sci-chemistry/autodock_vina: add 1.2.5

Signed-off-by: Alexey Shvetsov <alexxy@gentoo.org>

3 files changed, 115 insertions, 0 deletions

diff --git a/sci-chemistry/autodock_vina/Manifest b/sci-chemistry/autodock_vina/Manifest
index 67f2032d2856..e4088c449178 100644
--- a/sci-chemistry/autodock_vina/Manifest
+++ b/sci-chemistry/autodock_vina/Manifest
@@ -1 +1,2 @@
+DIST autodock_vina-1.2.5.tar.gz 24158966 BLAKE2B c11493fcb35d409b97f639c4da48967d5df450781d412d80a951b95162555f4b1dfba809a01062136a7f0664c0b9a01a42b5403ee1d278a57afd669cf1f96321 SHA512 d36908e5833d22bcbc4dae353ef32b905d6eb46511302f7583a291398bfadff5e75fc99ce7b380860578b2257e5c32434cc75b1ca51fafb4b5f12d9477a878e9
 DIST autodock_vina_1_1_2.tgz 67366 BLAKE2B dc754bf522795ebfbfcf89a2df4e3761d941c1f0ce05cf56898720c1e855f5dd00fd2a583f5a8d218fa2e738d37e014a9b3239b9aa989b9018a6a33f8f0bd02c SHA512 f704af322ebc192117c49d0cf8a3f217105beccb7b47d6361665470894ef7a9f91fc4b5f07cc9aff56e497bfa80953e40e39090c8394a095c61597756e333ae9
diff --git a/sci-chemistry/autodock_vina/autodock_vina-1.2.5.ebuild b/sci-chemistry/autodock_vina/autodock_vina-1.2.5.ebuild
new file mode 100644
index 000000000000..e9edf1f9c991
--- /dev/null
+++ b/sci-chemistry/autodock_vina/autodock_vina-1.2.5.ebuild
@@ -0,0 +1,50 @@
+# Copyright 1999-2024 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit flag-o-matic toolchain-funcs
+
+MY_PN=AutoDock-Vina
+
+DESCRIPTION="Program for drug discovery, molecular docking and virtual screening"
+HOMEPAGE="http://vina.scripps.edu/"
+SRC_URI="https://github.com/ccsb-scripps/AutoDock-Vina/archive/refs/tags/v${PV}.tar.gz -> ${P}.tar.gz"
+
+S="${WORKDIR}/${MY_PN}-${PV}/build/linux/release"
+
+LICENSE="Apache-2.0"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="debug"
+
+RDEPEND="dev-libs/boost:="
+DEPEND="${RDEPEND}"
+
+PATCHES=(
+	"${FILESDIR}"/${P}-gentoo.patch
+)
+
+src_prepare() {
+	cd "${WORKDIR}/${MY_PN}-${PV}" || die
+	pwd
+	sed -e "s:VERSION:\"${PV}\":g" \
+		-i src/main/main.cpp \
+		-i src/split/split.cpp || die
+	default
+}
+
+src_configure() {
+	append-cxxflags -DBOOST_FILESYSTEM_VERSION=3 -DBOOST_TIMER_ENABLE_DEPRECATED -std=c++14
+}
+
+src_compile() {
+	emake \
+		BASE="${EPREFIX}"/usr/ \
+		GPP="$(tc-getCXX)" \
+		C_OPTIONS=$(usex debug '' -DNDEBUG)
+}
+
+src_install() {
+	dobin vina{,_split}
+}
diff --git a/sci-chemistry/autodock_vina/files/autodock_vina-1.2.5-gentoo.patch b/sci-chemistry/autodock_vina/files/autodock_vina-1.2.5-gentoo.patch
new file mode 100644
index 000000000000..e7bf1d5007ff
--- /dev/null
+++ b/sci-chemistry/autodock_vina/files/autodock_vina-1.2.5-gentoo.patch
@@ -0,0 +1,64 @@
+diff -urN AutoDock-Vina-1.2.5.orig/build/linux/debug/Makefile AutoDock-Vina-1.2.5/build/linux/debug/Makefile
