QSScorerResult Class Reference

Public Member Functions
	__init__ (self, weighted_scores, weight_sum, weight_extra_mapped, weight_extra_all, complete_mapping)
	weighted_scores (self)
	weight_sum (self)
	weight_extra_mapped (self)
	weight_extra_all (self)
	complete_mapping (self)
	QS_best (self)
	QS_global (self)

Protected Attributes
	_weighted_scores
	_weight_sum
	_weight_extra_mapped
	_weight_extra_all
	_complete_mapping

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__()

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

Definition at line 215 of file qsscore.py.

Member Function Documentation

complete_mapping()

complete_mapping

(

self

)

 Whether the underlying mapping of the scored assemblies is complete

In other words: If they have the same stoichiometry. This is relevant
for :attr:`~QS_best` and :attr:`~QS_global` in case of no contacts in
any of the scored entities.

:type: :class:`bool`

Definition at line 256 of file qsscore.py.

QS_best()

QS_best

(

self

)

 QS_best - the actual score as described in formula section above

If there are no contacts observed in any of the scored entities this
score is 1.0 if we're comparing structures with
:attr:`~complete_mapping`, 0.0 otherwise. In the example of two
monomers, no contacts can be observed but they exactly match in terms
of quaternary structure. Thus a perfect score. In terms of higher order
structure that becomes a bit more abstract but in principle they still
have the exact same quaternary structure if they match in stoichiometry
but have no single contact.

:type: :class:`float`

Definition at line 268 of file qsscore.py.

QS_global()

QS_global

(

self

)

 QS_global - the actual score as described in formula section above

If there are no contacts observed in any of the scored entities this
score is 1.0 if we're comparing structures with
:attr:`~complete_mapping`, 0.0 otherwise. In the example of two
monomers, no contacts can be observed but they exactly match in terms
of quaternary structure. Thus a perfect score. In terms of higher order
structure that becomes a bit more abstract but in principle they still
have the exact same quaternary structure if they match in stoichiometry
but have no single contact.

:type: :class:`float`

Definition at line 292 of file qsscore.py.

weight_extra_all()

weight_extra_all

(

self

)

 weight_extra_all attribute as described in formula section above

:type: :class:`float`

Definition at line 248 of file qsscore.py.

weight_extra_mapped()

weight_extra_mapped

(

self

)

 weight_extra_mapped attribute as described in formula section above

:type: :class:`float`

Definition at line 240 of file qsscore.py.

weight_sum()

weight_sum

(

self

)

 weight_sum attribute as described in formula section above

:type: :class:`float`

Definition at line 232 of file qsscore.py.

weighted_scores()

weighted_scores

(

self

)

 weighted_scores attribute as described in formula section above

:type: :class:`float`

Definition at line 224 of file qsscore.py.

Field Documentation

_complete_mapping

_complete_mapping

protected

Definition at line 221 of file qsscore.py.

_weight_extra_all

_weight_extra_all

protected

Definition at line 220 of file qsscore.py.

_weight_extra_mapped

_weight_extra_mapped

protected

Definition at line 219 of file qsscore.py.

_weight_sum

_weight_sum

protected

Definition at line 218 of file qsscore.py.

_weighted_scores

_weighted_scores

protected

Definition at line 217 of file qsscore.py.

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

• build-dev/stage/lib/python3.11/site-packages/ost/mol/alg/qsscore.py