if-split 0.3.0

Reproducible, date-pinned, ligand-aware train/val/test splitter for the PDB (LigandMPNN-style).

IF-Split

A reproducible, date-pinned, ligand-aware train/val/test splitter for the PDB.

IF-Split borrows the split logic of LigandMPNN (Dauparas et al., Nature Methods 2025) — cluster proteins at 30% sequence identity, partition so no cluster spans two splits, categorize the test set by ligand class — but instead of inheriting a frozen 2022 snapshot it generates the split on demand from today's PDB, and emits a lock file so a collaborator can reproduce the exact dataset later. See PLAN.md for the full design spec.

It is built entirely on RCSB metadata (the Search + Data APIs): no structure coordinates are downloaded to build a split — only tiny per-entry records and sequences. Coordinates are an optional, downstream concern.

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Why it's different

Fresh	Builds from the current PDB, not a years-old frozen copy.
Reproducible	A dataset.lock pins the snapshot and the split output; verify re-derives both and certifies they reproduced byte-for-byte (or reports exactly what drifted).
Cheap	Metadata-only — a split is megabytes of JSON, not a terabyte of mmCIF.
Honest about quality	Every ligand is tiered (functional / ambiguous / artifact) with a reason; nothing is silently dropped.
Fold-aware	Controls structural leakage, not just sequence: same-fold chains can't straddle train/test — the leak that matters most for structure→sequence models.

Two reproducibility guarantees

1. Snapshot by release date, not query time. Entries are selected by release_date <= snapshot_date. Re-running with the same snapshot_date yields the same candidate set no matter when you run it (obsoleted entries are tracked, not silently dropped).
2. Deterministic cluster → split assignment. A cluster's split is decided by hashing a stable cluster key into the cumulative split fractions — independent of how many other clusters exist. Existing clusters never move when the PDB grows, which is what prevents train/test leakage on regeneration. A splits.registry.json pins prior assignments to make this exact even across re-clustering.

Fold-level leakage control

Sequence clustering alone is not enough for inverse folding. A model learns structure → sequence, so two chains below the 30% identity threshold that nonetheless share a fold (TIM barrels, Rossmann folds, globins…) leak structural information across the split — the model has effectively seen the test backbone during training. structural_clustering closes this: protein entities sharing a structural (super)family are union-merged into the same component in addition to shared sequence clusters, so a fold cannot straddle train/test.

It uses RCSB's precomputed CATH / ECOD / SCOP2 classifications — still metadata only, no coordinates — selectable per build (off | cath | ecod | scop2). It is purely additive: it can only merge components, never split them, and a chain with no classification simply contributes no structural edge. if-split stats reports how many components the structural pass folded together, so the effect is always measurable (scripts/eval_structural_clustering.py compares the methods).

Coverage is partial by nature: CATH ≈ 55%, ECOD ≈ 80%, SCOP2 ≈ 52% of protein chains are classified (measured on the full 2026-07-14 snapshot); the rest fall back to sequence-only.

Why it needs a balance-aware split. On its own, fold-merging collapses the dominant superfamilies (antibodies, TIM barrels) into mega-components that land wholesale in one split, skewing the entry balance to ~95/3/2 (the component split stays ~80/10/10). split_strategy: "balanced" fixes this: it caps the dominant folds to train and fills val/test to their entry targets from the tail of smaller folds — restoring ~80/10/10 by entries with thousands of distinct, held-out folds per split. It stays leakage-safe (whole components) and growth-stable (via the registry), and reports a gap if a method's tail is too thin (cath/ecod starve val; scop2 is the sweet spot). balanced also fixes the plain sequence-only skew (88/6/6 → 80/10/10) from the antibody mega-cluster.

The masterclass split

uv run if-split build --config config/masterclass.yaml --out data/mc

config/masterclass.yaml = default + structural_clustering: scop2 + split_strategy: balanced: a fold-honest ~80/10/10 split whose val/test are thousands of folds held entirely out of train — the truest generalization measure the tool can produce, still from metadata alone.

split	strategy	structural	entry balance	val/test
default	hash	off	88 / 6 / 6	sequence-clustered
masterclass	balanced	scop2	80 / 10 / 10	thousands of held-out folds

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Install

Requires Python ≥ 3.11. build needs only network access to RCSB — no external binaries.

pip install if-split          # from PyPI

Or for development, with uv:

git clone https://github.com/WSobo/IF-Split && cd IF-Split
uv sync          # creates .venv from uv.lock, installs deps + dev tools (ruff, pytest)

uv.lock is committed, so dev environments are reproducible. (The optional coordinate/featurization path via gemmi is Linux-native, so run under Linux/WSL if you use fetch.)

