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dssp
Commit 82d1f1c4 by Maarten L. Hekkelman
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Updated options, added manual

parent 9e1fdea3
Showing with 363 additions and 639 deletions
GNUmakefile.in
......@@ -22,11 +22,13 @@
# (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
firstTarget: all
CXX = @CXX@
CXXFLAGS = @CXXFLAGS@ @CPPFLAGS@ @BOOST_CPPFLAGS@ @PTHREAD_CFLAGS@ @CIFPP_CFLAGS@
LDFLAGS = @LDFLAGS@ @BOOST_LDFLAGS@ @PTHREAD_CFLAGS@
CXXFLAGS = @CXXFLAGS@ @CPPFLAGS@ @PTHREAD_CFLAGS@ @CIFPP_CFLAGS@
LDFLAGS = @LDFLAGS@ @PTHREAD_CFLAGS@
LIBS = @LIBS@ \
@CIFPP_LIBS@ \
@BOOST_IOSTREAMS_LIB@ \
......@@ -38,6 +40,7 @@ exec_prefix = @exec_prefix@
bindir = @bindir@
datarootdir = @datarootdir@
datadir = @datadir@
mandir = @mandir@
GNUmakefile: config.status GNUmakefile.in
$(SHELL) ./config.status
......@@ -53,6 +56,9 @@ configure: configure.ac
endif
# main build variables
VERSION = @PACKAGE_VERSION@.0
DEFINES += VERSION='"$(VERSION)"'
CXXFLAGS += -Wall -Wno-multichar
CIFPP_RSRC = @CIFPP_RSRC@
......@@ -97,14 +103,18 @@ $(OBJDIR)/%.o: %.cpp | $(OBJDIR)
@ echo ">>" $<
@ $(CXX) -MD -c -o $@ $< $(CFLAGS) $(CXXFLAGS)
COMMON_OBJECTS = pr-main.o
# We have development releases and official releases, for each we
# maintain different versioning schemes.
ifneq "x@UPDATE_REVISION@" "x"
REVISION = $(shell git log --pretty=format:%h --max-count=1)
REVISION_FILE = version-info-$(REVISION).txt
$(REVISION_FILE):
rm -f version-info-*.txt
git describe --match=build --dirty > $@
@ echo dssp-version: $(VERSION) > $@
@ git describe --match=build --dirty >> $@
@ git log --pretty=medium --date=iso8601 -1 >> $@
src/revision.hpp: $(REVISION_FILE)
......@@ -112,10 +122,17 @@ src/revision.hpp: $(REVISION_FILE)
@ cat $? >> $@
@ echo ')";' >> $@
$(OBJDIR)/pr-main.o: src/revision.hpp
else
src/revision.hpp:
@ echo 'const char kRevision[] = R"(' > $@
@ echo dssp-version: $(VERSION) >> $@
@ echo Date: $$(date --iso-8601) >> $@
@ echo ')";' >> $@
endif
ifneq "$(USE_RSRC)" "0"
COMMON_RSRC = $(DATADIR)/dictionaries
rsrc:
@ mkdir -p $@
......@@ -127,46 +144,39 @@ endif
# The program rules
# disabled for now: centrifuge map-maker
PROGRAMS = dssp
define PROGRAM_template =
$(1)_OBJECTS += $(1).o $(COMMON_OBJECTS)
OBJECTS = \
$(OBJDIR)/dssp.o
ifneq "$(USE_RSRC)" "0"
$(1)_OBJECTS += $(1).o $(1)_rsrc.o
$OBJECTS += dssp_rsrc.o
$$(OBJDIR)/$(1)_rsrc.o: $$($(1)_RSRC) $$(COMMON_RSRC)
$(OBJDIR)/dssp_rsrc.o: $(DATADIR)/mmcif_pdbx_v50.dic
$(MRC) -o $$@ $$^
endif
$(1): $$($(1)_OBJECTS:%=$(OBJDIR)/%)
$(OBJDIR)/dssp.o: src/revision.hpp
endef
$(foreach program,$(PROGRAMS),$(eval $(call PROGRAM_template,$(program))))
$(PROGRAMS):
mkdssp: $(OBJECTS)
@ echo '->' $@
@ $(CXX) -o $@ $^ $(CXXFLAGS) $(LDFLAGS) $(LIBS)
OBJECTS = $(sort $(foreach program,$(PROGRAMS),$($(program)_OBJECTS)))
$(OBJDIR)/%.d: $(OBJDIR)/%.o
-include $(OBJECTS:%.o=$(OBJDIR)/%.d)
.PHONY: clean all
clean:
rm -rf $(PROGRAMS) $(OBJDIR)/* $(REVISION_FILE)
rm -rf mkdssp $(OBJDIR)/* src/revision.hpp
all: $(PROGRAMS)
all: mkdssp
.PHONY: install
install: $(PROGRAMS)
install: mkdssp
install -d $(bindir)
for p in $(PROGRAMS); do install $$p $(bindir)/$$p; done
install mkdssp $(bindir)/mkdssp
install -d $(mandir)/man1
install -m 644 mkdssp.1 $(mandir)/man1/mkdssp.1;
gzip $(mandir)/man1/mkdssp.1;
.PHONY: FORCE
FORCE:
......
README.md
DSSP version 4
==============
DSSP 4.0
========
This is a rewrite of DSSP, now offering full mmCIF support. The difference
with previous releases of DSSP is that it now writes out an annotated mmCIF
file by default, storing the secondary structure information in the
_struct_conf category.
