fixing git repository

src/CifParser.cpp

@@ -888,8 +888,11 @@ void DictParser::linkItems()
 {
 	if (not mDataBlock)
 		error("no datablock");
+
+	auto& dict = *mDataBlock;
 	
-	std::map<std::tuple<std::string,std::string,int>,size_t> linkIndex;
+	std::map<std::tuple<std::string,std::string>,size_t> linkIndex;
+	std::map<std::tuple<std::string,std::string>,int> linkGroupIds;
 	std::vector<std::tuple<std::vector<std::string>,std::vector<std::string>>> linkKeys;
 	
 	for (auto gl: dict["pdbx_item_linked_group_list"])
@@ -906,11 +909,13 @@ void DictParser::linkItems()
 		if (piv == nullptr)
 			error("in pdbx_item_linked_group_list, item '" + parent + "' is not specified");
 		
-		auto key = make_tuple(piv->mCategory->mName, civ->mCategory->mName, link_group_id);
+		auto key = std::make_tuple(piv->mCategory->mName, civ->mCategory->mName);
 		if (not linkIndex.count(key))
 		{
 			linkIndex[key] = linkKeys.size();
 			linkKeys.push_back({});
+
+			linkGroupIds[key] = link_group_id;
 		}
 		
 		size_t ix = linkIndex.at(key);
@@ -919,39 +924,43 @@ void DictParser::linkItems()
 		std::get<1>(linkKeys.at(ix)).push_back(civ->mTag);
 	}
 
-//	for (auto li: mImpl->mLinkedItems)
-//	{
-//		std::string child, parent;
-//		std::tie(child, parent) = li;
-//		
-//		auto civ = mValidator.getValidatorForItem(child);
-//		if (civ == nullptr)
-//			error("in pdbx_item_linked_group_list, item '" + child + "' is not specified");
-//		
-//		auto piv = mValidator.getValidatorForItem(parent);
-//		if (piv == nullptr)
-//			error("in pdbx_item_linked_group_list, item '" + parent + "' is not specified");
-//		
-//		auto key = make_tuple(piv->mCategory->mName, civ->mCategory->mName, piv->mTag);
-//		if (not linkIndex.count(key))
-//		{
-//			linkIndex[key] = linkKeys.size();
-//			linkKeys.push_back({});
-//		}
-//		
-//		size_t ix = linkIndex.at(key);
-//		auto& keys = linkKeys.at(ix);
-//		
-//		keys.insert(civ->mTag);
-//	}
+	// for links recorded in categories but not in pdbx_item_linked_group_list
+	for (auto li: mImpl->mLinkedItems)
+	{
+		std::string child, parent;
+		std::tie(child, parent) = li;
+		
+		auto civ = mValidator.getValidatorForItem(child);
+		if (civ == nullptr)
+			error("in pdbx_item_linked_group_list, item '" + child + "' is not specified");
+		
+		auto piv = mValidator.getValidatorForItem(parent);
+		if (piv == nullptr)
+			error("in pdbx_item_linked_group_list, item '" + parent + "' is not specified");
+
+		auto key = std::make_tuple(piv->mCategory->mName, civ->mCategory->mName);
+		if (not linkIndex.count(key))
+		{
+			linkIndex[key] = linkKeys.size();
+			linkKeys.push_back({});
+		}
+		
+		size_t ix = linkIndex.at(key);
+		
+		std::get<0>(linkKeys.at(ix)).push_back(piv->mTag);
+		std::get<1>(linkKeys.at(ix)).push_back(civ->mTag);
+	}
 	
 	auto& linkedGroup = dict["pdbx_item_linked_group"];
 
 	// now store the links in the validator
 	for (auto& kv: linkIndex)
 	{
-		ValidateLink link;
-		std::tie(link.mParentCategory, link.mChildCategory, link.mLinkGroupID) = kv.first;
+		ValidateLink link = {};
+		std::tie(link.mParentCategory, link.mChildCategory) = kv.first;
+
+		if (linkGroupIds.count(kv.first))
+			link.mLinkGroupID = linkGroupIds[kv.first];
 		
 		std::tie(link.mParentKeys, link.mChildKeys) = linkKeys[kv.second];