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Merge timing-bench into rc175: battery.py timing, a three-set benchmark (myoglobin and cytochrome C from AlphaFold DB models, 4nwv from a moved deposited model) placed by molecular replacement, checked and timed per step

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Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
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leonarski_fandClaude Opus 5.5 committed 2026-10-15 09:25:34 +02:00
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@@ -32,6 +32,8 @@ rugnux_anomalous*/
# Test fixtures are checked in deliberately; add them with an explicit path.
!tests/**
# The timing benchmark's start models: public AlphaFold DB predictions (no measured cell, no sample)
!tools/battery/models/AF-*-model_v*.cif
# CMake configures GitInfo.cpp.in into the BINARY dir; a copy here is only ever the residue of an
# in-source configure, and a stale one shipped a wrong version string once already.
THIRD_PARTY_NOTICES.md
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@@ -72,6 +72,18 @@ These live in the source tree (see the path) rather than being fetched; traccc a
| [xbflash.qspi](https://github.com/Xilinx/XRT) | `tools/xbflash.qspi/` | Xilinx / AMD | Apache-2.0 | [xbflash-qspi.txt](licenses/xbflash-qspi.txt) |
| [wingetopt](https://github.com/alex85k/wingetopt) | `tools/wingetopt/` | Todd C. Miller; The NetBSD Foundation | ISC AND BSD-2-Clause | [wingetopt.txt](licenses/wingetopt.txt) |
## Data files in the repository
Not code and not linked into any binary: input files of the battery's timing benchmark
(`tools/battery/timing.json`), kept verbatim as downloaded.
| Component | Path | Copyright | License (SPDX) | License text |
|---|---|---|---|---|
| [AlphaFold Protein Structure Database](https://alphafold.ebi.ac.uk/) predictions AF-P68082-F1 and AF-P62894-F1 (v6), with their predicted aligned error | `tools/battery/models/` | DeepMind Technologies Limited; EMBL-EBI | CC-BY-4.0 | [alphafold-db.txt](licenses/alphafold-db.txt) |
The benchmark's third start model is made at run time from the deposited coordinates of PDB entry
4NWV, downloaded from the RCSB PDB (PDB data are CC0 1.0); nothing of it is committed.
## Runtime libraries and SDKs (shipped in binaries, not in the source tree)
| Component | Used by | License | Notice |
docs/ACKNOWLEDGEMENT.md
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@@ -616,6 +616,20 @@ J. Westbrook, Z. Feng, G. Gilliland, T. N. Bhat, H. Weissig, I. N. Shindyalov an
"The Protein Data Bank" (2000), Nucleic Acids Res. 28, 235-242
[doi:10.1093/nar/28.1.235](https://doi.org/10.1093/nar/28.1.235).
**The [AlphaFold Protein Structure Database](https://alphafold.ebi.ac.uk/)** (EMBL-EBI and Google
DeepMind) supplies the start models of the battery's timing benchmark: the predictions of horse
myoglobin (AF-P68082-F1) and bovine cytochrome c (AF-P62894-F1), model version 6, with their predicted
aligned error, kept unmodified in `tools/battery/models/` under CC BY 4.0. J. Jumper, R. Evans,
A. Pritzel et al., "Highly accurate protein structure prediction with AlphaFold" (2021), Nature 596,
583-589 [doi:10.1038/s41586-021-03819-2](https://doi.org/10.1038/s41586-021-03819-2); M. Varadi,
S. Anyango, M. Deshpande et al., "AlphaFold Protein Structure Database: massively expanding the
structural coverage of protein-sequence space with high-accuracy models" (2022), Nucleic Acids Res. 50,
D439-D444 [doi:10.1093/nar/gkab1061](https://doi.org/10.1093/nar/gkab1061); M. Varadi, D. Bertoni,
P. Magana et al., "AlphaFold Protein Structure Database in 2024: providing structure coverage for over
214 million protein sequences" (2024), Nucleic Acids Res. 52, D368-D375
[doi:10.1093/nar/gkad1011](https://doi.org/10.1093/nar/gkad1011). Its third start model is the
deposited model of PDB entry 4NWV, moved away from its place.
## Generative AI usage declaration
Large language models were used extensively in developing this code. Jungfraujoch development was
licenses/COLLECT.sh
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@@ -84,6 +84,9 @@ copy_license pegtl.txt gemmi_gph/gemmi/third_party/tao/LICENSE
copy_license xbflash-qspi.txt tools/xbflash.qspi/LICENSE
copy_license wingetopt.txt tools/wingetopt/LICENSE
# --- Data files in the repository --------------------------------------------------------------
copy_license alphafold-db.txt tools/battery/models/LICENSE.txt
# --- Runtime SDK license texts, copied from their system install (best effort) ---------------
# These come from outside the build tree; the committed copies are authoritative if absent here.
copy_license Qt6-LGPL-3.0.txt /usr/share/common-licenses/LGPL-3
licenses/alphafold-db.txt
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@@ -0,0 +1,429 @@
AlphaFold Protein Structure Database predictions (tools/battery/models/)
AF-P68082-F1-model_v6.cif, AF-P68082-F1-predicted_aligned_error_v6.json
myoglobin, Equus caballus (UniProt P68082), model version 6
AF-P62894-F1-model_v6.cif, AF-P62894-F1-predicted_aligned_error_v6.json
cytochrome c, Bos taurus (UniProt P62894), model version 6
Source: AlphaFold Protein Structure Database, https://alphafold.ebi.ac.uk/ (EMBL-EBI and Google
DeepMind), downloaded 2026-10-15 from https://alphafold.ebi.ac.uk/files/. The files are unmodified.
Licence: Creative Commons Attribution 4.0 International (CC BY 4.0),
https://creativecommons.org/licenses/by/4.0/ - the full legal code follows below.
Please cite: J. Jumper et al., "Highly accurate protein structure prediction with AlphaFold" (2021),
Nature 596, 583-589, doi:10.1038/s41586-021-03819-2; M. Varadi et al., "AlphaFold Protein Structure
Database: massively expanding the structural coverage of protein-sequence space with high-accuracy
models" (2022), Nucleic Acids Res. 50, D439-D444, doi:10.1093/nar/gkab1061; M. Varadi et al.,
"AlphaFold Protein Structure Database in 2024: providing structure coverage for over 214 million
protein sequences" (2024), Nucleic Acids Res. 52, D368-D375, doi:10.1093/nar/gkad1011.
The notice each model file carries (_pdbx_data_usage), verbatim:
ALPHAFOLD DATA, COPYRIGHT (2021) DEEPMIND TECHNOLOGIES LIMITED. THE INFORMATION
PROVIDED IS THEORETICAL MODELLING ONLY AND CAUTION SHOULD BE EXERCISED IN ITS
USE. IT IS PROVIDED "AS-IS" WITHOUT ANY WARRANTY OF ANY KIND, WHETHER EXPRESSED
OR IMPLIED. NO WARRANTY IS GIVEN THAT USE OF THE INFORMATION SHALL NOT INFRINGE
THE RIGHTS OF ANY THIRD PARTY. DISCLAIMER: THE INFORMATION IS NOT INTENDED TO BE
A SUBSTITUTE FOR PROFESSIONAL MEDICAL ADVICE, DIAGNOSIS, OR TREATMENT, AND DOES
NOT CONSTITUTE MEDICAL OR OTHER PROFESSIONAL ADVICE. IT IS AVAILABLE FOR
ACADEMIC AND COMMERCIAL PURPOSES, UNDER CC-BY 4.0 LICENCE.
