Package csb :: Package bio :: Package fragments :: Module hhsites :: Class HMMFragmentWrapper
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Class HMMFragmentWrapper

source code

       object --+            
                |            
   hmm.ProfileHMM --+        
                    |        
hmm.ProfileHMMSegment --+    
                        |    
              HMMFragment --+
                            |
                           HMMFragmentWrapper

Describes a HMM segment which can be slid over a subject profile. Wraps an existing ProfileHMMSegment to decorate it with a slide_over method.

Instance Methods
 
__init__(self, hmm_segment)
x.__init__(...) initializes x; see help(type(x)) for signature
source code
list
slide_over(self, other)
Find instances of self by sliding it over other and computing emission vector similarity and RSMD.
source code

Inherited from hmm.ProfileHMM: add_emission_pseudocounts, add_transition_pseudocounts, chain, convert_scores, emission_profile, emission_similarity, segment, serialize, structure, subregion, to_hmm

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

Static Methods

Inherited from hmm.ProfileHMM: deserialize

Properties

Inherited from hmm.ProfileHMMSegment: source_end, source_start

Inherited from hmm.ProfileHMM: alignment, all_layers, consensus, dssp, dssp_solvent, effective_matches, emission_pseudocounts, end, evd, family, has_structure, id, layers, length, logbase, name, pseudocounts, psipred, residues, scale, score_units, start, start_insertion, transition_pseudocounts, version

Inherited from object: __class__

Method Details

__init__(self, hmm_segment)
(Constructor)

source code 

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

Parameters:
Raises:
  • ValueError - when start or end positions are out of range
Overrides: object.__init__
(inherited documentation)

slide_over(self, other)

source code 

Find instances of self by sliding it over other and computing emission vector similarity and RSMD.

Parameters:
  • other - the subject HMM
Returns: list
a list of isites.ProfileMatch-es
Overrides: HMMFragment.slide_over
(inherited documentation)