From 18d4312458e7ef5c038d6c1d6a6295f0005b8e5b Mon Sep 17 00:00:00 2001
From: Thomas Duignan <thomas.j.duignan@gmail.com>
Date: Wed, 30 Sep 2026 14:16:15 +0200
Subject: [PATCH 01/26] fix: serve the 2026-09 release from R2 without a
 release-number prefix

---
 scripts/build_r2_manifest.py     |  4 ++--
 src/plinder/core/utils/config.py |  4 ++--
 src/plinder/core/utils/cpl.py    |  6 +++---
 tests/core/test_r2.py            | 10 +++++-----
 4 files changed, 12 insertions(+), 12 deletions(-)

diff --git a/scripts/build_r2_manifest.py b/scripts/build_r2_manifest.py
index 6627a57c..f3a56aee 100644
--- a/scripts/build_r2_manifest.py
+++ b/scripts/build_r2_manifest.py
@@ -20,9 +20,9 @@ def build(inventory: Path, destination: Path) -> int:
         with gzip.open(path, "rt") as stream:
             for line in stream:
                 r = json.loads(line)
-                if not r["name"].startswith("2024-06/v2/"):
+                if not r["name"].startswith("2026-09/"):
                     raise ValueError("Unexpected release")
-                key = r["name"][len("2024-06/v2/") :]
+                key = r["name"][len("2026-09/") :]
                 if key.endswith("/"):
                     continue
                 if (
diff --git a/src/plinder/core/utils/config.py b/src/plinder/core/utils/config.py
index ba8b3ce9..e462a8f5 100644
--- a/src/plinder/core/utils/config.py
+++ b/src/plinder/core/utils/config.py
@@ -224,10 +224,10 @@ class DataConfig:
     """
 
     plinder_release: str = field(
-        default_factory=partial(_getenv_default, "PLINDER_RELEASE", "2026-07")
+        default_factory=partial(_getenv_default, "PLINDER_RELEASE", "2026-09")
     )
     plinder_release_number: str = field(
-        default_factory=partial(_getenv_default, "PLINDER_RELEASE_NUMBER", "1")
+        default_factory=partial(_getenv_default, "PLINDER_RELEASE_NUMBER", "")
     )
     plinder_mount: str = field(
         default_factory=partial(
diff --git a/src/plinder/core/utils/cpl.py b/src/plinder/core/utils/cpl.py
index dff92604..7dc2bf71 100644
--- a/src/plinder/core/utils/cpl.py
+++ b/src/plinder/core/utils/cpl.py
@@ -41,10 +41,10 @@ def _get_client() -> ReleaseClient:
     cfg = get_config().data
     if (cfg.plinder_bucket, cfg.plinder_release, cfg.plinder_release_number) != (
         "plinder",
-        "2024-06",
-        "v2",
+        "2026-09",
+        "",
     ):
-        raise ValueError("R2 downloads support only plinder/2024-06/v2")
+        raise ValueError("R2 downloads support only plinder/2026-09")
     remote = str(cfg.plinder_remote).rstrip("/")
     url = urlsplit(remote)
     if (
diff --git a/tests/core/test_r2.py b/tests/core/test_r2.py
index 234272d2..25ea403f 100644
--- a/tests/core/test_r2.py
+++ b/tests/core/test_r2.py
@@ -17,7 +17,7 @@
 @pytest.fixture
 def mirror(tmp_path, monkeypatch):
     origin = tmp_path / "origin"
-    release = origin / "2024-06/v2"
+    release = origin / "2026-09"
     release.mkdir(parents=True)
     records = []
     for key, data in [
@@ -46,10 +46,10 @@ def mirror(tmp_path, monkeypatch):
     cfg = SimpleNamespace(
         data=SimpleNamespace(
             plinder_bucket="plinder",
-            plinder_release="2024-06",
-            plinder_release_number="v2",
+            plinder_release="2026-09",
+            plinder_release_number="",
             plinder_dir=str(tmp_path / "cache"),
-            plinder_remote=f"http://127.0.0.1:{server.server_port}/2024-06/v2",
+            plinder_remote=f"http://127.0.0.1:{server.server_port}/2026-09",
             force_update=False,
         )
     )
@@ -98,7 +98,7 @@ def test_path_traversal_rejected(mirror, rel):
 def test_unsupported_release_rejected(mirror):
     cfg, _ = mirror
     cfg.data.plinder_release_number = "v1"
-    with pytest.raises(ValueError, match="2024-06/v2"):
+    with pytest.raises(ValueError, match="2026-09"):
         cpl.get_plinder_path(rel="systems")
 
 

From b975dd326e4ffbbd54b338b538f5deb8148fe312 Mon Sep 17 00:00:00 2001
From: Thomas Duignan <thomas.j.duignan@gmail.com>
Date: Wed, 30 Sep 2026 14:36:02 +0200
Subject: [PATCH 02/26] fix: accept any YYYY-MM release stamp on R2 and drop
 legacy 2024-06/v2

---
 scripts/build_r2_manifest.py     | 10 ++++++----
 src/plinder/core/utils/config.py |  5 ++++-
 src/plinder/core/utils/cpl.py    | 11 ++++++-----
 tests/core/test_r2.py            |  9 ++++++---
 4 files changed, 22 insertions(+), 13 deletions(-)

diff --git a/scripts/build_r2_manifest.py b/scripts/build_r2_manifest.py
index f3a56aee..e9e7a95a 100644
--- a/scripts/build_r2_manifest.py
+++ b/scripts/build_r2_manifest.py
@@ -8,7 +8,8 @@
 from pathlib import Path
 
 
-def build(inventory: Path, destination: Path) -> int:
+def build(inventory: Path, destination: Path, release: str) -> int:
+    prefix = release.strip("/") + "/"
     shards = json.loads((inventory / "manifest-files.json").read_text())
     records = {}
     for shard in shards:
@@ -20,9 +21,9 @@ def build(inventory: Path, destination: Path) -> int:
         with gzip.open(path, "rt") as stream:
             for line in stream:
                 r = json.loads(line)
-                if not r["name"].startswith("2026-09/"):
+                if not r["name"].startswith(prefix):
                     raise ValueError("Unexpected release")
-                key = r["name"][len("2026-09/") :]
+                key = r["name"][len(prefix) :]
                 if key.endswith("/"):
                     continue
                 if (
@@ -47,5 +48,6 @@ def build(inventory: Path, destination: Path) -> int:
     parser = argparse.ArgumentParser(description=__doc__)
     parser.add_argument("inventory", type=Path)
     parser.add_argument("destination", type=Path)
+    parser.add_argument("release", help="release stamp, e.g. 2026-09")
     args = parser.parse_args()
-    print(build(args.inventory, args.destination))
+    print(build(args.inventory, args.destination, args.release))
diff --git a/src/plinder/core/utils/config.py b/src/plinder/core/utils/config.py
index e462a8f5..058f2224 100644
--- a/src/plinder/core/utils/config.py
+++ b/src/plinder/core/utils/config.py
@@ -15,6 +15,9 @@
 
 LOG = setup_logger(__name__)
 
+# Default public release: a YYYY-MM PDB snapshot stamp served flat on R2.
+DEFAULT_RELEASE = "2026-09"
+
 
 def _validate_cfg(*, cfg: DictConfig, schema: dict[str, Any]) -> DictConfig:
     """
@@ -224,7 +227,7 @@ class DataConfig:
     """
 
     plinder_release: str = field(
-        default_factory=partial(_getenv_default, "PLINDER_RELEASE", "2026-09")
+        default_factory=partial(_getenv_default, "PLINDER_RELEASE", DEFAULT_RELEASE)
     )
     plinder_release_number: str = field(
         default_factory=partial(_getenv_default, "PLINDER_RELEASE_NUMBER", "")
diff --git a/src/plinder/core/utils/cpl.py b/src/plinder/core/utils/cpl.py
index 7dc2bf71..3a48ff3f 100644
--- a/src/plinder/core/utils/cpl.py
+++ b/src/plinder/core/utils/cpl.py
@@ -1,6 +1,7 @@
 """Public dataset access with cloudpathlib and a local immutable-release cache."""
 
 import os
+import re
 from concurrent.futures import ThreadPoolExecutor
 from pathlib import Path
 from typing import Callable, Iterable, TypeVar
@@ -39,12 +40,12 @@ def thread_pool(func: Callable[[T], None], items: Iterable[T]) -> None:
 
 def _get_client() -> ReleaseClient:
     cfg = get_config().data
-    if (cfg.plinder_bucket, cfg.plinder_release, cfg.plinder_release_number) != (
-        "plinder",
-        "2026-09",
-        "",
+    if (
+        cfg.plinder_bucket != "plinder"
+        or cfg.plinder_release_number
+        or not re.fullmatch(r"\d{4}-(0[1-9]|1[0-2])", cfg.plinder_release)
     ):
-        raise ValueError("R2 downloads support only plinder/2026-09")
+        raise ValueError("R2 downloads support only plinder/YYYY-MM releases")
     remote = str(cfg.plinder_remote).rstrip("/")
     url = urlsplit(remote)
     if (
diff --git a/tests/core/test_r2.py b/tests/core/test_r2.py
index 25ea403f..ab80ac78 100644
--- a/tests/core/test_r2.py
+++ b/tests/core/test_r2.py
@@ -95,10 +95,13 @@ def test_path_traversal_rejected(mirror, rel):
         cpl.get_plinder_path(rel=rel)
 
 
-def test_unsupported_release_rejected(mirror):
+@pytest.mark.parametrize(
+    "release", [("2024-06", "v2"), ("2026-09", "1"), ("2026-9", ""), ("2026-13", "")]
+)
+def test_unsupported_release_rejected(mirror, release):
     cfg, _ = mirror
-    cfg.data.plinder_release_number = "v1"
-    with pytest.raises(ValueError, match="2026-09"):
+    cfg.data.plinder_release, cfg.data.plinder_release_number = release
+    with pytest.raises(ValueError, match="YYYY-MM"):
         cpl.get_plinder_path(rel="systems")
 
 

From 9fe285d2cf8aec6a3546c9b3a183e2d86bc600ac Mon Sep 17 00:00:00 2001
From: Thomas Duignan <thomas.j.duignan@gmail.com>
Date: Wed, 30 Sep 2026 18:56:17 +0200
Subject: [PATCH 03/26] ci: drop Docker and run tests directly on the runner

---
 .github/workflows/main.yaml       |  50 ++--
 .github/workflows/pr.yaml         |  57 ++--
 docker-compose.yml                |  30 ---
 dockerfiles/base/Dockerfile       |  70 -----
 dockerfiles/base/env.yml          |  17 --
 dockerfiles/base/requirements.txt | 185 -------------
 dockerfiles/main/Dockerfile       |  16 --
 dockerfiles/test/Dockerfile       |   8 -
 docs/contribution/development.md  |  16 --
 docs/contribution/release.md      |   2 -
 environment.yml                   |   1 -
 flows/docker.py                   | 419 ------------------------------
 flows/proc.py                     |  77 ------
 flows/version.py                  |  52 ++++
 pyproject.toml                    |   2 +-
 tox.ini                           |   7 +-
 16 files changed, 97 insertions(+), 912 deletions(-)
 delete mode 100644 docker-compose.yml
 delete mode 100644 dockerfiles/base/Dockerfile
 delete mode 100644 dockerfiles/base/env.yml
 delete mode 100644 dockerfiles/base/requirements.txt
 delete mode 100644 dockerfiles/main/Dockerfile
 delete mode 100644 dockerfiles/test/Dockerfile
 delete mode 100644 flows/docker.py
 delete mode 100644 flows/proc.py
 create mode 100644 flows/version.py

diff --git a/.github/workflows/main.yaml b/.github/workflows/main.yaml
index cf0e9405..c272507d 100644
--- a/.github/workflows/main.yaml
+++ b/.github/workflows/main.yaml
@@ -2,7 +2,6 @@ name: Package
 permissions:
   contents: write
   id-token: write
-  packages: write
 on:
   push:
     branches:
@@ -14,38 +13,38 @@ jobs:
     name: Package
     if: ${{ ! contains(toJSON(github.event.commits.*.message), '[skip ci]') }}
     runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash -l {0}
     steps:
       - name: Checkout repo
         uses: actions/checkout@v4
         with:
           fetch-depth: 0
-      - name: Setup python
-        uses: actions/setup-python@v5
+      - name: Setup micromamba
+        uses: mamba-org/setup-micromamba@v1
         with:
-          python-version: "3.12"
-      - name: Configure docker
-        run: echo ${{ secrets.GITHUB_TOKEN }} | docker login ghcr.io -u ${{ github.repository_owner }} --password-stdin
-      - name: Install build and tag requirements
-        run: python -m pip install build semver
+          environment-file: environment.yml
+          create-args: python=3.12
+          init-shell: bash
+          cache-downloads: true
+          cache-environment: true
+          post-cleanup: all
+      - name: Install Python requirements
+        run: |
+          pip install build semver -r requirements_data.txt
+          pip install -e ".[data,test,eval,plots]"
       - name: Get version bump
         id: get-tag
-        run: echo "bump=$(python flows/docker.py bump)" >> $GITHUB_OUTPUT
-      - name: Pull, build, tag, bump base image
-        if: steps.get-tag.outputs.bump != ''
-        run: python flows/docker.py pull --build --promote
-      - name: Build image
+        run: echo "bump=$(python flows/version.py)" >> $GITHUB_OUTPUT
+      - name: Run tests
         if: steps.get-tag.outputs.bump != ''
-        run: python flows/docker.py build
-      - name: Run tests against new image and save images
+        env:
+          PLINDER_OFFLINE: "true"
+        run: python -m pytest -n auto -v
+      - name: Tag release
         if: steps.get-tag.outputs.bump != ''
-        run: |
-          python flows/docker.py test --push
-          if ! test -f reports/.coverage; then
-            echo "Missing test coverage reports (reports/.coverage). Not all tests have passed?"
-            exit 1
-          else
-            echo "Test coverage report found!"
-          fi
+        run: git tag ${{ steps.get-tag.outputs.bump }}
       - name: Build distribution
         run: python -m build
       - name: Publish package distributions to PyPI
@@ -54,11 +53,6 @@ jobs:
       - name: Save git tag
         if: steps.get-tag.outputs.bump != ''
         run: git push origin ${{ steps.get-tag.outputs.bump }}
-      - name: Copy and surgery coverage
-        if: steps.get-tag.outputs.bump != ''
-        run: |
-          cp reports/.coverage .
-          sqlite3 .coverage "update file set path='src/' || substr(path, 40);"
       - name: Post coverage comment
         if: steps.get-tag.outputs.bump != ''
         uses: py-cov-action/python-coverage-comment-action@v3
diff --git a/.github/workflows/pr.yaml b/.github/workflows/pr.yaml
index 2a6a9597..74a6e8d6 100644
--- a/.github/workflows/pr.yaml
+++ b/.github/workflows/pr.yaml
@@ -3,7 +3,6 @@ name: CI Workflow
 permissions:
   contents: write
   id-token: write
-  packages: read
   pull-requests: write
 
 concurrency:
@@ -37,53 +36,35 @@ jobs:
             tox-${{ runner.os }}-3.12-
 
   test:
-    name: Build and test docker image
+    name: Test
     runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash -l {0}
     steps:
       - name: Checkout repo
         uses: actions/checkout@v4
         with:
           ref: ${{ github.event.pull_request.head.sha }}
           fetch-depth: 0
-      - name: Configure docker
-        run: echo ${{ secrets.GITHUB_TOKEN }} | docker login ghcr.io -u ${{ github.repository_owner }} --password-stdin
-      - name: Get changed source files
-        id: changed-src
-        uses: tj-actions/changed-files@v41
-        with:
-          files: src/**
-      - name: Get changed base image files
-        if: steps.changed-src.outputs.any_changed == 'true'
-        id: changed-base
-        uses: tj-actions/changed-files@v41
+      - name: Setup micromamba
+        uses: mamba-org/setup-micromamba@v1
         with:
-          files: dockerfiles/base/*
-      - name: Pull base image and build
-        if: steps.changed-src.outputs.any_changed == 'true' && steps.changed-base.outputs.any_changed == 'true'
-        run: python flows/docker.py pull --build
-      - name: Pull base image
-        if: steps.changed-src.outputs.any_changed == 'true' && steps.changed-base.outputs.any_changed != 'true'
-        run: python flows/docker.py pull
-      - name: Build image
-        if: steps.changed-base.outputs.any_changed == 'true' || steps.changed-src.outputs.any_changed == 'true'
-        run: python flows/docker.py build
-      - name: Run test image
-        if: steps.changed-base.outputs.any_changed == 'true' || steps.changed-src.outputs.any_changed == 'true'
-        run: |
-          python flows/docker.py test
-          if ! test -f reports/.coverage; then
-            echo "Missing test coverage reports (reports/.coverage). Not all tests have passed?"
-            exit 1
-          else
-            echo "Test coverage report found!"
-          fi
-      - name: Copy and surgery coverage
-        if: steps.changed-base.outputs.any_changed == 'true' || steps.changed-src.outputs.any_changed == 'true'
+          environment-file: environment.yml
+          create-args: python=3.12
+          init-shell: bash
+          cache-downloads: true
+          cache-environment: true
+          post-cleanup: all
+      - name: Install Python requirements
         run: |
-          cp reports/.coverage .
-          sqlite3 .coverage "update file set path='src/' || substr(path, 40);"
+          pip install -r requirements_data.txt
+          pip install -e ".[data,test,eval,plots]"
+      - name: Run tests
+        env:
+          PLINDER_OFFLINE: "true"
+        run: python -m pytest -n auto -v
       - name: Post coverage comment
-        if: steps.changed-src.outputs.any_changed == 'true'
         uses: py-cov-action/python-coverage-comment-action@v3
         with:
           GITHUB_TOKEN: ${{ github.token }}
diff --git a/docker-compose.yml b/docker-compose.yml
deleted file mode 100644
index 823953cb..00000000
--- a/docker-compose.yml
+++ /dev/null
@@ -1,30 +0,0 @@
-services:
-
-  base:
-    image: ${IMAGE_REPO:-ghcr.io/plinder-org}/plinder-base:${BASE_TAG:-latest}
-    build:
-      context: ./dockerfiles/base
-
-  plinder:
-    image: ${IMAGE_REPO:-ghcr.io/plinder-org}/plinder:${BUILD_TAG:-latest}
-    build:
-      context: .
-      dockerfile: ./dockerfiles/main/Dockerfile
-      args:
-        BASE_IMAGE: ${IMAGE_REPO:-ghcr.io/plinder-org}/plinder-base
-        BASE_TAG: ${BASE_TAG:-latest}
-    depends_on:
-      - base
-
-  test:
-    image: ${IMAGE_REPO:-ghcr.io/plinder-org}/plinder:${BUILD_TAG:-latest}
-    depends_on:
-      - plinder
-    volumes:
-      - ./tests/:/app/tests/
-      - ./docs/:/app/docs/
-      - ./pytest.ini:/app/pytest.ini
-      - ./.coveragerc:/app/.coveragerc
-      - ./reports/:/app/reports/
-      - ./examples/:/app/examples/
-    command: /bin/bash -c "python -m pytest -n auto -v && cp .coverage reports/.coverage"
diff --git a/dockerfiles/base/Dockerfile b/dockerfiles/base/Dockerfile
deleted file mode 100644
index 1b43378b..00000000
--- a/dockerfiles/base/Dockerfile
+++ /dev/null
@@ -1,70 +0,0 @@
-FROM --platform=linux/amd64 mambaorg/micromamba:git-c160e88-jammy
-
-USER root
-ENV DEBIAN_FRONTEND=noninteractive
-
-# Install OS dependencies
-RUN apt-get --allow-releaseinfo-change update \
-    && apt-get -y install --no-install-recommends \
-    apt-utils \
-    dialog 2>&1 \
-    && apt-get install -y --no-install-recommends \
-    git \
-    gpg \
-    wget \
-    man-db \
-    procps \
-    tree \
-    unzip \
-    gcc \
-    build-essential \
-    lsb-release \
-    curl \
-    vim \
-    exuberant-ctags \
-    apt-transport-https \
-    ca-certificates \
-    gnupg \
-    sudo \
-    libgl1-mesa-glx \
-    libxrender1 \
-    rsync \
-    libtiff-dev \
-    && apt-get autoclean \
-    && apt-get autoremove \
-    && rm -rf /var/lib/apt/lists/*
-
-# Install rust toolchain
-RUN curl https://sh.rustup.rs -sSf | sh -s -- -y
-ENV PATH=/root/.cargo/bin:${PATH}
-
-# Install conda env
-COPY env.yml /tmp/env.yml
-RUN micromamba install -y -f /tmp/env.yml && \
-    micromamba clean --all --yes && \
-    rm /tmp/env.yml
-
-# Install gsutil without full gcloud sdk
-RUN echo "deb [signed-by=/usr/share/keyrings/cloud.google.gpg] http://packages.cloud.google.com/apt cloud-sdk main" | \
-    tee -a /etc/apt/sources.list.d/google-cloud-sdk.list \
-    && curl https://packages.cloud.google.com/apt/doc/apt-key.gpg | \
-    apt-key --keyring /usr/share/keyrings/cloud.google.gpg add - \
-    && apt-get update -y \
-    && apt-get install google-cloud-cli -y \
-    && apt-get autoclean \
-    && apt-get autoremove \
-    && rm -rf /var/lib/apt/lists/*
-
-ENV BASH_ENV=/usr/local/bin/_activate_current_env.sh
-ENV LD_LIBRARY_PATH=/opt/conda/lib
-
-COPY requirements.txt /tmp/requirements.txt
-RUN --mount=type=secret,id=INDEX_URL \
-    PIP_KEYRING_PROVIDER=subprocess python -m pip install \
-    --extra-index-url "$(cat /run/secrets/INDEX_URL)" \
-    --no-cache-dir -r /tmp/requirements.txt && \
-    rm /tmp/requirements.txt
-
-ENTRYPOINT ["/usr/local/bin/_entrypoint.sh"]
-
-CMD ["/bin/bash"]
diff --git a/dockerfiles/base/env.yml b/dockerfiles/base/env.yml
deleted file mode 100644
index f3d4541f..00000000
--- a/dockerfiles/base/env.yml
+++ /dev/null
@@ -1,17 +0,0 @@
-name: base
-channels:
-  - conda-forge
-  - defaults
-  - bioconda
-dependencies:
-  - python=3.12.*
-  - pyopenssl=23.2.0
-  - requests=2.25.1
-  - google-cloud-storage
-  - gcsfs
-  - reduce
-  - openstructure>=2.12.0
-  - mmseqs2
-  - foldseek
-  - pip:
-    - keyrings.google-artifactregistry-auth==1.1.2
diff --git a/dockerfiles/base/requirements.txt b/dockerfiles/base/requirements.txt
deleted file mode 100644
index 55714ada..00000000
--- a/dockerfiles/base/requirements.txt
+++ /dev/null
@@ -1,185 +0,0 @@
-#
-# This file is autogenerated by pip-compile with Python 3.9
-# by the following command:
-#
-#    pip-compile --annotation-style=line --extra=test,pipeline,plots --output-file=/output/requirements.txt --strip-extras pyproject.toml
-#
-aiohappyeyeballs==2.4.0   # via aiohttp
-aiohttp==3.10.5           # via gcsfs
-aiosignal==1.3.1          # via aiohttp
-annotated-types==0.7.0    # via pydantic
-antlr4-python3-runtime==4.9.3  # via omegaconf
-anyio==4.4.0              # via httpx, jupyter-server
-argon2-cffi==23.1.0       # via jupyter-server
-argon2-cffi-bindings==21.2.0  # via argon2-cffi
-arrow==1.3.0              # via isoduration
-asttokens==2.4.1          # via stack-data
-async-lru==2.0.4          # via jupyterlab
-async-timeout==4.0.3      # via aiohttp
-attrs==24.2.0             # via aiohttp, jsonschema, pytest, referencing
-babel==2.16.0             # via jupyterlab-server
-beautifulsoup4==4.12.3    # via nbconvert
-biotite==1.0.1            # via plinder (pyproject.toml)
-bleach==6.1.0             # via nbconvert
-build==0.9.0              # via plinder (pyproject.toml)
-cachetools==5.5.0         # via google-auth, tox
-certifi==2024.8.30        # via httpcore, httpx, requests
-cffi==1.17.0              # via argon2-cffi-bindings
-chardet==5.2.0            # via tox
-charset-normalizer==3.3.2  # via requests
-cloudpathlib==0.19.0      # via plinder (pyproject.toml)
-colorama==0.4.6           # via tox
-comm==0.2.2               # via ipykernel, ipywidgets
-contourpy==1.3.0          # via matplotlib
-coverage==7.6.1           # via pytest-cov
-cycler==0.12.1            # via matplotlib
-debugpy==1.8.5            # via ipykernel
-decorator==5.1.1          # via gcsfs, ipython
-defusedxml==0.7.1         # via nbconvert
-distlib==0.3.8            # via virtualenv
-duckdb==1.5.2             # via plinder (pyproject.toml)
-eval-type-backport==0.2.0  # via plinder (pyproject.toml)
-exceptiongroup==1.2.2     # via anyio, ipython, pytest
-execnet==2.1.1            # via pytest-xdist
-executing==2.1.0          # via stack-data
-fastjsonschema==2.20.0    # via nbformat
-filelock==3.15.4          # via tox, virtualenv
-fonttools==4.53.1         # via matplotlib
-fqdn==1.5.1               # via jsonschema
-frozenlist==1.4.1         # via aiohttp, aiosignal
-fsspec==2024.6.1          # via gcsfs
-future==1.0.0             # via mmcif
-gcsfs==2024.6.1           # via plinder (pyproject.toml)
-gemmi==0.6.6              # via plinder (pyproject.toml)
-google-api-core==2.19.2   # via google-cloud-core, google-cloud-storage
-google-auth==2.34.0       # via gcsfs, google-api-core, google-auth-oauthlib, google-cloud-core, google-cloud-storage
-google-auth-oauthlib==1.2.1  # via gcsfs
-google-cloud-core==2.4.1  # via google-cloud-storage
-google-cloud-storage==2.18.2  # via gcsfs, plinder (pyproject.toml)
-google-crc32c==1.6.0      # via google-cloud-storage, google-resumable-media
-google-resumable-media==2.7.2  # via google-cloud-storage
-googleapis-common-protos==1.65.0  # via google-api-core
-h11==0.14.0               # via httpcore
-httpcore==1.0.5           # via httpx
-httpx==0.27.2             # via jupyterlab
-idna==3.8                 # via anyio, httpx, jsonschema, requests, yarl
-importlib-metadata==8.4.0  # via jupyter-client, jupyter-lsp, jupyterlab, jupyterlab-server, nbconvert
-importlib-resources==6.4.4  # via matplotlib
-iniconfig==2.0.0          # via pytest
-ipykernel==6.29.5         # via jupyterlab
-ipython==8.18.1           # via ipykernel, ipywidgets
-ipython-genutils==0.2.0   # via ipywidgets
-ipywidgets==7.8.4         # via mols2grid
-isoduration==20.11.0      # via jsonschema
-jedi==0.19.1              # via ipython
-jinja2==3.1.4             # via jupyter-server, jupyterlab, jupyterlab-server, mols2grid, nbconvert
-json5==0.9.25             # via jupyterlab-server
-jsonpointer==3.0.0        # via jsonschema
-jsonschema==4.23.0        # via jupyter-events, jupyterlab-server, nbformat
-jsonschema-specifications==2023.12.1  # via jsonschema
-jupyter-client==8.6.2     # via ipykernel, jupyter-server, nbclient
-jupyter-core==5.7.2       # via ipykernel, jupyter-client, jupyter-server, jupyterlab, nbclient, nbconvert, nbformat
-jupyter-events==0.10.0    # via jupyter-server
-jupyter-lsp==2.2.5        # via jupyterlab
-jupyter-server==2.14.2    # via jupyter-lsp, jupyterlab, jupyterlab-server, notebook, notebook-shim
-jupyter-server-terminals==0.5.3  # via jupyter-server
-jupyterlab==4.2.5         # via notebook
-jupyterlab-pygments==0.3.0  # via nbconvert
-jupyterlab-server==2.27.3  # via jupyterlab, notebook
-jupyterlab-widgets==1.1.10  # via ipywidgets
-kiwisolver==1.4.5         # via matplotlib
-markupsafe==2.1.5         # via jinja2, nbconvert
-matplotlib==3.9.2         # via matplotlib-venn, plinder (pyproject.toml), seaborn
-matplotlib-inline==0.1.7  # via ipykernel, ipython
-matplotlib-venn==1.1.1    # via plinder (pyproject.toml)
-mistune==3.0.2            # via nbconvert
-mmcif==0.89.0             # via plinder (pyproject.toml)
-mols2grid==2.0.0          # via plinder (pyproject.toml)
-msgpack==1.0.8            # via biotite, mmcif
-multidict==6.0.5          # via aiohttp, yarl
-nbclient==0.10.0          # via nbconvert
-nbconvert==7.16.4         # via jupyter-server
-nbformat==5.10.4          # via jupyter-server, nbclient, nbconvert, plinder (pyproject.toml)
-nest-asyncio==1.6.0       # via ipykernel
-networkx==3.2.1           # via biotite
-notebook==7.2.2           # via widgetsnbextension
-notebook-shim==0.2.4      # via jupyterlab, notebook
-numpy==1.26.4             # via biotite, contourpy, matplotlib, matplotlib-venn, mols2grid, pandas, plinder (pyproject.toml), posebusters, pyarrow, rdkit, scipy, seaborn
-oauthlib==3.2.2           # via requests-oauthlib
-omegaconf==2.3.0          # via plinder (pyproject.toml)
-overrides==7.7.0          # via jupyter-server
-packaging==24.1           # via build, ipykernel, jupyter-server, jupyterlab, jupyterlab-server, matplotlib, nbconvert, plotly, pyproject-api, pytest, setuptools-scm, tox
-pandas==2.2.2             # via mols2grid, plinder (pyproject.toml), posebusters, seaborn
-pandocfilters==1.5.1      # via nbconvert
-parso==0.8.4              # via jedi
-pep517==0.13.1            # via build
-pexpect==4.9.0            # via ipython
-pillow==10.4.0            # via matplotlib, rdkit
-platformdirs==4.2.2       # via jupyter-core, tox, virtualenv
-plotly==5.24.0            # via plinder (pyproject.toml)
-pluggy==1.5.0             # via pytest, tox
-posebusters==0.3.1        # via plinder (pyproject.toml)
-prometheus-client==0.20.0  # via jupyter-server
-prompt-toolkit==3.0.47    # via ipython
-proto-plus==1.24.0        # via google-api-core
-protobuf==5.28.0          # via google-api-core, googleapis-common-protos, proto-plus
-psutil==6.0.0             # via ipykernel
-ptyprocess==0.7.0         # via pexpect, terminado
-pure-eval==0.2.3          # via stack-data
-pyarrow==17.0.0           # via plinder (pyproject.toml)
-pyasn1==0.6.0             # via pyasn1-modules, rsa
-pyasn1-modules==0.4.0     # via google-auth
-pycparser==2.22           # via cffi
-pydantic==2.8.2           # via plinder (pyproject.toml)
-pydantic-core==2.20.1     # via pydantic
-pygments==2.18.0          # via ipython, nbconvert
-pyparsing==3.1.4          # via matplotlib
-pyproject-api==1.7.1      # via tox
-pytest==7.2.0             # via plinder (pyproject.toml), pytest-cov, pytest-xdist
-pytest-cov==4.0.0         # via plinder (pyproject.toml)
-pytest-xdist==3.6.1       # via plinder (pyproject.toml)
-python-dateutil==2.9.0.post0  # via arrow, jupyter-client, matplotlib, pandas
-python-json-logger==2.0.7  # via jupyter-events
-pytz==2024.1              # via pandas
-pyyaml==6.0.2             # via jupyter-events, omegaconf, posebusters
-pyzmq==26.2.0             # via ipykernel, jupyter-client, jupyter-server
-rdkit>=2023.9.5           # via plinder (pyproject.toml), posebusters
-referencing==0.35.1       # via jsonschema, jsonschema-specifications, jupyter-events
-requests==2.32.3          # via biotite, gcsfs, google-api-core, google-cloud-storage, jupyterlab-server, mmcif, requests-oauthlib
-requests-oauthlib==2.0.0  # via google-auth-oauthlib
-rfc3339-validator==0.1.4  # via jsonschema, jupyter-events
-rfc3986-validator==0.1.1  # via jsonschema, jupyter-events
-rpds-py==0.20.0           # via jsonschema, referencing
-rsa==4.9                  # via google-auth
-scipy==1.13.1             # via matplotlib-venn, plinder (pyproject.toml)
-seaborn==0.13.2           # via plinder (pyproject.toml)
-send2trash==1.8.3         # via jupyter-server
-setuptools-scm==7.0.5     # via plinder (pyproject.toml)
-six==1.16.0               # via asttokens, bleach, mmcif, plinder (pyproject.toml), python-dateutil, rfc3339-validator
-sniffio==1.3.1            # via anyio, httpx
-soupsieve==2.6            # via beautifulsoup4
-stack-data==0.6.3         # via ipython
-tenacity==9.0.0           # via plotly
-terminado==0.18.1         # via jupyter-server, jupyter-server-terminals
-tinycss2==1.3.0           # via nbconvert
-tomli==2.0.1              # via build, coverage, jupyterlab, pep517, pyproject-api, pytest, setuptools-scm, tox
-tornado==6.4.1            # via ipykernel, jupyter-client, jupyter-server, jupyterlab, notebook, terminado
-tox==4.18.0               # via plinder (pyproject.toml)
-tqdm==4.66.5              # via plinder (pyproject.toml)
-traitlets==5.14.3         # via comm, ipykernel, ipython, ipywidgets, jupyter-client, jupyter-core, jupyter-events, jupyter-server, jupyterlab, matplotlib-inline, nbclient, nbconvert, nbformat
-types-python-dateutil==2.9.0.20240821  # via arrow
-typing-extensions==4.12.2  # via anyio, async-lru, cloudpathlib, ipython, plinder (pyproject.toml), pydantic, pydantic-core, setuptools-scm
-tzdata==2024.1            # via pandas
-uri-template==1.3.0       # via jsonschema
-urllib3==2.2.2            # via requests
-virtualenv==20.26.3       # via tox
-wcwidth==0.2.13           # via prompt-toolkit
-webcolors==24.8.0         # via jsonschema
-webencodings==0.5.1       # via bleach, tinycss2
-websocket-client==1.8.0   # via jupyter-server
-widgetsnbextension==3.6.9  # via ipywidgets
-yarl==1.9.7               # via aiohttp
-zipp==3.20.1              # via importlib-metadata, importlib-resources
-
-# The following packages are considered to be unsafe in a requirements file:
-# setuptools
diff --git a/dockerfiles/main/Dockerfile b/dockerfiles/main/Dockerfile
deleted file mode 100644
index 1b449c6c..00000000
--- a/dockerfiles/main/Dockerfile
+++ /dev/null
@@ -1,16 +0,0 @@
-ARG BASE_IMAGE
-ARG BASE_TAG
-FROM --platform=linux/amd64 ${BASE_IMAGE}:${BASE_TAG}
-ARG MAMBA_DOCKERFILE_ACTIVATE=1
-ARG DEPENDENCY_BLOCKS=data,test,eval
-
-WORKDIR /app
-COPY requirements_data.txt requirements_data.txt
-RUN python -m pip install -r requirements_data.txt
-COPY src src
-COPY pyproject.toml pyproject.toml
-RUN --mount=source=.git,target=.git,type=bind \
-    --mount=type=secret,id=INDEX_URL \
-    PIP_KEYRING_PROVIDER=subprocess python -m pip install \
-    --extra-index-url "$(cat /run/secrets/INDEX_URL)" \
-    --no-cache-dir '.['"${DEPENDENCY_BLOCKS}"']'
diff --git a/dockerfiles/test/Dockerfile b/dockerfiles/test/Dockerfile
deleted file mode 100644
index 45451840..00000000
--- a/dockerfiles/test/Dockerfile
+++ /dev/null
@@ -1,8 +0,0 @@
-ARG BASE_IMAGE
-ARG BASE_TAG
-FROM --platform=linux/amd64 ${BASE_IMAGE}:${BASE_TAG}
-ARG MAMBA_DOCKERFILE_ACTIVATE=1
-COPY src src
-COPY pyproject.toml pyproject.toml
-RUN --mount=source=.git,target=.git,type=bind \
-    python -m pip install --no-cache-dir .
diff --git a/docs/contribution/development.md b/docs/contribution/development.md
index 01a08a39..6b5e2c7e 100644
--- a/docs/contribution/development.md
+++ b/docs/contribution/development.md
@@ -70,8 +70,6 @@ $ pip install -r requirements_data.txt
 ```
 
 This includes Linux pytorch (for the loader) and pipeline-specific tools.
-For Windows and MacOS users, please see the relevant
-[_Docker_](#docker-target) resources.
 :::
 
 ### Enabling Pre-commit hooks
@@ -82,20 +80,6 @@ Please install pre-commit hooks, that will run the same code quality checks as t
 $ pre-commit install
 ```
 
-(docker-target)=
-### Alternative: Using a Docker container
-
-We also publish the `plinder` project as a
-[docker container](https://github.com/plinder-org/plinder/pkgs/container/plinder)
-as alternative to the _Conda_-based installation, to ensure the highest level of
-compatibility with non-Linux platforms.
-See the relevant docker resources here for more details:
-
-- `docker-compose.yml`: defines a `base` image, the `plinder` "app" and a `test`
-  container
-- `dockerfiles/base/`: contains the files for the `base` image
-- `dockerfiles/main/`: contains the files for the `plinder` "app" image
-
 ## Testing and linting
 
 `plinder` uses [`tox`](https://tox.wiki) for running tests, type checks and code linting
diff --git a/docs/contribution/release.md b/docs/contribution/release.md
index b059375c..37065b21 100644
--- a/docs/contribution/release.md
+++ b/docs/contribution/release.md
@@ -19,6 +19,4 @@ The CI workflow will use the **most recent** match in the commit history to make
 Each new version release automatically triggers the following platforms:
 