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tools/battery/README.md
+71 -1
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@@ -231,7 +231,8 @@ export `JFJOCH_BATTERY_SITE=/data/battery/site.json`.
A relative `manifest` path is resolved against `tools/battery/`. `gpulock` is a command that
`rugnux` is prefixed with under `--gpulock`. At PSI it is a wrapper script that queues for one of
the shared GPU slots. Set it to `null` if you have no such wrapper. `pdb_cache` (optional) is where
the deposited models and their metadata are cached for `--model` and the REFMAC check.
the deposited models and their metadata are cached for `--model` and the REFMAC check. `baseline_timing`
(optional) is the timing run (`battery.py timing`, below) a new timing run is reported against.
`cod_cache` (optional, default `/data/battery/cod_cache`) caches the small molecules' COD structures,
and `shelxl` (optional; else `shelxl` on `PATH`, e.g. from CCP4) is the SHELXL the small-molecule
check calls - without one the check is skipped and says so.
@@ -248,6 +249,7 @@ $B run --rugnux $R --tier ci # 29 sets every recent relea
$B nullmodel --rugnux $R # the wrong-model null on its own (CI's second step)
$B run --rugnux $R --only 5reo,lyso_ref # named sets
$B run --rugnux $R --arm private # the private arm, on its own
$B timing --rugnux $R # the timing benchmark: 3 sets placed by MR (below)
```
Useful options:
@@ -346,6 +348,74 @@ at the top of the report; the sets' own rows in `results.json` are those of the
and exits with status 1 when a pair failed. It
adds 30 rugnux runs, about 6 minutes of rugnux on the RTX 5080 (measured: 6.1 min of WALL_TIME).
### The timing benchmark
`battery.py timing` is the run to repeat on every machine rugnux is measured on (the workstation, the
4x T4 server, a GB10, a Windows laptop, a Mac): three sets, each started from a model it has to place
by molecular replacement, so one run times the whole pipeline - reading, indexing, integration,
scaling, the space-group search, MR and model validation - and says whether its answers are right.
```
$B timing --rugnux $R [--gpulock] [--threads N] [--label L] [--baseline RUN|none]
```
| set | arm | start model (`--model`) | reference model it is checked against |
|---|---|---|---|
| `myob_x10sa` | inhouse | AlphaFold DB AF-P68082-F1 v6 (horse myoglobin, UniProt P68082), `models/` | 4DC8 |
| `cytc_x10sa` | inhouse | AlphaFold DB AF-P62894-F1 v6 (bovine cytochrome c, UniProt P62894), `models/` | `reference_model.cif` beside the data |
| `4nwv` | open | the deposited 4NWV, strict NCS expanded (45 chains), turned 30 deg about (0.36, 0.48, 0.80) through its centroid and shifted (12, -18, 25) A | 4NWV as deposited |
The two predictions are committed in `models/` exactly as the AlphaFold DB serves them, each with its
predicted aligned error under its own name, which rugnux finds beside the model and cuts the
prediction into rigid domains by. They are CC BY 4.0 (`models/LICENSE.txt`, `THIRD_PARTY_NOTICES.md`).
The moved 4NWV is not committed (10 MB): the runner makes it from the deposited coordinates in the
site's `pdb_cache` (fetched from the RCSB on first use, like every open-arm model) into the set's work
directory as `4nwv_moved.cif.gz`, with the transform in `timing.json`. That is far outside what the
rigid body corrects, so the model is rejected as read and MR places it. Each set otherwise runs the
battery's own command for its arm (above), so a timing run needs nothing beyond what the battery
needs, and a machine needs only those three dataset directories under its data roots
(`inhouse/myob_x10sa`, `inhouse/cytc_x10sa`, `open/4nwv`) and the usual site config.
A set passes when every check holds (`timing.py`; thresholds in `timing.json`):
| check | passes when |
|---|---|
| `space_group` | the battery's own verdict passes: lattice and space group against the reference, by the scorer's rules (the hand excepted) |
| `placed` | `MODEL_PLACEMENT` is `MR`: molecular replacement placed the model, and the R-factors, maps and model written are of that placement |
| `mr_group` | `MR_SPACE_GROUP` is the expected group, hand included (P 1 21 1, P 32 2 1, I 2 2 2): a model decides the hand |
| `r_free` | `R_FREE` at most 0.50 for the predictions and 0.35 for 4NWV. Measured: 0.44 (myoglobin, AlphaFold), 0.315 (4NWV after MR); the reference models placed by the rigid body give 0.246, 0.356 and 0.297; a random structure 0.586 |
| `confirmed` | `CC_MODEL_CONFIRMED_TO_D_MIN` is not `NONE`: some shell's CC(model, data) clears rugnux's empirical null |
| `placement_cc` | the placed model `p_model.pdb` has the reference model's intensities: the correlation of the two models' \|F\|^2, each shell normalised to its mean, 10-4 A, the best over the changes of basis the two lattices allow, is at least 0.30. \|F\| is the same for every origin and every symmetry copy, so this needs no superposition. Measured: 0.55 (myoglobin, AlphaFold against 4DC8: 0.9 A apart as models), 0.90 (cytochrome c), 0.96 (4NWV); a wrong placement 0.01-0.04, the cytochrome c placement relabelled to the other hand 0.18 |
`placement_cc` is independent of rugnux's own scores and is what catches a placement rugnux reports
as right: the myoglobin placement turned by 30 deg in a copy of its work directory, with rugnux's
report unchanged, fails it at 0.035, and the moved 4NWV start model at 0.011. A wrong model
(the cytochrome c prediction on the myoglobin data) is not placed by rugnux and fails `placed`.
The run is an ordinary run directory (`manifest.json`, `results.json`, `report.md`), so `list`,
`table`, `compare` and `keep` work on it. Each row carries `bench_verdict`, `bench_reason`,
`bench_checks` (`{check: [ok, value, limit]}`), `mr_seconds`, `mr_decision` and `steps` (seconds per
rugnux step, from the `TIMING step` lines of `p_log.txt`); the report opens with a **Timing benchmark**
section (the checks per set, then the step times), and the console prints both. `wall_s` is rugnux's
own WALL_TIME. The run exits with status 1 when a set failed a check or crashed. Its report is compared
against the site's `baseline_timing` (a timing run; none by default). As everywhere, `--gpulock`
marks the timing "NOT a reference": run it with the machine to itself when the numbers are the point.
On another machine: Python 3.9+ with `gemmi` and `numpy` (`pip install gemmi numpy`), a site config
whose data roots hold the three directories and whose `gpulock` is `null`, and the command above.
macOS runs it as Linux does. Windows has no process groups and no `flock`, which a timing run does not
need; run it as `python -X utf8 tools\battery\battery.py ...` (the report and the console table are
UTF-8), with `--rugnux` naming `rugnux.exe` (the run directory keeps its own copy, so any DLL it needs
must be found on `PATH`). Neither has been tried yet.
