
+		ids.insert(a.labelAtomID());
+	
+	return ids;
+}
+
+AtomView Residue::getAtomsByID(const std::string& atomID) const
+{
+	AtomView atoms;
+	for (auto a: mAtoms)
+	{
+		if (a.labelAtomID() == atomID)
+			atoms.push_back(a);
+	}
+	return atoms;
+}
+
 std::ostream& operator<<(std::ostream& os, const Residue& res)
 std::ostream& operator<<(std::ostream& os, const Residue& res)
 {
 {
 	os << res.compoundID() << ' ' << res.asymID() << ':' << res.seqID();
 	os << res.compoundID() << ' ' << res.asymID() << ':' << res.seqID();
@@ -1747,6 +1781,23 @@ Atom Structure::getAtomByLabel(const std::string& atomID, const std::string& asy
 	throw std::out_of_range("Could not find atom with specified label");
 	throw std::out_of_range("Could not find atom with specified label");
 }
 }
 
 
+const Residue& Structure::getResidue(const std::string& asymID, const std::string& compID, int seqID) const
+{
+	for (auto& poly: mPolymers)
+	{
+		if (poly.asymID() != asymID)
+			continue;
+		
+		for (auto& res: poly)
+		{
+			if (res.seqID() == seqID and res.compoundID() == compID)
+				return res;
+		}
+	}
+
+	throw std::out_of_range("Could not find residue " + asymID + '/' + std::to_string(seqID));
+}
+
 File& Structure::getFile() const
 File& Structure::getFile() const
 {
 {
 	return mFile;
 	return mFile;