From f5efafc7748ac323f3ca27647a001948c28e4b8e Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Tue, 31 Oct 2023 13:49:54 +0100
Subject: [PATCH] Scoring: add number of native and model contacts as
attributes to Scorer
---
actions/ost-compare-structures | 2 ++
modules/mol/alg/pymod/scoring.py | 32 +++++++++++++++++++++++++++-----
2 files changed, 29 insertions(+), 5 deletions(-)
diff --git a/actions/ost-compare-structures b/actions/ost-compare-structures
index f7021ffd9..9dacd7786 100644
--- a/actions/ost-compare-structures
+++ b/actions/ost-compare-structures
@@ -700,6 +700,8 @@ def _Process(model, reference, args):
out["fnat"] = scorer.fnat
out["irmsd"] = scorer.irmsd
out["lrmsd"] = scorer.lrmsd
+ out["nnat"] = scorer.nnat
+ out["nmdl"] = scorer.nmdl
out["dockq_ave"] = scorer.dockq_ave
out["dockq_wave"] = scorer.dockq_wave
out["dockq_ave_full"] = scorer.dockq_ave_full
diff --git a/modules/mol/alg/pymod/scoring.py b/modules/mol/alg/pymod/scoring.py
index 54dba0937..45ccb439e 100644
--- a/modules/mol/alg/pymod/scoring.py
+++ b/modules/mol/alg/pymod/scoring.py
@@ -289,6 +289,8 @@ class Scorer:
self._fnonnat = None
self._irmsd = None
self._lrmsd = None
+ self._nnat = None
+ self._nmdl = None
self._dockq_scores = None
self._dockq_ave = None
self._dockq_wave = None
@@ -953,6 +955,26 @@ class Scorer:
self._compute_dockq_scores()
return self._fnat
+ @property
+ def nnat(self):
+ """ N native contacts for interfaces in :attr:`~dockq_interfaces`
+
+ :class:`list` of :class:`int`
+ """
+ if self._nnat is None:
+ self._compute_dockq_scores()
+ return self._nnat
+
+ @property
+ def nmdl(self):
+ """ N model contacts for interfaces in :attr:`~dockq_interfaces`
+
+ :class:`list` of :class:`int`
+ """
+ if self._nmdl is None:
+ self._compute_dockq_scores()
+ return self._nmdl
+
@property
def fnonnat(self):
""" fnonnat scores for interfaces in :attr:`~dockq_interfaces`
@@ -1506,9 +1528,8 @@ class Scorer:
self._fnonnat = list()
self._irmsd = list()
self._lrmsd = list()
-
- # keep track of native counts for weights in dockq_wave/dockq_wave_full
- native_counts = list()
+ self._nnat = list()
+ self._nmdl = list()
dockq_alns = dict()
for aln in self.aln:
@@ -1531,7 +1552,8 @@ class Scorer:
self._irmsd.append(res["irmsd"])
self._lrmsd.append(res["lrmsd"])
self._dockq_scores.append(res["DockQ"])
- native_counts.append(res["nnat"])
+ self._nnat.append(res["nnat"])
+ self._nmdl.append(res["nmdl"])
# keep track of native counts in target interfaces which are
# not covered in model in order to compute
@@ -1554,7 +1576,7 @@ class Scorer:
# - average weighted by native_contacts
# - the two above including nonmapped_contact_interfaces => set DockQ to 0.0
scores = np.array([self._dockq_scores])
- weights = np.array([native_counts])
+ weights = np.array([self._nnat])
if len(scores) > 0:
self._dockq_ave = np.mean(scores)
else:
--
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