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

Class HMMFragment

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

Known Subclasses:

HMMFragmentWrapper

Describes a HMM segment which can be slid over a subject profile. See the documentation of the base class for the signature of the constructor.

Instance Methods

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.ProfileHMMSegment: __init__

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

slide_over(self, other)

source code

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

Parameters:

other (ProfileHMM) - the subject HMM

Returns: list

a list of isites.ProfileMatch-es