From 5e3b46679113297cb6349ab5960a81503f74a8d9 Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Tue, 17 Sep 2024 11:26:04 +0200
Subject: [PATCH] scoring: correctly handle per-atom lDDT scores in case of
stereochecks
---
modules/mol/alg/pymod/scoring.py | 57 +++++++++++++++++++++++++++++---
1 file changed, 52 insertions(+), 5 deletions(-)
diff --git a/modules/mol/alg/pymod/scoring.py b/modules/mol/alg/pymod/scoring.py
index c229aff4f..0626bff67 100644
--- a/modules/mol/alg/pymod/scoring.py
+++ b/modules/mol/alg/pymod/scoring.py
@@ -2148,16 +2148,53 @@ class Scorer:
score = round(r.GetFloatProp("lddt"), 3)
local_lddt[cname][rnum] = score
+ trg_r = None
+ mdl_r = None
+
for a in r.atoms:
if a.HasProp("lddt"):
score = round(a.GetFloatProp("lddt"), 3)
aa_local_lddt[cname][rnum][a.GetName()] = score
else:
- # must have been removed by stereochecks
- aa_local_lddt[cname][rnum][a.GetName()] = 0.0
+ # the target residue is there since we have a score
+ # for the residue.
+ # opt 1: The atom was never there in the
+ # stereochecked target => None
+ # opt 2: The atom has been removed in the model
+ # stereochecks but is there in stereochecked
+ # target => 0.0
+ if trg_r is 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 not None:
+ trg_cname = trg_r.GetChain().GetName()
+ trg_rnum = trg_r.GetNumber()
+ tmp = self.stereochecked_target.FindResidue(trg_cname,
+ trg_rnum)
+ if tmp.IsValid():
+ trg_r = tmp
+
+ if mdl_r is None:
+ tmp = self.stereochecked_model.FindResidue(cname, rnum)
+ if tmp.IsValid():
+ mdl_r = tmp
+
+ if trg_r is not None and not trg_r.FindAtom(a.GetName()).IsValid():
+ # opt 1
+ aa_local_lddt[cname][rnum][a.GetName()] = None
+ elif trg_r is not None and trg_r.FindAtom(a.GetName()).IsValid() and \
+ mdl_r is not None and not mdl_r.FindAtom(a.GetName()).IsValid():
+ # opt 2
+ aa_local_lddt[cname][rnum][a.GetName()] = 0.0
+ else:
+ # unknown issue
+ aa_local_lddt[cname][rnum][a.GetName()] = None
else:
- # rsc => residue stereo checked...
mdl_res = self.stereochecked_model.FindResidue(cname, rnum)
if mdl_res.IsValid():
# not covered by trg or skipped in chain mapping procedure
@@ -2177,15 +2214,25 @@ class Scorer:
if col.GetResidue(1).number == r.number:
trg_r = col.GetResidue(0)
break
+ if trg_r is not None:
+ trg_cname = trg_r.GetChain().GetName()
+ trg_rnum = trg_r.GetNumber()
+ tmp = self.stereochecked_target.FindResidue(trg_cname,
+ trg_rnum)
+ if tmp.IsValid():
+ trg_r = tmp
+
if trg_r is None:
local_lddt[cname][rnum] = None
for a in r.atoms:
aa_local_lddt[cname][rnum][a.GetName()] = None
-
else:
local_lddt[cname][rnum] = 0.0
for a in r.atoms:
- aa_local_lddt[cname][rnum][a.GetName()] = 0.0
+ if trg_r.FindAtom(a.GetName()).IsValid():
+ aa_local_lddt[cname][rnum][a.GetName()] = 0.0
+ else:
+ aa_local_lddt[cname][rnum][a.GetName()] = None
self._lddt = lddt_score
self._local_lddt = local_lddt
--
GitLab