Public Member Functions
def	__init__ (self, weighted_scores, weight_sum, weight_extra_mapped, weight_extra_all)

def	weighted_scores (self)

def	weight_sum (self)

def	weight_extra_mapped (self)

def	weight_extra_all (self)

def	QS_best (self)

def	QS_global (self)

Detailed Description

Holds data relevant for QS-score computation. Formulas for QS scores:

::

  - QS_best = weighted_scores / (weight_sum + weight_extra_mapped)
  - QS_global = weighted_scores / (weight_sum + weight_extra_all)
  -> weighted_scores = sum(w(min(d1,d2)) * (1 - abs(d1-d2)/12)) for shared
  -> weight_sum = sum(w(min(d1,d2))) for shared
  -> weight_extra_mapped = sum(w(d)) for all mapped but non-shared
  -> weight_extra_all = sum(w(d)) for all non-shared
  -> w(d) = 1 if d <= 5, exp(-2 * ((d-5.0)/4.28)^2) else

In the formulas above:

* "d": CA/CB-CA/CB distance of an "inter-chain contact" ("d1", "d2" for
  "shared" contacts).
* "mapped": we could map chains of two structures and align residues in
  :attr:`alignments`.
* "shared": pairs of residues which are "mapped" and have
  "inter-chain contact" in both structures.
* "inter-chain contact": CB-CB pairs (CA for GLY) with distance <= 12 A
  (fallback to CA-CA if :attr:`calpha_only` is True).
* "w(d)": weighting function (prob. of 2 res. to interact given CB distance)
  from `Xu et al. 2009 <https://dx.doi.org/10.1016%2Fj.jmb.2008.06.002>`_.

Definition at line 188 of file qsscore.py.

Constructor & Destructor Documentation

◆ init()

def __init__	(	self,
		weighted_scores,
		weight_sum,
		weight_extra_mapped,
		weight_extra_all
	)

Definition at line 215 of file qsscore.py.

Member Function Documentation

◆ QS_best()

def QS_best ( self )

 QS_best - the actual score as described in formula section above

:type: :class:`float`

Definition at line 255 of file qsscore.py.

◆ QS_global()

def QS_global ( self )

 QS_global - the actual score as described in formula section above

:type: :class:`float`

Definition at line 268 of file qsscore.py.

◆ weight_extra_all()

def weight_extra_all ( self )

 weight_extra_all attribute as described in formula section above

:type: :class:`float`

Definition at line 247 of file qsscore.py.

◆ weight_extra_mapped()

def weight_extra_mapped ( self )

 weight_extra_mapped attribute as described in formula section above

:type: :class:`float`

Definition at line 239 of file qsscore.py.

◆ weight_sum()

def weight_sum ( self )

 weight_sum attribute as described in formula section above

:type: :class:`float`

Definition at line 231 of file qsscore.py.

◆ weighted_scores()

def weighted_scores ( self )

 weighted_scores attribute as described in formula section above

:type: :class:`float`

Definition at line 223 of file qsscore.py.

The documentation for this class was generated from the following file:

build-dev-doc/stage/lib64/python3.9/site-packages/ost/mol/alg/qsscore.py

Public Member Functions