Package csb :: Package bio :: Package io :: Module wwpdb :: Class StructureProvider

Class StructureProvider

object --+
         |
        StructureProvider

Known Subclasses:

Base class for all PDB data source providers.

Concrete classes need to implement the find method, which abstracts the retrieval of a PDB structure file by a structure identifier. This is a hook method called internally by get, but subclasses can safely override both find and {get} to in order to achieve completely custom behavior.

Nested Classes
	__metaclass__ Metaclass for defining Abstract Base Classes (ABCs).

Instance Methods

__getitem__(self, id)

source code

str or None

find(self, id)
Attempt to discover a PDB file, given a specific PDB id. source code

csb.bio.Structure

get(self, id, model=None)
Discover, parse and return the PDB structure, corresponding to the specified id. source code

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

Class Variables
	__abstractmethods__ = `frozenset(['find'])`

Properties
Inherited from `object`: `__class__`

Method Details

find(self, id)

source code

Attempt to discover a PDB file, given a specific PDB id.

Parameters:

id (str) - structure identifier (e.g. 1x80)

Returns: str or None

path and file name on success, None otherwise

get(self, id, model=None)

source code

Discover, parse and return the PDB structure, corresponding to the specified id.

Parameters:

id (str) - structure identifier (e.g. 1x80)
model (str) - optional model identifier

Returns: csb.bio.Structure

Raises:

StructureNotFoundError - when id could not be found