Package csb :: Package bio :: Package fragments :: Module isites :: Class ProfileMatches

Class ProfileMatches

object --+
         |
        ProfileMatches

A collection of profile-database hits.

Instance Methods

__init__(self, size=20, cutoff=0.5, rmsd_cutoff=0.5)
x.__init__(...) initializes x; see help(type(x)) for signature

source code

add(self, id, start, score, rmsd=None)
Add a new match to the collection of hits if its score satisfies the cutoff.

source code

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

Properties
	best_match
	hits
	length
Inherited from `object`: `__class__`

Method Details

init(self, size=20, cutoff=0.5, rmsd_cutoff=0.5)
(Constructor)

source code

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

Parameters:

size (int) - target maximum size of the hitlist
cutoff (float) - inclusion score cutoff
rmsd_cutoff (float) - inclusion RMSD cutoff

Raises:

ValueError - on invalid hitlist size

Overrides: object.__init__

(inherited documentation)

add(self, id, start, score, rmsd=None)

source code

Add a new match to the collection of hits if its score satisfies the cutoff.

Parameters:

id (str) - id of the match
start (int) - start position of the match
score (float) - score
rmsd (float) - RMSD between the query and the representative structure of the fragment withing the matching region

Raises:

value_error - on invalid start position

Property Details

best_match

Get Method:: unreachable.best_match(self)

hits

Get Method:: unreachable.hits(self)

length

Get Method:: unreachable.length(self)

Class ProfileMatches

__init__(self, size=20, cutoff=0.5, rmsd_cutoff=0.5) (Constructor)

add(self, id, start, score, rmsd=None)

best_match

hits

length

init(self, size=20, cutoff=0.5, rmsd_cutoff=0.5)
(Constructor)