Commit 9f57e08d by Maarten L. Hekkelman

license added

parent 5bcd6b64
# Makefile for example app using libzeep
#
# Copyright Maarten L. Hekkelman, UMC St. Radboud 2008-2013.
# Copyright Maarten L. Hekkelman, 2014-2019
# Distributed under the Boost Software License, Version 1.0.
# (See accompanying file LICENSE_1_0.txt or copy at
# http://www.boost.org/LICENSE_1_0.txt)
#
# Use the make.config file in the uplevel directory to
# change the settings for this build
# 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.
SHELL := /bin/bash
......@@ -21,6 +34,7 @@ LIBS = -lcif++ \
@BOOST_THREAD_LIB@ \
@BOOST_REGEX_LIB@ \
@BOOST_PROGRAM_OPTIONS_LIB@ \
@BOOST_DATE_TIME_LIB@ \
-lboost_timer -lboost_chrono \
-Wl,-Bstatic -lstdc++ -Wl,-Bdynamic \
@LIBS@
......@@ -59,7 +73,7 @@ DEFINES += VERSION='"$(VERSION)"'
ifeq "$(DEBUG)" "1"
DEFINES += DEBUG
CXXFLAGS += -g -O0 -fstandalone-debug
CXXFLAGS += -g -O0
LDFLAGS += -g
else
CXXFLAGS += -O2
......
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.
\ No newline at end of file
......@@ -630,9 +630,7 @@ LIBBZ2_LDFLAGS
LIBBZ2_CPPFLAGS
LIBZ_LDFLAGS
LIBZ_CPPFLAGS
LIBCLIPPER_LDFLAGS
LIBCLIPPER_CPPFLAGS
CCP4
BOOST_DATE_TIME_LIB
BOOST_PROGRAM_OPTIONS_LIB
BOOST_REGEX_LIB
BOOST_THREAD_LIB
......@@ -725,8 +723,7 @@ with_boost_iostreams
with_boost_thread
with_boost_regex
with_boost_program_options
with_clipper
with_newuoa
with_boost_date_time
'
ac_precious_vars='build_alias
host_alias
......@@ -745,9 +742,6 @@ CPP
LIBCIFPP_CPPFLAGS
LIBCIFPP_LDFLAGS
CXXCPP
CCP4
LIBCLIPPER_CPPFLAGS
LIBCLIPPER_LDFLAGS
LIBZ_CPPFLAGS
LIBZ_LDFLAGS
LIBBZ2_CPPFLAGS
......@@ -1403,11 +1397,11 @@ Optional Packages:
possible to specify a certain library for the linker
e.g.
--with-boost-program-options=boost_program_options-gcc-mt-1_33_1
--with-clipper=[location]
Use the clipper library as specified.
[location=$CCP4]
--with-newuoa=[location]
Use the newuoa library as specified.
--with-boost-date-time[=special-lib]
use the Date_Time library from boost - it is
possible to specify a certain library for the linker
e.g.
--with-boost-date-time=boost_date_time-gcc-mt-d-1_33_1
Some influential environment variables:
CXX C++ compiler command
......@@ -1427,11 +1421,6 @@ Some influential environment variables:
LIBCIFPP_LDFLAGS
linker flags for LIBCIFPP libraries
CXXCPP C++ preprocessor
CCP4 The location where CCP4 is installed
LIBCLIPPER_CPPFLAGS
C preprocessor flags for LIBCLIPPER headers
LIBCLIPPER_LDFLAGS
linker flags for LIBCLIPPER libraries
LIBZ_CPPFLAGS
C preprocessor flags for LIBZ headers
LIBZ_LDFLAGS
......@@ -3650,6 +3639,44 @@ $as_echo "#define HAVE_CXX17 1" >>confdefs.h
{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether C++ compiler accepts -fstandalone-debug" >&5
$as_echo_n "checking whether C++ compiler accepts -fstandalone-debug... " >&6; }
if ${ax_cv_check_cxxflags__Werror__fstandalone_debug+:} false; then :
$as_echo_n "(cached) " >&6
else
ax_check_save_flags=$CXXFLAGS
CXXFLAGS="$CXXFLAGS -Werror -fstandalone-debug"
cat confdefs.h - <<_ACEOF >conftest.$ac_ext
/* end confdefs.h. */
int
main ()
{
;
return 0;
}
_ACEOF
if ac_fn_cxx_try_compile "$LINENO"; then :
ax_cv_check_cxxflags__Werror__fstandalone_debug=yes
else
ax_cv_check_cxxflags__Werror__fstandalone_debug=no
fi
rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
CXXFLAGS=$ax_check_save_flags
fi
{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ax_cv_check_cxxflags__Werror__fstandalone_debug" >&5
$as_echo "$ax_cv_check_cxxflags__Werror__fstandalone_debug" >&6; }
if test "x$ax_cv_check_cxxflags__Werror__fstandalone_debug" = xyes; then :
CXXFLAGS="$CXXFLAGS -fstandalone-debug"
else
:
