@platforma-open/milaboratories.3d-structure-prediction.software 1.0.7 → 1.1.0
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/.turbo/turbo-build.log +334 -336
- package/CHANGELOG.md +12 -0
- package/dist/artifacts/py-archive/archive.json +1 -1
- package/dist/artifacts/py-docker/docker_x64.json +1 -1
- package/dist/tengo/software/immunebuilder-predict.sw.json +1 -1
- package/package.json +2 -2
- package/pkg-platforma-open-milaboratories.3d-structure-prediction.software-py-archive-1.1.0.tgz +0 -0
- package/src_python/run_immunebuilder.py +53 -5
- package/pkg-platforma-open-milaboratories.3d-structure-prediction.software-py-archive-1.0.7.tgz +0 -0
package/.turbo/turbo-build.log
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WARN Issue while reading "/home/runner/work/3d-structure-prediction/3d-structure-prediction/.npmrc". Failed to replace env in config: ${NPMJS_TOKEN}
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> @platforma-open/milaboratories.3d-structure-prediction.software@1.0
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> @platforma-open/milaboratories.3d-structure-prediction.software@1.1.0 build /home/runner/work/3d-structure-prediction/3d-structure-prediction/software
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[32minfo[39m: Building docker images...
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#3 resolve image config for docker-image://docker.io/docker/dockerfile:1
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#4 docker-image://docker.io/docker/dockerfile:1@sha256:87999aa3d42bdc6bea60565083ee17e86d1f3339802f543c0d03998580f9cb89
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#4 resolve docker.io/docker/dockerfile:1@sha256:87999aa3d42bdc6bea60565083ee17e86d1f3339802f543c0d03998580f9cb89 done
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#8 [1/6] FROM docker.io/mambaorg/micromamba:1.5.10@sha256:e3797091302382ea841498bc93a7b0a50f7c1448333d5e946d2d1608d0c5f43d
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#8 resolve docker.io/mambaorg/micromamba:1.5.10@sha256:e3797091302382ea841498bc93a7b0a50f7c1448333d5e946d2d1608d0c5f43d done
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#10 [2/6] RUN micromamba install -y -n base -c bioconda -c conda-forge python=3.12.10 anarci hmmer biopython=1.85 openmm=8.3.1 pdbfixer=1.12.0 numpy=2.4.3 scipy=1.17.1 && micromamba clean --all --yes
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#10 16.69 + python_abi 3.12 8_cp312 conda-forge 7kB
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#10 16.69 + tzdata 2025c hc9c84f9_1 conda-forge 119kB
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#10 16.69 + ca-certificates 2026.5.20 hbd8a1cb_0 conda-forge 130kB
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#10 16.69 + cuda-version 12.9 h4f385c5_3 conda-forge 22kB
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#10 16.69 + ld_impl_linux-64 2.45.1 default_hbd61a6d_102 conda-forge 728kB
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#10 16.69 + tk 8.6.13 noxft_h366c992_103 conda-forge 3MB
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#10 16.69 + libsqlite 3.53.2 h0c1763c_0 conda-forge 958kB
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#10 16.69 + openssl 3.6.3 h35e630c_0 conda-forge 3MB
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#10 16.69 + ncurses 6.6 hdb14827_0 conda-forge 919kB
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#10 16.69 + liblzma 5.8.3 hb03c661_0 conda-forge 113kB
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#10 16.69 + bzip2 1.0.8 hda65f42_9 conda-forge 260kB
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#10 16.69 + libstdcxx-ng 15.2.0 hdf11a46_19 conda-forge 28kB
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#10 16.69 + libcufft 11.4.1.4 hecca717_1 conda-forge 162MB
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#10 16.69 + cuda-nvrtc 12.9.86 hecca717_1 conda-forge 67MB
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#10 16.69 + python 3.12.10 h9e4cc4f_0_cpython conda-forge 31MB
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#10 16.69 + setuptools 82.0.1 pyh332efcf_0 conda-forge 640kB
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#10 16.69 Install: 54 packages
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#10 16.69 Total download: 353MB
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#10 22.17 Equivalently, you can set the MCA parameters in the command line:
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#10 23.33 Cleaning index cache..