 - A new *PyPI* release is created.
-- A new *Docker* image is pushed to the
-  [registry](https://github.com/plinder-org/plinder/pkgs/container/plinder).
 - This documentation website is updated.
diff --git a/environment.yml b/environment.yml
index e415115f..2e270648 100644
--- a/environment.yml
+++ b/environment.yml
@@ -15,7 +15,6 @@ channels:
   - bioconda
 dependencies:
   - python=3.12.*
-  - reduce
   - mmseqs2
   - foldseek
   - bioconda::openstructure>=2.12.0
diff --git a/flows/docker.py b/flows/docker.py
deleted file mode 100644
index ec38e2f8..00000000
--- a/flows/docker.py
+++ /dev/null
@@ -1,419 +0,0 @@
-# Copyright (c) 2024, Plinder Development Team
-# Distributed under the terms of the Apache License 2.0
-from __future__ import annotations
-
-import logging
-from argparse import ArgumentParser
-from os import environ
-from pathlib import Path
-from shlex import split
-from shutil import which
-from subprocess import PIPE, check_output
-from sys import argv as sys_argv
-from typing import List, Optional
-
-from proc import Proc
-
-logging.basicConfig(level=logging.INFO)
-LOG = logging.getLogger("doc")
-DEPENDENCY_BLOCKS = "data,test,eval,plots"
-
-
-def get_dev_tag() -> str:
-    """
-    Get the current git describe which includes base image tag
-    and whether or not the repository is in a dirty (uncommitted)
-    state.
-
-    Returns
-    -------
-    tag : str
-        current git describe
-    """
-    return check_output(
-        [
-            "git",
-            "describe",
-            "--tags",
-            "--always",
-            "--dirty",
-            "--abbrev=8",
-        ],
-        text=True,
-    ).strip()
-
-
-def get_version_bump(base_tag: str | None = None) -> str:
-    """
-    Inspect the git history for "bumpversion {phrase}"
-    and return the new version.
-    """
-    if base_tag is None:
-        current = get_dev_tag()
-        base_tag = current.split("-")[0]
-    bump = "patch"
-    tokens = [
-        "bumpversion major",
-        "bumpversion minor",
-        "bumpversion skip",
-    ]
-    for token in tokens:
-        log = check_output(
-            split(
-                " ".join(
-                    [
-                        "git",
-                        "log",
-                        f"{base_tag}..HEAD",
-                        "--oneline",
-                        "--grep",
-                        f"'{token}'",
-                        "--format=%s",
-                    ]
-                )
-            ),
-            text=True,
-        ).strip()
-        # origin/main hack was to get around docs branch but isn'try:
-        # present before pushing the tag back to main so just search for PR number
-        if log and "(#" in log:
-            bump = token.split()[1]
-            break
-    if bump == "skip":
-        return ""
-    try:
-        import semver
-
-        new_version = getattr(semver, f"bump_{bump}")(base_tag.lstrip("v"))
-        new_version = f"v{new_version}"
-        print(new_version)
-        return new_version
-    except ImportError:
-        LOG.error("could not import semver")
-        return ""
-
-
-def get_image() -> str:
-    """
-    Minimize the diff if any of this changes
-    """
-    url = "ghcr.io"
-    organization = "plinder-org"
-    image_name = "plinder"
-    return f"{url}/{organization}/{image_name}"
-
-
-def get_docker() -> str:
-    """
-    Sanity check for docker in environment
-    """
-    docker = which("docker")
-    if docker is None:
-        raise ValueError("could not find docker executable!")
-    if not (Path.cwd() / "docker-compose.yml").is_file():
-        raise ValueError("could not find docker-compose.yml, are you in repo root?")
-    return docker
-
-
-def get_env(tag: str | None = None) -> dict[str, str]:
-    """
-    Get the build env that simulates docker compose
-
-    Parameters
-    ----------
-    tag : str, default=None
-        the tag to use instead of the current dev tag
-
-    Returns
-    -------
-    env : dict[str, str]
-        the build environment
-    """
-    image_repo = "/".join(get_image().split("/")[:-1])
-    dev_tag = get_dev_tag()
-    base_tag = dev_tag.split("-")[0]
-    build_tag = tag or dev_tag
-    LOG.info(f"get_env: base_tag={base_tag} build_tag={build_tag}")
-    return {
-        **environ,
-        **{
-            "BASE_TAG": base_tag,
-            "IMAGE_REPO": image_repo,
-            "BUILD_TAG": build_tag,
-            "INDEX_URL": "https://pypi.org/simple",
-        },
-    }
-
-
-def pull_base_image(build: bool = False, promote: bool = False) -> None:
-    """
-    Make sure the base image is up to date. Optionally
-    promote the image tag using semver by inspecting the
-    git history for "bumpverson {phrase}".
-
-    Parameters
-    ----------
-    promote : bool, default=False
-        if True, promote the image tag using semver
-    """
-    docker = get_docker()
-    env = get_env()
-    cmd = [docker, "compose", "pull", "base", "--quiet"]
-    Proc(cmd, env=env).execute()
-    if build:
-        cmd = [
-            docker,
-            "build",
-            "-f",
-            "dockerfiles/base/Dockerfile",
-            "-t",
-            f"{env['IMAGE_REPO']}/plinder-base:{env['BASE_TAG']}",
-            "--secret",
-            "id=INDEX_URL",
-            "--build-arg",
-            f"BASE_TAG={env['BASE_TAG']}",
-            "--build-arg",
-            f"DEPENDENCY_BLOCKS={DEPENDENCY_BLOCKS}",
-            (Path.cwd() / "dockerfiles/base").as_posix(),
-        ]
-        Proc(cmd, env=env).execute()
-    if promote:
-        promote_base_image(env)
-
-
-def promote_base_image(env: dict[str, str]) -> None:
-    """
-    Promote the base image
-    """
-    base_tag = env["BASE_TAG"]
-    new_tag = get_version_bump(base_tag)
-    if not new_tag:
-        LOG.info("skipping base image promotion")
-        return
-    image = f"{env['IMAGE_REPO']}/plinder-base"
-    orig_image = f"{image}:{base_tag}"
-    new_image = f"{image}:{new_tag}"
-    LOG.info(f"promoting base image to {new_tag}")
-    docker = get_docker()
-    Proc([docker, "tag", orig_image, new_image], env=env).execute()
-    check_output(["git", "tag", new_tag])
-
-
-def build_image(tag: str | None = None, push: bool = False) -> str:
-    """
-    Build the image
-
-    Parameters
-    ----------
-    tag : str, default=None
-        the tag to use instead of the current dev tag
-    push : bool, default=False
-        push the image to the artifact registry
-
-    Returns
-    -------
-    image : str
-        the full image including tag
-    """
-    check_output(["git", "fetch", "--tags"])
-    docker = get_docker()
-    env = get_env(tag)
-    image = f"{env['IMAGE_REPO']}/plinder"
-    build_tag = env["BUILD_TAG"]
-    registry = environ.get("PLINDER_REGISTRY", "/".join(get_image().split("/")[:-1]))
-    cmd = [
-        docker,
-        "build",
-        "-f",
-        "dockerfiles/main/Dockerfile",
-        "-t",
-        f"{env['IMAGE_REPO']}/plinder:{build_tag}",
-        "-t",
-        f"{registry}/plinder:{build_tag}",
-        "--secret",
-        "id=INDEX_URL",
-        "--build-arg",
-        f"BASE_IMAGE={env['IMAGE_REPO']}/plinder-base",
-        "--build-arg",
-        f"BASE_TAG={env['BASE_TAG']}",
-        "--build-arg",
-        f"DEPENDENCY_BLOCKS={DEPENDENCY_BLOCKS}",
-        Path.cwd().as_posix(),
-    ]
-    Proc(cmd, env=env).execute()
-    if push:
-        cmd = [docker, "push", f"{registry}/plinder:{build_tag}"]
-        Proc(cmd, env=env).execute()
-    return f"{image}:{build_tag}"
-
-
-def test_image(
-    tag: str,
-    push: bool = False,
-    args: Optional[List[str]] = None,
-    dirty: bool = False,
-) -> None:
-    """
-    Run the test service from docker compose. Optionally
-    push both the base and plinder images to the artifact
-    registry.
-
-    Parameters
-    ----------
-    tag : str
-        the tag to use instead of the current dev tag
-    push : bool, default=False
-        if True, push images to the artifact registry
-    args : List[str], default=None
-        the arguments to pass to the image
-    dirty : bool, default=False
-        if True, mount the current working tree
-    """
-    env = get_env(tag)
-    docker = get_docker()
-    cmd = [docker, "compose", "run", "-e", "PLINDER_OFFLINE=true"]
-    if dirty:
-        cmd.extend(["-v", f"{Path.cwd()}/src/plinder:/opt/conda/lib/python3.9/site-packages/plinder"])
-    cmd.append("test")
-    if args is not None and len(args):
-        cmd.extend(
-            split(f'''/bin/bash -c "python -m pytest -n auto -v {' '.join(args)} && cp .coverage reports/.coverage"''')
-        )
-    Proc(cmd, env=env).execute()
-    if push:
-        cmd = [docker, "compose", "push", "base", "plinder", "--quiet"]
-        Proc(cmd, env=env).execute()
-
-
-def run_image(
-    args: Optional[List[str]] = None,
-    build: bool = False,
-    tag: str | None = None,
-    dirty: bool = False,
-    it: bool = False,
-    script: str | None = None,
-) -> None:
-    """
-    Run the image mounting the current working tree. This can be
-    convenient for debugging during development.
-
-    Parameters
-    ----------
-    image : str
-        the image to run
-    args : List[str], default=None
-        the arguments to pass to the image
-    """
-    tag = tag or "latest"
-    image = build_image(tag=tag) if build else get_image() + ":" + tag
-    docker = which("docker")
-    if docker is None:
-        raise ValueError("could not find docker executable!")
-    home = Path.home()
-    host = Path.cwd() / "src"
-    guest = "/opt/conda/lib/python3.10/site-packages/plinder"
-    app = "/app/src"
-    if not host.is_dir():
-        raise RuntimeError(f"could not find {host}, please run from repo root")
-    cmd = [
-        docker,
-        "run",
-        "--platform",
-        "linux/amd64",
-        "-e",
-        "PLINDER_TEST_BASE_DIR=/app",
-        "-v",
-        f"{host.parent}/tests:/app/tests/",
-        "-v",
-        f"{host.parent}/column_descriptions:/app/column_descriptions/",
-        "-e",
-        "PLINDER_MOUNT=/plinder",
-        "-e",
-        "PLINDER_LOG_LEVEL=10",
-        "-v",
-        f"{home}/.local/share/plinder:/plinder",
-        "-v",
-        f"{host}/plinder:{guest}",
-        "-v",
-        f"{host}:{app}",
-    ]
-    if script:
-        cmd.extend(["-v", f"{host.parent}/{script}:{Path(app).parent}/{script}"])
-    if it:
-        import pty
-
-        pty.spawn(cmd + ["-it", image, "/bin/bash"])
-        return
-    cmd.append(image)
-    if args is not None:
-        cmd.extend(args)
-    Proc(cmd).execute()
-
-
-def main(argv: Optional[List[str]] = None):
-    """
-    The main entrypoint for the docker helper
-
-    Parameters
-    ----------
-    argv : List[str], default=None
-        the command line arguments
-    """
-    if argv is None:
-        argv = sys_argv[1:]
-    parser = ArgumentParser(prog="plinder docker helper")
-    subs = parser.add_subparsers(help="subcommand", dest="command")
-    subs.add_parser("bump", help="Get version bump")
-    pull = subs.add_parser("pull", help="Pull the base image")
-    pull.add_argument(
-        "--promote",
-        default=False,
-        action="store_true",
-        help="Promote the image tag using semver",
-    )
-    build = subs.add_parser("build", help="Build the app image")
-    test = subs.add_parser("test", help="Test the app image")
-    test.add_argument("--dirty", default=False, action="store_true", help="Mount current working tree")
-    run = subs.add_parser("run", help="Run the app image")
-    run.add_argument("--it", default=False, action="store_true", help="Run in interactive mode")
-    run.add_argument("--script", default="", help="Script to run")
-    run.add_argument("--dirty", default=False, action="store_true", help="Mount current working tree")
-    for sub in [build, test, run]:
-        sub.add_argument(
-            "--tag", default=None, help="The image tag to pass to build_image",
-        )
-    for sub in [build, test]:
-        sub.add_argument(
-            "--push",
-            default=False,
-            action="store_true",
-            help="Push the image to the artifact registry",
-        )
-    for sub in [pull, run]:
-        sub.add_argument(
-            "--build",
-            default=False,
-            action="store_true",
-            help="Build the image before running",
-        )
-    ns, args = parser.parse_known_args()
-    nsargs = vars(ns)
-    if len(args):
-        nsargs["args"] = args
-    command = nsargs.pop("command")
-    func = {
-        "bump": get_version_bump,
-        "pull": pull_base_image,
-        "build": build_image,
-        "test": test_image,
-        "run": run_image,
-    }
-    kwargs = {} if command == "bump" else nsargs
-    if command is None:
-        parser.print_help()
-        exit()
-    func[command](**kwargs)
-
-
-if __name__ == "__main__":
-    main()
diff --git a/flows/proc.py b/flows/proc.py
deleted file mode 100644
index 1c4b7459..00000000
--- a/flows/proc.py
+++ /dev/null
@@ -1,77 +0,0 @@
-# Copyright (c) 2024, Plinder Development Team
-# Distributed under the terms of the Apache License 2.0
-import io
-import logging
-from subprocess import PIPE, STDOUT, Popen
-from typing import Any, Dict, List, Optional, Union
-
-logging.basicConfig(level=logging.INFO)
-LOG = logging.getLogger("proc")
-
-
-class Proc(Popen):
-    """
-    An opinionated Popen with an execute method
-    to mirror communicate that handles input as strings,
-    supports early return, and logs as the process runs.
-    Also retain stdout and stderr as a list of strings
-    for downstream access.
-    """
-
-    def __init__(
-        self,
-        *args,
-        stdin=PIPE,
-        stdout=PIPE,
-        stderr=STDOUT,
-        text=True,
-        **kwargs,
-    ):
-        super().__init__(
-            *args,
-            stdin=stdin,
-            stdout=stdout,
-            stderr=stderr,
-            text=text,
-            **kwargs,
-        )
-        self._stderr = stderr
-        # squelch the static type checkers that
-        # see these pipes as None since we're using
-        # PIPEs for everything
-        self.stdin: io.TextIOWrapper
-        self.stdout: io.TextIOWrapper
-        self.stderr: io.TextIOWrapper
-
-    def execute(
-        self,
-        *,
-        inputs: Optional[str] = None,
-    ) -> None:
-        """
-        Like Popen.communicate but tail output
-
-        Parameters
-        ----------
-        inputs : str
-            a command to pass to the subprocess
-
-        """
-        if isinstance(self.args, list):
-            LOG.info(" ".join(map(str, self.args)))
-        else:
-            LOG.info(self.args)
-
-        streams = [("stdout", "stdout"), ("stderr", "stderr")]
-        if self._stderr == STDOUT:
-            streams = [("stdout", "stream")]
-        with self:
-            try:
-                if inputs is not None:
-                    self.stdin.write(inputs)
-                    self.stdin.close()
-                for attr, stream in streams:
-                    for line in getattr(self, attr):
-                        LOG.info(f"{stream}: {line.rstrip()}")
-            except Exception:
-                self.kill()
diff --git a/flows/version.py b/flows/version.py
new file mode 100644
index 00000000..dd25366f
--- /dev/null
+++ b/flows/version.py
@@ -0,0 +1,52 @@
+# Copyright (c) 2024, Plinder Development Team
+# Distributed under the terms of the Apache License 2.0
+"""Compute the next release tag from "bumpversion" markers in merged PR titles."""
+
+from __future__ import annotations
+
+from subprocess import check_output
+
+
+def get_dev_tag() -> str:
+    """Return the current ``git describe`` (latest tag, distance, dirty state)."""
+    return check_output(
+        ["git", "describe", "--tags", "--always", "--dirty", "--abbrev=8"],
+        text=True,
+    ).strip()
+
+
+def get_version_bump(base_tag: str | None = None) -> str:
+    """
+    Inspect the git history since the last tag for "bumpversion {major,minor,skip}"
+    in a merged PR title and return the new version, defaulting to a patch bump.
+    An empty string means no release.
+    """
+    if base_tag is None:
+        base_tag = get_dev_tag().split("-")[0]
+    bump = "patch"
+    for token in ["bumpversion major", "bumpversion minor", "bumpversion skip"]:
+        log = check_output(
+            [
+                "git",
+                "log",
+                f"{base_tag}..HEAD",
+                "--oneline",
+                "--grep",
+                token,
+                "--format=%s",
+            ],
+            text=True,
+        ).strip()
+        # only count merged PRs, whose titles carry the PR number
+        if log and "(#" in log:
+            bump = token.split()[1]
+            break
+    if bump == "skip":
+        return ""
+    import semver
+
+    return f"v{getattr(semver, f'bump_{bump}')(base_tag.lstrip('v'))}"
+
+
+if __name__ == "__main__":
+    print(get_version_bump())
diff --git a/pyproject.toml b/pyproject.toml
index 08d7bf25..89ae5768 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -13,7 +13,7 @@ dependencies = [
     "rdkit>=2025.09.1",
     "pyarrow",
     "omegaconf",
-    "duckdb",
+    "duckdb>=1.5",
     "cloudpathlib>=0.25,<0.26",
 ]
 description = "PLINDER: Protein & Ligand INteraction Dataset and Evaluation Resource"
diff --git a/tox.ini b/tox.ini
index 8384c91a..1e3a8ca2 100644
--- a/tox.ini
+++ b/tox.ini
@@ -36,7 +36,6 @@ commands = mypy src
 setenv =
     PLINDER_LOG_LEVEL=10
     PLINDER_OFFLINE=true
-passenv =
-    PLINDER_REGISTRY
-extras = test
-commands = python flows/docker.py test --dirty {posargs}
+extras = data,test,eval,plots
+deps = -r requirements_data.txt
+commands = python -m pytest -n auto {posargs}

From df4c714ecae055f6f39b82d589fae02e9cd99468 Mon Sep 17 00:00:00 2001
From: Thomas Duignan <thomas.j.duignan@gmail.com>
Date: Thu, 1 Oct 2026 09:25:59 +0200
Subject: [PATCH 04/26] build: cap pandas below 3 until string/NA dtype changes
 are handled

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 89ae5768..300a91d5 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -5,7 +5,7 @@ dependencies = [
     "biotite >= 1.2",
     "numpy",
     "threadpoolctl>=3.6",
-    "pandas",
+    "pandas<3",
     "pydantic",
     "tqdm",
     "peppr>=0.13",

From 4f55068ed43a93887fffac4b6b5abbad0f4b5ddd Mon Sep 17 00:00:00 2001
From: Thomas Duignan <thomas.j.duignan@gmail.com>
Date: Thu, 1 Oct 2026 09:28:54 +0200
Subject: [PATCH 05/26] fix: support pandas 3 string dtypes instead of capping
 pandas

- restore the original physical schema when DuckDB rewrites a patched
  alignment shard (DuckDB writes string; pandas 3 writes large_string)
- assert missing string values with isna() so the query test holds for
  pandas 2 (None) and pandas 3 (NaN)
---
 pyproject.toml                     |  2 +-
 src/plinder/data/pipeline/tasks.py | 17 +++++++++++++++++
 tests/core/test_table_query.py     |  4 +++-
 3 files changed, 21 insertions(+), 2 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 300a91d5..89ae5768 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -5,7 +5,7 @@ dependencies = [
     "biotite >= 1.2",
     "numpy",
     "threadpoolctl>=3.6",
-    "pandas<3",
+    "pandas",
     "pydantic",
     "tqdm",
     "peppr>=0.13",
diff --git a/src/plinder/data/pipeline/tasks.py b/src/plinder/data/pipeline/tasks.py
index 7badb195..0e903722 100644
--- a/src/plinder/data/pipeline/tasks.py
+++ b/src/plinder/data/pipeline/tasks.py
@@ -2513,6 +2513,22 @@ def alignment_mapping_shard_is_current(
     return True
 
 
+def _restore_parquet_schema(path: Path, schema: pa.Schema) -> None:
+    """Cast a DuckDB-written file back to the shard's original physical types.
+
+    DuckDB always writes text as ``string``, while pandas 3 writes ``large_string``;
+    the values are identical, so only the physical type is restored.
+    """
+    written = pq.read_schema(path)
+    if written.equals(schema) or written.names != schema.names:
+        return
+    restored = path.with_suffix(path.suffix + ".restored")
+    with pq.ParquetWriter(restored, schema, compression="zstd") as writer:
+        for batch in pq.ParquetFile(path).iter_batches():
+            writer.write_batch(batch.cast(schema))
+    restored.replace(path)
+
+
 def _replace_release_alignment_queries(
     *,
     old: Path,
@@ -2582,6 +2598,7 @@ def _replace_release_alignment_queries(
         )
     finally:
         connection.close()
+    _restore_parquet_schema(temporary, old_schema)
     if not pq.read_schema(temporary).equals(old_schema):
         raise ValueError(
             f"patched alignment shard has an unexpected schema: {old}; "
diff --git a/tests/core/test_table_query.py b/tests/core/test_table_query.py
index e7482e6f..849986a0 100644
--- a/tests/core/test_table_query.py
+++ b/tests/core/test_table_query.py
@@ -436,7 +436,9 @@ def test_annotation_binding_affinity_columns_join_from_sidecar(
         columns=["ligand_id", "ligand_binding_affinity_endpoint"],
         release=local_release,
     )
-    assert joined["ligand_binding_affinity_endpoint"].tolist() == [None, "Kd"]
+    endpoints = joined["ligand_binding_affinity_endpoint"]
+    assert endpoints.isna().tolist() == [True, False]
+    assert endpoints.iloc[1] == "Kd"
 
 
 def test_query_table_uses_bound_filter_parameters(

From 8344e7c17d0a613a66cd3573effdbf4385b3b400 Mon Sep 17 00:00:00 2001
From: Thomas Duignan <thomas.j.duignan@gmail.com>
Date: Thu, 1 Oct 2026 14:24:10 +0200
Subject: [PATCH 06/26] build: install everything from pyproject.toml with uv;
 drop requirements_data.txt

- dev dependency group is the complete CI/dev environment (adds plots
  extra and semver); networkit must come from a wheel via no-build-package
- commit uv.lock and install with uv sync --locked into the Conda env
  that provides the conda-only tools (openstructure, mmseqs2, foldseek)
- build release distributions with uv build
- pin the project Python to 3.12 with .python-version
---
 .github/workflows/main.yaml      |   12 +-
 .github/workflows/pr.yaml        |   10 +-
 .python-version                  |    1 +
 docs/contribution/development.md |   29 +-
 environment.yml                  |    2 -
 pyproject.toml                   |   11 +-
 requirements_data.txt            |    7 -
 tox.ini                          |    5 +-
 uv.lock                          | 5143 ++++++++++++++++++++++++++++++
 9 files changed, 5179 insertions(+), 41 deletions(-)
 create mode 100644 .python-version
 delete mode 100644 requirements_data.txt
 create mode 100644 uv.lock

diff --git a/.github/workflows/main.yaml b/.github/workflows/main.yaml
index c272507d..beb95fd3 100644
--- a/.github/workflows/main.yaml
+++ b/.github/workflows/main.yaml
@@ -30,10 +30,12 @@ jobs:
           cache-downloads: true
           cache-environment: true
           post-cleanup: all
-      - name: Install Python requirements
-        run: |
-          pip install build semver -r requirements_data.txt
-          pip install -e ".[data,test,eval,plots]"
+      - name: Setup uv
+        uses: astral-sh/setup-uv@v6
+        with:
+          enable-cache: true
+      - name: Install plinder
+        run: UV_PROJECT_ENVIRONMENT="$CONDA_PREFIX" uv sync --locked --inexact
       - name: Get version bump
         id: get-tag
         run: echo "bump=$(python flows/version.py)" >> $GITHUB_OUTPUT
@@ -46,7 +48,7 @@ jobs:
         if: steps.get-tag.outputs.bump != ''
         run: git tag ${{ steps.get-tag.outputs.bump }}
       - name: Build distribution
-        run: python -m build
+        run: uv build
       - name: Publish package distributions to PyPI
         if: steps.get-tag.outputs.bump != ''
         uses: pypa/gh-action-pypi-publish@release/v1
diff --git a/.github/workflows/pr.yaml b/.github/workflows/pr.yaml
index 74a6e8d6..c272367c 100644
--- a/.github/workflows/pr.yaml
+++ b/.github/workflows/pr.yaml
@@ -56,10 +56,12 @@ jobs:
           cache-downloads: true
           cache-environment: true
           post-cleanup: all
-      - name: Install Python requirements
-        run: |
-          pip install -r requirements_data.txt
-          pip install -e ".[data,test,eval,plots]"
+      - name: Setup uv
+        uses: astral-sh/setup-uv@v6
+        with:
+          enable-cache: true
+      - name: Install plinder
+        run: UV_PROJECT_ENVIRONMENT="$CONDA_PREFIX" uv sync --locked --inexact
       - name: Run tests
         env:
           PLINDER_OFFLINE: "true"
diff --git a/.python-version b/.python-version
new file mode 100644
index 00000000..e4fba218
--- /dev/null
+++ b/.python-version
@@ -0,0 +1 @@
+3.12
diff --git a/docs/contribution/development.md b/docs/contribution/development.md
index 6b5e2c7e..7530a9fe 100644
--- a/docs/contribution/development.md
+++ b/docs/contribution/development.md
@@ -16,8 +16,8 @@ $ git clone https://github.com/plinder-org/plinder.git
 
 ### Creating the Conda environment
 
-The data generation pipeline (`plinder.data`) requires a few tools that are only
-available via _Conda_ (mmseqs2, foldseek, reduce).
+The data generation pipeline (`plinder.data`) and evaluation require a few tools
+that are only available via _Conda_ (mmseqs2, foldseek, OpenStructure).
 If you have not _Conda_ installed yet, we recommend its installation via
 [miniforge](https://github.com/conda-forge/miniforge).
 
@@ -28,18 +28,19 @@ $ mamba activate plinder
 
 ### Installing `plinder`
 
-With [uv](https://docs.astral.sh/uv/), a single command installs `plinder` in
-editable mode with the `dev`, `eval` and `loader` extras and the data pipeline
-dependencies from `requirements_data.txt`:
+All Python dependencies are declared in `pyproject.toml` and locked in `uv.lock`.
+With [uv](https://docs.astral.sh/uv/), install `plinder` in editable mode with the
+complete `dev` dependency group (all extras used in CI, including CPU-only pytorch
+on Linux and the git-only pipeline packages) into the active Conda environment:
 
 ```console
-$ uv sync
+$ UV_PROJECT_ENVIRONMENT="$CONDA_PREFIX" uv sync --inexact
 ```
 
-No separate `pip install -r requirements_data.txt` step is needed.
-The Conda-only tools above are still required.
+CI runs the same command with `--locked`. Without the Conda environment, a plain `uv sync`
+installs into `.venv`; tests that need the Conda-only tools will then fail.
 
