From f8e75963d776ff41e52502658329bd13ad70cb6d Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Fri, 13 Sep 2024 17:20:18 +0200
Subject: [PATCH] ics/ips: make per-interface scores for trimmed variant
available
---
actions/ost-compare-structures | 36 +++++++--
modules/mol/alg/pymod/scoring.py | 135 ++++++++++++++++++++++++++++++-
2 files changed, 161 insertions(+), 10 deletions(-)
diff --git a/actions/ost-compare-structures b/actions/ost-compare-structures
index 57ed24b90..b38bb4b7e 100644
--- a/actions/ost-compare-structures
+++ b/actions/ost-compare-structures
@@ -444,10 +444,20 @@ def _ParseArgs():
"counterpart are removed. As a consequence, model contacts for "
"which we have no experimental evidence do not affect the score. "
"The effect of these added model contacts without mapping to "
- "target are decreased precision and thus lower ics. Recall is "
+ "target would be decreased precision and thus lower ics. Recall is "
"not affected. Enabling this flag adds the following keys: "
"\"ics_trimmed\", \"ics_precision_trimmed\", "
- "\"ics_recall_trimmed\" and \"model_contacts_trimmed\""))
+ "\"ics_recall_trimmed\", \"model_contacts_trimmed\". "
+ "The reference contacts and reference interfaces are the same "
+ "as for ics and available as keys: \"reference_contacts\", "
+ "\"contact_reference_interfaces\". "
+ "All these measures are also available on a per-interface basis "
+ "for each interface in the reference structure that are defined "
+ "as chain pairs with at least one contact (available as key "
+ " \"contact_reference_interfaces\"). The respective metrics are "
+ "available as keys \"per_interface_ics_precision_trimmed\", "
+ "\"per_interface_ics_recall_trimmed\" and "
+ "\"per_interface_ics_trimmed\"."))
parser.add_argument(
"--ips",
@@ -906,8 +916,13 @@ def _Process(model, reference, args, model_format, reference_format):
[_RoundOrNone(x) for x in scorer.per_interface_qs_best]
if args.ics or args.ips:
- out["reference_contacts"] = scorer.native_contacts
out["model_contacts"] = scorer.model_contacts
+
+ if args.ics_trimmed or args.ips_trimmed:
+ out["model_contacts_trimmed"] = scorer.trimmed_model_contacts
+
+ if args.ics or args.ips or args.ics_trimmed or args.ips_trimmed:
+ out["reference_contacts"] = scorer.native_contacts
out["contact_reference_interfaces"] = scorer.contact_target_interfaces
if args.ics:
@@ -932,18 +947,27 @@ def _Process(model, reference, args, model_format, reference_format):
out["per_interface_ips"] = \
[_RoundOrNone(x) for x in scorer.per_interface_ips]
- if args.ics_trimmed or args.ips_trimmed:
- out["model_contacts_trimmed"] = scorer.trimmed_model_contacts
-
if args.ics_trimmed:
out["ics_trimmed"] = _RoundOrNone(scorer.ics_trimmed)
out["ics_precision_trimmed"] = _RoundOrNone(scorer.ics_precision_trimmed)
out["ics_recall_trimmed"] = _RoundOrNone(scorer.ics_recall_trimmed)
+ out["per_interface_ics_precision_trimmed"] = \
+ [_RoundOrNone(x) for x in scorer.per_interface_ics_precision_trimmed]
+ out["per_interface_ics_recall_trimmed"] = \
+ [_RoundOrNone(x) for x in scorer.per_interface_ics_recall_trimmed]
+ out["per_interface_ics_trimmed"] = \
+ [_RoundOrNone(x) for x in scorer.per_interface_ics_trimmed]
if args.ips_trimmed:
out["ips_trimmed"] = _RoundOrNone(scorer.ips_trimmed)
out["ips_precision_trimmed"] = _RoundOrNone(scorer.ips_precision_trimmed)
out["ips_recall_trimmed"] = _RoundOrNone(scorer.ips_recall_trimmed)
