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OpenStructure
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Public Member Functions | |
| def | __init__ |
| def | weighted_scores |
| def | weight_sum |
| def | weight_extra_mapped |
| def | weight_extra_all |
| def | QS_best |
| def | QS_global |
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.
| def __init__ | ( | self, | |
| weighted_scores, | |||
| weight_sum, | |||
| weight_extra_mapped, | |||
| weight_extra_all | |||
| ) |
Definition at line 216 of file qsscore.py.
| 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.
| 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.
| 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.
| 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.
| def weight_sum | ( | self | ) |
weight_sum attribute as described in formula section above :type: :class:`float`
Definition at line 231 of file qsscore.py.
| def weighted_scores | ( | self | ) |
weighted_scores attribute as described in formula section above :type: :class:`float`
Definition at line 223 of file qsscore.py.
1.8.5