When converting pdb to cif, calculate distance for LINKR records

include/cif++/Cif++.hpp

@@ -1195,6 +1195,19 @@ inline Condition Not(Condition&& cond)
     return Condition(new detail::NotConditionImpl(std::move(cond)));
     return Condition(new detail::NotConditionImpl(std::move(cond)));
 }
 }
 
 
+namespace literals
+{
+
+inline Key operator""_key(const char* text, size_t length)
+{
+	return Key(std::string(text, length));
+}
+
+inline constexpr Empty Null = Empty();
+
+}
+
+
 // -----------------------------------------------------------------------
 // -----------------------------------------------------------------------
 // iterators
 // iterators
 
 

src/PDB2Cif.cpp

@@ -42,6 +42,7 @@
 #include "cif++/PDB2CifRemark3.hpp"
 #include "cif++/PDB2CifRemark3.hpp"
 #include "cif++/CifUtils.hpp"
 #include "cif++/CifUtils.hpp"
 #include "cif++/Symmetry.hpp"
 #include "cif++/Symmetry.hpp"
+#include "cif++/Point.hpp"
 
 
 namespace ba = boost::algorithm;
 namespace ba = boost::algorithm;
 
 
@@ -5772,6 +5773,50 @@ void PDBFileParser::Parse(std::istream& is, cif::File& result)
 //				continue;
 //				continue;
 //			}
 //			}
 //		}
 //		}
+
+		using namespace cif::literals;
+
+		auto& atom_site = *getCategory("atom_site");
+
+		// for (const auto& [asym1, seq1, atom1, asym2, seq2, atom2]: getCategory("struct_conn")
+		// 	->find<std::string,std::string,std::string,std::string,std::string,std::string>(
+		// 		"pdbx_dist_value"_key == 0 or "pdbx_dist_value"_key == Null,
+		// 		{ "ptnr1_label_asym_id", "ptnr1_label_seq_id", "ptnr1_label_atom_id",
+		// 		"ptnr2_label_asym_id", "ptnr2_label_seq_id", "ptnr2_label_atom_id" }))
+		// {
+		// 	auto a1 = atom_site.find1("label_asym_id"_key == asym1 and "label_seq_id"_key == seq1 and "label_atom_id"_key == atom1);
+		// 	auto a2 = atom_site.find1("label_asym_id"_key == asym2 and "label_seq_id"_key == seq2 and "label_atom_id"_key == atom2);
+
+		// 	const auto& [x1, y1, z1] = a1.get<float,float,float>({"cartn_x", "cartn_y", "cartn_z"});
+		// 	const auto& [x2, y2, z2] = a2.get<float,float,float>({"cartn_x", "cartn_y", "cartn_z"});
+
+		// 	float distance = mmcif::Distance(mmcif::Point{x1, y1, z1}, mmcif::Point{x2, y2, z2});
+
+		// 	std::cerr << "Distance for link: " << distance << std::endl;
+
+		// }
+
+		for (auto r: getCategory("struct_conn")->find("pdbx_dist_value"_key == 0 or "pdbx_dist_value"_key == Null))
+		{
+			const auto& [asym1, seq1, atom1, symm1, asym2, seq2, atom2, symm2] = r.get<std::string,std::string,std::string,std::string,std::string,std::string,std::string,std::string>(
+				{ "ptnr1_label_asym_id", "ptnr1_label_seq_id", "ptnr1_label_atom_id", "ptnr1_symmetry",
+				  "ptnr2_label_asym_id", "ptnr2_label_seq_id", "ptnr2_label_atom_id", "ptnr2_symmetry" });
+
+			auto a1 = atom_site.find1("label_asym_id"_key == asym1 and "label_seq_id"_key == seq1 and "label_atom_id"_key == atom1);
+			auto a2 = atom_site.find1("label_asym_id"_key == asym2 and "label_seq_id"_key == seq2 and "label_atom_id"_key == atom2);
+
+			const auto& [x1, y1, z1] = a1.get<float,float,float>({"cartn_x", "cartn_y", "cartn_z"});
+			const auto& [x2, y2, z2] = a2.get<float,float,float>({"cartn_x", "cartn_y", "cartn_z"});
+
+			float distance = 1.0f;
+
+			if (symm1 == "1_555" and symm2 == "1_555")
+				distance = mmcif::Distance(mmcif::Point{x1, y1, z1}, mmcif::Point{x2, y2, z2});
+			else if (cif::VERBOSE)
+				std::cerr << "Cannot calculate distance for link since one of the atoms is in another dimension" << std::endl;
+
+			r["pdbx_dist_value"] = distance;
+		}
 	}
 	}
 	catch (const std::exception& ex)
 	catch (const std::exception& ex)
 	{
 	{