Merge branch 'develop' into trunk

CMakeLists.txt

@@ -25,7 +25,7 @@
 cmake_minimum_required(VERSION 3.15)
 
 # set the project name
-project(mkdssp VERSION 4.3.2 LANGUAGES CXX)
+project(mkdssp VERSION 4.4.0 LANGUAGES CXX)
 
 list(APPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/cmake")
 
@@ -211,6 +211,10 @@ install(TARGETS ${PROJECT_NAME}
 	RUNTIME DESTINATION ${BIN_INSTALL_DIR}
 )
 
+set(CIFPP_DATA_DIR "${CMAKE_INSTALL_FULL_DATADIR}/libcifpp")
+install(FILES "${CMAKE_CURRENT_SOURCE_DIR}/mmcif_pdbx/dssp-extension.dic"
+        DESTINATION ${CIFPP_DATA_DIR})
+
 # manual
 find_program(PANDOC pandoc)
 
@@ -265,7 +269,9 @@ if(ENABLE_TESTING)
 	add_executable(unit-test-dssp ${PROJECT_SOURCE_DIR}/test/unit-test-dssp.cpp ${PROJECT_SOURCE_DIR}/src/dssp-io.cpp)
 
 	if(USE_RSRC)
-		mrc_target_resources(unit-test-dssp ${CIFPP_SHARE_DIR}/mmcif_pdbx.dic ${CIFPP_SHARE_DIR}/mmcif_ddl.dic)
+		mrc_target_resources(unit-test-dssp
+			${CIFPP_SHARE_DIR}/mmcif_pdbx.dic ${CIFPP_SHARE_DIR}/mmcif_ddl.dic
+			${CMAKE_CURRENT_SOURCE_DIR}/mmcif_pdbx/dssp-extension.dic)
 	endif()
 
 	target_include_directories(unit-test-dssp PRIVATE

changelog

-Version 4.3.2
+Version 4.4.0
 - Packaging (split out the web server again)
 - Added markdown doc file, all doc files are now created from mkdssp.1
   using pandoc, if that is installed.

include/dssp.hpp

@@ -172,6 +172,7 @@ class dssp
 		std::tuple<residue_info, int, bool> bridge_partner(int i) const;
 
 		int sheet() const;
+		int strand() const;
 
 		/// \brief return resinfo and the energy of the bond
 		std::tuple<residue_info, double> acceptor(int i) const;

mmcif_pdbx/dssp-extension.dic

@@ -477,6 +477,9 @@ save_dssp_struct_ladder
 ;
 ;
 	_dssp_struct_ladder.id                        A      
+	_dssp_struct_ladder.sheet_id                  A
+	_dssp_struct_ladder.range_id_1                   A
+	_dssp_struct_ladder.range_id_2                   B
 	_dssp_struct_ladder.type                      anti-parallel        
 	_dssp_struct_ladder.beg_1_label_comp_id       GLY                       
 	_dssp_struct_ladder.beg_1_label_asym_id       A                       
@@ -520,6 +523,39 @@ save__dssp_struct_ladder.id
 	_item_type.code          code
 	save_
 
