Fix importing sugars from PDB files

include/cif++/Structure.hpp

@@ -525,12 +525,12 @@ class Sugar : public Residue
 {
   public:
 	Sugar(const Branch &branch, const std::string &compoundID,
-		const std::string &asymID, int authSeqID, int number);
+		const std::string &asymID, int authSeqID);
 
 	Sugar(Sugar &&rhs);
 	Sugar &operator=(Sugar &&rhs);
 
-	int num() const { return mNumber; }
+	int num() const { return std::stoi(mAuthSeqID); }
 	std::string name() const;
 
 	/// \brief Return the atom the C1 is linked to
@@ -545,7 +545,6 @@ class Sugar : public Residue
   private:
 
 	const Branch *mBranch;
-	int mNumber;
 	Atom mLink;
 };
 

src/PDB2Cif.cpp

@@ -1077,6 +1077,7 @@ class PDBFileParser
 	std::map<std::string, std::string> mBranch2EntityID;
 	std::map<std::string, std::string> mAsymID2EntityID;
 	std::map<std::string, std::string> mMod2parent;
+	std::set<std::string> mSugarEntities;
 };
 
 // --------------------------------------------------------------------
@@ -3776,6 +3777,10 @@ void PDBFileParser::ConstructEntities()
 	for (auto &chain : mChains)
 	{
 		std::string asymID = cif::cifIdForNumber(asymNr++);
+
+		if (mMolID2EntityID.count(chain.mMolID) == 0)
+			continue;
+
 		std::string entityID = mMolID2EntityID[chain.mMolID];
 
 		mAsymID2EntityID[asymID] = entityID;
@@ -4601,14 +4606,20 @@ void PDBFileParser::ConstructSugarTrees(int &asymNr)
 					}
 				}
 
+				mSugarEntities.insert(entityID);
+
 				// create an asym for this sugar tree
 
 				std::string asymID = cif::cifIdForNumber(asymNr++);
 
-				getCategory("struct_asym")->emplace({{"id", asymID},
+				mAsymID2EntityID[asymID] = entityID;
+
+				getCategory("struct_asym")->emplace({
+					{"id", asymID},
 					{"pdbx_blank_PDB_chainid_flag", si->chainID == ' ' ? "Y" : "N"},
 					{"pdbx_modified", "N"},
-				{"entity_id", entityID}});
+					{"entity_id", entityID}
+				});
 
 				std::string iCode{si->iCode};
 				ba::trim(iCode);
@@ -5107,7 +5118,8 @@ void PDBFileParser::ParseConnectivtyAnnotation()
 				continue;
 			}
 
-			getCategory("struct_conn")->emplace({{"id", type + std::to_string(linkNr)},
+			getCategory("struct_conn")->emplace({
+				{"id", type + std::to_string(linkNr)},
 				{"conn_type_id", type},
 
 				// { "ccp4_link_id", ccp4LinkID },
@@ -5140,7 +5152,8 @@ void PDBFileParser::ParseConnectivtyAnnotation()
 
 				{"ptnr2_symmetry", sym2},
 
-			                                     {"pdbx_dist_value", distance}});
+				{"pdbx_dist_value", distance}
+			});
 
 			continue;
 		}
@@ -5181,7 +5194,8 @@ void PDBFileParser::ParseConnectivtyAnnotation()
 			std::string iCode1str = iCode1 == ' ' ? std::string() : std::string{iCode1};
 			std::string iCode2str = iCode2 == ' ' ? std::string() : std::string{iCode2};
 
-			getCategory("struct_mon_prot_cis")->emplace({{"pdbx_id", serNum},
+			getCategory("struct_mon_prot_cis")->emplace({
+				{"pdbx_id", serNum},
 				{"label_comp_id", pep1},
 				{"label_seq_id", lResSeq1},
 				{"label_asym_id", lAsym1},
@@ -5198,7 +5212,8 @@ void PDBFileParser::ParseConnectivtyAnnotation()
 				{"pdbx_auth_seq_id_2", seqNum2},
 				{"pdbx_auth_asym_id_2", std::string{chainID2}},
 				{"pdbx_PDB_model_num", modNum},
-			{"pdbx_omega_angle", measure}});
+				{"pdbx_omega_angle", measure}
+			});
 
 			continue;
 		}
@@ -5557,7 +5572,17 @@ void PDBFileParser::ParseCoordinate(int modelNr)
 			}
 		}
 
-		getCategory("atom_site")->emplace({{"group_PDB", groupPDB},
+		// if the atom is part of a sugar, we need to replace the auth_seq_id/resSeq
+		if (mSugarEntities.count(entityID))
+		{
+			using namespace cif::literals;
+
+			auto &branch_scheme = *getCategory("pdbx_branch_scheme");
+			resSeq = branch_scheme.find1<int>("asym_id"_key == asymID and "auth_seq_num"_key == resSeq, "pdb_seq_num");
+		}
+
+		getCategory("atom_site")->emplace({
+			{"group_PDB", groupPDB},
 			{"id", mAtomID},
 			{"type_symbol", element},
 			{"label_atom_id", name},
@@ -5577,7 +5602,8 @@ void PDBFileParser::ParseCoordinate(int modelNr)
 			{"auth_comp_id", resName},
 			{"auth_asym_id", std::string{chainID}},
 			{"auth_atom_id", name},
-		{"pdbx_PDB_model_num", modelNr}});
+			{"pdbx_PDB_model_num", modelNr}
+		});
 
 		InsertAtomType(element);
 

src/Structure.cpp

@@ -1123,17 +1123,15 @@ int Polymer::Distance(const Monomer &a, const Monomer &b) const
 // --------------------------------------------------------------------
 