Measured on the workstation (RTX 5080, rc175): myoglobin 10 s, cytochrome c 13 s, 4NWV 106 s
(of which MR 34 s and model validation 8 s; about 16 GB peak resident memory, the most of the
three by far). **cytochrome c fails today**: the prediction is a monomer and the crystal holds
three copies related by a pseudo-translation; MR places three copies in both P 32 2 1 (R-free 0.427)
and P 31 2 1 (0.437), the margin is under the 0.03 it needs to choose, and so it places neither
(`MR_DECISION= UNDECIDED`). The battery's own three-copy reference model, given to `--mr`, decides
the hand at once. The set stays in the benchmark and fails until MR can decide this case.
### Stress: hunting crashes that do not reproduce
One rugnux process runs several GPU users at once (image workers on every card, the space-group
tools/battery/battery.py
+62 -5
View File
@@ -19,6 +19,11 @@ Usage (README.md in this directory is the full guide):
the wrong-model null on its own, in a run directory of
its own: exit 1 if a pair failed (CI runs it as its own
step, after run --tier ci --no-nullmodel)
battery.py timing --rugnux BIN [--label L] [--build-dir DIR] [--gpulock] [--threads N] [--baseline RUN|none]
the timing benchmark (timing.json): myob_x10sa and cytc_x10sa
from their AlphaFold DB models, 4nwv from its deposited model
moved away, all placed by molecular replacement; checks each
answer and prints wall and step times; exit 1 if one is wrong
battery.py keep RUN --as workstation|server copy a finished open/inhouse run's report.md, results.json
and manifest.json into results/<role>/<run>/ (committed);
refuses a private run
@@ -58,7 +63,6 @@ A run that did not finish is never compared or reported on unless asked (--allow
import argparse
import concurrent.futures
import datetime
import fcntl
import hashlib
import json
import os
@@ -81,6 +85,7 @@ import score # noqa: E402
import model_check # noqa: E402 the deposited model (--model); REFMAC check (--model-check)
import nullmodel # noqa: E402 a wrong --model changes nothing and is recognised as wrong
import shelx_check # noqa: E402 SHELXL refinement of a small molecule's COD structure
import timing # noqa: E402 the timing benchmark: three sets placed by molecular replacement
import depdata_check # noqa: E402 our merge vs the depositor's data, shell by shell
PDB_ID = re.compile(r"^[0-9][A-Za-z0-9]{3}$")
@@ -341,7 +346,10 @@ def run_logged(cmd, wd, timeout, env=None):
return None
finally:
if proc.poll() is None:
os.killpg(proc.pid, signal.SIGKILL)
if hasattr(os, "killpg"):
os.killpg(proc.pid, signal.SIGKILL)
else: # Windows: no process groups
proc.kill()
proc.wait()
@@ -397,6 +405,11 @@ def run_one(run_dir, binary, e, opts):
meta, row["model_note"] = deposited_model(e, opts)
if meta:
row["model"], row["rfree_deposited"] = meta["xyz"], meta["rfree"]
reference = row["model"]
if e.get("timing"):
# the timing benchmark: rugnux starts from a model it has to place, and the set's own model
# (above) is the reference the placement is checked against
row["model"] = timing.start_model(e["timing"]["start"], wd, opts["pdb_cache"])
cmd = command(binary, e, opts, row["model"])
row["cmd"] = " ".join(cmd)
t0 = time.time()
@@ -417,7 +430,9 @@ def run_one(run_dir, binary, e, opts):
row["wall_s"] = row["rugnux_wall_s"] if row["rugnux_wall_s"] is not None else row["elapsed_s"]
if row["rfree"] and row["rfree_deposited"]:
row["rfree_ratio"] = round(row["rfree"] / row["rfree_deposited"], 4)
if e["reference"] == "deposition" and row["model"] and os.path.exists(os.path.join(wd, "p.mtz")):
if e.get("timing"):
row.update(timing.check(e["timing"], row, wd, reference))
elif e["reference"] == "deposition" and row["model"] and os.path.exists(os.path.join(wd, "p.mtz")):
row.update(depdata_check.check_set(wd, e["id"], opts["pdb_cache"]))
if opts["model_check"] and e["arm"] == "open":
row.update(check_model(e, wd))
@@ -551,6 +566,7 @@ def run_sets(site, sets, arms, binary_src, build_dir, label, opts, subset, basel
report.check_baseline(baseline, private)
lock_fh = None
if lock:
import fcntl # POSIX only; a subset run (and Windows) takes no lock
os.makedirs(os.path.dirname(lock), exist_ok=True)
lock_fh = open(lock, "w")
try:
@@ -564,7 +580,8 @@ def run_sets(site, sets, arms, binary_src, build_dir, label, opts, subset, basel
run_dir = os.path.join(opts["runs_root"],
f"{stamp}_{info['git']}_{label}" + ("_private" if private else ""))
os.makedirs(run_dir) # never reuse or overwrite a run directory
binary = os.path.join(run_dir, "bin", "rugnux")
# rugnux.exe keeps its extension, which Windows needs to run it
binary = os.path.join(run_dir, "bin", "rugnux" + os.path.splitext(binary_src)[1])
os.makedirs(os.path.dirname(binary))
shutil.copy2(binary_src, binary)
info.update(copied_from=os.path.realpath(binary_src), sha256=sha256(binary))
@@ -694,6 +711,32 @@ def cmd_nullmodel(a, site):
", ".join(f"{r['set']} --model {r['model']} ({r['reason']})" for r in bad))
def cmd_timing(a, site):
"""The timing benchmark (timing.json): its three sets, each with --model <a model it has to place>,
in a run directory of its own; prints the checks and the step times, exits 1 when a set failed."""
