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

source code

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)