upgrade c++ to 17

updates for refactoring libcif++

GNUmakefile.in

@@ -91,8 +91,8 @@ OBJECTS = $(APPLICATION:%=$(OBJDIR)/%.o)
 ifneq "$(MRC)" ""
 OBJECTS += $(APPLICATION:%=$(OBJDIR)/%_rsrc.o)
 
-$(OBJDIR)/$(APPLICATION)_rsrc.o: $(CIFPP_RSRC)/dictionaries
-	$(MRC) -o $@ $^
+$(OBJDIR)/$(APPLICATION)_rsrc.o: $(wildcard $(CIFPP_RSRC)/dictionaries/*)
+	$(MRC) -o $@ $(CIFPP_RSRC)/dictionaries
 endif
 
 -include $(OBJECTS:%.o=%.d)
@@ -121,3 +121,7 @@ distclean: clean
 
 .PHONY: FORCE
 FORCE:
+
+.PHONY: test
+test:
+	echo $(wildcard $(CIFPP_RSRC)/dictionaries/*)

configure

 #! /bin/sh
 # Guess values for system-dependent variables and create Makefiles.
-# Generated by GNU Autoconf 2.69 for dssp 3.0.
+# Generated by GNU Autoconf 2.69 for dssp 4.0.
 #
 # Report bugs to <m.hekkelman@nki.nl>.
 #
@@ -580,8 +580,8 @@ MAKEFLAGS=
 # Identity of this package.
 PACKAGE_NAME='dssp'
 PACKAGE_TARNAME='dssp'
-PACKAGE_VERSION='3.0'
-PACKAGE_STRING='dssp 3.0'
+PACKAGE_VERSION='4.0'
+PACKAGE_STRING='dssp 4.0'
 PACKAGE_BUGREPORT='m.hekkelman@nki.nl'
 PACKAGE_URL=''
 
@@ -668,7 +668,7 @@ DEBUG
 INSTALL_DATA
 INSTALL_SCRIPT
 INSTALL_PROGRAM
-HAVE_CXX14
+HAVE_CXX17
 OBJEXT
 EXEEXT
 ac_ct_CXX
@@ -1302,7 +1302,7 @@ if test "$ac_init_help" = "long"; then
   # Omit some internal or obsolete options to make the list less imposing.
   # This message is too long to be a string in the A/UX 3.1 sh.
   cat <<_ACEOF
-\`configure' configures dssp 3.0 to adapt to many kinds of systems.
+\`configure' configures dssp 4.0 to adapt to many kinds of systems.
 
 Usage: $0 [OPTION]... [VAR=VALUE]...
 
@@ -1368,7 +1368,7 @@ fi
 
 if test -n "$ac_init_help"; then
   case $ac_init_help in
-     short | recursive ) echo "Configuration of dssp 3.0:";;
+     short | recursive ) echo "Configuration of dssp 4.0:";;
    esac
   cat <<\_ACEOF
 
@@ -1507,7 +1507,7 @@ fi
 test -n "$ac_init_help" && exit $ac_status
 if $ac_init_version; then
   cat <<\_ACEOF
-dssp configure 3.0
+dssp configure 4.0
 generated by GNU Autoconf 2.69
 
 Copyright (C) 2012 Free Software Foundation, Inc.
@@ -1930,7 +1930,7 @@ cat >config.log <<_ACEOF
 This file contains any messages produced by compilers while
 running configure, to aid debugging if configure makes a mistake.
 
-It was created by dssp $as_me 3.0, which was
+It was created by dssp $as_me 4.0, which was
 generated by GNU Autoconf 2.69.  Invocation command line was
 
   $ $0 $@
@@ -2793,7 +2793,7 @@ ac_link='$CXX -o conftest$ac_exeext $CXXFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ex
 ac_compiler_gnu=$ac_cv_cxx_compiler_gnu
 