fi
ac_aux_dir=
for ac_dir in config "$srcdir"/config; do
......@@ -7170,146 +7197,232 @@ fi
# Check whether --with-boost-date-time was given.
if test "${with_boost_date_time+set}" = set; then :
withval=$with_boost_date_time;
if test "$withval" = "no"; then
want_boost="no"
elif test "$withval" = "yes"; then
want_boost="yes"
ax_boost_user_date_time_lib=""
else
want_boost="yes"
ax_boost_user_date_time_lib="$withval"
fi
if test x"$CCP4" != x""; then :
CPPFLAGS="$CPPFLAGS -I ${CCP4}/include"
CXXFLAGS="$CXXFLAGS -I ${CCP4}/include"
LDFLAGS="$LDFLAGS -L${CCP4}/lib -Wl,-rpath=${CCP4}/lib"
else
want_boost="yes"
fi
if test "x$want_boost" = "xyes"; then
# Check whether --with-clipper was given.
if test "${with_clipper+set}" = set; then :
withval=$with_clipper;
CPPFLAGS="$CPPFLAGS -I ${withval}/include"
CXXFLAGS="$CXXFLAGS -I ${withval}/include"
LDFLAGS="$LDFLAGS -L${withval}/lib"
LIBS="$LIBS -lclipper-ccp4 -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core"
CPPFLAGS_SAVED="$CPPFLAGS"
CPPFLAGS="$CPPFLAGS $BOOST_CPPFLAGS"
export CPPFLAGS
fi
LDFLAGS_SAVED="$LDFLAGS"
LDFLAGS="$LDFLAGS $BOOST_LDFLAGS"
export LDFLAGS
{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether the Boost::Date_Time library is available" >&5
$as_echo_n "checking whether the Boost::Date_Time library is available... " >&6; }
if ${ax_cv_boost_date_time+:} false; then :
$as_echo_n "(cached) " >&6
else
ac_ext=cpp
ac_cpp='$CXXCPP $CPPFLAGS'
ac_compile='$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
ac_fn_cxx_check_header_mongrel "$LINENO" "clipper/clipper.h" "ac_cv_header_clipper_clipper_h" "$ac_includes_default"
if test "x$ac_cv_header_clipper_clipper_h" = xyes; then :
cat confdefs.h - <<_ACEOF >conftest.$ac_ext
/* end confdefs.h. */
#include <boost/date_time/gregorian/gregorian_types.hpp>
int
main ()
{
using namespace boost::gregorian; date d(2002,Jan,10);
return 0;
;
return 0;
}
_ACEOF
if ac_fn_cxx_try_compile "$LINENO"; then :
ax_cv_boost_date_time=yes
else
as_fn_error $? "
Can't find the main clipper include file clipper/clipper.h. Please
specify either the CCP4 location of the location of the installed
clipper using --with-clipper=<path>
" "$LINENO" 5
ax_cv_boost_date_time=no
fi
rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
ac_ext=cpp
ac_cpp='$CXXCPP $CPPFLAGS'
ac_compile='$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
fi
{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ax_cv_boost_date_time" >&5
$as_echo "$ax_cv_boost_date_time" >&6; }
if test "x$ax_cv_boost_date_time" = "xyes"; then
$as_echo "#define HAVE_BOOST_DATE_TIME /**/" >>confdefs.h
if ${ax_cv_have_LIBCLIPPER+:} false; then :
BOOSTLIBDIR=`echo $BOOST_LDFLAGS | sed -e 's/[^\/]*//'`
if test "x$ax_boost_user_date_time_lib" = "x"; then
for libextension in `ls $BOOSTLIBDIR/libboost_date_time*.so* $BOOSTLIBDIR/libboost_date_time*.dylib* $BOOSTLIBDIR/libboost_date_time*.a* 2>/dev/null | sed 's,.*/,,' | sed -e 's;^lib\(boost_date_time.*\)\.so.*$;\1;' -e 's;^lib\(boost_date_time.*\)\.dylib.*$;\1;' -e 's;^lib\(boost_date_time.*\)\.a*$;\1;'` ; do
ax_lib=${libextension}
as_ac_Lib=`$as_echo "ac_cv_lib_$ax_lib''_exit" | $as_tr_sh`
{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for exit in -l$ax_lib" >&5
$as_echo_n "checking for exit in -l$ax_lib... " >&6; }
if eval \${$as_ac_Lib+:} false; then :
$as_echo_n "(cached) " >&6
else
save_CPPFLAGS="$CPPFLAGS"
save_LDFLAGS="$LDFLAGS"
save_LIBS="$LIBS"
ac_check_lib_save_LIBS=$LIBS
LIBS="-l$ax_lib $LIBS"
cat confdefs.h - <<_ACEOF >conftest.$ac_ext
/* end confdefs.h. */
if test "x$LIBCLIPPER_CPPFLAGS" != "x"; then :
CPPFLAGS="$CPPFLAGS $LIBCLIPPER_CPPFLAGS"
/* Override any GCC internal prototype to avoid an error.
