new DSSP output, dssp as shared lib

CMakeLists.txt

@@ -195,7 +195,6 @@ file(GENERATE OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/libdssp.pc
 	INPUT ${CMAKE_CURRENT_BINARY_DIR}/libdssp.pc.in)
 install(FILES ${CMAKE_CURRENT_BINARY_DIR}/libdssp.pc DESTINATION ${CMAKE_INSTALL_LIBDIR}/pkgconfig)
 
-
 install(TARGETS ${PROJECT_NAME}
 	RUNTIME DESTINATION ${BIN_INSTALL_DIR}
 )
@@ -248,8 +247,8 @@ set(CPACK_SOURCE_TBZ2 OFF)
 set(CPACK_SOURCE_TXZ OFF)
 set(CPACK_SOURCE_TZ OFF)
 set(CPACK_SOURCE_IGNORE_FILES "/data/components.cif;/build;/.vscode;/.git")
-set (CPACK_PACKAGE_FILE_NAME "${PROJECT_NAME}-${PROJECT_VERSION}")
-set (CPACK_SOURCE_PACKAGE_FILE_NAME ${CPACK_PACKAGE_FILE_NAME})
+set(CPACK_PACKAGE_FILE_NAME "${PROJECT_NAME}-${PROJECT_VERSION}")
+set(CPACK_SOURCE_PACKAGE_FILE_NAME ${CPACK_PACKAGE_FILE_NAME})
 
 # NSIS options
 set(CPACK_NSIS_MODIFY_PATH ON)

changelog

-Version 4.2
+Version 4.2.0
 - Changes for packaging
 - New mmCIF DSSP output, added several categories
 

include/dssp.hpp

@@ -97,7 +97,6 @@ class dssp
 		Gap
 	};
 
-	dssp(const std::filesystem::path &file, int model_nr, int min_poly_proline_stretch_length, bool calculateSurfaceAccessibility);
 	dssp(const cif::datablock &db, int model_nr, int min_poly_proline_stretch_length, bool calculateSurfaceAccessibility);
 	dssp(const cif::mm::structure &s, int min_poly_proline_stretch_length, bool calculateSurfaceAccessibility);
 

src/dssp-io.hpp

@@ -29,5 +29,5 @@
 #include "dssp.hpp"
 
 void writeDSSP(const dssp& dssp, std::ostream& os);
-void annotateDSSP(cif::datablock &db, const dssp& dssp, bool writeOther, std::ostream& os);
+void annotateDSSP(cif::datablock &db, const dssp& dssp, bool writeOther, bool writeExperimental, std::ostream& os);
 

src/dssp.cpp

@@ -2085,6 +2085,11 @@ dssp::iterator &dssp::iterator::operator--()
 
 // --------------------------------------------------------------------
 
+dssp::dssp(const cif::mm::structure &s, int min_poly_proline_stretch_length, bool calculateSurfaceAccessibility)
+	: dssp(s.get_datablock(), s.get_model_nr(), min_poly_proline_stretch_length, calculateSurfaceAccessibility)
+{
+}
+
 dssp::dssp(const cif::datablock &db, int model_nr, int min_poly_proline_stretch, bool calculateSurfaceAccessibility)
 	: m_impl(new DSSP_impl(db, model_nr, min_poly_proline_stretch))
 {

src/mkdssp.cpp

@@ -72,6 +72,7 @@ int d_main(int argc, const char *argv[])
 		mcfp::make_option<std::string>("output-format", "Output format, can be either 'dssp' for classic DSSP or 'mmcif' for annotated mmCIF. The default is chosen based on the extension of the output file, if any."),
 		mcfp::make_option<short>("min-pp-stretch", 3, "Minimal number of residues having PSI/PHI in range for a PP helix, default is 3"),
 		mcfp::make_option("write-other", "If set, write the type OTHER for loops, default is to leave this out"),
+		mcfp::make_option("write-experimental", "If set, write the new, experimental DSSP output in mmCIF format, default is to leave this out"),
 
 		// mcfp::make_option("components",			po::value<std::string,	"Location of the components.cif file from CCD")
 	    // mcfp::make_option("extra-compounds",		po::value<std::string,	"File containing residue information for extra compounds in this specific target, should be either in CCD format or a CCP4 restraints file")
@@ -185,14 +186,14 @@ int d_main(int argc, const char *argv[])
 		if (fmt == "dssp")
 			writeDSSP(dssp, out);
 		else
-			annotateDSSP(f.front(), dssp, writeOther, out);
+			annotateDSSP(f.front(), dssp, writeOther, config.has("write-experimental"), out);
 	}
 	else
 	{
 		if (fmt == "dssp")
 			writeDSSP(dssp, std::cout);
 		else
-			annotateDSSP(f.front(), dssp, writeOther, std::cout);
+			annotateDSSP(f.front(), dssp, writeOther, config.has("write-experimental"), std::cout);
 	}
 
 	return 0;

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.
- */
-