sets = []
for t in timing.load():
e = select(site, [t["arm"]], t["set"], None)[0]
e["timing"] = t
sets.append(e)
opts = {"threads": a.threads, "timeout": a.timeout, "model_check": False,
"pdb_cache": site.get("pdb_cache") or model_check.DEFAULT_CACHE,
"cod_cache": site.get("cod_cache") or shelx_check.DEFAULT_CACHE, "shelxl": None,
"gpulock": site["gpulock"] if a.gpulock else None, "extra_args": a.extra.split(),
"runs_root": a.runs_root or site["runs_root"], "nullmodel": False}
if a.gpulock and not site.get("gpulock"):
sys.exit("--gpulock: the site config names no gpulock")
baseline = None if a.baseline == "none" else a.baseline or site.get("baseline_timing")
run_dir = run_sets(site, sets, sorted({e["arm"] for e in sets}), a.rugnux, a.build_dir, a.label or "timing",
opts, "timing benchmark", baseline)
res = json.load(open(os.path.join(run_dir, "results.json")))
print("\n" + timing.console(res), flush=True)
bad = [r for r in res if r.get("bench_verdict") != "pass" or r["verdict"] == "crash"]
if bad:
sys.exit(f"timing benchmark: {len(bad)} of {len(res)} sets failed: " +
"; ".join(f"{r['set']} ({r.get('bench_reason') or r.get('reason')})" for r in bad))
KEPT_ROOT = os.path.join(HERE, "results")
KEPT_FILES = ("report.md", "results.json", "manifest.json")
PUBLIC_ARMS = {"open", "inhouse"}
@@ -1092,6 +1135,20 @@ def main():
nm.add_argument("--timeout", type=int, default=10800, help="per rugnux run, in s")
nm.add_argument("--runs-root")
tb = sub.add_parser("timing", help="the timing benchmark: three sets placed by molecular replacement, "
"checked and timed per step (timing.json); fail on any wrong answer")
tb.add_argument("--rugnux", required=True)
tb.add_argument("--label", help="short name, part of the run directory's name (default: timing)")
tb.add_argument("--build-dir", help="build tree whose CMakeCache.txt records the flags")
tb.add_argument("--gpulock", action="store_true",
help="queue each rugnux behind the site's GPU lock (timing is then not a reference)")
tb.add_argument("--threads", type=int, default=0, help="-N for rugnux (default: its own choice)")
tb.add_argument("--timeout", type=int, default=10800, help="per rugnux run, in s")
tb.add_argument("--extra", default="", help="extra rugnux arguments, applied to every set")
tb.add_argument("--baseline", help="earlier timing run to report the delta against (default: the "
"site's baseline_timing; 'none' for no delta)")
tb.add_argument("--runs-root")
kp = sub.add_parser("keep", help="copy a run's report.md, results.json and manifest.json into "
"results/<role>/<run>/ (open and inhouse runs only)")
kp.add_argument("run")
@@ -1171,7 +1228,7 @@ def main():
report.SHELXL = shelx_check.find_shelxl(site.get("shelxl"))
report.MANIFESTS = {arm: {e["id"]: e for e in load_sets(site, arm)}
for arm, cfg in site["arms"].items() if os.path.exists(cfg["manifest"])}
{"run": cmd_run, "nullmodel": cmd_nullmodel, "keep": cmd_keep, "stress": cmd_stress, "list": cmd_list, "compare": cmd_compare, "table": cmd_table, "report": cmd_report,
{"run": cmd_run, "nullmodel": cmd_nullmodel, "timing": cmd_timing, "keep": cmd_keep, "stress": cmd_stress, "list": cmd_list, "compare": cmd_compare, "table": cmd_table, "report": cmd_report,
"abort": cmd_abort, "recheck": cmd_recheck, "discover": cmd_discover, "refs": cmd_refs, "remap": cmd_remap}[a.cmd](a, site)
tools/battery/models/AF-P62894-F1-model_v6.cif
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tools/battery/models/AF-P62894-F1-predicted_aligned_error_v6.json
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@@ -0,0 +1 @@
[{"predicted_aligned_error":[[0,1,3,7,7,7,8,10,10,11,13,13,14,14,16,15,14,14,18,16,15,17,20,21,18,18,19,18,17,18,18,17,15,17,17,15,13,15,18,18,17,19,20,19,24,23,22,22,21,20,23,22,19,20,24,20,21,19,16,15,11,10,10,15,11,10,14,16,12,13,18,16,16,18,19,18,22,23,18,19,17,17,16,18,15,11,12,10,10,9,7,9,7,6,9,9,6,8,11,9,11,11,12,13,16],[2,0,1,1,2,2,2,2,3,4,4,4,7,6,7,7,8,11,9,8,6,5,7,8,8,6,10,9,9,10,9,10,8,7,8,7,5,6,8,7,7,11,8,8,8,8,12,9,10,11,10,12,10,9,10,9,9,7,7,6,4,3,3,5,5,2,4,6,6,5,8,6,10,9,9,9,10,10,8,9,9,9,7,10,6,6,5,4,3,2,4,3,2,2,3,3,2,2,3,3,2,4,5,6,6],[1,1,0,1,1,2,1,1,1,2,1,1,2,2,2,2,2,2,2,2,2,2,2,3,2,2,3,3,3,3,3,2,3,2,2,2,2,3,3,3,3,3,3,3,3,3,3,4,3,4,4,4,4,3,4,3,3,3,3,3,2,2,2,2,2,2,2,3,2,2,2,3,3,3,3,3,3,3,3,3,3,3,2,3,2,2,2,2,1,1,2,1,1,1,1,1,1,1,1,1,1,1,2,2,3],[2,1,1,0,1,1,1,1,1,1,1,1,1,1,1,1,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,3,3,2,3,3,2,3,3,3,3,3,3,3,3,3,3,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,3,2,2,3,3,3,3,3,3,2,2,2,2,2,2,2,2,1,1,1,1,1,1,1,1,1,1,1,1,1,1,2,3],[2,1,1,1,0,1,1,1,1,1,1,1,1,1,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,3,3,3,3,2,3,3,3,3,3,3,3,3,3,3,3,3,3,3,2,2,2,2,2,2,2,2,2,2,2,2,2,2,3,3,3,3,3,3,3,3,3,2,2,2,2,2,2,2,2,1,1,2,1,1,1,1,1,1,1,1,1,1,1,2,2],[2,1,1,1,1,0,1,1,1,1,1,1,1,1,1,1,2,2,1,2,1,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,3,3,2,2,2,2,3,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,1,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,1,1,2,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,2,3],[2,1,1,1,1,1,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,2,2,2,2,2,2,2,1