-With pip, the base install covers data generation and the core library (numpy 2 compatible):
+With pip, the base install covers data generation and the core library:
 
 ```console
 $ pip install -e ".[dev]"
@@ -62,14 +63,8 @@ is installed by `mamba env create -f environment.yml` above.
 Data generation (`plinder.data`) does **not** require OpenStructure and
 works with numpy 2.
 
-For the full data pipeline, pip installs need additional dependencies
-(`uv sync` already includes them):
-
-```console
-$ pip install -r requirements_data.txt
-```
-
-This includes Linux pytorch (for the loader) and pipeline-specific tools.
+The full data pipeline also needs the git-only packages in the `dev`
+dependency group, which only `uv sync` installs.
 :::
 
 ### Enabling Pre-commit hooks
diff --git a/environment.yml b/environment.yml
index 2e270648..51a580b6 100644
--- a/environment.yml
+++ b/environment.yml
@@ -18,5 +18,3 @@ dependencies:
   - mmseqs2
   - foldseek
   - bioconda::openstructure>=2.12.0
-  - pip:
-    - keyrings.google-artifactregistry-auth==1.1.2
diff --git a/pyproject.toml b/pyproject.toml
index 89ae5768..6a82efbb 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -87,15 +87,16 @@ docs = [
     "matplotlib",
 ]
 
-# Not published to PyPI; installed by default with `uv sync`.
-# Mirrors requirements_data.txt, which remains for pip-based installs.
+# Not published to PyPI (includes git-only packages); installed by default with
+# `uv sync`. This is the complete development and CI environment.
 [dependency-groups]
 dev = [
-    "plinder[dev,eval,loader]",
+    "plinder[dev,eval,loader,plots]",
     "networkit>11.0",
     "tabulate",
     "pdb-validation",
     "mmpdb",
+    "semver",
 ]
 
 [tool.uv.sources]
@@ -103,6 +104,10 @@ pdb-validation = { git = "https://git.scicore.unibas.ch/schwede/ligand-validatio
 mmpdb = { git = "https://github.com/rdkit/mmpdb.git" }
 torch = [{ index = "pytorch-cpu", marker = "sys_platform == 'linux'" }]
 
+[tool.uv]
+# networkit source builds need CMake; require a published wheel.
+no-build-package = ["networkit"]
+
 [[tool.uv.index]]
 name = "pytorch-cpu"
 url = "https://download.pytorch.org/whl/cpu"
diff --git a/requirements_data.txt b/requirements_data.txt
deleted file mode 100644
index 0b7aa95f..00000000
--- a/requirements_data.txt
+++ /dev/null
@@ -1,7 +0,0 @@
---only-binary=networkit
-  networkit > 11.0
-  tabulate
-  pdb-validation @ git+https://git.scicore.unibas.ch/schwede/ligand-validation.git
-  mmpdb @ git+https://github.com/rdkit/mmpdb.git
-  torch @ https://download.pytorch.org/whl/cpu/torch-2.5.1%2Bcpu-cp312-cp312-linux_x86_64.whl#sha256=4856f9d6925121d13c2df07aa7580b767f449dfe71ae5acde9c27535d5da4840 ; sys_platform == "linux"
-  torch >= 2.5 ; sys_platform == "darwin"
diff --git a/tox.ini b/tox.ini
index 1e3a8ca2..097c4d5a 100644
--- a/tox.ini
+++ b/tox.ini
@@ -36,6 +36,5 @@ commands = mypy src
 setenv =
     PLINDER_LOG_LEVEL=10
     PLINDER_OFFLINE=true
-extras = data,test,eval,plots
-deps = -r requirements_data.txt
-commands = python -m pytest -n auto {posargs}
+allowlist_externals = uv
+commands = uv run --locked python -m pytest -n auto {posargs}
diff --git a/uv.lock b/uv.lock
new file mode 100644
index 00000000..70faadac
--- /dev/null
+++ b/uv.lock
@@ -0,0 +1,5143 @@
+version = 1
+revision = 3
+requires-python = ">=3.12"
+resolution-markers = [
+    "python_full_version >= '3.14' and sys_platform == 'linux'",
+    "python_full_version < '3.14' and sys_platform == 'linux'",
+    "python_full_version >= '3.14' and sys_platform == 'win32'",
+    "python_full_version >= '3.14' and sys_platform == 'emscripten'",
+    "python_full_version >= '3.14' and sys_platform != 'emscripten' and sys_platform != 'linux' and sys_platform != 'win32'",
+    "python_full_version < '3.14' and sys_platform == 'win32'",
+    "python_full_version < '3.14' and sys_platform == 'emscripten'",
+    "python_full_version < '3.14' and sys_platform != 'emscripten' and sys_platform != 'linux' and sys_platform != 'win32'",
+]
+
+[[package]]
+name = "accessible-pygments"
+version = "0.0.5"
+source = { registry = "https://pypi.org/simple" }
+dependencies = [
+    { name = "pygments" },
+]
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+    { url = "https://files.pythonhosted.org/packages/62/49/5506e5b6d29aab91bd845cc9016d88c3d3f81b81bc242b8100bdd5737825/yarl-1.25.1-cp315-cp315t-musllinux_1_2_armv7l.whl", hash = "sha256:85a18376073f8a39aa07be34f9fc77e2869aa72c55c441efdd2cf79a0407504d", size = 106212, upload-time = "2026-09-15T19:34:42.768Z" },
+    { url = "https://files.pythonhosted.org/packages/46/8a/19877c193b7c5929f4b07118c18bbe390f3fadd0f59dd98c0cd12b31fa5c/yarl-1.25.1-cp315-cp315t-musllinux_1_2_ppc64le.whl", hash = "sha256:77716e245c90f058466a05e6a465bb8600f767a8f4b18b4d40f3aff958e5f73c", size = 119985, upload-time = "2026-09-15T19:34:44.976Z" },
+    { url = "https://files.pythonhosted.org/packages/4e/6c/0a46fbbf9ecbcbd0cc20d2193394254b9e19817f22c814aab60f99847400/yarl-1.25.1-cp315-cp315t-musllinux_1_2_riscv64.whl", hash = "sha256:1e80dcf1446e1b080b1932b0d103c464a04112f5bc31f0f983ad418172063cde", size = 112081, upload-time = "2026-09-15T19:34:47.45Z" },
+    { url = "https://files.pythonhosted.org/packages/ef/30/93f5d471230c74ccd06255d0842739f86551f937f9e63a5e947853c6244a/yarl-1.25.1-cp315-cp315t-musllinux_1_2_s390x.whl", hash = "sha256:bdc8d8b8c22e9e43ac68316b5e6cf083dec537f4ec213cb4aa967b583bc3fa64", size = 116995, upload-time = "2026-09-15T19:34:49.972Z" },
+    { url = "https://files.pythonhosted.org/packages/2b/80/c386593035ee3f9c6c6af0847b5578f2830c674794a9d7701b744a3ebd42/yarl-1.25.1-cp315-cp315t-musllinux_1_2_x86_64.whl", hash = "sha256:dfbf531053a0935f2e871bcd4753f90313688772ff8c017f5ea402e315a78c1f", size = 115570, upload-time = "2026-09-15T19:34:52.628Z" },
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+[[package]]
+name = "zipp"
+version = "4.1.0"
+source = { registry = "https://pypi.org/simple" }
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+wheels = [
+    { url = "https://files.pythonhosted.org/packages/3a/13/547360d81e6d88d58492968ffda9f9542854f11310ee556fef14260cc886/zipp-4.1.0-py3-none-any.whl", hash = "sha256:25ad4e16390cd314347dd8f1de67a2ac538ae658ed4ab9db16029c07c188e97f", size = 10238, upload-time = "2026-05-18T20:08:57.045Z" },
+]

From 2bc833d94082becb1b784be52fe025bc13e307c9 Mon Sep 17 00:00:00 2001
From: Thomas Duignan <thomas.j.duignan@gmail.com>
Date: Thu, 1 Oct 2026 16:07:27 +0200
Subject: [PATCH 07/26] fix: fetch protein score shards for lazy ligand
 similarity reconstruction

Published CIGAR shards omit alignment scores, so Scorer.load_alignments reads
the matching exports/protein_similarity_scores shard. prefetch only downloaded
the CIGAR shards, so reconstruct_similarity_scores failed on a lazily
populated cache. Register the score shard as a release path and fetch it when
include_protein_scores=True (used by ligand reconstruction only).
---
 src/plinder/core/release.py            |  4 ++++
 src/plinder/core/scores/reconstruct.py | 16 ++++++++++++++++
 tests/core/test_reconstruct_scores.py  | 24 ++++++++++++++++++++++++
 3 files changed, 44 insertions(+)

diff --git a/src/plinder/core/release.py b/src/plinder/core/release.py
index d825eda9..0d4121b8 100644
--- a/src/plinder/core/release.py
+++ b/src/plinder/core/release.py
@@ -80,6 +80,10 @@ def _release_file(
     "search_database_overlay": "search_databases/weekly_delta/holo_{backend}",
     "search_database_shadowed_entries": "search_databases/shadowed_entries.parquet",
     "protein_similarity_scores": "exports/protein_similarity_scores",
+    "protein_similarity_score_shard": (
+        "exports/protein_similarity_scores/alignment_type={alignment_type}/"
+        "shard={shard}.parquet"
+    ),
     "ligand_similarity_scores": "exports/ligand_similarity_scores.parquet",
     "interface_similarity_scores": "exports/interface_similarity_scores.parquet",
     "interface_half_similarity_scores": (
diff --git a/src/plinder/core/scores/reconstruct.py b/src/plinder/core/scores/reconstruct.py
index 7ec468fa..4068f73d 100644
--- a/src/plinder/core/scores/reconstruct.py
+++ b/src/plinder/core/scores/reconstruct.py
@@ -44,11 +44,15 @@ def prefetch_similarity_alignments(
     *,
     search_db: str = "holo",
     data_dir: Path | None = None,
+    include_protein_scores: bool = False,
 ) -> dict[str, dict[str, Path]]:
     """Download or verify only the mapped alignments needed by query systems.
 
     Calling this on an online node populates the normal PLINDER cache. Calling
     it later with offline mode enabled only checks those same local files.
+    With ``include_protein_scores``, each backend also needs its matching
+    protein-similarity export shard, which supplies the alignment scores that
+    the CIGAR shards omit (needed for ligand similarity reconstruction).
     """
     if search_db != "holo":
         raise NotImplementedError(
@@ -79,6 +83,17 @@ def prefetch_similarity_alignments(
                         alignment_type=alignment_type,
                         shard=shard,
                     )
+                    if include_protein_scores:
+                        _release_file(
+                            "protein_similarity_score_shard",
+                            data_dir=data_dir,
+                            description=(
+                                f"{alignment_type} protein similarity score "
+                                f"shard {shard}"
+                            ),
+                            alignment_type=alignment_type,
+                            shard=shard,
+                        )
                 except FileNotFoundError as exc:
                     resolved[key] = None
                     resolution_errors[key] = exc
@@ -458,6 +473,7 @@ def reconstruct_similarity_scores(
         query_systems,
         search_db=search_db,
         data_dir=data_dir,
+        include_protein_scores=True,
     )
     selected_pdb_ids = {
         _pdb_id(system_id) for system_id in query_systems | target_systems
diff --git a/tests/core/test_reconstruct_scores.py b/tests/core/test_reconstruct_scores.py
index 46835472..c2ad3a6c 100644
--- a/tests/core/test_reconstruct_scores.py
+++ b/tests/core/test_reconstruct_scores.py
@@ -65,6 +65,30 @@ def test_prefetch_accepts_one_available_alignment_backend(tmp_path):
     assert paths == {"1abc": {"foldseek": foldseek}}
 
 
+def test_prefetch_fetches_protein_score_shards_when_requested(tmp_path, monkeypatch):
+    requested: list[str] = []
+
+    def get_plinder_path(*, rel: str) -> Path:
+        requested.append(rel)
+        path = tmp_path / rel
+        path.parent.mkdir(parents=True, exist_ok=True)
+        path.touch()
+        return path
+
+    monkeypatch.setattr(release.cpl, "get_plinder_path", get_plinder_path)
+
+    reconstruct.prefetch_similarity_alignments(
+        ["1abc__1__1.A__1.L"], include_protein_scores=True
+    )
+
+    assert requested == [
+        "alignment_cigars/search_db=holo/alignment_type=foldseek/shard=ab.parquet",
+        "exports/protein_similarity_scores/alignment_type=foldseek/shard=ab.parquet",
+        "alignment_cigars/search_db=holo/alignment_type=mmseqs/shard=ab.parquet",
+        "exports/protein_similarity_scores/alignment_type=mmseqs/shard=ab.parquet",
+    ]
+
+
 def test_canonical_ligand_resolver_materializes_only_requested_member(tmp_path):
     archive = tmp_path / "ligand_archives" / "ab.parquet"
     archive.parent.mkdir(parents=True)

From a3cc88770311dbab74ebd3e48e3dad4f45820ad4 Mon Sep 17 00:00:00 2001
From: Thomas Duignan <thomas.j.duignan@gmail.com>
Date: Thu, 1 Oct 2026 16:07:27 +0200
Subject: [PATCH 08/26] docs: execute all example notebooks against the 2026-09
 release

- drop the PLINDER_RELEASE=2026-07 / PLINDER_RELEASE_NUMBER=1 overrides so
  notebooks use the default release and download lazily from R2
- remove the notebook execution skip list
- install docs builds with uv sync --locked --extra docs into the Conda env
  (OpenStructure and MMseqs2 are needed by the evaluation and search notebooks)
---
 .github/workflows/docs.yaml                    | 13 ++++++++-----
 .github/workflows/pr.yaml                      |  8 ++++++--
 docs/conf.py                                   | 17 -----------------
 docs/examples/1_download.ipynb                 | 18 ++----------------
 docs/examples/2_query_filter_index.ipynb       | 13 -------------
 docs/examples/3_access_system_files.ipynb      | 12 ------------
 docs/examples/4_align_mask_crop.ipynb          | 12 ------------
 docs/examples/custom_scoring.ipynb             |  3 ---
 docs/examples/evaluation.ipynb                 |  3 ---
 docs/examples/protein_interfaces.ipynb         | 12 ------------
 .../similarity_and_representatives.ipynb       | 12 ------------
 11 files changed, 16 insertions(+), 107 deletions(-)

diff --git a/.github/workflows/docs.yaml b/.github/workflows/docs.yaml
index aed210a6..dbcf5831 100644
--- a/.github/workflows/docs.yaml
+++ b/.github/workflows/docs.yaml
@@ -33,14 +33,17 @@ jobs:
           cache-downloads: true
           cache-environment: true
           post-cleanup: all
+      - name: Setup uv
+        uses: astral-sh/setup-uv@v6
+        with:
+          enable-cache: true
+      - name: Install plinder
+        shell: bash -el {0}
+        run: UV_PROJECT_ENVIRONMENT="$CONDA_PREFIX" uv sync --locked --inexact --extra docs
       - name: Build docs
         shell: bash -el {0}
         id: build
-        run: |
-          which python
-          python -m pip install six
-          python -m pip install '.[docs,loader]'
-          sphinx-build docs build/docs
+        run: sphinx-build docs build/docs
       - name: Upload build artifact
         uses: actions/upload-pages-artifact@v3
         with:
diff --git a/.github/workflows/pr.yaml b/.github/workflows/pr.yaml
index c272367c..942c9044 100644
--- a/.github/workflows/pr.yaml
+++ b/.github/workflows/pr.yaml
@@ -89,7 +89,11 @@ jobs:
           cache-downloads: true
           cache-environment: true
           post-cleanup: all
-      - name: Install Python requirements
-        run: pip install six ".[docs,loader]"
+      - name: Setup uv
+        uses: astral-sh/setup-uv@v6
+        with:
+          enable-cache: true
+      - name: Install plinder
+        run: UV_PROJECT_ENVIRONMENT="$CONDA_PREFIX" uv sync --locked --inexact --extra docs
       - name: Build the documentation
         run: sphinx-build --fail-on-warning docs build/docs
diff --git a/docs/conf.py b/docs/conf.py
index 84be4b12..19c80b83 100644
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -64,23 +64,6 @@
 nb_custom_formats = {".ipynb": ["jupytext.reads", {"fmt": "ipynb"}]}
 nb_execution_timeout = 720
 nb_kernel_rgx_aliases = {"plinder.*": "python3"}
-# TODO(docs-v3): these notebooks were migrated to the v3 schema (new cluster
-# column names, system_receptor_type, structure APIs) but the docs build
-# executes them against the published v2 dataset, so re-execution fails. Skip
-# executing them (committed outputs are rendered instead) until the v3 dataset
-# is published; then remove this list to restore live execution.
-nb_execution_excludepatterns = [
-    "examples/2_query_filter_index.ipynb",
-    "examples/3_access_system_files.ipynb",
-    "examples/4_align_mask_crop.ipynb",
-    "examples/5_dataset_and_loader.ipynb",
-    # TODO: v3-only: these fetch 2026-07 release artifacts (systems, interfaces,
-    # similarity exports) that are not published yet.
-    "examples/custom_scoring.ipynb",
-    "examples/evaluation.ipynb",
-    "examples/protein_interfaces.ipynb",
-    "examples/similarity_and_representatives.ipynb",
-]
 myst_enable_extensions = [
     "amsmath",
     "attrs_inline",
diff --git a/docs/examples/1_download.ipynb b/docs/examples/1_download.ipynb
index a116b049..e2769719 100644
--- a/docs/examples/1_download.ipynb
+++ b/docs/examples/1_download.ipynb
@@ -6,9 +6,7 @@
    "source": [
     "# Downloading the dataset\n",
     "\n",
-    "The default location for the dataset is `~/.local/share/plinder/<PLINDER_RELEASE>/<PLINDER_RELEASE_NUMBER>` where:\n",
-    "- `<PLINDER_RELEASE>` is the month of the PDB snapshot, formatted as `YYYY-MM`;\n",
-    "- `<PLINDER_RELEASE_NUMBER>` distinguishes PLINDER releases from the same month.\n",
+    "The default location for the dataset is `~/.local/share/plinder/<PLINDER_RELEASE>`, where `<PLINDER_RELEASE>` is the month of the PDB snapshot, formatted as `YYYY-MM` (currently `2026-09`).\n",
     "\n",
     "Set the `PLINDER_MOUNT` environment variable to use a different location."
    ]
@@ -37,7 +35,7 @@
     "  -y, --yes             skip confirmation\n",
     "```\n",
     "\n",
-    ":::{note} The public `2024-06/v2` release is served from Cloudflare R2 and contains about 220 GB of downloadable files. Allow additional space for extracted archives; download time depends on your connection. Completed files are reused on subsequent runs. Set `PLINDER_OFFLINE=true` to use the cache without network requests. :::"
+    ":::{note} The public `2026-09` release is served from Cloudflare R2 and contains about 135 GB of downloadable files. Allow additional space for extracted archives; download time depends on your connection. Completed files are reused on subsequent runs. Set `PLINDER_OFFLINE=true` to use the cache without network requests. :::"
    ]
   },
   {
@@ -49,18 +47,6 @@
     "Alternatively, if the `PLINDER_OFFLINE` environment variable **unset** (which is the default empty), the dataset will be downloaded on lazily and on the fly as you access the data. This is preferred for exploration and prototyping as you don't need to download the entire dataset at once and can just work with the assets you need for your use-case."
    ]
   },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "import os\n",
-    "\n",
-    "os.environ.setdefault(\"PLINDER_RELEASE\", \"2026-07\")\n",
-    "os.environ.setdefault(\"PLINDER_RELEASE_NUMBER\", \"1\")"
-   ]
-  },
   {
    "cell_type": "markdown",
    "metadata": {},
diff --git a/docs/examples/2_query_filter_index.ipynb b/docs/examples/2_query_filter_index.ipynb
index d13bc674..4316f9ff 100644
--- a/docs/examples/2_query_filter_index.ipynb
+++ b/docs/examples/2_query_filter_index.ipynb
@@ -10,19 +10,6 @@
     "Use {func}`plinder.core.query_table` to select and filter release records. The [dataset reference](../dataset.md) defines every table, key, relationship, and column."
    ]
   },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "select-release",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "import os\n",
-    "\n",
-    "os.environ.setdefault(\"PLINDER_RELEASE\", \"2026-07\")\n",
-    "os.environ.setdefault(\"PLINDER_RELEASE_NUMBER\", \"1\")"
-   ]
-  },
   {
    "cell_type": "code",
    "execution_count": null,
diff --git a/docs/examples/3_access_system_files.ipynb b/docs/examples/3_access_system_files.ipynb
index 736072fb..b9237ec3 100644
--- a/docs/examples/3_access_system_files.ipynb
+++ b/docs/examples/3_access_system_files.ipynb
@@ -7,18 +7,6 @@
     "# Access system files with PlinderSystem"
    ]
   },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "import os\n",
-    "\n",
-    "os.environ.setdefault(\"PLINDER_RELEASE\", \"2026-07\")\n",
-    "os.environ.setdefault(\"PLINDER_RELEASE_NUMBER\", \"1\")"
-   ]
-  },
   {
    "cell_type": "markdown",
    "metadata": {},
diff --git a/docs/examples/4_align_mask_crop.ipynb b/docs/examples/4_align_mask_crop.ipynb
index f876d304..a6cee989 100644
--- a/docs/examples/4_align_mask_crop.ipynb
+++ b/docs/examples/4_align_mask_crop.ipynb
@@ -9,18 +9,6 @@
     "This advanced guide starts from a reconstructed ligand system and shows the in-memory coordinate views used for featurization and structural comparison. For file access and linked apo reconstruction, begin with [Access system files with PlinderSystem](3_access_system_files.ipynb)."
    ]
   },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "import os\n",
-    "\n",
-    "os.environ.setdefault(\"PLINDER_RELEASE\", \"2026-07\")\n",
-    "os.environ.setdefault(\"PLINDER_RELEASE_NUMBER\", \"1\")"
-   ]
-  },
   {
    "cell_type": "code",
    "execution_count": null,
diff --git a/docs/examples/custom_scoring.ipynb b/docs/examples/custom_scoring.ipynb
index c235cdb0..ffde8f4b 100644
--- a/docs/examples/custom_scoring.ipynb
+++ b/docs/examples/custom_scoring.ipynb
@@ -31,9 +31,6 @@
     "import os\n",
     "from pathlib import Path\n",
     "\n",
-    "os.environ.setdefault(\"PLINDER_RELEASE\", \"2026-07\")\n",
-    "os.environ.setdefault(\"PLINDER_RELEASE_NUMBER\", \"1\")\n",
-    "\n",
     "import pandas as pd\n",
     "\n",
     "from plinder.core import PlinderSystem, PlinderRelease\n",
diff --git a/docs/examples/evaluation.ipynb b/docs/examples/evaluation.ipynb
index 8a5ac39b..1785a3c9 100644
--- a/docs/examples/evaluation.ipynb
+++ b/docs/examples/evaluation.ipynb
@@ -44,9 +44,6 @@
     "import yaml\n",
     "import pandas as pd\n",
     "\n",
-    "os.environ.setdefault(\"PLINDER_RELEASE\", \"2026-07\")\n",
-    "os.environ.setdefault(\"PLINDER_RELEASE_NUMBER\", \"1\")\n",
-    "\n",
     "from plinder.core import PlinderRelease\n",
     "from plinder.eval import evaluate_predictions\n",
     "\n",
diff --git a/docs/examples/protein_interfaces.ipynb b/docs/examples/protein_interfaces.ipynb
index 0328f8f1..efaf6c37 100644
--- a/docs/examples/protein_interfaces.ipynb
+++ b/docs/examples/protein_interfaces.ipynb
@@ -9,18 +9,6 @@
     "Start from a selected interface ID and rebuild its two-chain coordinate view. Use [Query the release tables](2_query_filter_index.ipynb) to select interfaces and {ref}`Protein interfaces <protein-interface-reference>` for the column definitions."
    ]
   },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "import os\n",
-    "\n",
-    "os.environ.setdefault(\"PLINDER_RELEASE\", \"2026-07\")\n",
-    "os.environ.setdefault(\"PLINDER_RELEASE_NUMBER\", \"1\")"
-   ]
-  },
   {
    "cell_type": "code",
    "execution_count": null,
diff --git a/docs/examples/similarity_and_representatives.ipynb b/docs/examples/similarity_and_representatives.ipynb
index 56b0cd09..c9f7a503 100644
--- a/docs/examples/similarity_and_representatives.ipynb
+++ b/docs/examples/similarity_and_representatives.ipynb
@@ -9,18 +9,6 @@
     "Reconstruct selected pairwise scores, read part of a complete score table, and query representative assignments. {ref}`Similarity scores <similarity-score-reference>` defines the metrics and files."
    ]
   },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "import os\n",
-    "\n",
-    "os.environ.setdefault(\"PLINDER_RELEASE\", \"2026-07\")\n",
-    "os.environ.setdefault(\"PLINDER_RELEASE_NUMBER\", \"1\")"
-   ]
-  },
   {
    "cell_type": "code",
    "execution_count": null,

From fcb9a019bcace8c2299547a4f7326d273375a9b0 Mon Sep 17 00:00:00 2001
From: Thomas Duignan <thomas.j.duignan@gmail.com>
Date: Thu, 1 Oct 2026 16:19:35 +0200
Subject: [PATCH 09/26] fix: don't CIGAR-decode custom alignments that already
 carry residue numbers

Custom-scoring alignments keep their CIGAR column but are already mapped to
query/target residue numbers. load_alignments only checked for decoded
positions, so it tried to decode them, which needs a release chain lookup the
custom scorer doesn't have (ValueError: CIGAR alignments require a chain
lookup). Found by executing docs/examples/custom_scoring.ipynb.
---
 src/plinder/data/annotations/get_similarity_scores.py | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/src/plinder/data/annotations/get_similarity_scores.py b/src/plinder/data/annotations/get_similarity_scores.py
index 49e07050..e0487d8e 100644
--- a/src/plinder/data/annotations/get_similarity_scores.py
+++ b/src/plinder/data/annotations/get_similarity_scores.py
@@ -2751,9 +2751,13 @@ def load_alignments(
                 aln_df = aln_df.drop(columns="_merge")
                 for column in score_columns:
                     aln_df[column] = aln_df[column].astype(float) / 100
+            # Custom-scoring alignments keep their CIGARs but are already
+            # mapped to residue numbers, so only undecoded release shards
+            # need the chain lookup.
             if (
                 "cigar" in aln_df.columns
                 and "query_selected_residue_positions" not in aln_df.columns
+                and "query_selected_residue_numbers" not in aln_df.columns
             ):
                 if self.alignment_chain_lookup is None:
                     raise ValueError("CIGAR alignments require a chain lookup")

From f67b308cb3ef293c6280d5bac70fa7646bbb63e4 Mon Sep 17 00:00:00 2001
From: Thomas Duignan <thomas.j.duignan@gmail.com>
Date: Thu, 1 Oct 2026 16:19:35 +0200
Subject: [PATCH 10/26] ci: print notebook tracebacks when the docs build fails

---
 .github/workflows/pr.yaml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/.github/workflows/pr.yaml b/.github/workflows/pr.yaml
index 942c9044..17b19505 100644
--- a/.github/workflows/pr.yaml
+++ b/.github/workflows/pr.yaml
@@ -97,3 +97,6 @@ jobs:
         run: UV_PROJECT_ENVIRONMENT="$CONDA_PREFIX" uv sync --locked --inexact --extra docs
       - name: Build the documentation
         run: sphinx-build --fail-on-warning docs build/docs
+      - name: Show notebook errors
+        if: failure()
+        run: cat build/docs/reports/examples/*.err.log 2>/dev/null || true

From e0a3aae794f4c4d10465837cdd91449a2dc6c259 Mon Sep 17 00:00:00 2001
From: Thomas Duignan <thomas.j.duignan@gmail.com>
Date: Fri, 2 Oct 2026 10:06:26 +0200
Subject: [PATCH 11/26] build: stop committing uv.lock; resolve from
 pyproject.toml in CI

CI now tests the dependency set users get from pip, catching upstream
breakage early rather than through a lockfile that must be refreshed.
---
 .github/workflows/main.yaml      |    2 +-
 .github/workflows/pr.yaml        |    2 +-
 .gitignore                       |    3 +
 docs/contribution/development.md |    4 +-
 tox.ini                          |    2 +-
 uv.lock                          | 5143 ------------------------------
 6 files changed, 8 insertions(+), 5148 deletions(-)
 delete mode 100644 uv.lock

diff --git a/.github/workflows/main.yaml b/.github/workflows/main.yaml
index beb95fd3..d37e73f3 100644
--- a/.github/workflows/main.yaml
+++ b/.github/workflows/main.yaml
@@ -35,7 +35,7 @@ jobs:
         with:
           enable-cache: true
       - name: Install plinder
-        run: UV_PROJECT_ENVIRONMENT="$CONDA_PREFIX" uv sync --locked --inexact
+        run: UV_PROJECT_ENVIRONMENT="$CONDA_PREFIX" uv sync --inexact
       - name: Get version bump
         id: get-tag
         run: echo "bump=$(python flows/version.py)" >> $GITHUB_OUTPUT
diff --git a/.github/workflows/pr.yaml b/.github/workflows/pr.yaml
index c272367c..7ff4ddee 100644
--- a/.github/workflows/pr.yaml
+++ b/.github/workflows/pr.yaml
@@ -61,7 +61,7 @@ jobs:
         with:
           enable-cache: true
       - name: Install plinder
-        run: UV_PROJECT_ENVIRONMENT="$CONDA_PREFIX" uv sync --locked --inexact
+        run: UV_PROJECT_ENVIRONMENT="$CONDA_PREFIX" uv sync --inexact
       - name: Run tests
         env:
           PLINDER_OFFLINE: "true"
diff --git a/.gitignore b/.gitignore
index 5e6fc822..313cf21b 100644
--- a/.gitignore
+++ b/.gitignore
@@ -195,3 +195,6 @@ tmp_foldseek
 tmp_mmseqs
 artifacts
 logs/
+
+# uv lockfile: not committed; CI resolves the latest versions allowed by pyproject.toml
+uv.lock
diff --git a/docs/contribution/development.md b/docs/contribution/development.md
index 7530a9fe..826400c0 100644
--- a/docs/contribution/development.md
+++ b/docs/contribution/development.md
@@ -28,7 +28,7 @@ $ mamba activate plinder
 
 ### Installing `plinder`
 
-All Python dependencies are declared in `pyproject.toml` and locked in `uv.lock`.
+All Python dependencies are declared in `pyproject.toml`.
 With [uv](https://docs.astral.sh/uv/), install `plinder` in editable mode with the
 complete `dev` dependency group (all extras used in CI, including CPU-only pytorch
 on Linux and the git-only pipeline packages) into the active Conda environment:
@@ -37,7 +37,7 @@ on Linux and the git-only pipeline packages) into the active Conda environment:
 $ UV_PROJECT_ENVIRONMENT="$CONDA_PREFIX" uv sync --inexact
 ```
 
-CI runs the same command with `--locked`. Without the Conda environment, a plain `uv sync`
+CI runs the same command. Without the Conda environment, a plain `uv sync`
 installs into `.venv`; tests that need the Conda-only tools will then fail.
 
 With pip, the base install covers data generation and the core library:
diff --git a/tox.ini b/tox.ini
index 097c4d5a..ddbff24b 100644
--- a/tox.ini
+++ b/tox.ini
@@ -37,4 +37,4 @@ setenv =
     PLINDER_LOG_LEVEL=10
     PLINDER_OFFLINE=true
 allowlist_externals = uv
-commands = uv run --locked python -m pytest -n auto {posargs}
+commands = uv run python -m pytest -n auto {posargs}
diff --git a/uv.lock b/uv.lock
deleted file mode 100644
index 70faadac..00000000
--- a/uv.lock
+++ /dev/null
@@ -1,5143 +0,0 @@
-version = 1
-revision = 3
-requires-python = ">=3.12"
-resolution-markers = [
-    "python_full_version >= '3.14' and sys_platform == 'linux'",
-    "python_full_version < '3.14' and sys_platform == 'linux'",
-    "python_full_version >= '3.14' and sys_platform == 'win32'",
-    "python_full_version >= '3.14' and sys_platform == 'emscripten'",
-    "python_full_version >= '3.14' and sys_platform != 'emscripten' and sys_platform != 'linux' and sys_platform != 'win32'",
-    "python_full_version < '3.14' and sys_platform == 'win32'",
-    "python_full_version < '3.14' and sys_platform == 'emscripten'",
-    "python_full_version < '3.14' and sys_platform != 'emscripten' and sys_platform != 'linux' and sys_platform != 'win32'",
-]
-
-[[package]]
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From 8996f82a811f234453502254eaf5c786718b8bb9 Mon Sep 17 00:00:00 2001
From: Thomas Duignan <thomas.j.duignan@gmail.com>
Date: Fri, 2 Oct 2026 10:06:32 +0200
Subject: [PATCH 12/26] ci: install docs builds without uv.lock

---
 .github/workflows/docs.yaml | 2 +-
 .github/workflows/pr.yaml   | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/docs.yaml b/.github/workflows/docs.yaml
index dbcf5831..f6edeac6 100644
--- a/.github/workflows/docs.yaml
+++ b/.github/workflows/docs.yaml
@@ -39,7 +39,7 @@ jobs:
           enable-cache: true
       - name: Install plinder
         shell: bash -el {0}
-        run: UV_PROJECT_ENVIRONMENT="$CONDA_PREFIX" uv sync --locked --inexact --extra docs
+        run: UV_PROJECT_ENVIRONMENT="$CONDA_PREFIX" uv sync --inexact --extra docs
       - name: Build docs
         shell: bash -el {0}
         id: build
diff --git a/.github/workflows/pr.yaml b/.github/workflows/pr.yaml
index 25c1b567..7657eeb0 100644
--- a/.github/workflows/pr.yaml
+++ b/.github/workflows/pr.yaml
@@ -94,7 +94,7 @@ jobs:
         with:
           enable-cache: true
       - name: Install plinder
-        run: UV_PROJECT_ENVIRONMENT="$CONDA_PREFIX" uv sync --locked --inexact --extra docs
+        run: UV_PROJECT_ENVIRONMENT="$CONDA_PREFIX" uv sync --inexact --extra docs
       - name: Build the documentation
         run: sphinx-build --fail-on-warning docs build/docs
       - name: Show notebook errors

From e2f654bf2c398e14d72994789299e2e5bf59b345 Mon Sep 17 00:00:00 2001
From: Thomas Duignan <thomas.j.duignan@gmail.com>
Date: Fri, 2 Oct 2026 10:07:12 +0200
Subject: [PATCH 13/26] build: move the release version script to the repo root

---
 .github/workflows/main.yaml    | 2 +-
 flows/version.py => version.py | 0
 2 files changed, 1 insertion(+), 1 deletion(-)
 rename flows/version.py => version.py (100%)

diff --git a/.github/workflows/main.yaml b/.github/workflows/main.yaml
index d37e73f3..9ef3df7b 100644
--- a/.github/workflows/main.yaml
+++ b/.github/workflows/main.yaml
@@ -38,7 +38,7 @@ jobs:
         run: UV_PROJECT_ENVIRONMENT="$CONDA_PREFIX" uv sync --inexact
       - name: Get version bump
         id: get-tag
-        run: echo "bump=$(python flows/version.py)" >> $GITHUB_OUTPUT
+        run: echo "bump=$(python version.py)" >> $GITHUB_OUTPUT
       - name: Run tests
         if: steps.get-tag.outputs.bump != ''
         env:
diff --git a/flows/version.py b/version.py
similarity index 100%
rename from flows/version.py
rename to version.py

From bfb2eae0f08d9771f06a70c8c633a1b7affaa035 Mon Sep 17 00:00:00 2001
From: Ninjani <janani.durairaj@gmail.com>
Date: Fri, 2 Oct 2026 11:44:02 +0200
Subject: [PATCH 14/26] Fix overlapping assembly copies and interface
 clustering

---
 src/plinder/data/annotations/cif_utils.py |  67 ++++++++-
 src/plinder/data/clusters.py              | 168 +++++++++++++++-------
 tests/data/test_clusters.py               |  83 +++++++++++
 tests/test_cif_utils.py                   |  66 +++++++++
 4 files changed, 334 insertions(+), 50 deletions(-)

diff --git a/src/plinder/data/annotations/cif_utils.py b/src/plinder/data/annotations/cif_utils.py
index d6efe789..9730a899 100644
--- a/src/plinder/data/annotations/cif_utils.py
+++ b/src/plinder/data/annotations/cif_utils.py
@@ -766,13 +766,17 @@ def drop_self_clashing_symmetry_copies(
     clash_ratio: float = 0.5,
     context: str = "assembly",
 ) -> struc.AtomArray:
-    """Drop symmetry copies overlapping a lower ``sym_id`` copy.
+    """Drop coincident symmetry copies and severely overlapping protein chains.
 
     Chains on a symmetry axis can expand into coincident copies of one
     ``label_asym_id``. Copies are visited in ascending ``sym_id``; one is
     dropped when more than ``clash_ratio`` of its atoms lie within
     ``clash_distance`` of an already kept copy. Waters are untouched.
-    Requires the ``sym_id`` and ``label_asym_id`` annotations.
+    Protein chains from different source asym IDs are also compared by their
+    C-alpha atoms: a chain is removed if at least five and more than 10%, or
+    at least twenty regardless of chain length, lie within 2 Å of previously
+    retained protein chains. Such C-alpha distances are nonphysical for
+    separate chains. Requires the ``sym_id`` and ``label_asym_id`` annotations.
     """
     categories = set(assembly.get_annotation_categories())
     if not {"sym_id", "label_asym_id"}.issubset(categories):
@@ -815,6 +819,65 @@ def drop_self_clashing_symmetry_copies(
                 asym_id,
                 [(sym_id, round(fraction, 2)) for sym_id, fraction in dropped],
             )
+    ca_indices = np.flatnonzero(
+        keep
+        & candidates
+        & (assembly.atom_name == "CA")
+        & struc.filter_amino_acids(assembly)
+    )
+    if len(ca_indices):
+        ca = assembly[ca_indices]
+        chain_names = np.array(
+            [
+                f"{int(sym_id)}.{asym_id}"
+                for sym_id, asym_id in zip(ca.sym_id, ca.label_asym_id, strict=True)
+            ]
+        )
+        unique_chains, chain_index = np.unique(chain_names, return_inverse=True)
+        chain_sizes = np.bincount(chain_index)
+        eligible = [index for index, size in enumerate(chain_sizes) if size >= 10]
+        if len(eligible) > 1:
+            cell_list = struc.CellList(ca, cell_size=3.0)
+            retained: list[int] = []
+            dropped_chains: list[tuple[str, int, float]] = []
+            for index in sorted(
+                eligible,
+                key=lambda value: (
+                    int(unique_chains[value].split(".", 1)[0]),
+                    unique_chains[value],
+                ),
+            ):
+                query_mask = chain_index == index
+                if retained:
+                    neighbors = cell_list.get_atoms(ca.coord[query_mask], radius=2.0)
+                    clashing = (
+                        (neighbors >= 0)
+                        & np.isin(chain_index[np.clip(neighbors, 0, None)], retained)
+                    ).any(axis=1)
+                    fraction = float(clashing.mean())
+                    clash_count = int(clashing.sum())
+                    if clash_count >= 20 or (clash_count >= 5 and fraction > 0.1):
+                        sym_id, asym_id = unique_chains[index].split(".", 1)
+                        keep &= ~(
+                            (assembly.sym_id == int(sym_id))
+                            & (assembly.label_asym_id == asym_id)
+                        )
+                        dropped_chains.append(
+                            (str(unique_chains[index]), clash_count, fraction)
+                        )
+                        continue
+                retained.append(index)
+            if dropped_chains:
+                LOG.info(
+                    "%s: dropped %d clashing protein chains (first 10 chain, "
+                    "C-alpha clash count, fraction): %s",
+                    context,
+                    len(dropped_chains),
+                    [
+                        (chain, count, round(fraction, 2))
+                        for chain, count, fraction in dropped_chains[:10]
+                    ],
+                )
     if keep.all():
         return assembly
     return assembly[keep]
diff --git a/src/plinder/data/clusters.py b/src/plinder/data/clusters.py
index d138f836..5b95b97e 100644
--- a/src/plinder/data/clusters.py
+++ b/src/plinder/data/clusters.py
@@ -23,7 +23,6 @@
 import networkit as nk
 import numpy as np
 import pandas as pd
-import pyarrow as pa
 import pyarrow.parquet as pq
 from numpy.typing import NDArray
 
@@ -583,13 +582,27 @@ def prepare_symmetric_edge_plan(
     score_metrics = [
         metric for metric in selected_metrics if not is_chemical_cluster_metric(metric)
     ]
-    # One aggregation group per distinct raw-source set: interface metrics share
-    # the interface score shards, all protein/pocket metrics share the holo
-    # search scores, and each chemical metric has its own directed-edge shards
-    # (e.g. ligand_scores / mhfp6_scores).
+    # Group metrics by score source; interface exports and chemical metrics
+    # have separate sources, while protein/pocket metrics share holo scores.
     source_groups: list[tuple[str, list[str]]] = []
     if entity_type == "interface":
-        source_groups.append(("interface", selected_metrics))
+        raw_metrics: list[str] = []
+        for metric in selected_metrics:
+            export = (
+                data_dir
+                / "exports"
+                / (
+                    "interface_similarity_scores.parquet"
+                    if metric == "interface_qcov"
+                    else "interface_half_similarity_scores.parquet"
+                )
+            )
+            if export.is_file():
+                source_groups.append((f"interface_export_{metric}", [metric]))
+            else:
+                raw_metrics.append(metric)
+        if raw_metrics:
+            source_groups.append(("interface", raw_metrics))
     else:
         if score_metrics:
             source_groups.append(("score", score_metrics))
@@ -598,11 +611,19 @@ def prepare_symmetric_edge_plan(
     for kind, source_metrics in source_groups:
         if not source_metrics:
             continue
-        sources = _raw_component_score_sources(
-            data_dir=data_dir,
-            metric=source_metrics[0],
-            entity_type=entity_type,
-        )
+        if kind.startswith("interface_export_"):
+            export_name = (
+                "interface_similarity_scores.parquet"
+                if source_metrics[0] == "interface_qcov"
+                else "interface_half_similarity_scores.parquet"
+            )
+            sources = [data_dir / "exports" / export_name]
+        else:
+            sources = _raw_component_score_sources(
+                data_dir=data_dir,
+                metric=source_metrics[0],
+                entity_type=entity_type,
+            )
         if not sources:
             if entity_type != "interface":
                 raise FileNotFoundError(
@@ -792,7 +813,7 @@ def write_symmetric_edge_fragment_batch(
     read_paths: Sequence[Path] | None = None,
     entity_type: ClusterEntity = "ligand",
 ) -> dict[str, Any]:
-    """Aggregate one raw-source batch into canonical-pair hash fragments."""
+    """Write one score batch into canonical-pair hash fragments."""
     if threads < 1:
         raise ValueError("symmetric-edge threads must be positive")
     plan = load_symmetric_edge_plan(data_dir, entity_type=entity_type)
@@ -825,6 +846,10 @@ def write_symmetric_edge_fragment_batch(
     import duckdb
 
     connection = duckdb.connect()
+    if slurm_memory_mb := os.environ.get("SLURM_MEM_PER_NODE"):
+        connection.execute(
+            "SET memory_limit = ?", [f"{int(slurm_memory_mb) * 3 // 5}MB"]
+        )
     connection.sql(f"SET threads={threads}")
     temporary_root = scratch_dir / "duckdb"
     temporary_root.mkdir(exist_ok=True, parents=True)
@@ -861,6 +886,26 @@ def write_symmetric_edge_fragment_batch(
             WHERE cast(metric AS VARCHAR) IN ({metrics_sql})
             """
         )
+    elif batch["kind"] in {
+        "interface_export_interface_qcov",
+        "interface_export_interface_side_qcov",
+    }:
+        metric = metrics[0]
+        query, target = (
+            ("query_system", "target_system")
+            if metric == "interface_qcov"
+            else ("query_half_interface_id", "target_half_interface_id")
+        )
+        selected_sql = dedent(
+            f"""
+            SELECT
+                '{metric}'::VARCHAR AS metric,
+                cast({query} AS VARCHAR) AS query_node,
+                cast({target} AS VARCHAR) AS target_node,
+                cast(similarity AS DOUBLE) AS similarity
+            FROM read_parquet([{paths_sql}], union_by_name=true)
+            """
+        )
     else:
         nodes, eligible_systems = component_node_universe(
             data_dir=data_dir,
@@ -930,6 +975,39 @@ def write_symmetric_edge_fragment_batch(
             max(similarity) FILTER (WHERE query_node = high_node)::DOUBLE
                 AS reverse_similarity
         """
+    compact_interface_export = batch["kind"] in {
+        "interface_export_interface_qcov",
+        "interface_export_interface_side_qcov",
+    }
+    edge_rows_sql = (
+        dedent(
+            """
+            SELECT
+                metric,
+                bucket,
+                low_node,
+                high_node,
+                CASE WHEN query_node = low_node THEN similarity END
+                    AS forward_similarity,
+                CASE WHEN query_node = high_node THEN similarity END
+                    AS reverse_similarity
+            FROM bucketed
+            """
+        )
+        if compact_interface_export
+        else dedent(
+            f"""
+            SELECT
+                metric,
+                bucket,
+                low_node,
+                high_node,
+                {aggregate_sql}
+            FROM bucketed
+            GROUP BY metric, bucket, low_node, high_node
+            """
+        )
+    )
     query = dedent(
         f"""
         COPY (
@@ -955,14 +1033,7 @@ def write_symmetric_edge_fragment_batch(
                     )::INTEGER AS bucket
                 FROM canonical
             )
-            SELECT
-                metric,
-                bucket,
-                low_node,
-                high_node,
-                {aggregate_sql}
-            FROM bucketed
-            GROUP BY metric, bucket, low_node, high_node
+            {edge_rows_sql}
         ) TO '{scratch_output.as_posix()}'
         (
             FORMAT PARQUET,
@@ -1102,6 +1173,10 @@ def write_symmetric_edge_shard(
     local_output = scratch_dir / f"{metric}-{bucket:03d}.parquet"
     local_output.unlink(missing_ok=True)
     connection = duckdb.connect()
+    if slurm_memory_mb := os.environ.get("SLURM_MEM_PER_NODE"):
+        connection.execute(
+            "SET memory_limit = ?", [f"{int(slurm_memory_mb) * 3 // 5}MB"]
+        )
     connection.sql(f"SET threads={threads}")
     connection.sql(f"SET temp_directory='{scratch_dir.as_posix()}'")
     if fragments:
@@ -2983,11 +3058,15 @@ def _stage_directed_cover_edges(
     import duckdb
 
     connection = duckdb.connect()
+    if slurm_memory_mb := os.environ.get("SLURM_MEM_PER_NODE"):
+        connection.execute(
+            "SET memory_limit = ?", [f"{int(slurm_memory_mb) * 4 // 5}MB"]
+        )
     connection.sql(f"SET threads={threads}")
+    connection.sql("SET preserve_insertion_order=false")
     temporary_root.mkdir(exist_ok=True, parents=True)
     escaped_temporary_root = temporary_root.as_posix().replace("'", "''")
     connection.sql(f"SET temp_directory='{escaped_temporary_root}'")
-    connection.sql("SET preserve_insertion_order=false")
     connection.register(
         "component_labels",
         labels[[node_column, "graph_node"]],
@@ -3041,35 +3120,30 @@ def _stage_directed_cover_edges(
     )
     staged_edges.unlink(missing_ok=True)
     incoming_counts_path.unlink(missing_ok=True)
-    staged_schema = pa.schema(
-        [
-            ("query_node", pa.uint32()),
-            ("target_node", pa.uint32()),
-            ("similarity", pa.uint8()),
-        ]
-    )
     staged_rows = 0
     incoming_counts = np.zeros(len(labels), dtype=np.int64)
     stage_started = time()
-    writer = pq.ParquetWriter(
-        staged_edges,
-        staged_schema,
-        compression="zstd",
-        use_dictionary=False,
-        write_statistics=False,
-    )
     try:
-        reader = connection.execute(query).fetch_record_batch(rows_per_batch=2_000_000)
-        for batch_index, record_batch in enumerate(reader, start=1):
-            compact = (
-                pa.Table.from_batches([record_batch])
-                .select(staged_schema.names)
-                .cast(staged_schema, safe=False)
-            )
-            writer.write_table(compact, row_group_size=2_000_000)
-            staged_rows += len(record_batch)
-            target_index = compact.schema.get_field_index("target_node")
-            targets = compact.column(target_index).to_numpy(zero_copy_only=False)
+        escaped_staged_edges = staged_edges.as_posix().replace("'", "''")
+        connection.execute(
+            f"COPY ({query}) TO '{escaped_staged_edges}' "
+            "(FORMAT PARQUET, COMPRESSION ZSTD, ROW_GROUP_SIZE 2000000)"
+        )
+        previous_target = -1
+        for batch_index, batch in enumerate(
+            pq.ParquetFile(staged_edges).iter_batches(
+                batch_size=2_000_000, columns=["target_node"]
+            ),
+            start=1,
+        ):
+            targets = batch.column(0).to_numpy(zero_copy_only=False)
+            if len(targets) and (
+                int(targets[0]) < previous_target or np.any(targets[1:] < targets[:-1])
+            ):
+                raise ValueError("directed-cover edges are not target-sorted")
+            if len(targets):
+                previous_target = int(targets[-1])
+            staged_rows += len(targets)
             incoming_counts += np.bincount(targets, minlength=len(labels))
             if batch_index % 5 == 0:
                 elapsed = time() - stage_started
@@ -3084,13 +3158,11 @@ def _stage_directed_cover_edges(
                     elapsed,
                 )
     except BaseException:
-        writer.close()
         connection.close()
         staged_edges.unlink(missing_ok=True)
         incoming_counts_path.unlink(missing_ok=True)
         raise
     else:
-        writer.close()
         connection.close()
     np.save(incoming_counts_path, incoming_counts, allow_pickle=False)
     LOG.info(
diff --git a/tests/data/test_clusters.py b/tests/data/test_clusters.py
index 55b3513d..5298b7aa 100644
--- a/tests/data/test_clusters.py
+++ b/tests/data/test_clusters.py
@@ -711,6 +711,89 @@ def test_interface_side_clusters_use_independent_side_nodes(tmp_path):
     assert edges.loc[("i1::side=1", "i2::side=2"), "similarity"] == pytest.approx(60.0)
 