The DSSP program was designed by Wolfgang Kabsch and Chris Sander to
standardize secondary structure assignment. DSSP is a database of secondary
structure assignments (and much more) for all protein entries in the Protein
Data Bank (PDB). DSSP is also the program that calculates DSSP entries from
PDB entries. DSSP does not predict secondary structure.
Requirements
------------
The tools are based on [libcif++](https://github.com/PDB-REDO/libcifpp)
and the code is written in modern C++ so you need a compiler capable
of handling C++17 code.
Building
--------
To build this, first install [libcif++](https://github.com/PDB-REDO/libcifpp.git)
and then run `configure`, `make` and `make install`.
Make sure you install libcif++ first before building.
After that, building should be as easy as typing:
```
./configure
make
make install
```
Usage
-----
See `man mkdssp` for more info.
configure
......@@ -625,10 +625,6 @@ ac_includes_default="\
ac_subst_vars='LTLIBOBJS
LIBOBJS
LIBBZ2_LDFLAGS
LIBBZ2_CPPFLAGS
LIBZ_LDFLAGS
LIBZ_CPPFLAGS
CIFPP_LDFLAGS
CIFPP_CPPFLAGS
AX_PACKAGE_REQUIRES_PRIVATE
......@@ -645,9 +641,6 @@ BOOST_IOSTREAMS_LIB
BOOST_LDFLAGS
BOOST_CPPFLAGS
CXXCPP
USE_RSRC
MRC
DEBUG
PTHREAD_CFLAGS
PTHREAD_LIBS
PTHREAD_CC
......@@ -667,6 +660,9 @@ build_os
build_vendor
build_cpu
build
UPDATE_REVISION
MRC
DEBUG
INSTALL_DATA
INSTALL_SCRIPT
INSTALL_PROGRAM
......@@ -720,7 +716,7 @@ SHELL'
ac_subst_files=''
ac_user_opts='
enable_option_checking
enable_resources
enable_revision
with_boost
with_boost_libdir
with_boost_iostreams
......@@ -737,11 +733,11 @@ LDFLAGS
LIBS
CPPFLAGS
CCC
DEBUG
MRC
CC
CFLAGS
CPP
DEBUG
MRC
CXXCPP
PKG_CONFIG
PKG_CONFIG_PATH
......@@ -749,11 +745,7 @@ PKG_CONFIG_LIBDIR
CIFPP_CFLAGS
CIFPP_LIBS
CIFPP_CPPFLAGS
CIFPP_LDFLAGS
LIBZ_CPPFLAGS
LIBZ_LDFLAGS
LIBBZ2_CPPFLAGS
LIBBZ2_LDFLAGS'
CIFPP_LDFLAGS'
# Initialize some variables set by options.
......@@ -1378,7 +1370,7 @@ Optional Features:
--disable-option-checking ignore unrecognized --enable/--with options
--disable-FEATURE do not include FEATURE (same as --enable-FEATURE=no)
--enable-FEATURE[=ARG] include FEATURE [ARG=yes]
--disable-resources Do not use mrc to store data in resources
--disable-revision Create a build number as revision
Optional Packages:
--with-PACKAGE[=ARG] use PACKAGE [ARG=yes]
......@@ -1417,11 +1409,11 @@ Some influential environment variables:
LIBS libraries to pass to the linker, e.g. -l<library>
CPPFLAGS (Objective) C/C++ preprocessor flags, e.g. -I<include dir> if
you have headers in a nonstandard directory <include dir>
DEBUG Build a debug version of the application
MRC Specify a location for the mrc executable
CC C compiler command
CFLAGS C compiler flags
CPP C preprocessor
DEBUG Build a debug version of the application
MRC Specify a location for the mrc executable
CXXCPP C++ preprocessor
PKG_CONFIG path to pkg-config utility
PKG_CONFIG_PATH
......@@ -1435,14 +1427,6 @@ Some influential environment variables:
C preprocessor flags for CIFPP headers
CIFPP_LDFLAGS
linker flags for CIFPP libraries
LIBZ_CPPFLAGS
C preprocessor flags for LIBZ headers
LIBZ_LDFLAGS
linker flags for LIBZ libraries
LIBBZ2_CPPFLAGS
C preprocessor flags for LIBBZ2 headers
LIBBZ2_LDFLAGS
linker flags for LIBBZ2 libraries
Use these variables to override the choices made by `configure' or to help
it to find libraries and programs with nonstandard names/locations.
......@@ -3683,7 +3667,9 @@ 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"
CXXFLAGS="$CXXFLAGS -fstandalone-debug"
else
:
fi
......@@ -3719,7 +3705,6 @@ ac_config_sub="$SHELL $ac_aux_dir/config.sub" # Please don't use this var.
ac_configure="$SHELL $ac_aux_dir/configure" # Please don't use this var.
ac_config_headers="$ac_config_headers src/config.hpp"
......@@ -3819,6 +3804,72 @@ test -z "$INSTALL_SCRIPT" && INSTALL_SCRIPT='${INSTALL}'
test -z "$INSTALL_DATA" && INSTALL_DATA='${INSTALL} -m 644'
if test "x$MRC" = "x"; then
# Extract the first word of "mrc", so it can be a program name with args.
set dummy mrc; ac_word=$2
{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
$as_echo_n "checking for $ac_word... " >&6; }
if ${ac_cv_path_MRC+:} false; then :
$as_echo_n "(cached) " >&6
else
case $MRC in
[\\/]* | ?:[\\/]*)
ac_cv_path_MRC="$MRC" # Let the user override the test with a path.
