Fix in REMARK3 parser for more strict mmcif_pdbx dictionary

src/model.cpp

@@ -807,11 +807,17 @@ float monomer::chi(size_t nr) const
 					atoms.back() = "CG2";
 					atoms.back() = "CG2";
 			}
 			}
 
 
+			auto atom_0 = get_atom_by_atom_id(atoms[nr + 0]);
+			auto atom_1 = get_atom_by_atom_id(atoms[nr + 1]);
+			auto atom_2 = get_atom_by_atom_id(atoms[nr + 2]);
+			auto atom_3 = get_atom_by_atom_id(atoms[nr + 3]);
+
+			if (atom_0 and atom_1 and atom_2 and atom_3)
 				result = static_cast<float>(dihedral_angle(
 				result = static_cast<float>(dihedral_angle(
-				get_atom_by_atom_id(atoms[nr + 0]).get_location(),
-				get_atom_by_atom_id(atoms[nr + 1]).get_location(),
-				get_atom_by_atom_id(atoms[nr + 2]).get_location(),
-				get_atom_by_atom_id(atoms[nr + 3]).get_location()));
+					atom_0.get_location(),
+					atom_1.get_location(),
+					atom_2.get_location(),
+					atom_3.get_location()));
 		}
 		}
 	}
 	}
 	catch (const std::exception &e)
 	catch (const std::exception &e)

src/pdb/cif2pdb.cpp

@@ -3359,7 +3359,7 @@ std::tuple<int, int> WriteCoordinatesForModel(std::ostream &pdbFile, const datab
 	auto &atom_site_anisotrop = db["atom_site_anisotrop"];
 	auto &atom_site_anisotrop = db["atom_site_anisotrop"];
 	auto &entity = db["entity"];
 	auto &entity = db["entity"];
 	auto &pdbx_poly_seq_scheme = db["pdbx_poly_seq_scheme"];
 	auto &pdbx_poly_seq_scheme = db["pdbx_poly_seq_scheme"];
-	auto &pdbx_nonpoly_scheme = db["pdbx_nonpoly_scheme"];
+	// auto &pdbx_nonpoly_scheme = db["pdbx_nonpoly_scheme"];
 	auto &pdbx_branch_scheme = db["pdbx_branch_scheme"];
 	auto &pdbx_branch_scheme = db["pdbx_branch_scheme"];
 
 
 	int serial = 1;
 	int serial = 1;
@@ -3434,7 +3434,11 @@ std::tuple<int, int> WriteCoordinatesForModel(std::ostream &pdbFile, const datab
 			r.get("id", "group_PDB", "label_atom_id", "label_alt_id", "auth_comp_id", "auth_asym_id", "auth_seq_id",
 			r.get("id", "group_PDB", "label_atom_id", "label_alt_id", "auth_comp_id", "auth_asym_id", "auth_seq_id",
 				"pdbx_PDB_ins_code", "Cartn_x", "Cartn_y", "Cartn_z", "occupancy", "B_iso_or_equiv", "type_symbol", "pdbx_formal_charge");
 				"pdbx_PDB_ins_code", "Cartn_x", "Cartn_y", "Cartn_z", "occupancy", "B_iso_or_equiv", "type_symbol", "pdbx_formal_charge");
 
 
+		if (resName != "HOH")
+		{
 			int entity_id = r.get<int>("label_entity_id");
 			int entity_id = r.get<int>("label_entity_id");
+			try
+			{
 				auto type = entity.find1<std::string>("id"_key == entity_id, "type");
 				auto type = entity.find1<std::string>("id"_key == entity_id, "type");
 
 
 				if (type == "branched")	// find the real auth_seq_num, since sugars have their auth_seq_num reused as sugar number... sigh.
 				if (type == "branched")	// find the real auth_seq_num, since sugars have their auth_seq_num reused as sugar number... sigh.
@@ -3443,6 +3447,12 @@ std::tuple<int, int> WriteCoordinatesForModel(std::ostream &pdbFile, const datab
 				// 	resSeq = pdbx_nonpoly_scheme.find1<int>("asym_id"_key == r.get<std::string>("label_asym_id") and "pdb_seq_num"_key == resSeq, "auth_seq_num");
 				// 	resSeq = pdbx_nonpoly_scheme.find1<int>("asym_id"_key == r.get<std::string>("label_asym_id") and "pdb_seq_num"_key == resSeq, "auth_seq_num");
 				else if (type == "polymer")
 				else if (type == "polymer")
 					resSeq = pdbx_poly_seq_scheme.find1<int>("asym_id"_key == r.get<std::string>("label_asym_id") and "pdb_seq_num"_key == resSeq, "auth_seq_num");
 					resSeq = pdbx_poly_seq_scheme.find1<int>("asym_id"_key == r.get<std::string>("label_asym_id") and "pdb_seq_num"_key == resSeq, "auth_seq_num");
+			}
+			catch (const std::exception &ex)
+			{
+				std::cerr << "Oops, there was not exactly one entity with id " << entity_id << std::endl;
+			}
+		}
 		
 		
 		if (chainID.length() > 1)
 		if (chainID.length() > 1)
 			throw std::runtime_error("Chain ID " + chainID + " won't fit into a PDB file");
 			throw std::runtime_error("Chain ID " + chainID + " won't fit into a PDB file");

src/pdb/pdb2cif_remark_3.cpp

@@ -1233,7 +1233,9 @@ void Remark3Parser::storeCapture(const char *category, std::initializer_list<con
 			{
 			{
 				cat.emplace({ // #warning("crystal id, diffrn id, what should be put here?")
 				cat.emplace({ // #warning("crystal id, diffrn id, what should be put here?")
 					{ "crystal_id", 1 },
 					{ "crystal_id", 1 },
-					{ "diffrn_id", 1 } });
+					{ "diffrn_id", 1 },
+					{ "operator", "" },
+					{ "fraction", 0.f } });
 			}
 			}
 			else if (iequals(category, "reflns"))
 			else if (iequals(category, "reflns"))
 				cat.emplace({ { "pdbx_ordinal", cat.size() + 1 },
 				cat.emplace({ { "pdbx_ordinal", cat.size() + 1 },