re-ref en pep-shuffle

git-svn-id: svn+ssh://gitlab/srv/svn-repos/pdb-redo/trunk@238 a1961a4f-ab94-4bcc-80e8-33b5a54de466

include/cif++/Compound.h

@@ -47,8 +47,19 @@ struct CompoundBond
 {
 	std::string			atomID[2];
 	CompoundBondType	type;
-	bool				aromatic;
 	float				distance;
+	float				esd;
+};
+
+// --------------------------------------------------------------------
+// struct containing information about the bond-angles
+// This information comes from the CCP4 monomer library. 
+
+struct CompoundAngle
+{
+	std::string			atomID[3];
+	float				angle;
+	float				esd;
 };
 
 // --------------------------------------------------------------------
@@ -76,15 +87,15 @@ class Compound
 
 	Compound(const std::string& id, const std::string& name,
 		const std::string& group, std::vector<CompoundAtom>&& atoms,
-		std::vector<CompoundBond>&& bonds, std::vector<ChiralCentre>&& chiralCentres)
+		std::vector<CompoundBond>&& bonds, std::vector<CompoundAngle>&& angles,
+		std::vector<ChiralCentre>&& chiralCentres)
 		: mId(id), mName(name), mGroup(group)
 		, mAtoms(std::move(atoms)), mBonds(std::move(bonds))
+		, mAngles(std::move(angles))
 		, mChiralCentres(std::move(chiralCentres))
 	{
 	}
 
-	~Compound();
-
 	// factory method, create a Compound based on the three letter code
 	// (for amino acids) or the one-letter code (for bases) or the
 	// code as it is known in the CCP4 monomer library.
@@ -101,12 +112,13 @@ class Compound
 	static void addMonomerLibraryPath(const std::string& dir);
 
 	// accessors
-	std::string id() const					{ return mId; }
-	std::string	name() const				{ return mName; }
+	std::string id() const						{ return mId; }
+	std::string	name() const					{ return mName; }
 	std::string	type() const;
-	std::string group() const				{ return mGroup; }
-	std::vector<CompoundAtom> atoms() const	{ return mAtoms; }
-	std::vector<CompoundBond> bonds() const	{ return mBonds; }
+	std::string group() const					{ return mGroup; }
+	std::vector<CompoundAtom> atoms() const		{ return mAtoms; }
+	std::vector<CompoundBond> bonds() const		{ return mBonds; }
+	std::vector<CompoundAngle> angles() const	{ return mAngles; }
 	
 	CompoundAtom getAtomById(const std::string& atomId) const;
 	
@@ -126,12 +138,16 @@ class Compound
 	std::vector<std::tuple<std::string,std::string>> mapToIsomer(const Compound& c) const;
 
   private:
+
+	~Compound();
+
 //	Entity&						mEntity;
 	std::string					mId;
 	std::string					mName;
 	std::string					mGroup;
 	std::vector<CompoundAtom>	mAtoms;
 	std::vector<CompoundBond>	mBonds;
+	std::vector<CompoundAngle>	mAngles;
 	std::vector<ChiralCentre>	mChiralCentres;
 };
 

include/cif++/Structure.h

@@ -155,7 +155,7 @@ class Residue
 		: mStructure(&structure), mCompoundID(compoundID)
 		, mAsymID(asymID), mAltID(altID), mSeqID(seqID) {}
 	
-	const Compound&		comp() const;
+	const Compound&		compound() const;
 	AtomView			atoms() const;
 	
 	Atom				atomByID(const std::string& atomID) const;

src/Compound.cpp

@@ -582,8 +582,8 @@ const Compound* CompoundFactory::create(std::string id)
 				CompoundBond b;
 				string type, aromatic;
 				
-				cif::tie(b.atomID[0], b.atomID[1], type, b.distance, aromatic) =
-					row.get("atom_id_1", "atom_id_2", "type", "distance", "aromatic");
+				cif::tie(b.atomID[0], b.atomID[1], type, b.distance, b.esd) =
+					row.get("atom_id_1", "atom_id_2", "type", "value_dist", "value_dist_esd");
 				
 				using cif::iequals;
 				
@@ -606,6 +606,19 @@ const Compound* CompoundFactory::create(std::string id)
 			}
 			sort(bonds.begin(), bonds.end(), CompoundBondLess());
 
+			auto& compAngles = cf["comp_" + id]["chem_comp_angle"];
+			
+			vector<CompoundAngle> angles;
+			for (auto row: compAngles)
+			{
+				CompoundAngle a;
+				
+				cif::tie(a.atomID[0], a.atomID[1], a.atomID[2], a.angle, a.esd) =
+					row.get("atom_id_1", "atom_id_2", "atom_id_3", "value_angle", "value_angle_esd");
+				
+				angles.push_back(a);
+			}
+
 			auto& compChir = cf["comp_" + id]["chem_comp_chir"];
 			
 			vector<ChiralCentre> chiralCentres;
@@ -636,7 +649,7 @@ const Compound* CompoundFactory::create(std::string id)
 			}
 
 			result = new Compound(id, name, group, move(atoms), move(bonds),
-				move(chiralCentres));
+				move(angles), move(chiralCentres));
 
 			boost::upgrade_to_unique_lock<boost::shared_mutex> uniqueLock(lock);
 			mCompounds.push_back(result);

src/PDB2Cif.cpp

@@ -4662,7 +4662,7 @@ void PDBFileParser::ParseConnectivtyAnnotation()
 		if (mRec->is("CISPEP"))
 		{
 											//	 1 -  6       Record name   "CISPEP"
-			int serNum = vI(8, 10);		//	 8 - 10       Integer       serNum        Record serial number.
+			int serNum = vI(8, 10);			//	 8 - 10       Integer       serNum        Record serial number.
 			string pep1 = vS(12, 14);		//	12 - 14       LString(3)    pep1          Residue name.
 			char chainID1 = vC(16); 		//	16            Character     chainID1      Chain identifier.
 			int seqNum1 = vI(18, 21);		//	18 - 21       Integer       seqNum1       Residue sequence number.

src/Structure.cpp

@@ -508,12 +508,12 @@ Residue& Residue::operator=(const Residue& rhs)
 	return *this;
 }
 
-const Compound& Residue::comp() const
+const Compound& Residue::compound() const
 {
-	auto compound = Compound::create(mCompoundID);
-	if (compound == nullptr)
+	auto result = Compound::create(mCompoundID);
+	if (result == nullptr)
 		throw runtime_error("Failed to create compound " + mCompoundID);
-	return *compound;
+	return *result;
 }
 
 AtomView Residue::atoms() const