CATH Access Functions

This module defines functions for query CATH database.

class CATHDB(source='http://download.cathdb.info')

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(identifier='root')

Find an xml.etree.Element object given identifier.

save(filename='cath.xml')

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

search(identifier)

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(source=None)

Update data and files from CATH.

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

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

parsePDBs(**kwargs)

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