Write BEND and (optionally) OTHER

src/dssp.cpp

@@ -269,7 +269,7 @@ void writeDSSP(const mmcif::Structure& structure, const mmcif::DSSP& dssp, std::
 	// }
 }
 
-void annotateDSSP(mmcif::Structure& structure, const mmcif::DSSP& dssp, std::ostream& os)
+void annotateDSSP(mmcif::Structure& structure, const mmcif::DSSP& dssp, bool writeOther, std::ostream& os)
 {
 	auto& db = structure.getFile().data();
 
@@ -291,7 +291,6 @@ void annotateDSSP(mmcif::Structure& structure, const mmcif::DSSP& dssp, std::ost
 
 		auto st = dssp.begin(), lt = st;
 		auto lastSS = st->ss();
-		std::string id;
 
 		for (auto t = dssp.begin(); ; lt = t, ++t)
 		{
@@ -299,52 +298,13 @@ void annotateDSSP(mmcif::Structure& structure, const mmcif::DSSP& dssp, std::ost
 
 			bool flush = (stop or t->ss() != lastSS);
 
-			if (flush and lastSS != mmcif::SecondaryStructureType::ssLoop)
+			if (flush and (writeOther or lastSS != mmcif::SecondaryStructureType::ssLoop))
 			{
 				auto& rb = st->residue();
 				auto& re = lt->residue();
 
-				structConf.emplace({
-					{ "conf_type_id", id },
-					{ "id", id + std::to_string(foundTypes[id]++) },
-					// { "pdbx_PDB_helix_id", vS(12, 14) },
-					{ "beg_label_comp_id", rb.compoundID() },
-					{ "beg_label_asym_id", rb.asymID() },
-					{ "beg_label_seq_id", rb.seqID() },
-					{ "pdbx_beg_PDB_ins_code", rb.authInsCode() },
-					{ "end_label_comp_id", re.compoundID() },
-					{ "end_label_asym_id", re.asymID() },
-					{ "end_label_seq_id", re.seqID() },
-					{ "pdbx_end_PDB_ins_code", re.authInsCode() },
-		
-					{ "beg_auth_comp_id", rb.compoundID() },
-					{ "beg_auth_asym_id", rb.authAsymID() },
-					{ "beg_auth_seq_id", rb.authSeqID() },
-					{ "end_auth_comp_id", re.compoundID() },
-					{ "end_auth_asym_id", re.authAsymID() },
-					{ "end_auth_seq_id", re.authSeqID() }
-
-					// { "pdbx_PDB_helix_class", vS(39, 40) },
-					// { "details", vS(41, 70) },
-					// { "pdbx_PDB_helix_length", vI(72, 76) }
-				});
-
-				st = t;
-			}
-
-			if (lastSS != t->ss())
-			{
-				st = t;
-				lastSS = t->ss();
-			}
-
-			if (stop)
-				break;
-
-			if (not flush)
-				continue;
-
-			switch (t->ss())
+				std::string id;
+				switch (lastSS)
 				{
 					case mmcif::SecondaryStructureType::ssHelix_3:
 						id = "HELX_RH_3T_P";
@@ -367,7 +327,7 @@ void annotateDSSP(mmcif::Structure& structure, const mmcif::DSSP& dssp, std::ost
 						break;
 
 					case mmcif::SecondaryStructureType::ssBend:
-					id = "TURN_P";
+						id = "BEND";
 						break;
 
 					case mmcif::SecondaryStructureType::ssBetabridge:
@@ -375,14 +335,11 @@ void annotateDSSP(mmcif::Structure& structure, const mmcif::DSSP& dssp, std::ost
 						id = "STRN";
 						break;
 
-				default:
-					id.clear();
+					case mmcif::SecondaryStructureType::ssLoop:
+						id = "OTHER";
 						break;
 				}
 
-			if (id.empty())
-				continue;
-
 				if (foundTypes.count(id) == 0)
 				{
 					structConfType.emplace({
@@ -391,6 +348,43 @@ void annotateDSSP(mmcif::Structure& structure, const mmcif::DSSP& dssp, std::ost
 					});
 					foundTypes[id] = 1;
 				}
+
+				structConf.emplace({
+					{ "conf_type_id", id },
+					{ "id", id + std::to_string(foundTypes[id]++) },
+					// { "pdbx_PDB_helix_id", vS(12, 14) },
+					{ "beg_label_comp_id", rb.compoundID() },
+					{ "beg_label_asym_id", rb.asymID() },
+					{ "beg_label_seq_id", rb.seqID() },
+					{ "pdbx_beg_PDB_ins_code", rb.authInsCode() },
+					{ "end_label_comp_id", re.compoundID() },
+					{ "end_label_asym_id", re.asymID() },
+					{ "end_label_seq_id", re.seqID() },
+					{ "pdbx_end_PDB_ins_code", re.authInsCode() },
+		
+					{ "beg_auth_comp_id", rb.compoundID() },
+					{ "beg_auth_asym_id", rb.authAsymID() },
+					{ "beg_auth_seq_id", rb.authSeqID() },
+					{ "end_auth_comp_id", re.compoundID() },
+					{ "end_auth_asym_id", re.authAsymID() },
+					{ "end_auth_seq_id", re.authSeqID() }
+
+					// { "pdbx_PDB_helix_class", vS(39, 40) },
+					// { "details", vS(41, 70) },
+					// { "pdbx_PDB_helix_length", vI(72, 76) }
+				});
+
+				st = t;
+			}
+
+			if (lastSS != t->ss())
+			{
+				st = t;
+				lastSS = t->ss();
+			}
+
+			if (stop)
+				break;
 		}
 	}
 
@@ -631,6 +625,8 @@ int pr_main(int argc, char* argv[])
 
 		("min-pp-stretch",		po::value<short>(),			"Minimal number of residues having PSI/PHI in range for a PP helix, default is 3")
 
+		("write-other",										"If set, write the type OTHER for loops, default is to leave this out")
+
 		("verbose,v",										"verbose output")
 		;
 	
@@ -703,6 +699,8 @@ int pr_main(int argc, char* argv[])
 	if (vm.count("min-pp-stretch"))
 		pp_stretch = vm["min-pp-stretch"].as<short>();
 
+	bool writeOther = vm.count("write-other");
+
 	std::string fmt;
 	if (vm.count("output-format"))
 		fmt = vm["output-format"].as<std::string>();
@@ -748,14 +746,14 @@ int pr_main(int argc, char* argv[])
 		if (fmt == "dssp")
 			writeDSSP(structure, dssp, out);
 		else
-			annotateDSSP(structure, dssp, out);
+			annotateDSSP(structure, dssp, writeOther, out);
 	}
 	else
 	{
 		if (fmt == "dssp")
 			writeDSSP(structure, dssp, std::cout);
 		else
-			annotateDSSP(structure, dssp, std::cout);
+			annotateDSSP(structure, dssp, writeOther, std::cout);
 	}
 	
 	return 0;