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add failsafe for nucleic ss metric

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This commit is contained in:
Raktim Mitra
2026-02-19 01:59:11 -08:00
committed by Raktim Mitra
parent 212082581b
commit d04989f65f
2 changed files with 20 additions and 14 deletions
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4
models/rfd3/configs/datasets/val/pseudoknot.yaml
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@@ -6,5 +6,5 @@ defaults:
dataset:
name: pseudoknot
eval_every_n: 1
data: ${paths.data.design_benchmark_data_dir}/pseudoknot_debug.json
#data: ${paths.data.design_benchmark_data_dir}/pseudoknot.json
#data: ${paths.data.design_benchmark_data_dir}/pseudoknot_debug.json
data: ${paths.data.design_benchmark_data_dir}/pseudoknot.json

30
models/rfd3/src/rfd3/metrics/nucleic_ss_metrics.py
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@@ -230,18 +230,24 @@ class NucleicSSSimilarityMetrics(Metric):
# prediction can inherit it, yielding artificially perfect scores.
# Optionally recompute bp_partners from the *predicted coordinates*.
if self.annotate_predicted_fresh:
# Infer res name from geometry first
pred_arr = _readout_seq_from_struc(
pred_arr,
central_atom="C1'",
threshold=0.5,
association_scheme="atom23",
)
# strip virtuals and set final atom names/elements
pred_arr = _cleanup_virtual_atoms_and_assign_atom_name_elements(
pred_arr,
association_scheme="atom23",
)
try:
# Infer res name from geometry first
pred_arr = _readout_seq_from_struc(
pred_arr,
central_atom="C1'",
threshold=0.5,
association_scheme="atom23",
)
# strip virtuals and set final atom names/elements
pred_arr = _cleanup_virtual_atoms_and_assign_atom_name_elements(
pred_arr,
association_scheme="atom23",
)
except:
# this can fail early in training
print("could not cleanup virtuals for nucleic ss metric compute")
pass
# clear annotation to avoid potential info leak
if "bp_partners" in pred_arr.get_annotation_categories():
pred_arr.del_annotation("bp_partners")