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#10 23.47 anarci-2024.05.21-pyhdfd78af_0.tar.bz2 1MB
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#10 23.47 bzip2-1.0.8-hda65f42_9.conda 260kB
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#10 23.47 libcblas-3.11.0-8_h0358290_openblas.conda 19kB
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#10 23.47 libcufft-11.4.1.4-hecca717_1.conda 162MB
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#10 23.47 libexpat-2.8.1-hecca717_0.conda 77kB
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#10 23.47 libffi-3.4.6-h2dba641_1.conda 57kB
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#10 23.47 libgcc-ng-15.2.0-h69a702a_19.conda 28kB
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#10 23.47 libgfortran-15.2.0-h69a702a_19.conda 28kB
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#10 23.47 libgfortran5-15.2.0-h68bc16d_19.conda 2MB
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#10 23.47 libgomp-15.2.0-he0feb66_19.conda 604kB
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#10 23.47 liblapack-3.11.0-8_h47877c9_openblas.conda 19kB
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#10 23.47 liblzma-5.8.3-hb03c661_0.conda 113kB
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#10 23.47 libnsl-2.0.1-hb9d3cd8_1.conda 34kB
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#10 23.47 libopenblas-0.3.33-pthreads_h94d23a6_0.conda 6MB
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#10 23.47 libsqlite-3.53.2-h0c1763c_0.conda 958kB
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#10 23.47 libstdcxx-15.2.0-h934c35e_19.conda 6MB
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#10 23.47 libstdcxx-ng-15.2.0-hdf11a46_19.conda 28kB
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#10 23.47 libuuid-2.42.1-h5347b49_0.conda 40kB
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#10 23.47 libxcrypt-4.4.36-hd590300_1.conda 100kB
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#10 23.47 libzlib-1.3.2-h25fd6f3_2.conda 64kB
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#10 23.47 mpi-1.0-openmpi.tar.bz2 4kB
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#10 23.47 ncurses-6.6-hdb14827_0.conda 919kB
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#10 23.47 numpy-2.4.3-py312h33ff503_0.conda 9MB
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#10 23.47 ocl-icd-2.3.4-hb03c661_1.conda 110kB
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#10 23.47 ocl-icd-system-1.0.0-1.tar.bz2 4kB
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#10 23.47 opencl-headers-2025.06.13-hecca717_0.conda 56kB
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#10 23.47 openmm-8.3.1-py312h50c43f0_0.conda 13MB
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#10 23.47 openmpi-4.1.6-hc5af2df_101.conda 4MB
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#10 23.47 openssl-3.6.3-h35e630c_0.conda 3MB
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#10 23.47 packaging-26.2-pyhc364b38_0.conda 92kB
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#10 23.47 pdbfixer-1.12-pyhd8ed1ab_1.conda 546kB
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#10 23.47 pip-26.1.2-pyh8b19718_0.conda 1MB
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platforma-open.milaboratories.3d-structure-prediction.software.py-docker.
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platforma-open.milaboratories.3d-structure-prediction.software.py-docker.c57294107f92: digest: sha256:6516e709cede5d5769159706ffc2a967bb6373238964c9ae0f717f05600c6c7a size: 3860
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package/CHANGELOG.md
CHANGED
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@@ -1,5 +1,17 @@
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1
1
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# @platforma-open/milaboratories.3d-structure-prediction.software
|
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2
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3
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+
## 1.1.0
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4
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+
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5
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+
### Minor Changes
|
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6
|
+
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|
7
|
+
- 37da856: Export only confident structures. The PDB ResourceMap now contains only confident clonotypes — prediction succeeded AND the selected error metric is within threshold — and the `confident` / `predictionSuccessful` subset filter columns are no longer exported. Downstream blocks consume confident structures directly, with no all-vs-confident selection to make. The results table still shows every clonotype and every column (confidence values, failure reasons, warnings); failed and unconfident clonotypes simply have no downloadable PDB. Confident filtering is applied once, in the Python wrapper's manifest, so the PDB map is built by the existing stable path (no post-hoc rebuild).
