From 4f2d7949f03e1c198bc888f2d05f421d35c57e21 Mon Sep 17 00:00:00 2001 From: V3n3RiX Date: Mon, 9 Oct 2017 18:53:29 +0100 Subject: reinit the tree, so we can have metadata --- sci-chemistry/apbs/Manifest | 8 ++ sci-chemistry/apbs/apbs-1.4.1-r2.ebuild | 127 +++++++++++++++++++++ sci-chemistry/apbs/files/apbs-1.4.1-manip.patch | 50 ++++++++ sci-chemistry/apbs/files/apbs-1.4.1-multilib.patch | 92 +++++++++++++++ sci-chemistry/apbs/files/apbs-1.4.1-python.patch | 122 ++++++++++++++++++++ sci-chemistry/apbs/metadata.xml | 25 ++++ 6 files changed, 424 insertions(+) create mode 100644 sci-chemistry/apbs/Manifest create mode 100644 sci-chemistry/apbs/apbs-1.4.1-r2.ebuild create mode 100644 sci-chemistry/apbs/files/apbs-1.4.1-manip.patch create mode 100644 sci-chemistry/apbs/files/apbs-1.4.1-multilib.patch create mode 100644 sci-chemistry/apbs/files/apbs-1.4.1-python.patch create mode 100644 sci-chemistry/apbs/metadata.xml (limited to 'sci-chemistry/apbs') diff --git a/sci-chemistry/apbs/Manifest b/sci-chemistry/apbs/Manifest new file mode 100644 index 000000000000..244816343796 --- /dev/null +++ b/sci-chemistry/apbs/Manifest @@ -0,0 +1,8 @@ +AUX apbs-1.4.1-manip.patch 1522 SHA256 155c6fcd777c1c00e313bbdae60b6ccf373af0d50b05398d928bb7662378801c SHA512 b2517b86b688091a9ae6a78132e8cd5a451eff6150211459dae6919bf2ee61edcf2cf1b95d8b2922050a3a7a3aaaa9ce8e2be6766116a1e66d413339b291326b WHIRLPOOL a215daf24985d7847210b4286a662b461d5c4b714a5585eb21b781911f95853c41c1f40109e53d6f8008c0c5c291c0d8b4f06044bf767d6049bff3e6167162c2 +AUX apbs-1.4.1-multilib.patch 3301 SHA256 21c1934eb5694737d6049eb8da868ee81f15ff86dacc09f89f0024c263929ddc SHA512 cdd72fd23a57ee8413f72bf674ae246543b1c9f326727ff07c3b8848d59f98ab7d2daf28677460cb4726f919832079c1d280bcdc86a8bef5c0875583c789b7c0 WHIRLPOOL 07ae32ecd14c21d3cce59bb904533faa1b9de532d6411176d5ee2d52ed91ef6da88b52cec0ef7b989dab253300a9d89182ddc25323347a48eb8d3355c16cb3a4 +AUX apbs-1.4.1-python.patch 4109 SHA256 793257f3581c768951c27742ecf299f462fbc7fc78635e2d7c8dd0ade69c9738 SHA512 369c0fa08187ba80d8ce72542fc2942f28426beed39619dd6a90a9ef8dfecb47ea6dc7aa20994629a69d63b55d72d1f837c442744bf5499a942bf312f6723092 WHIRLPOOL 39d2445e7d3ed1974dffeaad4c0772238cf6e508f4e002636c833921f124fe7d7d9732d23a7ffc5341815152d4ddc6cd0565bebc46988caf7f742bb2f3031033 +DIST apbs-1.4.1.zip 37999283 SHA256 1156c44fb65bb7c884801f3111ca1cdb1dfba6f5308226587db112aac4969027 SHA512 3a127af3940054e5a43b3c0c620507f4f9baa69049e5a0933d8e8825458ad2faba840392752de49fe68d91e2054fb1394cf87bb5bb1c0b48305368e2f404cf6a WHIRLPOOL 6729571f13c953ec0bcf90da73ef0c39cf769f1498a767d3280de3ffbeea18eda718373efca0468436c4b18357fe450865f661daba79eeb66778c572c43ff39a +EBUILD apbs-1.4.1-r2.ebuild 3117 SHA256 5507aca1b88d0adda0c2be27909003fc883389fba4432904c675e15950e5ecc5 SHA512 e8f20517537119640c8f12accdcc37a2f25b30d3b25923f54a5bff3c88b679219f029b49ae96ac66acf04599877f1b33289e1ce15462a0e7a6a4cd5f979ac3fc WHIRLPOOL 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7d68049cb9b044676430fe879890cc4cd869b99f85696f579d9cbf3b156081301792fd7f03205a9b9d429d71c9a35b4815f4236573f68d3ef6b4718e6e1f0bb3 