Added test case

CMakeLists.txt

@@ -45,8 +45,8 @@ if(MSVC)
 
 	# On Windows, do not install in the system location
 	if(CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT AND NOT ($ENV{LOCALAPPDATA} STREQUAL ""))
-		message(WARNING "The executable will be installed in $ENV{LOCALAPPDATA}/${PROJECT_NAME}")
-		set(CMAKE_INSTALL_PREFIX "$ENV{LOCALAPPDATA}/${PROJECT_NAME}" CACHE PATH "..." FORCE)
+		message(WARNING "The executable will be installed in $ENV{LOCALAPPDATA}")
+		set(CMAKE_INSTALL_PREFIX "$ENV{LOCALAPPDATA}" CACHE PATH "..." FORCE)
 	endif()
 
 	# Find out the processor type for the target
@@ -92,7 +92,7 @@ string(TIMESTAMP BUILD_DATE_TIME "%Y-%m-%d" UTC)
 configure_file("${CMAKE_SOURCE_DIR}/src/revision.hpp.in" "${CMAKE_BINARY_DIR}/revision.hpp" @ONLY)
 
 # Optionally use mrc to create resources
-find_program(MRC mrc HINTS "$ENV{LOCALAPPDATA}/mrc" "${CMAKE_INSTALL_PREFIX}/../mrc" "/usr/local/bin")
+find_program(MRC mrc HINTS "$ENV{LOCALAPPDATA}/bin"  "$ENV{LOCALAPPDATA}/mrc" "${CMAKE_INSTALL_PREFIX}/../mrc" "/usr/local/bin")
 
 if(MRC)
 	option(USE_RSRC "Use mrc to create resources" ON)
@@ -119,7 +119,7 @@ message(STATUS "Boost libraries in: ${Boost_LIBRARY_DIRS}")
 
 find_package(ZLIB)
 find_package(BZip2)
-find_package(cifpp 1.0 REQUIRED)
+find_package(cifpp 1.0 REQUIRED HINTS $ENV{LOCALAPPDATA}/cifpp)
 
 if(CIFPP_FOUND)
 	add_compile_definitions("DATA_DIR=\"${CIFPP_SHARE_DIR}\"")
@@ -150,6 +150,8 @@ include_directories(
 )
 
 add_executable(mkdssp
+	${PROJECT_SOURCE_DIR}/src/dssp.cpp
+	${PROJECT_SOURCE_DIR}/src/dssp.hpp
 	${PROJECT_SOURCE_DIR}/src/mkdssp.cpp
 	${DSSP_RESOURCE})
 
@@ -159,5 +161,32 @@ install(TARGETS ${PROJECT_NAME}
 
 # manual
 
-install(FILES doc/mkdssp.1 DESTINATION ${CMAKE_INSTALL_DATADIR}/man/man1)
+install(FILES doc/mkdssp.1
+	DESTINATION ${CMAKE_INSTALL_DATADIR}/man/man1)
 
+# test
+
+add_executable(unit-test ${PROJECT_SOURCE_DIR}/test/unit-test.cpp ${PROJECT_SOURCE_DIR}/src/dssp.cpp ${DSSP_RESOURCE})
+
+target_include_directories(unit-test PRIVATE
+	${CMAKE_CURRENT_SOURCE_DIR}/include
+)
+
+target_link_libraries(unit-test Threads::Threads ${Boost_LIBRARIES} cifpp::cifpp)
+
+if(${ZLIB_FOUND})
+	target_link_libraries(unit-test ZLIB::ZLIB)
+endif()
+
+if(${BZip2_FOUND})
+	target_link_libraries(unit-test BZip2::BZip2)
+endif()
+
+if(MSVC)
+	# Specify unwind semantics so that MSVC knowns how to handle exceptions
+	target_compile_options(unit-test PRIVATE /EHsc)
+endif()
+
+add_test(NAME unit-test
+	COMMAND $<TARGET_FILE:unit-test>
+	WORKING_DIRECTORY ${CMAKE_SOURCE_DIR}/test)
\ No newline at end of file

