From 0fd7f322d33692ff13bc8aca60656c6349805647 Mon Sep 17 00:00:00 2001
From: Xavier Robin <xavier.robin@unibas.ch>
Date: Fri, 5 Apr 2024 15:45:37 +0200
Subject: [PATCH] Add logging output to the scoring
---
actions/ost-compare-structures | 11 +++++++++++
modules/mol/alg/pymod/scoring.py | 24 +++++++++++++++++++++++-
2 files changed, 34 insertions(+), 1 deletion(-)
diff --git a/actions/ost-compare-structures b/actions/ost-compare-structures
index 02fa365c0..4cf9ef75f 100644
--- a/actions/ost-compare-structures
+++ b/actions/ost-compare-structures
@@ -526,6 +526,14 @@ def _ParseArgs():
"problematic as they may produce high sequence identity "
"alignments by pure chance.")
)
+
+ parser.add_argument(
+ '-v',
+ '--verbosity',
+ dest="verbosity",
+ type=int,
+ default=2,
+ help="Set verbosity level. Defaults to 3 (Script).")
return parser.parse_args()
@@ -862,6 +870,9 @@ def _Process(model, reference, args, model_format, reference_format):
def _Main():
args = _ParseArgs()
+ ost.PushVerbosityLevel(args.verbosity)
+ if args.verbosity < 4:
+ sys.tracebacklimit = 0
_CheckCompoundLib()
try:
compute_cad = args.cad_score or args.local_cad_score
diff --git a/modules/mol/alg/pymod/scoring.py b/modules/mol/alg/pymod/scoring.py
index d0d3cf84d..53a596f52 100644
--- a/modules/mol/alg/pymod/scoring.py
+++ b/modules/mol/alg/pymod/scoring.py
@@ -5,6 +5,7 @@ from ost import io
from ost import conop
from ost import settings
from ost import geom
+from ost import LogScript, LogInfo, LogDebug
from ost.mol.alg import lddt
from ost.mol.alg import qsscore
from ost.mol.alg import chain_mapping
@@ -191,6 +192,7 @@ class Scorer:
colored=False,
map_nonstd_res=True,
assign_elem=True)
+ LogScript("Cleaning up input structures")
Molck(self._model, conop.GetDefaultLib(), molck_settings)
Molck(self._target, conop.GetDefaultLib(), molck_settings)
self._model = self._model.Select("peptide=True or nucleotide=True")
@@ -343,6 +345,7 @@ class Scorer:
if custom_mapping is not None:
self._set_custom_mapping(custom_mapping)
+ LogDebug("Scorer sucessfully initialized")
@property
def model(self):
@@ -526,6 +529,7 @@ class Scorer:
:type: :class:`ost.mol.alg.chain_mapping.MappingResult`
"""
if self._mapping is None:
+ LogScript("Computing chain mapping")
self._mapping = \
self.chain_mapper.GetMapping(self.model,
n_max_naive = self.n_max_naive)
@@ -1220,6 +1224,7 @@ class Scorer:
:type: :class:`float`
"""
if self._gdtts is None:
+ LogScript("Computing GDT-TS score")
n = \
self.mapped_target_pos.GetGDTTS(self.transformed_mapped_model_pos,
norm=False)
@@ -1240,6 +1245,7 @@ class Scorer:
:type: :class:`float`
"""
if self._gdtha is None:
+ LogScript("Computing GDT-HA score")
n = \
self.mapped_target_pos.GetGDTHA(self.transformed_mapped_model_pos,
norm=False)
@@ -1260,6 +1266,7 @@ class Scorer:
:type: :class:`float`
"""
if self._rmsd is None:
+ LogScript("Computing RMSD")
self._rmsd = \
self.mapped_target_pos.GetRMSD(self.transformed_mapped_model_pos)
return self._rmsd
@@ -1413,6 +1420,7 @@ class Scorer:
self.stereochecked_model)
def _compute_lddt(self):
+ LogScript("Computing all-atom lDDT")
# lDDT requires a flat mapping with mdl_ch as key and trg_ch as value
flat_mapping = self.mapping.GetFlatMapping(mdl_as_key=True)
@@ -1499,7 +1507,7 @@ class Scorer:
self._local_lddt = local_lddt
def _compute_bb_lddt(self):
-
+ LogScript("Computing backbone lDDT")