;;
*)
as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
for as_dir in $PATH
do
IFS=$as_save_IFS
test -z "$as_dir" && as_dir=.
for ac_exec_ext in '' $ac_executable_extensions; do
if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
ac_cv_path_MRC="$as_dir/$ac_word$ac_exec_ext"
$as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
break 2
fi
done
done
IFS=$as_save_IFS
;;
esac
fi
MRC=$ac_cv_path_MRC
if test -n "$MRC"; then
{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $MRC" >&5
$as_echo "$MRC" >&6; }
else
{ $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
$as_echo "no" >&6; }
fi
fi
if test "x$MRC" = "x"; then
as_fn_error $? "mrc not found, the application will be built without resources" "$LINENO" 5
fi
# Check whether --enable-revision was given.
if test "${enable_revision+set}" = set; then :
enableval=$enable_revision;
fi
if test "x$enable_revision" != "xno" ; then :
UPDATE_REVISION=1
fi
UPDATE_REVISION=$UPDATE_REVISION
# Make sure we can run config.sub.
$SHELL "$ac_aux_dir/config.sub" sun4 >/dev/null 2>&1 ||
as_fn_error $? "cannot run $SHELL $ac_aux_dir/config.sub" "$LINENO" 5
......@@ -5409,81 +5460,6 @@ ac_compiler_gnu=$ac_cv_cxx_compiler_gnu
USE_RSRC=0
if test "x$MRC" = "x"; then
# Extract the first word of "mrc", so it can be a program name with args.
set dummy mrc; ac_word=$2
{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
$as_echo_n "checking for $ac_word... " >&6; }
if ${ac_cv_path_MRC+:} false; then :
$as_echo_n "(cached) " >&6
else
case $MRC in
[\\/]* | ?:[\\/]*)
ac_cv_path_MRC="$MRC" # Let the user override the test with a path.
;;
*)
as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
for as_dir in $PATH
do
IFS=$as_save_IFS
test -z "$as_dir" && as_dir=.
for ac_exec_ext in '' $ac_executable_extensions; do
if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
ac_cv_path_MRC="$as_dir/$ac_word$ac_exec_ext"
$as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
break 2
fi
done
done
IFS=$as_save_IFS
;;
esac
fi
MRC=$ac_cv_path_MRC
if test -n "$MRC"; then
{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $MRC" >&5
$as_echo "$MRC" >&6; }
else
{ $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
$as_echo "no" >&6; }
fi
fi
if test "x$MRC" = "x"; then
{ $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: The mrc application was not found, not using resources." >&5
$as_echo "$as_me: WARNING: The mrc application was not found, not using resources." >&2;}
else
# Check whether --enable-resources was given.
if test "${enable_resources+set}" = set; then :
enableval=$enable_resources;
fi
if test "x$enable_resources" != "xno" ; then :
USE_RSRC=1
fi
fi
USE_RSRC=$USE_RSRC
cat >>confdefs.h <<_ACEOF
#define USE_RSRC $USE_RSRC
_ACEOF
ac_ext=cpp
ac_cpp='$CXXCPP $CPPFLAGS'
ac_compile='$CXX -c $CXXFLAGS $CPPFLAGS conftest.$ac_ext >&5'
......@@ -7017,7 +6993,7 @@ fi
AX_PACKAGE_REQUIRES="$AX_PACKAGE_REQUIRES libcif++"
AX_PACKAGE_REQUIRES="$AX_PACKAGE_REQUIRES libcifpp"
AX_PACKAGE_REQUIRES_PRIVATE="$AX_PACKAGE_REQUIRES_PRIVATE "
......@@ -7029,12 +7005,12 @@ if test -n "$CIFPP_CFLAGS"; then
pkg_cv_CIFPP_CFLAGS="$CIFPP_CFLAGS"
elif test -n "$PKG_CONFIG"; then
if test -n "$PKG_CONFIG" && \
{ { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"libcif++ \""; } >&5
($PKG_CONFIG --exists --print-errors "libcif++ ") 2>&5
{ { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"libcifpp \""; } >&5
($PKG_CONFIG --exists --print-errors "libcifpp ") 2>&5
ac_status=$?
$as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
test $ac_status = 0; }; then
pkg_cv_CIFPP_CFLAGS=`$PKG_CONFIG --cflags "libcif++ " 2>/dev/null`
pkg_cv_CIFPP_CFLAGS=`$PKG_CONFIG --cflags "libcifpp " 2>/dev/null`
test "x$?" != "x0" && pkg_failed=yes
else
pkg_failed=yes
......@@ -7046,12 +7022,12 @@ if test -n "$CIFPP_LIBS"; then
pkg_cv_CIFPP_LIBS="$CIFPP_LIBS"
elif test -n "$PKG_CONFIG"; then
if test -n "$PKG_CONFIG" && \
{ { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"libcif++ \""; } >&5
($PKG_CONFIG --exists --print-errors "libcif++ ") 2>&5
{ { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"libcifpp \""; } >&5
($PKG_CONFIG --exists --print-errors "libcifpp ") 2>&5
ac_status=$?