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.
+ */
+
+#pragma once
+
+#include <cif++/Structure.hpp>
+#include <cif++/Secondary.hpp>
+
+void load_version_info();
+std::string get_version_nr();
+std::string get_version_date();
+std::string get_version_string();
+
+void writeDSSP(const mmcif::Structure& structure, const mmcif::DSSP& dssp, std::ostream& os);
+void annotateDSSP(mmcif::Structure& structure, const mmcif::DSSP& dssp, bool writeOther, std::ostream& os);
+

src/mkdssp.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.
+ */
+

test/unit-test.cpp

+/*-
+ * 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.
+ */
+
+#define BOOST_TEST_MODULE DSSP_Test
+#include <boost/test/included/unit_test.hpp>
+#include <boost/algorithm/string.hpp>
+
+#include <stdexcept>
+
+#include <cif++/Structure.hpp>
+#include <cif++/Secondary.hpp>
+#include <cif++/CifUtils.hpp>
+#include <cif++/Cif2PDB.hpp>
+
+#include "dssp.hpp"
+
+namespace ba = boost::algorithm;
+
+// --------------------------------------------------------------------
+
+BOOST_AUTO_TEST_CASE(ut_dssp)
+{
+	using namespace std::literals;
+
+	mmcif::File f("1cbs.cif.gz");
+	mmcif::Structure structure(f, 1, mmcif::StructureOpenOptions::SkipHydrogen);
+
+	mmcif::DSSP dssp(structure, 3, true);
+
+	std::stringstream test;
+
+	writeDSSP(structure, dssp, test);
+
+	std::ifstream reference("1cbs.dssp");
+
+	BOOST_ASSERT(reference.is_open());
+
+	std::string line_t, line_r;
+	BOOST_ASSERT (std::getline(test, line_t) and std::getline(reference, line_r));
+	BOOST_ASSERT(line_t.compare(0, 104,  "==== Secondary Structure Definition by the program DSSP, NKI version 4.0                           ==== ") == 0);
+
+	for (int line_nr = 1; ; ++line_nr)
+	{
+		bool done_t = not std::getline(test, line_t);
+		bool done_r = not std::getline(reference, line_r);
+
+		BOOST_CHECK_EQUAL(done_r, done_t);
+		if (done_r)
+			break;
+
+		if (line_t != line_r)
+			std::cerr << line_nr << std::endl
+					<< line_t << std::endl
+					<< line_r << std::endl;
+
+		BOOST_CHECK(line_t == line_r);
+	}
+
+	BOOST_CHECK(test.eof());
+	BOOST_CHECK(reference.eof());
+}
+
+
+BOOST_AUTO_TEST_CASE(ut_mmcif)
+{
+	using namespace std::literals;
+
+	mmcif::File f("1cbs.cif.gz");
+	mmcif::Structure structure(f, 1, mmcif::StructureOpenOptions::SkipHydrogen);
+
+	mmcif::DSSP dssp(structure, 3, true);
+
+	std::stringstream test;
+
+	annotateDSSP(structure, dssp, true, test);
+
+	std::ifstream reference("1cbs-dssp.cif");
+
+	BOOST_ASSERT(reference.is_open());
+
+	std::string line_t, line_r;
+	BOOST_ASSERT (std::getline(test, line_t) and std::getline(reference, line_r));
+	BOOST_ASSERT(line_t.compare(0, 104,  "==== Secondary Structure Definition by the program DSSP, NKI version 4.0                           ==== ") == 0);
+
+	for (int line_nr = 1; ; ++line_nr)
+	{
+		bool done_t = not std::getline(test, line_t);
+		bool done_r = not std::getline(reference, line_r);
+
+		BOOST_CHECK_EQUAL(done_r, done_t);
+		if (done_r)
+			break;
+
+		if (line_t != line_r)
+			std::cerr << line_nr << std::endl
+					<< line_t << std::endl
+					<< line_r << std::endl;
+
+		BOOST_CHECK(line_t == line_r);
+	}
+
+	BOOST_CHECK(test.eof());
+	BOOST_CHECK(reference.eof());
+}