+ out["per_interface_ips_precision_trimmed"] = \
+ [_RoundOrNone(x) for x in scorer.per_interface_ips_precision_trimmed]
+ out["per_interface_ips_recall_trimmed"] = \
+ [_RoundOrNone(x) for x in scorer.per_interface_ips_recall_trimmed]
+ out["per_interface_ips_trimmed"] = \
+ [_RoundOrNone(x) for x in scorer.per_interface_ips_trimmed]
if args.dockq:
out["dockq_reference_interfaces"] = scorer.dockq_target_interfaces
diff --git a/modules/mol/alg/pymod/scoring.py b/modules/mol/alg/pymod/scoring.py
index d1ec0705d..710223b68 100644
--- a/modules/mol/alg/pymod/scoring.py
+++ b/modules/mol/alg/pymod/scoring.py
@@ -374,9 +374,9 @@ class Scorer:
self._ips_precision = None
self._ips_recall = None
self._ips = None
- self._per_interface_ics_precision = None
- self._per_interface_ics_recall = None
- self._per_interface_ics = None
+ self._per_interface_ips_precision = None
+ self._per_interface_ips_recall = None
+ self._per_interface_ips = None
# subset of contact scores that operate on trimmed model
# i.e. no contacts from model residues that are not present in
@@ -384,9 +384,15 @@ class Scorer:
self._ics_trimmed = None
self._ics_precision_trimmed = None
self._ics_recall_trimmed = None
+ self._per_interface_ics_precision_trimmed = None
+ self._per_interface_ics_recall_trimmed = None
+ self._per_interface_ics_trimmed = None
self._ips_trimmed = None
self._ips_precision_trimmed = None
self._ips_recall_trimmed = None
+ self._per_interface_ips_precision_trimmed = None
+ self._per_interface_ips_recall_trimmed = None
+ self._per_interface_ips_trimmed = None
self._dockq_target_interfaces = None
self._dockq_interfaces = None
@@ -1096,7 +1102,6 @@ class Scorer:
if self._per_interface_ics is None:
self._compute_ics_scores()
return self._per_interface_ics
-
@property
def ips_precision(self):
@@ -1175,6 +1180,47 @@ class Scorer:
self._compute_ics_scores_trimmed()
return self._ics_recall_trimmed
+ @property
+ def per_interface_ics_precision_trimmed(self):
+ """ Same as :attr:`per_interface_ics_precision` but with :attr:`trimmed_model`
+
+ :attr:`~ics_precision_trimmed` for each interface in
+ :attr:`~contact_target_interfaces`
+
+ :type: :class:`list` of :class:`float`
+ """
+ if self._per_interface_ics_precision_trimmed is None:
+ self._compute_ics_scores_trimmed()
+ return self._per_interface_ics_precision_trimmed
+
+
+ @property
+ def per_interface_ics_recall_trimmed(self):
+ """ Same as :attr:`per_interface_ics_recall` but with :attr:`trimmed_model`
+
+ :attr:`~ics_recall_trimmed` for each interface in
+ :attr:`~contact_target_interfaces`
+
+ :type: :class:`list` of :class:`float`
+ """
+ if self._per_interface_ics_recall_trimmed is None:
+ self._compute_ics_scores_trimmed()
+ return self._per_interface_ics_recall_trimmed
+
+ @property
+ def per_interface_ics_trimmed(self):
+ """ Same as :attr:`per_interface_ics` but with :attr:`trimmed_model`
+
+ :attr:`~ics` for each interface in
+ :attr:`~contact_target_interfaces`
+
+ :type: :class:`float`
+ """
+
+ if self._per_interface_ics_trimmed is None:
+ self._compute_ics_scores_trimmed()
+ return self._per_interface_ics_trimmed
+
@property
def ips_trimmed(self):
""" Same as :attribute:`ips` but with trimmed model
@@ -1257,6 +1303,47 @@ class Scorer:
self._compute_ips_scores()
return self._per_interface_ips
+ @property
+ def per_interface_ips_precision_trimmed(self):
+ """ Same as :attr:`per_interface_ips_precision` but with :attr:`trimmed_model`
