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

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object --+
         |
        ProfileMatch

Describes a profile-query match

Instance Methods
 
__init__(self, id, start, score, rmsd=None, rmsd_dih=None, tm_score=None, tm_scoreout=None)
x.__init__(...) initializes x; see help(type(x)) for signature
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__lt__(self, other) source code
 
__repr__(self)
repr(x)
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float
confidence(self, b0, b1, b2, b3=1.0)
Convert the raw profile score to probability.
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Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __setattr__, __sizeof__, __str__, __subclasshook__

Properties

Inherited from object: __class__

Method Details

__init__(self, id, start, score, rmsd=None, rmsd_dih=None, tm_score=None, tm_scoreout=None)
(Constructor)

source code 

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

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
  • rmsd_dih (float) - circular (torsion) RMSD between the query and the representative structure of the fragment withing the matching region
  • tm_score (float) - TM-Score between the query and the representative structure of the fragment withing the matching region
  • tm_scoreout (float) - TM-Score, but calculated with local structural alignment
Overrides: object.__init__
(inherited documentation)

__repr__(self)
(Representation operator)

source code 

repr(x)

Overrides: object.__repr__
(inherited documentation)

confidence(self, b0, b1, b2, b3=1.0)

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Convert the raw profile score to probability.

Parameters:
  • b0 (float) - cluster.linearfit[0]
  • b1 (float) - cluster.linearfit[1]
  • b2 (float) - cluster.linearfit[2]
  • b3 (float) - cluster.linearfit[3]
Returns: float
probability for the hit being a true positive