$as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
test $ac_status = 0; }; then
pkg_cv_CIFPP_LIBS=`$PKG_CONFIG --libs "libcif++ " 2>/dev/null`
pkg_cv_CIFPP_LIBS=`$PKG_CONFIG --libs "libcifpp " 2>/dev/null`
test "x$?" != "x0" && pkg_failed=yes
else
pkg_failed=yes
......@@ -7072,18 +7048,18 @@ else
_pkg_short_errors_supported=no
fi
if test $_pkg_short_errors_supported = yes; then
CIFPP_PKG_ERRORS=`$PKG_CONFIG --short-errors --print-errors --cflags --libs "libcif++ " 2>&1`
CIFPP_PKG_ERRORS=`$PKG_CONFIG --short-errors --print-errors --cflags --libs "libcifpp " 2>&1`
else
CIFPP_PKG_ERRORS=`$PKG_CONFIG --print-errors --cflags --libs "libcif++ " 2>&1`
CIFPP_PKG_ERRORS=`$PKG_CONFIG --print-errors --cflags --libs "libcifpp " 2>&1`
fi
# Put the nasty error message in config.log where it belongs
echo "$CIFPP_PKG_ERRORS" >&5
as_fn_error $? "the required package libcif++ is not installed" "$LINENO" 5
as_fn_error $? "the required package libcifpp is not installed" "$LINENO" 5
elif test $pkg_failed = untried; then
{ $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
$as_echo "no" >&6; }
as_fn_error $? "the required package libcif++ is not installed" "$LINENO" 5
as_fn_error $? "the required package libcifpp is not installed" "$LINENO" 5
else
CIFPP_CFLAGS=$pkg_cv_CIFPP_CFLAGS
CIFPP_LIBS=$pkg_cv_CIFPP_LIBS
......@@ -7197,170 +7173,6 @@ fi
fi
if ${ax_cv_have_LIBZ+:} false; then :
$as_echo_n "(cached) " >&6
else
save_CPPFLAGS="$CPPFLAGS"
save_LDFLAGS="$LDFLAGS"
save_LIBS="$LIBS"
if test "x$LIBZ_CPPFLAGS" != "x"; then :
CPPFLAGS="$CPPFLAGS $LIBZ_CPPFLAGS"
fi
if test "x$LIBZ_LDFLAGS" != "x"; then :
LDFLAGS="$LDFLAGS $LIBZ_LDFLAGS"
fi
ac_fn_cxx_check_header_mongrel "$LINENO" "zlib.h" "ac_cv_header_zlib_h" "$ac_includes_default"
if test "x$ac_cv_header_zlib_h" = xyes; then :
{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for main in -lz" >&5
$as_echo_n "checking for main in -lz... " >&6; }
if ${ac_cv_lib_z_main+:} false; then :
$as_echo_n "(cached) " >&6
else
ac_check_lib_save_LIBS=$LIBS
LIBS="-lz $LIBS"
cat confdefs.h - <<_ACEOF >conftest.$ac_ext
/* end confdefs.h. */
int
main ()
{
return main ();
;
return 0;
}
_ACEOF
if ac_fn_cxx_try_link "$LINENO"; then :
ac_cv_lib_z_main=yes
else
ac_cv_lib_z_main=no
fi
rm -f core conftest.err conftest.$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_z_main" >&5
$as_echo "$ac_cv_lib_z_main" >&6; }
if test "x$ac_cv_lib_z_main" = xyes; then :
ax_cv_have_LIBZ=yes
else
ax_cv_have_LIBZ=no
fi
else
ax_cv_have_LIBZ=no
fi
CPPFLAGS="$save_CPPFLAGS"
LDFLAGS="$save_LDFLAGS"
LIBS="$save_LIBS"
fi
if test "$ax_cv_have_LIBZ" = "yes"; then :
$as_echo "#define HAVE_LIBZ 1" >>confdefs.h
LIBS="$LIBS -lz"
else
as_fn_error $? "libz not found - compressed files not supported" "$LINENO" 5
fi
if ${ax_cv_have_LIBBZ2+:} false; then :
$as_echo_n "(cached) " >&6
else
save_CPPFLAGS="$CPPFLAGS"
save_LDFLAGS="$LDFLAGS"
save_LIBS="$LIBS"
if test "x$LIBBZ2_CPPFLAGS" != "x"; then :
CPPFLAGS="$CPPFLAGS $LIBBZ2_CPPFLAGS"
fi
if test "x$LIBBZ2_LDFLAGS" != "x"; then :
LDFLAGS="$LDFLAGS $LIBBZ2_LDFLAGS"
fi
ac_fn_cxx_check_header_mongrel "$LINENO" "bzlib.h" "ac_cv_header_bzlib_h" "$ac_includes_default"
if test "x$ac_cv_header_bzlib_h" = xyes; then :
{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for main in -lbz2" >&5
$as_echo_n "checking for main in -lbz2... " >&6; }
if ${ac_cv_lib_bz2_main+:} false; then :
$as_echo_n "(cached) " >&6
else
ac_check_lib_save_LIBS=$LIBS
LIBS="-lbz2 $LIBS"
cat confdefs.h - <<_ACEOF >conftest.$ac_ext
/* end confdefs.h. */
int
main ()
{
return main ();
;
return 0;
}
_ACEOF
if ac_fn_cxx_try_link "$LINENO"; then :
ac_cv_lib_bz2_main=yes
else
ac_cv_lib_bz2_main=no
fi
rm -f core conftest.err conftest.$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_bz2_main" >&5
$as_echo "$ac_cv_lib_bz2_main" >&6; }
if test "x$ac_cv_lib_bz2_main" = xyes; then :
ax_cv_have_LIBBZ2=yes
else
ax_cv_have_LIBBZ2=no
fi
else
ax_cv_have_LIBBZ2=no
fi
CPPFLAGS="$save_CPPFLAGS"
LDFLAGS="$save_LDFLAGS"
LIBS="$save_LIBS"
fi
if test "$ax_cv_have_LIBBZ2" = "yes"; then :
$as_echo "#define HAVE_LIBBZ2 1" >>confdefs.h
LIBS="$LIBS -lbz2"
else
as_fn_error $? "libbz2 not found - compressed files not supported" "$LINENO" 5
fi
ac_config_files="$ac_config_files GNUmakefile"
cat >confcache <<\_ACEOF
......
