Package csb :: Package bio :: Package io :: Module isites :: Class ISitesParser

Class ISitesParser

object --+
         |
        ISitesParser

Implements an I-Sites fragment library parser v.5.1+ (2008).

Instance Methods

__del__(self)

source code

__enter__(self)

source code

__exit__(self, exc_type, exc_value, traceback)

source code

__init__(self, flatfile, express=False)
x.__init__(...) initializes x; see help(type(x)) for signature

source code

Library

parse(self)
Parse I-sites library common/general properties.

source code

Cluster

parse_entry(self, entry)
Parse a single I-Sites entry.

source code

Library

parseall(self)
Parse the whole library to end.

source code

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

Properties
	clusters Efficient iterator over all Cluster objects.
	library Return the general properties of the library.
Inherited from `object`: `__class__`

Method Details

init(self, flatfile, express=False)
(Constructor)

source code

x.__init__(...) initializes x; see help(type(x)) for signature

Parameters:

flatfile (str) - input *.isl I-Sites library file name
express (bool) - if True, speeds up the parser by ignoring the covariance tensors

Raises:

IOError - when the source file cannot be found

Overrides: object.__init__

(inherited documentation)

parse(self)

source code

Parse I-sites library common/general properties. Clusters are not parsed, but can be fetched on demand while iterating over library.clusters.

Returns: Library: object representation of the library with a bound clusters generator

parse_entry(self, entry)

source code

Parse a single I-Sites entry.

Returns: Cluster: object representation of the entry

parseall(self)

source code

Parse the whole library to end.

Returns: Library: object representation of the library with all clusters pre-parsed

Property Details

clusters

Efficient iterator over all Cluster objects.

Get Method:: unreachable.clusters(self) - Efficient iterator over all Cluster objects.

library

Return the general properties of the library. Library Clusters are iterable, but read efficiently only on demand.

Get Method:: unreachable.library(self) - Return the general properties of the library.

Class ISitesParser

__init__(self, flatfile, express=False) (Constructor)

parse(self)

parse_entry(self, entry)

parseall(self)

clusters

library

init(self, flatfile, express=False)
(Constructor)