WHIRLPOOL e317d7b4cc4b18c66f1943a87a69e173abd9fd151f5610881fbb8a7955e993954209f504cafce053c2e95eda94ecd394c742483b6b55e0f3b3e553f55d1a79b0 diff --git a/sci-chemistry/apbs/apbs-1.4.1-r2.ebuild b/sci-chemistry/apbs/apbs-1.4.1-r2.ebuild new file mode 100644 index 000000000000..aecbcd3ce745 --- /dev/null +++ b/sci-chemistry/apbs/apbs-1.4.1-r2.ebuild @@ -0,0 +1,127 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) +DISTUTILS_SINGLE_IMPL=true + +inherit cmake-utils distutils-r1 flag-o-matic multilib 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 iapbs mpi openmp python tools" + +REQUIRED_USE=" + iapbs? ( fetk ) + mpi? ( !python ) + python? ( tools fetk iapbs ${PYTHON_REQUIRED_USE} )" + +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 + "${FILESDIR}"/${P}-manip.patch + "${FILESDIR}"/${P}-python.patch +) + +src_prepare() { + cmake-utils_src_prepare + append-cppflags $($(tc-getPKG_CONFIG) --cflags eigen3) + + sed \ + -e "s:-lblas:$($(tc-getPKG_CONFIG) --libs blas):g" \ + -e "/TOOLS_PATH/d" \ + -i CMakeLists.txt || die + use doc && MAKEOPTS+=" -j1" + if use python; then + unset PATCHES || die + cd tools/python && distutils-r1_src_prepare + fi +} + +src_configure() { + local mycmakeargs=( + -DCMAKE_SKIP_RPATH=ON + -DTOOLS_PATH="${ED}"/usr + -DSYS_LIBPATHS="${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 + $(cmake-utils_use_enable iapbs iAPBS) +# MAX_MEMORY: Set the maximum memory (in MB) to be used for a job + ) + cmake-utils_src_configure + if use python; then + cd tools/python && distutils-r1_src_configure + fi +} + +src_compile(){ + cmake-utils_src_compile + if use python; then + append-ldflags -L"${S}"/lib + cd tools/python && distutils-r1_src_compile + fi +} + +src_test() { + python_export_best + cd tests || die + LD_LIBRARY_PATH="${S}"/lib "${PYTHON}" apbs_tester.py -l log || die + grep -q 'FAILED' log && die "Tests failed" +} + +src_install() { + dodir /usr/bin + cmake-utils_src_install + local i + for i in "${ED}"/usr/bin/*; do + if [[ ! "${i}" =~ .*apbs$ ]]; then + mv "${i}" "${i}-apbs" || die + fi + done + if use python; then + cd tools/python && distutils-r1_src_install + rm -rf "${ED}"/usr/share/apbs/tools/python || die + fi +} diff --git a/sci-chemistry/apbs/files/apbs-1.4.1-manip.patch b/sci-chemistry/apbs/files/apbs-1.4.1-manip.patch new file mode 100644 index 000000000000..378223397594 --- /dev/null +++ b/sci-chemistry/apbs/files/apbs-1.4.1-manip.patch @@ -0,0 +1,50 @@ + apbs/CMakeLists.txt | 2 +- + apbs/tools/CMakeLists.txt | 4 ---- + apbs/tools/mesh/CMakeLists.txt | 4 ++-- + 4 files changed, 5 insertions(+), 9 deletions(-) + +diff --git a/apbs/CMakeLists.txt b/apbs/CMakeLists.txt +index 8917fc4..5152008 100644 +--- a/apbs/CMakeLists.txt ++++ b/apbs/CMakeLists.txt +@@ -293,7 +293,7 @@ option(ENABLE_FETK "Enable the finite element solver" OFF) + + if(ENABLE_FETK) + message(STATUS "Checking for fetk components") +- set(FETK_ENALBED 1) ++ set(FETK_ENABLED 1) + + list(APPEND APBS_LIBS "-lstdc++") + list(APPEND APBS_LIBS "-L${FETK_PATH}/lib") +diff --git a/apbs/tools/manip/CMakeLists.txt b/apbs/tools/manip/CMakeLists.txt +index 937dac7..5768cc5 100644 +--- a/apbs/tools/manip/CMakeLists.txt ++++ b/apbs/tools/manip/CMakeLists.txt +@@ -4,9 +4,9 @@ set(LIBS "") + list(APPEND LIBS "apbs_generic") + list(APPEND LIBS "apbs_mg") + list(APPEND LIBS "apbs_pmgc") +-if(FETK_ENALBED) ++if(FETK_ENABLED) + list(APPEND LIBS "apbs_fem") +-endif(FETK_ENALBED) ++endif(FETK_ENABLED) + + message(STATUS "libraries: ${LIBS}") + +diff --git a/apbs/tools/mesh/CMakeLists.txt b/apbs/tools/mesh/CMakeLists.txt +index 1406377..6e6dfb9 100644 +--- a/apbs/tools/mesh/CMakeLists.txt ++++ b/apbs/tools/mesh/CMakeLists.txt +@@ -4,9 +4,9 @@ set(LIBS "") + list(APPEND LIBS "apbs_generic") + list(APPEND LIBS "apbs_mg") + list(APPEND LIBS "apbs_pmgc") +-if(FETK_ENALBED) ++if(FETK_ENABLED) + list(APPEND LIBS "apbs_fem") +-endif(FETK_ENALBED) ++endif(FETK_ENABLED) + + message(STATUS "libraries: ${LIBS}") + 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..a4e2d1761cf4 --- /dev/null +++ b/sci-chemistry/apbs/files/apbs-1.4.1-multilib.patch @@ -0,0 +1,92 @@ + 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/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/files/apbs-1.4.1-python.patch b/sci-chemistry/apbs/files/apbs-1.4.1-python.patch new file mode 100644 index 000000000000..db9f86ba120a --- /dev/null +++ b/sci-chemistry/apbs/files/apbs-1.4.1-python.patch @@ -0,0 +1,122 @@ + apbs/contrib/iapbs/src/apbs_driver.c | 6 +++--- + apbs/src/CMakeLists.txt | 1 + + apbs/tools/CMakeLists.txt | 2 +- + apbs/tools/python/CMakeLists.txt | 1 + + apbs/tools/python/apbslib.c | 4 ++-- + apbs/tools/python/apbslib.i | 4 ++-- + apbs/tools/python/setup.py | 16 ++++++++++++++++ + 7 files changed, 26 insertions(+), 8 deletions(-) + +diff --git a/apbs/contrib/iapbs/src/apbs_driver.c b/apbs/contrib/iapbs/src/apbs_driver.c +index c9e443b..e1ad67f 100644 +--- a/apbs/contrib/iapbs/src/apbs_driver.c ++++ b/apbs/contrib/iapbs/src/apbs_driver.c +@@ -595,7 +595,7 @@ int apbsdrv_( + printPBEPARM(pbeparm); + + /* Refine mesh */ +- if (!preRefineFE(i, nosh, feparm, fetk)) { ++ if (!preRefineFE(i, feparm, fetk)) { + Vnm_tprint( 2, "Error pre-refining mesh!\n"); + VJMPERR1(0); + } +@@ -609,7 +609,7 @@ int apbsdrv_( + Vnm_tprint(1, " Beginning solve-estimate-refine cycle:\n"); + for (isolve=0; isolvemaxsolve; isolve++) { + Vnm_tprint(1, " Solve #%d...\n", isolve); +- if (!solveFE(i, nosh, pbeparm, feparm, fetk)) { ++ if (!solveFE(i, pbeparm, feparm, fetk)) { + Vnm_tprint(2, "ERROR SOLVING EQUATION!\n"); + VJMPERR1(0); + } +@@ -622,7 +622,7 @@ int apbsdrv_( + /* We're not going to refine if we've hit the max number + * of solves */ + if (isolve < (feparm->maxsolve)-1) { +- if (!postRefineFE(i, nosh, feparm, fetk)) break; ++ if (!postRefineFE(i, feparm, fetk)) break; + } + bytesTotal = Vmem_bytesTotal(); + highWater = Vmem_highWaterTotal(); +diff --git a/apbs/src/CMakeLists.txt b/apbs/src/CMakeLists.txt +index 44d20fa..2577343 100644 +--- a/apbs/src/CMakeLists.txt ++++ b/apbs/src/CMakeLists.txt +@@ -68,6 +68,7 @@ configure_file( + + if(ENABLE_iAPBS) + ADD_LIBRARY(apbs_routines routines.c routines.h) ++ target_link_libraries(apbs_routines apbs_mg apbs_fem) + INSTALL(TARGETS apbs_routines DESTINATION ${LIBRARY_INSTALL_PATH}) + INSTALL(FILES apbscfg.h DESTINATION ${HEADER_INSTALL_PATH}) + endif() +diff --git a/apbs/tools/CMakeLists.txt b/apbs/tools/CMakeLists.txt +index 1982a3c..4acbe68 100644 +--- a/apbs/tools/CMakeLists.txt ++++ b/apbs/tools/CMakeLists.txt +@@ -4,5 +4,5 @@ add_subdirectory(mesh) + add_subdirectory(manip) + + if(ENABLE_PYTHON) +- add_subdirectory(manip) ++ add_subdirectory(python) + endif(ENABLE_PYTHON) +diff --git a/apbs/tools/python/CMakeLists.txt b/apbs/tools/python/CMakeLists.txt +new file mode 100644 +index 0000000..8b13789 +--- /dev/null ++++ b/apbs/tools/python/CMakeLists.txt +@@ -0,0 +1 @@ ++ +diff --git a/apbs/tools/python/apbslib.c b/apbs/tools/python/apbslib.c +index fef5cc8..feaaa2c 100644 +--- a/apbs/tools/python/apbslib.c ++++ b/apbs/tools/python/apbslib.c +@@ -2504,8 +2504,8 @@ static swig_module_info swig_module = {swig_types, 24, 0, 0, 0, 0}; + #include "maloc/maloc.h" + #include "apbscfg.h" + #include "routines.h" +-#include "apbs/valist.h" +-#include "apbs/vatom.h" ++#include "generic/valist.h" ++#include "generic/vatom.h" + + + #include +diff --git a/apbs/tools/python/apbslib.i b/apbs/tools/python/apbslib.i +index 17fe521..44d05ea 100644 +--- a/apbs/tools/python/apbslib.i ++++ b/apbs/tools/python/apbslib.i +@@ -15,8 +15,8 @@ Header files: + #include "maloc/maloc.h" + #include "apbscfg.h" + #include "routines.h" +-#include "apbs/valist.h" +-#include "apbs/vatom.h" ++#include "generic/valist.h" ++#include "generic/vatom.h" + %} + + /* +diff --git a/apbs/tools/python/setup.py b/apbs/tools/python/setup.py +new file mode 100644 +index 0000000..4a20198 +--- /dev/null ++++ b/apbs/tools/python/setup.py +@@ -0,0 +1,16 @@ ++from distutils.core import setup, Extension ++setup(name='apbs', ++ version='1.4.1', ++ package_dir={'apbs': '', 'vgrid': 'vgrid'}, ++ packages=['apbs', 'vgrid'], ++ py_modules=['apbslib', 'main', 'noinput'], ++ ext_modules=[ ++ Extension( ++ '_apbslib', ++ ['apbslib.i'], ++ swig_opts=['-module', 'apbslib', '-I../include'], ++ include_dirs=["../../src"], ++ libraries=["apbs_generic", "apbs_routines"] ++ ) ++ ], ++ ) diff --git a/sci-chemistry/apbs/metadata.xml b/sci-chemistry/apbs/metadata.xml new file mode 100644 index 000000000000..a33a5468d19c --- /dev/null +++ b/sci-chemistry/apbs/metadata.xml @@ -0,0 +1,25 @@ + + + + + sci-chemistry@gentoo.org + Gentoo Chemistry Project + + + Include support for FeTK + APBS fast mode (experimental) + C/C++/Fortran interface + Install optional tools + + +APBS is a software package for modeling biomolecular solvation through solution +of the Poisson-Boltzmann equation (PBE), one of the most popular continuum +models for describing electrostatic interactions between molecular solutes in +salty, aqueous media. Continuum electrostatics plays an important role in +several areas of biomolecular simulation + + + Electrostatics/apbs-pdb2pqr + apbs + + -- cgit v1.2.3