+save__dssp_struct_ladder.sheet_id
+	_item.description
+;	This data item is a pointer to _struct_sheet.id in the
+	STRUCT_SHEET category.
+;
+	_item.name               '_dssp_struct_ladder.sheet_id'
+	_item.category_id        dssp_struct_ladder
+	_item.mandatory_code     yes
+	_item_type.code          code
+	save_
+
+save__dssp_struct_ladder.range_id_1
+	_item.description
+;   This data item is a pointer to _struct_sheet_range.id in
+    the STRUCT_SHEET_RANGE category.
+;
+	_item.name               '_dssp_struct_ladder.range_id_1'
+	_item.category_id        dssp_struct_ladder
+	_item.mandatory_code     yes
+	_item_type.code          code
+	save_
+
+save__dssp_struct_ladder.range_id_2
+	_item.description
+;   This data item is a pointer to _struct_sheet_range.id in
+    the STRUCT_SHEET_RANGE category.
+;
+	_item.name               '_dssp_struct_ladder.range_id_2'
+	_item.category_id        dssp_struct_ladder
+	_item.mandatory_code     yes
+	_item_type.code          code
+	save_
+
 save__dssp_struct_ladder.type
 	_item.description
 ;	The type of the ladder, be it parallel or anti-parallel
@@ -1466,9 +1502,10 @@ save_dssp_struct_summary
 	_dssp_struct_summary.helix_pp               .     
 	_dssp_struct_summary.bend                   S 
 	_dssp_struct_summary.chirality              +      
+	_dssp_struct_summary.sheet                  .  
+	_dssp_struct_summary.strand                 .
 	_dssp_struct_summary.ladder_1               .     
 	_dssp_struct_summary.ladder_2               .     
-	_dssp_struct_summary.sheet                  .  
 	_dssp_struct_summary.accessibility         23.1           
 	_dssp_struct_summary.TCO                    0.940
 	_dssp_struct_summary.kappa                  73.9  
@@ -1655,31 +1692,43 @@ save__dssp_struct_summary.chirality
 	                         '-'
 	save_
 
-save__dssp_struct_summary.ladder_1
+save__dssp_struct_summary.sheet
 	_item.description
-;	Label for the first beta bridge of which this residue is part.
+;   This data item is a pointer to _struct_sheet.id in
+    the STRUCT_SHEET category.
 ;
-	_item.name             '_dssp_struct_summary.ladder_1'
+	_item.name             '_dssp_struct_summary.sheet'
 	_item.category         dssp_struct_summary
 	_item.mandatory_code   no
 	_item_type.code        code
 	save_
 
-save__dssp_struct_summary.ladder_2
+save__dssp_struct_summary.strand
 	_item.description
-;	Label for the second beta bridge of which this residue is part.
+;   This data item is a pointer to _struct_sheet_range.id in
+    the STRUCT_SHEET_RANGE category.
 ;
-	_item.name             '_dssp_struct_summary.ladder_2'
+	_item.name             '_dssp_struct_summary.strand'
 	_item.category         dssp_struct_summary
 	_item.mandatory_code   no
 	_item_type.code        code
 	save_
 
-save__dssp_struct_summary.sheet
+save__dssp_struct_summary.ladder_1
 	_item.description
-;	Label for the sheet of which this residue is part.
+;	Label for the first beta bridge of which this residue is part.
 ;
-	_item.name             '_dssp_struct_summary.sheet'
+	_item.name             '_dssp_struct_summary.ladder_1'
+	_item.category         dssp_struct_summary
+	_item.mandatory_code   no
+	_item_type.code        code
+	save_
+
+save__dssp_struct_summary.ladder_2
+	_item.description
+;	Label for the second beta bridge of which this residue is part.
+;
+	_item.name             '_dssp_struct_summary.ladder_2'
 	_item.category         dssp_struct_summary
 	_item.mandatory_code   no
 	_item_type.code        code

src/dssp.cpp

@@ -27,7 +27,6 @@
 // Calculate DSSP-like secondary structure information
 
 #include "dssp.hpp"
-#include "queue.hpp"
 
 #include "dssp-io.hpp"
 
@@ -43,8 +42,6 @@ using helix_type = dssp::helix_type;
 using helix_position_type = dssp::helix_position_type;
 using chain_break_type = dssp::chain_break_type;
 
-using queue_type = blocking_queue<std::tuple<uint32_t,uint32_t>>;
-
 // --------------------------------------------------------------------
 
 const double
@@ -421,6 +418,9 @@ struct dssp::residue
 	void SetSheet(uint32_t inSheet) { mSheet = inSheet; }
 	uint32_t GetSheet() const { return mSheet; }
 
