From 8984d76f0282c1f5cf5b4c4a60e5eed5d2d6dc69 Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Thu, 20 Jun 2024 09:54:46 +0200
Subject: [PATCH] SCHWED-6298: QS-score for two monomers is defined as 1.0
They have the exact same quaternary structure in the end... This definition
has been generalized to: if there are no contacts observed, QS-score is 1.0
if the scored structures have the same stoichiometry, 0.0 otherwise.
This becomes a bit more abstract for higher order complexes but in principle
they still have the exact same quaternary structure if they match in
stoichiometry but have no single contact.
---
modules/mol/alg/pymod/qsscore.py | 63 ++++++++++++++++++++++++++++----
1 file changed, 55 insertions(+), 8 deletions(-)
diff --git a/modules/mol/alg/pymod/qsscore.py b/modules/mol/alg/pymod/qsscore.py
index 3b32746d6..2c98d9fa7 100644
--- a/modules/mol/alg/pymod/qsscore.py
+++ b/modules/mol/alg/pymod/qsscore.py
@@ -213,11 +213,12 @@ class QSScorerResult:
from `Xu et al. 2009 <https://dx.doi.org/10.1016%2Fj.jmb.2008.06.002>`_.
"""
def __init__(self, weighted_scores, weight_sum, weight_extra_mapped,
- weight_extra_all):
+ weight_extra_all, complete_mapping):
self._weighted_scores = weighted_scores
self._weight_sum = weight_sum
self._weight_extra_mapped = weight_extra_mapped
self._weight_extra_all = weight_extra_all
+ self._complete_mapping = complete_mapping
@property
def weighted_scores(self):
@@ -251,11 +252,30 @@ class QSScorerResult:
"""
return self._weight_extra_all
+ @property
+ def 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`
+ """
+ return self._complete_mapping
+
@property
def QS_best(self):
""" QS_best - the actual score as described in formula section above
- Returns None if there are no contacts in the compared structures
+ 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`
"""
@@ -263,14 +283,23 @@ class QSScorerResult:
denominator = self.weight_sum + self.weight_extra_mapped
if denominator != 0.0:
return nominator/denominator
+ elif self.complete_mapping:
+ return 1.0
else:
- return None
+ return 0.0
@property
def QS_global(self):
""" QS_global - the actual score as described in formula section above
- Returns None if there are no contacts in the compared structures
+ 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`
"""
@@ -278,8 +307,10 @@ class QSScorerResult:
denominator = self.weight_sum + self.weight_extra_all
if denominator != 0.0:
return nominator/denominator
+ elif self.complete_mapping:
+ return 1.0
else:
- return None
+ return 0.0
class QSScorer:
@@ -457,6 +488,11 @@ class QSScorer:
This only works for interfaces that are computed in :func:`Score`, i.e.
interfaces for which the alignments are set up correctly.
+ As all specified chains must be present, the mapping is considered
+ complete which affects
+ :attr:`QSScorerResult.QS_global`/:attr:`QSScorerResult.QS_best` in
+ edge cases of no observed contacts.
+
:param trg_ch1: Name of first interface chain in target
:type trg_ch1: :class:`str`
:param trg_ch2: Name of second interface chain in target
@@ -484,7 +520,10 @@ class QSScorer:
trg_int = (trg_ch1, trg_ch2)
mdl_int = (mdl_ch1, mdl_ch2)
a, b, c, d = self._MappedInterfaceScores(trg_int, mdl_int)
- return QSScorerResult(a, b, c, d)
+
+ # complete_mapping is True by definition, as the requested chain pairs
+ # are both present
+ return QSScorerResult(a, b, c, d, True)
def FromFlatMapping(self, flat_mapping):
""" Same as :func:`Score` but with flat mapping
@@ -530,8 +569,16 @@ class QSScorer:
else:
weight_extra_all += self._InterfacePenalty2(int2)
+ trg_chains = sorted(self.qsent1.chain_names) # should be sorted already
+ mdl_chains = sorted(self.qsent2.chain_names) # should be sorted already
+ mapped_trg_chains = sorted(flat_mapping.keys())
+ mapped_mdl_chains = sorted(flat_mapping.values())
+ trg_complete = trg_chains == mapped_trg_chains
+ mdl_complete = mdl_chains == mapped_mdl_chains
+ complete_mapping = trg_complete and mdl_complete
+
return QSScorerResult(weighted_scores, weight_sum, weight_extra_mapped,
- weight_extra_all)
+ weight_extra_all, complete_mapping)
def _MappedInterfaceScores(self, int1, int2):
key_one = (int1, int2)
@@ -704,4 +751,4 @@ class QSScorer:
return penalty
# specify public interface
-__all__ = ('QSEntity', 'QSScorer')
+__all__ = ('QSEntity', 'QSScorer', 'QSScorerResult')
--
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