 
+def test_interface_clusters_prefer_compact_similarity_tables(tmp_path):
+    from plinder.data.clusters import (
+        prepare_component_node_universe,
+        prepare_symmetric_edge_plan,
+        write_symmetric_edge_fragment_batch,
+        write_symmetric_edge_shard,
+    )
+
+    index_dir = tmp_path / "index"
+    index_dir.mkdir()
+    pd.DataFrame({"system_id": ["i1", "i2"]}).to_parquet(
+        index_dir / "interface_annotation_table.parquet", index=False
+    )
+    _write_interface_cluster_universe(index_dir, ["i1", "i2"])
+    raw_dir = tmp_path / "interface_scores"
+    raw_dir.mkdir()
+    pd.DataFrame(
+        {
+            "query_system": ["i1"],
+            "target_system": ["i2"],
+            "metric": ["interface_qcov"],
+            "similarity": [5],
+        }
+    ).to_parquet(raw_dir / "shard=ab.parquet", index=False)
+    exports = tmp_path / "exports"
+    exports.mkdir()
+    pd.DataFrame(
+        {
+            "query_system": ["i1", "i1", "i2"],
+            "target_system": ["i2", "i2", "i1"],
+            "similarity": [80, 75, 60],
+        }
+    ).to_parquet(exports / "interface_similarity_scores.parquet", index=False)
+    pd.DataFrame(
+        {
+            "query_half_interface_id": ["i1::side=1", "i2::side=2"],
+            "target_half_interface_id": ["i2::side=2", "i1::side=1"],
+            "similarity": [90, 70],
+        }
+    ).to_parquet(exports / "interface_half_similarity_scores.parquet", index=False)
+
+    prepare_component_node_universe(tmp_path, entity_type="interface")
+    plan = prepare_symmetric_edge_plan(
+        data_dir=tmp_path,
+        metrics=["interface_qcov", "interface_side_qcov"],
+        source_batch_size=1,
+        bucket_count=1,
+        entity_type="interface",
+    )
+    assert {batch["kind"] for batch in plan["batches"]} == {
+        "interface_export_interface_qcov",
+        "interface_export_interface_side_qcov",
+    }
+    for batch in plan["batches"]:
+        write_symmetric_edge_fragment_batch(
+            data_dir=tmp_path,
+            batch=batch,
+            scratch_dir=tmp_path / "scratch-fragments" / batch["key"],
+            threads=1,
+            entity_type="interface",
+        )
+    for metric, pair, expected in (
+        ("interface_qcov", ("i1", "i2"), 60.0),
+        ("interface_side_qcov", ("i1::side=1", "i2::side=2"), 70.0),
+    ):
+        write_symmetric_edge_shard(
+            data_dir=tmp_path,
+            metric=metric,
+            bucket=0,
+            scratch_dir=tmp_path / "scratch-shards" / metric,
+            threads=1,
+            entity_type="interface",
+        )
+        edges = pd.read_parquet(
+            tmp_path
+            / "interface_clusters/symmetric_edges"
+            / f"metric={metric}/bucket=000.parquet"
+        ).set_index(["query_node", "target_node"])
+        assert edges.loc[pair, "similarity"] == pytest.approx(expected)
+        if metric == "interface_qcov":
+            assert edges.loc[pair, "forward_similarity"] == pytest.approx(80.0)
+
+
 def test_empty_interface_universe_publishes_typed_empty_cover(tmp_path):
     from plinder.data.clusters import (
         make_directed_cover_component_reduction,
diff --git a/tests/test_cif_utils.py b/tests/test_cif_utils.py
index e4cf8489..cbbae686 100644
--- a/tests/test_cif_utils.py
+++ b/tests/test_cif_utils.py
@@ -1377,3 +1377,69 @@ def test_drop_self_clashing_symmetry_copies_keeps_lowest_and_distant_copies():
     assert sorted(set(kept.sym_id[kept.label_asym_id == "L"])) == [0, 2, 3]
     assert sorted(set(kept.sym_id[kept.label_asym_id == "P"])) == [0, 2]
     assert drop_self_clashing_symmetry_copies(kept) is kept
+
+
+def test_drop_overlapping_protein_chains_with_distinct_asym_ids():
+    import biotite.structure as struc
+
+    from plinder.data.annotations.cif_utils import drop_self_clashing_symmetry_copies
+
+    base = np.column_stack((np.arange(20) * 3.8, np.zeros(20), np.zeros(20)))
+    partial = base.copy()
+    partial[8:, 1] = 10.0
+    isolated_errors = base.copy()
+    isolated_errors[3:, 1] = 15.0
+    split_contacts = base.copy()
+    split_contacts[3:6, 1] = 4.5
+    split_contacts[6:, 1] = 30.0
+    blocks = [
+        ("A", base),
+        ("B", base.copy()),  # identical protein, but a different source asym ID
+        ("C", partial),  # eight clashing C-alpha atoms out of twenty
+        ("D", base + np.array([0.0, 4.5, 0.0])),  # plausible close contact
+        ("E", base + np.array([0.0, 20.0, 0.0])),
+        ("F", isolated_errors),  # three collisions do not remove a whole chain
+        ("G", split_contacts),  # six collisions across two other chains
+    ]
+    atoms = struc.AtomArray(20 * len(blocks))
+    atoms.coord = np.concatenate([coord for _, coord in blocks]).astype(np.float32)
+    atoms.set_annotation("label_asym_id", np.repeat([asym for asym, _ in blocks], 20))
+    atoms.set_annotation("sym_id", np.zeros(len(atoms), dtype=int))
+    atoms.chain_id = atoms.label_asym_id.copy()
+    atoms.atom_name = np.repeat("CA", len(atoms))
+    atoms.element = np.repeat("C", len(atoms))
+    atoms.res_name = np.repeat("ALA", len(atoms))
+    atoms.res_id = np.tile(np.arange(1, 21), len(blocks))
+    atoms.hetero = np.zeros(len(atoms), dtype=bool)
+
+    kept = drop_self_clashing_symmetry_copies(atoms)
+
+    assert set(kept.label_asym_id) == {"A", "D", "E", "F"}
+    assert drop_self_clashing_symmetry_copies(kept) is kept
+
+
+def test_drop_long_protein_chain_with_many_absolute_ca_clashes():
+    import biotite.structure as struc
+
+    from plinder.data.annotations.cif_utils import drop_self_clashing_symmetry_copies
+
+    base = np.column_stack((np.arange(300) * 3.8, np.zeros(300), np.zeros(300)))
+    twenty_clashes = base.copy()
+    twenty_clashes[20:, 1] = 10.0
+    nineteen_clashes = base.copy()
+    nineteen_clashes[19:, 1] = 20.0
+    blocks = [("A", base), ("B", twenty_clashes), ("C", nineteen_clashes)]
+    atoms = struc.AtomArray(300 * len(blocks))
+    atoms.coord = np.concatenate([coords for _, coords in blocks]).astype(np.float32)
+    atoms.set_annotation("label_asym_id", np.repeat([name for name, _ in blocks], 300))
+    atoms.set_annotation("sym_id", np.zeros(len(atoms), dtype=int))
+    atoms.chain_id = atoms.label_asym_id.copy()
+    atoms.atom_name = np.repeat("CA", len(atoms))
+    atoms.element = np.repeat("C", len(atoms))
+    atoms.res_name = np.repeat("ALA", len(atoms))
+    atoms.res_id = np.tile(np.arange(1, 301), len(blocks))
+    atoms.hetero = np.zeros(len(atoms), dtype=bool)
+
+    kept = drop_self_clashing_symmetry_copies(atoms)
+
+    assert set(kept.label_asym_id) == {"A", "C"}

From 4024193fd22d124762b2cbb89b35e711870870c8 Mon Sep 17 00:00:00 2001
From: Ninjani <janani.durairaj@gmail.com>
Date: Fri, 2 Oct 2026 11:44:38 +0200
Subject: [PATCH 15/26] Fix weekly release repair and update planning

---
 src/plinder/data/pipeline/update_release.py | 134 +++++++++-----------
 src/plinder/data/pipeline/updates.py        |  33 ++++-
 tests/data/pipeline/test_update_release.py  |  85 ++++++++++++-
 tests/data/pipeline/test_updates.py         |  19 +++
 4 files changed, 193 insertions(+), 78 deletions(-)

diff --git a/src/plinder/data/pipeline/update_release.py b/src/plinder/data/pipeline/update_release.py
index 97f005b4..4a4ff723 100644
--- a/src/plinder/data/pipeline/update_release.py
+++ b/src/plinder/data/pipeline/update_release.py
@@ -12,6 +12,7 @@
 import os
 from concurrent.futures import ProcessPoolExecutor, ThreadPoolExecutor, as_completed
 from dataclasses import replace
+from itertools import groupby
 from multiprocessing import get_context
 from pathlib import Path
 from shutil import copyfile, rmtree
@@ -33,7 +34,7 @@
     write_json_atomic,
 )
 from plinder.data import clusters, databases
-from plinder.data.annotations import get_similarity_scores
+from plinder.data.annotations import ccd_ligand_dbs, get_similarity_scores
 from plinder.data.pipeline import config, score, tasks, utils
 from plinder.data.pipeline.update_archives import update_ligand_archives
 from plinder.data.pipeline.update_entries import apply_entry_update
@@ -297,25 +298,19 @@ def _queries_with_old_target_hits(
     ]
     if not paths:
         return set()
-    connection = duckdb.connect()
-    try:
-        connection.register(
-            "affected_targets",
-            pd.DataFrame({"target_entry": sorted(affected)}),
-        )
-        sources = ", ".join(
-            f"'{path.as_posix().replace(chr(39), chr(39) * 2)}'" for path in paths
-        )
-        hits = connection.sql(
-            f"""
-            SELECT DISTINCT query_entry
-            FROM read_parquet([{sources}], union_by_name=true) AS alignments
-            INNER JOIN affected_targets USING (target_entry)
-            """
-        ).df()
-    finally:
-        connection.close()
-    return set(hits["query_entry"].dropna().astype(str))
+    target_ids = pa.array(sorted(affected), type=pa.string())
+    hits: set[str] = set()
+    for path in paths:
+        for batch in pq.ParquetFile(path).iter_batches(
+            columns=["query_entry", "target_entry"], batch_size=131_072
+        ):
+            mask = pc.is_in(batch.column("target_entry"), value_set=target_ids)
+            if pc.any(mask).as_py():
+                matches = pc.unique(pc.filter(batch.column("query_entry"), mask))
+                hits.update(
+                    str(value) for value in matches.to_pylist() if value is not None
+                )
+    return hits
 
 
 def _changed_target_database(
@@ -323,46 +318,17 @@ def _changed_target_database(
     *,
     search_db: str,
     affected: set[str],
-    scratch_dir: Path,
-    threads: int,
 ) -> Path | None:
     chains = _scoring_chains(data_dir, search_db)
     chains = chains.loc[chains["entry_pdb_id"].astype(str).isin(affected)]
-    identifiers = {
-        f"{search_db}_{alignment_type}": _database_identifiers(chains, alignment_type)
-        for alignment_type in ("foldseek", "mmseqs")
-    }
-    if not any(identifiers.values()):
-        return None
-    target_dir = scratch_dir / f"changed-{search_db}-targets"
-    if target_dir.exists():
-        rmtree(target_dir)
-    selected = {
-        key: ids
-        for key, ids in identifiers.items()
-        if ids
-        and (
-            data_dir
-            / "dbs/weekly_delta"
-            / key.rsplit("_", 1)[1]
-            / f"{key.rsplit('_', 1)[1]}.dbtype"
-        ).is_file()
-    }
-    if not selected:
+    if not any(_database_identifiers(chains, kind) for kind in ("foldseek", "mmseqs")):
         return None
-    databases.make_sub_dbs(
-        target_dir,
-        {
-            key: data_dir
-            / "dbs/weekly_delta"
-            / key.rsplit("_", 1)[1]
-            / key.rsplit("_", 1)[1]
-            for key in selected
-        },
-        identifiers_by_database=selected,
-        tmp_dir=scratch_dir / f"changed-{search_db}-target-work",
-        threads=threads,
-    )
+    target_dir = data_dir / "dbs/weekly_delta/subdbs"
+    if not any(
+        (target_dir / f"{search_db}_{kind}/exact_cluster.json").is_file()
+        for kind in ("foldseek", "mmseqs")
+    ):
+        raise FileNotFoundError(f"missing changed-target database for {search_db}")
     return target_dir
 
 
@@ -582,8 +548,6 @@ def _plan_alignment_repairs(
         data_dir,
         search_db=search_db,
         affected=affected,
-        scratch_dir=scratch_dir,
-        threads=threads,
     )
     reverse_hits = _search_changed_targets(
         data_dir,
@@ -678,8 +642,6 @@ def repair_alignments(
             data_dir,
             search_db=search_db,
             affected=affected,
-            scratch_dir=scratch_dir / "changed-targets",
-            threads=threads,
         )
         if changed_targets is None:
             # Obsolete targets have no database to search. Re-search their old
@@ -1141,17 +1103,35 @@ def _restore_score_query_caches(
             if not missing:
                 continue
             packed = base_data_dir / "scores" / packed_name / f"shard={shard}.parquet"
-            rows = pq.read_table(
-                packed,
-                columns=schema.names,
-                filters=[("query_entry", "in", list(missing))],
-            ).cast(schema)
-            for pdb_id, destination in missing.items():
+            rows = (
+                pq.read_table(
+                    packed,
+                    columns=schema.names,
+                    filters=[("query_entry", "in", list(missing))],
+                )
+                .cast(schema)
+                .sort_by([("query_entry", "ascending")])
+            )
+            seen = set()
+            offset = 0
+            for pdb_id, group in groupby(rows["query_entry"].to_pylist()):
+                count = sum(1 for _ in group)
+                selected = rows.slice(offset, count)
+                offset += count
+                if pdb_id not in missing:
+                    continue
+                seen.add(pdb_id)
+                destination = missing[pdb_id]
                 destination.parent.mkdir(parents=True, exist_ok=True)
-                selected = rows.filter(pc.equal(rows["query_entry"], pdb_id))
                 temporary = destination.with_suffix(".parquet.tmp")
                 pq.write_table(selected, temporary, compression="zstd")
                 temporary.replace(destination)
+            for pdb_id in missing.keys() - seen:
+                destination = missing[pdb_id]
+                destination.parent.mkdir(parents=True, exist_ok=True)
+                temporary = destination.with_suffix(".parquet.tmp")
+                pq.write_table(rows.slice(0, 0), temporary, compression="zstd")
+                temporary.replace(destination)
 
 
 def _repair_score_batches(
@@ -2134,12 +2114,15 @@ def refresh_ligand_chemistry(
     )
     ccd = None
     if "make_ccd_ligand_dbs" not in cfg.flow.skip_specific_stages:
-        ccd = tasks.make_ccd_ligand_dbs(
-            data_dir=data_dir,
-            scratch_dir=scratch_dir / "ccd",
-            threads=threads,
-            minimum_similarity=float(cfg.ligand.minimum_similarity),
-        )
+        if (ccd_ligand_dbs.ccd_dbs_dir(data_dir) / "ccd_dbs.manifest.json").is_file():
+            ccd = ccd_ligand_dbs.make_ligand_ccd_match(data_dir=data_dir)
+        else:
+            ccd = tasks.make_ccd_ligand_dbs(
+                data_dir=data_dir,
+                scratch_dir=scratch_dir / "ccd",
+                threads=threads,
+                minimum_similarity=float(cfg.ligand.minimum_similarity),
+            )
     return {
         "status": "complete",
         "tanimoto": ligand_scores,
@@ -2465,6 +2448,11 @@ def apply_release_update(
             entries.action.isin(["added", "revised", "obsolete"]), "pdb_id"
         ].astype(str)
     )
+    if affected and (base / "exports/monomer_similarity_scores").exists():
+        raise NotImplementedError(
+            "weekly updates of releases with monomer similarity pairs require "
+            "a monomer delta-refresh stage"
+        )
     if report is None:
         entry_report = apply_entry_update(
             plan_dir,
diff --git a/src/plinder/data/pipeline/updates.py b/src/plinder/data/pipeline/updates.py
index b2bff78a..9982b0a1 100644
--- a/src/plinder/data/pipeline/updates.py
+++ b/src/plinder/data/pipeline/updates.py
@@ -218,14 +218,15 @@ def plan_update(
     threads: int = 8,
     previous_snapshot: Path | None = None,
     pdb_ids: Collection[str] | None = None,
+    refresh_pdb_ids: Collection[str] | None = None,
 ) -> dict[str, Any]:
     """Write an update report and work lists into a new, separate directory.
 
     Nothing is applied to the release. Blocked plans are review reports, not
     executable work lists. A partial ``pdb_ids`` scope is useful for testing;
     omit it for a complete release comparison. Coordinate revisions determine
-    changes here; validation-only or NextGen enrichment changes without a PDB
-    revision need a separate annotation refresh.
+    changes unless ``refresh_pdb_ids`` explicitly requests re-annotation of
+    unchanged entries against the same source revision.
     """
     data_dir = data_dir.resolve(strict=True)
     nextgen_root = nextgen_root.resolve(strict=True)
@@ -259,6 +260,23 @@ def plan_update(
         pdb_ids=scope,
     )
     entries = compare_entries(sources, snapshot, read_obsolete(obsolete_path))
+    refresh = {normalize_pdb_id(value) for value in refresh_pdb_ids or ()}
+    missing_refresh = refresh.difference(entries.pdb_id)
+    if missing_refresh:
+        raise ValueError(
+            f"refresh PDB IDs are outside the update scope: {sorted(missing_refresh)}"
+        )
+    unavailable_refresh = refresh.intersection(
+        entries.loc[entries.action != "unchanged", "pdb_id"]
+    )
+    if unavailable_refresh:
+        raise ValueError(
+            f"refresh PDB IDs must be unchanged entries: {sorted(unavailable_refresh)}"
+        )
+    entries.loc[entries.pdb_id.isin(refresh), ["action", "reason"]] = [
+        "revised",
+        "annotation refresh",
+    ]
     counts = dict(sorted(Counter(entries.action).items()))
     changed = bool(entries.action.isin(["added", "revised", "obsolete"]).any())
     status = (
@@ -269,6 +287,7 @@ def plan_update(
         "data_dir": str(data_dir),
         "nextgen_root": str(nextgen_root),
         "scope": scope,
+        "refresh_pdb_ids": sorted(refresh),
         "inputs": signatures,
         "counts": counts,
         "work": {
@@ -295,8 +314,8 @@ def plan_update(
             "Search directions are candidate work, not a complete search-cache repair plan: "
             "changed representatives and capped hit lists can require full-query searches.",
             "Recompute covers globally; their representatives and labels can change.",
-            "This plan compares PDB coordinate revisions, not independent changes to "
-            "validation reports, NextGen enrichment, CCD, or annotation settings.",
+            "This plan compares PDB coordinate revisions and explicitly refreshed "
+            "entries; other annotation changes are not detected automatically.",
         ],
     }
     # Check small catalogues again in case a source changed during revision reads.
@@ -339,6 +358,7 @@ def main() -> None:
     parser.add_argument("--obsolete", type=Path, required=True)
     parser.add_argument("--previous-snapshot", type=Path)
     parser.add_argument("--pdb-manifest", type=Path)
+    parser.add_argument("--refresh-pdb-manifest", type=Path)
     parser.add_argument("--threads", type=int, default=8)
     args = parser.parse_args()
     plan = plan_update(
@@ -349,6 +369,11 @@ def main() -> None:
         threads=args.threads,
         previous_snapshot=args.previous_snapshot,
         pdb_ids=load_manifest(args.pdb_manifest) if args.pdb_manifest else None,
+        refresh_pdb_ids=(
+            load_manifest(args.refresh_pdb_manifest)
+            if args.refresh_pdb_manifest
+            else None
+        ),
     )
     print(json.dumps(plan, indent=2, sort_keys=True))
     if plan["status"] == "blocked":
diff --git a/tests/data/pipeline/test_update_release.py b/tests/data/pipeline/test_update_release.py
index e3c3afe4..cb458993 100644
--- a/tests/data/pipeline/test_update_release.py
+++ b/tests/data/pipeline/test_update_release.py
@@ -659,6 +659,51 @@ def test_weekly_target_repair_restores_only_needed_query_caches(tmp_path):
         ).exists()
 
 
+def test_weekly_target_repair_splits_interleaved_packed_rows_once(tmp_path):
+    base = tmp_path / "base"
+    workspace = tmp_path / "workspace"
+    score_root = base / "dbs/subdbs/search_db=holo"
+    score_root.mkdir(parents=True)
+    for pdb_id in ("1abc", "2abc", "3abc"):
+        pd.DataFrame({"query_system": [f"{pdb_id}__1"]}).to_parquet(
+            score_root / f"{pdb_id}.parquet", index=False
+        )
+    for folder, schema in (
+        ("ligand_3d_candidate_shards", schemas.LIGAND_3D_CANDIDATE_SCHEMA),
+        ("ligand_pair_score_shards", schemas.LIGAND_PAIR_SCORE_SCHEMA),
+    ):
+        packed = base / "scores" / folder / "shard=ab.parquet"
+        packed.parent.mkdir(parents=True)
+        pq.write_table(
+            pa.Table.from_pylist(
+                [
+                    {"query_entry": "2abc", "target_entry": "4def"},
+                    {"query_entry": "1abc", "target_entry": "5def"},
+                    {"query_entry": "2abc", "target_entry": "6def"},
+                ],
+                schema=schema,
+            ),
+            packed,
+        )
+
+    update_release._restore_score_query_caches(
+        base_data_dir=base,
+        data_dir=workspace,
+        query_ids={"1abc", "2abc", "3abc"},
+    )
+
+    for folder in ("ligand_3d_candidates", "ligand_pair_scores"):
+        cache = workspace / "scores" / folder / "search_db=holo/shard=ab"
+        assert pd.read_parquet(cache / "1abc.parquet")["target_entry"].tolist() == [
+            "5def"
+        ]
+        assert pd.read_parquet(cache / "2abc.parquet")["target_entry"].tolist() == [
+            "4def",
+            "6def",
+        ]
+        assert pd.read_parquet(cache / "3abc.parquet").empty
+
+
 def test_ligand_score_export_removes_stale_shards(tmp_path, monkeypatch):
     shard_dir = tmp_path / "exports" / "ligand_similarity_scores"
     shard_dir.mkdir(parents=True)
@@ -823,10 +868,21 @@ def test_old_target_discovery_reads_retained_cigars(tmp_path):
             "target_entry": ["9xyz", "8xyz", "9xyz"],
         }
     ).to_parquet(cigar, index=False)
+    foldseek = (
+        tmp_path
+        / "alignment_cigars/search_db=holo/alignment_type=foldseek/shard=cd.parquet"
+    )
+    foldseek.parent.mkdir(parents=True)
+    pd.DataFrame(
+        {
+            "query_entry": ["1abc", "4abc", None],
+            "target_entry": ["9xyz", "9xyz", "9xyz"],
+        }
+    ).to_parquet(foldseek, index=False)
 
     assert update_release._queries_with_old_target_hits(
         tmp_path, search_db="holo", affected={"9xyz"}
-    ) == {"1abc", "3abc"}
+    ) == {"1abc", "3abc", "4abc"}
 
 
 def test_changed_target_probe_searches_in_reverse_once_per_backend(
@@ -1097,6 +1153,33 @@ def unexpected(*_args, **_kwargs):
     ) == {"1abc"}
 
 
+def test_changed_target_database_reuses_weekly_subdb(tmp_path, monkeypatch):
+    monkeypatch.setattr(
+        update_release,
+        "_scoring_chains",
+        lambda *_args: pd.DataFrame(
+            {
+                "entry_pdb_id": ["1abc"],
+                "chain_asym_id": ["A"],
+                "chain_auth_id": ["A"],
+            }
+        ),
+    )
+    subdb = tmp_path / "dbs/weekly_delta/subdbs"
+    exact = subdb / "holo_mmseqs/exact_cluster.json"
+    exact.parent.mkdir(parents=True)
+    exact.write_text("{}")
+
+    assert (
+        update_release._changed_target_database(
+            tmp_path,
+            search_db="holo",
+            affected={"1abc"},
+        )
+        == subdb
+    )
+
+
 def test_release_update_runs_only_configured_search_databases(tmp_path, monkeypatch):
     plan_dir = tmp_path / "plan"
     plan_dir.mkdir()
diff --git a/tests/data/pipeline/test_updates.py b/tests/data/pipeline/test_updates.py
index 9783de3e..66968bfd 100644
--- a/tests/data/pipeline/test_updates.py
+++ b/tests/data/pipeline/test_updates.py
@@ -117,6 +117,25 @@ def test_plan_classifies_entries_and_both_search_directions(inputs, tmp_path):
     assert before == _bytes(inputs["data_dir"])
 
 
+def test_plan_refreshes_unchanged_entry_without_new_revision(inputs, tmp_path):
+    output = tmp_path / "refresh_plan"
+    plan = updates.plan_update(
+        **inputs,
+        output_dir=output,
+        pdb_ids=["1abc"],
+        refresh_pdb_ids=["1ABC"],
+    )
+    assert plan["status"] == "ready"
+    assert plan["refresh_pdb_ids"] == ["1abc"]
+    assert load_manifest(output / "ingest.txt") == ["1abc"]
+    assert load_manifest(output / "invalidate.txt") == ["1abc"]
+    row = pd.read_parquet(output / "entries.parquet").iloc[0]
+    assert row.action == "revised"
+    assert row.reason == "annotation refresh"
+    assert row.previous_major_revision == row.current_major_revision == 1
+    assert row.previous_minor_revision == row.current_minor_revision == 0
+
+
 def test_obsolete_preserves_multiple_successors_and_withdrawals(tmp_path):
     path = tmp_path / "obsolete.dat"
     path.write_text(

From d0da6e37ca38f4a3787f176000cc8139dfd97373 Mon Sep 17 00:00:00 2001
From: Ninjani <janani.durairaj@gmail.com>
Date: Fri, 2 Oct 2026 11:44:42 +0200
Subject: [PATCH 16/26] Add monomer search and precomputed protein similarities

---
 docs/dataset.md                        |  21 +-
 src/plinder/core/index/utils.py        |   1 +
 src/plinder/core/release.py            |   7 +-
 src/plinder/core/scores/custom.py      | 353 ++++++++++++++++++-------
 src/plinder/core/scores/protein.py     |  17 +-
 src/plinder/core/scores/search.py      |   8 +
 src/plinder/data/databases.py          |   2 +-
 src/plinder/data/monomer_similarity.py | 306 +++++++++++++++++++++
 src/plinder/data/pipeline/pipeline.py  |   5 +-
 src/plinder/data/pipeline/score.py     |  31 +--
 src/plinder/data/pipeline/tasks.py     |  48 +++-
 src/plinder/data/pipeline/utils.py     |   3 +
 tests/core/test_core_scores.py         |  29 ++
 tests/core/test_custom_scores.py       | 131 ++++++---
 tests/data/pipeline/test_tasks.py      |  38 ++-
 tests/data/test_monomer_similarity.py  | 177 +++++++++++++
 16 files changed, 1013 insertions(+), 164 deletions(-)
 create mode 100644 src/plinder/data/monomer_similarity.py
 create mode 100644 tests/data/test_monomer_similarity.py