# make alignments accessible by mdl seq name
alns = dict()
for aln in self.aln:
@@ -1535,11 +1543,13 @@ class Scorer:
self._bb_local_lddt = local_lddt
def _compute_qs(self):
+ LogScript("Computing global QS-score")
qs_score_result = self.qs_scorer.Score(self.mapping.mapping)
self._qs_global = qs_score_result.QS_global
self._qs_best = qs_score_result.QS_best
def _compute_per_interface_qs_scores(self):
+ LogScript("Computing per-interface QS-score")
self._per_interface_qs_global = list()
self._per_interface_qs_best = list()
@@ -1554,6 +1564,7 @@ class Scorer:
self._per_interface_qs_global.append(qs_res.QS_global)
def _compute_ics_scores(self):
+ LogScript("Computing ICS scores")
contact_scorer_res = self.contact_scorer.ScoreICS(self.mapping.mapping)
self._ics_precision = contact_scorer_res.precision
self._ics_recall = contact_scorer_res.recall
@@ -1579,6 +1590,7 @@ class Scorer:
self._per_interface_ics.append(None)
def _compute_ips_scores(self):
+ LogScript("Computing IPS scores")
contact_scorer_res = self.contact_scorer.ScoreIPS(self.mapping.mapping)
self._ips_precision = contact_scorer_res.precision
self._ips_recall = contact_scorer_res.recall
@@ -1605,6 +1617,7 @@ class Scorer:
self._per_interface_ips.append(None)
def _compute_dockq_scores(self):
+ LogScript("Computing DockQ")
# lists with values in contact_target_interfaces
self._dockq_scores = list()
self._fnat = list()
@@ -1708,6 +1721,7 @@ class Scorer:
"chains, i.e. only work if resnum_alignments "
"is True at Scorer construction.")
try:
+ LogScript("Computing CAD score")
cad_score_exec = \
settings.Locate("voronota-cadscore",
explicit_file_name=self.cad_score_exec)
@@ -1774,6 +1788,7 @@ class Scorer:
def _do_stereochecks(self):
""" Perform stereochemistry checks on model and target
"""
+ LogInfo("Performing stereochemistry checks on model and target")
data = stereochemistry.GetDefaultStereoData()
l_data = stereochemistry.GetDefaultStereoLinkData()
@@ -1908,6 +1923,7 @@ class Scorer:
trg_patch_one, trg_patch_two)
def _compute_patchqs_scores(self):
+ LogScript("Computing patch QS-scores")
self._patch_qs = dict()
for cname, rnums in self.model_interface_residues.items():
scores = list()
@@ -1925,6 +1941,7 @@ class Scorer:
self._patch_qs[cname] = scores
def _compute_patchdockq_scores(self):
+ LogScript("Computing patch DockQ scores")
self._patch_dockq = dict()
for cname, rnums in self.model_interface_residues.items():
scores = list()
@@ -2034,6 +2051,7 @@ class Scorer:
:param mapping: mapping with trg chains as key and mdl ch as values
:type mapping: :class:`dict`
"""
+ LogInfo("Setting custom chain mapping")
chain_mapper = self.chain_mapper
chem_mapping, chem_group_alns, mdl = \
@@ -2125,14 +2143,18 @@ class Scorer:
def _compute_tmscore(self):
res = None
if self.usalign_exec is None:
+ LogScript("Computing patch TM-score with USalign exectuable")
if self.oum:
flat_mapping = self.mapping.GetFlatMapping()
+ LogInfo("Overriding TM-score chain mapping")
res = res = bindings.WrappedMMAlign(self.model, self.target,
mapping=flat_mapping)
else:
res = bindings.WrappedMMAlign(self.model, self.target)
else:
+ LogScript("Computing patch TM-score with built-in USalign")
if self.oum:
+ LogInfo("Overriding TM-score chain mapping")
flat_mapping = self.mapping.GetFlatMapping()
res = tmtools.USAlign(self.model, self.target,
usalign = self.usalign_exec,
--
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