Bio.SCOP.Scop

Class Scop

object --+ | Scop

The entire SCOP hierarchy.

root -- The root node of the hierarchy

Instance Methods

__init__(self, cla_handle=None, des_handle=None, hie_handle=None, dir_path=None, db_handle=None, version=None)
Build the SCOP hierarchy from the SCOP parsable files, or a sql backend.

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getRoot(self)

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getDomainBySid(self, sid)
Return a domain from its sid

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getNodeBySunid(self, sunid)
Return a node from its sunid

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getDomains(self)
Returns an ordered tuple of all SCOP Domains

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write_hie(self, handle)
Build an HIE SCOP parsable file from this object

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write_des(self, handle)
Build a DES SCOP parsable file from this object

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write_cla(self, handle)
Build a CLA SCOP parsable file from this object

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getDomainFromSQL(self, sunid=None, sid=None)
Load a node from the SQL backend using sunid or sid

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getAscendentFromSQL(self, node, type)
Get ascendents using SQL backend

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getDescendentsFromSQL(self, node, type)
Get descendents of a node using the database backend.

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write_hie_sql(self, handle)
Write HIE data to SQL database

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write_cla_sql(self, handle)
Write CLA data to SQL database

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write_des_sql(self, handle)
Write DES data to SQL database

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Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __str__, __subclasshook__

Properties

[hide private]

Inherited from object: __class__

init(self, cla_handle=None, des_handle=None, hie_handle=None, dir_path=None, db_handle=None, version=None)
(Constructor)

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Build the SCOP hierarchy from the SCOP parsable files, or a sql backend.

If no file handles are given, then a Scop object with a single empty root node is returned.

If a directory and version are given (with dir_path=.., version=...) or file handles for each file, the whole scop tree will be built in memory.

If a MySQLdb database handle is given, the tree will be built as needed, minimising construction times. To build the SQL database to the methods write_xxx_sql to create the tables.

Overrides: object.__init__

getDescendentsFromSQL(self, node, type)

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Get descendents of a node using the database backend. This avoids repeated iteration of SQL calls and is therefore much quicker than repeatedly calling node.getChildren().

Class Scop

__init__(self, cla_handle=None, des_handle=None, hie_handle=None, dir_path=None, db_handle=None, version=None) (Constructor)

getDescendentsFromSQL(self, node, type)

init(self, cla_handle=None, des_handle=None, hie_handle=None, dir_path=None, db_handle=None, version=None)
(Constructor)