Use char because int might match the return type of a GCC
builtin and then its argument prototype would still apply. */
#ifdef __cplusplus
extern "C"
#endif
char exit ();
int
main ()
{
return exit ();
;
return 0;
}
_ACEOF
if ac_fn_cxx_try_link "$LINENO"; then :
eval "$as_ac_Lib=yes"
else
eval "$as_ac_Lib=no"
fi
if test "x$LIBCLIPPER_LDFLAGS" != "x"; then :
LDFLAGS="$LDFLAGS $LIBCLIPPER_LDFLAGS"
rm -f core conftest.err conftest.$ac_objext \
conftest$ac_exeext conftest.$ac_ext
LIBS=$ac_check_lib_save_LIBS
fi
eval ac_res=\$$as_ac_Lib
{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_res" >&5
$as_echo "$ac_res" >&6; }
if eval test \"x\$"$as_ac_Lib"\" = x"yes"; then :
BOOST_DATE_TIME_LIB="-l$ax_lib"; link_date_time="yes"; break
else
link_date_time="no"
fi
ac_fn_cxx_check_header_mongrel "$LINENO" "clipper/clipper.h" "ac_cv_header_clipper_clipper_h" "$ac_includes_default"
if test "x$ac_cv_header_clipper_clipper_h" = xyes; then :
{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for main in -lclipper-core" >&5
$as_echo_n "checking for main in -lclipper-core... " >&6; }
if ${ac_cv_lib_clipper_core_main+:} false; then :
done
if test "x$link_date_time" != "xyes"; then
for libextension in `ls $BOOSTLIBDIR/boost_date_time*.dll* $BOOSTLIBDIR/boost_date_time*.a* 2>/dev/null | sed 's,.*/,,' | sed -e 's;^\(boost_date_time.*\)\.dll.*$;\1;' -e 's;^\(boost_date_time.*\)\.a.*$;\1;'` ; do
ax_lib=${libextension}
as_ac_Lib=`$as_echo "ac_cv_lib_$ax_lib''_exit" | $as_tr_sh`
{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for exit in -l$ax_lib" >&5
$as_echo_n "checking for exit in -l$ax_lib... " >&6; }
if eval \${$as_ac_Lib+:} false; then :
$as_echo_n "(cached) " >&6
else
ac_check_lib_save_LIBS=$LIBS
LIBS="-lclipper-core $LIBS"
LIBS="-l$ax_lib $LIBS"
cat confdefs.h - <<_ACEOF >conftest.$ac_ext
/* end confdefs.h. */
/* Override any GCC internal prototype to avoid an error.
