Moved DSSP code back here from libcifpp

CMakeLists.txt

@@ -123,13 +123,19 @@ find_package(Threads)
 find_package(cifpp 5.0.0 REQUIRED)
 find_package(Boost COMPONENTS date_time program_options)
 
+# The DSSP code is in a separate library, optionally to be used by others
+
+add_library(dssp_library OBJECT ${PROJECT_SOURCE_DIR}/src/DSSP.cpp)
+target_link_libraries(dssp_library cifpp::cifpp)
+
 add_executable(mkdssp
-	${PROJECT_SOURCE_DIR}/src/dssp.cpp
-	${PROJECT_SOURCE_DIR}/src/dssp.hpp
-	${PROJECT_SOURCE_DIR}/src/mkdssp.cpp)
+	${PROJECT_SOURCE_DIR}/src/dssp_wrapper.cpp
+	${PROJECT_SOURCE_DIR}/src/dssp_wrapper.hpp
+	${PROJECT_SOURCE_DIR}/src/mkdssp.cpp
+	$<TARGET_OBJECTS:dssp_library>)
 
-target_include_directories(mkdssp PRIVATE cifpp::cifpp ${CMAKE_SOURCE_DIR}/include ${CMAKE_BINARY_DIR})
-target_link_libraries(mkdssp PRIVATE cifpp::cifpp Boost::date_time Boost::program_options)
+target_include_directories(mkdssp PRIVATE ${CMAKE_BINARY_DIR})
+target_link_libraries(mkdssp PRIVATE dssp_library cifpp::cifpp Boost::date_time Boost::program_options)
 	
 if(USE_RSRC)
 	mrc_target_resources(mkdssp ${CIFPP_SHARE_DIR}/mmcif_pdbx.dic)
@@ -153,7 +159,7 @@ endif()
 
 # test
 
-add_executable(unit-test ${PROJECT_SOURCE_DIR}/test/unit-test.cpp ${PROJECT_SOURCE_DIR}/src/dssp.cpp)
+add_executable(unit-test ${PROJECT_SOURCE_DIR}/test/unit-test.cpp ${PROJECT_SOURCE_DIR}/src/dssp_wrapper.cpp)
 
 if(USE_RSRC)
 	mrc_target_resources(unit-test ${CIFPP_SHARE_DIR}/mmcif_pdbx.dic)
@@ -164,7 +170,7 @@ target_include_directories(unit-test PRIVATE
 	${CMAKE_CURRENT_SOURCE_DIR}/include
 )
 
-target_link_libraries(unit-test cifpp::cifpp Boost::date_time)
+target_link_libraries(unit-test dssp_library cifpp::cifpp Boost::date_time)
 
 if(MSVC)
 	# Specify unwind semantics so that MSVC knowns how to handle exceptions

