A mysql database on cumin.rcsb.org contains all the information generated by the program.  There are two tables:

automeths
Table containing the domains assigned by all the domain assignment algorithms.  Though originally called automeths as this was only going to contain the results from the automatic methods, the definitions by CATH and SCOP are also in the table - maybe the name will be changed at some stage - yet this features in a lot of programs.

Fields:

• domain (joint key) - the domain identifier - made up of pdbId+chain+domainId (a number) - for example 1HTBA1
• fragment (joint key) - the fragment of this domain that this assignment represents
• start - an integer (positive - must be in CIF format) noting the start position of the domain
• end - an integer (positive - must be in CIF format) noting the start position of the domain
• method (joint key) - the method which has generated this assignment

The java program DomainDB.java creates a link to this database, as well as the following methods:

• Insert a Record (used by the programs which parse the output from the domain assignment algorithms)
• Delete a Record
• Query the database
• Get the size of a ResultSet (useful to some classes when calculating statistics or generating consensus)
• Close the connection

dssp
Table containing the secondary structure for each amino acid or each chain, for each pdbId.  This is calculated by the dssp program and parsed into this table by LoadDSSP.java.  This information is used to generate the consensus and to generate statistics

Fields:

• structId
• residue Number CIF
• chainId
• auth Residue Number
• insertion Code
• Amino Acid Code
• Secondary Struct
• Turn Helix 3
• Turn Helix 4
• Turn Helix 5
• geometric Bend
• chirality
• Beta Bridge Label 1
• Beta Bridge Label 2
• Beta Bridge Part Residue Number 1
  
• Beta Bridge Part RN2
• Beta Sheet Label
• Solvent Accessibility
• H1 Offset
• H1 Energy
• H2 Offset
• H2 Energy
• H3 Offset
• H3 Energy
• H4 Offset
• H4 Energy
• tco
• kappa
• alpha
• phi
• psi
• cAlphaX
• cAlphaY
• cAlphaZ
  

The java program DsspDB.java creates a link to this database, as well as the same functionality provided by DomainDB.java.

When the dssp table is loaded by DsspDB.java, the utility class DSSPObj.java is used - this is similar to the pdb version, which creates an object containing variables representing all the dssp fields.  This object is then used when the record is added to the table.