+	void SetStrand(uint32_t inStrand) { mStrand = inStrand; }
+	uint32_t GetStrand() const { return mStrand; }
+
 	bool IsBend() const { return mBend; }
 	void SetBend(bool inBend) { mBend = inBend; }
 
@@ -548,6 +548,7 @@ struct dssp::residue
 	HBond mHBondDonor[2] = {}, mHBondAcceptor[2] = {};
 	bridge_partner mBetaPartner[2] = {};
 	uint32_t mSheet = 0;
+	uint32_t mStrand = 0;	// Added to ease the writing of mmCIF's struct_sheet and friends
 	helix_position_type mHelixFlags[4] = { helix_position_type::None, helix_position_type::None, helix_position_type::None, helix_position_type::None }; //
 	bool mBend = false;
 	chain_break_type mChainBreak = chain_break_type::None;
@@ -1099,6 +1100,26 @@ void CalculateBetaSheets(std::vector<residue> &inResidues, statistics &stats, st
 			inResidues[i].SetSheet(bridge.sheet);
 		}
 	}
+
+	// Create 'strands'. A strand is a range of residues without a gap in between
+	// that belong to the same sheet.
+
+	int strand = 0;
+	for (uint32_t iSheet = 1; iSheet < sheet; ++iSheet)
+	{
+		int lastNr = -1;
+		for (auto &res : inResidues)
+		{
+			if (res.mSheet != iSheet)
+				continue;
+			
+			if (lastNr + 1 < res.mNumber)
+				++strand;
+			
+			res.mStrand = strand;
+			lastNr = res.mNumber;
+		}
+	}
 }
 
 // --------------------------------------------------------------------
@@ -1487,7 +1508,10 @@ DSSP_impl::DSSP_impl(const cif::datablock &db, int model_nr, int min_poly_prolin
 					nextNext.mCAlpha,
 					cur.mCAlpha);
 				float skap = std::sqrt(1 - ckap * ckap);
-				cur.mKappa = std::atan2(skap, ckap) * static_cast<float>(180 / kPI);
+
+				auto kappa = std::atan2(skap, ckap) * static_cast<float>(180 / kPI);
+				if (not std::isnan(kappa))
+					cur.mKappa = kappa;
 			}
 		}
 
@@ -2138,6 +2162,11 @@ int dssp::residue_info::sheet() const
 	return m_impl->GetSheet();
 }
 
+int dssp::residue_info::strand() const
+{
+	return m_impl->GetStrand();
+}
+
 std::tuple<dssp::residue_info, double> dssp::residue_info::acceptor(int i) const
 {
 	auto &a = m_impl->mHBondAcceptor[i];

