Summary
Rapid Software Prototyping can significantly reduce development times in the field of Computational Molecular Biology and Molecular Modeling. BALL (Biochemical Algorithms Library) is an application framework in C++ that has been specifically designed for this purpose. It provides an extensive set of data structures as well as classes for Molecular Mechanics, advanced solvation methods, comparison and analysis of protein structures, file import/export, and visualization . BALL has been carefully designed to be robust, easy to use, and open to extensions. Especially its extensibility which results from an object-oriented and generic programming approach distinguishes it from other software packages. BALL is well suited to serve as a public repository for reliable data structures and algorithms. Based on BALL we have developed a stand-alone tool for molecular visualization, BALLView . BALLView makes the broad functionality available through an integrated user-friendly GUI.
Versions
v1.5.0_pre20180419 :: 0 :: gentoo
- Modified
- License
- LGPL-2 fftw? ( GPL-3 ) openbabel? ( GPL-3 )
- Keywords
- ~amd64 ~amd64-linux ~x86 ~x86-linux
- USE flags
- cuda doc fftw gui lpsolve mpi openbabel python svm test threads webengine
USE flags
General
- cuda
- Missing description
- doc
- Add extra documentation (API, Javadoc, etc). It is recommended to enable per package instead of globally
- fftw
- Use FFTW library for computing Fourier transforms
- gui
- Missing description
- lpsolve
- Missing description
- mpi
- Add MPI (Message Passing Interface) layer to the apps that support it
- openbabel
- Missing description
- python
- Add optional support/bindings for the Python language
- svm
- Missing description
- test
- Enable dependencies and/or preparations necessary to run tests (usually controlled by FEATURES=test but can be toggled independently)
- threads
- Add threads support for various packages. Usually pthreads
- webengine
- Missing description
python_targets
- python2_7
- Build with Python 2.7
Dependencies
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 / boost : Boost Libraries for C++
dev-python / sip : Python extension module generator for C and C++ libraries
dev-qt / linguist-tools : Tools for working with Qt translation data files
dev-qt / qtcore : Cross-platform application development framework
dev-qt / qtgui : The GUI module and platform plugins for the Qt5 framework
dev-qt / qtnetwork : Network abstraction library for the Qt5 framework
dev-qt / qtopengl : OpenGL support library for the Qt5 framework (deprecated)
dev-qt / qtprintsupport : Printing support library for the Qt5 framework
dev-qt / qttest : Unit testing library for the Qt5 framework
dev-qt / qtwebchannel : Qt5 module for integrating C++ and QML applications with HTML/JavaScript clients
dev-qt / qtwebengine : Library for rendering dynamic web content in Qt5 C++ and QML applications
dev-qt / qtwidgets : Set of components for creating classic desktop-style UIs for the Qt5 framework
dev-qt / qtxml : Implementation of SAX and DOM for the Qt5 framework
dev-util / cmake : Cross platform Make
dev-util / nvidia-cuda-toolkit : NVIDIA CUDA Toolkit (compiler and friends)
media-libs / glew : The OpenGL Extension Wrangler Library
sci-chemistry / openbabel : Interconverts file formats used in molecular modeling
sci-libs / fftw : Fast C library for the Discrete Fourier Transform
sci-libs / libsvm : Library for Support Vector Machines
sci-mathematics / lpsolve : Mixed Integer Linear Programming (MILP) solver
sys-devel / bison : A general-purpose (yacc-compatible) parser generator
sys-devel / make : Standard tool to compile source trees
virtual / mpi : Virtual for Message Passing Interface (MPI) v2.0 implementation
virtual / opengl : Virtual for OpenGL implementation
virtual / yacc : virtual for yacc (yet another compiler compiler)
Runtime Dependencies
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 / boost : Boost Libraries for C++
dev-qt / qtcore : Cross-platform application development framework
dev-qt / qtgui : The GUI module and platform plugins for the Qt5 framework
dev-qt / qtnetwork : Network abstraction library for the Qt5 framework
dev-qt / qtopengl : OpenGL support library for the Qt5 framework (deprecated)
dev-qt / qtprintsupport : Printing support library for the Qt5 framework
dev-qt / qttest : Unit testing library for the Qt5 framework
dev-qt / qtwebchannel : Qt5 module for integrating C++ and QML applications with HTML/JavaScript clients
dev-qt / qtwebengine : Library for rendering dynamic web content in Qt5 C++ and QML applications
dev-qt / qtwidgets : Set of components for creating classic desktop-style UIs for the Qt5 framework
dev-qt / qtxml : Implementation of SAX and DOM for the Qt5 framework
dev-util / nvidia-cuda-toolkit : NVIDIA CUDA Toolkit (compiler and friends)
media-libs / glew : The OpenGL Extension Wrangler Library
sci-chemistry / openbabel : Interconverts file formats used in molecular modeling
sci-libs / fftw : Fast C library for the Discrete Fourier Transform
sci-libs / libsvm : Library for Support Vector Machines
sci-mathematics / lpsolve : Mixed Integer Linear Programming (MILP) solver
virtual / mpi : Virtual for Message Passing Interface (MPI) v2.0 implementation
Bugs
- 593644
- sci-chemistry/ball-1.4.2-r1 : /.../MPISupport.C:1142:83: error: declaration of ‘void BALL::MPISupport::combineDatapoints(const std::vector<valuetype>&) [with valuetype = BALL::TVector3<float>]’ has a different exception specifier
- 656096
- sci-chemistry/ball-1.5.0_pre20180419 : CMake Error at cmake/BALLConfigXDR.cmake:38 (MESSAGE):
Change logs
- Andreas Sturmlechner · gentoo
sci-chemistry/ball: Drop old Qt4-based
Closes: https://bugs.gentoo.org/639000 Package-Manager: Portage-2.3.31, Repoman-2.3.9 - Andreas Sturmlechner · gentoo
sci-chemistry/ball: Add 1.5.0_pre20180419 Qt5-based snapshot
Bug: https://bugs.gentoo.org/639000 Package-Manager: Portage-2.3.31, Repoman-2.3.9 - Michael Palimaka · gentoo
sci-chemistry/ball: remove bogus dev-qt/qtwebkit:4 dependency
Also pin media-libs/glew to the source SLOT. Package-Manager: Portage-2.3.5, Repoman-2.3.2 - Robin H. Johnson · gentoo
Drop $Id$ per council decision in bug #611234.
Signed-off-by: Robin H. Johnson <robbat2@gentoo.org> - David Seifert · gentoo
sci-chemistry/ball: Fix Swig bug, qualify std::isnan
Gentoo-Bug: 583932 * EAPI=6 * Also fix GCC warning pollution due to misplaced attributes * Add subslot operator for dev-libs/boost * Remove USE=webkit, as webkit is no longer supported Package-Manager: portage-2.3.0_rc1 - 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