{"id":1056,"date":"2019-04-25T21:51:27","date_gmt":"2019-04-25T21:51:27","guid":{"rendered":"https:\/\/ccsb.scripps.edu\/adfr\/?page_id=1056"},"modified":"2019-04-25T21:51:27","modified_gmt":"2019-04-25T21:51:27","slug":"implementation","status":"publish","type":"page","link":"https:\/\/ccsb.scripps.edu\/adfr\/implementation\/","title":{"rendered":"implementation"},"content":{"rendered":"

ADFR<\/em> suite implementation<\/h3>\n

the ADFR<\/em> 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.<\/p>\n

To avoid Python packages mismatches we opted to shift ADFR<\/em> 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<\/em> script located in $WHERE_YOU_INSTALLED\/ADFRsuite-1.0\/bin\/pythonsh.<\/em> This folder also contains the other executable shipped with the ADFR<\/em> suite.<\/p>\n

Included Python package developed, extended, or wrapped by us:<\/h4>\n

these packages are located in\u00a0$WHERE_YOU_INSTALLED\/ADFRsuite-1.0\/CCSBpckgs\/<\/p>\n\n\n\n\n\t\n\n\t\n\t\n\t\n\t\n\t\n\t\n\t\n\t\n\t\n\t\n\t\n\t\n\t\n\t\n\t\n\t\n\t\n\t\n\t\n\t\n\t\n\t
Package name<\/th>Language(s)<\/th>Functionality<\/th>Dependencies<\/th>\n<\/tr>\n<\/thead>\n
ADFR<\/td>Python<\/td>Ligand docking<\/td><\/td>\n<\/tr>\n
ADFRcc<\/td>C++<\/td>AutoDock4 scoring function, Flexibility Tree, Solis Wets local search<\/td><\/td>\n<\/tr>\n
AppFramework<\/td>Python<\/td>Base class for writing applications<\/td><\/td>\n<\/tr>\n
AutoDockTools<\/td>Python<\/td>Legacy package used by prepare_ligand and prepare_receptor<\/td><\/td>\n<\/tr>\n
AutoSite<\/td>Python<\/td>Binding pocket identification<\/td><\/td>\n<\/tr>\n
bhtree<\/td>C<\/td>Spatial hashing<\/td><\/td>\n<\/tr>\n
DejaVu2<\/td>Python<\/td>OpenGL 3D Viewer with Qt Camera widget<\/td><\/td>\n<\/tr>\n
geomutils<\/td>Python \/ C++<\/td>Geometry utility functions <\/td><\/td>\n<\/tr>\n
gle<\/td>C++<\/td>OpenGL extrusion library wrapper for Python<\/td><\/td>\n<\/tr>\n
mglkey<\/td>Python<\/td>Software keys validation<\/td><\/td>\n<\/tr>\n
mglutil<\/td>Python<\/td>Utilities<\/td><\/td>\n<\/tr>\n
MolKit<\/td>Python<\/td>Legacy package used by prepare_ligand and prepare_receptor<\/td><\/td>\n<\/tr>\n
MolKit2<\/td>Python<\/td>Read\/Write\/Query molecules<\/td>prody, openbabel<\/td>\n<\/tr>\n
mslib<\/td>C<\/td>Python wrapper of the MSMS library for computing molecular surfaces<\/td><\/td>\n<\/tr>\n
opengltk<\/td>C<\/td>Python wrapper of the OpenGL library<\/td><\/td>\n<\/tr>\n
PmvApp<\/td>Python<\/td>Generic molecular visualization application<\/td><\/td>\n<\/tr>\n
prody<\/td>Python<\/td>CCSB version of the ProDy package<\/td><\/td>\n<\/tr>\n
PyBabel<\/td>Python<\/td>Legacy package used by prepare_ligand and prepare_receptor<\/td><\/td>\n<\/tr>\n
pyglf<\/td>C<\/td>Python wrapper for OpenGL fonts<\/td><\/td>\n<\/tr>\n
Support<\/td>Python<\/td><\/td><\/td>\n<\/tr>\n
UTpackages<\/td>C++<\/td>Fast iso-contouring and volume rendering<\/td><\/td>\n<\/tr>\n
Volume<\/td>Python<\/td>Support for 3D rectilinear data grids<\/td><\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n\n

Included Python package developed, extended, or wrapped by others:<\/h4>\n

these packages are located in\u00a0$WHERE_YOU_INSTALLED\/ADFRsuite-1.0\/lib\/python2.7\/site-packages\/<\/p>\n\n\n\n\n\t\n\n\t\n\t\n\t\n\t\n\t\n\t\n\t\n\t\n\t\n\t
Name<\/th>Functionality<\/th>version<\/th>\n<\/tr>\n<\/thead>\n
Bio<\/td>BioPython<\/td>1.59<\/td>\n<\/tr>\n
dateutil<\/td>extension to datetime<\/td>1.5-mpl<\/td>\n<\/tr>\n
IPython<\/td>Improved Python shell<\/td>2.2.0<\/td>\n<\/tr>\n
matplotlib<\/td>2D ploting<\/td>1.2.0<\/td>\n<\/tr>\n
mmtf<\/td>compressed PDB format<\/td><\/td>\n<\/tr>\n
nlopt<\/td>linear optimization<\/td>2.5.0<\/td>\n<\/tr>\n
numpy<\/td>Numeric arrays extension<\/td>1.9.2<\/td>\n<\/tr>\n
openbabel<\/td>small molecules<\/td>2.4.1 <\/td>\n<\/tr>\n
PIL<\/td>
\nPython Imaging Library<\/td>		4.3.0<\/td>\n<\/tr>\n
PySide<\/td>Python wrapper for Qt 4.8<\/td>1.2.2<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n\n<\/div>
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