The subpages below notes how each of the loaders runs and the locations of the files needed to run them.

The following files are used:

LoadCath.java	Loader to parse through the CATH Domall domain definition file and insert the assigned domains into the database
LoadDDomain.java	Runs DDomain algorithm for all pdbIds currently in the databank and inserts domains assigned into database
LoadDhCL.java	Runs DHcL algorithm for all pdbIds currently in the databank and inserts domains assigned into database
LoadDodis.java	Runs dodis algorithm for all pdbIds currently in the databank and inserts domains assigned into database
GetChain.java	Used by LoadDodis - creates a pdb file containing a single chain from a pdbId
Loaddp.java	Runs domain parser algorithm for all pdbIds currently in the databank and inserts domains assigned into database
LoadNCBI.java	For each pdbId in the databank, gets the domains assigned by the NCBI-Vast program as shown on their webpage
ReadNCBI.java	Recovers the web page for the NCBI domain assignment, stores locally, and then parses to recover the domain assignments
Loadpdp.java	Runs pdp algorithm for all pdbIds currently in the databank and inserts domains assigned into database
LoadPUU.java	Runs pdp algorithm for all pdbIds currently in the databank and inserts domains assigned into database
LoadSCOP.java	Loader to parse through the SCOP domain definition file and insert the assigned domains into the database

The following utility classes are also used:

GetPDBFile.java	Returns the pdb FIle that the algorithm needs from the databank, and deletes all temporary directories used while retrieving it
DomainDB.java	Creates a link to the domain assignment database held on cumin, including methods to query database, insert and delete records, and close the connection
ExecExternalAlg.java	Utility program which runs the external algorithm (i.e. any of the domain assignment algorithms).  This can set a timeout to stop the external algorithm should a problem be encountered, thus meaning the whole loader does not hang