|
|
8
|
+
|
|
9
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+
Clonotypes whose prediction succeeded but whose error exceeds the confidence threshold now carry a failure reason — "Prediction confidence above threshold (<value> Å)" — so the table explains why they have no downloadable structure (their error values remain visible).
|
|
10
|
+
|
|
11
|
+
Output column traces are now rooted in the Lead Selection filter when present, so predictions off the same dataset with different filters carry distinguishable provenance (dataset → lead selection → prediction) in downstream labels.
|
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12
|
+
|
|
13
|
+
The error-distribution histogram now shows the confidence threshold as a dashed vertical line (via a `pl7.app/graph/thresholds` annotation on the selected-metric column) — on the CDR-H3 page for the `cdrh3Mean` metric, or the Mean page for `overallMean`.
|
|
14
|
+
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3
15
|
## 1.0.7
|
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4
16
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5
17
|
### Patch Changes
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|
@@ -1 +1 @@
|
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1
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-
{"type":"python","platform":"linux-x64","registryURL":"https://bin.pl-open.science/","registryName":"platforma-open","remoteArtifactLocation":"software/platforma-open/milaboratories.3d-structure-prediction.software/py-archive/1.0.
|
|
1
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+
{"type":"python","platform":"linux-x64","registryURL":"https://bin.pl-open.science/","registryName":"platforma-open","remoteArtifactLocation":"software/platforma-open/milaboratories.3d-structure-prediction.software/py-archive/1.1.0.tgz","uploadPath":"software/platforma-open/milaboratories.3d-structure-prediction.software/py-archive/1.1.0.tgz"}
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@@ -1 +1 @@
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1
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-
{"type":"docker","platform":"linux-x64","remoteArtifactLocation":"containers.pl-open.science/milaboratories/pl-containers:platforma-open.milaboratories.3d-structure-prediction.software.py-docker.
|
|
1
|
+
{"type":"docker","platform":"linux-x64","remoteArtifactLocation":"containers.pl-open.science/milaboratories/pl-containers:platforma-open.milaboratories.3d-structure-prediction.software.py-docker.c57294107f92","entrypoint":["/usr/local/bin/_entrypoint.sh"]}
|
|
@@ -1 +1 @@
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|
|
1
|
-
{"name":"@platforma-open/milaboratories.3d-structure-prediction.software:immunebuilder-predict","docker":{"tag":"containers.pl-open.science/milaboratories/pl-containers:platforma-open.milaboratories.3d-structure-prediction.software.py-docker.
|
|
1
|
+
{"name":"@platforma-open/milaboratories.3d-structure-prediction.software:immunebuilder-predict","docker":{"tag":"containers.pl-open.science/milaboratories/pl-containers:platforma-open.milaboratories.3d-structure-prediction.software.py-docker.c57294107f92","entrypoint":["/usr/local/bin/_entrypoint.sh"],"cmd":["python","/app/run_immunebuilder.py"],"pkg":"/app"},"binary":{"type":"python","registry":"platforma-open","package":"software/platforma-open/milaboratories.3d-structure-prediction.software/py-archive/1.1.0.tgz","cmd":["python","{pkg}/run_immunebuilder.py"],"envVars":[],"runEnv":{"name":"@platforma-open/milaboratories.runenv-python-3:3.12.10-atls","type":"python","registry":"platforma-open","package":"software/platforma-open/milaboratories.runenv-python-3.12.10-atls/main/1.2.7-{os}-{arch}.tgz","python-version":"3.12.10","envVars":[],"binDir":"bin"},"toolset":"pip","dependencies":{"requirements":"requirements.txt"}}}
|
package/package.json
CHANGED
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
{
|
|
2
2
|
"name": "@platforma-open/milaboratories.3d-structure-prediction.software",
|
|
3
|
-
"version": "1.0
|
|
3
|
+
"version": "1.1.0",
|
|
4
4
|
"type": "module",
|
|
5
5
|
"description": "Block Software",
|
|
6
6
|
"block-software": {
|
|
@@ -42,7 +42,7 @@
|
|
|
42
42
|
},
|
|
43
43
|
"devDependencies": {
|
|
44
44
|
"@platforma-open/milaboratories.runenv-python-3": "1.8.6",
|
|
45
|
-
"@platforma-sdk/package-builder": "3.