diff --git a/docs/dataset.md b/docs/dataset.md
index 52ed0430..7a10590f 100644
--- a/docs/dataset.md
+++ b/docs/dataset.md
@@ -57,16 +57,20 @@ differ from the current release.
     ├── interface_sampling/
     │   └── directed_set_cover/metric=interface_qcov/threshold={threshold}.parquet
     ├── search_databases/
-    │   ├── manifest.json
     │   ├── holo_foldseek/
-    │   └── holo_mmseqs/
+    │   ├── holo_mmseqs/
+    │   ├── monomer_foldseek/
+    │   └── monomer_mmseqs/
     └── exports/
         ├── ligand_similarity_scores.parquet
         ├── interface_similarity_scores.parquet
         ├── interface_half_similarity_scores.parquet
-        └── protein_similarity_scores/
+        ├── protein_similarity_scores/
+        │   └── alignment_type={foldseek,mmseqs}/
+        │       └── shard={two_char_code}.parquet
+        └── monomer_similarity_scores/
             └── alignment_type={foldseek,mmseqs}/
-                └── shard={two_char_code}.parquet
+                └── monomer_{holo,monomer}_{batch}.parquet
 ```
 
 `plinder_download` downloads the index and representative-cover tables by
@@ -234,6 +238,15 @@ exact assembly-chain instance selected for reconstruction.
 chain-pair scores, including query and target coverage, sequence identity,
 sequence similarity, and Foldseek lDDT. Percentage values are stored as
 integers from 0 to 100.
+`exports/monomer_similarity_scores/` adds query chains outside ligand pockets
+and protein interfaces. Pass `include_monomers=True` to
+`query_protein_similarity()` to read both sets of chain pairs.
+
+For a custom structure or FASTA search, `search()` returns
+`result.chain_similarity_scores`, a Parquet file of direct chain-level hits
+with the same score fields. FASTA results retain the original sequence IDs.
+By default, chain hits also include protein chains outside ligand pockets
+and protein interfaces. Pocket and interface scores use their own targets.
 
 The optional `alignment_cigars/` files contain full-chain CIGARs, alignment
 starts, and bit-packed residue identity flags. Holo chain-pair statistics are
diff --git a/src/plinder/core/index/utils.py b/src/plinder/core/index/utils.py
index 6455d735..f5a1aed0 100644
--- a/src/plinder/core/index/utils.py
+++ b/src/plinder/core/index/utils.py
@@ -31,6 +31,7 @@
         "complete similarity exports",
         (
             "protein_similarity_scores",
+            "monomer_similarity_scores",
             "ligand_similarity_scores",
             "interface_similarity_scores",
             "interface_half_similarity_scores",
diff --git a/src/plinder/core/release.py b/src/plinder/core/release.py
index d825eda9..473917ec 100644
--- a/src/plinder/core/release.py
+++ b/src/plinder/core/release.py
@@ -70,16 +70,19 @@ def _release_file(
     ),
     "ligand_archives": "ligand_archives",
     "ligand_archive": "ligand_archives/{shard}.parquet",
-    "ligand_archives_manifest": "ligand_archives/manifest.json",
     "ligand_scores": "ligand_scores",
     "ligand_sampling": "ligand_sampling",
     "interface_sampling": "interface_sampling",
     "search_databases": "search_databases",
     "search_database": "search_databases/holo_{backend}",
-    "search_databases_manifest": "search_databases/manifest.json",
     "search_database_overlay": "search_databases/weekly_delta/holo_{backend}",
+    "monomer_search_database": "search_databases/monomer_{backend}",
+    "monomer_search_database_overlay": (
+        "search_databases/weekly_delta/monomer_{backend}"
+    ),
     "search_database_shadowed_entries": "search_databases/shadowed_entries.parquet",
     "protein_similarity_scores": "exports/protein_similarity_scores",
+    "monomer_similarity_scores": "exports/monomer_similarity_scores",
     "ligand_similarity_scores": "exports/ligand_similarity_scores.parquet",
     "interface_similarity_scores": "exports/interface_similarity_scores.parquet",
     "interface_half_similarity_scores": (
diff --git a/src/plinder/core/scores/custom.py b/src/plinder/core/scores/custom.py
index 26d424f5..c491558c 100644
--- a/src/plinder/core/scores/custom.py
+++ b/src/plinder/core/scores/custom.py
@@ -4,7 +4,6 @@
 
 from __future__ import annotations
 
-import json
 import logging
 import re
 import shutil
@@ -32,12 +31,6 @@
 CIF_SEARCH_BACKENDS = ("foldseek", "mmseqs")
 SEQUENCE_SEARCH_BACKENDS = ("mmseqs",)
 SEARCH_BACKENDS = CIF_SEARCH_BACKENDS
-EXACT_CLUSTER_CONTRACT: Mapping[str, object] = {
-    "identity": 1.0,
-    "coverage": 1.0,
-    "coverage_mode": 0,
-    "compressed_search_target": False,
-}
 
 
 @dataclass(frozen=True)
@@ -62,9 +55,15 @@ class CustomScoringAssets:
     alignment_chain_lookup: Path
     search_databases: Mapping[str, SearchDatabaseBundle]
     ligand_archives: Mapping[str, Path]
+    monomer_search_databases: Mapping[str, SearchDatabaseBundle] = field(
+        default_factory=dict
+    )
     overlay_search_databases: Mapping[str, SearchDatabaseBundle] = field(
         default_factory=dict
     )
+    overlay_monomer_search_databases: Mapping[str, SearchDatabaseBundle] = field(
+        default_factory=dict
+    )
     shadowed_entries: frozenset[str] = frozenset()
 
 
@@ -153,6 +152,7 @@ class CustomScoringResult:
     query_inputs: CustomQueryInputs
     query_databases: CustomQueryDatabases
     protein_hits: Mapping[str, Path]
+    chain_similarity_scores: Path
     score_alignments: Mapping[str, Path]
     protein_score_alignments: Mapping[str, Path]
     protein_scores: Path
@@ -168,6 +168,7 @@ class CustomSequenceScoringResult:
     query_inputs: CustomQueryInputs
     query_databases: CustomQueryDatabases
     protein_hits: Mapping[str, Path]
+    chain_similarity_scores: Path
     protein_score_alignments: Mapping[str, Path]
     protein_scores: Path
     aligned_pocket_residues: Path | None
@@ -182,15 +183,6 @@ class _SequenceEntry:
     pdb_id: str
 
 
-def _manifest_member(root: Path, value: object, *, field: str) -> Path:
-    if not isinstance(value, str) or not value:
-        raise ValueError(f"invalid {field} in {root / 'exact_cluster.json'}")
-    relative = Path(value)
-    if relative.is_absolute() or relative.name != value:
-        raise ValueError(f"unsafe {field} in {root / 'exact_cluster.json'}: {value}")
-    return root / relative
-
-
 def _require_database_prefix(
     prefix: Path,
     *,
@@ -219,12 +211,16 @@ def _validate_portable_links(root: Path) -> None:
             raise ValueError(f"non-portable database link: {path} -> {path.readlink()}")
 
 
-def _local_search_database_root(data_dir: Path, backend: str) -> Path:
+def _local_search_database_root(
+    data_dir: Path, backend: str, *, monomer: bool = False
+) -> Path:
     """Resolve either a published bundle or an unmodified ingest output."""
-    published = PlinderRelease(data_dir).path("search_database", backend=backend)
+    artifact = "monomer_search_database" if monomer else "search_database"
+    prefix = "monomer" if monomer else "holo"
+    published = PlinderRelease(data_dir).path(artifact, backend=backend)
     if published.is_dir():
         return published
-    ingest = data_dir / "dbs" / "subdbs" / f"holo_{backend}"
+    ingest = data_dir / "dbs" / "subdbs" / f"{prefix}_{backend}"
     return ingest if ingest.is_dir() else published
 
 
@@ -232,67 +228,35 @@ def resolve_search_database(
     backend: str,
     *,
     data_dir: Path | None = None,
+    monomer: bool = False,
 ) -> SearchDatabaseBundle:
     """Download or validate one portable PLINDER search database bundle."""
     if backend not in SEARCH_BACKENDS:
         raise ValueError(
             f"unsupported search backend {backend!r}; expected one of {SEARCH_BACKENDS}"
         )
+    artifact = "monomer_search_database" if monomer else "search_database"
     if data_dir is None:
         root = _release_file(
-            "search_database",
+            artifact,
             data_dir=None,
             description=f"{backend} search database",
             backend=backend,
         )
     else:
-        root = _local_search_database_root(Path(data_dir), backend)
+        root = _local_search_database_root(Path(data_dir), backend, monomer=monomer)
     return _validate_search_database(backend, Path(root))
 
 
 def _validate_search_database(backend: str, root: Path) -> SearchDatabaseBundle:
     root = Path(root)
-    manifest_path = _require_file(
-        root / "exact_cluster.json",
-        description=f"{backend} search database manifest",
-    )
-    try:
-        manifest = json.loads(manifest_path.read_text())
-    except (OSError, json.JSONDecodeError) as exc:
-        raise ValueError(f"invalid search database manifest: {manifest_path}") from exc
-    if not isinstance(manifest, dict):
-        raise ValueError(f"invalid search database manifest: {manifest_path}")
-    if manifest.get("alignment_type") != backend:
-        raise ValueError(
-            f"search database backend mismatch in {manifest_path}: "
-            f"{manifest.get('alignment_type')!r}"
-        )
-    if manifest.get("portable") is not True:
-        raise ValueError(f"search database is not portable: {manifest_path}")
-    mismatches = {
-        key: manifest.get(key)
-        for key, expected in EXACT_CLUSTER_CONTRACT.items()
-        if manifest.get(key) != expected
-    }
-    if mismatches:
-        raise ValueError(
-            f"search database does not satisfy the exact-cluster contract in "
-            f"{manifest_path}: {mismatches}"
-        )
-
-    search_target = _manifest_member(
-        root, manifest.get("search_target"), field="search_target"
-    )
-    conversion_target = _manifest_member(
-        root, manifest.get("conversion_target"), field="conversion_target"
-    )
-    cluster_alignments = None
-    if backend == "mmseqs":
-        cluster_alignments = _manifest_member(
-            root,
-            manifest.get("cluster_alignments"),
-            field="cluster_alignments",
-        )
+    if backend == "foldseek":
+        search_target = conversion_target = root / "clustered"
+        cluster_alignments = None
+    else:
+        search_target = root / "representatives"
+        conversion_target = root / root.name
+        cluster_alignments = root / "cluster_alignments"
 
     _require_database_prefix(
         search_target,
@@ -315,7 +279,7 @@ def _validate_search_database(backend: str, root: Path) -> SearchDatabaseBundle:
         search_target=search_target,
         conversion_target=conversion_target,
         cluster_alignments=cluster_alignments,
-        manifest=manifest,
+        manifest={},
     )
 
 
@@ -349,6 +313,7 @@ def resolve_custom_scoring_assets(
     data_dir: Path | None = None,
     backends: Iterable[str] = CIF_SEARCH_BACKENDS,
     ligand_pdb_ids: Iterable[str] = (),
+    include_monomers: bool = False,
 ) -> CustomScoringAssets:
     """Download or validate the bounded asset set for custom scoring.
 
@@ -376,34 +341,47 @@ def resolve_custom_scoring_assets(
         backend: resolve_search_database(backend, data_dir=data_dir)
         for backend in selected_backends
     }
+    monomer_databases = (
+        {
+            backend: resolve_search_database(backend, data_dir=data_dir, monomer=True)
+            for backend in selected_backends
+        }
+        if include_monomers
+        else {}
+    )
     release = PlinderRelease(data_dir)
+    overlay_databases = {}
+    overlay_monomer_databases = {}
+    for backend in selected_backends:
+        try:
+            overlay = release.fetch("search_database_overlay", backend=backend)
+        except FileNotFoundError:
+            pass
+        else:
+            overlay_databases[backend] = _validate_search_database(backend, overlay)
+        if include_monomers:
+            try:
+                monomer_overlay = release.fetch(
+                    "monomer_search_database_overlay", backend=backend
+                )
+            except FileNotFoundError:
+                pass
+            else:
+                overlay_monomer_databases[backend] = _validate_search_database(
+                    backend, monomer_overlay
+                )
+    shadowed_entries: frozenset[str] = frozenset()
     try:
-        manifest_path = release.fetch("search_databases_manifest")
+        shadowed_path = release.fetch("search_database_shadowed_entries")
     except FileNotFoundError:
-        manifest = {}
+        if overlay_databases or overlay_monomer_databases:
+            raise ValueError(
+                "search database overlay is missing shadowed entries"
+            ) from None
     else:
-        manifest = json.loads(manifest_path.read_text())
-        if not isinstance(manifest, dict):
-            raise ValueError(f"invalid search database manifest: {manifest_path}")
-    overlays = manifest.get("overlays", {})
-    if not isinstance(overlays, dict):
-        raise ValueError("invalid search database overlay list")
-    overlay_databases = {
-        backend: _validate_search_database(
-            backend,
-            release.fetch("search_database_overlay", backend=backend),
-        )
-        for backend in selected_backends
-        if backend in overlays
-    }
-    shadowed_entries: frozenset[str] = frozenset()
-    if manifest.get("shadowed_entries"):
-        shadowed_path = release.fetch("search_database_shadowed_entries")
         shadowed_entries = frozenset(
             pd.read_parquet(shadowed_path, columns=["pdb_id"])["pdb_id"].astype(str)
         )
-    if overlay_databases and not shadowed_entries:
-        raise ValueError("search database overlay is missing its shadowed entry list")
     ligand_archives = resolve_ligand_archives(
         ligand_pdb_ids,
         data_dir=data_dir,
@@ -415,7 +393,9 @@ def resolve_custom_scoring_assets(
         alignment_chain_lookup=resolved_index["alignment_chain_lookup"],
         search_databases=databases,
         ligand_archives=ligand_archives,
+        monomer_search_databases=monomer_databases,
         overlay_search_databases=overlay_databases,
+        overlay_monomer_search_databases=overlay_monomer_databases,
         shadowed_entries=shadowed_entries,
     )
 
@@ -1129,8 +1109,9 @@ def _build_mmseqs_target_subset(
     entry_ids: Iterable[str],
     output_dir: Path,
     threads: int = 1,
-) -> SearchDatabaseBundle:
-    """Build an MMseqs target from scoreable chains in selected entries."""
+    monomer_only: bool = False,
+) -> SearchDatabaseBundle | None:
+    """Build a bounded MMseqs target from selected release chains."""
     selected = _plinder_entry_subset(entry_ids)
     assert selected is not None
     if threads < 1:
@@ -1147,6 +1128,7 @@ def _build_mmseqs_target_subset(
             "chain_receptor_type",
             "chain_is_holo",
             "chain_sequence",
+            *(["chain_is_ligand_like"] if monomer_only else []),
         ],
         filters=[("entry_pdb_id", "in", list(selected))],
     )
@@ -1175,18 +1157,25 @@ def _build_mmseqs_target_subset(
         how="left",
         validate="one_to_one",
     )
+    scoreable = chains["chain_is_holo"].fillna(False).astype(bool) | chains[
+        "chain_is_interface"
+    ].eq(True)
+    selected_chains = (
+        ~scoreable & ~chains["chain_is_ligand_like"].fillna(False)
+        if monomer_only
+        else scoreable
+    )
     chains = chains.loc[
         chains["chain_receptor_type"].fillna("").astype(str).eq("protein")
-        & (
-            chains["chain_is_holo"].fillna(False).astype(bool)
-            | chains["chain_is_interface"].eq(True)
-        )
+        & selected_chains
         & chains["chain_auth_id"].notna()
         & chains["chain_sequence"].notna()
     ].copy()
+    if monomer_only and chains.empty:
+        return None
     found = set(chains["entry_pdb_id"].astype(str))
     missing = sorted(set(selected).difference(found))
-    if missing:
+    if missing and not monomer_only:
         raise ValueError(
             "selected PLINDER entries have no scoreable receptor or interface "
             f"chains: {missing[:10]}"
@@ -1248,12 +1237,14 @@ def _resolve_workflow_assets(
     plinder_entry_ids: tuple[str, ...] | None,
     work_dir: Path,
     threads: int,
+    include_monomers: bool = False,
 ) -> CustomScoringAssets:
     if plinder_entry_ids is not None and backends != ("mmseqs",):
         raise ValueError("plinder_entry_ids currently requires backends=('mmseqs',)")
     assets = resolve_custom_scoring_assets(
         data_dir=data_dir,
         backends=() if plinder_entry_ids is not None else backends,
+        include_monomers=include_monomers and plinder_entry_ids is None,
     )
     if plinder_entry_ids is None:
         return assets
@@ -1264,7 +1255,27 @@ def _resolve_workflow_assets(
         output_dir=work_dir / "plinder_target_subset",
         threads=threads,
     )
-    return replace(assets, search_databases={"mmseqs": subset})
+    assert subset is not None
+    monomer_subset = (
+        _build_mmseqs_target_subset(
+            assets.entry_chains,
+            assets.interface_annotations,
+            entry_ids=plinder_entry_ids,
+            output_dir=work_dir / "plinder_monomer_subset",
+            threads=threads,
+            monomer_only=True,
+        )
+        if include_monomers
+        else None
+    )
+    return replace(
+        assets,
+        search_databases={"mmseqs": subset},
+        monomer_search_databases=(
+            {"mmseqs": monomer_subset} if monomer_subset is not None else {}
+        ),
+        shadowed_entries=frozenset(),
+    )
 
 
 def _parse_plinder_target_identifier(
@@ -1938,6 +1949,7 @@ def prepare_custom_protein_score_alignments(
             columns=[
                 "qaln",
                 "taln",
+                "cigar",
                 "target_selected_residue_indices",
             ],
             errors="ignore",
@@ -2067,6 +2079,122 @@ def run_custom_protein_searches(
     return outputs
 
 
+def run_custom_monomer_searches(
+    *,
+    query_databases: CustomQueryDatabases,
+    assets: CustomScoringAssets,
+    output_dir: Path,
+    scratch_dir: Path,
+    config: CustomProteinSearchConfig | None,
+    backends: Iterable[str],
+    threads: int,
+) -> dict[str, Path]:
+    """Search protein chains absent from pocket/interface targets."""
+    if not assets.monomer_search_databases:
+        return {}
+    monomer_assets = replace(
+        assets,
+        search_databases=assets.monomer_search_databases,
+        overlay_search_databases=assets.overlay_monomer_search_databases,
+    )
+    return run_custom_protein_searches(
+        query_databases=query_databases,
+        assets=monomer_assets,
+        output_dir=output_dir,
+        scratch_dir=scratch_dir,
+        config=config,
+        backends=(
+            backend
+            for backend in backends
+            if backend in assets.monomer_search_databases
+        ),
+        threads=threads,
+    )
+
+
+def write_custom_chain_similarity_scores(
+    protein_hits: Mapping[str, Path],
+    *,
+    output_path: Path,
+    chain_manifest: Path | None = None,
+    monomer_hits: Mapping[str, Path] | None = None,
+) -> Path:
+    """Write direct custom-to-PLINDER protein-chain alignment scores.
+
+    Coverage and similarity values use integer percentages, as in the release
+    protein similarity table. Each alignment remains a separate row.
+    """
+    from plinder.data.annotations.get_similarity_scores import (
+        get_sequence_similarity_helper,
+    )
+
+    columns = [
+        "sequence_id",
+        "query_id",
+        "query_chain_id",
+        "structure_id",
+        "query_chain_asym_id",
+        "target_entry",
+        "target_chain_asym_id",
+        "source",
+        "qcov",
+        "tcov",
+        "fident",
+        "seqsim",
+        "lddt",
+    ]
+    frames = []
+    for backend, path in [*protein_hits.items(), *(monomer_hits or {}).items()]:
+        hits = pd.read_parquet(path)
+        if hits.empty:
+            continue
+        required = set(columns).difference({"sequence_id", "seqsim", "lddt"}) | {
+            "qaln",
+            "taln",
+        }
+        if backend == "foldseek":
+            required.add("lddt")
+        missing = sorted(required.difference(hits.columns))
+        if missing:
+            raise ValueError(f"{backend} custom hit table is missing columns {missing}")
+        scores = hits[[column for column in columns if column in hits]].copy()
+        scores["seqsim"] = [
+            get_sequence_similarity_helper(str(query).upper(), str(target).upper())
+            for query, target in zip(hits["qaln"], hits["taln"], strict=True)
+        ]
+        if "lddt" not in scores:
+            scores["lddt"] = pd.NA
+        for column in ("qcov", "tcov", "fident", "seqsim", "lddt"):
+            scores[column] = (
+                (pd.to_numeric(scores[column], errors="coerce") * 100)
+                .round()
+                .clip(0, 100)
+                .astype("UInt8")
+            )
+        frames.append(scores)
+    result = (
+        pd.concat(frames, ignore_index=True)
+        if frames
+        else pd.DataFrame(columns=columns)
+    )
+    if chain_manifest is not None:
+        manifest = pd.read_parquet(chain_manifest, columns=["query_id", "sequence_id"])
+        if manifest["query_id"].duplicated().any():
+            raise ValueError("query chain manifest contains duplicate query IDs")
+        result = result.merge(
+            manifest, on="query_id", how="left", validate="many_to_one"
+        )
+        if result["sequence_id"].isna().any():
+            raise ValueError("custom chain scores contain unknown query IDs")
+    else:
+        result["sequence_id"] = pd.NA
+    result = result[columns]
+    output_path = Path(output_path)
+    output_path.parent.mkdir(parents=True, exist_ok=True)
+    result.to_parquet(output_path, index=False, compression="zstd")
+    return output_path
+
+
 def _target_entry_ids(score_alignments: Mapping[str, Path]) -> set[str]:
     target_ids: set[str] = set()
     for path in score_alignments.values():
@@ -2674,6 +2802,7 @@ def score_custom_sequence_file(
     plinder_entry_ids: Iterable[str] | None = None,
     threads: int = 1,
     store_aligned_pocket_residues: bool = False,
+    include_monomers: bool = False,
 ) -> CustomSequenceScoringResult:
     """Search protein sequences and score PLINDER ligand-pocket identity.
 
@@ -2710,6 +2839,7 @@ def score_custom_sequence_file(
         plinder_entry_ids=selected_plinder_entries,
         work_dir=work_dir,
         threads=threads,
+        include_monomers=include_monomers,
     )
     protein_hits = run_custom_protein_searches(
         query_databases=query_databases,
@@ -2722,6 +2852,24 @@ def score_custom_sequence_file(
         backends=selected_backends,
         threads=threads,
     )
+    monomer_hits = run_custom_monomer_searches(
+        query_databases=query_databases,
+        assets=assets,
+        output_dir=work_dir / "monomer_hits",
+        scratch_dir=(
+            Path(scratch_dir) if scratch_dir is not None else work_dir / "scratch"
+        )
+        / "monomer",
+        config=search_config,
+        backends=selected_backends,
+        threads=threads,
+    )
+    chain_similarity_scores = write_custom_chain_similarity_scores(
+        protein_hits,
+        output_path=work_dir / "chain_similarity_scores.parquet",
+        chain_manifest=query_inputs.chain_manifest,
+        monomer_hits=monomer_hits,
+    )
     manifest = pd.read_parquet(query_inputs.chain_manifest)
     entries_by_structure = {
         str(structure_id): _SequenceEntry(pdb_id=str(structure_id))
@@ -2766,6 +2914,7 @@ def score_custom_sequence_file(
         query_inputs=query_inputs,
         query_databases=query_databases,
         protein_hits=protein_hits,
+        chain_similarity_scores=chain_similarity_scores,
         protein_score_alignments=protein_score_alignments,
         protein_scores=protein_score_path,
         aligned_pocket_residues=aligned_pocket_residue_path,
@@ -2940,6 +3089,7 @@ def score_custom_cif_files(
     threads: int = 1,
     shape_score_threads: int = 1,
     store_aligned_pocket_residues: bool = False,
+    include_monomers: bool = False,
 ) -> CustomScoringResult:
     """Run custom-CIF annotation, protein search, and PLINDER scoring.
 
@@ -3008,6 +3158,7 @@ def score_custom_cif_files(
         plinder_entry_ids=selected_plinder_entries,
         work_dir=work_dir,
         threads=threads,
+        include_monomers=include_monomers,
     )
     protein_hits = run_custom_protein_searches(
         query_databases=query_databases,
@@ -3020,6 +3171,23 @@ def score_custom_cif_files(
         backends=selected_backends,
         threads=threads,
     )
+    monomer_hits = run_custom_monomer_searches(
+        query_databases=query_databases,
+        assets=assets,
+        output_dir=work_dir / "monomer_hits",
+        scratch_dir=(
+            Path(scratch_dir) if scratch_dir is not None else work_dir / "scratch"
+        )
+        / "monomer",
+        config=search_config,
+        backends=selected_backends,
+        threads=threads,
+    )
+    chain_similarity_scores = write_custom_chain_similarity_scores(
+        protein_hits,
+        output_path=work_dir / "chain_similarity_scores.parquet",
+        monomer_hits=monomer_hits,
+    )
     score_alignments = prepare_custom_score_alignments(
         protein_hits,
         entries_by_structure=annotations.entries_by_structure,
@@ -3091,6 +3259,7 @@ def score_custom_cif_files(
         query_inputs=query_inputs,
         query_databases=query_databases,
         protein_hits=protein_hits,
+        chain_similarity_scores=chain_similarity_scores,
         score_alignments=score_alignments,
         protein_score_alignments=protein_score_alignments,
         protein_scores=protein_score_path,
diff --git a/src/plinder/core/scores/protein.py b/src/plinder/core/scores/protein.py
index 7e8b1a7c..e1079654 100644
--- a/src/plinder/core/scores/protein.py
+++ b/src/plinder/core/scores/protein.py
@@ -39,10 +39,21 @@ def query_protein_similarity(
     columns: list[str] | None = None,
     filters: Filters = None,
     release: PlinderRelease | None = None,
+    include_monomers: bool = False,
 ) -> pd.DataFrame:
-    """Query chain-level Foldseek and MMseqs similarities in integer percent."""
-    dataset = (release or PlinderRelease()).fetch("protein_similarity_scores")
-    return read_score_table(dataset, columns=columns, filters=filters)
+    """Query chain-level Foldseek and MMseqs similarities in integer percent.
+
+    Set ``include_monomers`` to include queries from protein chains outside
+    ligand pockets and protein interfaces.
+    """
+    selected_release = release or PlinderRelease()
+    paths = [selected_release.fetch("protein_similarity_scores")]
+    if include_monomers:
+        paths.append(selected_release.fetch("monomer_similarity_scores"))
+    return pd.concat(
+        [read_score_table(path, columns=columns, filters=filters) for path in paths],
+        ignore_index=True,
+    )
 
 
 def _selected_residue_positions(
diff --git a/src/plinder/core/scores/search.py b/src/plinder/core/scores/search.py
index 564de5f0..9e845e18 100644
--- a/src/plinder/core/scores/search.py
+++ b/src/plinder/core/scores/search.py
@@ -36,6 +36,7 @@ def search(
     search_config: CustomProteinSearchConfig | None = None,
     plinder_entry_ids: Iterable[str] | None = None,
     store_aligned_pocket_residues: bool = False,
+    include_monomers: bool = True,
 ) -> CustomScoringResult | CustomSequenceScoringResult:
     """Search with the same structure table accepted by evaluation.
 
@@ -54,6 +55,12 @@ def search(
     other PDB components are omitted. Supply ligand poses through ``ligand_path``.
 
     The returned result contains paths to score tables and alignment files.
+    ``chain_similarity_scores`` gives direct protein-chain hits, with query and
+    target coverage, identity, sequence similarity, and Foldseek lDDT as
+    integer percentages. FASTA results include the original ``sequence_id``.
+    With ``include_monomers=True``, chain hits also cover proteins outside
+    ligand pockets and protein interfaces. Pocket and interface scores still
+    use their own targets.
     ``search_config`` controls search filters. Its shared ``evalue`` defaults to
     0.01; ``foldseek_evalue``, ``mmseqs_evalue`` and ``steam_evalue`` override it
     independently for their respective backends.
@@ -70,6 +77,7 @@ def search(
         search_config=search_config,
         plinder_entry_ids=plinder_entry_ids,
         store_aligned_pocket_residues=store_aligned_pocket_residues,
+        include_monomers=include_monomers,
     )
     path = None if isinstance(inputs, pd.DataFrame) else Path(inputs).resolve()
     if path is not None and path.name.lower().endswith(
diff --git a/src/plinder/data/databases.py b/src/plinder/data/databases.py
index 88e18bef..7d1c8308 100644
--- a/src/plinder/data/databases.py
+++ b/src/plinder/data/databases.py
@@ -280,7 +280,7 @@ def _search_database_bundle_sources(
             f"unsafe database prefix in {source_root / 'exact_cluster.json'}"
         )
     prefixes = {value for value in values if isinstance(value, str)}
-    sources = {source_root / "exact_cluster.json"}
+    sources: set[Path] = set()
     for prefix in prefixes:
         sources.update(
             path
diff --git a/src/plinder/data/monomer_similarity.py b/src/plinder/data/monomer_similarity.py
new file mode 100644
index 00000000..68021b8f
--- /dev/null
+++ b/src/plinder/data/monomer_similarity.py
@@ -0,0 +1,306 @@
+"""Precompute chain scores for proteins outside ligand pockets and interfaces."""
+
+from __future__ import annotations
+
+import argparse
+import shutil
+from collections.abc import Iterator
+from functools import lru_cache
+from pathlib import Path
+
+import numpy as np
+import pandas as pd
+import pyarrow as pa
+import pyarrow.dataset as ds
+import pyarrow.parquet as pq
+
+from plinder.core.scores.custom import resolve_search_database
+from plinder.core.utils.schemas import PROTEIN_SIMILARITY_EXPORT_SCHEMA
+from plinder.data import databases
+from plinder.data.annotations.get_similarity_scores import (
+    get_sequence_similarity_helper,
+    run_alignment,
+)
+from plinder.data.pipeline.config import FoldseekConfig, MMSeqsConfig
+
+
+def _chain_ids(data_dir: Path, backend: str) -> dict[str, tuple[str, str]]:
+    chains = pd.read_parquet(
+        data_dir / "index/alignment_chain_lookup.parquet",
+        columns=["entry_pdb_id", "chain_auth_id", "chain_asym_id"],
+    )
+    prefix = "pdb_0000" if backend == "foldseek" else ""
+    infix = "_xyz-enrich_" if backend == "foldseek" else "_"
+    identifiers = (
+        prefix
+        + chains["entry_pdb_id"].astype(str)
+        + infix
+        + chains["chain_auth_id"].astype(str)
+    )
+    if identifiers.duplicated().any():
+        raise ValueError("release chain lookup has ambiguous author-chain IDs")
+    return dict(
+        zip(
+            identifiers,
+            zip(chains["entry_pdb_id"], chains["chain_asym_id"], strict=True),
+            strict=True,
+        )
+    )
+
+
+def _percent(values: pd.Series, *, allow_missing: bool = False) -> pa.Array:
+    numeric = pd.to_numeric(values, errors="raise").to_numpy(dtype=float)
+    missing = np.isnan(numeric)
+    if (not allow_missing and missing.any()) or np.isinf(numeric).any():
+        raise ValueError("protein alignment contains a non-finite score")
+    scaled = np.floor(np.nan_to_num(numeric, nan=0) * 100 + 0.5)
+    return pa.array(scaled.clip(0, 100).astype("uint8"), mask=missing)
+
+
+def _alignment_frames(scanner: ds.Scanner) -> Iterator[pd.DataFrame]:
+    """Combine small search row groups before converting and writing scores."""
+    pending: list[pa.RecordBatch] = []
+    count = 0
+    for batch in scanner.to_batches():
+        if not batch.num_rows:
+            continue
+        pending.append(batch)
+        count += batch.num_rows
+        if count >= 100_000:
+            yield pa.Table.from_batches(pending).to_pandas()
+            pending.clear()
+            count = 0
+    if pending:
+        yield pa.Table.from_batches(pending).to_pandas()
+
+
+def _score_alignment_batches(
+    raw_path: Path,
+    output_path: Path,
+    *,
+    backend: str,
+    chain_ids: dict[str, tuple[str, str]],
+) -> int:
+    output_path.parent.mkdir(parents=True, exist_ok=True)
+    temporary = output_path.with_suffix(".tmp.parquet")
+    count = 0
+
+    @lru_cache(maxsize=100_000)
+    def sequence_similarity(query: str, target: str) -> float:
+        return get_sequence_similarity_helper(query, target)
+
+    with pq.ParquetWriter(
+        temporary, PROTEIN_SIMILARITY_EXPORT_SCHEMA, compression="zstd"
+    ) as writer:
+        scanner = ds.dataset(raw_path, format="parquet").scanner(
+            columns=[
+                "query",
+                "target",
+                "qcov",
+                "tcov",
+                "fident",
+                "qaln",
+                "taln",
+                *(["lddt"] if backend == "foldseek" else []),
+            ],
+            batch_size=100_000,
+        )
+        for rows in _alignment_frames(scanner):
+            query_ids = rows["query"]
+            target_ids = rows["target"]
+            if backend == "foldseek":
+                model_prefix = r"_xyz-enrich_MODEL_\d+_"
+                query_ids = query_ids.str.replace(
+                    model_prefix, "_xyz-enrich_", regex=True
+                )
+                target_ids = target_ids.str.replace(
+                    model_prefix, "_xyz-enrich_", regex=True
+                )
+            queries = query_ids.map(chain_ids)
+            targets = target_ids.map(chain_ids)
+            if queries.isna().any() or targets.isna().any():
+                unknown = {
+                    "query": rows.loc[queries.isna(), "query"].head(5).tolist(),
+                    "target": rows.loc[targets.isna(), "target"].head(5).tolist(),
+                }
+                raise ValueError(f"monomer alignment has unknown chains: {unknown}")
+            query_entry, query_chain = zip(*queries, strict=True)
+            target_entry, target_chain = zip(*targets, strict=True)
+            similarity = pd.Series(
+                [
+                    sequence_similarity(str(q).upper(), str(t).upper())
+                    for q, t in zip(rows["qaln"], rows["taln"], strict=True)
+                ]
+            )
+            size = len(rows)
+            table = pa.Table.from_arrays(
+                [
+                    pa.array(query_entry, type=pa.string()),
+                    pa.array(target_entry, type=pa.string()),
+                    pa.array(query_chain, type=pa.string()),
+                    pa.array(target_chain, type=pa.string()),
+                    pa.array([backend] * size, type=pa.string()),
+                    _percent(rows["qcov"]),
+                    _percent(rows["tcov"]),
+                    _percent(rows["fident"]),
+                    _percent(similarity),
+                    (
+                        _percent(rows["lddt"], allow_missing=True)
+                        if backend == "foldseek"
+                        else pa.nulls(size, type=pa.uint8())
+                    ),
+                ],
+                schema=PROTEIN_SIMILARITY_EXPORT_SCHEMA,
+            )
+            writer.write_table(table)
+            count += size
+    temporary.replace(output_path)
+    return count
+
+
+def score_monomer_pairs(
+    data_dir: Path,
+    *,
+    backend: str,
+    target_kind: str,
+    scratch_dir: Path,
+    output_path: Path,
+    threads: int,
+    pilot_queries: int | None = None,
+    query_batch_index: int | None = None,
+    query_batch_count: int | None = None,
+) -> int:
+    """Score unrepresented protein query chains against one target universe."""
+    if backend not in {"foldseek", "mmseqs"}:
+        raise ValueError(f"unsupported backend: {backend}")
+    if target_kind not in {"holo", "monomer"}:
+        raise ValueError(f"unsupported target universe: {target_kind}")
+    if threads < 1:
+        raise ValueError("threads must be positive")
+    data_dir = Path(data_dir)
+    scratch_dir = Path(scratch_dir)
+    scratch_dir.mkdir(parents=True, exist_ok=True)
+    query = data_dir / "dbs/subdbs" / f"monomer_{backend}" / f"monomer_{backend}"
+    if pilot_queries is not None or query_batch_index is not None:
+        identifiers = sorted(databases.database_identifiers(query))
+        if pilot_queries is not None:
+            if pilot_queries < 1 or query_batch_index is not None:
+                raise ValueError("pilot_queries must be positive and unbatched")
+            identifiers = identifiers[:pilot_queries]
+        else:
+            if (
+                query_batch_count is None
+                or not 0 <= query_batch_index < query_batch_count
+            ):
+                raise ValueError("invalid monomer query batch")
+            start = len(identifiers) * query_batch_index // query_batch_count
+            stop = len(identifiers) * (query_batch_index + 1) // query_batch_count
+            identifiers = identifiers[start:stop]
+        print(f"Searching {len(identifiers):,} monomer query chains", flush=True)
+        subset_root = scratch_dir / "query_subset"
+        subset_root.mkdir(exist_ok=True)
+        missing = databases.make_sub_db(set(identifiers), query, subset_root, backend)
+        if missing:
+            raise ValueError(f"missing pilot query chains: {sorted(missing)[:10]}")
+        query = subset_root / subset_root.name
+
+    target = resolve_search_database(
+        backend, data_dir=data_dir, monomer=target_kind == "monomer"
+    )
+    config = FoldseekConfig() if backend == "foldseek" else MMSeqsConfig()
+    raw = scratch_dir / "raw_alignment"
+    run_alignment(
+        aln_type=backend,
+        query_db=query,
+        target_db=target.conversion_target,
+        search_target_db=target.search_target,
+        cluster_alignment_db=target.cluster_alignments,
+        search_db=scratch_dir / "results",
+        aln_file=raw,
+        alignment_config=config,
+        tmp_dir=scratch_dir / "search_tmp",
+        threads=threads,
+    )
+    try:
+        return _score_alignment_batches(
+            raw.with_suffix(".parquet"),
+            Path(output_path),
+            backend=backend,
+            chain_ids=_chain_ids(data_dir, backend),
+        )
+    finally:
+        shutil.rmtree(raw.with_suffix(".parquet"), ignore_errors=True)
+
+
+def finalize_monomer_similarity_scores(
+    data_dir: Path, *, query_batch_count: int = 8
+) -> int:
+    """Install the complete monomer-pair table after every batch succeeds."""
+    exports = Path(data_dir) / "exports"
+    staging = exports / ".monomer_similarity_scores_staging"
+    installing = exports / ".monomer_similarity_scores_installing"
+    installed = exports / "monomer_similarity_scores"
+    if installed.exists():
+        raise FileExistsError(installed)
+    total_rows = 0
+    for backend in ("mmseqs", "foldseek"):
+        for target_kind in ("holo", "monomer"):
+            for batch_index in range(query_batch_count):
+                path = (
+                    staging
+                    / f"alignment_type={backend}"
+                    / f"target_kind={target_kind}"
+                    / f"part-{batch_index}.parquet"
+                )
+                if not path.is_file():
+                    raise FileNotFoundError(path)
+                file = pq.ParquetFile(path)
+                if not file.schema_arrow.equals(PROTEIN_SIMILARITY_EXPORT_SCHEMA):
+                    raise ValueError(f"invalid monomer score schema: {path}")
+                total_rows += file.metadata.num_rows
+    if installing.exists():
+        shutil.rmtree(installing)
+    for backend in ("mmseqs", "foldseek"):
+        backend_root = installing / f"alignment_type={backend}"
+        backend_root.mkdir(parents=True)
+        for target_kind in ("holo", "monomer"):
+            target_root = (
+                staging / f"alignment_type={backend}" / f"target_kind={target_kind}"
+            )
+            for batch_index in range(query_batch_count):
+                (
+                    backend_root / f"monomer_{target_kind}_{batch_index}.parquet"
+                ).hardlink_to(target_root / f"part-{batch_index}.parquet")
+    installing.rename(installed)
+    shutil.rmtree(staging, ignore_errors=True)
+    return total_rows
+
+
+def main() -> None:
+    parser = argparse.ArgumentParser(description=__doc__)
+    parser.add_argument("data_dir", type=Path)
+    parser.add_argument("--backend", choices=("foldseek", "mmseqs"), required=True)
+    parser.add_argument("--target-kind", choices=("holo", "monomer"), required=True)
+    parser.add_argument("--scratch-dir", type=Path, required=True)
+    parser.add_argument("--output", type=Path, required=True)
+    parser.add_argument("--threads", type=int, default=16)
+    parser.add_argument("--pilot-queries", type=int)
+    parser.add_argument("--query-batch-index", type=int)
+    parser.add_argument("--query-batch-count", type=int)
+    args = parser.parse_args()
+    count = score_monomer_pairs(
+        args.data_dir,
+        backend=args.backend,
+        target_kind=args.target_kind,
+        scratch_dir=args.scratch_dir,
+        output_path=args.output,
+        threads=args.threads,
+        pilot_queries=args.pilot_queries,
+        query_batch_index=args.query_batch_index,
+        query_batch_count=args.query_batch_count,
+    )
+    print(f"Wrote {count:,} {args.backend}/{args.target_kind} pair rows", flush=True)
+
+
+if __name__ == "__main__":
+    main()
diff --git a/src/plinder/data/pipeline/pipeline.py b/src/plinder/data/pipeline/pipeline.py
index fc8142a6..bfa509d4 100644
--- a/src/plinder/data/pipeline/pipeline.py
+++ b/src/plinder/data/pipeline/pipeline.py
@@ -342,9 +342,12 @@ def finalize_ligand_archives(self) -> None:
 
     @utils.ingest_flow_control
     def make_sub_dbs(self) -> None:
+        search_databases = list(self.cfg.scorer.sub_databases)
+        if "holo" in search_databases:
+            search_databases.append("monomer")
         tasks.make_sub_dbs(
             data_dir=self.plinder_dir,
-            sub_databases=self.cfg.scorer.sub_databases,
+            sub_databases=search_databases,
             cpu=self.cfg.flow.make_sub_dbs_cpu,
             scratch_dir=Path(tempfile.gettempdir()) / "plinder-exact-search-dbs",
         )
diff --git a/src/plinder/data/pipeline/score.py b/src/plinder/data/pipeline/score.py
index 8d19e73a..8d272df3 100644
--- a/src/plinder/data/pipeline/score.py
+++ b/src/plinder/data/pipeline/score.py
@@ -3417,7 +3417,6 @@ def publish_search_database_bundles(
             rmtree(path)
     staging.mkdir(parents=True)
     reports: dict[str, dict[str, int | str]] = {}
-    overlay_reports: dict[str, dict[str, int | str]] = {}
     try:
         for alignment_type in alignment_types:
             reports[alignment_type] = databases.publish_search_database_bundle(
@@ -3425,31 +3424,25 @@ def publish_search_database_bundles(
                 target_root=staging / f"holo_{alignment_type}",
                 aln_type=alignment_type,
             )
+            monomer_source = data_dir / "dbs" / "subdbs" / f"monomer_{alignment_type}"
+            if (monomer_source / "exact_cluster.json").is_file():
+                databases.publish_search_database_bundle(
+                    source_root=monomer_source,
+                    target_root=staging / f"monomer_{alignment_type}",
+                    aln_type=alignment_type,
+                )
             overlay_source = (
                 data_dir / "dbs/weekly_delta/subdbs" / f"holo_{alignment_type}"
             )
             if (overlay_source / "exact_cluster.json").is_file():
-                overlay_reports[alignment_type] = (
-                    databases.publish_search_database_bundle(
-                        source_root=overlay_source,
-                        target_root=staging / "weekly_delta" / f"holo_{alignment_type}",
-                        aln_type=alignment_type,
-                    )
+                databases.publish_search_database_bundle(
+                    source_root=overlay_source,
+                    target_root=staging / "weekly_delta" / f"holo_{alignment_type}",
+                    aln_type=alignment_type,
                 )
         shadowed = data_dir / "manifests/weekly_shadowed_entries.parquet"
         if shadowed.is_file():
             copyfile(shadowed, staging / "shadowed_entries.parquet")
-        write_json_atomic(
-            staging / "manifest.json",
-            {
-                "status": "complete",
-                "bundles": reports,
-                "overlays": overlay_reports,
-                "shadowed_entries": (
-                    "shadowed_entries.parquet" if shadowed.is_file() else None
-                ),
-            },
-        )
         if output.exists():
             output.rename(backup)
         staging.rename(output)
@@ -7571,7 +7564,7 @@ def main() -> None:
     elif args.command == "make-sub-dbs":
         tasks.make_sub_dbs(
             data_dir=data_dir,
-            sub_databases=args.search_dbs or ["holo"],
+            sub_databases=args.search_dbs or ["holo", "monomer"],
             cpu=args.threads,
             scratch_dir=args.scratch_dir.resolve(),
         )
diff --git a/src/plinder/data/pipeline/tasks.py b/src/plinder/data/pipeline/tasks.py
index 7badb195..f1f530f2 100644
--- a/src/plinder/data/pipeline/tasks.py
+++ b/src/plinder/data/pipeline/tasks.py
@@ -655,14 +655,20 @@ def make_sub_dbs(
     """
     entries = None
     identifiers_by_database: dict[str, set[str]] = {}
-    indexed_search_databases = (
-        sub_databases if set(sub_databases) <= {"holo", "apo"} else []
-    )
+    indexed_search_databases = []
+    if set(sub_databases) <= {"holo", "apo", "monomer"}:
+        indexed_search_databases = list(sub_databases)
+    elif "monomer" in sub_databases:
+        indexed_search_databases = ["monomer"]
     for search_db in indexed_search_databases:
         chains = (
             _protein_scoring_chains(data_dir)
             if search_db == "holo"
-            else _apo_scoring_chains(data_dir)
+            else (
+                _monomer_scoring_chains(data_dir)
+                if search_db == "monomer"
+                else _apo_scoring_chains(data_dir)
+            )
         )
         if search_db == "holo":
             chain_auth_ids = pd.read_parquet(
@@ -684,7 +690,7 @@ def make_sub_dbs(
             f"{row.entry_pdb_id}_{row.chain_auth_id}"
             for row in chains.itertuples(index=False)
         }
-    if set(sub_databases).difference({"holo", "apo"}):
+    if set(sub_databases).difference({"holo", "apo", "monomer"}):
         from plinder.core.scores.entries import entry_views_from_df
 
         entries = entry_views_from_df(
@@ -717,7 +723,7 @@ def make_sub_dbs(
         tmp_dir=scratch_dir,
         threads=cpu,
     )
-    if set(sub_databases).intersection({"holo", "apo"}):
+    if set(sub_databases).intersection({"holo", "apo", "monomer"}):
         make_alignment_chain_lookup(
             data_dir=data_dir,
             scratch_dir=scratch_dir,
@@ -1853,6 +1859,36 @@ def _protein_scoring_chains(data_dir: Path) -> pd.DataFrame:
     ].copy()
 
 
+def _monomer_scoring_chains(data_dir: Path) -> pd.DataFrame:
+    """Return protein chains absent from pocket/interface search targets."""
+    chains = pd.read_parquet(
+        data_dir / "index" / "entry_chains.parquet",
+        columns=[
+            "entry_pdb_id",
+            "chain_asym_id",
+            "chain_auth_id",
+            "chain_receptor_type",
+            "chain_is_ligand_like",
+        ],
+    )
+    chains = chains.loc[
+        chains["chain_receptor_type"].eq("protein")
+        & ~chains["chain_is_ligand_like"].fillna(False)
+        & chains["chain_auth_id"].notna()
+    ]
+    holo = _protein_scoring_chains(data_dir)[["entry_pdb_id", "chain_asym_id"]]
+    return (
+        chains.merge(
+            holo.drop_duplicates(),
+            on=["entry_pdb_id", "chain_asym_id"],
+            how="left",
+            indicator=True,
+        )
+        .loc[lambda rows: rows["_merge"].eq("left_only")]
+        .drop(columns="_merge")
+    )
+
+
 def _ligand_apo_query_chains(data_dir: Path) -> pd.DataFrame:
     """Return proper-ligand protein receptor chains used as apo queries."""
     from plinder.data.linked_apo import ligand_holo_chain_keys
diff --git a/src/plinder/data/pipeline/utils.py b/src/plinder/data/pipeline/utils.py
index c07fc107..eb8e5c75 100644
--- a/src/plinder/data/pipeline/utils.py
+++ b/src/plinder/data/pipeline/utils.py
@@ -39,6 +39,9 @@ def get_db_sources(
     if "holo" in sub_databases or not len(sub_databases):
         dbs["holo_foldseek"] = data_dir / "dbs" / "foldseek" / "foldseek"
         dbs["holo_mmseqs"] = data_dir / "dbs" / "mmseqs" / "mmseqs"
+    if "monomer" in sub_databases:
+        dbs["monomer_foldseek"] = data_dir / "dbs" / "foldseek" / "foldseek"
+        dbs["monomer_mmseqs"] = data_dir / "dbs" / "mmseqs" / "mmseqs"
     if "apo" in sub_databases or not len(sub_databases):
         dbs["apo_foldseek"] = data_dir / "dbs" / "foldseek" / "foldseek"
         dbs["apo_mmseqs"] = data_dir / "dbs" / "mmseqs" / "mmseqs"
diff --git a/tests/core/test_core_scores.py b/tests/core/test_core_scores.py
index 3d992eef..f960dc06 100644
--- a/tests/core/test_core_scores.py
+++ b/tests/core/test_core_scores.py
@@ -88,6 +88,22 @@ def similarity_release(tmp_path):
             "lddt": pd.Series([80], dtype="uint8"),
         }
     ).to_parquet(protein_scores / "shard=ab.parquet", index=False)
+    monomer_scores = exports / "monomer_similarity_scores/alignment_type=mmseqs"
+    monomer_scores.mkdir(parents=True)
+    pd.DataFrame(
+        {
+            "query_entry": ["3ghi"],
+            "target_entry": ["1abc"],
+            "query_chain_mapped": ["C"],
+            "target_chain_mapped": ["A"],
+            "source": ["mmseqs"],
+            "qcov": pd.Series([95], dtype="uint8"),
+            "tcov": pd.Series([75], dtype="uint8"),
+            "fident": pd.Series([65], dtype="uint8"),
+            "seqsim": pd.Series([72], dtype="uint8"),
+            "lddt": pd.Series([pd.NA], dtype="UInt8"),
+        }
+    ).to_parquet(monomer_scores / "part-0.parquet", index=False)
     alignment_shard = (
         tmp_path / "alignments/search_db=holo/alignment_type=mmseqs/shard=ab.parquet"
     )
@@ -185,6 +201,19 @@ def test_query_protein_similarity_reads_integer_scores(similarity_release):
     ]
 
 
+def test_query_protein_similarity_can_include_monomer_pairs(similarity_release):
+    result = scores.query_protein_similarity(
+        columns=["query_entry", "target_entry", "fident"],
+        filters=[("target_entry", "==", "1abc")],
+        release=similarity_release,
+        include_monomers=True,
+    )
+
+    assert result.to_dict("records") == [
+        {"query_entry": "3ghi", "target_entry": "1abc", "fident": 65}
+    ]
+
+
 @pytest.mark.parametrize(
     ("kind", "expected"),
     [
diff --git a/tests/core/test_custom_scores.py b/tests/core/test_custom_scores.py
index 834e83dd..36cc1f55 100644
--- a/tests/core/test_custom_scores.py
+++ b/tests/core/test_custom_scores.py
@@ -23,6 +23,73 @@
 )
 
 
+def test_custom_chain_similarity_scores_keep_each_alignment(tmp_path):
+    hits = {}
+    for backend, rows in {
+        "mmseqs": [
+            ("1abc", "A", 0.8, 0.5, 0.75, "ACDE", "ACDF"),
+            ("1abc", "A", 0.6, 0.4, 0.5, "AC-E", "ACDE"),
+        ],
+        "foldseek": [("2def", "B", 0.9, 0.8, 0.5, "AAAA", "AATA")],
+    }.items():
+        path = tmp_path / f"{backend}.parquet"
+        frame = pd.DataFrame(
+            [
+                {
+                    "query_id": "model2" if backend == "foldseek" else "model",
+                    "query_chain_id": (
+                        "model2__A" if backend == "foldseek" else "model__A"
+                    ),
+                    "structure_id": "model2" if backend == "foldseek" else "model",
+                    "query_chain_asym_id": "A",
+                    "target_entry": entry,
+                    "target_chain_asym_id": chain,
+                    "source": backend,
+                    "qcov": qcov,
+                    "tcov": tcov,
+                    "fident": fident,
+                    "qaln": qaln,
+                    "taln": taln,
+                    **({"lddt": 0.7} if backend == "foldseek" else {}),
+                }
+                for entry, chain, qcov, tcov, fident, qaln, taln in rows
+            ]
+        )
+        frame.to_parquet(path, index=False)
+        hits[backend] = path
+
+    manifest = tmp_path / "query_chains.parquet"
+    pd.DataFrame(
+        {
+            "query_id": ["model", "model2"],
+            "sequence_id": ["original-first", "original-second"],
+        }
+    ).to_parquet(manifest, index=False)
+    output = custom.write_custom_chain_similarity_scores(
+        hits,
+        output_path=tmp_path / "chain_scores.parquet",
+        chain_manifest=manifest,
+    )
+    scores = pd.read_parquet(output)
+    assert len(scores) == 3
+    assert scores["qcov"].tolist() == [80, 60, 90]
+    assert scores["fident"].tolist() == [75, 50, 50]
+    assert scores["sequence_id"].tolist() == [
+        "original-first",
+        "original-first",
+        "original-second",
+    ]
+    assert scores["lddt"].isna().tolist() == [True, True, False]
+    assert scores.iloc[2]["lddt"] == 70
+
+    empty = tmp_path / "empty.parquet"
+    pd.DataFrame().to_parquet(empty, index=False)
+    empty_output = custom.write_custom_chain_similarity_scores(
+        {"mmseqs": empty}, output_path=tmp_path / "empty_scores.parquet"
+    )
+    assert pd.read_parquet(empty_output).empty
+
+
 def _write_database_prefix(prefix: Path, *, indexed: bool = False) -> None:
     prefix.parent.mkdir(parents=True, exist_ok=True)
     prefix.with_suffix(".dbtype").write_bytes(b"db")
@@ -53,11 +120,11 @@ def _write_search_bundle(root: Path, backend: str) -> None:
             "alignment_type": backend,
             "portable": True,
             "search_target": "representatives",
-            "conversion_target": "holo_mmseqs",
+            "conversion_target": root.name,
             "cluster_alignments": "cluster_alignments",
         }
         _write_database_prefix(root / "representatives", indexed=True)
-        _write_database_prefix(root / "holo_mmseqs")
+        _write_database_prefix(root / root.name)
         _write_database_prefix(root / "cluster_alignments")
     (root / "exact_cluster.json").write_text(json.dumps(manifest))
 
@@ -93,6 +160,24 @@ def test_resolve_custom_scoring_assets_accepts_ingest_layout(tmp_path):
     assert assets.ligand_archives == {"ab": archive}
 
 
+def test_resolve_custom_scoring_assets_includes_monomer_targets(tmp_path):
+    _write_index(tmp_path)
+    for backend in custom.SEARCH_BACKENDS:
+        _write_search_bundle(tmp_path / "search_databases" / f"holo_{backend}", backend)
+        _write_search_bundle(
+            tmp_path / "search_databases" / f"monomer_{backend}", backend
+        )
+
+    assets = custom.resolve_custom_scoring_assets(
+        data_dir=tmp_path, include_monomers=True
+    )
+    assert set(assets.monomer_search_databases) == set(custom.SEARCH_BACKENDS)
+    assert (
+        assets.monomer_search_databases["mmseqs"].conversion_target.name
+        == "monomer_mmseqs"
+    )
+
+
 def test_remote_resolution_requests_only_bounded_assets(tmp_path, monkeypatch):
     _write_index(tmp_path)
     for backend in custom.SEARCH_BACKENDS:
@@ -117,7 +202,9 @@ def get_plinder_path(*, rel: str) -> Path:
         "index/alignment_chain_lookup.parquet",
         "search_databases/holo_foldseek",
         "search_databases/holo_mmseqs",
-        "search_databases/manifest.json",
+        "search_databases/weekly_delta/holo_foldseek",
+        "search_databases/weekly_delta/holo_mmseqs",
+        "search_databases/shadowed_entries.parquet",
         "ligand_archives/xy.parquet",
     }
     assert assets.ligand_archives == {"xy": archive}
@@ -132,15 +219,6 @@ def test_resolve_custom_scoring_assets_includes_weekly_search_overlay(tmp_path):
     pd.DataFrame({"pdb_id": ["1abc"]}).to_parquet(
         tmp_path / "search_databases/shadowed_entries.parquet", index=False
     )
-    (tmp_path / "search_databases/manifest.json").write_text(
-        json.dumps(
-            {
-                "overlays": {"mmseqs": {}},
-                "shadowed_entries": "shadowed_entries.parquet",
-            }
-        )
-    )
-
     assets = custom.resolve_custom_scoring_assets(data_dir=tmp_path)
 
     assert assets.shadowed_entries == {"1abc"}
@@ -231,34 +309,21 @@ def get_plinder_path(*, rel: str) -> Path:
     assert not any(path.startswith("ligand_archives/") for path in requested)
 
 
-def test_search_database_requires_portable_manifest(tmp_path):
+def test_search_database_does_not_require_build_manifest(tmp_path):
     root = tmp_path / "search_databases" / "holo_foldseek"
     _write_search_bundle(root, "foldseek")
-    manifest = json.loads((root / "exact_cluster.json").read_text())
-    manifest["portable"] = False
-    (root / "exact_cluster.json").write_text(json.dumps(manifest))
+    (root / "exact_cluster.json").unlink()
 
-    with pytest.raises(ValueError, match="not portable"):
-        custom.resolve_search_database("foldseek", data_dir=tmp_path)
+    bundle = custom.resolve_search_database("foldseek", data_dir=tmp_path)
+    assert bundle.search_target == root / "clustered"
 
 
-@pytest.mark.parametrize(
-    ("field", "value"),
-    [
-        ("identity", 0.9),
-        ("coverage", 0.9),
-        ("coverage_mode", 1),
-        ("compressed_search_target", True),
-    ],
-)
-def test_search_database_requires_exact_cluster_contract(tmp_path, field, value):
+def test_search_database_requires_indexed_target(tmp_path):
     root = tmp_path / "search_databases" / "holo_foldseek"
     _write_search_bundle(root, "foldseek")
-    manifest = json.loads((root / "exact_cluster.json").read_text())
-    manifest[field] = value
-    (root / "exact_cluster.json").write_text(json.dumps(manifest))
+    (root / "clustered.idx.dbtype").unlink()
 
-    with pytest.raises(ValueError, match="exact-cluster contract"):
+    with pytest.raises(FileNotFoundError, match="indexed"):
         custom.resolve_search_database("foldseek", data_dir=tmp_path)
 
 
@@ -903,6 +968,7 @@ def test_prepare_custom_score_alignments_maps_selected_residues(
         "tstart": 1,
         "qcov": 1.0,
         "fident": 1.0,
+        "cigar": "2M",
         "qaln": "AC",
         "taln": "AC",
     }
@@ -992,6 +1058,7 @@ def test_prepare_custom_protein_score_alignments_reverses_direction(
     assert result.loc[0, "target_selected_residue_numbers"].tolist() == [custom_number]
     assert result.loc[0, "selected_residue_identity_bits"] == b"\x01"
     assert result.loc[0, "fident_qcov"] == pytest.approx(0.75)
+    assert "cigar" not in result
 
 
 def test_prepare_custom_score_alignments_maps_coordinate_fasta_positions(tmp_path):
diff --git a/tests/data/pipeline/test_tasks.py b/tests/data/pipeline/test_tasks.py
index 48c88645..cf5d4f79 100644
--- a/tests/data/pipeline/test_tasks.py
+++ b/tests/data/pipeline/test_tasks.py
@@ -1765,6 +1765,9 @@ def test_search_bundle_includes_weekly_overlay(tmp_path, monkeypatch) -> None:
 
     base = tmp_path / "dbs/subdbs/holo_mmseqs"
     base.mkdir(parents=True)
+    monomer = tmp_path / "dbs/subdbs/monomer_mmseqs"
+    monomer.mkdir(parents=True)
+    (monomer / "exact_cluster.json").write_text("{}")
     overlay = tmp_path / "dbs/weekly_delta/subdbs/holo_mmseqs"
     overlay.mkdir(parents=True)
     (overlay / "exact_cluster.json").write_text("{}")
@@ -1784,9 +1787,10 @@ def publish_bundle(*, source_root, target_root, aln_type):
 
     score.publish_search_database_bundles(tmp_path, alignment_types=["mmseqs"])
 
-    assert sources == [base, overlay]
-    manifest = json.loads((tmp_path / "search_databases/manifest.json").read_text())
-    assert set(manifest["overlays"]) == {"mmseqs"}
+    assert sources == [base, monomer, overlay]
+    assert not (tmp_path / "search_databases/manifest.json").exists()
+    assert (tmp_path / "search_databases/monomer_mmseqs").is_dir()
+    assert (tmp_path / "search_databases/weekly_delta/holo_mmseqs").is_dir()
     assert pd.read_parquet(tmp_path / "search_databases/shadowed_entries.parquet")[
         "pdb_id"
     ].tolist() == ["1abc"]
@@ -1925,7 +1929,7 @@ def test_protein_scoring_plan_and_alignment_finalization(tmp_path, monkeypatch)
     assert report["target_clustering"]["expand_to_chain_level"] is True
     assert report["skipped_queries"] == {}
     assert (tmp_path / "alignments/manifest.json").is_file()
-    assert (tmp_path / "search_databases/manifest.json").is_file()
+    assert not (tmp_path / "search_databases/manifest.json").exists()
     assert (tmp_path / "search_databases/holo_foldseek/clustered.dbtype").is_file()
     assert (
         tmp_path / "search_databases/holo_mmseqs/cluster_alignments.dbtype"
@@ -7281,6 +7285,32 @@ def fake_entry_views(annotation, *, entry_chains):
     assert lookup_calls == [{"data_dir": tmp_path, "scratch_dir": None, "threads": 1}]
 
 
+def test_monomer_scoring_chains_excludes_holo_and_ligand_like_chains(
+    tmp_path, monkeypatch
+):
+    index = tmp_path / "index"
+    index.mkdir()
+    pd.DataFrame(
+        {
+            "entry_pdb_id": ["1abc"] * 4,
+            "chain_asym_id": ["A", "B", "C", "D"],
+            "chain_auth_id": ["A", "B", "C", "D"],
+            "chain_receptor_type": ["protein", "protein", "protein", "dna"],
+            "chain_is_ligand_like": [False, False, True, False],
+        }
+    ).to_parquet(index / "entry_chains.parquet", index=False)
+    monkeypatch.setattr(
+        tasks,
+        "_protein_scoring_chains",
+        lambda _data_dir: pd.DataFrame(
+            {"entry_pdb_id": ["1abc"], "chain_asym_id": ["A"]}
+        ),
+    )
+
+    result = tasks._monomer_scoring_chains(tmp_path)
+    assert result["chain_asym_id"].tolist() == ["B"]
+
+
 def test_make_holo_sub_dbs_selects_protein_receptor_and_interface_chains(
     tmp_path, monkeypatch
 ):
diff --git a/tests/data/test_monomer_similarity.py b/tests/data/test_monomer_similarity.py
new file mode 100644
index 00000000..4e6efdfa
--- /dev/null
+++ b/tests/data/test_monomer_similarity.py
@@ -0,0 +1,177 @@
+from pathlib import Path
+
+import pandas as pd
+import pyarrow.parquet as pq
+import pytest
+
+from plinder.core.utils.schemas import PROTEIN_SIMILARITY_EXPORT_SCHEMA
+from plinder.data import monomer_similarity
+from plinder.data.monomer_similarity import (
+    _chain_ids,
+    _score_alignment_batches,
+    finalize_monomer_similarity_scores,
+)
+
+
+@pytest.mark.parametrize("backend", ["mmseqs", "foldseek"])
+def test_monomer_pair_scores_map_release_chains(tmp_path: Path, backend: str) -> None:
+    index = tmp_path / "index"
+    index.mkdir()
+    pd.DataFrame(
+        {
+            "entry_pdb_id": ["1abc", "2def"],
+            "chain_auth_id": ["R", "S"],
+            "chain_asym_id": ["A", "C"],
+        }
+    ).to_parquet(index / "alignment_chain_lookup.parquet", index=False)
+    query = "1abc_R" if backend == "mmseqs" else "pdb_00001abc_xyz-enrich_R"
+    target = "2def_S" if backend == "mmseqs" else "pdb_00002def_xyz-enrich_MODEL_1_S"
+    raw = tmp_path / "raw"
+    raw.mkdir()
+    pd.DataFrame(
+        {
+            "query": [query],
+            "target": [target],
+            "qcov": [0.8],
+            "tcov": [0.6],
+            "fident": [0.75],
+            "qaln": ["ACDE"],
+            "taln": ["ACDF"],
+            **({"lddt": [0.7]} if backend == "foldseek" else {}),
+        }
+    ).to_parquet(raw / "batch.parquet", index=False)
+    output = tmp_path / "scores.parquet"
+    assert (
+        _score_alignment_batches(
+            raw, output, backend=backend, chain_ids=_chain_ids(tmp_path, backend)
+        )
+        == 1
+    )
+    assert pq.read_schema(output).equals(PROTEIN_SIMILARITY_EXPORT_SCHEMA)
+    row = pd.read_parquet(output).iloc[0]
+    assert (row.query_entry, row.query_chain_mapped) == ("1abc", "A")
+    assert (row.target_entry, row.target_chain_mapped) == ("2def", "C")
+    assert (row.qcov, row.tcov, row.fident) == (80, 60, 75)
+    assert row.lddt == 70 if backend == "foldseek" else pd.isna(row.lddt)
+
+
+def test_repeated_aligned_sequences_are_scored_once(
+    tmp_path: Path, monkeypatch
+) -> None:
+    raw = tmp_path / "raw"
+    raw.mkdir()
+    alignments = pd.DataFrame(
+        {
+            "query": ["1abc_R", "1abc_R"],
+            "target": ["2def_S", "2def_S"],
+            "qcov": [0.8, 0.8],
+            "tcov": [0.6, 0.6],
+            "fident": [0.75, 0.75],
+            "qaln": ["ACDE", "ACDE"],
+            "taln": ["ACDF", "ACDF"],
+        }
+    )
+    for index in range(len(alignments)):
+        alignments.iloc[[index]].to_parquet(raw / f"batch-{index}.parquet", index=False)
+    calls = []
+    monkeypatch.setattr(
+        monomer_similarity,
+        "get_sequence_similarity_helper",
+        lambda query, target: calls.append((query, target)) or 0.5,
+    )
+    assert (
+        _score_alignment_batches(
+            raw,
+            tmp_path / "scores.parquet",
+            backend="mmseqs",
+            chain_ids={"1abc_R": ("1abc", "A"), "2def_S": ("2def", "C")},
+        )
+        == 2
+    )
+    assert calls == [("ACDE", "ACDF")]
+    assert pq.ParquetFile(tmp_path / "scores.parquet").num_row_groups == 1
+
+
+def test_monomer_score_writer_accepts_empty_alignments(tmp_path: Path) -> None:
+    raw = tmp_path / "raw"
+    raw.mkdir()
+    pd.DataFrame(
+        {
+            column: pd.Series(dtype=dtype)
+            for column, dtype in {
+                "query": "string",
+                "target": "string",
+                "qcov": "float64",
+                "tcov": "float64",
+                "fident": "float64",
+                "qaln": "string",
+                "taln": "string",
+            }.items()
+        }
+    ).to_parquet(raw / "empty.parquet", index=False)
+    output = tmp_path / "scores.parquet"
+    assert _score_alignment_batches(raw, output, backend="mmseqs", chain_ids={}) == 0
+    assert pq.read_schema(output).equals(PROTEIN_SIMILARITY_EXPORT_SCHEMA)
+
+
+def test_foldseek_missing_lddt_remains_null(tmp_path: Path) -> None:
+    raw = tmp_path / "raw"
+    raw.mkdir()
+    pd.DataFrame(
+        {
+            "query": ["pdb_00001abc_xyz-enrich_R"],
+            "target": ["pdb_00002def_xyz-enrich_S"],
+            "qcov": [0.8],
+            "tcov": [0.6],
+            "fident": [0.75],
+            "qaln": ["ACDE"],
+            "taln": ["ACDF"],
+            "lddt": [None],
+        }
+    ).to_parquet(raw / "batch.parquet", index=False)
+    output = tmp_path / "scores.parquet"
+    assert (
+        _score_alignment_batches(
+            raw,
+            output,
+            backend="foldseek",
+            chain_ids={
+                "pdb_00001abc_xyz-enrich_R": ("1abc", "A"),
+                "pdb_00002def_xyz-enrich_S": ("2def", "C"),
+            },
+        )
+        == 1
+    )
+    assert pd.isna(pd.read_parquet(output).iloc[0].lddt)
+
+
+def test_finalize_monomer_scores_has_only_alignment_partition(tmp_path: Path) -> None:
+    staging = tmp_path / "exports/.monomer_similarity_scores_staging"
+    for backend in ("mmseqs", "foldseek"):
+        for target_kind in ("holo", "monomer"):
+            source = (
+                staging / f"alignment_type={backend}" / f"target_kind={target_kind}"
+            )
+            source.mkdir(parents=True)
+            pq.write_table(
+                PROTEIN_SIMILARITY_EXPORT_SCHEMA.empty_table(),
+                source / "part-0.parquet",
+            )
+
+    assert finalize_monomer_similarity_scores(tmp_path, query_batch_count=1) == 0
+    installed = tmp_path / "exports/monomer_similarity_scores"
+    assert len(list(installed.rglob("*.parquet"))) == 4
+    assert not list(installed.rglob("target_kind=*"))
+    assert set(pd.read_parquet(installed).columns) == {
+        *PROTEIN_SIMILARITY_EXPORT_SCHEMA.names,
+        "alignment_type",
+    }
+
+
+def test_finalize_monomer_scores_requires_every_batch(tmp_path: Path) -> None:
+    staging = tmp_path / "exports/.monomer_similarity_scores_staging"
+    staging.mkdir(parents=True)
+    with pytest.raises(FileNotFoundError):
+        finalize_monomer_similarity_scores(tmp_path, query_batch_count=1)
+    assert staging.is_dir()
+    assert not (tmp_path / "exports/monomer_similarity_scores").exists()

From 08eab089a955e115c46ddae2902143106306ee87 Mon Sep 17 00:00:00 2001
From: Ninjani <janani.durairaj@gmail.com>
Date: Fri, 2 Oct 2026 12:07:37 +0200
Subject: [PATCH 17/26] Separate public release artifacts from working ingest

---
 pyproject.toml                              |   1 +
 scripts/slurm/README.md                     |  21 +++
 src/plinder/data/pipeline/public_release.py | 147 ++++++++++++++++++++
 tests/data/pipeline/test_public_release.py  |  95 +++++++++++++
 4 files changed, 264 insertions(+)
 create mode 100644 src/plinder/data/pipeline/public_release.py
 create mode 100644 tests/data/pipeline/test_public_release.py

diff --git a/pyproject.toml b/pyproject.toml
index 08d7bf25..317459c7 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -32,6 +32,7 @@ Issues = "https://github.com/plinder-org/plinder/issues"
 [project.scripts]
 plinder_download = "plinder.core.index.utils:download_plinder_cmd"
 plinder_eval = "plinder.eval.cli:main"
+plinder_prepare_release = "plinder.data.pipeline.public_release:main"
 
 [project.optional-dependencies]
 data = ["google-cloud-storage", "gcsfs", "numba"]
diff --git a/scripts/slurm/README.md b/scripts/slurm/README.md
index bd445c95..b4b5283d 100644
--- a/scripts/slurm/README.md
+++ b/scripts/slurm/README.md
@@ -619,3 +619,24 @@ the validated alignment shards under
 `alignment_cigars/search_db=holo/alignment_type=*/shard=*.parquet`. Per-PDB raw
 search files and the other derived score datasets are generation intermediates;
 mapped per-PDB files exist only transiently on node-local scratch.
+
+## Separate the public release from working data
+
+Keep the completed ingest as the working directory. Build a sibling directory
+containing only the files used by the release API:
+
+```bash
+python -m plinder.data.pipeline.public_release \
+  /path/to/ingest_2026-09 /path/to/PLINDER-2026-09
+```
+
+The public directory includes the index tables, similarity tables, cover tables,
+ligand archives and scores, alignment CIGARs, and MMseqs/Foldseek search databases.
+It excludes raw alignments, score caches, scratch files, STEAM databases, and JSON
+files containing local paths. By default the files are hard-linked, so this adds
+almost no data storage but is not an independent copy: do not edit either tree's
+files in place. Pass `--copy` for an independent copy. After a working-release
+repair, rerun with `--replace` to refresh the public tree.
+
+Upload the public directory, not the working ingest. The Foldseek databases
+contain internal symlinks, so use `--no-ignore-symlinks` when syncing to GCS.
diff --git a/src/plinder/data/pipeline/public_release.py b/src/plinder/data/pipeline/public_release.py
new file mode 100644
index 00000000..975d0a03
--- /dev/null
+++ b/src/plinder/data/pipeline/public_release.py
@@ -0,0 +1,147 @@
+# Copyright (c) 2024, Plinder Development Team
+# Distributed under the terms of the Apache License 2.0
+"""Build a clean public release tree from a working ingest."""
+
+from __future__ import annotations
+
+import argparse
+import os
+import shutil
+import tempfile
+from pathlib import Path
+
+from plinder.core.release import RELEASE_PATHS, RELEASE_TABLES
+
+_FILE_ARTIFACTS = (
+    *(table["artifact"] for table in RELEASE_TABLES.values()),
+    "ligand_similarity_scores",
+    "interface_similarity_scores",
+    "interface_half_similarity_scores",
+)
+_PARQUET_DIRECTORIES = (
+    "protein_similarity_scores",
+    "monomer_similarity_scores",
+    "ligand_archives",
+    "ligand_scores",
+    "ligand_sampling",
+    "interface_sampling",
+    "alignment_cigars",
+)
+_SEARCH_DATABASES = (
+    "holo_mmseqs",
+    "holo_foldseek",
+    "monomer_mmseqs",
+    "monomer_foldseek",
+)
+
+
+def _public_files(source: Path) -> list[Path]:
+    files = {Path(RELEASE_PATHS[name]) for name in _FILE_ARTIFACTS}
+    for name in _PARQUET_DIRECTORIES:
+        directory = source / RELEASE_PATHS.get(name, name)
+        if not directory.is_dir():
+            raise FileNotFoundError(directory)
+        files.update(path.relative_to(source) for path in directory.rglob("*.parquet"))
+
+    database_root = source / RELEASE_PATHS["search_databases"]
+    for name in _SEARCH_DATABASES:
+        directory = database_root / name
+        if not directory.is_dir():
+            raise FileNotFoundError(directory)
+        files.update(
+            path.relative_to(source)
+            for path in directory.rglob("*")
+            if path.is_file() and path.suffix != ".json"
+        )
+    shadowed = database_root / "shadowed_entries.parquet"
+    if shadowed.is_file():
+        files.add(shadowed.relative_to(source))
+    overlay = database_root / "weekly_delta"
+    if overlay.is_dir():
+        files.update(
+            path.relative_to(source)
+            for path in overlay.rglob("*")
+            if path.is_file() and path.suffix != ".json"
+        )
+
+    missing = [str(source / path) for path in files if not (source / path).is_file()]
+    if missing:
+        raise FileNotFoundError(f"missing public release files: {missing[:10]}")
+    included = {source / item for item in files}
+    for relative in files:
+        path = source / relative
+        if path.is_symlink() and path.resolve() not in included:
+            raise ValueError(f"search database link leaves the public release: {path}")
+    return sorted(files)
+
+
+def prepare_public_release(
+    source: Path, destination: Path, *, replace: bool = False, copy: bool = False
+) -> int:
+    """Stage only public files beside an ingest; return the number of files."""
+    source = source.resolve(strict=True)
+    if destination.is_symlink():
+        raise ValueError("public release destination cannot be a symlink")
+    destination = destination.parent.resolve() / destination.name
+    if (
+        source == destination
+        or source in destination.parents
+        or destination in source.parents
+    ):
+        raise ValueError("working and public release directories must be separate")
+    if destination.exists() and not replace:
+        raise FileExistsError(destination)
+    if destination.exists() and not destination.is_dir():
+        raise NotADirectoryError(destination)
+    files = _public_files(source)
+    destination.parent.mkdir(parents=True, exist_ok=True)
+    staging = Path(
+        tempfile.mkdtemp(prefix=f".{destination.name}-", dir=destination.parent)
+    )
+    previous = staging.with_name(staging.name + "-previous")
+    try:
+        for relative in files:
+            original = source / relative
+            target = staging / relative
+            target.parent.mkdir(parents=True, exist_ok=True)
+            if original.is_symlink():
+                target.symlink_to(os.readlink(original))
+            elif copy:
+                shutil.copy2(original, target)
+            else:
+                os.link(original, target)
+        if destination.exists():
+            destination.rename(previous)
+        try:
+            staging.rename(destination)
+        except OSError:
+            if previous.exists():
+                previous.rename(destination)
+            raise
+        if previous.exists():
+            shutil.rmtree(previous)
+    finally:
+        if staging.exists():
+            shutil.rmtree(staging)
+    return len(files)
+
+
+def main() -> None:
+    parser = argparse.ArgumentParser(description=__doc__)
+    parser.add_argument("working", type=Path, help="completed working ingest")
+    parser.add_argument("public", type=Path, help="separate public release directory")
+    parser.add_argument(
+        "--replace", action="store_true", help="replace an existing public tree"
+    )
+    parser.add_argument(
+        "--copy", action="store_true", help="copy bytes instead of hard-linking"
+    )
+    args = parser.parse_args()
+    count = prepare_public_release(
+        args.working, args.public, replace=args.replace, copy=args.copy
+    )
+    print(f"Prepared {count} public files in {args.public}")
+
+
+if __name__ == "__main__":
+    main()
diff --git a/tests/data/pipeline/test_public_release.py b/tests/data/pipeline/test_public_release.py
new file mode 100644
index 00000000..904ac3fa
--- /dev/null
+++ b/tests/data/pipeline/test_public_release.py
@@ -0,0 +1,95 @@
+from pathlib import Path
+
+import pytest
+from plinder.core.release import RELEASE_PATHS
+from plinder.data.pipeline.public_release import (
+    _FILE_ARTIFACTS,
+    _PARQUET_DIRECTORIES,
+    _SEARCH_DATABASES,
+    prepare_public_release,
+)
+
+
+def _working_release(root: Path) -> None:
+    for name in _FILE_ARTIFACTS:
+        path = root / RELEASE_PATHS[name]
+        path.parent.mkdir(parents=True, exist_ok=True)
+        path.write_bytes(b"table")
+    for name in _PARQUET_DIRECTORIES:
+        path = root / RELEASE_PATHS.get(name, name) / "part.parquet"
+        path.parent.mkdir(parents=True, exist_ok=True)
+        path.write_bytes(b"scores")
+        (path.parent / "local.json").write_text("/scicore/private/path")
+    for name in _SEARCH_DATABASES:
+        folder = root / "search_databases" / name
+        folder.mkdir(parents=True)
+        (folder / "db").write_bytes(b"database")
+        (folder / "alias").symlink_to("db")
+        (folder / "local.json").write_text("/scicore/private/path")
+    (root / "search_databases" / "holo_steam").mkdir()
+    (root / "search_databases" / "holo_steam" / "db").write_bytes(b"tea")
+    (root / "scores").mkdir()
+    (root / "scores" / "temporary.parquet").write_bytes(b"work")
+
+
+def test_public_release_contains_only_reader_artifacts(tmp_path: Path) -> None:
+    working = tmp_path / "working"
+    public = tmp_path / "public"
+    _working_release(working)
+
+    count = prepare_public_release(working, public)
+
+    assert count > len(_FILE_ARTIFACTS)
+    assert (public / RELEASE_PATHS["annotation_table"]).read_bytes() == b"table"
+    assert (public / "search_databases/holo_foldseek/alias").read_bytes() == b"database"
+    assert (public / "search_databases/holo_foldseek/alias").is_symlink()
+    assert (public / "search_databases/holo_foldseek/db").stat().st_ino == (
+        working / "search_databases/holo_foldseek/db"
+    ).stat().st_ino
+    assert not list(public.rglob("*.json"))
+    assert not (public / "search_databases/holo_steam").exists()
+    assert not (public / "scores").exists()
+
+
+def test_public_release_replacement_drops_old_files(tmp_path: Path) -> None:
+    working = tmp_path / "working"
+    public = tmp_path / "public"
+    _working_release(working)
+    prepare_public_release(working, public)
+    (public / "stale.parquet").write_bytes(b"old")
+
+    with pytest.raises(FileExistsError):
+        prepare_public_release(working, public)
+    prepare_public_release(working, public, replace=True, copy=True)
+
+    assert not (public / "stale.parquet").exists()
+    assert (public / "search_databases/holo_foldseek/db").stat().st_ino != (
+        working / "search_databases/holo_foldseek/db"
+    ).stat().st_ino
+
+
+def test_missing_public_file_does_not_replace_release(tmp_path: Path) -> None:
+    working = tmp_path / "working"
+    public = tmp_path / "public"
+    _working_release(working)
+    prepare_public_release(working, public)
+    (working / RELEASE_PATHS["annotation_table"]).unlink()
+
+    with pytest.raises(FileNotFoundError, match="annotation_table.parquet"):
+        prepare_public_release(working, public, replace=True)
+
+    assert (public / RELEASE_PATHS["annotation_table"]).is_file()
+
+
+def test_public_release_rejects_external_database_links(tmp_path: Path) -> None:
+    working = tmp_path / "working"
+    public = tmp_path / "public"
+    _working_release(working)
+    alias = working / "search_databases/holo_foldseek/alias"
+    alias.unlink()
+    alias.symlink_to(working / "scores/temporary.parquet")
+
+    with pytest.raises(ValueError, match="link leaves the public release"):
+        prepare_public_release(working, public)
+
+    assert not public.exists()

From 0e940ec71c582b716677fa5fc33d23b633b9083c Mon Sep 17 00:00:00 2001
From: Ninjani <janani.durairaj@gmail.com>
Date: Fri, 2 Oct 2026 13:59:07 +0200
Subject: [PATCH 18/26] Fix release packaging and weekly update edge cases

---
 src/plinder/core/scores/custom.py           |   3 +-
 src/plinder/data/clusters.py                |  21 ++--
 src/plinder/data/monomer_similarity.py      |  14 +++
 src/plinder/data/pipeline/public_release.py |  21 +++-
 src/plinder/data/pipeline/tasks.py          |   3 +-
 src/plinder/data/pipeline/update_release.py |  40 ++++----
 tests/core/test_custom_scores.py            |  27 +++++
 tests/data/pipeline/test_public_release.py  |  34 ++++++-
 tests/data/pipeline/test_tasks.py           |  24 +++++
 tests/data/pipeline/test_update_release.py  | 104 ++++++++++++++++++++
 tests/data/test_clusters.py                 |  18 ++++
 tests/data/test_monomer_similarity.py       |  23 +++++
 12 files changed, 290 insertions(+), 42 deletions(-)

diff --git a/src/plinder/core/scores/custom.py b/src/plinder/core/scores/custom.py
index c491558c..3a9a46d6 100644
--- a/src/plinder/core/scores/custom.py
+++ b/src/plinder/core/scores/custom.py
@@ -2166,8 +2166,7 @@ def write_custom_chain_similarity_scores(
             scores["lddt"] = pd.NA
         for column in ("qcov", "tcov", "fident", "seqsim", "lddt"):
             scores[column] = (
-                (pd.to_numeric(scores[column], errors="coerce") * 100)
-                .round()
+                np.floor(pd.to_numeric(scores[column], errors="coerce") * 100 + 0.5)
                 .clip(0, 100)
                 .astype("UInt8")
             )
diff --git a/src/plinder/data/clusters.py b/src/plinder/data/clusters.py
index 5b95b97e..9bfadb7d 100644
--- a/src/plinder/data/clusters.py
+++ b/src/plinder/data/clusters.py
@@ -48,6 +48,12 @@
 INTERFACE_MEMBERSHIP = Path("index/interface_membership.parquet")
 
 
+def _set_slurm_memory_limit(connection: Any, share: int) -> None:
+    memory_mb = int(os.environ.get("SLURM_MEM_PER_NODE", "0"))
+    if memory_mb > 0:
+        connection.execute("SET memory_limit = ?", [f"{memory_mb * share // 5}MB"])
+
+
 def _cluster_root(data_dir: Path, entity_type: ClusterEntity) -> Path:
     if entity_type == "ligand":
         return data_dir / "ligand_clusters"
@@ -846,10 +852,7 @@ def write_symmetric_edge_fragment_batch(
     import duckdb
 
     connection = duckdb.connect()
-    if slurm_memory_mb := os.environ.get("SLURM_MEM_PER_NODE"):
-        connection.execute(
-            "SET memory_limit = ?", [f"{int(slurm_memory_mb) * 3 // 5}MB"]
-        )
+    _set_slurm_memory_limit(connection, 3)
     connection.sql(f"SET threads={threads}")
     temporary_root = scratch_dir / "duckdb"
     temporary_root.mkdir(exist_ok=True, parents=True)
@@ -1173,10 +1176,7 @@ def write_symmetric_edge_shard(
     local_output = scratch_dir / f"{metric}-{bucket:03d}.parquet"
     local_output.unlink(missing_ok=True)
     connection = duckdb.connect()
-    if slurm_memory_mb := os.environ.get("SLURM_MEM_PER_NODE"):
-        connection.execute(
-            "SET memory_limit = ?", [f"{int(slurm_memory_mb) * 3 // 5}MB"]
-        )
+    _set_slurm_memory_limit(connection, 3)
     connection.sql(f"SET threads={threads}")
     connection.sql(f"SET temp_directory='{scratch_dir.as_posix()}'")
     if fragments:
@@ -3058,10 +3058,7 @@ def _stage_directed_cover_edges(
     import duckdb
 
     connection = duckdb.connect()
-    if slurm_memory_mb := os.environ.get("SLURM_MEM_PER_NODE"):
-        connection.execute(
-            "SET memory_limit = ?", [f"{int(slurm_memory_mb) * 4 // 5}MB"]
-        )
+    _set_slurm_memory_limit(connection, 4)
     connection.sql(f"SET threads={threads}")
     connection.sql("SET preserve_insertion_order=false")
     temporary_root.mkdir(exist_ok=True, parents=True)
diff --git a/src/plinder/data/monomer_similarity.py b/src/plinder/data/monomer_similarity.py
index 68021b8f..306af956 100644
--- a/src/plinder/data/monomer_similarity.py
+++ b/src/plinder/data/monomer_similarity.py
@@ -236,12 +236,26 @@ def finalize_monomer_similarity_scores(
     data_dir: Path, *, query_batch_count: int = 8
 ) -> int:
     """Install the complete monomer-pair table after every batch succeeds."""
+    if query_batch_count < 1:
+        raise ValueError("query_batch_count must be positive")
     exports = Path(data_dir) / "exports"
     staging = exports / ".monomer_similarity_scores_staging"
     installing = exports / ".monomer_similarity_scores_installing"
     installed = exports / "monomer_similarity_scores"
     if installed.exists():
         raise FileExistsError(installed)
+    expected = {
+        staging
+        / f"alignment_type={backend}"
+        / f"target_kind={target_kind}"
+        / f"part-{batch_index}.parquet"
+        for backend in ("mmseqs", "foldseek")
+        for target_kind in ("holo", "monomer")
+        for batch_index in range(query_batch_count)
+    }
+    extra = set(staging.rglob("*.parquet")) - expected
+    if extra:
+        raise ValueError(f"unexpected monomer score batches: {sorted(extra)[:5]}")
     total_rows = 0
     for backend in ("mmseqs", "foldseek"):
         for target_kind in ("holo", "monomer"):
diff --git a/src/plinder/data/pipeline/public_release.py b/src/plinder/data/pipeline/public_release.py
index 975d0a03..8e179e2f 100644
--- a/src/plinder/data/pipeline/public_release.py
+++ b/src/plinder/data/pipeline/public_release.py
@@ -23,10 +23,9 @@
     "monomer_similarity_scores",
     "ligand_archives",
     "ligand_scores",
-    "ligand_sampling",
-    "interface_sampling",
     "alignment_cigars",
 )
+_SAMPLING_DIRECTORIES = ("ligand_sampling", "interface_sampling")
 _SEARCH_DATABASES = (
     "holo_mmseqs",
     "holo_foldseek",
@@ -42,6 +41,15 @@ def _public_files(source: Path) -> list[Path]:
         if not directory.is_dir():
             raise FileNotFoundError(directory)
         files.update(path.relative_to(source) for path in directory.rglob("*.parquet"))
+    for name in _SAMPLING_DIRECTORIES:
+        directory = source / RELEASE_PATHS.get(name, name)
+        if not directory.is_dir():
+            raise FileNotFoundError(directory)
+        for cover in ("set_cover", "directed_set_cover"):
+            files.update(
+                path.relative_to(source)
+                for path in (directory / cover).glob("metric=*/threshold=*.parquet")
+            )
 
     database_root = source / RELEASE_PATHS["search_databases"]
     for name in _SEARCH_DATABASES:
@@ -70,8 +78,13 @@ def _public_files(source: Path) -> list[Path]:
     included = {source / item for item in files}
     for relative in files:
         path = source / relative
-        if path.is_symlink() and path.resolve() not in included:
-            raise ValueError(f"search database link leaves the public release: {path}")
+        if path.is_symlink():
+            if Path(os.readlink(path)).is_absolute():
+                raise ValueError(f"absolute link in public release: {path}")
+            if path.resolve() not in included:
+                raise ValueError(
+                    f"search database link leaves the public release: {path}"
+                )
     return sorted(files)
 
 
diff --git a/src/plinder/data/pipeline/tasks.py b/src/plinder/data/pipeline/tasks.py
index f1f530f2..163a5a5a 100644
--- a/src/plinder/data/pipeline/tasks.py
+++ b/src/plinder/data/pipeline/tasks.py
@@ -1792,6 +1792,7 @@ def make_ccd_ligand_dbs(
     threads: int,
     force_update: bool = False,
     minimum_similarity: float = 30.0,
+    build_parity_scores: bool = False,
 ) -> Path:
     """Build the CCD-anchored MMP/ECFP4 databases and the ligand-to-CCD match sidecar."""
     ccd_ligand_dbs.make_ccd_ligand_dbs(
@@ -1800,7 +1801,7 @@ def make_ccd_ligand_dbs(
         threads=threads,
         force_update=force_update,
         minimum_similarity=minimum_similarity,
-        build_parity_scores=False,
+        build_parity_scores=build_parity_scores,
     )
     return ccd_ligand_dbs.make_ligand_ccd_match(data_dir=data_dir)
 
diff --git a/src/plinder/data/pipeline/update_release.py b/src/plinder/data/pipeline/update_release.py
index 4a4ff723..f35d5729 100644
--- a/src/plinder/data/pipeline/update_release.py
+++ b/src/plinder/data/pipeline/update_release.py
@@ -637,6 +637,10 @@ def repair_alignments(
         raw_dir = data_dir / "dbs/subdbs" / f"{search_db}_{alignment_type}" / "aln"
         for pdb_id in full_queries | targeted_queries:
             (raw_dir / f"{pdb_id}.parquet").unlink(missing_ok=True)
+    shadowed_path = data_dir / "manifests/weekly_shadowed_entries.parquet"
+    shadowed = set(
+        map(str, pq.read_table(shadowed_path, columns=["pdb_id"])["pdb_id"].to_pylist())
+    )
     if targeted_queries:
         changed_targets = _changed_target_database(
             data_dir,
@@ -659,15 +663,6 @@ def repair_alignments(
                     changed_targets / f"{search_db}_{backend}/exact_cluster.json"
                 ).is_file()
             ]
-            shadowed_path = data_dir / "manifests/weekly_shadowed_entries.parquet"
-            shadowed = set(
-                map(
-                    str,
-                    pq.read_table(shadowed_path, columns=["pdb_id"])[
-                        "pdb_id"
-                    ].to_pylist(),
-                )
-            )
             for source_label, query_ids in (
                 ("base", targeted_queries - shadowed),
                 ("overlay", targeted_queries & shadowed),
@@ -701,7 +696,7 @@ def repair_alignments(
                 search_db=search_db,
                 shards=targeted_shards,
                 replacement_query_ids=targeted_queries,
-                replacement_target_ids=affected,
+                replacement_target_ids=shadowed,
                 scorer_cfg=selected_cfg,
                 scratch_dir=scratch_dir / f"map-targeted-{search_db}",
                 threads=threads,
@@ -712,10 +707,6 @@ def repair_alignments(
                 )
                 for pdb_id in targeted_queries:
                     (raw_dir / f"{pdb_id}.parquet").unlink(missing_ok=True)
-    shadowed_path = data_dir / "manifests/weekly_shadowed_entries.parquet"
-    shadowed = set(
-        map(str, pq.read_table(shadowed_path, columns=["pdb_id"])["pdb_id"].to_pylist())
-    )
     for source_label, query_ids in (
         ("base", full_queries - shadowed),
         ("overlay", full_queries & shadowed),
@@ -2114,15 +2105,20 @@ def refresh_ligand_chemistry(
     )
     ccd = None
     if "make_ccd_ligand_dbs" not in cfg.flow.skip_specific_stages:
-        if (ccd_ligand_dbs.ccd_dbs_dir(data_dir) / "ccd_dbs.manifest.json").is_file():
-            ccd = ccd_ligand_dbs.make_ligand_ccd_match(data_dir=data_dir)
-        else:
-            ccd = tasks.make_ccd_ligand_dbs(
-                data_dir=data_dir,
-                scratch_dir=scratch_dir / "ccd",
-                threads=threads,
-                minimum_similarity=float(cfg.ligand.minimum_similarity),
+        ccd_manifest = (
+            read_json_cache(
+                ccd_ligand_dbs.ccd_dbs_dir(data_dir) / "ccd_dbs.manifest.json"
             )
+            or {}
+        )
+        ccd = tasks.make_ccd_ligand_dbs(
+            data_dir=data_dir,
+            scratch_dir=scratch_dir / "ccd",
+            threads=threads,
+            minimum_similarity=float(cfg.ligand.minimum_similarity),
+            build_parity_scores=bool(ccd_manifest.get("build_parity_scores"))
+            or ccd_ligand_dbs.ccd_parity_path(data_dir).is_file(),
+        )
     return {
         "status": "complete",
         "tanimoto": ligand_scores,
diff --git a/tests/core/test_custom_scores.py b/tests/core/test_custom_scores.py
index 36cc1f55..d1e41f6f 100644
--- a/tests/core/test_custom_scores.py
+++ b/tests/core/test_custom_scores.py
@@ -90,6 +90,33 @@ def test_custom_chain_similarity_scores_keep_each_alignment(tmp_path):
     assert pd.read_parquet(empty_output).empty
 
 
+def test_custom_chain_similarity_scores_round_half_up(tmp_path):
+    hits = tmp_path / "hits.parquet"
+    pd.DataFrame(
+        {
+            "query_id": ["model"],
+            "query_chain_id": ["model__A"],
+            "structure_id": ["model"],
+            "query_chain_asym_id": ["A"],
+            "target_entry": ["1abc"],
+            "target_chain_asym_id": ["B"],
+            "source": ["mmseqs"],
+            "qcov": [0.625],
+            "tcov": [0.125],
+            "fident": [0.125],
+            "qaln": ["ACDE"],
+            "taln": ["ACDF"],
+        }
+    ).to_parquet(hits, index=False)
+
+    output = custom.write_custom_chain_similarity_scores(
+        {"mmseqs": hits}, output_path=tmp_path / "scores.parquet"
+    )
+
+    scores = pd.read_parquet(output)
+    assert scores.loc[0, ["qcov", "tcov", "fident"]].tolist() == [63, 13, 13]
+
+
 def _write_database_prefix(prefix: Path, *, indexed: bool = False) -> None:
     prefix.parent.mkdir(parents=True, exist_ok=True)
     prefix.with_suffix(".dbtype").write_bytes(b"db")
diff --git a/tests/data/pipeline/test_public_release.py b/tests/data/pipeline/test_public_release.py
index 904ac3fa..136387d5 100644
--- a/tests/data/pipeline/test_public_release.py
+++ b/tests/data/pipeline/test_public_release.py
@@ -1,10 +1,12 @@
 from pathlib import Path
 
 import pytest
+
 from plinder.core.release import RELEASE_PATHS
 from plinder.data.pipeline.public_release import (
     _FILE_ARTIFACTS,
     _PARQUET_DIRECTORIES,
+    _SAMPLING_DIRECTORIES,
     _SEARCH_DATABASES,
     prepare_public_release,
 )
@@ -20,6 +22,14 @@ def _working_release(root: Path) -> None:
         path.parent.mkdir(parents=True, exist_ok=True)
         path.write_bytes(b"scores")
         (path.parent / "local.json").write_text("/scicore/private/path")
+    for name in _SAMPLING_DIRECTORIES:
+        directory = root / RELEASE_PATHS.get(name, name)
+        cover = directory / "directed_set_cover/metric=pocket_qcov/threshold=50.parquet"
+        cover.parent.mkdir(parents=True, exist_ok=True)
+        cover.write_bytes(b"cover")
+        cache = directory / "directed_set_cover/reductions/part.parquet"
+        cache.parent.mkdir(parents=True, exist_ok=True)
+        cache.write_bytes(b"cache")
     for name in _SEARCH_DATABASES:
         folder = root / "search_databases" / name
         folder.mkdir(parents=True)
@@ -49,6 +59,12 @@ def test_public_release_contains_only_reader_artifacts(tmp_path: Path) -> None:
     assert not list(public.rglob("*.json"))
     assert not (public / "search_databases/holo_steam").exists()
     assert not (public / "scores").exists()
+    for name in _SAMPLING_DIRECTORIES:
+        directory = public / RELEASE_PATHS.get(name, name)
+        assert (
+            directory / "directed_set_cover/metric=pocket_qcov/threshold=50.parquet"
+        ).read_bytes() == b"cover"
+        assert not (directory / "directed_set_cover/reductions").exists()
 
 
 def test_public_release_replacement_drops_old_files(tmp_path: Path) -> None:
@@ -87,9 +103,25 @@ def test_public_release_rejects_external_database_links(tmp_path: Path) -> None:
     _working_release(working)
     alias = working / "search_databases/holo_foldseek/alias"
     alias.unlink()
-    alias.symlink_to(working / "scores/temporary.parquet")
+    alias.symlink_to("../../scores/temporary.parquet")
 
     with pytest.raises(ValueError, match="link leaves the public release"):
         prepare_public_release(working, public)
 
     assert not public.exists()
+
+
+def test_public_release_rejects_absolute_internal_database_links(
+    tmp_path: Path,
+) -> None:
+    working = tmp_path / "working"
+    public = tmp_path / "public"
+    _working_release(working)
+    alias = working / "search_databases/holo_foldseek/alias"
+    alias.unlink()
+    alias.symlink_to(working / "search_databases/holo_foldseek/db")
+
+    with pytest.raises(ValueError, match="absolute link"):
+        prepare_public_release(working, public, copy=True)
+
+    assert not public.exists()
diff --git a/tests/data/pipeline/test_tasks.py b/tests/data/pipeline/test_tasks.py
index cf5d4f79..8e4526ea 100644
--- a/tests/data/pipeline/test_tasks.py
+++ b/tests/data/pipeline/test_tasks.py
@@ -25,6 +25,30 @@
 from plinder.data.pipeline.config import LigandConfig
 
 
+def test_ccd_builder_forwards_parity_selection(tmp_path, monkeypatch):
+    calls = []
+    monkeypatch.setattr(
+        tasks.ccd_ligand_dbs,
+        "make_ccd_ligand_dbs",
+        lambda **kwargs: calls.append(kwargs),
+    )
+    match = tmp_path / "ccd_dbs/ligand_ccd_match.parquet"
+    monkeypatch.setattr(
+        tasks.ccd_ligand_dbs, "make_ligand_ccd_match", lambda **_kwargs: match
+    )
+
+    assert (
+        tasks.make_ccd_ligand_dbs(
+            data_dir=tmp_path,
+            scratch_dir=tmp_path / "scratch",
+            threads=1,
+            build_parity_scores=True,
+        )
+        == match
+    )
+    assert calls[0]["build_parity_scores"] is True
+
+
 def test_foldseek_manifest_signature_reads_references_in_parallel(
     tmp_path: Path,
 ) -> None:
diff --git a/tests/data/pipeline/test_update_release.py b/tests/data/pipeline/test_update_release.py
index cb458993..aa312507 100644
--- a/tests/data/pipeline/test_update_release.py
+++ b/tests/data/pipeline/test_update_release.py
@@ -1180,6 +1180,110 @@ def test_changed_target_database_reuses_weekly_subdb(tmp_path, monkeypatch):
     )
 
 
+def test_targeted_weekly_repair_replaces_cumulative_delta_targets(
+    tmp_path, monkeypatch
+):
+    manifest = tmp_path / update_release.score.MANIFEST_RELATIVE
+    manifest.parent.mkdir(parents=True)
+    pd.DataFrame({"pdb_id": ["1abc", "2def"]}).to_parquet(manifest, index=False)
+    shadowed = tmp_path / "manifests/weekly_shadowed_entries.parquet"
+    shadowed.parent.mkdir(parents=True, exist_ok=True)
+    pd.DataFrame({"pdb_id": ["2def", "3ghi"]}).to_parquet(shadowed, index=False)
+    target_dir = tmp_path / "changed"
+    marker = target_dir / "holo_mmseqs/exact_cluster.json"
+    marker.parent.mkdir(parents=True)
+    marker.write_text("{}")
+    monkeypatch.setattr(
+        update_release, "_changed_target_database", lambda *_args, **_kwargs: target_dir
+    )
+    monkeypatch.setattr(update_release.tasks, "run_batch_searches", lambda **_kw: None)
+    monkeypatch.setattr(
+        update_release, "_rebase_unchanged_alignment_manifests", lambda *_a, **_kw: None
+    )
+    replacements = []
+    monkeypatch.setattr(
+        update_release,
+        "_refresh_alignment_shards",
+        lambda *_args, **kwargs: replacements.append(kwargs),
+    )
+
+    update_release.repair_alignments(
+        tmp_path,
+        search_db="holo",
+        affected={"2def"},
+        full_queries=set(),
+        targeted_queries={"1abc"},
+        scorer_cfg=OmegaConf.create({}),
+        foldseek_cfg=OmegaConf.create({}),
+        mmseqs_cfg=OmegaConf.create({}),
+        scratch_dir=tmp_path / "scratch",
+        threads=1,
+        batch_size=10,
+    )
+
+    assert len(replacements) == 1
+    assert replacements[0]["replacement_query_ids"] == {"1abc"}
+    assert replacements[0]["replacement_target_ids"] == {"2def", "3ghi"}
+
+
+def test_weekly_ccd_refresh_preserves_parity_from_manifest(tmp_path, monkeypatch):
+    fingerprint_path = tmp_path / "fingerprints/ligands_per_smiles.parquet"
+    fingerprint_path.parent.mkdir(parents=True)
+    pd.DataFrame(
+        {
+            "ligand_smiles_id": [1],
+            "ligand_rdkit_canonical_smiles": ["CCO"],
+            "fingerprint": [b"fingerprint"],
+        }
+    ).to_parquet(fingerprint_path, index=False)
+    ccd_manifest = tmp_path / "ccd_dbs/ccd_dbs.manifest.json"
+    ccd_manifest.parent.mkdir()
+    ccd_manifest.write_text('{"build_parity_scores": true}')
+    monkeypatch.setattr(
+        update_release.get_similarity_scores,
+        "ligand_score_manifest_payload",
+        lambda **_kwargs: {},
+    )
+    monkeypatch.setattr(
+        update_release.tasks, "compute_ligand_fingerprints", lambda **_kwargs: None
+    )
+    monkeypatch.setattr(
+        update_release, "_refresh_chemical_score_shards", lambda **_kwargs: {}
+    )
+    monkeypatch.setattr(
+        update_release.tasks, "annotate_ligand_similarity", lambda **_kwargs: None
+    )
+    monkeypatch.setattr(
+        update_release.tasks, "make_ligand_mmp_pairs", lambda **_kwargs: tmp_path
+    )
+    ccd_calls = []
+    monkeypatch.setattr(
+        update_release.tasks,
+        "make_ccd_ligand_dbs",
+        lambda **kwargs: ccd_calls.append(kwargs) or tmp_path / "ccd_dbs",
+    )
+    cfg = OmegaConf.create(
+        {
+            "ligand": {
+                "number_id_col": "ligand_smiles_id",
+                "minimum_similarity": 30.0,
+                "cofactor_similarity_threshold": 90.0,
+            },
+            "flow": {
+                "cluster_metrics": [],
+                "make_ligands_batch_size": 10,
+                "skip_specific_stages": [],
+            },
+        }
+    )
+
+    update_release.refresh_ligand_chemistry(
+        tmp_path, cfg=cfg, scratch_dir=tmp_path / "scratch", threads=1
+    )
+
+    assert ccd_calls[0]["build_parity_scores"] is True
+
+
 def test_release_update_runs_only_configured_search_databases(tmp_path, monkeypatch):
     plan_dir = tmp_path / "plan"
     plan_dir.mkdir()
diff --git a/tests/data/test_clusters.py b/tests/data/test_clusters.py
index 5298b7aa..71d8c027 100644
--- a/tests/data/test_clusters.py
+++ b/tests/data/test_clusters.py
@@ -8,6 +8,24 @@
 import pytest
 
 
+def test_slurm_zero_memory_does_not_limit_duckdb(monkeypatch):
+    from plinder.data.clusters import _set_slurm_memory_limit
+
+    calls = []
+
+    class Connection:
+        def execute(self, query, values):
+            calls.append((query, values))
+
+    monkeypatch.setenv("SLURM_MEM_PER_NODE", "0")
+    _set_slurm_memory_limit(Connection(), 3)
+    assert calls == []
+
+    monkeypatch.setenv("SLURM_MEM_PER_NODE", "1000")
+    _set_slurm_memory_limit(Connection(), 4)
+    assert calls == [("SET memory_limit = ?", ["800MB"])]
+
+
 def _component_partition(labels: pd.DataFrame) -> set[frozenset[str]]:
     return {
         frozenset(group["ligand_id"].astype(str))
diff --git a/tests/data/test_monomer_similarity.py b/tests/data/test_monomer_similarity.py
index 4e6efdfa..575735eb 100644
--- a/tests/data/test_monomer_similarity.py
+++ b/tests/data/test_monomer_similarity.py
@@ -175,3 +175,26 @@ def test_finalize_monomer_scores_requires_every_batch(tmp_path: Path) -> None:
         finalize_monomer_similarity_scores(tmp_path, query_batch_count=1)
     assert staging.is_dir()
     assert not (tmp_path / "exports/monomer_similarity_scores").exists()
+
+
+def test_finalize_monomer_scores_rejects_extra_or_zero_batches(tmp_path: Path) -> None:
+    staging = tmp_path / "exports/.monomer_similarity_scores_staging"
+    for backend in ("mmseqs", "foldseek"):
+        for target_kind in ("holo", "monomer"):
+            source = (
+                staging / f"alignment_type={backend}" / f"target_kind={target_kind}"
+            )
+            source.mkdir(parents=True)
+            for index in range(2):
+                pq.write_table(
+                    PROTEIN_SIMILARITY_EXPORT_SCHEMA.empty_table(),
+                    source / f"part-{index}.parquet",
+                )
+
+    with pytest.raises(ValueError, match="positive"):
+        finalize_monomer_similarity_scores(tmp_path, query_batch_count=0)
+    with pytest.raises(ValueError, match="unexpected monomer score batches"):
+        finalize_monomer_similarity_scores(tmp_path, query_batch_count=1)
+
+    assert staging.is_dir()
+    assert not (tmp_path / "exports/monomer_similarity_scores").exists()

From 7cc72eec04bb6dd09856425f42d57e7c17c2a482 Mon Sep 17 00:00:00 2001
From: Ninjani <janani.durairaj@gmail.com>
Date: Sat, 3 Oct 2026 13:12:09 +0200
Subject: [PATCH 19/26] Fix duplicate sequence ID columns in custom chain
 scores

---
 src/plinder/core/scores/custom.py | 1 +
 tests/core/test_custom_scores.py  | 1 +
 2 files changed, 2 insertions(+)

diff --git a/src/plinder/core/scores/custom.py b/src/plinder/core/scores/custom.py
index 3a9a46d6..cb500645 100644
--- a/src/plinder/core/scores/custom.py
+++ b/src/plinder/core/scores/custom.py
@@ -2180,6 +2180,7 @@ def write_custom_chain_similarity_scores(
         manifest = pd.read_parquet(chain_manifest, columns=["query_id", "sequence_id"])
         if manifest["query_id"].duplicated().any():
             raise ValueError("query chain manifest contains duplicate query IDs")
+        result = result.drop(columns="sequence_id", errors="ignore")
         result = result.merge(
             manifest, on="query_id", how="left", validate="many_to_one"
         )
diff --git a/tests/core/test_custom_scores.py b/tests/core/test_custom_scores.py
index d1e41f6f..dd0c8929 100644
--- a/tests/core/test_custom_scores.py
+++ b/tests/core/test_custom_scores.py
@@ -36,6 +36,7 @@ def test_custom_chain_similarity_scores_keep_each_alignment(tmp_path):
         frame = pd.DataFrame(
             [
                 {
+                    "sequence_id": "generated-placeholder",
                     "query_id": "model2" if backend == "foldseek" else "model",
                     "query_chain_id": (
                         "model2__A" if backend == "foldseek" else "model__A"

From 31b6dd2914e473c9ccdf54a17c0b14d7f01eb969 Mon Sep 17 00:00:00 2001
From: Thomas Duignan <thomas.j.duignan@gmail.com>
Date: Sun, 4 Oct 2026 11:10:16 -0400
Subject: [PATCH 20/26] fix: skip empty monomer search databases and narrow
 monomer batch index

- make_sub_dbs now also builds monomer databases whenever holo is built; when
  no monomer chains exist (e.g. the end-to-end test entry) linclust segfaults
  on the empty database. Skip monomer databases with no chains; downstream
  bundling already treats them as optional.
- check query_batch_index is not None so mypy can narrow the batch slice.
---
 src/plinder/data/monomer_similarity.py |  3 ++-
 src/plinder/data/pipeline/tasks.py     | 13 ++++++++++++-
 2 files changed, 14 insertions(+), 2 deletions(-)

diff --git a/src/plinder/data/monomer_similarity.py b/src/plinder/data/monomer_similarity.py
index 306af956..a76ecc7d 100644
--- a/src/plinder/data/monomer_similarity.py
+++ b/src/plinder/data/monomer_similarity.py
@@ -189,7 +189,8 @@ def score_monomer_pairs(
             identifiers = identifiers[:pilot_queries]
         else:
             if (
-                query_batch_count is None
+                query_batch_index is None
+                or query_batch_count is None
                 or not 0 <= query_batch_index < query_batch_count
             ):
                 raise ValueError("invalid monomer query batch")
diff --git a/src/plinder/data/pipeline/tasks.py b/src/plinder/data/pipeline/tasks.py
index 5f5518e8..9f7ed14a 100644
--- a/src/plinder/data/pipeline/tasks.py
+++ b/src/plinder/data/pipeline/tasks.py
@@ -655,6 +655,7 @@ def make_sub_dbs(
     """
     entries = None
     identifiers_by_database: dict[str, set[str]] = {}
+    skipped: set[str] = set()
     indexed_search_databases = []
     if set(sub_databases) <= {"holo", "apo", "monomer"}:
         indexed_search_databases = list(sub_databases)
@@ -682,6 +683,12 @@ def make_sub_dbs(
                 validate="one_to_one",
             )
         chains = chains[chains["chain_auth_id"].notna()]
+        if search_db == "monomer" and chains.empty:
+            # linclust crashes on an empty database; with no monomer chains
+            # there is no monomer target universe to build.
+            LOG.info("make_sub_dbs: no monomer chains; skipping monomer databases")
+            skipped.add(search_db)
+            continue
         identifiers_by_database[f"{search_db}_foldseek"] = {
             f"pdb_0000{row.entry_pdb_id}_xyz-enrich_{row.chain_auth_id}"
             for row in chains.itertuples(index=False)
@@ -710,7 +717,11 @@ def make_sub_dbs(
     db_dir = data_dir / "dbs" / "subdbs"
     db_dir.mkdir(exist_ok=True)
     LOG.info("making sub-databases for scoring")
-    db_sources = utils.get_db_sources(data_dir=data_dir, sub_databases=sub_databases)
+    built = [search_db for search_db in sub_databases if search_db not in skipped]
+    # get_db_sources treats an empty list as "all defaults", so skip it instead.
+    db_sources = (
+        utils.get_db_sources(data_dir=data_dir, sub_databases=built) if built else {}
+    )
     if "apo" in sub_databases:
         db_sources.update(
             utils.get_db_sources(data_dir=data_dir, sub_databases=["interface_apo"])

From d689da8369862bc945cb053a3296071b14eb7c6f Mon Sep 17 00:00:00 2001
From: Thomas Duignan <thomas.j.duignan@gmail.com>
Date: Sun, 4 Oct 2026 12:27:38 -0400
Subject: [PATCH 21/26] fix: skip empty monomer sub-databases after chain
 selection

The end-to-end entry has monomer chains, but none are selected into the
MMseqs sub-database, so the chain-count check in make_sub_dbs never fired and
linclust still crashed. Check the selected database instead and skip
clustering an empty monomer universe; revert the earlier chain-count check.
---
 src/plinder/data/databases.py      |  9 +++++++++
 src/plinder/data/pipeline/tasks.py | 13 +------------
 2 files changed, 10 insertions(+), 12 deletions(-)

diff --git a/src/plinder/data/databases.py b/src/plinder/data/databases.py
index 7d1c8308..b58df9ab 100644
--- a/src/plinder/data/databases.py
+++ b/src/plinder/data/databases.py
@@ -812,6 +812,15 @@ def make_sub_dbs(
                 )
             )
             working_database = working_subdb / working_subdb.name
+            if search_db_aln_type.startswith("monomer_") and not (
+                working_database.with_suffix(".index").is_file()
+                and _database_entry_count(working_database)
+            ):
+                # linclust crashes on an empty database. An empty monomer
+                # universe is not an error: downstream bundling skips it.
+                LOG.info(f"no {search_db_aln_type} chains selected; skipping")
+                report[search_db_aln_type] = missing
+                continue
             cluster_manifest = make_exact_search_db(
                 full_db=working_database,
                 aln_type=aln_type,
diff --git a/src/plinder/data/pipeline/tasks.py b/src/plinder/data/pipeline/tasks.py
index 9f7ed14a..5f5518e8 100644
--- a/src/plinder/data/pipeline/tasks.py
+++ b/src/plinder/data/pipeline/tasks.py
@@ -655,7 +655,6 @@ def make_sub_dbs(
     """
     entries = None
     identifiers_by_database: dict[str, set[str]] = {}
-    skipped: set[str] = set()
     indexed_search_databases = []
     if set(sub_databases) <= {"holo", "apo", "monomer"}:
         indexed_search_databases = list(sub_databases)
@@ -683,12 +682,6 @@ def make_sub_dbs(
                 validate="one_to_one",
             )
         chains = chains[chains["chain_auth_id"].notna()]
-        if search_db == "monomer" and chains.empty:
-            # linclust crashes on an empty database; with no monomer chains
-            # there is no monomer target universe to build.
-            LOG.info("make_sub_dbs: no monomer chains; skipping monomer databases")
-            skipped.add(search_db)
-            continue
         identifiers_by_database[f"{search_db}_foldseek"] = {
             f"pdb_0000{row.entry_pdb_id}_xyz-enrich_{row.chain_auth_id}"
             for row in chains.itertuples(index=False)
@@ -717,11 +710,7 @@ def make_sub_dbs(
     db_dir = data_dir / "dbs" / "subdbs"
     db_dir.mkdir(exist_ok=True)
     LOG.info("making sub-databases for scoring")
-    built = [search_db for search_db in sub_databases if search_db not in skipped]
-    # get_db_sources treats an empty list as "all defaults", so skip it instead.
-    db_sources = (
-        utils.get_db_sources(data_dir=data_dir, sub_databases=built) if built else {}
-    )
+    db_sources = utils.get_db_sources(data_dir=data_dir, sub_databases=sub_databases)
     if "apo" in sub_databases:
         db_sources.update(
             utils.get_db_sources(data_dir=data_dir, sub_databases=["interface_apo"])

From 1cd10a3cbf932618335c179b80be6990cdb38ecb Mon Sep 17 00:00:00 2001
From: Thomas Duignan <thomas.j.duignan@gmail.com>
Date: Sun, 4 Oct 2026 13:34:56 -0400
Subject: [PATCH 22/26] docs: describe the flat YYYY-MM release layout served
 from R2

- README, getting-started and migration pages now point at 2026-09 on
  plinderdata.org instead of 2024-06/v2 and the release-number layout
- regenerate the release tree in docs/dataset.md from the published manifest
  (adds protein_clusters, ligand_pocket_residues, apo/interface_apo CIGARs and
  the manifest; drops ligand_archives/manifest.json and per-fragment
  ligand_scores)
- document the manifest builder's prefix argument and the publish order /
  Cache-Control needed for manifest updates
---
 README.md                |  15 +++---
 docs/dataset.md          | 110 ++++++++++++++++++++-------------------
 docs/migration/r2.md     |  18 +++++--
 docs/tutorial/dataset.md |  11 ++--
 4 files changed, 82 insertions(+), 72 deletions(-)

diff --git a/README.md b/README.md
index ed199b1b..572f48c4 100644
--- a/README.md
+++ b/README.md
@@ -43,10 +43,9 @@ More details about the competition and other helpful practical tips can be found
 
 ## 🔢 Plinder versions
 
-We version the `plinder` dataset with two controls:
-
-- `PLINDER_RELEASE`: the month stamp of the last RCSB sync
-- `PLINDER_RELEASE_NUMBER`: numbered release within that ingest month
+We version the `plinder` dataset by the month stamp (`YYYY-MM`) of the RCSB
+sync it was built from, set with `PLINDER_RELEASE`. The current release,
+`2026-09`, is the default.
 
 We version the `plinder` application using an automated semantic
 versioning scheme based on the `git` commit history.
@@ -57,7 +56,7 @@ with the dataset.
 #### Changelog:
 
 - WIP (Current — unreleased):
-    - **Public downloads on Cloudflare R2**: `2024-06/v2` now downloads from `https://plinderdata.org` instead of GCS; `PLINDER_MIRROR_URL` selects another HTTP mirror. Downloads stream to disk and verify size and MD5 before atomic replacement, interrupted transfers retry from the start, and cached files with the expected size are reused (force a refresh to repair same-size local corruption). Google storage dependencies are now optional: install `plinder[data]` for the GCS data-generation utilities.
+    - **Public downloads on Cloudflare R2**: releases download from `https://plinderdata.org/<YYYY-MM>/` (currently `2026-09`) instead of GCS; `PLINDER_MIRROR_URL` selects another HTTP mirror. Downloads stream to disk and verify size and MD5 before atomic replacement, interrupted transfers retry from the start, and cached files with the expected size are reused (force a refresh to repair same-size local corruption). Google storage dependencies are now optional: install `plinder[data]` for the GCS data-generation utilities.
     - **Major backend refactor**: replaced OST, gemmi, plip, openbabel with biotite + peppr for data generation; removed 6 dependencies from ingest pipeline
     - **Nucleic acid support**: DNA/RNA chains now correctly included as receptor neighbors, mainchain/sidechain detection works for both protein and nucleic acids ([#61](https://github.com/plinder-org/plinder/issues/61))
     - **Custom CIF support**: new `Entry.from_custom_cif_file` for structure-prediction outputs (Boltz, AlphaFold3, Chai-1) that ship CIFs without `_chem_comp_bond` ([#117](https://github.com/plinder-org/plinder/issues/117)). Bond orders come from `ligand_smiles_dict` via positional atom-order match (the convention these tools follow); element/count mismatches raise with the offending position, `force_substructure_match=True` opts into substructure matching when atom order isn't preserved. User SMILES win over CCD for both `smiles` and `resolved_stereo_matches_template` — closes a silent gap where biotite's `LIG` placeholder would pass any 3D conformer. Input CIFs are never mutated; optional `save_fixed_cif` persists the enriched copy.
@@ -118,14 +117,14 @@ After installing the package, download the index tables and cluster assignments
 for a release with:
 
