- fix new row iterators

- Residue constructor for sugars

.gitignore

@@ -16,3 +16,4 @@ libtool
 rsrc/lib-version.txt
 version-info*.txt
 src/revision.hpp
+test/pdb2cif-test

include/cif++/Structure.hpp

@@ -484,59 +484,8 @@ class Structure
 	/// Will asssign new atom_id's to all atoms. Be carefull
 	void sortAtoms();
 	
-	// // iterator for all residues
-	
-	// class residue_iterator : public std::iterator<std::forward_iterator_tag, const Residue>
-	// {
-	//   public:
-	// 	typedef std::iterator<std::forward_iterator_tag, const Residue>	baseType;
-	// 	typedef typename baseType::pointer								pointer;
-	// 	typedef typename baseType::reference							reference;
-		
-	// 	typedef std::list<Polymer>::const_iterator						poly_iterator;
-		
-	// 	residue_iterator(const Structure* s, poly_iterator polyIter, size_t polyResIndex, size_t nonPolyIndex);
-		
-	// 	reference operator*();
-	// 	pointer operator->();
-		
-	// 	residue_iterator& operator++();
-	// 	residue_iterator operator++(int);
-		
-	// 	bool operator==(const residue_iterator& rhs) const;
-	// 	bool operator!=(const residue_iterator& rhs) const;
-		
-	//   private:
-	// 	const Structure&	mStructure;
-	// 	poly_iterator		mPolyIter;
-	// 	size_t				mPolyResIndex;
-	// 	size_t				mNonPolyIndex;
-	// };
-	
-	// class residue_view
-	// {
-	//   public:
-	// 	residue_view(const Structure* s) : mStructure(s) {}
-	// 	residue_view(const residue_view& rhs) : mStructure(rhs.mStructure) {}
-	// 	residue_view& operator=(residue_view& rhs)
-	// 	{
-	// 		mStructure = rhs.mStructure;
-	// 		return *this;
-	// 	}
-		
-	// 	residue_iterator begin() const		{ return residue_iterator(mStructure, mStructure->mPolymers.begin(), 0, 0); }
-	// 	residue_iterator end() const		{ return residue_iterator(mStructure, mStructure->mPolymers.end(), 0, mStructure->mNonPolymers.size()); }
-	// 	size_t size() const
-	// 	{
-	// 		size_t ps = std::accumulate(mStructure->mPolymers.begin(), mStructure->mPolymers.end(), 0UL, [](size_t s, auto& p) { return s + p.size(); });
-	// 		return ps + mStructure->mNonPolymers.size();
-	// 	}
-
-	//   private:
-	// 	const Structure* mStructure;
-	// };
-	
-	// residue_view residues() const			{ return residue_view(this); }
+	const std::vector<Residue>& getNonPolymers() const					{ return mNonPolymers; }
+	const std::vector<Residue>& getBranchResidues() const				{ return mBranchResidues; }
 	
   private:
 	friend Polymer;

src/Cif++.cpp

@@ -1741,7 +1741,17 @@ Category::iterator Category::begin()
 
 Category::iterator Category::end()
 {
-	return iterator(nullptr);
+	return iterator();
+}
+
+Category::const_iterator Category::cbegin() const
+{
+	return const_iterator(mHead);
+}
+
+Category::const_iterator Category::cend() const
+{
+	return const_iterator();
 }
 
 Category::const_iterator Category::begin() const
@@ -1751,7 +1761,7 @@ Category::const_iterator Category::begin() const
 
 Category::const_iterator Category::end() const
 {
-	return const_iterator(nullptr);
+	return const_iterator();
 }
 
 bool Category::hasParent(Row r, const Category& parentCat, const ValidateLink& link) const

src/Structure.cpp

@@ -716,21 +716,29 @@ std::ostream& operator<<(std::ostream& os, const Atom& atom)
 // --------------------------------------------------------------------
 // residue
 
+// First constructor used to be for waters only, but now accepts sugars as well.
+
 Residue::Residue(const Structure& structure, const std::string& compoundID,
 	const std::string& asymID, const std::string& authSeqID)
 	: mStructure(&structure), mCompoundID(compoundID)
 	, mAsymID(asymID), mAuthSeqID(authSeqID)
 {
-	assert(mCompoundID == "HOH");
-	
 	for (auto& a: mStructure->atoms())
 	{
 		if (a.labelAsymID() != mAsymID or
 			a.labelCompID() != mCompoundID)
 				continue;
 
-		if (not mAuthSeqID.empty() and a.authSeqID() != mAuthSeqID)		// water!
+		if (compoundID == "HOH")
+		{
+			if (not mAuthSeqID.empty() and a.authSeqID() != mAuthSeqID)
+				continue;
+		}
+		else
+		{
+			if (mSeqID > 0 and a.labelSeqID() != mSeqID)
 				continue;
+		}
 		
 		mAtoms.push_back(a);
 	}
@@ -1842,6 +1850,25 @@ const Residue& Structure::getResidue(const std::string& asymID, const std::strin
 		}
 	}
 
+	if (seqID == 0)
+	{
+		for (auto& res: mNonPolymers)
+		{
+			if (res.asymID() != asymID or res.compoundID() != compID)
+				continue;
+
+			return res;
+		}
+	}
+
+	for (auto& res: mBranchResidues)
+	{
+		if (res.asymID() != asymID or res.compoundID() != compID or res.seqID() != seqID)
+			continue;
+		
+		return res;
+	}
+
 	throw std::out_of_range("Could not find residue " + asymID + '/' + std::to_string(seqID));
 }
 

test/unit-test.cpp

@@ -1154,6 +1154,41 @@ _test.name
 
     // query tests
 
+    for (const auto& [id, name]: db["test"].rows<int, std::optional<std::string>>({ "id", "name" }))
+    {
+        switch (id)
+        {
+            case 1: BOOST_CHECK(name == "aap"); break;
+            case 2: BOOST_CHECK(name == "noot"); break;
+            case 3: BOOST_CHECK(name == "mies"); break;
+            case 4:
+            case 5: BOOST_CHECK(not name); break;
+            default: 
+                    BOOST_CHECK(false);
+        }
+    }
+}
+
+
+BOOST_AUTO_TEST_CASE(c3)
+{
+    cif::VERBOSE = 1;
+
+    auto f = R"(data_TEST
+#
+loop_
+_test.id
+_test.name
+1 aap
+2 noot
+3 mies
+4 .
+5 ?
+    )"_cf;
+
+    auto& db = f.firstDatablock();
+
+    // query tests
     for (const auto& [id, name]: db["test"].find<int, std::optional<std::string>>(cif::All(), { "id", "name" }))
     {
         switch (id)