 
-  ax_cxx_compile_alternatives="14 1y"    ax_cxx_compile_cxx14_required=true
+  ax_cxx_compile_alternatives="17 1z"    ax_cxx_compile_cxx17_required=true
   ac_ext=cpp
 ac_cpp='$CXXCPP $CPPFLAGS'
 ac_compile='$CXX -c $CXXFLAGS $CPPFLAGS conftest.$ac_ext >&5'
@@ -2806,9 +2806,9 @@ ac_compiler_gnu=$ac_cv_cxx_compiler_gnu
     if test x$ac_success = xno; then
                 for alternative in ${ax_cxx_compile_alternatives}; do
       for switch in -std=c++${alternative} +std=c++${alternative} "-h std=c++${alternative}"; do
-        cachevar=`$as_echo "ax_cv_cxx_compile_cxx14_$switch" | $as_tr_sh`
-        { $as_echo "$as_me:${as_lineno-$LINENO}: checking whether $CXX supports C++14 features with $switch" >&5
-$as_echo_n "checking whether $CXX supports C++14 features with $switch... " >&6; }
+        cachevar=`$as_echo "ax_cv_cxx_compile_cxx17_$switch" | $as_tr_sh`
+        { $as_echo "$as_me:${as_lineno-$LINENO}: checking whether $CXX supports C++17 features with $switch" >&5
+$as_echo_n "checking whether $CXX supports C++17 features with $switch... " >&6; }
 if eval \${$cachevar+:} false; then :
   $as_echo_n "(cached) " >&6
 else
@@ -3222,6 +3222,384 @@ namespace cxx14
 
 
 