+
+ :attr:`~ips_precision_trimmed` for each interface in
+ :attr:`~contact_target_interfaces`
+
+ :type: :class:`list` of :class:`float`
+ """
+ if self._per_interface_ips_precision_trimmed is None:
+ self._compute_ips_scores_trimmed()
+ return self._per_interface_ips_precision_trimmed
+
+
+ @property
+ def per_interface_ips_recall_trimmed(self):
+ """ Same as :attr:`per_interface_ips_recall` but with :attr:`trimmed_model`
+
+ :attr:`~ics_recall_trimmed` for each interface in
+ :attr:`~contact_target_interfaces`
+
+ :type: :class:`list` of :class:`float`
+ """
+ if self._per_interface_ips_recall_trimmed is None:
+ self._compute_ips_scores_trimmed()
+ return self._per_interface_ips_recall_trimmed
+
+ @property
+ def per_interface_ips_trimmed(self):
+ """ Same as :attr:`per_interface_ips` but with :attr:`trimmed_model`
+
+ :attr:`~ics` for each interface in
+ :attr:`~contact_target_interfaces`
+
+ :type: :class:`float`
+ """
+
+ if self._per_interface_ips_trimmed is None:
+ self._compute_ips_scores_trimmed()
+ return self._per_interface_ips_trimmed
+
@property
def dockq_target_interfaces(self):
""" Interfaces in :attr:`target` that are relevant for DockQ
@@ -2266,6 +2353,26 @@ class Scorer:
self._ics_precision_trimmed = contact_scorer_res.precision
self._ics_recall_trimmed = contact_scorer_res.recall
+ self._per_interface_ics_precision_trimmed = list()
+ self._per_interface_ics_recall_trimmed = list()
+ self._per_interface_ics_trimmed = list()
+ flat_mapping = self.mapping.GetFlatMapping()
+ for trg_int in self.contact_target_interfaces:
+ trg_ch1 = trg_int[0]
+ trg_ch2 = trg_int[1]
+ if trg_ch1 in flat_mapping and trg_ch2 in flat_mapping:
+ mdl_ch1 = flat_mapping[trg_ch1]
+ mdl_ch2 = flat_mapping[trg_ch2]
+ res = self.trimmed_contact_scorer.ScoreICSInterface(trg_ch1, trg_ch2,
+ mdl_ch1, mdl_ch2)
+ self._per_interface_ics_precision_trimmed.append(res.precision)
+ self._per_interface_ics_recall_trimmed.append(res.recall)
+ self._per_interface_ics_trimmed.append(res.ics)
+ else:
+ self._per_interface_ics_precision_trimmed.append(None)
+ self._per_interface_ics_recall_trimmed.append(None)
+ self._per_interface_ics_trimmed.append(None)
+
def _compute_ips_scores(self):
LogScript("Computing IPS scores")
contact_scorer_res = self.contact_scorer.ScoreIPS(self.mapping.mapping)
@@ -2304,6 +2411,26 @@ class Scorer:
self._ips_recall_trimmed = contact_scorer_res.recall
self._ips_trimmed = contact_scorer_res.ips
+ self._per_interface_ips_precision_trimmed = list()
+ self._per_interface_ips_recall_trimmed = list()
+ self._per_interface_ips_trimmed = list()
+ flat_mapping = self.mapping.GetFlatMapping()
+ for trg_int in self.contact_target_interfaces:
+ trg_ch1 = trg_int[0]
+ trg_ch2 = trg_int[1]
+ if trg_ch1 in flat_mapping and trg_ch2 in flat_mapping:
+ mdl_ch1 = flat_mapping[trg_ch1]
+ mdl_ch2 = flat_mapping[trg_ch2]
+ res = self.trimmed_contact_scorer.ScoreIPSInterface(trg_ch1, trg_ch2,
+ mdl_ch1, mdl_ch2)
+ self._per_interface_ips_precision_trimmed.append(res.precision)
+ self._per_interface_ips_recall_trimmed.append(res.recall)
+ self._per_interface_ips_trimmed.append(res.ips)
+ else:
+ self._per_interface_ips_precision_trimmed.append(None)
+ self._per_interface_ips_recall_trimmed.append(None)
+ self._per_interface_ips_trimmed.append(None)
+
def _compute_dockq_scores(self):
LogScript("Computing DockQ")
--
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