+--- AutoDock-Vina-1.2.5.orig/build/linux/debug/Makefile	2024-03-05 13:23:49.210511903 +0300
++++ AutoDock-Vina-1.2.5/build/linux/debug/Makefile	2024-03-05 13:25:34.028499976 +0300
+@@ -1,7 +1,7 @@
+ BASE=/usr
+ BOOST_VERSION=
+ BOOST_INCLUDE = $(BASE)/include
+-C_PLATFORM=-static -pthread
++C_PLATFORM=-pthread
+ GPP=g++
+ C_OPTIONS= -g -std=gnu++11
+ BOOST_LIB_VERSION=
+diff -urN AutoDock-Vina-1.2.5.orig/build/linux/release/Makefile AutoDock-Vina-1.2.5/build/linux/release/Makefile
+--- AutoDock-Vina-1.2.5.orig/build/linux/release/Makefile	2024-03-05 13:23:49.213845279 +0300
++++ AutoDock-Vina-1.2.5/build/linux/release/Makefile	2024-03-05 13:26:10.285621339 +0300
+@@ -1,7 +1,7 @@
+ BASE=/usr/local
+ BOOST_VERSION=
+ BOOST_INCLUDE = $(BASE)/include
+-C_PLATFORM=-static -pthread
++C_PLATFORM=-pthread
+ GPP=g++
+ C_OPTIONS= -O3 -DNDEBUG -std=c++11
+ BOOST_LIB_VERSION=
+diff -urN AutoDock-Vina-1.2.5.orig/build/makefile_common AutoDock-Vina-1.2.5/build/makefile_common
+--- AutoDock-Vina-1.2.5.orig/build/makefile_common	2024-03-05 13:23:49.213845279 +0300
++++ AutoDock-Vina-1.2.5/build/makefile_common	2024-03-05 13:28:30.557370911 +0300
+@@ -14,7 +14,7 @@
+ #CC = ${GPP} ${C_PLATFORM} -ansi -pedantic -Wno-long-long ${C_OPTIONS} $(INCFLAGS)
+ CC = ${GPP} ${C_PLATFORM} -ansi -Wno-long-long ${C_OPTIONS} $(INCFLAGS)
+ 
+-LDFLAGS = -L$(BASE)/lib -L.
++LDFLAGS = -L.
+ 
+ # test if boost_thread-mt exists, this is
+ # necessary as some versions of boost only
+@@ -32,22 +32,22 @@
+ ifeq ($(BOOST_STATIC), y)
+ LIBS = ${BASE}/lib/libboost_system${BOOST_LIB_VERSION}.a ${BASE}/lib/libboost_thread${threadmt}${BOOST_LIB_VERSION}.a ${BASE}/lib/libboost_serialization${BOOST_LIB_VERSION}.a ${BASE}/lib/libboost_filesystem${BOOST_LIB_VERSION}.a ${BASE}/lib/libboost_program_options${BOOST_LIB_VERSION}.a
+ else
+-LIBS = -l boost_system${BOOST_LIB_VERSION} -l boost_thread${threadmt}${BOOST_LIB_VERSION} -l boost_serialization${BOOST_LIB_VERSION} -l boost_filesystem${BOOST_LIB_VERSION} -l boost_program_options${BOOST_LIB_VERSION}#-l pthread
++LIBS = -l boost_system -l boost_thread -l boost_serialization -l boost_filesystem -l boost_program_options -l pthread
+ endif
+ 
+ .SUFFIXES: .cpp .o
+ 
+ %.o : ../../../src/lib/%.cpp 
+-	$(CC) $(CFLAGS) -o $@ -c $< 
++	$(CC) $(CXXFLAGS) -o $@ -c $< 
+ 
+ %.o : ../../../src/design/%.cpp 
+-	$(CC) $(CFLAGS) -I ../../../src/lib -o $@ -c $< 
++	$(CC) $(CXXFLAGS) -I ../../../src/lib -o $@ -c $< 
+ 	
+ %.o : ../../../src/main/%.cpp 
+-	$(CC) $(CFLAGS) -I ../../../src/lib -o $@ -c $< 
++	$(CC) $(CXXFLAGS) -I ../../../src/lib -o $@ -c $< 
+ 
+ %.o : ../../../src/split/%.cpp 
+-	$(CC) $(CFLAGS) -I ../../../src/lib -o $@ -c $< 
++	$(CC) $(CXXFLAGS) -I ../../../src/lib -o $@ -c $< 
+ 
+ all: vina vina_split
+