configure.ac
......@@ -2,48 +2,48 @@ AC_PREREQ([2.69])
AC_INIT([dssp], 4.0, [m.hekkelman@nki.nl])
dnl Switch to a decent C++ compiler, and check if it works.
dnl Switch to a C++ compiler, and check if it works.
AC_LANG(C++)
AX_CXX_COMPILE_STDCXX_17([noext])
AX_CHECK_COMPILE_FLAG([-fstandalone-debug], [ CXXFLAGS="$CXXFLAGS -fstandalone-debug" ], , [-Werror])
AX_CHECK_COMPILE_FLAG([-fstandalone-debug],
[
CXXFLAGS="$CXXFLAGS -fstandalone-debug"
] , , [-Werror])
AC_CONFIG_SRCDIR([src/dssp.cpp])
AC_CONFIG_AUX_DIR(config)
AC_CONFIG_MACRO_DIR([config/m4])
AC_CONFIG_HEADERS([src/config.hpp])
AC_PREFIX_DEFAULT(/usr/local)
AC_PROG_INSTALL
AX_PTHREAD
AC_ARG_VAR([DEBUG], [Build a debug version of the application])
AC_ARG_VAR([MRC], [Specify a location for the mrc executable])
USE_RSRC=0
dnl We would like to use mrc
if test "x$MRC" = "x"; then
AC_PATH_PROG([MRC], [mrc])
fi
if test "x$MRC" = "x"; then
AC_MSG_WARN([The mrc application was not found, not using resources.])
else
AC_ARG_ENABLE(
resources,
[AS_HELP_STRING([--disable-resources], [Do not use mrc to store data in resources])])
AS_IF([test "x$enable_resources" != "xno" ], [
USE_RSRC=1
])
AC_MSG_ERROR([mrc not found, the application will be built without resources])
fi
AC_SUBST([USE_RSRC], [$USE_RSRC])
dnl revision numbering is something used internally at the NKI
AC_ARG_ENABLE(
revision,
[AS_HELP_STRING([--disable-revision], [Create a build number as revision])])
AS_IF([test "x$enable_revision" != "xno" ], [
UPDATE_REVISION=1
])
AC_SUBST([UPDATE_REVISION], [$UPDATE_REVISION])
AC_DEFINE_UNQUOTED([USE_RSRC], [$USE_RSRC], [Use mrc to store resources])
AX_PTHREAD
AC_CHECK_HEADER([filesystem], [], [AC_MSG_ERROR([The file <filesystem> is missing, perhaps you should install a more recent libstdc++ implementation.])])
......@@ -98,7 +98,7 @@ AS_IF([test "x$CIFPP_LIBS" = "x"], [
AC_PATH_PROG([PKG_CONFIG], [pkg-config])
if test -x "$PKG_CONFIG"
then
AX_PKG_CHECK_MODULES([CIFPP], [libcif++], [], [], [AC_MSG_ERROR([the required package libcif++ is not installed])])
AX_PKG_CHECK_MODULES([CIFPP], [libcifpp], [], [], [AC_MSG_ERROR([the required package libcifpp is not installed])])
else
AC_CHECK_HEADER(
[cif++/Config.hpp],
......@@ -118,13 +118,5 @@ pkg-config.])])
fi
])
AX_CHECK_LIBRARY([LIBZ], [zlib.h], [z],
[ LIBS="$LIBS -lz" ],
[AC_MSG_ERROR([libz not found - compressed files not supported])])
AX_CHECK_LIBRARY([LIBBZ2], [bzlib.h], [bz2],
[ LIBS="$LIBS -lbz2"],
[AC_MSG_ERROR([libbz2 not found - compressed files not supported])])
dnl Process Makefile.in to create Makefile
AC_OUTPUT([GNUmakefile])
mkdssp.1 0 → 100644
.TH mkdssp 1 "2020-11-23" "version 1.0.0" "User Commands"
.if n .ad l
.nh
.SH NAME
mkdssp \- Assign secondary structure to proteins
.SH SYNOPSIS
mkdssp [OPTION] input [output]
.SH DESCRIPTION
The DSSP program was designed by Wolfgang Kabsch and Chris Sander to
standardize secondary structure assignment. DSSP is a database of
secondary structure assignments (and much more) for all protein entries
in the Protein Data Bank (PDB). mkdssp is the program that calculates
DSSP entries from PDB entries. mkdssp does \fBnot\fR predict secondary structure.
.sp
The original DSSP program wrote output in a fixed format, this version
by default writes annotated mmCIF files, storing the secondary structure
information in the _struct_conf category.
.sp
Since version 4.0 the mkdssp program also assigns PP helices.
.SH OPTIONS
The input file can be either mmCIF or PDB format and the file may be
gzip or bzip2 compressed.
