Skip to content

D
dssp
Commit 9f57e08d by Maarten L. Hekkelman
Options

license added

parent 5bcd6b64
Showing with 84 additions and 87 deletions
GNUmakefile.in
# 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
......
LICENSE 0 → 100644
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
configure.ac
......@@ -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])
src/dssp.cpp
// 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);
// --------------------------------------------------------------------
......
Markdown is supported
0% or
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment