4 files changed, 206 insertions, 2 deletions
diff --git a/sci-chemistry/apbs/ChangeLog b/sci-chemistry/apbs/ChangeLog
index eb04e2ef697a..c62536ea7a15 100644
--- a/sci-chemistry/apbs/ChangeLog
+++ b/sci-chemistry/apbs/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-chemistry/apbs
-# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/apbs/ChangeLog,v 1.63 2013/05/02 15:16:35 jlec Exp $
+# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/apbs/ChangeLog,v 1.64 2014/08/15 08:50:33 jlec Exp $
+
+*apbs-1.4.1 (15 Aug 2014)
+
+  15 Aug 2014; Justin Lecher <jlec@gentoo.org> +apbs-1.4.1.ebuild,
+  +files/apbs-1.4.1-multilib.patch, metadata.xml:
+  Version BUmp
 
   02 May 2013; Justin Lecher <jlec@gentoo.org> apbs-1.3-r3.ebuild:
   Fix obsolete macros in automake-1.13
diff --git a/sci-chemistry/apbs/apbs-1.4.1.ebuild b/sci-chemistry/apbs/apbs-1.4.1.ebuild
new file mode 100644
index 000000000000..a3201f1faaa3
--- /dev/null
+++ b/sci-chemistry/apbs/apbs-1.4.1.ebuild
@@ -0,0 +1,93 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/apbs/apbs-1.4.1.ebuild,v 1.1 2014/08/15 08:50:33 jlec Exp $
+
+EAPI=5
+
+PYTHON_COMPAT=( python2_7 )
+
+inherit cmake-utils flag-o-matic multilib python-single-r1 toolchain-funcs
+
+GITHUB_REV="74fcb8676de69ed04ddab8976a8b05a6caaf4d65"
+
+DESCRIPTION="Evaluation of electrostatic properties of nanoscale biomolecular systems"
+HOMEPAGE="http://www.poissonboltzmann.org/apbs/"
+#SRC_URI="mirror://sourceforge/${PN}/${P}-source.tar.gz"
+SRC_URI="https://github.com/Electrostatics/apbs-pdb2pqr/archive/${GITHUB_REV}.zip -> ${P}.zip"
+
+SLOT="0"
+LICENSE="BSD"
+KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux"
+IUSE="debug doc examples fast +fetk mpi openmp python tools"
+
+REQUIRED_USE="mpi? ( !python )"
+
+RDEPEND="
+	dev-cpp/eigen:3
+	dev-libs/maloc[mpi=]
+	virtual/blas
+	sys-libs/readline
+	fetk? (
+		sci-libs/fetk
+		sci-libs/amd
+		sci-libs/umfpack
+		sci-libs/superlu
+	)
+	mpi? ( virtual/mpi )
+	python? ( ${PYTHON_DEPS} )
+"
+DEPEND="${DEPEND}
+	virtual/pkgconfig
+	doc? ( app-doc/doxygen )
+"
+
+S="${WORKDIR}"/${PN}-pdb2pqr-${GITHUB_REV}/${PN}
+
+PATCHES=(
+	"${FILESDIR}"/${P}-multilib.patch
+)
+
+src_prepare() {
+	cmake-utils_src_prepare
+	append-cppflags $($(tc-getPKG_CONFIG) --cflags eigen3)
+
+	sed \
+		-e "s:-lblas:$($(tc-getPKG_CONFIG) --libs blas):g" \
+		-i CMakeLists.txt || die
+}
+
+src_configure() {
+	local mycmakeargs=(
+	-DSYS_LIBPATHS="${EPREFIX}"/usr/$(get_libdir)
+		-DLIBRARY_INSTALL_PATH=$(get_libdir)
+		-DFETK_PATH="${EPREFIX}"/usr/
+		-DBUILD_SHARED_LIBS=ON
+		-DENABLE_QUIT=OFF
+		$(cmake-utils_use_build doc DOC)
+		$(cmake-utils_use_build tools TOOLS)
+		-DENABLE_BEM=OFF
+# ENABLE_BEM: Boundary element method using TABIPB
+		$(cmake-utils_use_enable debug DEBUG)
+		$(cmake-utils_use_enable debug VERBOSE_DEBUG)
+		$(cmake-utils_use_enable fast FAST)
+		$(cmake-utils_use_enable fetk FETK)
+		$(cmake-utils_use_enable mpi MPI)
+		$(cmake-utils_use_enable python PYTHON)
+# ENABLE_TINKER: Enable TINKER support
+		$(cmake-utils_use_enable python PYTHON)
+# ENABLE_iAPBS: Enable iAPBS
+# MAX_MEMORY: Set the maximum memory (in MB) to be used for a job
+	)
+	cmake-utils_src_configure
+}
+
+src_test() {
+	cd tests || die
+	"${PYTHON}" apbs_tester.py -l log || die
+	grep -q 'FAILED' log && die "Tests failed"
+}
+
+src_install() {
+	cmake-utils_src_install
+	python_optimize "${ED}"
+}
diff --git a/sci-chemistry/apbs/files/apbs-1.4.1-multilib.patch b/sci-chemistry/apbs/files/apbs-1.4.1-multilib.patch
new file mode 100644
index 000000000000..78061c76b6c2
--- /dev/null
+++ b/sci-chemistry/apbs/files/apbs-1.4.1-multilib.patch
@@ -0,0 +1,104 @@
+ CMakeLists.txt          | 18 +++++++++---------
+ src/CMakeLists.txt      |  1 -
+ src/fem/CMakeLists.txt  |  2 +-
+ src/pmgc/CMakeLists.txt |  2 +-
+ 4 files changed, 11 insertions(+), 12 deletions(-)
+
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index 75ddbdd..c46f5e7 100644
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -61,7 +61,7 @@ set(LIBRARY_OUTPUT_PATH ${APBS_ROOT}/lib)
+ set(TOOLS_PATH ${APBS_ROOT}/tools)
+ set(APBS_BINARY ${EXECUTABLE_OUTPUT_PATH}/apbs)
+ 
+-set(LIBRARY_INSTALL_PATH lib)
++set(LIBRARY_INSTALL_PATH ${CMAKE_INSTALL_LIBDIR})
+ set(HEADER_INSTALL_PATH include/apbs)
+ set(EXECUTABLE_INSTALL_PATH bin)
+ set(SHARE_INSTALL_PATH share/apbs)
+@@ -93,8 +93,6 @@ set(CMAKE_INCLUDE_PATH "${CMAKE_INCLUDE_PATH}")
+ list(APPEND CMAKE_INCLUDE_PATH /usr/include)
+ list(APPEND CMAKE_INCLUDE_PATH /usr/local/include)
+ 
+-set(APBS_LIBS "-L${APBS_ROOT}/lib -lapbs_geoflow")
+-
+ ################################################################################
+ # Enable ansi pedantic compiling                                               #
+ ################################################################################
+@@ -193,9 +191,11 @@ if(ENABLE_BEM)
+     else()
+         set(TABI_LIBRARY_BASENAME ${CMAKE_STATIC_LIBRARY_PREFIX}${TABI}${CMAKE_STATIC_LIBRARY_SUFFIX})
+     endif()
+-    
++	
++    file(GLOB MODS ${LIBRARY_OUTPUT_PATH}/*.mod)
++
+     install(
+-        FILES ${LIBRARY_OUTPUT_PATH}/${TABI_LIBRARY_BASENAME} ${LIBRARY_OUTPUT_PATH}/*.mod
++        FILES ${LIBRARY_OUTPUT_PATH}/${TABI_LIBRARY_BASENAME} ${MODS}
+         DESTINATION ${LIBRARY_INSTALL_PATH}
+     )
+     set(TABI_LIBRARY ${APBS_ROOT}/${LIBRARY_INSTALL_PATH}/${TABI_LIBRARY_BASENAME})
+@@ -210,7 +210,7 @@ if(ENABLE_BEM)
+     endif()
+     get_filename_component(LIBGFORTRANPATH ${LIBGFORTRANPATH} PATH)
+     find_path(LIBGFORTRAN_PATH ${LIBGFORTRAN_NAME} PATH ${LIBGFORTRANPATH})
+-    list(APPEND APBS_LIBS "-L${APBS_ROOT}/${LIBRARY_INSTALL_PATH} -L${LIBGFORTRAN_PATH} -lgfortran -ltabipb" )
++    list(APPEND APBS_LIBS "-L${APBS_ROOT}/lib -L${LIBGFORTRAN_PATH} -lgfortran -ltabipb" )
+ endif() # ENABLE_BEM
+ 
+ find_file( # this should be find path...
+@@ -228,7 +228,7 @@ endif()
+ 
+ 
+ find_library(MALOC_LIBRARY  "maloc"
+-    PATHS ${FETK_PATH}/lib ${CONTRIB_PATH}
++    PATHS ${FETK_PATH}/${CMAKE_INSTALL_LIBDIR} ${CONTRIB_PATH}
+     DOC   "The fetk/maloc library"
+ )
+ if(MALOC_LIBRARY)
+@@ -296,9 +296,9 @@ if(ENABLE_FETK)
+     set(FETK_ENALBED 1)
+ 
+     list(APPEND APBS_LIBS "-lstdc++")
+-    list(APPEND APBS_LIBS "-L${FETK_PATH}/lib")
++    list(APPEND APBS_LIBS "-L${FETK_PATH}/${CMAKE_INSTALL_LIBDIR}")
+     list(APPEND APBS_LIBS -lamd -lpunc -lmc -lgamer -lsuperlu -lumfpack
+--lblas -lvf2c -ltetgen -ltriangle -lg2c -lreadline )
++-lblas -lvf2c -ltetgen -ltriangle -lreadline )
+     
+     SET(HAVE_MC_H YES)
+ endif()
+diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
+index 44d20fa..5d5150b 100644
+--- a/src/CMakeLists.txt
++++ b/src/CMakeLists.txt
+@@ -23,7 +23,6 @@ macro(add_items TYPE)
+ endmacro()
+ 
+ 
+-
+ macro(add_sublibrary LIBRARY)
+     set(LIBRARY_NAME "apbs_${LIBRARY}")
+     set(LIBRARY_DEPENDENCIES ${APBS_LIBS} ${ARGN})
+diff --git a/src/fem/CMakeLists.txt b/src/fem/CMakeLists.txt
+index 5a950c2..dc37f48 100644
+--- a/src/fem/CMakeLists.txt
++++ b/src/fem/CMakeLists.txt
+@@ -12,4 +12,4 @@ add_items(
+     vpee.h
+ )
+ 
+-add_sublibrary(fem)
++add_sublibrary(fem apbs_geoflow)
+diff --git a/src/pmgc/CMakeLists.txt b/src/pmgc/CMakeLists.txt
+index 85b0c1e..97c95f0 100644
+--- a/src/pmgc/CMakeLists.txt
++++ b/src/pmgc/CMakeLists.txt
+@@ -42,4 +42,4 @@ add_items(
+     mgfasd.h
+ )
+ 
+-add_sublibrary(pmgc)
++add_sublibrary(pmgc apbs_geoflow)
diff --git a/sci-chemistry/apbs/metadata.xml b/sci-chemistry/apbs/metadata.xml
index cf9d997042f2..151466467f18 100644
--- a/sci-chemistry/apbs/metadata.xml
+++ b/sci-chemistry/apbs/metadata.xml
@@ -10,6 +10,7 @@
   <use>
     <flag name="arpack">Include support for arpack libs</flag>
     <flag name="fetk">Include support for FeTK</flag>
+    <flag name="fast">APBS fast mode (experimental)</flag>
     <flag name="tools">Install optional tools</flag>
   </use>
   <longdescription>