.sp
The output is optional, if ommited the output is written to \fIstdout\fR. If
the name of the output file ends with either \fI.gz\fR or \fI.bz2\fR the
output is compressed accordingly.
.TP
\fB--output-format\fR=[dssp|mmcif]
If an output file is specified, the extension of the filename is used to
choose to output format, but if it is unclear, mmcif is the default. Use
this option to force output in either the old fixed column DSSP format or
the new annotated mmCIF format.
.TP
\fB--min-pp-stretch\fR
This option can be used to define the minimal number of residues with PHI/PSI
angles within the range required to assing a PP helix.
.TP
\fB--write-other\fR
By default the new format does not write the structure information for OTHER.
Use this flag to change that.
.SH DETAILS
The DSSP algorithm assings secondary structure based on the energy calculated
for H-bonds.
.br
.B Table\ \&1.\ \&Secondary\ Structures\ recognized
.TS
allbox;
cb cb cb .
DSSP Code mmCIF Code Description
.T&
l l l.
H HELX_RH_AL_P Alphahelix
B STRN Betabridge
E STRN Strand
G HELX_RH_3T_P Helix_3
I HELX_RH_PI_P Helix_5
P HELX_LH_PP_P Helix_PPII
T TURN_TY1_P Turn
S BEND Bend
' ' OTHER Loop
.TE
.SH BUGS
The mmCIF format currently lacks a lot of information that was available
in the old format like information about the bridge pairs or the span
of the various helices recognized. Also the accessibility information
is left out.
.sp
If you think this information should be part of the output, please contact
the author.
.SH AUTHOR
Written by Maarten L. Hekkelman <maarten@hekkelman.com>
.SH "REPORTING BUGS"
Report bugs at https://github.com/PDB-REDO/cif-tools/issues
.SH "SEE ALSO"
\fBcif-drop\fR, \fBcif-grep\fR, \fBcif-merge\fR, \fBcif-validate\fR,
\fBcif2pdb\fR, \fBmmCQL\fR, \fBpdb2cif\fR.
src/config.hpp.in
......@@ -21,12 +21,6 @@
/* Define to 1 if you have the <inttypes.h> header file. */
#undef HAVE_INTTYPES_H
/* Define to 1 if LIBBZ2 is found */
#undef HAVE_LIBBZ2
/* Define to 1 if LIBZ is found */
#undef HAVE_LIBZ
/* Define to 1 if you have the <memory.h> header file. */
#undef HAVE_MEMORY_H
......@@ -81,6 +75,3 @@
/* Define to 1 if you have the ANSI C header files. */
#undef STDC_HEADERS
/* Use mrc to store resources */
#undef USE_RSRC
src/dssp.cpp
......@@ -24,12 +24,12 @@
* SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
*/
#include "dssp.hpp"
#include "config.hpp"
#include <exception>
#include <iostream>
#include <fstream>
#include <filesystem>
#include <fstream>
#include <boost/format.hpp>
#include <boost/date_time/gregorian/formatters.hpp>
......@@ -49,7 +49,87 @@ namespace fs = std::filesystem;
namespace io = boost::iostreams;
namespace po = boost::program_options;
extern std::string VERSION_STRING;
// --------------------------------------------------------------------
// recursively print exception whats:
void print_what (const std::exception& e)
{
std::cerr << e.what() << std::endl;
try
{
std::rethrow_if_nested(e);
}
catch (const std::exception& nested)
{
std::cerr << " >> ";
print_what(nested);
}
}
// --------------------------------------------------------------------
namespace {
std::string gVersionNr, gVersionDate, VERSION_STRING;
}
void load_version_info()
{
const std::regex
rxVersionNr(R"(build-(\d+)-g[0-9a-f]{7}(-dirty)?)"),
rxVersionDate(R"(Date: +(\d{4}-\d{2}-\d{2}).*)"),
rxVersionNr2(R"(dssp-version: (\d+(?:\.\d+)+))");
#include "revision.hpp"
struct membuf : public std::streambuf
{
membuf(char* data, size_t length) { this->setg(data, data, data + length); }
} buffer(const_cast<char*>(kRevision), sizeof(kRevision));
std::istream is(&buffer);
std::string line;
while (getline(is, line))
{
std::smatch m;
if (std::regex_match(line, m, rxVersionNr))
{
gVersionNr = m[1];
if (m[2].matched)
gVersionNr += '*';
continue;
}
if (std::regex_match(line, m, rxVersionDate))
{
gVersionDate = m[1];
continue;
}
// always the first, replace with more specific if followed by the other info
if (std::regex_match(line, m, rxVersionNr2))
{
gVersionNr = m[1];
continue;
}
}
if (not VERSION_STRING.empty())
VERSION_STRING += "\n";
VERSION_STRING += gVersionNr + " " + gVersionDate;
}
std::string get_version_nr()
{
return gVersionNr/* + '/' + cif::get_version_nr()*/;
}
std::string get_version_date()
{
return gVersionDate;
}
// --------------------------------------------------------------------
......@@ -240,33 +320,6 @@ void writeDSSP(const mmcif::Structure& structure, const mmcif::DSSP& dssp, std::
os << ResidueToDSSPLine(ri) << std::endl;
last = ri.nr();
}
// std::vector<const MResidue*> residues;
// foreach (const MChain* chain, protein.GetChains())
// {
// foreach (const MResidue* residue, chain->GetResidues())
