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|
Description: assorted fixes
[Maarten L. Hekkelman <m.hekkelman@cmbi.ru.nl>]
* DEST_DIR patched to DESTDIR
.
[Laszlo Kajan <lkajan@rostlab.org>]
* stripping is patched out so that it can be done by dh into a debug package
* line echo suppression is removed
* spelling errors in man page fixed
.
Upstream is aware of this patch.
Author: Maarten L. Hekkelman <m.hekkelman@cmbi.ru.nl>
Author: Laszlo Kajan <lkajan@rostlab.org>
--- a/makefile
+++ b/makefile
@@ -9,37 +9,36 @@
# new one if it doesn't exist. In this make.config you can set site
# specific variables like the Boost library location.
-firstTarget: mkdssp
-
-include make.config
+all: mkdssp
VERSION = 2.0.4
-DEST_DIR ?= /usr/local/
-LIB_DIR = $(BOOST_LIB_DIR)
-INC_DIR = $(BOOST_INC_DIR)
-MAN_DIR = $(DEST_DIR)man/man1/
+CXXFLAGS := $(shell dpkg-buildflags --get CXXFLAGS)
+LDFLAGS := $(shell dpkg-buildflags --get LDFLAGS)
+
+BIN_DIR = $(DESTDIR)/usr/bin
+MAN_DIR = $(DESTDIR)/usr/share/man/man1
-BOOST_LIBS = thread regex filesystem program_options date_time iostreams math_c99 system
-LIBS = $(BOOST_LIBS:%=boost_%$(BOOST_LIB_SUFFIX)) z bz2
+BOOST_LIBS = thread program_options iostreams system
+LIBS = $(BOOST_LIBS:%=boost_%)
DEFINES = USE_COMPRESSION LINUX VERSION='"$(VERSION)"'
-CC = c++
+CXX = g++
-CFLAGS = $(INC_DIR:%=-I%) -iquote src -g -Wall -Wno-multichar -pthread
-LDOPTS = $(LIB_DIR:%=-L%) $(LIBS:%=-l%) -g -pthread
+CXXFLAGS += -I $(HOME)/projects/boost/include -iquote src -g -Wall -Wno-multichar -pthread
+LDOPTS += -L $(HOME)/projects/boost/lib $(LIBS:%=-l%) -g -pthread
OBJ_DIR = obj
ifeq ($(DEBUG),1)
OBJ_DIR := $(OBJ_DIR).dbg
-CFLAGS += -g3
+CXXFLAGS += -g3
else
DEFINES += NDEBUG
-CFLAGS += -O3
+CXXFLAGS += -O3
endif
-CFLAGS += $(DEFINES:%=-D%)
+CXXFLAGS += $(DEFINES:%=-D%)
DIST_NAME = dssp-$(VERSION)
@@ -48,25 +47,21 @@
OBJECTS = $(OBJ_DIR)/mkdssp.o $(OBJ_DIR)/dssp.o $(OBJ_DIR)/primitives-3d.o $(OBJ_DIR)/structure.o $(OBJ_DIR)/utils.o
mkdssp: $(OBJECTS)
- @ echo linking $@
- @ $(CC) -static -o $@ $^ $(LDOPTS)
- @ echo OK
-
-include $(OBJECTS:%.o=%.d)
-
-$(OBJECTS:.o=.d):
-
-$(OBJ_DIR)/%.o: %.cpp
- @ if [ ! -d $(OBJ_DIR) ]; then mkdir $(OBJ_DIR); fi
- @ echo compiling $@
- @ $(CC) -MD -c -o $@ $< $(CFLAGS)
+ $(CXX) -o $@ $^ $(LDOPTS)
+
+$(OBJ_DIR):
+ mkdir -p $(OBJ_DIR)
+
+$(OBJ_DIR)/%.o: %.cpp | $(OBJ_DIR)
+ $(CXX) -MD -c -o $@ $< $(CXXFLAGS)
clean:
rm -rf $(OBJ_DIR)/* mkdssp
install: mkdssp
- sudo install -m 755 mkdssp $(DEST_DIR)bin/mkdssp
- sudo install doc/mkdssp.1 $(MAN_DIR)mkdssp.1
+ install -d $(BIN_DIR) $(MAN_DIR)
+ install -m 755 mkdssp $(BIN_DIR)/mkdssp
+ install doc/mkdssp.1 $(MAN_DIR)/mkdssp.1
dist: $(OBJECTS)
@ rm -rf $(DIST_NAME)
@@ -81,11 +76,3 @@
@ cp doc/mkdssp.1 $(DIST_NAME)/doc/mkdssp.1
tar czf $(DIST_NAME).tgz $(DIST_NAME)
cp $(DIST_NAME).tgz dssp_$(VERSION).orig.tar.gz
-
-make.config:
- @echo "creating empty make.config file"
- @echo "# Set local options for make here" > make.config
- @echo "#BOOST_LIB_SUFFIX = -mt" >> make.config
- @echo "#BOOST_LIB_DIR = $(HOME)/projects/boost/lib" >> make.config
- @echo "#BOOST_INC_DIR = $(HOME)/projects/boost/include" >> make.config
-
--- a/doc/mkdssp.1
+++ b/doc/mkdssp.1
@@ -13,7 +13,7 @@
Please note that \fImkdssp\fP \fBdoes not predict\fP secondary structure.
.SH OPTIONS
If you invoke \fImkdssp\fP with only one parameter, it will be
-interpreted as the PDB file to process and output will be send to
+interpreted as the PDB file to process and output will be sent to
stdout. If a second parameter is specified this is interpreted as
the name of the DSSP file to create. Both the input and the output
file names may have either \.gz or \.bz2 as extension resulting in
@@ -159,7 +159,7 @@
.SH TODO
The code desperately needs an update. The first thing that needs
implementing is the improved recognition of pi\-helices. A second
-improvement would be to use angle dependant H\-bond energy calculation.
+improvement would be to use angle dependent H\-bond energy calculation.
.SH BUGS
If you find any, please let me know.
.SH AUTHOR
|
