From a04a397b70e645a533b81242d3369660496b6863 Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Wed, 18 Jan 2023 08:25:34 +0100
Subject: [PATCH] integrate OST DockQ implementation in Scorer object
---
modules/mol/alg/pymod/scoring.py | 72 ++++++++------------------------
1 file changed, 17 insertions(+), 55 deletions(-)
diff --git a/modules/mol/alg/pymod/scoring.py b/modules/mol/alg/pymod/scoring.py
index 359aa0e67..b09c0d9df 100644
--- a/modules/mol/alg/pymod/scoring.py
+++ b/modules/mol/alg/pymod/scoring.py
@@ -9,10 +9,10 @@ from ost.mol.alg import lddt
from ost.mol.alg import qsscore
from ost.mol.alg import chain_mapping
from ost.mol.alg import stereochemistry
+from ost.mol.alg import dockq
from ost.mol.alg.lddt import lDDTScorer
from ost.mol.alg.qsscore import QSScorer
from ost.mol.alg import Molck, MolckSettings
-from ost.bindings import dockq
from ost.bindings import cadscore
import numpy as np
@@ -114,11 +114,6 @@ class Scorer:
to optimize for QS-score. Everything
above is treated with a heuristic.
:type naive_chain_mapping_thresh: :class:`int`
- :param dockq_exec: Explicit path to DockQ.py script from DockQ installation
- from https://github.com/bjornwallner/DockQ. If not given,
- DockQ.py must be in PATH if any of the DockQ related
- attributes is requested.
- :type dockq_exec: :class:`str`
:param cad_score_exec: Explicit path to voronota-cadscore executable from
voronota installation from
https://github.com/kliment-olechnovic/voronota. If
@@ -128,7 +123,7 @@ class Scorer:
"""
def __init__(self, model, target, resnum_alignments=False,
molck_settings = None, naive_chain_mapping_thresh=12,
- dockq_exec = None, cad_score_exec = None):
+ cad_score_exec = None):
if isinstance(model, mol.EntityView):
self._model = mol.CreateEntityFromView(model, False)
@@ -183,7 +178,6 @@ class Scorer:
Molck(self._target, conop.GetDefaultLib(), molck_settings)
self.resnum_alignments = resnum_alignments
self.naive_chain_mapping_thresh = naive_chain_mapping_thresh
- self.dockq_exec = dockq_exec
self.cad_score_exec = cad_score_exec
# lazily evaluated attributes
@@ -868,12 +862,6 @@ class Scorer:
"that are consistent between target and model "
"chains, i.e. only work if resnum_alignments "
"is True at Scorer construction.")
- try:
- dockq_exec = settings.Locate("DockQ.py",
- explicit_file_name=self.dockq_exec)
- except Exception as e:
- raise RuntimeError("DockQ.py must be in PATH for DockQ "
- "scoring") from e
flat_mapping = self.mapping.GetFlatMapping()
# list of [trg_ch1, trg_ch2, mdl_ch1, mdl_ch2]
@@ -896,38 +884,22 @@ class Scorer:
if trg_ch1 in flat_mapping and trg_ch2 in flat_mapping:
mdl_ch1 = flat_mapping[trg_ch1]
mdl_ch2 = flat_mapping[trg_ch2]
- try:
- res = dockq.DockQ(dockq_exec, self.model, self.target,
- mdl_ch1, mdl_ch2, trg_ch1, trg_ch2)
- except Exception as e:
- if "AssertionError: length of native is zero" in str(e):
- # happens if target interface has no native contacts
- continue
- else:
- raise
-
- if res.native_contacts > 0:
+ res = dockq.DockQ(self.model, self.target, mdl_ch1, mdl_ch2,
+ trg_ch1, trg_ch2)
+ if res["nnat"] > 0:
self._dockq_interfaces.append((trg_ch1, trg_ch2,
mdl_ch1, mdl_ch2))
- self._dockq_native_contacts.append(res.native_contacts)
- self._dockq_scores.append(res.DockQ)
+ self._dockq_native_contacts.append(res["nnat"])
+ self._dockq_scores.append(res["DockQ"])
else:
# interface which is not covered by mdl... let's run DockQ with
# trg as trg/mdl in order to get the native contacts out
- try:
- res = dockq.DockQ(dockq_exec, self.target, self.target,
- trg_ch1, trg_ch2, trg_ch1, trg_ch2)
- counts = res.native_contacts
- if counts > 0:
- self._dockq_nonmapped_interfaces.append((trg_ch1,
- trg_ch2))
- self._dockq_nonmapped_interfaces_counts.append(counts)
- except Exception as e:
- if "AssertionError: length of native is zero" in str(e):
- # happens if target interface has no native contacts
- continue
- else:
- raise
+ res = dockq.DockQ(self.target, self.target,
+ trg_ch1, trg_ch2, trg_ch1, trg_ch2)
+ if res["nnat"] > 0:
+ self._dockq_nonmapped_interfaces.append((trg_ch1,
+ trg_ch2))
+ self._dockq_nonmapped_interfaces_counts.append(res["nnat"])
# there are 4 types of combined scores
# - simple average
@@ -1273,22 +1245,12 @@ class Scorer:
"that are consistent between target and model "
"chains, i.e. only work if resnum_alignments "
"is True at Scorer construction.")
- try:
- dockq_exec = settings.Locate("DockQ.py",
- explicit_file_name=self.dockq_exec)
- except Exception as e:
- raise RuntimeError("DockQ.py must be in PATH for DockQ "
- "scoring") from e
m = self._qs_ent_from_patches(mdl_patch_one, mdl_patch_two)
t = self._qs_ent_from_patches(trg_patch_one, trg_patch_two)
- try:
- dockq_result = dockq.DockQ(dockq_exec, t, m, "A", "B", "A", "B")
- except Exception as e:
- if "AssertionError: length of native is zero" in str(e):
- return 0.0
- else:
- raise
- return dockq_result.DockQ
+ dockq_result = dockq.DockQ(t, m, "A", "B", "A", "B")
+ if dockq_result["nnat"] > 0:
+ return 0.0
+ return dockq_result["DockQ"]
def _qs_ent_from_patches(self, patch_one, patch_two):
""" Constructs Entity with two chains named "A" and "B""
--
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