src/DSSP.hpp

+/*-
+ * SPDX-License-Identifier: BSD-2-Clause
+ *
+ * Copyright (c) 2020 NKI/AVL, Netherlands Cancer Institute
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions are met:
+ *
+ * 1. Redistributions of source code must retain the above copyright notice, this
+ *    list of conditions and the following disclaimer
+ * 2. Redistributions in binary form must reproduce the above copyright notice,
+ *    this list of conditions and the following disclaimer in the documentation
+ *    and/or other materials provided with the distribution.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+ * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+ * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+ * DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
+ * ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+ * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+ * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+ * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+ * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+ * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ */
+
+/// \file DSSP.hpp
+/// Calculate DSSP-like secondary structure information.
+
+#pragma once
+
+#include <cif++/cif.hpp>
+
+namespace dssp
+{
+
+struct residue;
+
+enum class structure_type : char
+{
+	Loop = ' ',
+	Alphahelix = 'H',
+	Betabridge = 'B',
+	Strand = 'E',
+	Helix_3 = 'G',
+	Helix_5 = 'I',
+	Helix_PPII = 'P',
+	Turn = 'T',
+	Bend = 'S'
+};
+
+enum class helix_type
+{
+	_3_10,
+	alpha,
+	pi,
+	pp
+};
+
+enum class helix_position_type
+{
+	None,
+	Start,
+	End,
+	StartAndEnd,
+	Middle
+};
+
+const size_t
+	kHistogramSize = 30;
+
+struct statistics
+{
+	struct
+	{
+		uint32_t residues, chains, SS_bridges, intra_chain_SS_bridges, H_bonds;
+		uint32_t H_bonds_in_antiparallel_bridges, H_bonds_in_parallel_bridges;
+		uint32_t H_Bonds_per_distance[11];
+	} count;
+
+	double accessible_surface;
+
+	struct
+	{
+		uint32_t residues_per_alpha_helix[kHistogramSize];
+		uint32_t parallel_bridges_per_ladder[kHistogramSize];
+		uint32_t antiparallel_bridges_per_ladder[kHistogramSize];
+		uint32_t ladders_per_sheet[kHistogramSize];
+	} histogram;
+};
+
+enum class chain_break_type
+{
+	None,
+	NewChain,
+	Gap
+};
+
+class DSSP
+{
+  public:
+	DSSP(const cif::datablock &db, int model_nr, int min_poly_proline_stretch_length, bool calculateSurfaceAccessibility);
+	~DSSP();
+
+	DSSP(const DSSP &) = delete;
+	DSSP &operator=(const DSSP &) = delete;
+
+	statistics get_statistics() const;
+
+	class iterator;
+	using res_iterator = typename std::vector<residue>::iterator;
+
+	class residue_info
+	{
+	  public:
+		friend class iterator;
+
+		residue_info() = default;
+		residue_info(const residue_info &rhs) = default;
+		residue_info &operator=(const residue_info &rhs) = default;
+
+		explicit operator bool() const { return not empty(); }
+		bool empty() const { return m_impl == nullptr; }
+
+		std::string asym_id() const;
+		int seq_id() const;
+		std::string alt_id() const;
+		std::string compound_id() const;
+
+		std::string auth_asym_id() const;
+		int auth_seq_id() const;
+
+		std::string pdb_strand_id() const;
+		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;
+		std::tuple<float, float, float> ca_location() const;
+
+		chain_break_type chain_break() const;
+
+		/// \brief the internal number in DSSP
+		int nr() const;
+
+		structure_type type() const;
+
+		int ssBridgeNr() const;
+
+		helix_position_type helix(helix_type helixType) const;
+
+		bool is_alpha_helix_end_before_start() const;
+
+		bool bend() const;
+
+		double accessibility() const;
+
+		/// \brief returns resinfo, ladder and parallel
+		std::tuple<residue_info, int, bool> bridge_partner(int i) const;
+
+		int sheet() const;
+
+		/// \brief return resinfo and the energy of the bond
+		std::tuple<residue_info, double> acceptor(int i) const;
+		std::tuple<residue_info, double> donor(int i) const;
+
+		/// \brief Simple compare equals
+		bool operator==(const residue_info &rhs) const
+		{
+			return m_impl == rhs.m_impl;
+		}
+
+		/// \brief Returns \result true if there is a bond between two residues
+		friend bool test_bond(residue_info const &a, residue_info const &b);
+
+	  private:
+		residue_info(residue *res)
+			: m_impl(res)
+		{
+		}
+
+		residue *m_impl = nullptr;
+	};
+
+	class iterator
+	{
+	  public:
+		using iterator_category = std::bidirectional_iterator_tag;
+		using value_type = residue_info;
+		using difference_type = std::ptrdiff_t;
+		using pointer = value_type *;
+		using reference = value_type &;
+
+		iterator(const iterator &i) = default;
+		iterator(residue *res);
+		iterator &operator=(const iterator &i) = default;
+
+		reference operator*() { return m_current; }
+		pointer operator->() { return &m_current; }
+
+		iterator &operator++();
+		iterator operator++(int)
+		{
+			auto tmp(*this);
+			this->operator++();
+			return tmp;
+		}
+
+		iterator &operator--();
+		iterator operator--(int)
+		{
+			auto tmp(*this);
+			this->operator--();
+			return tmp;
+		}
+
+		bool operator==(const iterator &rhs) const { return m_current.m_impl == rhs.m_current.m_impl; }
+		bool operator!=(const iterator &rhs) const { return m_current.m_impl != rhs.m_current.m_impl; }
+
+	  private:
+		residue_info m_current;
+	};
+
+	using value_type = residue_info;
+
+	// To access residue info by key, i.e. LabelAsymID and LabelSeqID
+	using key_type = std::tuple<std::string,int>;
+
+	iterator begin() const;
+	iterator end() const;
+
+	residue_info operator[](const key_type &key) const;
+
+	bool empty() const { return begin() == end(); }
+
+	// convenience method, when creating old style DSSP files
+
+	enum class pdb_record_type { HEADER, COMPND, SOURCE, AUTHOR };
+
+	std::string get_pdb_header_line(pdb_record_type pdb_record) const;
+
+  private:
+	struct DSSP_impl *m_impl;
+};
+
+} // namespace dssp

src/dssp.cpp → src/dssp_wrapper.cpp

@@ -39,7 +39,7 @@
 #include <cif++/structure/Compound.hpp>
 #include <cif++/utilities.hpp>
 
-#include "dssp.hpp"
+#include "dssp_wrapper.hpp"
 #include "revision.hpp"
 
 // --------------------------------------------------------------------

src/mkdssp.cpp

@@ -38,12 +38,11 @@
 #include <boost/format.hpp>
 #include <boost/date_time/gregorian/formatters.hpp>
 
-#include <cif++/dssp/DSSP.hpp>
-// #include <cif++/structure/Compound.hpp>
+#include "DSSP.hpp"
 
 #include <boost/program_options.hpp>
 
-#include "dssp.hpp"
+#include "dssp_wrapper.hpp"
 #include "revision.hpp"
 
 namespace fs = std::filesystem;

test/unit-test.cpp

@@ -30,9 +30,9 @@
 
 #include <stdexcept>
 
-#include <cif++/dssp/DSSP.hpp>
+#include "DSSP.hpp"
 
-#include "dssp.hpp"
+#include "dssp_wrapper.hpp"
 
 namespace ba = boost::algorithm;