Utilities

Below is a selection of utilities that have been implemented for analyzing and using the Protein Coil Library. As additional utilities are implemented, they will make their way here. If you have written code for the coil library that may be useful to others, please let us know, and we will post it here.

All programs listed below are provided "as is" and without warranty.

Torsion Angle Search

This code allows one to search exhaustively for patterns of structure in the coil library. Given a list of torsion angle files, and some hard-coded (but documented) φ-ψ definitions, the program will count how many times each structural conformation occurs in the library.

PDB Fragment Extraction

Given a torsion file and a local copy of the PDB, this utility will reconstruct the fragment PDB structure files included in the coil library but not included in custom search results. Although wget or some other utility can be used to download the corresponding files individually, this utility saves bandwidth if you already maintain your own local PDB.

PDB Fragment Download

If you don't maintain a local copy of the PDB, this program will allow you to download the contents of a PDB file list from the Coil Library's anonymous FTP server. Simply put yourself in the top directory of your torsion file search results, run this program, and you will have all the corresponding structure files to go with your torsion files.

Torsion File Python Library

This is a simple Python object that allows easy access to the torsion file data stored in the coil library. It can be imported as a module and used in searching and tabulating data.