 Sugar::Sugar(const Branch &branch, const std::string &compoundID,
-	const std::string &asymID, int authSeqID, int number)
+	const std::string &asymID, int authSeqID)
 	: Residue(branch.structure(), compoundID, asymID, 0, std::to_string(authSeqID))
 	, mBranch(&branch)
-	, mNumber(number)
 {
 }
 
 Sugar::Sugar(Sugar &&rhs)
 	: Residue(std::forward<Residue>(rhs))
 	, mBranch(rhs.mBranch)
-	, mNumber(rhs.mNumber)
 {
 
 }
@@ -1144,7 +1142,6 @@ Sugar &Sugar::operator=(Sugar &&rhs)
 	{
 		Residue::operator=(std::forward<Residue>(rhs));
 		mBranch = rhs.mBranch;
-		mNumber = rhs.mNumber;
 	}
 
 	return *this;
@@ -1206,10 +1203,10 @@ Branch::Branch(Structure &structure, const std::string &asymID)
 
 	for (const auto &[entity_id] : struct_asym.find<std::string>("id"_key == asymID, "entity_id"))
 	{
-		for (const auto &[comp_id, number, auth_seq_num] : branch_scheme.find<std::string, int, int>(
-				 "asym_id"_key == asymID, "mon_id", "pdb_seq_num", "auth_seq_num"))
+		for (const auto &[comp_id, num] : branch_scheme.find<std::string, int>(
+				 "asym_id"_key == asymID, "mon_id", "pdb_seq_num"))
 		{
-			emplace_back(*this, comp_id, asymID, auth_seq_num, number);
+			emplace_back(*this, comp_id, asymID, num);
 		}
 
 		for (const auto &[num1, num2, atom1, atom2] : branch_link.find<size_t, size_t, std::string, std::string>(
@@ -2260,11 +2257,13 @@ std::string Structure::createNonpoly(const std::string &entity_id, const std::ve
 	auto &struct_asym = db["struct_asym"];
 	std::string asym_id = struct_asym.getUniqueID();
 
-	struct_asym.emplace({{"id", asym_id},
+	struct_asym.emplace({
+		{"id", asym_id},
 		{"pdbx_blank_PDB_chainid_flag", "N"},
 		{"pdbx_modified", "N"},
 		{"entity_id", entity_id},
-		{"details", "?"}});
+		{"details", "?"}
+	});
 
 	std::string comp_id = db["pdbx_entity_nonpoly"].find1<std::string>("entity_id"_key == entity_id, "comp_id");
 
@@ -2276,7 +2275,8 @@ std::string Structure::createNonpoly(const std::string &entity_id, const std::ve
 	{
 		auto atom_id = atom_site.getUniqueID("");
 
-		auto &&[row, inserted] = atom_site.emplace({{"group_PDB", atom.get_property<std::string>("group_PDB")},
+		auto &&[row, inserted] = atom_site.emplace({
+			{"group_PDB", atom.get_property<std::string>("group_PDB")},
 			{"id", atom_id},
 			{"type_symbol", atom.get_property<std::string>("type_symbol")},
 			{"label_atom_id", atom.get_property<std::string>("label_atom_id")},
@@ -2296,7 +2296,8 @@ std::string Structure::createNonpoly(const std::string &entity_id, const std::ve
 			{"auth_comp_id", comp_id},
 			{"auth_asym_id", asym_id},
 			{"auth_atom_id", atom.get_property<std::string>("label_atom_id")},
-			{"pdbx_PDB_model_num", 1}});
+			{"pdbx_PDB_model_num", 1}
+		});
 
 		auto &newAtom = emplace_atom(std::make_shared<Atom::AtomImpl>(db, atom_id, row));
 		res.addAtom(newAtom);
@@ -2328,11 +2329,13 @@ std::string Structure::createNonpoly(const std::string &entity_id, std::vector<s
 	auto &struct_asym = db["struct_asym"];
 	std::string asym_id = struct_asym.getUniqueID();
 
-	struct_asym.emplace({{"id", asym_id},
+	struct_asym.emplace({
+		{"id", asym_id},
 		{"pdbx_blank_PDB_chainid_flag", "N"},
 		{"pdbx_modified", "N"},
 		{"entity_id", entity_id},
-		{"details", "?"}});
+		{"details", "?"}
+	});
 
 	std::string comp_id = db["pdbx_entity_nonpoly"].find1<std::string>("entity_id"_key == entity_id, "comp_id");
 
@@ -2406,7 +2409,7 @@ Branch &Structure::createBranch(std::vector<std::vector<cif::Item>> &nag_atoms)
 	std::string asym_id = struct_asym.getUniqueID();
 
 	auto &branch = mBranches.emplace_back(*this, asym_id);
-	auto &sugar = branch.emplace_back(branch, "NAG", asym_id, 1, 1);
+	auto &sugar = branch.emplace_back(branch, "NAG", asym_id, 1);
 	auto tmp_entity_id = db["entity"].getUniqueID("");
 
 	auto &atom_site = db["atom_site"];
@@ -2520,7 +2523,7 @@ Branch &Structure::extendBranch(const std::string &asym_id, std::vector<std::vec
 
 	int sugarNum = branch.size() + 1;
 
-	auto &sugar = branch.emplace_back(branch, compoundID, asym_id, sugarNum, sugarNum);
+	auto &sugar = branch.emplace_back(branch, compoundID, asym_id, sugarNum);
 
 	for (auto &atom : atom_info)
 	{