sci-chemistry / apbs

Evaluation of electrostatic properties of nanoscale biomolecular systems

Official package sites : https://www.poissonboltzmann.org/apbs/ ·

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

v1.4.1-r2 :: 0 :: gentoo

Modified
License
BSD
Keywords
amd64 ppc x86 ~amd64-linux ~x86-linux
USE flags
debug doc examples fast fetk iapbs mpi openmp python tools

General

debug
Enable extra debug codepaths, like asserts and extra output. If you want to get meaningful backtraces see https://wiki.gentoo.org/wiki/Project:Quality_Assurance/Backtraces
doc
Add extra documentation (API, Javadoc, etc). It is recommended to enable per package instead of globally
examples
Install examples, usually source code
fast
APBS fast mode (experimental)
fetk
Include support for FeTK
iapbs
C/C++/Fortran interface
mpi
Add MPI (Message Passing Interface) layer to the apps that support it
openmp
Build support for the OpenMP (support parallel computing), requires >=sys-devel/gcc-4.2 built with USE="openmp"
python
Add optional support/bindings for the Python language
tools
Install optional tools

python_targets

python2_7
Build with Python 2.7

app-doc / doxygen : Documentation system for most programming languages

dev-cpp / eigen : C++ template library for linear algebra

dev-lang / python : An interpreted, interactive, object-oriented programming language

dev-lang / python-exec : Python script wrapper

dev-libs / maloc : Minimal Abstraction Layer for Object-oriented C/C++ programs

dev-util / cmake : Cross platform Make

sci-libs / amd : Library to order a sparse matrix prior to Cholesky factorization

sci-libs / fetk : The Finite Element ToolKit - Meta package

sci-libs / superlu : Sparse LU factorization library

sci-libs / umfpack : Unsymmetric multifrontal sparse LU factorization library

sys-devel / make : Standard tool to compile source trees

sys-libs / readline : Another cute console display library

virtual / blas : Virtual for FORTRAN 77 BLAS implementation

virtual / mpi : Virtual for Message Passing Interface (MPI) v2.0 implementation

virtual / pkgconfig : Virtual for the pkg-config implementation

dev-cpp / eigen : C++ template library for linear algebra

dev-lang / python : An interpreted, interactive, object-oriented programming language

dev-lang / python-exec : Python script wrapper

dev-libs / maloc : Minimal Abstraction Layer for Object-oriented C/C++ programs

sci-libs / amd : Library to order a sparse matrix prior to Cholesky factorization

sci-libs / fetk : The Finite Element ToolKit - Meta package

sci-libs / superlu : Sparse LU factorization library

sci-libs / umfpack : Unsymmetric multifrontal sparse LU factorization library

sys-libs / readline : Another cute console display library

virtual / blas : Virtual for FORTRAN 77 BLAS implementation

virtual / mpi : Virtual for Message Passing Interface (MPI) v2.0 implementation

sci-chemistry / pdb2pqr : Automated pipeline for performing Poisson-Boltzmann electrostatics calculations

359785
sci-chemistry/apbs fails tests
446122
[science overlay] sci-chemistry/apbs-1.3-r3 with sci-libs/mkl-11.0.0.079 - ../../src/aaa_lib/.libs/libapbs.so: undefined reference to `GOMP_parallel_start'
547210
sci-chemistry/apbs migrate to sys-cluster/mpich
571396
sci-chemistry/apbs-1.4.2 + 1.5 version bump
600754
sci-chemistry/apbs: useless USE=tools description
677830
sci-chemistry/apbs-1.4.1-r2 : [QA] One or more CMake variables were not used by the project:
Repository mirror & CI · gentoo
Merge updates from master
Andreas Sturmlechner · gentoo
sci-chemistry/apbs: EAPI-6 bump
Package-Manager: Portage-2.3.52, Repoman-2.3.12 Signed-off-by: Andreas Sturmlechner <asturm@gentoo.org>
Repository mirror & CI · gentoo
Merge updates from master
Andreas Sturmlechner · gentoo
sci-chemistry/apbs: https
Signed-off-by: Andreas Sturmlechner <asturm@gentoo.org> Package-Manager: Portage-2.3.51, Repoman-2.3.11
Andreas Sturmlechner · gentoo
sci-chemistry/apbs: Sort and fix DEPENDs
Signed-off-by: Andreas Sturmlechner <asturm@gentoo.org> Package-Manager: Portage-2.3.51, Repoman-2.3.11
Andreas Sturmlechner · gentoo
sci-chemistry/apbs: Several missing || die
Signed-off-by: Andreas Sturmlechner <asturm@gentoo.org> Package-Manager: Portage-2.3.51, Repoman-2.3.11
Robin H. Johnson · gentoo
Drop $Id$ per council decision in bug #611234.
Signed-off-by: Robin H. Johnson <robbat2@gentoo.org>
Robin H. Johnson · gentoo
proj/gentoo: Initial commit
This commit represents a new era for Gentoo: Storing the gentoo-x86 tree in Git, as converted from CVS. This commit is the start of the NEW history. Any historical data is intended to be grafted onto this point. Creation process: 1. Take final CVS checkout snapshot 2. Remove ALL ChangeLog* files 3. Transform all Manifests to thin 4. Remove empty Manifests 5. Convert all stale $Header$/$Id$ CVS keywords to non-expanded Git $Id$ 5.1. Do not touch files with -kb/-ko keyword flags. Signed-off-by: Robin H. Johnson <robbat2@gentoo.org> X-Thanks: Alec Warner <antarus@gentoo.org> - did the GSoC 2006 migration tests X-Thanks: Robin H. Johnson <robbat2@gentoo.org> - infra guy, herding this project X-Thanks: Nguyen Thai Ngoc Duy <pclouds@gentoo.org> - Former Gentoo developer, wrote Git features for the migration X-Thanks: Brian Harring <ferringb@gentoo.org> - wrote much python to improve cvs2svn X-Thanks: Rich Freeman <rich0@gentoo.org> - validation scripts X-Thanks: Patrick Lauer <patrick@gentoo.org> - Gentoo dev, running new 2014 work in migration X-Thanks: Michał Górny <mgorny@gentoo.org> - scripts, QA, nagging X-Thanks: All of other Gentoo developers - many ideas and lots of paint on the bikeshed