,2,1,1,2,2,1,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,1,2,2,1,1,2,2,1,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,2,2],[2,1,1,1,1,1,1,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,2,2,2,2,2,1,2,1,2,1,1,1,2,1,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,1,2,2,1,1,2,2,1,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,1,1,2,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,2,2],[2,1,1,1,1,1,1,1,0,1,1,1,1,1,1,1,1,1,1,1,1,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,3,2,2,2,3,2,3,2,2,2,2,2,2,2,2,2,2,2,1,2,2,2,2,2,2,2,2,2,2,2,2,2,1,2,1,1,2,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,2,2],[2,1,1,1,1,1,1,1,1,0,1,1,1,1,1,1,1,1,1,1,1,1,2,2,2,2,1,1,1,1,1,1,1,1,1,1,1,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,1,1,2,1,1,1,1,1,1,1,1,1,2,2,2,2,2,2,2,2,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,2,2],[2,1,1,1,1,1,1,1,1,1,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,2,2,2,2,2,2,2,2,1,2,2,2,2,2,2,2,2,2,2,2,2,1,1,1,1,1,1,1,1,1,1,1,1,1,1,2,1,1,2,2,2,2,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,2],[2,2,1,1,1,1,1,1,1,1,1,0,1,1,1,1,1,1,1,1,1,2,2,2,2,2,2,1,1,1,1,1,1,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,1,2,2,2,1,1,1,1,1,1,1,1,1,1,1,1,1,1,2,2],[3,2,1,1,1,1,1,1,1,1,1,1,0,1,1,1,1,1,1,1,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,3,2,2,2,2,2,3,2,2,3,3,3,3,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,1,2,1,2,2,2,2,2,1,2,2,1,1,1,1,1,1,2,2,1,2,2,3],[3,2,2,1,1,1,1,1,1,1,1,1,1,0,1,1,1,1,1,1,1,2,2,2,2,2,1,1,1,1,1,1,1,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,1,2,2,2,2,2,2,2,2,2,2,2,1,2,1,2,1,1,2,2,2,2,1,1,2,1,1,1,1,1,1,2,2,2,2,2,3],[3,2,2,1,1,1,1,1,1,1,1,1,1,1,0,1,1,1,1,1,1,1,1,2,1,1,1,1,1,1,1,1,1,1,2,1,2,2,2,2,2,2,2,2,2,2,1,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,1,2,1,1,1,1,1,2,2,2,2,2,2,2,2,1,1,1,1,1,1,1,1,2,2,1,1,1,1,1,1,1,1,1,1,1,1,1,2,2],[3,2,2,2,2,1,1,1,1,1,1,1,1,1,1,0,1,1,1,1,1,1,2,2,1,2,1,1,1,1,1,1,1,1,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,1,2,2,1,2,2,2,2,2,2,2,1,1,1,2,1,1,2,2,1,2,2,2],[4,2,2,2,2,2,2,1,1,1,1,1,1,1,1,1,0,1,1,1,1,2,2,2,2,2,1,1,1,1,1,1,1,2,2,2,2,3,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,3,3,3,3,3,2,2,2,3,2,2,2,2,2,2,2,2,2,2,3,2,2,3,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,3],[4,2,2,2,2,2,2,1,1,1,1,1,1,1,1,1,1,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,2,2,2,2,2,2,2,1,2,2,1,2,1,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,1,2,2,1,2,2,2,2,2,2,2,2,1,1,1,2,1,2,2,2,2,2,2,2,2,2,1,2,2,1,1,2,2,1,1,2,2],[3,2,2,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,2,1,2,1,1,1,1,1,1,1,1,1,1,2,2,2,2,2,2,2,2,2,2,1,2,2,2,1,2,2,2,1,1,2,1,2,2,2,2,2,2,1,2,1,1,1,2,1,1,2,2,2,2,1,2,1,1,1,1,1,1,1,1,1,1,1,1,2],[3,2,2,1,2,2,1,1,1,1,1,1,1,1,1,1,1,1,1,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,2,2,2,2,1,1,1,2,1,1,1,1,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,1,2,2,2,2,2,2,2,2,2,2,2,1,1,1,1,1,1,1,1,1,1,2],[3,2,2,2,2,2,2,1,2,2,1,1,1,1,1,1,1,1,1,1,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,2,2,2,2,2,2,2,2,2,1,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,1,1,1,1,1,1,1,2],[4,3,2,2,2,2,2,2,2,2,2,1,2,2,2,1,2,1,1,1,1,0,1,1,1,1,1,2,2,2,2,1,1,1,1,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,3,3,3,3,3,3,3,3,3,2,2,3,3,2,2,2,3,2,2,3,3,2,3,3,3,3,3,3,2,3,2,2,2,2,2,2,3,3,3,3,2,2,3,2,2,2,2,2,1,2,1,1,1,2,2],[4,3,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,1,1,1,1,0,1,1,1,1,2,2,2,1,1,1,1,1,1,2,2,2,2,2,2,2,2,2,2,2,2,2,3,3,3,3,3,3,3,3,2,2,2,2,2,3,2,2,2,3,2,2,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,2,2,2,2,2,2,2,2,2Line truncated
tools/battery/models/AF-P68082-F1-model_v6.cif
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tools/battery/models/AF-P68082-F1-predicted_aligned_error_v6.json
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[{"predicted_aligned_error":[[0,2,4,7,10,12,9,10,14,14,13,15,17,18,15,18,21,21,19,22,24,22,26,26,24,25,27,26,23,26,27,26,24,28,28,26,25,28,26,25,28,28,27,28,28,28,29,29,29,29,28,28,28,28,29,29,28,29,29,28,29,28,27,27,26,26,25,24,24,22,21,20,18,19,18,16,14,16,13,10,10,11,12,13,18,17,15,20,21,20,19,22,23,23,23,25,25,24,25,25,22,19,22,23,18,19,24,21,18,21,23,20,19,24,23,19,22,25,23,21,24,23,19,20,20,20,15,15,17,14,12,12,14,11,9,14,13,11,12,14,14,12,16,16,13,16,19,15,17,21,21,22,21,21],[3,0,1,2,5,5,3,5,7,6,6,9,11,10,11,12,11,12,12,14,15,14,17,18,14,16,17,16,14,17,18,15,15,19,17,18,16,18,17,17,20,18,17,20,21,22,21,20,21,20,21,20,18,19,21,19,19,20,21,20,21,21,18,19,18,18,16,16,15,13,12,14,11,13,13,8,7,9,8,5,5,7,7,7,11,10,8,12,12,12,11,13,14,14,13,14,17,15,15,16,14,11,14,13,12,12,14,13,10,14,13,13,11,13,13,12,12,14,13,11,11,11,10,10,9,10,6,7,8,7,5,7,9,4,6,8,6,5,8,10,6,6,8,8,7,10,12,9,10,12,13,13,12,13],[3,1,0,1,1,2,2,1,2,2,2,2,3,4,3,3,4,3,4,4,5,4,5,6,5,4,6,6,5,5,7,5,5,6,7,6,6,6,7,6,7,7,6,6,7,8,7,7,8,7,7,8,7,8,8,7,6,8,8,7,7,6,6,6,6,5,5,5,5,4,4,4,3,3,3,3,2,2,3,2,2,2,3,3,4,4,3,4,5,4,4,5,5,5,5,5,6,6,5,5,5,4,5,5,3,3,5,4,3,4,5,3,3,5,5,4,4,5,5,4,4,4,4,3,3,3,2,3,4,2,2,2,2,1,2,2,2,2,2,3,3,2,3,3,3,3,4,5,6,5,5,5,6,6],[3,1,1,0,1,1,1,1,1,2,2,2,2,2,3,2,3,3,3,3,4,3,4,4,3,3,4,4,3,4,4,3,4,4,4,4,4,5,5,