From e56b1d2101ee3feed111fdec378c416c14bd7de7 Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Wed, 4 May 2022 08:43:48 +0200
Subject: [PATCH] lDDT: avoid zero divisions - return None for scores with 0
expected contacts
---
modules/mol/alg/pymod/lddt.py | 10 ++++++----
1 file changed, 6 insertions(+), 4 deletions(-)
diff --git a/modules/mol/alg/pymod/lddt.py b/modules/mol/alg/pymod/lddt.py
index b7147b5f3..1e1230f89 100644
--- a/modules/mol/alg/pymod/lddt.py
+++ b/modules/mol/alg/pymod/lddt.py
@@ -508,7 +508,6 @@ class lDDTScorer:
self._ResolveSymmetries(pos, thresholds, symmetries, sym_ref_indices,
sym_ref_distances)
-
per_res_exp = np.asarray([self._GetNExp(res_ref_atom_indices[idx],
ref_indices) for idx in range(len(res_indices))], dtype=np.int32)
per_res_conserved = self._EvalResidues(pos, thresholds,
@@ -521,8 +520,9 @@ class lDDTScorer:
per_res_lDDT = [None] * len(model.residues)
for idx in range(len(res_indices)):
n_exp = n_thresh * per_res_exp[idx]
- score = np.sum(per_res_conserved[idx,:]) / n_exp
- per_res_lDDT[res_indices[idx]] = score
+ if n_exp > 0:
+ score = np.sum(per_res_conserved[idx,:]) / n_exp
+ per_res_lDDT[res_indices[idx]] = score
# do full model score
if penalize_extra_chains:
@@ -530,7 +530,9 @@ class lDDTScorer:
lDDT_tot = int(n_thresh * n_distances)
lDDT_cons = int(np.sum(per_res_conserved))
- lDDT = float(lDDT_cons) / lDDT_tot
+ lDDT = None
+ if lDDT_tot > 0:
+ lDDT = float(lDDT_cons) / lDDT_tot
# set properties if necessary
if local_lddt_prop:
--
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