// residues.push_back(residue);
// }
// // keep residues sorted by residue number as assigned during reading the PDB file
// sort(residues.begin(), residues.end(), boost::bind(&MResidue::GetNumber, _1) < boost::bind(&MResidue::GetNumber, _2));
// const MResidue* last = nullptr;
// foreach (const MResidue* residue, residues)
// {
// // insert a break line whenever we detect missing residues
// // can be the transition to a different chain, or missing residues in the current chain
// if (last != nullptr and last->GetNumber() + 1 != residue->GetNumber())
// {
// char breaktype = ' ';
// if (last->GetChainID() != residue->GetChainID())
// breaktype = '*';
// os << (kDSSPResidueLine % (last->GetNumber() + 1) % breaktype) << std::endl;
// }
// os << ResidueToDSSPLine(*residue) << std::endl;
// last = residue;
// }
}
void annotateDSSP(mmcif::Structure& structure, const mmcif::DSSP& dssp, bool writeOther, std::ostream& os)
......@@ -388,250 +441,34 @@ void annotateDSSP(mmcif::Structure& structure, const mmcif::DSSP& dssp, bool wri
}
}
db.add_software("dssp " PACKAGE_VERSION, "other", get_version_nr(), get_version_date());
db.add_software("dssp", "other", get_version_nr(), get_version_date());
db.write(os);
// cif::File df;
// df.append(new cif::Datablock("DSSP_" + structure.getFile().data().getName()));
// auto& db = df.firstDatablock();
// int last = 0;
// for (auto info: dssp)
// {
// // insert a break line whenever we detect missing residues
// // can be the transition to a different chain, or missing residues in the current chain
// // os << (kDSSPResidueLine % (last + 1) % (ri.chainBreak() == mmcif::ChainBreak::NewChain ? '*' : ' ')) << std::endl;
// // os << ResidueToDSSPLine(ri) << std::endl;
// auto& mon = info.residue();
// auto&& [row, rn] = db["struct_mon_prot"].emplace({
// { "chain_break", (info.chainBreak() == mmcif::ChainBreak::Gap ? 'Y' : '.') },
// { "label_comp_id", mon.compoundID() },
// { "label_asym_id", mon.asymID() },
// { "label_seq_id", mon.seqID() },
// { "label_alt_id", info.alt_id() },
// { "auth_asym_id", mon.authAsymID() },
// { "auth_seq_id", mon.authSeqID() },
// { "auth_ins_code", mon.authInsCode() },
// });
// if (mon.is_first_in_chain())
// row["phi"] = ".";
// else
// row["phi"].os(std::fixed, std::setprecision(1), mon.phi());
// if (mon.is_last_in_chain())
// row["psi"] = ".";
// else
// row["psi"].os(std::fixed, std::setprecision(1), mon.psi());
// if (mon.is_last_in_chain())
// row["omega"] = ".";
// else
// row["omega"].os(std::fixed, std::setprecision(1), mon.omega());
// int nrOfChis = mon.nrOfChis();
// for (int i = 0; i < 5; ++i)
// {
// auto cl = "chi" + std::to_string(i + 1);
// if (i < nrOfChis)
// row[cl].os(std::fixed, std::setprecision(1), mon.chi(i));
// else
// row[cl] = '.';
// }
// if (not mon.has_alpha())
// row["alpha"] = ".";
// else
// row["alpha"].os(std::fixed, std::setprecision(1), mon.alpha());
// if (not mon.has_kappa())
// row["kappa"] = ".";
// else
// row["kappa"].os(std::fixed, std::setprecision(1), mon.kappa());
// if (mon.is_first_in_chain())
// row["tco"] = ".";
// else
// row["tco"].os(std::fixed, std::setprecision(1), mon.tco());
// // sec structure info
// char ss;
// switch (info.ss())
// {
// case mmcif::ssAlphahelix: ss = 'H'; break;
// case mmcif::ssBetabridge: ss = 'B'; break;
// case mmcif::ssStrand: ss = 'E'; break;
// case mmcif::ssHelix_3: ss = 'G'; break;
// case mmcif::ssHelix_5: ss = 'I'; break;
// case mmcif::ssHelix_PPII: ss = 'P'; break;
// case mmcif::ssTurn: ss = 'T'; break;
// case mmcif::ssBend: ss = 'S'; break;
// case mmcif::ssLoop: ss = '.'; break;
// }
// row["dssp_symbol"] = ss;
// if (mon.has_alpha())
// row["Calpha_chiral_sign"] = mon.alpha() < 0 ? "neg" : "pos";
// else
// row["Calpha_chiral_sign"] = ".";
// row["sheet_id"] = info.sheet() ? std::to_string(info.sheet()) : ".";
// for (uint32_t i: { 0, 1 })
// {
// std::string il = "bridge_partner_" + std::to_string(i + 1);
// const auto& [p, ladder, parallel] = info.bridgePartner(i);
// if (not p)
// {
// row[il + "_label_comp_id"] = ".";
// row[il + "_label_asym_id"] = ".";
// row[il + "_label_seq_id"] = ".";
// row[il + "_auth_asym_id"] = ".";
// row[il + "_auth_seq_id"] = ".";
// row[il + "_ladder"] = ".";
// row[il + "_sense"] = ".";
// continue;
// }
// auto& pm = p.residue();
// row[il + "_label_comp_id"] = pm.compoundID();
// row[il + "_label_asym_id"] = pm.asymID();
// row[il + "_label_seq_id"] = pm.seqID();
// row[il + "_auth_asym_id"] = pm.authAsymID();
// row[il + "_auth_seq_id"] = pm.authSeqID();
// row[il + "_ladder"] = ladder;
// row[il + "_sense"] = parallel ? "parallel" : "anti-parallel";
// }
// for (auto stride: { 3, 4, 5})
// {