 ```console
-$ plinder_download --release 2024-06 --release-number v2
+$ plinder_download --release 2026-09
 ```
 
 The command offers the larger ligand, alignment, score, export, and search
 database groups separately, and dataset APIs also download required files
-lazily. No Google Cloud credentials or SDK are needed: `2024-06/v2` downloads
+lazily. No Google Cloud credentials or SDK are needed: releases download
 from `https://plinderdata.org`; `PLINDER_MIRROR_URL` can select another HTTP
-mirror. Other release versions are unavailable through the public downloader.
+mirror. The legacy `2024-06/v2` layout requires an earlier `plinder` version.
 For details on the release paths, see [Documentation](https://plinder-org.github.io/plinder/tutorial/dataset.html).
 
 ## Installing the Python package
diff --git a/docs/dataset.md b/docs/dataset.md
index 7a10590f..c1c01b67 100644
--- a/docs/dataset.md
+++ b/docs/dataset.md
@@ -9,8 +9,9 @@ extracts protein-ligand systems and protein-protein interfaces from the PDB.
 
 ## Release layout
 
-PLINDER releases are identified by the month of their PDB snapshot and a
-release number within that month. The file layout is:
+PLINDER releases are identified by the month of their PDB snapshot
+(`YYYY-MM`; the current release is `2026-09`) and served from
+`https://plinderdata.org/<release-month>/`. The file layout is:
 
 :::{note}
 Historical releases remain available at `gs://plinder/2024-04/v0`,
@@ -20,57 +21,60 @@ differ from the current release.
 
