SSP (Disulfide Bond Analysis Tool)

Wong and Hogg (2010) Analysis of disulfide bonds in protein structures. J Thromb Haemost 8:2345 (https://doi.org/10.1111/j.1538-7836.2010.03894.x)

This repository contains the SSP (disulfide bond analysis tool) python web application, the webpage and a difficult to find precompile apache module for mod_wsgi.

Requirements:

• Python 2.7
• XAMPP 32 bit

Setting up SSP tool

1. Create SSP folder (for example to C:\htdocs\SSP).
2. Create directories:

• ../Analysis
• ../Errors
• ../upload
• ../../pdb_files
• ../../pdb_files/dsspout

Other directory locations can be used but more paths would have to be modified in the scripts.
Paths in scripts and files that have to be modified include:

• absolute_path_of_dssp_files
• absolute_path_of_pdb_files
• create_dssp.py - line 30, 58
• analysis.py - line 31
• index.wsgi - line 5, 108, 146, 407, 422, 536
• run.py - line 18, 33, 38, 59, 106, 107, 234

Also change new PDB download URL in download_from_rscb2.py: https://files.wwpdb.org/pub/pdb/data/structures/all/pdb/

3. Install Python2.7 (32 bit)
4. pip2 install pyExcelerator
5. Install wget for windows (http://gnuwin32.sourceforge.net/packages/wget.htm). Make sure that it is accessible from the command prompt.
6. Install 7zip (https://www.7-zip.org/download.html). Make sure 7z.exe is accessible from the command prompt
7. run UpdatePDB2.bat from a command prompt (this will take a while)
8. run run_all.bat from a command prompt (this will take a hour or more on the first run). It is possible that it doesn't run to completion because it found some errors in a PDB file. This could be due to a corrupt download in the last step or a real invalid PDB file. For the latter, the file has to be removed from the PDB directory. This can be added to the top of the run_all.bat file, a copy of examples are already there. If you get a message that the task has been completed successfully then it means the SSP tool is setup correctly.

Setting SSP up to run from apache

9. Install xampp (32 bit). The lastest version with 32 bit should be 7.3.2 (https://sourceforge.net/projects/xampp/files/XAMPP%20Windows/7.3.2/)
10. Install VC9 for python (https://download.microsoft.com/download/7/9/6/796EF2E4-801B-4FC4-AB28-B59FBF6D907B/VCForPython27.msi)
11. pip2 install mod_wsgi (open command prompt as Administrator and type "pip install mod-wsgi")
12. Copy mod_wsgi-py27-VC9.so from Apache24-win32-VC9 in mod_wsgi-windows-4.4.12.tar.gz (included in the SSP zip package) to apache modules folder (i.e. X:\xampp\modules).
13. setup apache httpd.conf to load mod_wsgi and access appropriate directories (see example included in SSP zip package).
14. Start up apache. Should be able to access the SSP tool from a browser using https://localhost/SSP

Setting up SSP webpage

15. Unpack disulfideanalysis (for example to C:\htdocs\disulfideanalyis).
16. Change URL path to point to SSP web tool in search.html line 56

Setting up Windows task scheduler

17. Add tasks to run once per month: SSP\updatePDB2.bat, then ~1 hour later SSP\run_all.bat, then ~2 hours later disulfide_analysis\task_schedular