Merge branch 'trunk' of github.com:PDB-REDO/dssp into trunk

CMakeLists.txt

@@ -25,7 +25,7 @@
 cmake_minimum_required(VERSION 3.15)
 cmake_minimum_required(VERSION 3.15)
 
 
 # set the project name
 # set the project name
-project(mkdssp VERSION 4.3 LANGUAGES CXX)
+project(mkdssp VERSION 4.3.1 LANGUAGES CXX)
 
 
 list(APPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/cmake")
 list(APPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/cmake")
 
 
@@ -105,7 +105,7 @@ find_package(Threads)
 
 
 if(NOT PDB_REDO_META)
 if(NOT PDB_REDO_META)
 	find_package(libmcfp REQUIRED)
 	find_package(libmcfp REQUIRED)
-	find_package(cifpp 5.0.8 REQUIRED)
+	find_package(cifpp 5.1.0 REQUIRED)
 
 
 	if(BUILD_WEBSERVER)
 	if(BUILD_WEBSERVER)
 		find_package(zeep REQUIRED)
 		find_package(zeep REQUIRED)
@@ -135,7 +135,8 @@ target_link_libraries(mkdssp PRIVATE dssp cifpp::cifpp libmcfp::libmcfp dssp::ds
 if(USE_RSRC)
 if(USE_RSRC)
 	mrc_target_resources(mkdssp
 	mrc_target_resources(mkdssp
 		${CIFPP_SHARE_DIR}/mmcif_pdbx.dic
 		${CIFPP_SHARE_DIR}/mmcif_pdbx.dic
-		${CIFPP_SHARE_DIR}/mmcif_ddl.dic)
+		${CIFPP_SHARE_DIR}/mmcif_ddl.dic
+		${PROJECT_SOURCE_DIR}/mmcif_pdbx/dssp-extension.dic)
 endif()
 endif()
 
 
 if(BUILD_WEBSERVER)
 if(BUILD_WEBSERVER)

changelog

+Version 4.3.1
+- Optimised for speed
+- Fix in sheet numbering (mmCIF output)
+
 Version 4.3
 Version 4.3
 - Write new output by default
 - Write new output by default
 - Fix some issues with this new output, typo e.g.
 - Fix some issues with this new output, typo e.g.

mmcif_pdbx/dssp-extension.dic

@@ -173,7 +173,7 @@ save__dssp_struct_bridge_pairs.acceptor_1_label_asym_id
 ;
 ;
 	_item.name                  '_dssp_struct_bridge_pairs.acceptor_1_label_asym_id'
 	_item.name                  '_dssp_struct_bridge_pairs.acceptor_1_label_asym_id'
 	_item.category_id           dssp_struct_bridge_pairs
 	_item.category_id           dssp_struct_bridge_pairs
-	_item.mandatory_code        yes
+	_item.mandatory_code        no
 	_item_type.code             code
 	_item_type.code             code
 	save_
 	save_
 
 
@@ -250,7 +250,7 @@ save__dssp_struct_bridge_pairs.acceptor_2_label_asym_id
 ;
 ;
 	_item.name                  '_dssp_struct_bridge_pairs.acceptor_2_label_asym_id'
 	_item.name                  '_dssp_struct_bridge_pairs.acceptor_2_label_asym_id'
 	_item.category_id           dssp_struct_bridge_pairs
 	_item.category_id           dssp_struct_bridge_pairs
-	_item.mandatory_code        yes
+	_item.mandatory_code        no
 	_item_type.code             code
 	_item_type.code             code
 	save_
 	save_
 
 
@@ -327,7 +327,7 @@ save__dssp_struct_bridge_pairs.donor_1_label_asym_id
 ;
 ;
 	_item.name                  '_dssp_struct_bridge_pairs.donor_1_label_asym_id'
 	_item.name                  '_dssp_struct_bridge_pairs.donor_1_label_asym_id'
 	_item.category_id           dssp_struct_bridge_pairs
 	_item.category_id           dssp_struct_bridge_pairs
-	_item.mandatory_code        yes
+	_item.mandatory_code        no
 	_item_type.code             code
 	_item_type.code             code
 	save_
 	save_
 
 
@@ -404,7 +404,7 @@ save__dssp_struct_bridge_pairs.donor_2_label_asym_id
 ;
 ;
 	_item.name                  '_dssp_struct_bridge_pairs.donor_2_label_asym_id'
 	_item.name                  '_dssp_struct_bridge_pairs.donor_2_label_asym_id'
 	_item.category_id           dssp_struct_bridge_pairs
 	_item.category_id           dssp_struct_bridge_pairs
-	_item.mandatory_code        yes
+	_item.mandatory_code        no
 	_item_type.code             code
 	_item_type.code             code
 	save_
 	save_
 
 

src/mkdssp.cpp

@@ -74,6 +74,8 @@ int d_main(int argc, const char *argv[])
 		mcfp::make_option("write-other", "If set, write the type OTHER for loops, default is to leave this out"),
 		mcfp::make_option("write-other", "If set, write the type OTHER for loops, default is to leave this out"),
 		mcfp::make_option("no-dssp-categories", "If set, will suppress output of new DSSP output in mmCIF format"),
 		mcfp::make_option("no-dssp-categories", "If set, will suppress output of new DSSP output in mmCIF format"),
 
 
+		mcfp::make_option("calculate-accessibility", "Default is to not calculate the surface accessibility when the output format is mmCIF"),
+
 		mcfp::make_option<std::string>("mmcif-dictionary", "Path to the mmcif_pdbx.dic file to use instead of default"),
 		mcfp::make_option<std::string>("mmcif-dictionary", "Path to the mmcif_pdbx.dic file to use instead of default"),
 
 
 		mcfp::make_option("help,h", "Display help message"),
 		mcfp::make_option("help,h", "Display help message"),
@@ -93,16 +95,10 @@ int d_main(int argc, const char *argv[])
 		exit(0);
 		exit(0);
 	}
 	}
 
 
-	if (config.has("help"))
+	if (config.has("help") or config.operands().empty())
 	{
 	{
 		std::cerr << config << std::endl;
 		std::cerr << config << std::endl;
-		exit(0);
-	}
-
-	if (config.operands().empty())
-	{
-		std::cerr << "Input file not specified" << std::endl;
-		exit(1);
+		exit(config.has("help") ? 0 : 1);
 	}
 	}
 
 
 	if (config.has("output-format") and config.get<std::string>("output-format") != "dssp" and config.get<std::string>("output-format") != "mmcif")
 	if (config.has("output-format") and config.get<std::string>("output-format") != "dssp" and config.get<std::string>("output-format") != "mmcif")
@@ -130,8 +126,6 @@ int d_main(int argc, const char *argv[])
 	}
 	}
 
 
 	cif::file f = cif::pdb::read(in);
 	cif::file f = cif::pdb::read(in);
-	if (cif::VERBOSE > 0 and not f.is_valid())
-		std::cerr << "Warning, the input file is not valid. Run with --verbose to see why." << std::endl;
 
 
 	// --------------------------------------------------------------------
 	// --------------------------------------------------------------------
 
 
@@ -164,7 +158,7 @@ int d_main(int argc, const char *argv[])
 			fmt = "cif";
 			fmt = "cif";
 	}
 	}
 
 
-	dssp dssp(f.front(), 1, pp_stretch, true);
+	dssp dssp(f.front(), 1, pp_stretch, fmt == "dssp" or config.has("calculate-accessibility"));
 
 
 	if (not output.empty())
 	if (not output.empty())
 	{
 	{

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