4,5,5,5,5,5,6,5,5,6,6,6,5,5,5,6,5,5,5,6,5,5,5,4,4,4,4,3,4,3,3,3,3,3,2,3,2,2,2,2,2,2,2,2,3,3,3,3,3,4,4,4,4,5,4,4,5,5,5,4,4,4,3,3,4,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,2,3,2,2,2,2,1,2,2,1,2,2,2,2,2,2,2,2,3,3,3,3,3,3,4,5,4,5,5,5],[4,2,1,1,0,1,1,1,1,1,1,1,2,2,2,2,2,2,2,3,3,3,3,3,3,3,4,4,3,4,4,4,4,4,4,5,5,5,5,5,5,5,5,5,6,6,5,5,6,5,5,5,5,5,5,5,4,5,5,4,5,5,4,4,4,4,3,3,3,3,3,3,3,2,2,2,2,2,2,2,2,2,3,3,3,3,3,3,3,4,4,4,4,4,4,5,5,5,5,4,4,3,4,4,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,2,2,2,3,2,2,2,2,2,2,2,2,2,2,2,2,2,3,3,3,3,3,3,3,4,4,4,4,5,5,5,6],[4,2,1,1,1,0,1,1,1,1,1,2,1,2,2,2,2,2,2,3,3,3,3,3,2,3,3,3,3,3,3,3,3,4,4,4,4,4,4,4,4,4,5,4,5,5,4,5,5,5,5,4,4,4,5,4,3,4,5,4,4,4,3,4,4,3,3,3,3,3,3,3,3,2,3,2,2,2,2,2,2,2,3,3,3,4,4,3,4,4,4,4,4,4,4,5,5,5,4,4,4,4,3,3,3,3,3,3,3,2,3,2,2,2,2,2,2,2,3,2,2,3,2,2,2,2,2,1,2,2,1,1,2,2,2,2,2,2,2,2,3,3,3,3,3,4,4,4,4,5,5,5,5,6],[4,2,1,1,1,1,0,1,1,1,1,1,1,1,1,1,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,4,3,4,3,3,3,3,3,3,3,3,3,3,3,2,2,2,2,2,2,2,2,2,2,2,1,2,1,1,1,1,1,2,2,2,2,2,2,2,2,2,3,3,3,3,3,3,3,3,3,3,3,3,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,1,1,1,1,1,1,1,1,1,2,2,1,2,2,2,2,2,2,2,2,3,3,3,3,3,3,4,4],[3,2,1,1,1,1,1,0,1,1,1,1,1,1,1,1,1,1,1,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,2,3,2,2,2,2,2,2,2,2,2,2,2,2,1,2,1,1,1,1,1,1,2,2,2,2,2,2,2,2,2,2,3,2,2,3,3,3,3,3,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,1,1,1,1,1,1,1,1,1,1,1,1,1,2,2,2,2,2,2,2,2,3,3,3,3,3,4,4],[3,2,1,1,1,1,1,1,0,1,1,1,1,1,1,1,1,1,2,2,2,2,2,2,2,2,2,2,2,3,3,2,3,3,3,3,3,4,4,3,4,4,4,4,4,4,4,4,4,4,4,4,3,4,4,3,3,3,4,3,3,3,3,3,3,2,2,2,2,2,2,2,2,2,2,2,1,1,1,1,2,2,2,2,2,3,3,2,3,3,3,3,3,3,3,4,4,4,3,3,3,3,3,3,3,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,1,1,1,1,1,1,1,1,2,2,2,2,2,2,2,2,2,2,3,3,3,3,3,4,4,4,5],[4,2,1,1,1,1,1,1,1,0,1,1,1,1,1,1,1,1,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,3,3,3,3,3,3,3,3,3,3,3,3,4,3,3,4,3,3,3,3,3,3,3,3,3,3,3,3,3,2,2,2,2,2,2,2,2,2,2,2,2,2,2,1,2,2,2,2,2,2,2,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,1,2,2,1,1,1,1,1,2,2,2,2,2,2,2,3,2,3,3,3,3,4,4,4,4,4,4],[4,2,1,1,1,1,1,1,1,1,0,1,1,1,1,1,1,1,1,1,2,1,2,2,1,2,2,2,2,2,2,2,2,2,2,2,2,2,3,2,2,3,3,3,3,3,3,3,3,3,3,3,3,3,3,2,2,3,2,2,2,2,2,2,2,2,2,2,2,1,1,1,1,1,1,1,1,1,1,1,1,2,2,2,2,2,2,2,2,2,2,2,2,2,2,3,3,2,3,2,2,2,2,2,2,2,2,2,2,2,2,1,1,2,1,1,2,2,1,1,2,2,2,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,2,2,2,2,2,2,2,2,3,3,3,3,3,4,4],[3,2,1,1,1,1,1,1,1,1,1,0,1,1,1,1,1,1,1,1,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,3,2,3,3,2,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,2,3,3,2,2,2,2,2,2,2,2,2,2,2,2,2,1,1,1,1,1,1,1,1,2,2,2,2,2,2,2,3,3,2,3,2,2,2,3,3,3,3,3,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,1,2,2,2,1,1,1,1,1,1,1,1,1,2,1,2,2,2,2,2,2,2,3,3,3,3,3,3,3,4,4],[4,2,2,2,1,1,1,1,1,1,1,1,0,1,1,1,1,1,1,1,2,2,2,2,2,2,2,2,2,2,2,2,3,3,3,3,3,3,3,3,3,4,4,4,4,4,3,4,4,4,4,3,3,3,3,3,3,3,3,3,3,3,2,2,2,2,2,2,2,2,2,2,2,2,2,2,1,1,2,1,2,2,2,2,2,2,3,3,3,3,3,3,3,3,3,4,4,4,3,3,3,3,3,3,3,2,2,2,2,2,2,2,2,2,2,2,2,2,2,1,2,2,2,2,2,2,2,2,1,2,1,1,2,2,1,2,2,2,2,2,2,2,3,3,3,3,3,3,3,4,4,4,4,5],[4,2,2,2,2,1,1,1,1,1,1,1,1,0,1,1,1,1,1,1,1,1,2,2,1,2,2,2,2,2,2,2,2,2,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,2,2,2,2,2,2,2,2,2,2,1,2,2,2,1,2,2,1,2,2,2,2,2,2,2,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,2,2,2,2,2,2,2,2,1,2,2,1,2,2,1,1,2,2,2,2,2,2,2,1,1,2,1,1,2,2,2,2,2,2,2,2,3,2,3,3,3,3,3,3,4,4,4,4,4,4],[4,2,2,2,2,1,1,1,1,1,1,1,1,1,0,1,1,1,1,1,1,1,1,1,1,1,2,2,1,2,2,2,2,2,2,2,2,2,3,2,2,3,3,3,3,3,3,3,3,3,3,3,3,3,2,2,2,2,2,2,2,2,2,2,2,2,1,2,2,1,1,1,1,1,1,1,1,1,1,1,2,2,2,2,2,2,2,3,3,3,3,3,3,3,3,3,3,3,3,3,3,2,2,2,2,2,2,2,2,2,2,1,1,1,1,1,2,2,1,1,2,2,2,1,1,2,2,1,1,1,1,2,2,2,1,2,2,2,2,2,2,2,2,3,3,3,3,3,3,3,4,3,4,4],[5,2,2,2,2,2,2,1,1,1,1,1,1,1,1,0,1,1,1,1,1,1,2,2,2,2,2,2,2,2Line truncated
tools/battery/models/LICENSE.txt
+429
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AlphaFold Protein Structure Database predictions (tools/battery/models/)
AF-P68082-F1-model_v6.cif, AF-P68082-F1-predicted_aligned_error_v6.json
myoglobin, Equus caballus (UniProt P68082), model version 6
AF-P62894-F1-model_v6.cif, AF-P62894-F1-predicted_aligned_error_v6.json
cytochrome c, Bos taurus (UniProt P62894), model version 6
Source: AlphaFold Protein Structure Database, https://alphafold.ebi.ac.uk/ (EMBL-EBI and Google
DeepMind), downloaded 2026-10-15 from https://alphafold.ebi.ac.uk/files/. The files are unmodified.
Licence: Creative Commons Attribution 4.0 International (CC BY 4.0),
https://creativecommons.org/licenses/by/4.0/ - the full legal code follows below.
Please cite: J. Jumper et al., "Highly accurate protein structure prediction with AlphaFold" (2021),
Nature 596, 583-589, doi:10.1038/s41586-021-03819-2; M. Varadi et al., "AlphaFold Protein Structure
Database: massively expanding the structural coverage of protein-sequence space with high-accuracy
models" (2022), Nucleic Acids Res. 50, D439-D444, doi:10.1093/nar/gkab1061; M. Varadi et al.,
"AlphaFold Protein Structure Database in 2024: providing structure coverage for over 214 million
protein sequences" (2024), Nucleic Acids Res. 52, D368-D375, doi:10.1093/nar/gkad1011.