+
+// If the compiler admits that it is not ready for C++17, why torture it?
+// Hopefully, this will speed up the test.
+
+#ifndef __cplusplus
+
+#error "This is not a C++ compiler"
+
+#elif __cplusplus < 201703L
+
+#error "This is not a C++17 compiler"
+
+#else
+
+#include <initializer_list>
+#include <utility>
+#include <type_traits>
+
+namespace cxx17
+{
+
+  namespace test_constexpr_lambdas
+  {
+
+    constexpr int foo = [](){return 42;}();
+
+  }
+
+  namespace test::nested_namespace::definitions
+  {
+
+  }
+
+  namespace test_fold_expression
+  {
+
+    template<typename... Args>
+    int multiply(Args... args)
+    {
+      return (args * ... * 1);
+    }
+
+    template<typename... Args>
+    bool all(Args... args)
+    {
+      return (args && ...);
+    }
+
+  }
+
+  namespace test_extended_static_assert
+  {
+
+    static_assert (true);
+
+  }
+
+  namespace test_auto_brace_init_list
+  {
+
+    auto foo = {5};
+    auto bar {5};
+
+    static_assert(std::is_same<std::initializer_list<int>, decltype(foo)>::value);
+    static_assert(std::is_same<int, decltype(bar)>::value);
+  }
+
+  namespace test_typename_in_template_template_parameter
+  {
+
+    template<template<typename> typename X> struct D;
+
+  }
+
+  namespace test_fallthrough_nodiscard_maybe_unused_attributes
+  {
+
+    int f1()
+    {
+      return 42;
+    }
+
+    [[nodiscard]] int f2()
+    {
+      [[maybe_unused]] auto unused = f1();
+
+      switch (f1())
+      {
+      case 17:
+        f1();
+        [[fallthrough]];
+      case 42:
+        f1();
+      }
+      return f1();
+    }
+
+  }
+
+  namespace test_extended_aggregate_initialization
+  {
+
+    struct base1
+    {
+      int b1, b2 = 42;
+    };
+
+    struct base2
+    {
+      base2() {
+        b3 = 42;
+      }
+      int b3;
+    };
+
+    struct derived : base1, base2
+    {
+        int d;
+    };
+
+    derived d1 {{1, 2}, {}, 4};  // full initialization
+    derived d2 {{}, {}, 4};      // value-initialized bases
+
+  }
+
+  namespace test_general_range_based_for_loop
+  {
+
+    struct iter
+    {
+      int i;
+
+      int& operator* ()
+      {
+        return i;
+      }
+
+      const int& operator* () const
+      {
+        return i;
+      }
+
+      iter& operator++()
+      {
+        ++i;
+        return *this;
+      }
+    };
+
+    struct sentinel
+    {
+      int i;
+    };
+
+    bool operator== (const iter& i, const sentinel& s)
+    {
+      return i.i == s.i;
+    }
+
+    bool operator!= (const iter& i, const sentinel& s)
+    {
+      return !(i == s);
+    }
+
+    struct range
+    {
+      iter begin() const
+      {
+        return {0};
+      }
+
+      sentinel end() const
+      {
+        return {5};
+      }
+    };
+
+    void f()
+    {
+      range r {};
+
+      for (auto i : r)
+      {
+        [[maybe_unused]] auto v = i;
+      }
+    }
+
+  }
+
+  namespace test_lambda_capture_asterisk_this_by_value
+  {
+
+    struct t
+    {
+      int i;
+      int foo()
+      {
+        return [*this]()
+        {
+          return i;
+        }();
+      }
+    };
+
+  }
+
+  namespace test_enum_class_construction
+  {
+
+    enum class byte : unsigned char
+    {};
+
+    byte foo {42};
+
+  }
+
+  namespace test_constexpr_if
+  {
+
+    template <bool cond>
+    int f ()
+    {
+      if constexpr(cond)
+      {
+        return 13;
+      }
+      else
+      {
+        return 42;
+      }
+    }
+
+  }
+
+  namespace test_selection_statement_with_initializer
+  {
+
+    int f()
+    {
+      return 13;
+    }
+
+    int f2()
+    {
+      if (auto i = f(); i > 0)
+      {
+        return 3;
+      }
+
+      switch (auto i = f(); i + 4)
+      {
+      case 17:
+        return 2;
+
+      default:
+        return 1;
+      }
+    }
+
+  }
+
+  namespace test_template_argument_deduction_for_class_templates
+  {
+
+    template <typename T1, typename T2>
+    struct pair
+    {
+      pair (T1 p1, T2 p2)
+        : m1 {p1},
+          m2 {p2}
+      {}
+
+      T1 m1;
+      T2 m2;
+    };
+
+    void f()
+    {
+      [[maybe_unused]] auto p = pair{13, 42u};
+    }
+
+  }
+
+  namespace test_non_type_auto_template_parameters
+  {
+
+    template <auto n>
+    struct B
+    {};
+
+    B<5> b1;
+    B<'a'> b2;
+
+  }
+
+  namespace test_structured_bindings
+  {
+
+    int arr[2] = { 1, 2 };
+    std::pair<int, int> pr = { 1, 2 };
+
+    auto f1() -> int(&)[2]
+    {
+      return arr;
+    }
+
+    auto f2() -> std::pair<int, int>&
+    {
+      return pr;
+    }
+
+    struct S
+    {
+      int x1 : 2;
+      volatile double y1;
+    };
+
+    S f3()
+    {
+      return {};
+    }
+
+    auto [ x1, y1 ] = f1();
+    auto& [ xr1, yr1 ] = f1();
+    auto [ x2, y2 ] = f2();
+    auto& [ xr2, yr2 ] = f2();
+    const auto [ x3, y3 ] = f3();
+
+  }
+
+  namespace test_exception_spec_type_system
+  {
+
+    struct Good {};
+    struct Bad {};
+
+    void g1() noexcept;
+    void g2();
+
+    template<typename T>
+    Bad
+    f(T*, T*);
+
+    template<typename T1, typename T2>
+    Good
+    f(T1*, T2*);
+
+    static_assert (std::is_same_v<Good, decltype(f(g1, g2))>);
+
+  }
+
+  namespace test_inline_variables
+  {
+
+    template<class T> void f(T)
+    {}
+
+    template<class T> inline T g(T)
+    {
+      return T{};
+    }
+
+    template<> inline void f<>(int)
+    {}
+
+    template<> int g<>(int)
+    {
+      return 5;
+    }
+
+  }
+
+}  // namespace cxx17
+
+#endif  // __cplusplus < 201703L
+
+
+
 _ACEOF
 if ac_fn_cxx_try_compile "$LINENO"; then :
   eval $cachevar=yes
@@ -3254,19 +3632,19 @@ ac_compile='$CXX -c $CXXFLAGS $CPPFLAGS conftest.$ac_ext >&5'
 ac_link='$CXX -o conftest$ac_exeext $CXXFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
 ac_compiler_gnu=$ac_cv_cxx_compiler_gnu
 
