From 94618420e88851c49a919f53f42bb1ca6287f8f1 Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Fri, 12 May 2023 00:09:45 +0200
Subject: [PATCH] add TM-score to Scorer object
---
modules/mol/alg/pymod/scoring.py | 61 +++++++++++++++++++++++++++++++-
1 file changed, 60 insertions(+), 1 deletion(-)
diff --git a/modules/mol/alg/pymod/scoring.py b/modules/mol/alg/pymod/scoring.py
index 79fd4a29f..1a11304c8 100644
--- a/modules/mol/alg/pymod/scoring.py
+++ b/modules/mol/alg/pymod/scoring.py
@@ -13,7 +13,9 @@ 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 import bindings
from ost.bindings import cadscore
+from ost.bindings import tmtools
import numpy as np
class lDDTBSScorer:
@@ -125,10 +127,15 @@ class Scorer:
*target*. Dictionary with target chain names as key
and model chain names as value.
:type custom_mapping: :class:`dict`
+ :param usalign_exec: Explicit path to USalign executable used to compute
+ TM-score. If not given, TM-score will be computed
+ with OpenStructure internal copy of USalign code.
+ :type usalign_exec: :class:`str`
"""
def __init__(self, model, target, resnum_alignments=False,
molck_settings = None, naive_chain_mapping_thresh=12,
- cad_score_exec = None, custom_mapping=None):
+ cad_score_exec = None, custom_mapping=None,
+ usalign_exec = None):
if isinstance(model, mol.EntityView):
model = mol.CreateEntityFromView(model, False)
@@ -195,6 +202,7 @@ class Scorer:
self.resnum_alignments = resnum_alignments
self.naive_chain_mapping_thresh = naive_chain_mapping_thresh
self.cad_score_exec = cad_score_exec
+ self.usalign_exec = usalign_exec
# lazily evaluated attributes
self._stereochecked_model = None
@@ -258,6 +266,9 @@ class Scorer:
self._patch_qs = None
self._patch_dockq = None
+ self._tm_score = None
+ self._usalign_mapping = None
+
if custom_mapping is not None:
self._set_custom_mapping(custom_mapping)
@@ -961,6 +972,35 @@ class Scorer:
self._compute_patchdockq_scores()
return self._patch_dockq
+ @property
+ def tm_score(self):
+ """ TM-score computed with USalign
+
+ USalign executable can be specified with usalign_exec kwarg at Scorer
+ construction, an OpenStructure internal copy of the USalign code is
+ used otherwise.
+
+ :type: :class:`float`
+ """
+ if self._tm_score is None:
+ self._compute_tmscore()
+ return self._tm_score
+
+ @property
+ def usalign_mapping(self):
+ """ Mapping computed with USalign
+
+ Dictionary with target chain names as key and model chain names as
+ values. No guarantee that all chains are mapped. USalign executable
+ can be specified with usalign_exec kwarg at Scorer construction, an
+ OpenStructure internal copy of the USalign code is used otherwise.
+
+ :type: :class:`dict`
+ """
+ if self._usalign_mapping is None:
+ self._compute_tmscore()
+ return self._usalign_mapping
+
def _aln_helper(self, target, model):
# perform required alignments - cannot take the alignments from the
# mapping results as we potentially remove stuff there as compared
@@ -1644,3 +1684,22 @@ class Scorer:
self._mapping = chain_mapping.MappingResult(chain_mapper.target, mdl,
chain_mapper.chem_groups,
final_mapping, alns)
+
+ def _compute_tmscore(self):
+ res = None
+ if self.usalign_exec is not None:
+ if not os.path.exists(self.usalign_exec):
+ raise RuntimeError(f"USalign exec ({self.usalign_exec}) "
+ f"not found")
+ if not os.access(self.usalign_exec, os.X_OK):
+ raise RuntimeError(f"USalign exec ({self.usalign_exec}) "
+ f"is not executable")
+ res = tmtools.USAlign(self.model, self.target,
+ usalign = self.usalign_exec)
+ else:
+ res = bindings.WrappedMMAlign(self.model, self.target)
+
+ self._tm_score = res.tm_score
+ self._usalign_mapping = dict()
+ for a,b in zip(res.ent1_mapped_chains, res.ent2_mapped_chains):
+ self._usalign_mapping[b] = a
--
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