Quickstart

# Build the full split from today's PDB (metadata only).
uv run if-split build --config config/default.yaml --out data/out

# Dev: cap to the first N candidates (by sorted entry id — still reproducible).
uv run if-split build --limit 50 --out /tmp/ifs

# Summarize a build: split sizes, per-class test counts, curation tiers.
uv run if-split stats data/out/manifest.json

# Reproduce-check: re-derive from a lock, report candidate drift vs the live PDB,
# and (when candidates reproduce) certify the split output matches its hash.
uv run if-split verify data/out/dataset.lock

# Offline verify: integrity-check a distributed candidates.jsonl + lock, no network.
uv run if-split verify data/out/dataset.lock --candidates data/out/candidates.jsonl

# Re-derive the split from a CACHED candidates.jsonl — no RCSB. Ablate curation,
# clustering, split strategy, or TIGHTEN a filter (e.g. resolution) on a fixed
# snapshot in ~seconds instead of re-enumerating the whole PDB.
uv run if-split resplit --candidates data/out/candidates.jsonl \
    --config config/masterclass.yaml --out data/mc

# Growth-stable regeneration: pin prior cluster→split assignments.
uv run if-split build --registry data/out/splits.registry.json --out data/out2

# OPTIONAL: download the actual structures for a built split (see below).
uv run if-split fetch data/out/manifest.json --split test --out data/structures

# Emit a portable, shareable split spec (see "Sharing a split spec" below).
uv run if-split spec data/out/manifest.json --name my-split --out my-split.ifsplit.yaml

Outputs (--out directory)

File	Purpose
candidates.jsonl	The snapshot definition — one canonical JSON record per entry. Hashed into the lock.
dataset.lock	Reproduction anchor: embedded config + candidates SHA-256 + entry list + a split hash of the entry→split partition (so verify certifies the split output, not just the inputs).
manifest.json	Human-facing run record: per-split entry lists, ligand classes + tiers, per-class (and ambiguous) counts, drop log, cluster/leakage stats, entry→cluster map.
splits.registry.json	cluster key → split, for growth-stable regeneration.

Downloading structures (fetch)

build produces a tiny, coordinate-free split. When you actually want the mmCIF files — to featurize or train — fetch hydrates a built manifest into a clean, ML-ready tree. It is opt-in and downstream: nothing about a split requires coordinates.

# Scope is explicit by design (no accidental terabyte): choose splits or --all.
uv run if-split fetch data/out/manifest.json --split test                 # just test
uv run if-split fetch data/out/manifest.json --split train --split val    # repeatable
uv run if-split fetch data/out/manifest.json --all --yes --workers 16     # everything
uv run if-split fetch data/out/manifest.json --all --asymmetric-unit      # AU not assembly 1

fetch prints an estimated download size first and refuses pulls over ~1000 structures without --yes. It is resumable (existing, valid files are skipped) and parallel (--workers).

Layout — browsable and scalable

Files are split-partitioned (so you can ls a split) and sharded by the PDB "divided" scheme — the middle two characters of the entry id — so no single directory holds an unwieldy number of files:

data/structures/
  structures/
    train/  hh/4hhb-assembly1.cif.gz   01/101m-assembly1.cif.gz   02/102l-… 102m-…
    val/    …
    test/   0a/10ad-assembly1.cif.gz
  index.jsonl            # one row per structure (zero-dep, greppable)
  index.parquet          # same, columnar (written if pyarrow is installed)
  manifest.json          # copy of the source split manifest
  DATASET_CARD.md        # provenance + how-to-load

The index is the ML entry point — one row per structure with entry_id, split, path, sha256 (integrity + dedupe), cluster (for cluster-balanced batches), and ligand_classes / ligand_tiers:

import pandas as pd
df = pd.read_parquet("data/structures/index.parquet")   # or read_json(..., lines=True)
train = df[df.split == "train"]
metal_train = train[train.ligand_classes.str.contains("metal")]
# de-redundified epoch: one structure per sequence cluster
epoch = train.sort_values("entry_id").groupby("cluster").head(1)

The columnar index.parquet needs pyarrow: uv sync --extra mlops (the zero-dependency index.jsonl is always written regardless).