 ```text
 <release-month>/
-└── <release-number>/
-    ├── index/
-    │   ├── annotation_table.parquet
-    │   ├── system_validation.parquet
-    │   ├── entry_chains.parquet
-    │   ├── entry_biounit_chains.parquet
-    │   ├── entry_metadata.parquet
-    │   ├── entry_sources.parquet
-    │   ├── interface_annotation_table.parquet
-    │   ├── alignment_chain_lookup.parquet
-    │   ├── linked_apo_structures.parquet
-    │   ├── interface_apo_structures.parquet
-    │   ├── ligand_pocket_membership.parquet
-    │   ├── ligand_pocket_representatives.parquet
-    │   ├── ligand_clusters.parquet
-    │   ├── ligand_affinity.parquet
-    │   ├── bindingdb_measurements.parquet
-    │   ├── ligand_mmp_pairs.parquet
-    │   ├── interface_half_representatives.parquet
-    │   ├── interface_membership.parquet
-    │   ├── interface_representatives.parquet
-    │   └── interface_clusters.parquet
-    ├── ligand_archives/
-    │   ├── {two_char_code}.parquet
-    │   └── manifest.json
-    ├── alignment_cigars/
-    │   └── search_db=holo/
-    │       └── alignment_type={foldseek,mmseqs}/
-    │           └── shard={two_char_code}.parquet
-    ├── ligand_scores/
-    │   └── {fragment}.parquet
-    ├── ligand_sampling/
-    │   ├── set_cover/metric={metric}/threshold={threshold}.parquet
-    │   └── directed_set_cover/metric={metric}/threshold={threshold}.parquet
-    ├── interface_sampling/
-    │   └── directed_set_cover/metric=interface_qcov/threshold={threshold}.parquet
-    ├── search_databases/
-    │   ├── holo_foldseek/
-    │   ├── holo_mmseqs/
-    │   ├── monomer_foldseek/
-    │   └── monomer_mmseqs/
-    └── exports/
-        ├── ligand_similarity_scores.parquet
-        ├── interface_similarity_scores.parquet
-        ├── interface_half_similarity_scores.parquet
-        ├── protein_similarity_scores/
-        │   └── alignment_type={foldseek,mmseqs}/
-        │       └── shard={two_char_code}.parquet
-        └── monomer_similarity_scores/
-            └── alignment_type={foldseek,mmseqs}/
-                └── monomer_{holo,monomer}_{batch}.parquet
+├── manifest.jsonl.gz
+├── index/
+│   ├── annotation_table.parquet
+│   ├── system_validation.parquet
+│   ├── entry_chains.parquet
+│   ├── entry_biounit_chains.parquet
+│   ├── entry_metadata.parquet
+│   ├── entry_sources.parquet
+│   ├── interface_annotation_table.parquet
+│   ├── alignment_chain_lookup.parquet
+│   ├── linked_apo_structures.parquet
+│   ├── interface_apo_structures.parquet
+│   ├── ligand_pocket_membership.parquet
+│   ├── ligand_pocket_residues.parquet
+│   ├── ligand_pocket_representatives.parquet
+│   ├── ligand_clusters.parquet
+│   ├── ligand_affinity.parquet
+│   ├── bindingdb_measurements.parquet
+│   ├── ligand_mmp_pairs.parquet
+│   ├── interface_half_representatives.parquet
+│   ├── interface_membership.parquet
+│   ├── interface_representatives.parquet
+│   └── interface_clusters.parquet
+├── protein_clusters/
+│   ├── sequence.parquet
+│   └── structure.parquet
+├── ligand_archives/
+│   └── {two_char_code}.parquet
+├── alignment_cigars/
+│   └── search_db={holo,apo,interface_apo}/
+│       └── alignment_type={foldseek,mmseqs}/
+│           └── shard={two_char_code}.parquet
+├── ligand_scores/
+│   └── retained.parquet
+├── ligand_sampling/
+│   ├── set_cover/metric={metric}/threshold={threshold}.parquet
+│   └── directed_set_cover/metric={metric}/threshold={threshold}.parquet
+├── interface_sampling/
+│   └── directed_set_cover/metric=interface_qcov/threshold={threshold}.parquet
+├── search_databases/
+│   ├── holo_foldseek/
+│   ├── holo_mmseqs/
+│   ├── monomer_foldseek/
+│   └── monomer_mmseqs/
+└── exports/
+    ├── ligand_similarity_scores.parquet
+    ├── interface_similarity_scores.parquet
+    ├── interface_half_similarity_scores.parquet
+    ├── protein_similarity_scores/
+    │   └── alignment_type={foldseek,mmseqs}/
+    │       └── shard={two_char_code}.parquet
+    └── monomer_similarity_scores/
+        └── alignment_type={foldseek,mmseqs}/
+            └── monomer_{holo,monomer}_{batch}.parquet
 ```
 
 `plinder_download` downloads the index and representative-cover tables by
diff --git a/docs/migration/r2.md b/docs/migration/r2.md
index bcfad88d..9967651f 100644
--- a/docs/migration/r2.md
+++ b/docs/migration/r2.md
@@ -1,8 +1,9 @@
 # Static release downloads from R2
 
-Public dataset reads for `2024-06/v2` use `https://plinderdata.org`. No S3 keys
-or Google credentials are required. Other online release/bucket combinations
-are rejected. `PLINDER_MIRROR_URL` may select another HTTP(S) bucket root with
+Public dataset reads for `YYYY-MM` releases (currently `2026-09`) use
+`https://plinderdata.org/<YYYY-MM>/`. No S3 keys or Google credentials are
+required. Releases with a release number, such as the legacy `2024-06/v2`, are
+rejected; use an earlier `plinder` version for them. `PLINDER_MIRROR_URL` may select another HTTP(S) bucket root with
 the same release layout and manifest. The local cache layout is unchanged.
 
 ## Download and cache behavior
@@ -30,13 +31,20 @@ Ingestion and generation compatibility are outside this static-release change.
 ## Building the static manifest
 
 ```bash
-python scripts/build_r2_manifest.py INVENTORY_DIR OUTPUT.jsonl.gz
+python scripts/build_r2_manifest.py INVENTORY_DIR OUTPUT.jsonl.gz RELEASE_PREFIX
 ```
 
 `INVENTORY_DIR/manifest-files.json` lists shard paths and SHA256 values. Each
 compressed JSONL shard contains source rows with `name`, `size` and `md5Hash`.
 The builder verifies shard checksums, rejects duplicate/invalid keys and writes
-sorted release-relative records for `2024-06/v2`. It performs no cloud I/O.
+sorted records relative to `RELEASE_PREFIX` (the object-name prefix of the
+release in the inventory, e.g. `PLINDER-2026-09` for the GCS staging copy). It performs no cloud I/O.
+
+Upload changed objects first, then the manifest, then delete removed objects,
+so clients never see a manifest that lists missing files. Cloudflare caches
+`.gz` responses by default; upload the manifest with
+`--header-upload "Cache-Control: public, max-age=60"` (rclone) so a new
+manifest is served within a minute.
 
 The existing public manifest lists 5,891 objects totaling 219,677,619,278 bytes.
 Its 207,150 published bytes were checked on 2026-09-14 against SHA256
diff --git a/docs/tutorial/dataset.md b/docs/tutorial/dataset.md
index 51ec10f3..d77a5b93 100644
--- a/docs/tutorial/dataset.md
+++ b/docs/tutorial/dataset.md
@@ -9,17 +9,16 @@ files, querying annotations, and reconstructing structures.
 pip install plinder
 ```
 
-The published `2024-06/v2` release downloads from Cloudflare R2
-(`https://plinderdata.org`) with checksum verification and automatic retries;
+Releases download from Cloudflare R2
+(`https://plinderdata.org/<release-month>/`) with checksum verification and automatic retries;
 no Google Cloud SDK is required. `PLINDER_MIRROR_URL` selects another HTTP(S)
 mirror serving the same release layout and manifest.
 
