ADFR suite implementation
the ADFR software suite provides a number of software tools for automated docking and peripheral tasks. These tools are implemented using the Python, C++ and C programming languages and a re-usable component philosophy.
To avoid Python packages mismatches we opted to shift ADFR suite with a self-contain Python interpreter that is isolated from the default Python interpreter installed on your computer (except for Windows installations). The ADFR suite Python interpreter can be invoked using the pythonsh script located in $WHERE_YOU_INSTALLED/ADFRsuite-1.0/bin/pythonsh. This folder also contains the other executable shipped with the ADFR suite.
Included Python package developed, extended, or wrapped by us:
these packages are located in $WHERE_YOU_INSTALLED/ADFRsuite-1.0/CCSBpckgs/
| Package name | Language(s) | Functionality | Dependencies |
|---|---|---|---|
| ADFR | Python | Ligand docking | |
| ADFRcc | C++ | AutoDock4 scoring function, Flexibility Tree, Solis Wets local search | |
| AppFramework | Python | Base class for writing applications | |
| AutoDockTools | Python | Legacy package used by prepare_ligand and prepare_receptor | |
| AutoSite | Python | Binding pocket identification | |
| bhtree | C | Spatial hashing | |
| DejaVu2 | Python | OpenGL 3D Viewer with Qt Camera widget | |
| geomutils | Python / C++ | Geometry utility functions | |
| gle | C++ | OpenGL extrusion library wrapper for Python | |
| mglkey | Python | Software keys validation | |
| mglutil | Python | Utilities | |
| MolKit | Python | Legacy package used by prepare_ligand and prepare_receptor | |
| MolKit2 | Python | Read/Write/Query molecules | prody, openbabel |
| mslib | C | Python wrapper of the MSMS library for computing molecular surfaces | |
| opengltk | C | Python wrapper of the OpenGL library | |
| PmvApp | Python | Generic molecular visualization application | |
| prody | Python | CCSB version of the ProDy package | |
| PyBabel | Python | Legacy package used by prepare_ligand and prepare_receptor | |
| pyglf | C | Python wrapper for OpenGL fonts | |
| Support | Python | ||
| UTpackages | C++ | Fast iso-contouring and volume rendering | |
| Volume | Python | Support for 3D rectilinear data grids |
Included Python package developed, extended, or wrapped by others:
these packages are located in $WHERE_YOU_INSTALLED/ADFRsuite-1.0/lib/python2.7/site-packages/
| Name | Functionality | version |
|---|---|---|
| Bio | BioPython | 1.59 |
| dateutil | extension to datetime | 1.5-mpl |
| IPython | Improved Python shell | 2.2.0 |
| matplotlib | 2D ploting | 1.2.0 |
| mmtf | compressed PDB format | |
| nlopt | linear optimization | 2.5.0 |
| numpy | Numeric arrays extension | 1.9.2 |
| openbabel | small molecules | 2.4.1 |
| PIL | Python Imaging Library | 4.3.0 |
| PySide | Python wrapper for Qt 4.8 | 1.2.2 |