Use char because int might match the return type of a GCC
builtin and then its argument prototype would still apply. */
#ifdef __cplusplus
extern "C"
#endif
char exit ();
int
main ()
{
return main ();
return exit ();
;
return 0;
}
_ACEOF
if ac_fn_cxx_try_link "$LINENO"; then :
ac_cv_lib_clipper_core_main=yes
eval "$as_ac_Lib=yes"
else
ac_cv_lib_clipper_core_main=no
eval "$as_ac_Lib=no"
fi
rm -f core conftest.err conftest.$ac_objext \
conftest$ac_exeext conftest.$ac_ext
LIBS=$ac_check_lib_save_LIBS
fi
{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_clipper_core_main" >&5
$as_echo "$ac_cv_lib_clipper_core_main" >&6; }
if test "x$ac_cv_lib_clipper_core_main" = xyes; then :
ax_cv_have_LIBCLIPPER=yes
eval ac_res=\$$as_ac_Lib
{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_res" >&5
$as_echo "$ac_res" >&6; }
if eval test \"x\$"$as_ac_Lib"\" = x"yes"; then :
BOOST_DATE_TIME_LIB="-l$ax_lib"; link_date_time="yes"; break
else
ax_cv_have_LIBCLIPPER=no
link_date_time="no"
fi
done
fi
else
for ax_lib in $ax_boost_user_date_time_lib boost_date_time-$ax_boost_user_date_time_lib; do
as_ac_Lib=`$as_echo "ac_cv_lib_$ax_lib''_main" | $as_tr_sh`
{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for main in -l$ax_lib" >&5
$as_echo_n "checking for main in -l$ax_lib... " >&6; }
if eval \${$as_ac_Lib+:} false; then :
$as_echo_n "(cached) " >&6
else
ax_cv_have_LIBCLIPPER=no
fi
CPPFLAGS="$save_CPPFLAGS"
LDFLAGS="$save_LDFLAGS"
LIBS="$save_LIBS"
fi
if test "$ax_cv_have_LIBCLIPPER" = "yes"; then :
$as_echo "#define HAVE_LIBCLIPPER 1" >>confdefs.h
ac_check_lib_save_LIBS=$LIBS
LIBS="-l$ax_lib $LIBS"
cat confdefs.h - <<_ACEOF >conftest.$ac_ext
/* end confdefs.h. */
int
main ()
{
return main ();
;
return 0;
}
_ACEOF
if ac_fn_cxx_try_link "$LINENO"; then :
eval "$as_ac_Lib=yes"
else
as_fn_error $? "libclipper not found - cannot continue" "$LINENO" 5
eval "$as_ac_Lib=no"
fi
# Check whether --with-newuoa was given.
if test "${with_newuoa+set}" = set; then :
withval=$with_newuoa;
CPPFLAGS="$CPPFLAGS -I ${withval}/include"
CXXFLAGS="$CXXFLAGS -I ${withval}/include"
LDFLAGS="$LDFLAGS -L${withval}/lib"
LIBS="$LIBS -lnewuoa"
rm -f core conftest.err conftest.$ac_objext \
conftest$ac_exeext conftest.$ac_ext
LIBS=$ac_check_lib_save_LIBS
fi
ac_fn_cxx_check_header_mongrel "$LINENO" "newuoa.h" "ac_cv_header_newuoa_h" "$ac_includes_default"
if test "x$ac_cv_header_newuoa_h" = xyes; then :
eval ac_res=\$$as_ac_Lib
{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_res" >&5
$as_echo "$ac_res" >&6; }
if eval test \"x\$"$as_ac_Lib"\" = x"yes"; then :
BOOST_DATE_TIME_LIB="-l$ax_lib"; link_date_time="yes"; break
else
as_fn_error $? "
Can't find the newuoa include file newuoa.h. Please install this
library and specify its location with --with-newuoa=<path>.
You can find newuoa at https://github.com/elsid/newuoa-cpp.git
" "$LINENO" 5
link_date_time="no"
fi
done
fi
if test "x$ax_lib" = "x"; then
as_fn_error $? "Could not find a version of the library!" "$LINENO" 5
fi
if test "x$link_date_time" != "xyes"; then
as_fn_error $? "Could not link against $ax_lib !" "$LINENO" 5
fi
fi
CPPFLAGS="$CPPFLAGS_SAVED"
LDFLAGS="$LDFLAGS_SAVED"
fi
......@@ -7538,7 +7651,6 @@ fi
ac_config_files="$ac_config_files GNUmakefile"
cat >confcache <<\_ACEOF
......
......@@ -4,6 +4,11 @@ dnl Switch to a C++ compiler, and check if it works.
