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

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Class ProfileMatch

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

source code

__lt__(self, other)

source code

__repr__(self)
repr(x)

source code

float

confidence(self, b0, b1, b2, b3=1.0)
Convert the raw profile score to probability.

source code

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)

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)

repr(x)

Overrides: object.__repr__: (inherited documentation)

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

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