src/queue.hpp

-/*-
- * SPDX-License-Identifier: BSD-2-Clause
- * 
- * Copyright (c) 2021 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.
- */
-
-#pragma once
-
-#include <condition_variable>
-#include <mutex>
-#include <queue>
-
-template <typename T, size_t N = 100>
-class blocking_queue
-{
-  public:
-	void push(T const &value)
-	{
-		std::unique_lock<std::mutex> lock(m_guard);
-
-		while (m_queue.size() >= N)
-			m_full_signal.wait(lock);
-
-		m_queue.push(value);
-
-		m_empty_signal.notify_one();
-	}
-
-	T pop()
-	{
-		std::unique_lock<std::mutex> lock(m_guard);
-		while (m_queue.empty())
-			m_empty_signal.wait(lock);
-
-		auto value = m_queue.front();
-		m_queue.pop();
-
-		m_full_signal.notify_one();
-
-		return value;
-	}
-
-	template<class Rep, class Period>
-	std::tuple<bool,T> pop(const std::chrono::duration<Rep, Period>& wait_for)
-	{
-		std::unique_lock<std::mutex> lock(m_guard);
-		while (m_queue.empty())
-		{
-		    auto now = std::chrono::system_clock::now();
-			if (m_empty_signal.wait_until(lock, now + wait_for) == std::cv_status::timeout)
-				return { true , T{} };
-		}
-
-		auto value = m_queue.front();
-		m_queue.pop();
-
-		m_full_signal.notify_one();
-
-		return { false, value };
-	}
-
-	bool is_full() const
-	{
-		std::unique_lock<std::mutex> lock(m_guard);
-		return m_queue.size() >= N;
-	}
-
-  private:
-	std::queue<T> m_queue;
-	mutable std::mutex m_guard;
-	std::condition_variable m_empty_signal, m_full_signal;
-};
-
-template <typename T, size_t N = 10>
-class non_blocking_queue
-{
-  public:
-	bool push(T const &value)
-	{
-		bool result = false;
-
-		std::unique_lock<std::mutex> lock(m_guard);
-
-		if (m_queue.size() < N)
-		{
-			m_queue.push(value);
-			m_empty_signal.notify_one();
-			result = true;
-		}
-			
-		return result;
-	}
-
-	T pop()
-	{
-		std::unique_lock<std::mutex> lock(m_guard);
-		while (m_queue.empty())
-			m_empty_signal.wait(lock);
-
-		auto value = m_queue.front();
-		m_queue.pop();
-
-		return value;
-	}
-
-  private:
-	std::queue<T> m_queue;
-	mutable std::mutex m_guard;
-	std::condition_variable m_empty_signal;
-};
\ No newline at end of file

test/1cbs.dssp

-==== Secondary Structure Definition by the program DSSP, NKI version 4.0                           ==== DATE=2021-08-25        .
+==== Secondary Structure Definition by the program DSSP, NKI version 4.4.0                         ==== DATE=2021-08-25        .
 REFERENCE W. KABSCH AND C.SANDER, BIOPOLYMERS 22 (1983) 2577-2637                                                              .
 HEADER    RETINOIC-ACID TRANSPORT                 28-SEP-94   1CBS                                                             .
 COMPND    MOL_ID: 1; MOLECULE: CELLULAR RETINOIC ACID BINDING PROTEIN TYPE II; CHAIN: A; ENGINEERED: YES                       .

test/unit-test-dssp.cpp

@@ -32,6 +32,8 @@
 #include "dssp.hpp"
 #include "dssp-io.hpp"
 
+#include <cif++/dictionary_parser.hpp>
+
 namespace fs = std::filesystem;
 
 // --------------------------------------------------------------------
@@ -97,7 +99,7 @@ BOOST_AUTO_TEST_CASE(ut_dssp)
 	std::string line_t, line_r;
 	BOOST_CHECK(std::getline(test, line_t) and std::getline(reference, line_r));
 
-	const char *kHeaderLineStart = "==== Secondary Structure Definition by the program DSSP, NKI version 4.3                           ====";
+	const char *kHeaderLineStart = "==== Secondary Structure Definition by the program DSSP, NKI version 4.4.0                         ====";
 	BOOST_CHECK(line_t.compare(0, std::strlen(kHeaderLineStart), kHeaderLineStart) == 0);
 	// BOOST_CHECK(line_r.compare(0, std::strlen(kHeaderLineStart), kHeaderLineStart) == 0);
 
@@ -225,4 +227,19 @@ BOOST_AUTO_TEST_CASE(dssp_2)
 		BOOST_CHECK_EQUAL(ri.seq_id(), seqID);
 		BOOST_CHECK_EQUAL((char)ri.type(), secstr.front());
 	}
+}
+
+// --------------------------------------------------------------------
+
+BOOST_AUTO_TEST_CASE(dssp_3)
+{
+	cif::file f(gTestDir / "1cbs.cif.gz");
+
+	BOOST_ASSERT(f.is_valid());
+
+	dssp dssp(f.front(), 1, 3, true);
+
+	dssp.annotate(f.front(), true, true);
+
+	BOOST_TEST(f.is_valid());
 }
\ No newline at end of file