From b7163962dfbd0f8939bcd8c2ee187d2294e4beb0 Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Wed, 24 May 2023 14:15:43 +0200
Subject: [PATCH] flag to disable lddt stereochemistry checks in
ost.mol.alg.Scorer
---
modules/mol/alg/pymod/scoring.py | 109 ++++++++++++++++++++-----------
1 file changed, 71 insertions(+), 38 deletions(-)
diff --git a/modules/mol/alg/pymod/scoring.py b/modules/mol/alg/pymod/scoring.py
index 1a11304c8..f9e7ec864 100644
--- a/modules/mol/alg/pymod/scoring.py
+++ b/modules/mol/alg/pymod/scoring.py
@@ -131,11 +131,14 @@ class Scorer:
TM-score. If not given, TM-score will be computed
with OpenStructure internal copy of USalign code.
:type usalign_exec: :class:`str`
+ :param lddt_no_stereochecks: Whether to compute lDDT without stereochemistry
+ checks
+ :type lddt_no_stereochecks: :class:`bool`
"""
def __init__(self, model, target, resnum_alignments=False,
molck_settings = None, naive_chain_mapping_thresh=12,
cad_score_exec = None, custom_mapping=None,
- usalign_exec = None):
+ usalign_exec = None, lddt_no_stereochecks=False):
if isinstance(model, mol.EntityView):
model = mol.CreateEntityFromView(model, False)
@@ -203,6 +206,7 @@ class Scorer:
self.naive_chain_mapping_thresh = naive_chain_mapping_thresh
self.cad_score_exec = cad_score_exec
self.usalign_exec = usalign_exec
+ self.lddt_no_stereochecks = lddt_no_stereochecks
# lazily evaluated attributes
self._stereochecked_model = None
@@ -474,7 +478,10 @@ class Scorer:
:type: :class:`ost.mol.alg.lddt.lDDTScorer`
"""
if self._lddt_scorer is None:
- self._lddt_scorer = lDDTScorer(self.stereochecked_target)
+ if self.lddt_no_stereochecks:
+ self._lddt_scorer = lDDTScorer(self.target)
+ else:
+ self._lddt_scorer = lDDTScorer(self.stereochecked_target)
return self._lddt_scorer
@property
@@ -1062,48 +1069,74 @@ class Scorer:
mdl_seq = aln.GetSequence(1)
alns[mdl_seq.name] = aln
- lddt_chain_mapping = dict()
- for mdl_ch, trg_ch in flat_mapping.items():
- if mdl_ch in stereochecked_alns:
- lddt_chain_mapping[mdl_ch] = trg_ch
-
- lddt_score = self.lddt_scorer.lDDT(self.stereochecked_model,
- chain_mapping = lddt_chain_mapping,
- residue_mapping = stereochecked_alns,
- check_resnames=False,
- local_lddt_prop="lddt")[0]
- local_lddt = dict()
- for r in self.model.residues:
- cname = r.GetChain().GetName()
- if cname not in local_lddt:
- local_lddt[cname] = dict()
- if r.HasProp("lddt"):
- score = round(r.GetFloatProp("lddt"), 3)
- local_lddt[cname][r.GetNumber()] = score
- else:
- # rsc => residue stereo checked...
- mdl_res = self.stereochecked_model.FindResidue(cname, r.GetNumber())
- if mdl_res.IsValid():
+ # score variables to be set
+ lddt_score = None
+ local_lddt = None
+
+ if self.lddt_no_stereochecks:
+ lddt_chain_mapping = dict()
+ for mdl_ch, trg_ch in flat_mapping.items():
+ if mdl_ch in alns:
+ lddt_chain_mapping[mdl_ch] = trg_ch
+ lddt_score = self.lddt_scorer.lDDT(self.model,
+ chain_mapping = lddt_chain_mapping,
+ residue_mapping = alns,
+ check_resnames=False,
+ local_lddt_prop="lddt")[0]
+ local_lddt = dict()
+ for r in self.model.residues:
+ cname = r.GetChain().GetName()
+ if cname not in local_lddt:
+ local_lddt[cname] = dict()
+ if r.HasProp("lddt"):
+ score = round(r.GetFloatProp("lddt"), 3)
+ local_lddt[cname][r.GetNumber()] = score
+ else:
# not covered by trg or skipped in chain mapping procedure
# the latter happens if its part of a super short chain
local_lddt[cname][r.GetNumber()] = None
+
+ else:
+ lddt_chain_mapping = dict()
+ for mdl_ch, trg_ch in flat_mapping.items():
+ if mdl_ch in stereochecked_alns:
+ lddt_chain_mapping[mdl_ch] = trg_ch
+ lddt_score = self.lddt_scorer.lDDT(self.stereochecked_model,
+ chain_mapping = lddt_chain_mapping,
+ residue_mapping = stereochecked_alns,
+ check_resnames=False,
+ local_lddt_prop="lddt")[0]
+ local_lddt = dict()
+ for r in self.model.residues:
+ cname = r.GetChain().GetName()
+ if cname not in local_lddt:
+ local_lddt[cname] = dict()
+ if r.HasProp("lddt"):
+ score = round(r.GetFloatProp("lddt"), 3)
+ local_lddt[cname][r.GetNumber()] = score
else:
- # opt 1: removed by stereochecks => assign 0.0
- # opt 2: removed by stereochecks AND not covered by ref
- # => assign None
-
- # fetch trg residue from non-stereochecked aln
- trg_r = None
- if cname in flat_mapping:
- for col in alns[cname]:
- if col[0] != '-' and col[1] != '-':
- if col.GetResidue(1).number == r.number:
- trg_r = col.GetResidue(0)
- break
- if trg_r is None:
+ # rsc => residue stereo checked...
+ mdl_res = self.stereochecked_model.FindResidue(cname, r.GetNumber())
+ if mdl_res.IsValid():
+ # not covered by trg or skipped in chain mapping procedure
+ # the latter happens if its part of a super short chain
local_lddt[cname][r.GetNumber()] = None
else:
- local_lddt[cname][r.GetNumber()] = 0.0
+ # opt 1: removed by stereochecks => assign 0.0
+ # opt 2: removed by stereochecks AND not covered by ref
+ # => assign None
+ # fetch trg residue from non-stereochecked aln
+ trg_r = None
+ if cname in flat_mapping:
+ for col in alns[cname]:
+ if col[0] != '-' and col[1] != '-':
+ if col.GetResidue(1).number == r.number:
+ trg_r = col.GetResidue(0)
+ break
+ if trg_r is None:
+ local_lddt[cname][r.GetNumber()] = None
+ else:
+ local_lddt[cname][r.GetNumber()] = 0.0
self._lddt = lddt_score
self._local_lddt = local_lddt
--
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