// std::string hs = "helix_info_" + std::to_string(stride);
// switch (info.helix(stride))
// {
// #if 0
// case mmcif::Helix::None: row[hs] = '.'; break;
// case mmcif::Helix::Start: row[hs] = "start"; break;
// case mmcif::Helix::End: row[hs] = "end"; break;
// case mmcif::Helix::StartAndEnd: row[hs] = "start-and-end"; break;
// case mmcif::Helix::Middle: row[hs] = "middle"; break;
// #else
// case mmcif::Helix::None: row[hs] = '.'; break;
// case mmcif::Helix::Start: row[hs] = '>'; break;
// case mmcif::Helix::End: row[hs] = '<'; break;
// case mmcif::Helix::StartAndEnd: row[hs] = 'X'; break;
// case mmcif::Helix::Middle: row[hs] = '0' + stride; break;
// #endif
// }
// }
// if (info.bend())
// row["bend"] = 'S';
// else
// row["bend"] = ".";
// for (int i: { 0, 1 })
// {
// const auto& [donor, donorE] = info.donor(i);
// const auto& [acceptor, acceptorE] = info.acceptor(i);
// std::string ds = "O_donor_" + std::to_string(i + 1);
// std::string as = "NH_acceptor_" + std::to_string(i + 1);
// if (acceptor)
// {
// auto& am = acceptor.residue();
// row[as + "_label_comp_id"] = am.compoundID();
// row[as + "_label_asym_id"] = am.asymID();
// row[as + "_label_seq_id"] = am.seqID();
// row[as + "_auth_asym_id"] = am.authAsymID();
// row[as + "_auth_seq_id"] = am.authSeqID();
// row[as + "_energy"].os(std::fixed, std::setprecision(2), acceptorE);
// }
// else
// {
// row[as + "_label_comp_id"] = ".";
// row[as + "_label_asym_id"] = ".";
// row[as + "_label_seq_id"] = ".";
// row[as + "_auth_asym_id"] = ".";
// row[as + "_auth_seq_id"] = ".";
// row[as + "_energy"] = ".";
// }
// if (donor)
// {
// auto& dm = donor.residue();
// row[ds + "_label_comp_id"] = dm.compoundID();
// row[ds + "_label_asym_id"] = dm.asymID();
// row[ds + "_label_seq_id"] = dm.seqID();
// row[ds + "_auth_asym_id"] = dm.authAsymID();
// row[ds + "_auth_seq_id"] = dm.authSeqID();
// row[ds + "_energy"].os(std::fixed, std::setprecision(2), donorE);
// }
// else
// {
// row[ds + "_label_comp_id"] = ".";
// row[ds + "_label_asym_id"] = ".";
// row[ds + "_label_seq_id"] = ".";
// row[ds + "_auth_asym_id"] = ".";
// row[ds + "_auth_seq_id"] = ".";
// row[ds + "_energy"] = ".";
// }
// }
// last = info.nr();
// }
// df.write(os, {});
}
// --------------------------------------------------------------------
int pr_main(int argc, char* argv[])
int d_main(int argc, const char* argv[])
{
using namespace std::literals;
po::options_description visible_options(argv[0] + " input-file [output-file] [options]"s);
po::options_description visible_options(argv[0] + " [options] input-file [output-file]"s);
visible_options.add_options()
("xyzin", po::value<std::string>(), "coordinates file")
("output", po::value<std::string>(), "Output to this file")
("dict", po::value<std::vector<std::string>>(),
"Dictionary file containing restraints for residues in this specific target, can be specified multiple times.")
("help,h", "Display help message")
("version", "Print version")
("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
("min-pp-stretch", po::value<short>(), "Minimal number of residues having PSI/PHI in range for a PP helix, default is 3")
("write-other", "If set, write the type OTHER for loops, default is to leave this out")
("help,h", "Display help message")
("version", "Print version")
("verbose,v", "verbose output")
;
po::options_description hidden_options("hidden options");
hidden_options.add_options()
("xyzin", po::value<std::string>(), "coordinates file")
("output", po::value<std::string>(), "Output to this file")
("debug,d", po::value<int>(), "Debug level (for even more verbose output)")
;
......@@ -651,7 +488,7 @@ int pr_main(int argc, char* argv[])
if (vm.count("version"))
{
std::cout << argv[0] << ' ' << PACKAGE_VERSION " version " << VERSION_STRING << std::endl;
std::cout << argv[0] << " version " << VERSION_STRING << std::endl;
exit(0);
}
......@@ -688,11 +525,6 @@ int pr_main(int argc, 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);
// --------------------------------------------------------------------
short pp_stretch = 3;
......@@ -758,3 +590,24 @@ int pr_main(int argc, char* argv[])
return 0;
}
// --------------------------------------------------------------------
int main(int argc, const char* argv[])
{
int result = 0;
try
{
load_version_info();
result = d_main(argc, argv);
}
catch (const std::exception& ex)
{
print_what(ex);
exit(1);
}
return result;
}
src/dssp.hpp deleted 100644 → 0
/*-
* 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 <string>
#include "config.hpp"
extern std::string VERSION_STRING;
std::string get_version_nr();
std::string get_version_date();
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