CATH Access Functions

This module defines functions for query CATH database.

class CATHDB(source='')[source]

This class is for handing the data in the CATH database. It facilitates tree navigation and ID-based searching.

The class is initialised using data from source, which is downloaded from the CATH website by default, but can also be parsed from an XML file.


Find an xml.etree.Element object given identifier.


Write local CATH database to an XML file. filename can either be a file name or a handle.


Search the identifier against the local CATH database and return a list of ElementTree instances. identifier can be a 4-digit PDB ID plus an 1-digit chain ID (optional), 7-digit domain ID, or CATH ID.


Update data and files from CATH.

class CATHElement(tag, attrib={}, parent=None, **extra)[source]

This class handles individual elements from the cath tree including tree navigation and the getting of associated CATH domains, PDB IDs and selection strings.


Load PDB into memory as AtomGroup instances using parsePDB() and perform selection based on residue ranges given by CATH.