How it works

A build runs eight stages; none touch coordinates.

Stage	Module	What it does
1 — enumerate	enumerate.py, rcsb.py	RCSB Search → entry IDs; Data API (GraphQL, batched) → sequences, ligands, residue counts, cluster membership → candidates.jsonl.
3 — filter	parse.py	Drop no-protein / no-usable-sequence (empty or all-X poly-UNK) / too-short (opt-in min_modeled_residues) / oversized entries (assembly-1 residue count > max_total_residues) / over-resolution (re-derived here so it is auditable; per-method caps via resolution_max_A_by_method), plus optional wwPDB validation-report quality caps (clashscore, R-free, Ramachandran/rotamer/RSRZ, cryo-EM map-fit floor) — all from metadata. Every drop is logged with its reason.
4 — ligands	ligands.py	Tier each non-protein component functional/ambiguous/artifact; derive class labels (metal / small-molecule / nucleic-acid). nucleic_acid = a protein↔DNA/RNA complex (verified assembly interface), not a bound mononucleotide. Annotate, never drop.
5 — cluster	cluster.py	Group protein entities by RCSB precomputed cluster id at identity_threshold; canonical key = smallest member id. Optionally union same-fold entities (CATH/ECOD/SCOP2) for structural-leakage control.
6 — split	split.py	Assign components → train/val/test (hash, or balanced for entry-balanced fold-tail val/test); assert no cluster spans two splits; audit residual secondary-chain overlap.
7 — manifest	manifest.py	Emit lock + manifest + registry (all deterministic, no wall-clock fields).
8 — loader	dataset.py	Read a manifest into train/val/test views with cluster-balanced sampling.
2 — fetch (opt-in)	download.py, hydrate.py	Download mmCIF for a built manifest into a sharded, indexed, ML-ready tree.

Stage 2 (mmCIF coordinate download) is optional and downstream — only needed to extract ligand context or feed a model, never to build a split. See Downloading structures for the fetch command.

Structure quality (validation report)

For the highest-quality backbones, build can filter on the wwPDB validation report — fetched as metadata, so the no-download invariant still holds. The metrics come straight from the deposited report:

Cap	Metric	Applies to
max_clashscore	all-atom clashscore	X-ray + cryo-EM
max_ramachandran_outlier_pct	% backbone Ramachandran outliers	X-ray + cryo-EM
max_rotamer_outlier_pct	% sidechain rotamer outliers	X-ray + cryo-EM
max_rfree	R-free (DCC)	X-ray
max_rsrz_outlier_pct	% real-space-R Z-score outliers	X-ray
min_em_backbone_inclusion	backbone atom-in-density (a floor — higher is better)	cryo-EM

Two rules keep it honest: a cap fires only when the metric is present, so a cryo-EM entry is never dropped for a missing R-free; and every cap is off by default, so the snapshot is unchanged until you opt in. require_validation_report drops entries with no report at all. Each drop is logged with its reason and value (e.g. clashscore_too_high) and is summarised by if-split stats.

Strict starting point: max_clashscore: 40, max_rfree: 0.30, max_ramachandran_outlier_pct: 1.0. Some classic low-quality depositions drop out — e.g. the 1984 entry 4HHB has a clashscore of 142.

Ligand quality: annotate, don't destroy

IF-Split is a tool, not one frozen dataset, so it won't make an irreversible quality call for you. Every non-protein component is tiered, with a machine-readable reason, from RCSB metadata signals:

Tier	Meaning	Example reasons
functional	Real ligand/site → gets a class label	metal_bound/ligand_bound (contacts protein), *_affinity (measured), *_investigated (RCSB SOI), metal_annotated (protein annotated to bind this metal)
ambiguous	Present but uncorroborated → reported, not labelled	metal_unbound, ligand_unbound, metal_site_nonnative, glycan, purification_metal_uncorroborated
artifact	Buffer / counterion / purification tag → excluded from labels	additive, counterion, histag_metal

Holo gating (metadata-only). Presence isn't enough. A small molecule or metal is functional only if RCSB reports it contacting the protein (bound_components) or it has a measured binding affinity; an unbound one is ambiguous. A DNA/RNA chain is functional nucleic_acid only when the biological assembly has a verified protein↔nucleic-acid interface (num_prot_na_interface_entities > 0) — a co-deposited but non-contacting oligo is reported ambiguous, never silently labelled. (Interfaces are RCSB-computed metadata, available for X-ray and cryo-EM, so no coordinates are downloaded.)

