Installation

Windows installer

github repo

Linux

You'll need python 2.7, numpy, scipy, biopython, and vtk*, then clone the spade repo and run "python SPADE.py", or run "python MolecularViewer.py" for just the light weight viewer. The MolecularSystem library imports with no dependencies, and robustly loads at least old PDB structure formats. The MolecularViewer can be imported and launches from the python command prompt.

*wget http://dl.fedoraproject.org/pub/epel/7/x86_64/e/epel-release-7-10.noarch.rpm; rpm -Uvh epel-release-7-10.noarch.rpm; yum install vtk-python

Windows Users

Windows users can use the executable installer and run SPADE from the Desktop or Quick-Launch icons. The molecular viewer and database manager are immediately available for use. Use the menu command File>>Download a PDB to query the RCSB database by accession name. Try 1otc for instance, the dimeric Telomere End-Binding Protein. Once downloaded, the given project title appears in the 'systems' listings. Select it, and launch its molecular viewer by pressing the button on its right hand side.

Windows Developers

There are several dependencies required for running SPADE without the executable installer. First, download the zip file for the most recent SPADE version from the SourceForge Files page. Then go to http://www.lfd.uci.edu/~gohlke/pythonlibs/ to obtain and install the following packages, as appropriate for your operating system and the Python 2.7 that SPADE currently runs on: NumPy, SciPy, MatPlotLib, BioPython, Pillow, VTK (not VTK-Qt) On older systems I used to have to then copy vtkRenderingPythonTkWidgets.dll from C:\Python27\Lib\site-packages\vtk to my System directory (e.g. C:\Windows\System32), but my current installation did not require that. That should be it. If there are any issues please let us know in the forums. If you need them, some of the vtk binaries are here.