-  if test x$ax_cxx_compile_cxx14_required = xtrue; then
+  if test x$ax_cxx_compile_cxx17_required = xtrue; then
     if test x$ac_success = xno; then
-      as_fn_error $? "*** A compiler with support for C++14 language features is required." "$LINENO" 5
+      as_fn_error $? "*** A compiler with support for C++17 language features is required." "$LINENO" 5
     fi
   fi
   if test x$ac_success = xno; then
-    HAVE_CXX14=0
-    { $as_echo "$as_me:${as_lineno-$LINENO}: No compiler with C++14 support was found" >&5
-$as_echo "$as_me: No compiler with C++14 support was found" >&6;}
+    HAVE_CXX17=0
+    { $as_echo "$as_me:${as_lineno-$LINENO}: No compiler with C++17 support was found" >&5
+$as_echo "$as_me: No compiler with C++17 support was found" >&6;}
   else
-    HAVE_CXX14=1
+    HAVE_CXX17=1
 
-$as_echo "#define HAVE_CXX14 1" >>confdefs.h
+$as_echo "#define HAVE_CXX17 1" >>confdefs.h
 
   fi
 
@@ -6677,8 +7055,8 @@ fi
   LDFLAGS="$LDFLAGS $LIBCIFPP_LDFLAGS"
 fi
 
-     ac_fn_cxx_check_header_mongrel "$LINENO" "cif++/Config.h" "ac_cv_header_cifpp_Config_h" "$ac_includes_default"
-if test "x$ac_cv_header_cifpp_Config_h" = xyes; then :
+     ac_fn_cxx_check_header_mongrel "$LINENO" "cif++/Config.hpp" "ac_cv_header_cifpp_Config_hpp" "$ac_includes_default"
+if test "x$ac_cv_header_cifpp_Config_hpp" = xyes; then :
 
        { $as_echo "$as_me:${as_lineno-$LINENO}: checking for main in -lcif++" >&5
 $as_echo_n "checking for main in -lcif++... " >&6; }
@@ -7654,7 +8032,7 @@ cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
 # report actual input values of CONFIG_FILES etc. instead of their
 # values after options handling.
 ac_log="
-This file was extended by dssp $as_me 3.0, which was
+This file was extended by dssp $as_me 4.0, which was
 generated by GNU Autoconf 2.69.  Invocation command line was
 
   CONFIG_FILES    = $CONFIG_FILES
@@ -7707,7 +8085,7 @@ _ACEOF
 cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
 ac_cs_config="`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`"
 ac_cs_version="\\
-dssp config.status 3.0
+dssp config.status 4.0
 configured by $0, generated by GNU Autoconf 2.69,
   with options \\"\$ac_cs_config\\"
 

configure.ac

-AC_INIT([dssp], 3.0, [m.hekkelman@nki.nl])
+AC_INIT([dssp], 4.0, [m.hekkelman@nki.nl])
 
 dnl Switch to a C++ compiler, and check if it works.
 AC_LANG(C++)
-AX_CXX_COMPILE_STDCXX_14([noext])
+AX_CXX_COMPILE_STDCXX_17([noext])
 
 AC_CONFIG_SRCDIR([src/dssp.cpp])
 AC_CONFIG_AUX_DIR(config)
@@ -47,7 +47,7 @@ AC_ARG_WITH([cif++],
 		])
 
 
-AX_CHECK_LIBRARY([LIBCIFPP], [cif++/Config.h], [cif++],
+AX_CHECK_LIBRARY([LIBCIFPP], [cif++/Config.hpp], [cif++],
 	[],
 	[AC_MSG_ERROR([libcif++ not found - cannot continue])])
 

src/dssp.cpp

@@ -10,11 +10,12 @@
 #include <boost/format.hpp>
 #include <boost/date_time/gregorian/formatters.hpp>
 
