Searching a cavity database

The script utilities/cavity_database_search/cavity_database_search.py provides tools to search for and compare cavities stored in an SQLite database. If you wish to make a database, the utility script utilities/cavity_database_search/cavity_database_search.py may be used. The search script can be used to find cavities that fulfil certain criteria, such as those containing particular pseudocenter types or certain ligands. Three cavity comparison methods are provided: fast cavity graph comparison (the default method), cavity graph comparison and cavity histograms comparison. More information on these methods can be found in the descriptive documentation for the cavity module. Cavities for comparison against those in the database can be provided using PDB files (for which LIGSITE cavity detection will be performed), cavity XML files or as identifiers from the database. If no query cavities are provided, a simple search for cavities will be performed. The report on the search can be configured using a variety of options and can be output to the screen or to a file in either tab-separated or HTML format. Invoking the script with the argument ‘-h’ provides full information on usage options, including example searches.