Better output format

Added dictionary extension

include/dssp.hpp

@@ -135,15 +135,15 @@ class dssp
 		int pdb_seq_num() const;
 		std::string pdb_ins_code() const;
 
-		float alpha() const;
-		float kappa() const;
-		float phi() const;
-		float psi() const;
-		float tco() const;
-		float omega() const;
+		std::optional<float> alpha() const;
+		std::optional<float> kappa() const;
+		std::optional<float> phi() const;
+		std::optional<float> psi() const;
+		std::optional<float> tco() const;
+		std::optional<float> omega() const;
 
 		bool is_pre_pro() const;
-		bool is_cis() const { return std::abs(omega()) < 30.0f; }
+		bool is_cis() const { return std::abs(omega().value_or(360)) < 30.0f; }
 
 		float chiral_volume() const;
 		std::size_t nr_of_chis() const;

src/dssp-io.cpp

@@ -91,7 +91,7 @@ std::string ResidueToDSSPLine(const dssp::residue_info &info)
 	if (info.bend())
 		bend = 'S';
 
-	double alpha = residue.alpha();
+	double alpha = residue.alpha().value_or(360);
 	char chirality = alpha == 360 ? ' ' : (alpha < 0 ? '-' : '+');
 
 	uint32_t bp[2] = {};
@@ -882,7 +882,7 @@ void writeStatistics(cif::datablock &db, const dssp &dssp)
 
 	using histogram_data_type = std::tuple<const char *, const uint32_t *>;
 	for (const auto &[type, values] : std::vector<histogram_data_type>{
-			 { "parallel_bridges_per_ladder", stats.histogram.residues_per_alpha_helix },
+			 { "residues_per_alpha_helix", stats.histogram.residues_per_alpha_helix },
 			 { "parallel_bridges_per_ladder", stats.histogram.parallel_bridges_per_ladder },
 			 { "antiparallel_bridges_per_ladder", stats.histogram.antiparallel_bridges_per_ladder },
 			 { "ladders_per_sheet", stats.histogram.ladders_per_sheet } })
@@ -930,6 +930,11 @@ void writeSummary(cif::datablock &db, const dssp &dssp)
 
 	auto &dssp_struct_summary = db["dssp_struct_summary"];
 
+	// prime the category with the field labels we need, this is to ensure proper order in writing out the data.
+
+	for (auto label : { "entry_id", "label_comp_id", "label_asym_id", "label_seq_id", "secondary_structure", "ss_bridge", "helix_3_10", "helix_alpha", "helix_pi", "helix_pp", "bend", "chirality", "ladder_1", "ladder_2", "sheet", "accessibility", "TCO", "kappa", "alpha", "phi", "psi", "x_ca", "y_ca", "z_ca"})
+		dssp_struct_summary.add_column(label);
+
 	for (auto res : dssp)
 	{
 
@@ -979,10 +984,9 @@ void writeSummary(cif::datablock &db, const dssp &dssp)
 		if (res.bend())
 			bend = "S";
 
-		double alpha = res.alpha();
 		std::string chirality = ".";
-		if (alpha != 360)
-			chirality = alpha < 0 ? "-" : "+";
+		if (res.alpha().has_value())
+			chirality = *res.alpha() < 0 ? "-" : "+";
 
 		std::string ladders[2] = { ".", "." };
 
@@ -997,7 +1001,7 @@ void writeSummary(cif::datablock &db, const dssp &dssp)
 
 		auto const &[cax, cay, caz] = res.ca_location();
 
-		dssp_struct_summary.emplace({
+		cif::row_initializer data{
 			{ "entry_id", db.name() },
 			{ "label_comp_id", res.compound_id() },
 			{ "label_asym_id", res.asym_id() },
@@ -1020,18 +1024,39 @@ void writeSummary(cif::datablock &db, const dssp &dssp)
 
 			{ "sheet", res.sheet() ? cif::cif_id_for_number(res.sheet() - 1) : "." },
 
-			{ "accesssibility", res.accessibility(), 1 },
-
-			{ "TCO", res.tco(), 3 },
-			{ "kappa", res.kappa(), 1 },
-			{ "alpha", res.alpha(), 1 },
-			{ "phi", res.phi(), 1 },
-			{ "psi", res.psi(), 1 },
+			{ "accessibility", res.accessibility(), 1 },
 
