From c10df1cb0cdba9d4bb05bdffbf4747a481b06063 Mon Sep 17 00:00:00 2001 From: Petar Petrov Date: Sun, 30 Jun 2013 15:09:57 -0500 Subject: [PATCH] academic/mkDSSP: Added (A program that calculates DSSP entries from PDB entries) Signed-off-by: Erik Hanson --- academic/mkDSSP/README | 16 ++++ academic/mkDSSP/References | 10 +++ academic/mkDSSP/makefile.patch | 76 +++++++++++++++++++ academic/mkDSSP/mkDSSP.SlackBuild | 109 +++++++++++++++++++++++++++ academic/mkDSSP/mkDSSP.info | 10 +++ academic/mkDSSP/slack-desc | 19 +++++ academic/mkDSSP/thread_include.patch | 23 ++++++ 7 files changed, 263 insertions(+) create mode 100644 academic/mkDSSP/README create mode 100644 academic/mkDSSP/References create mode 100644 academic/mkDSSP/makefile.patch create mode 100644 academic/mkDSSP/mkDSSP.SlackBuild create mode 100644 academic/mkDSSP/mkDSSP.info create mode 100644 academic/mkDSSP/slack-desc create mode 100644 academic/mkDSSP/thread_include.patch diff --git a/academic/mkDSSP/README b/academic/mkDSSP/README new file mode 100644 index 0000000000..e5eea2580f --- /dev/null +++ b/academic/mkDSSP/README @@ -0,0 +1,16 @@ +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. + +If you use DSSP, please quote: +Dictionary of protein secondary structure: pattern recognition of +hydrogen-bonded and geometrical features. Kabsch W, Sander C, +Biopolymers. 1983 22 2577-2637 + +A series of PDB related databases for everyday needs. Joosten RP, Te +Beek TAH, Krieger E, Hekkelman ML, Hooft RWW, Schneider R, Sander C, +Vriend G, NAR 2010 diff --git a/academic/mkDSSP/References b/academic/mkDSSP/References new file mode 100644 index 0000000000..052633cece --- /dev/null +++ b/academic/mkDSSP/References @@ -0,0 +1,10 @@ +If you use DSSP, please quote: + +Dictionary of protein secondary structure: pattern recognition of +hydrogen-bonded and geometrical features. Kabsch W, Sander C, +Biopolymers. 1983 22 2577-2637. PMID: 6667333; UI: 84128824. + +A series of PDB related databases for everyday needs. Joosten RP, Te +Beek TAH, Krieger E, Hekkelman ML, Hooft RWW, Schneider R, Sander C, +Vriend G, NAR 2010; doi: 10.1093/nar/gkq1105. +http://swift.cmbi.ru.nl/gv/facilities/HTML/facilities.pdf diff --git a/academic/mkDSSP/makefile.patch b/academic/mkDSSP/makefile.patch new file mode 100644 index 0000000000..f50f53a426 --- /dev/null +++ b/academic/mkDSSP/makefile.patch @@ -0,0 +1,76 @@ +Description: assorted fixes + [Maarten L. Hekkelman ] + * DEST_DIR patched to DESTDIR + . + [Laszlo Kajan ] + * 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 +Author: Laszlo Kajan +--- a/makefile ++++ b/makefile +@@ -11,18 +11,16 @@ + + all: mkdssp + +-include make.config +- + VERSION = 2.1.0 + + DEST_DIR ?= /usr/local + LIB_DIR = $(BOOST_LIB_DIR) + INC_DIR = $(BOOST_INC_DIR) +-BIN_DIR = $(DEST_DIR)/bin +-MAN_DIR = $(DEST_DIR)/man/man1 ++BIN_DIR = $(DESTDIR)$(DEST_DIR)/bin ++MAN_DIR = $(DESTDIR)$(DEST_DIR)/share/man/man1 + +-BOOST_LIBS = thread filesystem program_options iostreams system +-LIBS = $(BOOST_LIBS:%=boost_%$(BOOST_LIB_SUFFIX)) z bz2 ++BOOST_LIBS = thread program_options iostreams system ++LIBS = $(BOOST_LIBS:%=boost_%$(BOOST_LIB_SUFFIX)) + + DEFINES = USE_COMPRESSION LINUX VERSION='"$(VERSION)"' + CXX = g++ +@@ -49,22 +47,19 @@ + OBJECTS = $(OBJ_DIR)/mkdssp.o $(OBJ_DIR)/dssp.o $(OBJ_DIR)/primitives-3d.o $(OBJ_DIR)/structure.o $(OBJ_DIR)/utils.o $(OBJ_DIR)/mas.o + + mkdssp: $(OBJECTS) +- @ echo linking $@ +- @ $(CXX) -static -o $@ $^ $(LDOPTS) ++ $(CXX) -o $@ $^ $(LDOPTS) + +-include $(OBJECTS:%.o=%.d) ++-include $(OBJECTS:%.o=%.d) + + $(OBJECTS:.o=.d): + + $(OBJ_DIR): +- @ mkdir -p $(OBJ_DIR) ++ mkdir -p $(OBJ_DIR) + + $(OBJ_DIR)/%.o: %.cpp | $(OBJ_DIR) +- @ echo compiling $@ +- @ $(CXX) -MD -c -o $@ $< $(CFLAGS) ++ $(CXX) -MD -c -o $@ $< $(CPPFLAGS) $(CFLAGS) + + clean: +- install -d $(BIN_DIR) $(MAN_DIR) + rm -rf $(OBJ_DIR)/* mkdssp + + install: mkdssp +@@ -85,11 +80,3 @@ + @ 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 = $(HOME)/projects/boost/include" >> make.config +- diff --git a/academic/mkDSSP/mkDSSP.SlackBuild b/academic/mkDSSP/mkDSSP.SlackBuild new file mode 100644 index 0000000000..31b109cb18 --- /dev/null +++ b/academic/mkDSSP/mkDSSP.SlackBuild @@ -0,0 +1,109 @@ +#!