access to atoms

include/cif++/Structure.hpp

@@ -551,6 +551,8 @@ class Structure
 	~Structure();
 
 	const AtomView &atoms() const { return mAtoms; }
+	AtomView &atoms() { return mAtoms; }
+
 	AtomView waters() const;
 
 	const std::list<Polymer> &polymers() const { return mPolymers; }
@@ -580,6 +582,9 @@ class Structure
 	/// \brief Get a the single residue for an asym with id \a asymID
 	const Residue &getResidue(const std::string &asymID) const;
 
+	/// \brief Get a the single residue for an asym with id \a asymID and seq id \a seqID
+	const Residue &getResidue(const std::string &asymID, int seqID) const;
+
 	/// \brief Get a the single residue for an asym with id \a asymID
 	Residue &getResidue(const std::string &asymID);
 

src/Point.cpp

@@ -302,7 +302,8 @@ Quaternion ConstructFromAngleAxis(float angle, Point axis)
 
 	axis.normalize();
 
-	return Normalize(Quaternion{q,
+	return Normalize(Quaternion{
+		static_cast<float>(q),
 		static_cast<float>(s * axis.mX),
 		static_cast<float>(s * axis.mY),
 		static_cast<float>(s * axis.mZ)});

src/Structure.cpp

@@ -1429,10 +1429,21 @@ Atom Structure::getAtomByID(std::string id) const
 	//	auto i = find_if(mAtoms.begin(), mAtoms.end(),
 	//		[&id](auto& a) { return a.id() == id; });
 
+	Atom result;
+
 	if (i == mAtomIndex.end() or mAtoms[*i].id() != id)
-		throw std::out_of_range("Could not find atom with id " + id);
+	{
+		auto j = std::find_if(mAtoms.begin(), mAtoms.end(), [id](const Atom &a) { return a.id() == id; });
+
+		if (j == mAtoms.end())
+			throw std::out_of_range("Could not find atom with id " + id);
+		
+		result = *j;
+	}
+	else
+		result = mAtoms[*i];
 
-	return mAtoms[*i];
+	return result;
 }
 
 Atom Structure::getAtomByLabel(const std::string &atomID, const std::string &asymID, const std::string &compID, int seqID, const std::string &altID)
@@ -1558,6 +1569,42 @@ const Residue &Structure::getResidue(const std::string &asymID) const
 	throw std::out_of_range("Could not find residue " + asymID);
 }
 
+const Residue &Structure::getResidue(const std::string &asymID, int seqID) const
+{
+	if (seqID == 0)
+	{
+		for (auto &res : mNonPolymers)
+		{
+			if (res.asymID() != asymID)
+				continue;
+
+			return res;
+		}
+	}
+
+	for (auto &poly : mPolymers)
+	{
+		if (poly.asymID() != asymID)
+			continue;
+
+		for (auto &res : poly)
+		{
+			if (res.seqID() == seqID)
+				return res;
+		}
+	}
+
+	for (auto &res : mBranchResidues)
+	{
+		if (res.asymID() != asymID or res.seqID() != seqID)
+			continue;
+
+		return res;
+	}
+
+	throw std::out_of_range("Could not find residue " + asymID + '/' + std::to_string(seqID));
+}
+
 Residue &Structure::getResidue(const std::string &asymID)
 {
 	return const_cast<Residue &>(const_cast<Structure const &>(*this).getResidue(asymID));