Fix loading embedded restraint data

src/compound.cpp

@@ -550,12 +550,6 @@ class local_compound_factory_impl : public compound_factory_impl
 		for (const auto &[id, name, threeLetterCode, group] :
 		for (const auto &[id, name, threeLetterCode, group] :
 			file["comp_list"]["chem_comp"].rows<std::string, std::string, std::string, std::string>("id", "name", "three_letter_code", "group"))
 			file["comp_list"]["chem_comp"].rows<std::string, std::string, std::string, std::string>("id", "name", "three_letter_code", "group"))
 		{
 		{
-			// if (std::regex_match(group, peptideRx))
-			// 	mKnownPeptides.insert(threeLetterCode);
-			// else if (cif::iequals(group, "DNA") or cif::iequals(group, "RNA"))
-			// 	mKnownBases.insert(threeLetterCode);
-			
-			// Test if this compound is known in CCD
 			auto &rdb = m_local_file["comp_" + id];
 			auto &rdb = m_local_file["comp_" + id];
 			if (rdb.empty())
 			if (rdb.empty())
 			{
 			{
@@ -563,6 +557,53 @@ class local_compound_factory_impl : public compound_factory_impl
 				continue;
 				continue;
 			}
 			}
 
 
+			construct_compound(rdb, id, name, threeLetterCode, group);
+		}
+	}
+
+	compound *create(const std::string &id) override;
+
+  private:
+
+	compound *construct_compound(const datablock &db, const std::string &id, const std::string &name, const std::string &three_letter_code, const std::string &group);
+
+	cif::file m_local_file;
+};
+
+compound *local_compound_factory_impl::create(const std::string &id)
+{
+	compound *result = nullptr;
+
+	for (auto &db : m_local_file)
+	{
+		if (db.name() == "comp_" + id)
+		{
+			auto chem_comp = db.get("chem_comp");
+			if (not chem_comp)
+				break;
+
+			try
+			{
+				const auto &[id, name, threeLetterCode, group] =
+					chem_comp->front().get<std::string, std::string, std::string, std::string>("id", "name", "three_letter_code", "group");
+
+				result = construct_compound(db, id, name, threeLetterCode, group);
+			}
+			catch (const std::exception &ex)
+			{
+				std::throw_with_nested(std::runtime_error("Error loading compound " + id));
+			}
+
+			break;
+		}
+	}
+
+	return result;
+}
+
+compound *local_compound_factory_impl::construct_compound(const datablock &rdb, const std::string &id,
+	const std::string &name, const std::string &three_letter_code, const std::string &group)
+{
 	cif::datablock db(id);
 	cif::datablock db(id);
 
 
 	float formula_weight = 0;
 	float formula_weight = 0;
@@ -644,48 +685,15 @@ class local_compound_factory_impl : public compound_factory_impl
 		{ "formula", formula },
 		{ "formula", formula },
 		{ "pdbx_formal_charge", formal_charge },
 		{ "pdbx_formal_charge", formal_charge },
 		{ "formula_weight", formula_weight },
 		{ "formula_weight", formula_weight },
-				{ "three_letter_code", threeLetterCode }
+		{ "three_letter_code", three_letter_code }
 	});
 	});
 
 
-			m_compounds.push_back(new compound(db));
-		}
-	}
-
-	// compound *create(const std::string &id) override;
-
-  private:
-	cif::file m_local_file;
-};
-
-// compound *local_compound_factory_impl::create(const std::string &id)
-// {
-// 	compound *result = nullptr;
-
-// 	for (auto &db : m_local_file)
-// 	{
-// 		if (db.name() == id)
-// 		{
-// 			cif::datablock db_copy(db);
-
-// 			try
-// 			{
-// 				result = new compound(db_copy, 1);
-// 			}
-// 			catch (const std::exception &ex)
-// 			{
-// 				std::throw_with_nested(std::runtime_error("Error loading compound " + id));
-// 			}
-
-
-// 			std::shared_lock lock(mMutex);
-// 			m_compounds.push_back(result);
-
-// 			break;
-// 		}
-// 	}
+	std::shared_lock lock(mMutex);
 
 
-// 	return result;
-// }
+	auto result = new compound(db);
+	m_compounds.push_back(result);
+	return result;
+}
 
 
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