AC_LANG(C++)
AX_CXX_COMPILE_STDCXX_17([noext])
AX_CHECK_COMPILE_FLAG([-fstandalone-debug],
[
CXXFLAGS="$CXXFLAGS -fstandalone-debug"
] , , [-Werror])
AC_CONFIG_SRCDIR([src/dssp.cpp])
AC_CONFIG_AUX_DIR(config)
dnl AC_CONFIG_MACRO_DIR([config/m4])
......@@ -69,59 +74,7 @@ AX_BOOST_IOSTREAMS
AX_BOOST_THREAD
AX_BOOST_REGEX
AX_BOOST_PROGRAM_OPTIONS
AC_ARG_VAR([CCP4], [The location where CCP4 is installed])
AS_IF([test x"$CCP4" != x""],
[
CPPFLAGS="$CPPFLAGS -I ${CCP4}/include"
CXXFLAGS="$CXXFLAGS -I ${CCP4}/include"
LDFLAGS="$LDFLAGS -L${CCP4}/lib -Wl,-rpath=${CCP4}/lib"
])
AC_ARG_WITH([clipper],
AS_HELP_STRING([--with-clipper=@<:@location@:>@],
[Use the clipper library as specified.
@<:@location=$CCP4@:>@]),
[
CPPFLAGS="$CPPFLAGS -I ${withval}/include"
CXXFLAGS="$CXXFLAGS -I ${withval}/include"
LDFLAGS="$LDFLAGS -L${withval}/lib"
LIBS="$LIBS -lclipper-ccp4 -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core"
])
AC_CHECK_HEADER(
[clipper/clipper.h],
[],
[AC_MSG_ERROR([
Can't find the main clipper include file clipper/clipper.h. Please
specify either the CCP4 location of the location of the installed
clipper using --with-clipper=<path>
])])
AX_CHECK_LIBRARY([LIBCLIPPER], [clipper/clipper.h], [clipper-core],
[],
[AC_MSG_ERROR([libclipper not found - cannot continue])])
AC_ARG_WITH([newuoa],
AS_HELP_STRING([--with-newuoa=@<:@location@:>@],
[Use the newuoa library as specified.]),
[
CPPFLAGS="$CPPFLAGS -I ${withval}/include"
CXXFLAGS="$CXXFLAGS -I ${withval}/include"
LDFLAGS="$LDFLAGS -L${withval}/lib"
LIBS="$LIBS -lnewuoa"
])
AC_CHECK_HEADER(
[newuoa.h],
[],
[AC_MSG_ERROR([
Can't find the newuoa include file newuoa.h. Please install this
library and specify its location with --with-newuoa=<path>.
You can find newuoa at https://github.com/elsid/newuoa-cpp.git
])])
AX_BOOST_DATE_TIME
AX_CHECK_LIBRARY([LIBZ], [zlib.h], [z],
[ LIBS="$LIBS -lz" ],
......@@ -137,20 +90,5 @@ AC_SEARCH_LIBS([dladdr1], [dl],
AC_SUBST([HAVE_DLADDR])
dnl AC_MSG_CHECKING([clipper version])
dnl AC_COMPILE_IFELSE(
dnl [read_test(clipper-test.cpp)],
dnl [],
dnl [AC_MSG_ERROR([The version of clipper is not up to date])])
dnl
dnl AC_CHECK_HEADER(
dnl [newuoa.h],
dnl [],
dnl [AC_MSG_ERROR([
dnl Can't find the newuoa include file newuoa.h. Please install this
dnl library and specify its location with --with-newuoa=<path>.
dnl You can find newuoa at https://github.com/elsid/newuoa-cpp.git
dnl ])])
dnl Process Makefile.in to create Makefile
AC_OUTPUT([GNUmakefile])
// Copyright Maarten L. Hekkelman 2020
// Distributed under the Boost Software License, Version 1.0.
// (See accompanying file LICENSE_1_0.txt or copy at
// http://www.boost.org/LICENSE_1_0.txt)
/*-
* 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.
*/
#include <exception>
#include <iostream>
......@@ -673,7 +694,7 @@ int d_main(int argc, const 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")
// ("create-missing", "Create missing backbone atoms")
#if not USE_RSRC
("rsrc-dir", po::value<std::string>(), "Directory containing the 'resources' used by this application")
......@@ -742,10 +763,10 @@ int d_main(int argc, const char* argv[])
mmcif::File f(vm["xyzin"].as<std::string>());
mmcif::Structure structure(f, 1, mmcif::StructureOpenOptions::SkipHydrogen);
// --------------------------------------------------------------------
// // --------------------------------------------------------------------
if (vm.count("create-missing"))
mmcif::CreateMissingBackboneAtoms(structure, true);
// if (vm.count("create-missing"))
// mmcif::CreateMissingBackboneAtoms(structure, true);
// --------------------------------------------------------------------
......
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