The nucleic_acid class is the protein–nucleic-acid complex category (DNA/RNA polymer chains), matching LigandMPNN's "nucleotide" split. Bound mononucleotide ligands (ATP, GTP, NAD, SAM, …) are not this class — they fall under small_molecule.

The His-tag/Ni curation catches a known blemish in the LigandMPNN metal set: structures whose only "metal site" is a poly-His tag chelating Ni/Co from affinity purification. A poly-His run anywhere — or a short run at a chain terminus (histag_terminal_min_run, catching 6×His tags left partial by unmodeled or trimmed residues) — flags the entry's Ni/Co as an artifact.

But an audit (reproducible via scripts/audit_nico_histag.py) showed a subtler issue: ~82% of lone Ni/Co entries carry no detectable His-tag in the deposited sequence — IMAC tags are frequently absent from the SEQRES record, not just unmodeled, so a sequence scan can't recover them. So even with no detectable tag, a lone Ni/Co (the entry's only metal) with no corroboration is demoted from functional to ambiguous — reported, not labelled.

To avoid over-firing on genuine bare-Ni/Co enzymes (urease, cobalt methionine aminopeptidase, nitrile hydratase, …), a lone Ni/Co is rescued to functional (metal_annotated) when the protein's RCSB GO/InterPro/Pfam annotation says it binds that metal. A protein that binds a different native metal (Ni/Co as an isomorphous substitute — e.g. Co in a Mg enzyme) is reported metal_site_nonnative so a consumer can choose to keep it; one with no metal annotation at all stays purification_metal_uncorroborated. All from RCSB's own metadata (no extra UniProt call). Real metals (Zn, Mg, Fe, …), and Ni/Co with affinity/SOI or beside a genuine metal, are untouched. Rerun scripts/eval_metal_tiering.py to measure the tier distribution over the whole lone-Ni/Co set.

Crucially, the structure always stays in its split — a protein with a junk ion is still a good backbone; we just don't label the junk. A consumer wanting "pristine metal sites only" vs "maximum scale, I'll filter myself" changes a threshold, not the build. The same per-component tier is what a downstream featurizer reads to decide what counts as real ligand context.

Per-instance is a featurizer concern. These tiers are per component — they establish whether a structure contains a real Ni/Co site, not which of several same-element ions is it. A deposition can hold both a catalytic Ni and a surface crystallization Ni under one NI id, and no metadata separates them (adventitious Ni binds surface His/Asp with the same geometry as a catalytic site). Deciding which individual ion to featurize is left to the coordinate-level featurizer.

Glycans aren't ligand pockets. A carbohydrate (RCSB CCD type *saccharide* — NAG/BMA/MAN/…, and sugar-detergents like LMT) is overwhelmingly decorative glycosylation or a purification detergent, not a site an inverse-folding model conditions on. So a carbohydrate is tiered glycan (reported, not a small-molecule target) unless it has a measured binding affinity — RCSB's is_subject_of_investigation flag is too noisy for sugars (it flags glycosylation and detergents), so it doesn't rescue here. A genuine lectin/glycosidase ligand is recoverable as an opt-in target (include_ambiguous=True). Real cofactors (ATP, NAD, HEM, FAD) and structural lipids (cardiolipin, phosphatidyl-*) are non-polymer, not saccharides, so they're untouched.

Test-set representation

The split is deterministic (a per-component hash, or the balanced fold-tail fill), so the test set's ligand mix is reported but not forced by default: manifest.json carries per-split, per-class functional counts plus ambiguous counts, so under-representation is visible. An opt-in --enforce-minimums top-up (recruit functional-only ligand clusters into test in deterministic order) is scoped for a future release.