The notice each model file carries (_pdbx_data_usage), verbatim:
ALPHAFOLD DATA, COPYRIGHT (2021) DEEPMIND TECHNOLOGIES LIMITED. THE INFORMATION
PROVIDED IS THEORETICAL MODELLING ONLY AND CAUTION SHOULD BE EXERCISED IN ITS
USE. IT IS PROVIDED "AS-IS" WITHOUT ANY WARRANTY OF ANY KIND, WHETHER EXPRESSED
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ACADEMIC AND COMMERCIAL PURPOSES, UNDER CC-BY 4.0 LICENCE.
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tools/battery/report.py
+2
View File
@@ -12,6 +12,7 @@ import depdata_check
import nullmodel
import score
import shelx_check
import timing
from render import Doc, ratio_dots, verdict_bars
# A change smaller than these is treated as run-to-run noise. They are a starting point, to be
@@ -408,6 +409,7 @@ def build(run_dir, baseline=None, allow_incomplete=False):
null_path = os.path.join(run_dir, "nullmodel_results.json")
if os.path.exists(null_path):
nullmodel.section(doc, json.load(open(null_path)))
timing.section(doc, res)
if not res: # the wrong-model null on its own (battery.py nullmodel): that section is the report
return doc
tools/battery/site.example.json
+1
View File
@@ -5,6 +5,7 @@
"gpulock": null,
"baseline": null,
"baseline_private": null,
"baseline_timing": null,
"pdb_cache": "/path/to/battery/pdb_cache",
"cod_cache": "/path/to/battery/cod_cache",
"shelxl": null,
tools/battery/timing.json
+17
View File
@@ -0,0 +1,17 @@
{
"about": "Timing benchmark (README: 'The timing benchmark'): three sets, each started from a model rugnux has to place by molecular replacement, timed per step and checked for a right answer. 'start' is the model given to --model: an AlphaFold DB prediction committed in models/ (with its predicted aligned error beside it), or a deposited entry from the site's pdb_cache moved by a fixed rigid-body transform (strict NCS expanded first, then x' = R (x - c) + c + t, R a rotation by 'deg' about the unit 'axis', c the centroid of the expanded asymmetric unit, t 'shift' in A). The reference model the placement is checked against is the one the battery itself uses for the set (its manifest row's 'model', else the PDB entry of the set id). 'expect': 'mr_sgno' the space group the placed model is in (the model decides the hand), 'rfree_max' the highest R_FREE accepted, 'cc_min' the lowest correlation of the placed model's intensities with the reference model's (shell-normalised, 10-4 A, best over the lattice's reindexing operators).",
"sets": [
{"set": "myob_x10sa", "arm": "inhouse",
"start": {"alphafold": "models/AF-P68082-F1-model_v6.cif",
"why": "AlphaFold DB AF-P68082-F1 v6: myoglobin, Equus caballus (UniProt P68082), the species of the battery's reference model 4DC8 (horse heart). No heme"},
"expect": {"mr_sgno": 4, "rfree_max": 0.50, "cc_min": 0.30}},
{"set": "cytc_x10sa", "arm": "inhouse",
"start": {"alphafold": "models/AF-P62894-F1-model_v6.cif",
"why": "AlphaFold DB AF-P62894-F1 v6: cytochrome c, Bos taurus (UniProt P62894), the protein of the battery's reference model (bovine heart, placed with 6FF5). No heme; three copies to place, related by a pseudo-translation"},
"expect": {"mr_sgno": 154, "rfree_max": 0.50, "cc_min": 0.30}},
{"set": "4nwv", "arm": "open",
"start": {"moved": {"pdb": "4nwv", "axis": [0.36, 0.48, 0.80], "deg": 30.0, "shift": [12.0, -18.0, 25.0]},
"why": "the deposited model of 4NWV (I222, a virus capsid: 3 chains and 14 strict NCS operators, 45 chains once expanded), turned 30 deg and shifted 33 A: far outside what the rigid body corrects, so it is rejected and molecular replacement places the whole asymmetric unit"},
"expect": {"mr_sgno": 23, "rfree_max": 0.35, "cc_min": 0.30}}
]
}
tools/battery/timing.py
+208
View File
@@ -0,0 +1,208 @@
"""The timing benchmark: three sets, each started from a model rugnux has to place by molecular
replacement, timed per step and checked for a right answer.
timing.json lists the sets (README, 'The timing benchmark'). Two are in-house standard proteins
started from their AlphaFold DB prediction (models/, committed with its predicted aligned error);
one is an open-arm entry started from its deposited model moved by a fixed rigid-body transform,
made at run time from the site's pdb_cache (`start_model`). Each runs the battery's own command for
its arm with --model <start model>. A set passes (`check`) when every one of these holds:
space_group the battery's own verdict (score.judge: lattice and space group against the
reference, the hand excepted) is a pass
placed MODEL_PLACEMENT is MR: molecular replacement placed the model, and the R-factors,
maps and model written are of that placement
mr_group MR_SPACE_GROUP is the expected group, hand included - the model decides it
r_free R_FREE <= rfree_max (a random structure: 0.586 acentric, Wilson 1950)
confirmed CC_MODEL_CONFIRMED_TO_D_MIN is not NONE: some shell's CC(model, data) clears
rugnux's empirical null
placement_cc the placed model (p_model.pdb) has the reference model's intensities: their
correlation, shell by shell normalised, 10-4 A, the best over the reindexing
operators the two lattices allow, is >= cc_min. Independent of rugnux's own scores:
|F| is the same for every origin the space group allows and every symmetry copy, so
a right placement correlates highly and a wrong one (or the wrong hand) near zero.
"""
import gzip
import json
import math
import os
import re
import gemmi
import numpy as np
import model_check
import score
HERE = os.path.dirname(os.path.abspath(__file__))
MANIFEST = os.path.join(HERE, "timing.json")
CC_D_MAX, CC_D_MIN = 10.0, 4.0 # the placement check's resolution range (A)
CC_SHELLS = 8 # equal-count shells for the normalisation
STEP_LINE = re.compile(r"TIMING step (.+?)(?:, \d+ images)? ([\d.]+)$")
def load():
return json.load(open(MANIFEST))["sets"]
def read_model(path):
"""A model with strict NCS expanded (as rugnux's validation does) and no hydrogens or waters."""
st = gemmi.read_structure(path)
st.setup_entities()
if any(not op.given for op in st.ncs):
st.expand_ncs(gemmi.HowToNameCopiedChain.Short)
st.remove_hydrogens()
st.remove_waters()
return st
def rotation(axis, deg):
x, y, z = np.asarray(axis, float) / np.linalg.norm(axis)
c, s = math.cos(math.radians(deg)), math.sin(math.radians(deg))
t = 1 - c
return [[c + x * x * t, x * y * t - z * s, x * z * t + y * s],
[y * x * t + z * s, c + y * y * t, y * z * t - x * s],
[z * x * t - y * s, z * y * t + x * s, c + z * z * t]]
def start_model(start, wd, pdb_cache):
"""The file given to --model: the committed prediction, or the deposited model moved by the
manifest's transform, written into the set's work directory."""