|
|
45
|
+
"@platforma-sdk/package-builder": "3.13.0"
|
|
46
46
|
},
|
|
47
47
|
"scripts": {
|
|
48
48
|
"do-pack": "shx rm -f *.tgz && pl-pkg build && pnpm pack && shx mv platforma-open*.tgz package.tgz",
|
package/pkg-platforma-open-milaboratories.3d-structure-prediction.software-py-archive-1.1.0.tgz
ADDED
|
Binary file
|
|
@@ -4,9 +4,12 @@ Reads a batch TSV of clonotypes and predicts structures via ABodyBuilder2 or
|
|
|
4
4
|
NanoBodyBuilder2 (spec R22). Emits:
|
|
5
5
|
|
|
6
6
|
- Per-clonotype PDB files named `<sha1(clonotypeKey)>.pdb` (R30).
|
|
7
|
-
- `manifest.tsv` : (clonotypeKey, pdb_filename)
|
|
7
|
+
- `manifest.tsv` : (clonotypeKey, pdb_filename) — confident clonotypes only
|
|
8
|
+
(success AND selected metric ≤ threshold); drives the
|
|
9
|
+
exported/UI PDB ResourceMap.
|
|
8
10
|
- `confidence.tsv`: aggregate + per-residue confidence (Å error, R32-R36)
|
|
9
|
-
plus failureReason (R40) and warning columns
|
|
11
|
+
plus failureReason (R40) and warning columns — every row,
|
|
12
|
+
confident or not.
|
|
10
13
|
|
|
11
14
|
Dependencies (ImmuneBuilder, torch) ride the venv that pl-pkg's install-deps
|
|
12
15
|
creates. ANARCI and pdbfixer are not on PyPI; the atls runenv builds them
|
|
@@ -138,6 +141,18 @@ def _failure_reason_label(code: str) -> str:
|
|
|
138
141
|
def _warning_label(code: str) -> str:
|
|
139
142
|
return WARNING_LABELS.get(code, code)
|
|
140
143
|
|
|
144
|
+
# Failure-reason code for a successful prediction whose selected error metric
|
|
145
|
+
# is above the confidence threshold (so it's excluded from the PDB map). The
|
|
146
|
+
# code is stable for grouping; the human text (with the threshold value) is set
|
|
147
|
+
# per-run via RowResult.failure_reason_text.
|
|
148
|
+
CONFIDENCE_ABOVE_THRESHOLD_REASON = "confidence_above_threshold"
|
|
149
|
+
|
|
150
|
+
# Failure-reason code for a successful prediction whose selected confidence
|
|
151
|
+
# metric could not be computed (so no threshold comparison was possible). Kept
|
|
152
|
+
# distinct from CONFIDENCE_ABOVE_THRESHOLD_REASON so the table doesn't imply a
|
|
153
|
+
# numeric comparison that never happened.
|
|
154
|
+
CONFIDENCE_METRIC_UNAVAILABLE_REASON = "confidence_metric_unavailable"
|
|
155
|
+
|
|
141
156
|
MANIFEST_FIELDS = [KEY_COLUMN_PLACEHOLDER, "pdb_filename"]
|
|
142
157
|
|
|
143
158
|
|
|
@@ -183,6 +198,10 @@ class RowResult:
|
|
|
183
198
|
per_residue_json: str = ""
|
|
184
199
|
cdrh3_len: str = ""
|
|
185
200
|
failure_reason: str = ""