Using a split (loader)

from ifsplit.dataset import load_dataset

ds = load_dataset("data/out/manifest.json")
print(len(ds.train), len(ds.val), len(ds.test))

# Ligand-class views.
metal_test = ds.test.with_class("metal")

# Cluster-balanced sampling: one representative per sequence cluster per epoch,
# so over-represented folds (lysozyme, common kinases) don't dominate.
for epoch in range(3):
    batch_ids = ds.train.sample_by_cluster(seed=epoch)

Training strategies for inverse folding

An inverse-folding model consumes two different things, with opposite scale/quality tradeoffs. IF-Split emits both from the same leakage-safe split, so you pick a strategy without re-deriving the split:

Corpus	What	Use it for
Backbones — every kept structure	ds.train.backbones	ProteinMPNN-style, ligand-agnostic. The scale lever — a structure with only junk ions or no ligand is still a good backbone.
Conditioning targets — the functional-tier ligands	ds.train.conditioning_targets()	LigandMPNN-style. One row per (structure, ligand); junk is never a target. The quality lever.

ds = load_dataset("data/out/manifest.json")

# 1. Backbone-only training (max data): every structure.
backbones = ds.train.backbones

# 2. Ligand-conditioned training: condition on the real ligands only.
targets = ds.train.conditioning_targets()                 # metal / small_molecule / nucleic_acid
metal_targets = ds.train.conditioning_targets(classes=["metal"])

# 3. Condition on ALL of a structure's ligands at once (group by entry), or one at a time:
for entry_id, ligs in ds.train.targets_by_entry().items():
    ctx = [(t.ligand_class, t.comp_id) for t in ligs]     # e.g. [("small_molecule","HEM")]

# 4. Only structures that actually carry a conditioning target:
conditioned = ds.train.conditioned_entry_ids()            # subset of backbones

# 5. Opt in to ambiguous targets — non-native metal pockets (Ni/Co substituting the
#    native metal) and glycans (glycosylation / lectin ligands) — off by default:
any_site = ds.train.conditioning_targets(include_ambiguous=True)

The full corpus is also written to targets.jsonl (one row per target: entry, split, cluster, class, comp_id, tier, reason) and mirrored into index.parquet's conditioning_targets column after fetch.

From a target to its pocket (your featurizer owns this)

IF-Split stops at the labels — it never parses coordinates. The last mile is yours: join a target's comp_id to a fetched structure with your own parser and pull the ligand atoms + pocket. This is deliberate — featurization is model-specific (ligand atoms? SMILES? a pocket mask? all-atom context?), and every inverse-folding model already has its own pipeline. comp_id is the join key:

from pathlib import Path

import gemmi  # or biotite / Biopython — same pattern
from ifsplit.dataset import load_dataset
from ifsplit.download import rel_path_for

ds = load_dataset("data/out/manifest.json")
for entry_id, targets in ds.test.targets_by_entry().items():
    path = Path("data/structures") / rel_path_for(entry_id, "test", assembly=True)
    model = gemmi.read_structure(str(path))[0]
    for t in targets:
        # A structure may hold several copies of one ligand (plus adventitious ions).
        # Surface ALL copies; pick the instance to condition on per your model.
        copies = [r for ch in model for r in ch if r.name == t.comp_id]
        # ... extract residues within config.ligand_context_radius_A of each copy ...

When an entry has several functional ligands (e.g. a cofactor and an inhibitor, or a catalytic metal alongside an adventitious one), that shows up as multiple target rows — condition on all (group by entry_id) or one per example, your call. A runnable, copy-and-adapt version with pocket extraction is scripts/consume_split.py.

Sharing a split spec

The config is the shareable recipe. Everything that affects the split lives in one small YAML file with a content hash, so you can hand someone that file and they reproduce your methodology exactly — like params.yaml in DVC. if-split spec emits a portable, self-identifying version from any build or config:

# Extract a stand-alone spec from a finished build (config is embedded in the manifest):
uv run if-split spec data/out/manifest.json --name "my-split" --author "you" \
    --out my-split.ifsplit.yaml

# Anyone reproduces your split from just that file:
uv run if-split build --config my-split.ifsplit.yaml --out their/out

The emitted file carries a spec: header that announces what it is and pins the expected hash:

spec:
  ifsplit_spec: ifsplit/config@1          # schema id — the file says what it is
  name: my-split
  author: you
  created_with: if-split 0.3.0
  expected_config_hash: 3b63318286fd2ac4994f34d10936be05
snapshot_date: '2026-07-14'
resolution_max_A: 3.5
# ... all output-affecting settings ...