/bin/sh + +# Slackware build script for mkDSSP + +# Copyright 2013 Petar Petrov, ppetrov@paju.oulu.fi +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +PRGNAM=mkDSSP +SRCNAM=dssp +VERSION=${VERSION:-2.1.0} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i486 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +CWD=$(pwd) +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i486" ]; then + SLKCFLAGS="-O2 -march=i486 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" +fi + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $SRCNAM-$VERSION +tar xvf $CWD/$SRCNAM-$VERSION.tgz +cd $SRCNAM-$VERSION +chown -R root:root . +find . \ + \( -perm 777 -o -perm 775 -o -perm 711 -o -perm 555 -o -perm 511 \) \ + -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \ + -exec chmod 644 {} \; + +# Thanks to Debian for the patches! +patch -p1 -i $CWD/makefile.patch +patch -p1 -i $CWD/thread_include.patch + +CFLAGS="$SLKCFLAGS" \ +CXXFLAGS="$SLKCFLAGS" \ +BIN_DIR=/usr/bin \ +MAN_DIR=/usr/man/man1 \ +make + +make install DEST_DIR=$PKG \ +BIN_DIR=$PKG/usr/bin \ +MAN_DIR=$PKG/usr/man/man1 + +# Some programs (like aline) expect the binary to be called just "dssp" +cd $PKG/usr/bin +ln -s mkdssp dssp +cd - + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +find $PKG/usr/man -type f -exec gzip -9 {} \; +for i in $( find $PKG/usr/man -type l ) ; do ln -s $( readlink $i ).gz $i.gz ; rm $i ; done + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a \ + changelog LICENSE_1_0.txt README.txt \ + $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild +cat $CWD/References > $PKG/usr/doc/$PRGNAM-$VERSION/References + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} diff --git a/academic/mkDSSP/mkDSSP.info b/academic/mkDSSP/mkDSSP.info new file mode 100644 index 0000000000..3396b9a658 --- /dev/null +++ b/academic/mkDSSP/mkDSSP.info @@ -0,0 +1,10 @@ +PRGNAM="mkDSSP" +VERSION="2.1.0" +HOMEPAGE="http://swift.cmbi.ru.nl/gv/dssp/" +DOWNLOAD="ftp://ftp.cmbi.ru.nl/pub/software/dssp/dssp-2.1.0.tgz" +MD5SUM="950c2563d8cbeed445101d85f5a66ce7" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="" +MAINTAINER="Petar Petrov" +EMAIL="ppetrov@paju.oulu.fi" diff --git a/academic/mkDSSP/slack-desc b/academic/mkDSSP/slack-desc new file mode 100644 index 0000000000..eefbaea9dc --- /dev/null +++ b/academic/mkDSSP/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +mkDSSP: mkDSSP (A program that calculates DSSP entries from PDB entries) +mkDSSP: +mkDSSP: The DSSP program was designed by Wolfgang Kabsch and Chris Sander +mkDSSP: to standardize secondary structure assignment. DSSP is a database +mkDSSP: of secondary structure assignments (and much more) for all protein +mkDSSP: entries in the Protein Data Bank (PDB). DSSP is also the program +mkDSSP: that calculates DSSP entries from PDB entries. DSSP does not +mkDSSP: predict secondary structure. +mkDSSP: +mkDSSP: Home: http://swift.cmbi.ru.nl/gv/dssp/ +mkDSSP: References: /usr/doc/mkDSSP:-$VERSION/References diff --git a/academic/mkDSSP/thread_include.patch b/academic/mkDSSP/thread_include.patch new file mode 100644 index 0000000000..f0b462b19c --- /dev/null +++ b/academic/mkDSSP/thread_include.patch @@ -0,0 +1,23 @@ +Description: moving boost thread include out of header that does not use it + Patch is not yet forwarded upstream. +Author: Laszlo Kajan +--- a/src/utils.h ++++ b/src/utils.h +@@ -10,7 +10,6 @@ + #endif + + #include +-#include + #include + #include + #include +--- a/src/structure.cpp ++++ b/src/structure.cpp +@@ -18,6 +18,7 @@ + #define foreach BOOST_FOREACH + #include + #include ++#include + + #include "align-2d.h" + #include "utils.h"