|
|
201
|
+
# Optional human text override; when set, used verbatim instead of the
|
|
202
|
+
# static FAILURE_REASON_LABELS lookup (lets us embed runtime values such as
|
|
203
|
+
# the confidence threshold).
|
|
204
|
+
failure_reason_text: str = ""
|
|
186
205
|
warnings: list[str] = field(default_factory=list)
|
|
187
206
|
pdb_filename: str = ""
|
|
188
207
|
|
|
@@ -208,7 +227,7 @@ class RowResult:
|
|
|
208
227
|
"perResidueError": self.per_residue_json,
|
|
209
228
|
"cdrh3Length": self.cdrh3_len,
|
|
210
229
|
"failureReason": self.failure_reason,
|
|
211
|
-
"failureReasonText": _failure_reason_label(self.failure_reason),
|
|
230
|
+
"failureReasonText": self.failure_reason_text or _failure_reason_label(self.failure_reason),
|
|
212
231
|
"warning": self.warning_str,
|
|
213
232
|
"warningText": self.warning_text,
|
|
214
233
|
}
|
|
@@ -543,13 +562,43 @@ def process_batch(
|
|
|
543
562
|
manifest_fields = [key_col if f == KEY_COLUMN_PLACEHOLDER else f for f in MANIFEST_FIELDS]
|
|
544
563
|
confidence_fields = build_confidence_fields(key_col)
|
|
545
564
|
|
|
565
|
+
# Build the summary BEFORE the confident-marking loop below, so its
|
|
566
|
+
# semantics stay stable: `succeeded` = a structure was produced (regardless
|
|
567
|
+
# of confidence) and `confidentCount` = the within-threshold subset. The
|
|
568
|
+
# loop then tags above-threshold / metric-unavailable rows with a failure
|
|
569
|
+
# reason for the per-row table; that must not retroactively inflate the
|
|
570
|
+
# summary's failure count or collapse `succeeded` onto `confidentCount`.
|
|
571
|
+
summary = _build_summary(results, metric, threshold)
|
|
572
|
+
|
|
573
|
+
# A structure was produced, but it isn't confident enough to export. Two
|
|
574
|
+
# distinct cases, surfaced as distinct failure reasons so the user (and any
|
|
575
|
+
# downstream tooling) can tell them apart — the confidence values still
|
|
576
|
+
# appear in the table either way. This is the single confident filter for
|
|
577
|
+
# the block.
|
|
578
|
+
for r in results:
|
|
579
|
+
if r.failure_reason or not r.pdb_filename:
|
|
580
|
+
continue
|
|
581
|
+
v = _metric_value(r, metric)
|
|
582
|
+
if v is None:
|
|
583
|
+
# The selected metric couldn't be computed (e.g. the CDR-H3 region
|
|
584
|
+
# produced no numbered residues) — no comparison was made.
|
|
585
|
+
r.failure_reason = CONFIDENCE_METRIC_UNAVAILABLE_REASON
|
|
586
|
+
r.failure_reason_text = "Confidence metric unavailable"
|
|
587
|
+
elif v > threshold:
|
|
588
|
+
r.failure_reason = CONFIDENCE_ABOVE_THRESHOLD_REASON
|
|
589
|
+
r.failure_reason_text = f"Prediction confidence above threshold ({threshold} Å)"
|
|
590
|
+
|
|
591
|
+
# The manifest selects which PDBs become the exported/UI ResourceMap: only
|
|
592
|
+
# clonotypes that have a structure and no failure reason. Failed and the
|
|
593
|
+
# low-confidence rows just marked are excluded, so the map is confident-only
|
|
594
|
+
# by construction.
|
|
546
595
|
with open(manifest_tsv, "w", newline="") as f:
|
|
547
596
|
writer = csv.DictWriter(
|
|
548
597
|
f, fieldnames=manifest_fields, delimiter="\t", lineterminator="\n"
|
|
549
598
|
)
|
|
550
599
|
writer.writeheader()
|
|
551
600
|
for r in results:
|
|
552
|
-
if r.pdb_filename:
|
|
601
|
+
if r.pdb_filename and not r.failure_reason:
|
|
553
602
|
writer.writerow({key_col: r.clonotype_key, "pdb_filename": r.pdb_filename})
|
|
554
603
|
|
|
555
604
|
with open(confidence_tsv, "w", newline="") as f:
|
|
@@ -558,7 +607,6 @@ def process_batch(
|
|
|
558
607
|
for r in results:
|
|
559
608
|
writer.writerow(r.to_tsv_row(key_col))
|
|
560
609
|
|
|
561
|
-
summary = _build_summary(results, metric, threshold)
|
|
562
610
|
if summary_json is not None:
|
|
563
611
|
summary_json.parent.mkdir(parents=True, exist_ok=True)
|
|
564
612
|
with open(summary_json, "w") as f:
|