if start.get("alphafold"):
return os.path.join(HERE, start["alphafold"])
mv = start["moved"]
meta = model_check.deposition(mv["pdb"], pdb_cache)
if meta is None:
return None
st = read_model(meta["xyz"])
pos = np.array([a.pos.tolist() for ch in st[0] for r in ch for a in r])
centre = pos.mean(axis=0)
rot = np.array(rotation(mv["axis"], mv["deg"]))
tr = gemmi.Transform(gemmi.Mat33(rot.tolist()),
gemmi.Vec3(*(centre - rot @ centre + np.asarray(mv["shift"], float))))
st[0].transform_pos_and_adp(tr)
out = os.path.join(wd, f"{mv['pdb']}_moved.cif.gz")
with gzip.open(out, "wt") as fh:
fh.write(st.make_mmcif_document().as_string())
return out
def intensities(st):
hkl, f = model_check.fcalc(st, CC_D_MIN)
return hkl, f.astype(float) ** 2
def normalised(i, d):
"""Each intensity over its shell's mean (equal-count shells in d)."""
out = np.empty_like(i)
for sel in np.array_split(np.argsort(d), CC_SHELLS):
out[sel] = i[sel] / max(i[sel].mean(), 1e-30)
return out
def placement_cc(placed_path, reference_path):
"""Correlation of the placed model's intensities with the reference model's, each in its own cell
and space group, the placed model's indices carried into the reference's frame by every change of
basis the two lattices allow; the best one."""
placed, ref = read_model(placed_path), read_model(reference_path)
sg_p, sg_r = placed.find_spacegroup(), ref.find_spacegroup()
hp, ip = intensities(placed)
hr, ir = intensities(ref)
d_r = ref.cell.calculate_d_array(hr)
keep = d_r <= CC_D_MAX
hr, ir = hr[keep], ir[keep]
best = None
for t in model_check.basis_changes(placed.cell, sg_p, ref.cell, sg_r):
hm = hp @ t
whole = np.all(np.abs(hm - np.round(hm)) < 1e-3, axis=1)
n = int(whole.sum())
h, i, _, _ = model_check.to_group(np.round(hm[whole]).astype(int), ip[whole], np.ones(n),
np.zeros(n, int), ref.cell, sg_r, np.arange(n))
_, a, b = np.intersect1d(model_check.hkl_key(h), model_check.hkl_key(hr), return_indices=True)
if len(a) < 100:
continue
d = ref.cell.calculate_d_array(hr[b])
cc = float(np.corrcoef(normalised(i[a], d), normalised(ir[b], d))[0, 1])
if best is None or cc > best[0]:
best = (cc, len(a), model_check.op_string(t))
return best
def steps(wd):
"""{step: seconds} from the TIMING step lines of rugnux's log, in run order."""
out = {}
log = os.path.join(wd, "p_log.txt")
if os.path.exists(log):
for line in open(log, errors="replace"):
m = STEP_LINE.search(line.rstrip())
if m:
out[m.group(1)] = out.get(m.group(1), 0.0) + float(m.group(2))
return out
def check(t, row, wd, reference_path):
"""The benchmark's verdict on one finished set: bench_checks {name: [ok, value, limit]},
bench_verdict pass/fail, bench_reason (the checks that failed) and steps."""
rep = score.read_report(os.path.join(wd, "p_report.txt"))
exp = t["expect"]
mr_sg = gemmi.find_spacegroup_by_name(rep.get("MR_SPACE_GROUP") or "")
checks = {
"space_group": [row["verdict"] == "pass", row.get("sg"), row.get("sg_ref")],
"placed": [rep.get("MODEL_PLACEMENT") == "MR", rep.get("MODEL_PLACEMENT"), "MR"],
"mr_group": [bool(mr_sg) and mr_sg.number == exp["mr_sgno"], rep.get("MR_SPACE_GROUP"),
gemmi.find_spacegroup_by_number(exp["mr_sgno"]).hm],
"r_free": [row.get("rfree") is not None and row["rfree"] <= exp["rfree_max"], row.get("rfree"),
exp["rfree_max"]],
"confirmed": [rep.get("CC_MODEL_CONFIRMED_TO_D_MIN") not in (None, "NONE"),
rep.get("CC_MODEL_CONFIRMED_TO_D_MIN"), "not NONE"],
}
placed = os.path.join(wd, "p_model.pdb")
cc = None
if os.path.exists(placed) and reference_path:
cc = placement_cc(placed, reference_path)
checks["placement_cc"] = [cc is not None and cc[0] >= exp["cc_min"], cc and round(cc[0], 3), exp["cc_min"]]
bad = [k for k, (ok, _, _) in checks.items() if not ok]
return {"bench_checks": checks, "bench_verdict": "fail" if bad else "pass",
"bench_reason": ", ".join(f"{k} {checks[k][1]} (want {checks[k][2]})" for k in bad) or None,
"bench_cc_op": cc and cc[2], "bench_cc_n": cc and cc[1],
"mr_seconds": score.fnum(rep.get("MR_SECONDS")), "mr_decision": rep.get("MR_DECISION"),
"steps": steps(wd)}
def console(rows):
"""One block per set: verdict, wall time, the checks, the step times."""
out = []
for r in rows:
out.append(f"{r['set']:12s} {r.get('bench_verdict') or '-':5s} wall {r.get('wall_s') or 0:7.1f} s"
f" MR {r.get('mr_seconds') or 0:.1f} s {r.get('bench_reason') or ''}")
for k, (ok, v, lim) in (r.get("bench_checks") or {}).items():
out.append(f" {'ok ' if ok else 'BAD'} {k:13s} {v} (want {lim})")
out.append(" " + ", ".join(f"{k} {v:.1f}" for k, v in (r.get("steps") or {}).items()))
return "\n".join(out)
def section(doc, rows):
"""The report's section for a timing run (rows of results.json carrying bench_* keys)."""
rows = [r for r in rows if r.get("bench_checks")]
if not rows:
return
bad = [r for r in rows if r["bench_verdict"] != "pass"]
doc.h(2, f"Timing benchmark: {len(rows) - len(bad)} of {len(rows)} pass")
doc.p("Each set started from a model it has to place by molecular replacement (timing.json). A set "
"passes when the battery's verdict passes, MODEL_PLACEMENT is MR, MR_SPACE_GROUP is the expected "
"group (hand included), R_FREE is at most its limit, CC_MODEL_CONFIRMED_TO_D_MIN is not NONE, "
f"and the placed model's intensities correlate with the reference model's ({CC_D_MAX:.0f}-{CC_D_MIN:.0f} A, "
"shell-normalised) at least as much as its limit.")
names = list(rows[0]["bench_checks"])
doc.table(["set", "verdict", "wall s", "MR s"] + names + ["why"],
[[r["set"], r["bench_verdict"], f"{r['wall_s']:.1f}" if r.get("wall_s") else "-",
f"{r['mr_seconds']:.1f}" if r.get("mr_seconds") else "-"]
+ [("" if r["bench_checks"][k][0] else "BAD ") + str(r["bench_checks"][k][1]) for k in names]
+ [r.get("bench_reason") or ""] for r in rows],
row_class=lambda row: "fail" if row[1] != "pass" else "")
step_names = []
for r in rows:
step_names += [k for k in r.get("steps", {}) if k not in step_names]
doc.table(["step"] + [r["set"] for r in rows],
[[k] + [f"{r['steps'][k]:.1f}" if k in r.get("steps", {}) else "-" for r in rows]
for k in step_names])