 			{ "x_ca", cax, 1 },
 			{ "y_ca", cay, 1 },
 			{ "z_ca", caz, 1 },
-		});
+		};
+
+		if (res.tco().has_value())
+			data.emplace_back("TCO", *res.tco(), 3);
+		else
+			data.emplace_back("TCO", ".");
+
+		if (res.kappa().has_value())
+			data.emplace_back("kappa", *res.kappa(), 1);
+		else
+			data.emplace_back("kappa", ".");
+
+		if (res.alpha().has_value())
+			data.emplace_back("alpha", *res.alpha(), 1);
+		else
+			data.emplace_back("alpha", ".");
+
+		if (res.phi().has_value())
+			data.emplace_back("phi", *res.phi(), 1);
+		else
+			data.emplace_back("phi", ".");
+
+		if (res.psi().has_value())
+			data.emplace_back("psi", *res.psi(), 1);
+		else
+			data.emplace_back("psi", ".");
+		
+		dssp_struct_summary.emplace(std::move(data));
 	}
 }
 

src/dssp.cpp

@@ -531,7 +531,8 @@ struct dssp::residue
 	float mAccessibility = 0;
 	float mChiralVolume = 0;
 
-	float mAlpha = 360, mKappa = 360, mPhi = 360, mPsi = 360, mTCO = 0, mOmega = 360;
+	// float mAlpha = 360, mKappa = 360, mPhi = 360, mPsi = 360, mTCO = 0, mOmega = 360;
+	std::optional<float> mAlpha, mKappa, mPhi, mPsi, mTCO, mOmega;
 
 	residue_type mType;
 	uint8_t mSSBridgeNr = 0;
@@ -1114,8 +1115,8 @@ void CalculateAlphaHelices(std::vector<residue> &inResidues, statistics &stats,
 
 	for (auto &r : inResidues)
 	{
-		double kappa = r.mKappa;
-		r.SetBend(kappa != 360 and kappa > 70);
+		if (r.mKappa.has_value())
+			r.SetBend(*r.mKappa > 70);
 	}
 
 	for (uint32_t i = 1; i + 4 < inResidues.size(); ++i)
@@ -1216,8 +1217,8 @@ void CalculatePPHelices(std::vector<residue> &inResidues, statistics &stats, int
 
 	for (uint32_t i = 1; i + 1 < inResidues.size(); ++i)
 	{
-		phi[i] = static_cast<float>(inResidues[i].mPhi);
-		psi[i] = static_cast<float>(inResidues[i].mPsi);
+		phi[i] = static_cast<float>(inResidues[i].mPhi.value_or(360));
+		psi[i] = static_cast<float>(inResidues[i].mPsi.value_or(360));
 	}
 
 	for (uint32_t i = 1; i + 3 < inResidues.size(); ++i)
@@ -1888,32 +1889,32 @@ std::string dssp::residue_info::pdb_ins_code() const
 	return m_impl->mPDBInsCode;
 }
 
-float dssp::residue_info::alpha() const
+std::optional<float> dssp::residue_info::alpha() const
 {
 	return m_impl->mAlpha;
 }
 
-float dssp::residue_info::kappa() const
+std::optional<float> dssp::residue_info::kappa() const
 {
 	return m_impl->mKappa;
 }
 
-float dssp::residue_info::omega() const
+std::optional<float> dssp::residue_info::omega() const
 {
 	return m_impl->mOmega;
 }
 
-float dssp::residue_info::phi() const
+std::optional<float> dssp::residue_info::phi() const
 {
 	return m_impl->mPhi;
 }
 
-float dssp::residue_info::psi() const
+std::optional<float> dssp::residue_info::psi() const
 {
 	return m_impl->mPsi;
 }
 
-float dssp::residue_info::tco() const
+std::optional<float> dssp::residue_info::tco() const
 {
 	return m_impl->mTCO;
 }