-#include <cif++/Config.h>
-#include <cif++/Structure.h>
-#include <cif++/Secondary.h>
-#include <cif++/CifUtils.h>
-#include <cif++/Cif2PDB.h>
+#include <cif++/Config.hpp>
+#include <cif++/Structure.hpp>
+#include <cif++/Secondary.hpp>
+#include <cif++/CifUtils.hpp>
+#include <cif++/Cif2PDB.hpp>
+#include <cif++/FixDMC.hpp>
 
 #include <boost/program_options.hpp>
 
@@ -54,8 +55,6 @@ std::string ResidueToDSSPLine(const mmcif::DSSP::ResidueInfo& info)
 	if (residue.asymID().length() > 1)
 		throw std::runtime_error("This file contains data that won't fit in the original DSSP format");
 
-	auto ca = residue.atomByID("CA");
-
 	char code = 'X';
 	if (mmcif::kAAMap.find(residue.compoundID()) != mmcif::kAAMap.end())
 		code = mmcif::kAAMap.at(residue.compoundID());
@@ -137,9 +136,10 @@ std::string ResidueToDSSPLine(const mmcif::DSSP::ResidueInfo& info)
 		}
 	}
 
+	auto ca = residue.atomByID("CA");
 	auto const& [cax, cay, caz] = ca.location();
 
-	return (kDSSPResidueLine % info.nr() % ca.authSeqId() % ca.pdbxAuthInsCode() % ca.authAsymId() % code %
+	return (kDSSPResidueLine % info.nr() % ca.authSeqID() % ca.pdbxAuthInsCode() % ca.authAsymID() % code %
 		ss % helix[0] % helix[1] % helix[2] % bend % chirality % bridgelabel[0] % bridgelabel[1] %
 		bp[0] % bp[1] % sheet % floor(info.accessibility() + 0.5) %
 		NHO[0] % ONH[0] % NHO[1] % ONH[1] %
@@ -220,9 +220,8 @@ void writeDSSP(const mmcif::Structure& structure, const mmcif::DSSP& dssp, std::
 		// insert a break line whenever we detect missing residues
 		// can be the transition to a different chain, or missing residues in the current chain
 
-		auto b = ri.chainBreak();
-		if (b != mmcif::ChainBreak::None)
-			os << (kDSSPResidueLine % (last + 1) % (b == mmcif::ChainBreak::Gap ? '*' : ' ')) << std::endl;
+		if (ri.nr() != last + 1)
+			os << (kDSSPResidueLine % (last + 1) % (ri.chainBreak() == mmcif::ChainBreak::NewChain ? '*' : ' ')) << std::endl;
 		
 		os << ResidueToDSSPLine(ri) << std::endl;
 		last = ri.nr();
@@ -263,7 +262,7 @@ void annotateDSSP(const mmcif::Structure& structure, const mmcif::DSSP& dssp, st
 
 // --------------------------------------------------------------------
 
-int main(int argc, char* argv[])
+int d_main(int argc, const char* argv[])
 {
 	using namespace std::literals;
 
@@ -280,6 +279,8 @@ int main(int argc, char* argv[])
 
 		("output-format",		po::value<std::string>(),	"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.")
 
+		("create-missing",									"Create missing backbone atoms")
+
 #if not USE_RSRC
 		("rsrc-dir",			po::value<std::string>(),	"Directory containing the 'resources' used by this application")
 #endif
@@ -352,8 +353,13 @@ int main(int argc, char* argv[])
 	}
 
 	mmcif::File f(vm["xyzin"].as<std::string>());
-	mmcif::Structure structure(f);
+	mmcif::Structure structure(f, mmcif::StructureOpenOptions::SkipHydrogen);
+
+	// --------------------------------------------------------------------
 	
+	if (vm.count("create-missing"))
+		mmcif::CreateMissingBackboneAtoms(structure, true);
+
 	// --------------------------------------------------------------------
 
 	mmcif::DSSP dssp(structure);
@@ -384,3 +390,22 @@ int main(int argc, char* argv[])
 	
 	return 0;
 }
+
+// --------------------------------------------------------------------
+
+int main(int argc, const char* argv[])
+{
+	int result = 0;
+
+	try
+	{
+		result = d_main(argc, argv);
+	}
+	catch (const std::exception& ex)
+	{
+		print_what(ex);
+		exit(1);
+	}
+
+	return result;
+}