On load, if expected_config_hash no longer matches the settings (someone edited them after stamping), IF-Split warns. The spec: metadata is excluded from the hash, so name/author/description never change the split identity — two specs that differ only in their labels produce byte-identical outputs.

Artifact	Question it answers	Size
*.ifsplit.yaml (or config.yaml)	"How did you make this split?" — the recipe	~KB
manifest.json	"What's in it?" — counts, provenance, file index	~KB
dataset.lock	"Reproduce the exact bytes" — pins entry set + candidates SHA + split-output hash	~MB

Configuration

Everything that affects the output lives in one YAML file (config/default.yaml); its canonical hash is embedded in every manifest, so two builds with the same hash used identical settings. It doubles as a shareable split spec — see Sharing a split spec.

Key	Default	Meaning
snapshot_date	2026-05-30	release_date <= this — the reproducibility anchor.
experimental_methods	X-ray, EM	Allowed exptl.method values.
resolution_max_A	3.5	Resolution cutoff (re-derived in Stage 3, so it is auditable from candidates.jsonl).
resolution_max_A_by_method	{}	Optional per-method resolution overrides, e.g. {ELECTRON MICROSCOPY: 3.0} — cryo-EM 3.5 Å ≠ X-ray 3.5 Å. Empty = one cap for all.
max_total_residues	5999	Max residues kept (drop if > this) — LigandMPNN kept < 6000, i.e. <= 5999.
min_modeled_residues	0	Opt-in floor on modeled (non-X) residues in a protein chain. 0 = off; only the always-on empty/all-X (poly-UNK) drop applies. ~20 also drops tiny/mostly-unknown chains.
excluded_het	waters + common ions	Extra components forced to artifact.
use_biological_assembly	true	Count residues from assembly 1, not the deposited asymmetric unit.
purification_metals	[NI, CO]	Metals treated as IMAC tags; [] disables the heuristic.
histag_min_run	6	His-run length (anywhere) that marks a purification tag.
histag_terminal_min_run	3	Shorter His-run at a chain terminus that also counts as a tag (partial/unmodeled 6×His).
exclude_purification_artifacts	true	Demote His-tag metals to artifact; lone uncorroborated Ni/Co → ambiguous.
identity_threshold	0.30	Clustering cutoff (RCSB levels: 30/50/70/90/95/100).
clustering_backend	precomputed	precomputed (RCSB clusters) or mmseqs2 (run your own).
split_fractions	0.80 / 0.10 / 0.10	train / val / test.
split_salt	snapsplit-v1	Bump to intentionally reshuffle the split.
max_clashscore, max_rfree, max_ramachandran_outlier_pct, max_rotamer_outlier_pct, max_rsrz_outlier_pct, min_em_backbone_inclusion, require_validation_report	off	Optional validation-report quality caps — see Structure quality.
ligand_context_radius_A, max_ligand_atoms	8.0, 25	Featurization only (not part of the split).

Develop

uv run pytest              # tests (offline; 1 opt-in network test, see below)
uv run ruff check .        # lint
uv run ruff format .       # format

# Run the opt-in live RCSB round-trip test.
IFSPLIT_NETWORK_TESTS=1 uv run pytest tests/test_integration.py

Layout

config/default.yaml      # single source of truth for a run (hashed into the manifest)
src/ifsplit/             # config.py + one module per pipeline stage
  enumerate.py rcsb.py   #   Stage 1: RCSB Search + Data API
  parse.py               #   Stage 3: metadata filters
  ligands.py             #   Stage 4: ligand tiering + classification
  cluster.py split.py    #   Stages 5-6: clustering + deterministic split
  manifest.py            #   Stage 7: lock + manifest + registry, verify/stats
  dataset.py             #   Stage 8: loader + cluster-balanced sampling
  download.py            #   Stage 2: optional mmCIF fetch (featurization only)
data/cache/              # downloaded mmCIF, if ever used (gitignored)
data/out/                # generated manifests + lock files
tests/

Changelog

Release history is in CHANGELOG.md. The current release is 0.3.0 (fold-honest splitting, split-output certification, the two-corpus training model, a metadata-only curation overhaul, and offline resplit / verify).

License

MIT — see LICENSE.