-A release is identified by the month of its PDB snapshot and a number within
-that month:
+A release is identified by the month of its PDB snapshot. The current release
+(`2026-09`) is the default; select another with:
 
 ```bash
-export PLINDER_RELEASE=2026-07
-export PLINDER_RELEASE_NUMBER=1
+export PLINDER_RELEASE=2026-09
 ```
 
 ## Continue with a runnable guide

From b37a5f91705f78f197aeaca5ac67d62a8fe1dcac Mon Sep 17 00:00:00 2001
From: Thomas Duignan <thomas.j.duignan@gmail.com>
Date: Sun, 4 Oct 2026 14:01:00 -0400
Subject: [PATCH 23/26] fix: handle in-place release updates and empty monomer
 universes

- directory downloads drop cached Parquet files the release no longer lists,
  so dataset readers never mix removed fragments (e.g. the 290 old
  ligand_scores files removed from 2026-09) with their replacements
- skipping an empty monomer sub-database also retires an earlier build, so a
  stale monomer target is never published as current
- custom scoring treats monomer search databases as optional per backend, and
  public_release no longer requires monomer artifacts, matching the pipeline
- monomer chain masks cast fillna results to bool for pandas 3
- build_r2_manifest skips a root folder placeholder; clarify its prefix
  argument
---
 scripts/build_r2_manifest.py                |  8 +++-
 src/plinder/core/scores/custom.py           | 19 ++++-----
 src/plinder/core/utils/cpl.py               | 16 ++++++++
 src/plinder/data/databases.py               | 11 ++++++
 src/plinder/data/pipeline/public_release.py |  6 +++
 src/plinder/data/pipeline/tasks.py          |  2 +-
 tests/core/test_custom_scores.py            | 14 +++++++
 tests/core/test_r2.py                       | 18 +++++++++
 tests/data/pipeline/test_public_release.py  | 18 +++++++++
 tests/data/test_databases.py                | 43 +++++++++++++++++++++
 10 files changed, 143 insertions(+), 12 deletions(-)

diff --git a/scripts/build_r2_manifest.py b/scripts/build_r2_manifest.py
index e9e7a95a..28fba050 100644
--- a/scripts/build_r2_manifest.py
+++ b/scripts/build_r2_manifest.py
@@ -24,7 +24,7 @@ def build(inventory: Path, destination: Path, release: str) -> int:
                 if not r["name"].startswith(prefix):
                     raise ValueError("Unexpected release")
                 key = r["name"][len(prefix) :]
-                if key.endswith("/"):
+                if not key or key.endswith("/"):
                     continue
                 if (
                     not key
@@ -48,6 +48,10 @@ def build(inventory: Path, destination: Path, release: str) -> int:
     parser = argparse.ArgumentParser(description=__doc__)
     parser.add_argument("inventory", type=Path)
     parser.add_argument("destination", type=Path)
-    parser.add_argument("release", help="release stamp, e.g. 2026-09")
+    parser.add_argument(
+        "release",
+        help="object-name prefix of the release in the inventory, "
+        "e.g. 2026-09 or PLINDER-2026-09",
+    )
     args = parser.parse_args()
     print(build(args.inventory, args.destination, args.release))
diff --git a/src/plinder/core/scores/custom.py b/src/plinder/core/scores/custom.py
index cb500645..7492e8ee 100644
--- a/src/plinder/core/scores/custom.py
+++ b/src/plinder/core/scores/custom.py
@@ -341,14 +341,15 @@ def resolve_custom_scoring_assets(
         backend: resolve_search_database(backend, data_dir=data_dir)
         for backend in selected_backends
     }
-    monomer_databases = (
-        {
-            backend: resolve_search_database(backend, data_dir=data_dir, monomer=True)
-            for backend in selected_backends
-        }
-        if include_monomers
-        else {}
-    )
+    monomer_databases = {}
+    for backend in selected_backends if include_monomers else ():
+        try:
+            monomer_databases[backend] = resolve_search_database(
+                backend, data_dir=data_dir, monomer=True
+            )
+        except FileNotFoundError as exc:
+            # A release or ingest may have no monomer universe for a backend.
+            LOG.warning(f"no {backend} monomer search database; skipping: {exc}")
     release = PlinderRelease(data_dir)
     overlay_databases = {}
     overlay_monomer_databases = {}
@@ -1161,7 +1162,7 @@ def _build_mmseqs_target_subset(
         "chain_is_interface"
     ].eq(True)
     selected_chains = (
-        ~scoreable & ~chains["chain_is_ligand_like"].fillna(False)
+        ~scoreable & ~chains["chain_is_ligand_like"].fillna(False).astype(bool)
         if monomer_only
         else scoreable
     )
diff --git a/src/plinder/core/utils/cpl.py b/src/plinder/core/utils/cpl.py
index 3a48ff3f..005c0d13 100644
--- a/src/plinder/core/utils/cpl.py
+++ b/src/plinder/core/utils/cpl.py
@@ -106,6 +106,20 @@ def download_paths(*, paths: list[Path], force_progress: bool = False) -> None:
         _download(_get_client(), paths, force_progress)
 
 
+def _prune_unpublished(client: ReleaseClient, directory: Path) -> None:
+    """Remove cached Parquet files that the release no longer lists.
+
+    Directory artifacts are read as whole Parquet datasets, so a file dropped
+    from an updated release would otherwise be read alongside its replacement.
+    """
+    root = Path(get_config().data.plinder_dir)
+    for path in directory.rglob("*.parquet"):
+        if path.is_symlink() or not path.is_file():
+            continue
+        if path.relative_to(root).as_posix() not in client.records:
+            path.unlink()
+
+
 def get_plinder_path(
     *, rel: str = "", download: bool = True, force_progress: bool = False
 ) -> Path:
@@ -141,4 +155,6 @@ def get_plinder_path(
         [remote] if remote.is_file() else [p for p in remote.rglob("*") if p.is_file()]
     )
     _download(client, [root / client.key(p) for p in files], force_progress)
+    if not remote.is_file():
+        _prune_unpublished(client, local)
     return local
diff --git a/src/plinder/data/databases.py b/src/plinder/data/databases.py
index b58df9ab..16846291 100644
--- a/src/plinder/data/databases.py
+++ b/src/plinder/data/databases.py
@@ -818,7 +818,18 @@ def make_sub_dbs(
             ):
                 # linclust crashes on an empty database. An empty monomer
                 # universe is not an error: downstream bundling skips it.
+                # Retire any earlier build so it is not published as current.
                 LOG.info(f"no {search_db_aln_type} chains selected; skipping")
+                for stale in ("exact_cluster.json", "selection.json"):
+                    (subdb / stale).unlink(missing_ok=True)
+                for prefix in (
+                    subdb.name,
+                    "exact_clusters",
+                    "representatives",
+                    "cluster_alignments",
+                    "clustered",
+                ):
+                    _remove_database_prefix(subdb / prefix)
                 report[search_db_aln_type] = missing
                 continue
             cluster_manifest = make_exact_search_db(
diff --git a/src/plinder/data/pipeline/public_release.py b/src/plinder/data/pipeline/public_release.py
index 8e179e2f..efcb05f6 100644
--- a/src/plinder/data/pipeline/public_release.py
+++ b/src/plinder/data/pipeline/public_release.py
@@ -32,6 +32,8 @@
     "monomer_mmseqs",
     "monomer_foldseek",
 )
+# Monomer artifacts exist only when the ingest had monomer chains to search.
+_OPTIONAL = {"monomer_similarity_scores", "monomer_mmseqs", "monomer_foldseek"}
 
 
 def _public_files(source: Path) -> list[Path]:
@@ -39,6 +41,8 @@ def _public_files(source: Path) -> list[Path]:
     for name in _PARQUET_DIRECTORIES:
         directory = source / RELEASE_PATHS.get(name, name)
         if not directory.is_dir():
+            if name in _OPTIONAL:
+                continue
             raise FileNotFoundError(directory)
         files.update(path.relative_to(source) for path in directory.rglob("*.parquet"))
     for name in _SAMPLING_DIRECTORIES:
@@ -55,6 +59,8 @@ def _public_files(source: Path) -> list[Path]:
     for name in _SEARCH_DATABASES:
         directory = database_root / name
         if not directory.is_dir():
+            if name in _OPTIONAL:
+                continue
             raise FileNotFoundError(directory)
         files.update(
             path.relative_to(source)
diff --git a/src/plinder/data/pipeline/tasks.py b/src/plinder/data/pipeline/tasks.py
index 5f5518e8..1f285c38 100644
--- a/src/plinder/data/pipeline/tasks.py
+++ b/src/plinder/data/pipeline/tasks.py
@@ -1874,7 +1874,7 @@ def _monomer_scoring_chains(data_dir: Path) -> pd.DataFrame:
     )
     chains = chains.loc[
         chains["chain_receptor_type"].eq("protein")
-        & ~chains["chain_is_ligand_like"].fillna(False)
+        & ~chains["chain_is_ligand_like"].fillna(False).astype(bool)
         & chains["chain_auth_id"].notna()
     ]
     holo = _protein_scoring_chains(data_dir)[["entry_pdb_id", "chain_asym_id"]]
diff --git a/tests/core/test_custom_scores.py b/tests/core/test_custom_scores.py
index dd0c8929..fd51d531 100644
--- a/tests/core/test_custom_scores.py
+++ b/tests/core/test_custom_scores.py
@@ -206,6 +206,20 @@ def test_resolve_custom_scoring_assets_includes_monomer_targets(tmp_path):
     )
 
 
+def test_resolve_custom_scoring_assets_skips_missing_monomer_targets(tmp_path):
+    _write_index(tmp_path)
+    for backend in custom.SEARCH_BACKENDS:
+        _write_search_bundle(tmp_path / "search_databases" / f"holo_{backend}", backend)
+    _write_search_bundle(tmp_path / "search_databases" / "monomer_mmseqs", "mmseqs")
+
+    assets = custom.resolve_custom_scoring_assets(
+        data_dir=tmp_path, include_monomers=True
+    )
+
+    assert set(assets.search_databases) == set(custom.SEARCH_BACKENDS)
+    assert set(assets.monomer_search_databases) == {"mmseqs"}
+
+
 def test_remote_resolution_requests_only_bounded_assets(tmp_path, monkeypatch):
     _write_index(tmp_path)
     for backend in custom.SEARCH_BACKENDS:
diff --git a/tests/core/test_r2.py b/tests/core/test_r2.py
index ab80ac78..49a896ca 100644
--- a/tests/core/test_r2.py
+++ b/tests/core/test_r2.py
@@ -73,6 +73,24 @@ def test_directory_download_and_truncated_cache_repair(mirror):
     assert not (Path(cfg.data.plinder_dir) / "systems/ab.zip").exists()
 
 
+def test_directory_download_prunes_parquet_files_the_release_dropped(mirror):
+    cfg, _ = mirror
+    cache = Path(cfg.data.plinder_dir)
+    stale = cache / "scores/old.parquet"
+    stale.parent.mkdir(parents=True)
+    stale.write_bytes(b"stale")
+    (cache / "scores/notes.txt").write_text("kept")
+    elsewhere = cache / "other/x.parquet"
+    elsewhere.parent.mkdir()
+    elsewhere.write_bytes(b"kept")
+
+    path = cpl.get_plinder_path(rel="scores")
+
+    assert sorted(p.name for p in path.glob("*.parquet")) == ["a.parquet", "b.parquet"]
+    assert (path / "notes.txt").read_text() == "kept"
+    assert elsewhere.read_bytes() == b"kept"
+
+
 def test_small_batch_failure_propagates(mirror):
     cfg, origin = mirror
     (origin / "systems/ab.zip").write_bytes(b"corrupt")
diff --git a/tests/data/pipeline/test_public_release.py b/tests/data/pipeline/test_public_release.py
index 136387d5..e44080f7 100644
--- a/tests/data/pipeline/test_public_release.py
+++ b/tests/data/pipeline/test_public_release.py
@@ -67,6 +67,24 @@ def test_public_release_contains_only_reader_artifacts(tmp_path: Path) -> None:
         assert not (directory / "directed_set_cover/reductions").exists()
 
 
+def test_public_release_allows_an_empty_monomer_universe(tmp_path: Path) -> None:
+    working = tmp_path / "working"
+    _working_release(working)
+    for name in ("monomer_mmseqs", "monomer_foldseek"):
+        for path in sorted((working / "search_databases" / name).iterdir()):
+            path.unlink()
+        (working / "search_databases" / name).rmdir()
+    monomer_scores = working / RELEASE_PATHS["monomer_similarity_scores"]
+    for path in monomer_scores.iterdir():
+        path.unlink()
+    monomer_scores.rmdir()
+
+    prepare_public_release(working, tmp_path / "public")
+
+    assert (tmp_path / "public/search_databases/holo_mmseqs/db").is_file()
+    assert not (tmp_path / "public/search_databases/monomer_mmseqs").exists()
+
+
 def test_public_release_replacement_drops_old_files(tmp_path: Path) -> None:
     working = tmp_path / "working"
     public = tmp_path / "public"
diff --git a/tests/data/test_databases.py b/tests/data/test_databases.py
index c8cb5197..7d3ce954 100644
--- a/tests/data/test_databases.py
+++ b/tests/data/test_databases.py
@@ -305,3 +305,46 @@ def fake_make_exact_search_db(*, full_db, **_kwargs):
     assert (target / "exact_cluster.json").is_file()
     assert original_missing.read_text() == '{"old": true}\n'
     assert not os.path.samefile(original_missing, db_dir / "missing.json")
+
+
+def test_make_sub_dbs_retires_monomer_db_when_selection_becomes_empty(
+    tmp_path, monkeypatch
+):
+    full_db = tmp_path / "full" / "mmseqs"
+    full_db.parent.mkdir()
+    full_db.with_suffix(".lookup").write_text("0 1abc_A 0\n")
+    db_dir = tmp_path / "subdbs"
+    db_dir.mkdir()
+    clustered: list[str] = []
+
+    def fake_make_sub_db(ids, _full_db, subdb, _aln_type, *, portable):
+        database = subdb / subdb.name
+        _touch_database(database)
+        database.with_suffix(".index").write_text("".join(f"{i}\t0\t1\n" for i in ids))
+        return []
+
+    def fake_make_exact_search_db(*, full_db, **_kwargs):
+        clustered.append(full_db.name)
+        (full_db.parent / "exact_cluster.json").write_text("{}")
+        return {"status": "complete"}
+
+    monkeypatch.setattr(databases, "make_sub_db", fake_make_sub_db)
+    monkeypatch.setattr(databases, "make_exact_search_db", fake_make_exact_search_db)
+    monkeypatch.setattr(
+        databases, "_completed_exact_search_manifest", lambda *_args: None
+    )
+    target = db_dir / "monomer_mmseqs"
+    for identifiers in ({"1abc_A"}, set()):
+        databases.make_sub_dbs(
+            db_dir,
+            {"monomer_mmseqs": full_db},
+            identifiers_by_database={"monomer_mmseqs": identifiers},
+            tmp_dir=tmp_path / "scratch",
+        )
+        if identifiers:
+            assert (target / "exact_cluster.json").is_file()
+
+    assert clustered == ["monomer_mmseqs"]
+    assert not (target / "exact_cluster.json").exists()
+    assert not (target / "selection.json").exists()
+    assert not list(target.glob("monomer_mmseqs*"))

From 79f3883dec5f216b5fc7875ffdfb16bff6164cd4 Mon Sep 17 00:00:00 2001
From: Thomas Duignan <thomas.j.duignan@gmail.com>
Date: Sun, 4 Oct 2026 14:01:00 -0400
Subject: [PATCH 24/26] docs: refresh R2 manifest facts and published cover
 families

---
 docs/dataset.md      | 11 ++++++-----
 docs/migration/r2.md | 20 +++++++++++++-------
 2 files changed, 19 insertions(+), 12 deletions(-)

diff --git a/docs/dataset.md b/docs/dataset.md
index c1c01b67..39d4847d 100644
--- a/docs/dataset.md
+++ b/docs/dataset.md
@@ -59,7 +59,7 @@ differ from the current release.
 │   ├── set_cover/metric={metric}/threshold={threshold}.parquet
 │   └── directed_set_cover/metric={metric}/threshold={threshold}.parquet
 ├── interface_sampling/
-│   └── directed_set_cover/metric=interface_qcov/threshold={threshold}.parquet
+│   └── directed_set_cover/metric={interface_qcov,interface_side_qcov}/threshold={threshold}.parquet
 ├── search_databases/
 │   ├── holo_foldseek/
 │   ├── holo_mmseqs/
@@ -296,12 +296,13 @@ in `::side=1` or `::side=2`. Use `query_interface_similarity()` or
 
 ## Representative covers
 
-- `ligand_sampling/set_cover/` contains an undirected set cover for reciprocal
-  Tanimoto similarity;
+- `ligand_sampling/set_cover/` contains undirected set covers for reciprocal
+  Tanimoto (ECFP4) and Jaccard (MHFP6) similarity;
 - `ligand_sampling/directed_set_cover/` contains directed covers for pocket,
   interaction, and pocket-weighted ligand 3D metrics;
-- `interface_sampling/directed_set_cover/` contains directed covers for protein
-  interfaces.
+- `interface_sampling/directed_set_cover/` contains directed covers for whole
+  protein interfaces (`interface_qcov`) and interface sides
+  (`interface_side_qcov`).
 
 Each metric has files named `metric={metric}/threshold={threshold}.parquet`.
 The release also includes one row per ligand in
diff --git a/docs/migration/r2.md b/docs/migration/r2.md
index 9967651f..e6835ba7 100644
--- a/docs/migration/r2.md
+++ b/docs/migration/r2.md
@@ -24,10 +24,12 @@ Refreshing a ZIP clears its extraction marker. `PLINDER_OFFLINE` bypasses all
 network access when set to any nonempty value; unset it to return online.
 
 Google libraries are optional for consumers and available through `plinder[data]`.
-The docs extra still declares Google storage because `docs/tablegen.py` uses it
-for annotation-table generation. That docs download has not yet moved to R2.
 Ingestion and generation compatibility are outside this static-release change.
 
+When a published release is updated in place, a directory download also removes
+cached Parquet files under that directory that the manifest no longer lists, so
+dataset readers never mix removed fragments with their replacements.
+
 ## Building the static manifest
 
 ```bash
@@ -46,12 +48,16 @@ so clients never see a manifest that lists missing files. Cloudflare caches
 `--header-upload "Cache-Control: public, max-age=60"` (rclone) so a new
 manifest is served within a minute.
 
-The existing public manifest lists 5,891 objects totaling 219,677,619,278 bytes.
-Its 207,150 published bytes were checked on 2026-09-14 against SHA256
-`9b520375910b2e9bc7d258b0186e21488dc2236991976683a4bfa0ccbaa04e1b`.
-The full download validation below also checked every object's size and MD5.
+The current `2026-09` manifest lists 11,099 objects totaling 139,592,033,582
+bytes. Its 288,878 published bytes have SHA256
+`50640faf0eb855b9dc042a8e4c82127b54e7cc6479853966f3d4f55b3415eff9`. On
+2026-10-04, `rclone check` against the GCS staging copy found every object
+identical (MD5), and the R2 listing matched the manifest exactly.
+
+## Initial migration validation (2026-09-14, legacy `2024-06/v2`)
 
-## Validation
+These results record the original migration of the legacy release; that
+release's commands (e.g. `--iteration`) predate the current CLI.
 
 ```bash
 python -m pytest --noconftest tests/core/test_r2.py tests/core/test_core_config.py tests/core/test_atoms.py::test_default_sequence_alignment -q -o addopts=''

From 3473710231de5144d3c430c79702e4dc85dee8f2 Mon Sep 17 00:00:00 2001
From: Thomas Duignan <thomas.j.duignan@gmail.com>
Date: Thu, 8 Oct 2026 15:03:52 -0400
Subject: [PATCH 25/26] fix: serve releases directly from the Cameo file server

---
 README.md                               |   9 +-
 docs/dataset.md                         |   5 +-
 docs/examples/1_download.ipynb          |   2 +-
 docs/index.md                           |   2 +-
 docs/migration/http.md                  |  62 ++++++
 docs/migration/r2.md                    |  98 ---------
 docs/tutorial/dataset.md                |  10 +-
 scripts/build_r2_manifest.py            |  57 ------
 src/plinder/core/__init__.py            |   9 +-
 src/plinder/core/utils/config.py        |   9 +-
 src/plinder/core/utils/cpl.py           |  43 ++--
 src/plinder/core/utils/http.py          | 232 +++++++++++++++++++++
 src/plinder/core/utils/r2.py            | 166 ---------------
 tests/core/test_core_config.py          |  21 +-
 tests/core/{test_r2.py => test_http.py} | 255 ++++++++++++++++--------
 15 files changed, 530 insertions(+), 450 deletions(-)
 create mode 100644 docs/migration/http.md
 delete mode 100644 docs/migration/r2.md
 delete mode 100644 scripts/build_r2_manifest.py
 create mode 100644 src/plinder/core/utils/http.py
 delete mode 100644 src/plinder/core/utils/r2.py
 rename tests/core/{test_r2.py => test_http.py} (58%)

diff --git a/README.md b/README.md
index 572f48c4..f0ecc951 100644
--- a/README.md
+++ b/README.md
@@ -56,7 +56,7 @@ with the dataset.
 #### Changelog:
 
 - WIP (Current — unreleased):
-    - **Public downloads on Cloudflare R2**: releases download from `https://plinderdata.org/<YYYY-MM>/` (currently `2026-09`) instead of GCS; `PLINDER_MIRROR_URL` selects another HTTP mirror. Downloads stream to disk and verify size and MD5 before atomic replacement, interrupted transfers retry from the start, and cached files with the expected size are reused (force a refresh to repair same-size local corruption). Google storage dependencies are now optional: install `plinder[data]` for the GCS data-generation utilities.
+    - **Public downloads from Cameo**: releases download directly from `https://cameo3d.org/plinder/PLINDER-<YYYY-MM>/` (currently `2026-09`); `PLINDER_MIRROR_URL` selects another HTTP file server with the same directory layout. Downloads stream to disk, validate HTTP Content-Length, and replace cached files atomically. Interrupted transfers retry from the start. Cached files are reused when their size and Last-Modified time match the server, so data hotfixes are fetched on the next access. Google storage dependencies are optional: install `plinder[data]` for the GCS data-generation utilities.
     - **Major backend refactor**: replaced OST, gemmi, plip, openbabel with biotite + peppr for data generation; removed 6 dependencies from ingest pipeline
     - **Nucleic acid support**: DNA/RNA chains now correctly included as receptor neighbors, mainchain/sidechain detection works for both protein and nucleic acids ([#61](https://github.com/plinder-org/plinder/issues/61))
     - **Custom CIF support**: new `Entry.from_custom_cif_file` for structure-prediction outputs (Boltz, AlphaFold3, Chai-1) that ship CIFs without `_chem_comp_bond` ([#117](https://github.com/plinder-org/plinder/issues/117)). Bond orders come from `ligand_smiles_dict` via positional atom-order match (the convention these tools follow); element/count mismatches raise with the offending position, `force_substructure_match=True` opts into substructure matching when atom order isn't preserved. User SMILES win over CCD for both `smiles` and `resolved_stereo_matches_template` — closes a silent gap where biotite's `LIG` placeholder would pass any 3D conformer. Input CIFs are never mutated; optional `save_fixed_cif` persists the enriched copy.
@@ -107,7 +107,7 @@ Moreover, as we enticipate this resource to be used for benchmarking a wide rang
 The *PLINDER* dataset is provided in two ways:
 
 - You can either use the files from the dataset directly using your preferred tooling
-  by downloading the data from `https://plinderdata.org` (Cloudflare R2),
+  by downloading the data from the [Cameo file server](https://cameo3d.org/plinder/PLINDER-2026-09/),
 - or you can utilize the dedicated `plinder` Python package for interfacing the data.
 
 
@@ -123,8 +123,9 @@ $ plinder_download --release 2026-09
 The command offers the larger ligand, alignment, score, export, and search
 database groups separately, and dataset APIs also download required files
 lazily. No Google Cloud credentials or SDK are needed: releases download
-from `https://plinderdata.org`; `PLINDER_MIRROR_URL` can select another HTTP
-mirror. The legacy `2024-06/v2` layout requires an earlier `plinder` version.
+from `https://cameo3d.org/plinder/PLINDER-2026-09/`; `PLINDER_MIRROR_URL`
+can select another HTTP file-server root containing `PLINDER-<YYYY-MM>/`
+directories. The legacy `2024-06/v2` layout requires an earlier `plinder` version.
 For details on the release paths, see [Documentation](https://plinder-org.github.io/plinder/tutorial/dataset.html).
 
 ## Installing the Python package
diff --git a/docs/dataset.md b/docs/dataset.md
index 39d4847d..d38441e4 100644
--- a/docs/dataset.md
+++ b/docs/dataset.md
@@ -11,7 +11,7 @@ extracts protein-ligand systems and protein-protein interfaces from the PDB.
 
 PLINDER releases are identified by the month of their PDB snapshot
 (`YYYY-MM`; the current release is `2026-09`) and served from
-`https://plinderdata.org/<release-month>/`. The file layout is:
+`https://cameo3d.org/plinder/PLINDER-<release-month>/`. The file layout is:
 
 :::{note}
 Historical releases remain available at `gs://plinder/2024-04/v0`,
@@ -20,8 +20,7 @@ differ from the current release.
 :::
 
 ```text
-<release-month>/
-├── manifest.jsonl.gz
+PLINDER-<release-month>/
 ├── index/
 │   ├── annotation_table.parquet
 │   ├── system_validation.parquet
diff --git a/docs/examples/1_download.ipynb b/docs/examples/1_download.ipynb
index e2769719..938dcadb 100644
--- a/docs/examples/1_download.ipynb
+++ b/docs/examples/1_download.ipynb
@@ -35,7 +35,7 @@
     "  -y, --yes             skip confirmation\n",
     "```\n",
     "\n",
-    ":::{note} The public `2026-09` release is served from Cloudflare R2 and contains about 135 GB of downloadable files. Allow additional space for extracted archives; download time depends on your connection. Completed files are reused on subsequent runs. Set `PLINDER_OFFLINE=true` to use the cache without network requests. :::"
+    ":::{note} The public `2026-09` release is served directly from the [Cameo file server](https://cameo3d.org/plinder/PLINDER-2026-09/) and contains about 140 GB of downloadable files. Allow additional space for extracted archives; download time depends on your connection. Completed files are reused when their size and server modification time match; data hotfixes are fetched on the next access. Set `PLINDER_OFFLINE=true` to use the cache without network requests. :::"
    ]
   },
   {
diff --git a/docs/index.md b/docs/index.md
index 22d1d195..8072a735 100644
--- a/docs/index.md
+++ b/docs/index.md
@@ -86,6 +86,6 @@ dataset
 evaluation
 api/index
 contribution/index
-migration/r2
+migration/http
 citation
 :::
diff --git a/docs/migration/http.md b/docs/migration/http.md
new file mode 100644
index 00000000..62e48a27
--- /dev/null
+++ b/docs/migration/http.md
@@ -0,0 +1,62 @@
+# Release downloads from the Cameo file server
+
+Public dataset reads for `YYYY-MM` releases (currently `2026-09`) use
+[the Cameo file server](https://cameo3d.org/plinder/PLINDER-2026-09/) directly.
+No S3 keys, Google credentials, or separately published manifest are required.
+Releases with a release number, such as the legacy `2024-06/v2`, are rejected;
+use an earlier `plinder` version for them.
+
+`PLINDER_MIRROR_URL` may select another HTTP(S) file-server root containing
+`PLINDER-<YYYY-MM>/` directories with nginx or Python-style directory indexes.
+For example, setting it to `https://mirror.example/datasets` selects
+`https://mirror.example/datasets/PLINDER-2026-09/` for the default release.
+The local cache remains `<PLINDER_MOUNT>/<PLINDER_BUCKET>/<YYYY-MM>/`.
+
+## Download and cache behavior
+
+The consumer uses cloudpathlib HTTP paths. Directory indexes provide file
+listings; HEAD responses provide exact sizes and Last-Modified times. Listings
+and metadata are fetched afresh for each API download call, so additions,
+removals, and hotfixes are visible without restarting Python. Directory links
+are restricted to immediate children within the release.
+
+Transfers stream into temporary files, validate HTTP Content-Length, and
+atomically replace the destination. Interrupted transfers retry from the start,
+with up to three attempts. They do not resume at a byte offset. Failed transfers
+preserve an existing destination. Metadata and directory requests use the same
+retry policy. Parallel download batches use eight workers and propagate errors.
+
+The file server does not publish per-file checksums. Content-Length validation
+detects truncated transfers; it does not detect same-size content corruption.
+
+Downloaded files retain the server's Last-Modified time. Cached files are reused
+when both size and modification time match. A changed server timestamp triggers
+a new download even for a same-size hotfix. Files without Last-Modified are
+fetched again on access. Publishers must update Last-Modified when changing a
+file; a same-size edit preserving that timestamp requires a forced refresh
+(`data.force_update=true`) or deletion of the affected cached file.
+Refreshing a ZIP clears its extraction marker.
+
+When a published release is updated in place, a directory download also removes
+cached Parquet files under that directory that the server no longer lists.
+Pruning happens only after the complete listing and all downloads succeed, so
+readers do not mix removed fragments with their replacements.
+
+`PLINDER_OFFLINE=true` bypasses all network access; unset it to return online.
+`PLINDER_OFFLINE_MODE` is also accepted. Empty values and `0`, `false`, `no`,
+and `off` leave networking enabled. Google libraries are optional for consumers
+and available through `plinder[data]` for data generation.
+
+## Focused validation
+
+```bash
+python -m pytest --noconftest tests/core/test_http.py tests/core/test_core_config.py -q -o addopts=''
+```
+
+The local HTTP-server tests exercise directory and direct-file access without a
+manifest, encoded and nested paths, cache reuse, same-size server hotfixes,
+forced refresh, removed Parquet fragments, offline behavior, path containment,
+atomic replacement, and recovery from interrupted transfers and HTTP errors.
+`--noconftest` excludes the repository-wide fixtures; full project CI also runs
+the release APIs and executes all documentation notebooks against the default
+public server.
diff --git a/docs/migration/r2.md b/docs/migration/r2.md
deleted file mode 100644
index e6835ba7..00000000
--- a/docs/migration/r2.md
+++ /dev/null
@@ -1,98 +0,0 @@
-# Static release downloads from R2
-
-Public dataset reads for `YYYY-MM` releases (currently `2026-09`) use
-`https://plinderdata.org/<YYYY-MM>/`. No S3 keys or Google credentials are
-required. Releases with a release number, such as the legacy `2024-06/v2`, are
-rejected; use an earlier `plinder` version for them. `PLINDER_MIRROR_URL` may select another HTTP(S) bucket root with
-the same release layout and manifest. The local cache layout is unchanged.
-
-## Download and cache behavior
-
-The consumer uses cloudpathlib HTTP paths. A release-relative `manifest.jsonl.gz`
-provides listing, sizes and base64 MD5 checksums. Directory traversal and file
-transfers use cloudpathlib; the manifest is cached in-process.
-
-Transfers stream into temporary files, verify size and MD5, and atomically
-replace the destination. Interrupted transfers retry from the start, with up to
-three attempts. They do not resume at a byte offset. Failed validation preserves
-an existing destination. Parallel batches use eight workers and propagate errors.
-
-Cached files with the expected size are reused without rehashing. Missing and
-size-mismatched files are fetched again. Same-size local corruption requires a
-forced refresh (`data.force_update=true`) or deletion of the affected file.
-Refreshing a ZIP clears its extraction marker. `PLINDER_OFFLINE` bypasses all
-network access when set to any nonempty value; unset it to return online.
-
-Google libraries are optional for consumers and available through `plinder[data]`.
-Ingestion and generation compatibility are outside this static-release change.
-
-When a published release is updated in place, a directory download also removes
-cached Parquet files under that directory that the manifest no longer lists, so
-dataset readers never mix removed fragments with their replacements.
-
-## Building the static manifest
-
-```bash
-python scripts/build_r2_manifest.py INVENTORY_DIR OUTPUT.jsonl.gz RELEASE_PREFIX
-```
-
-`INVENTORY_DIR/manifest-files.json` lists shard paths and SHA256 values. Each
-compressed JSONL shard contains source rows with `name`, `size` and `md5Hash`.
-The builder verifies shard checksums, rejects duplicate/invalid keys and writes
-sorted records relative to `RELEASE_PREFIX` (the object-name prefix of the
-release in the inventory, e.g. `PLINDER-2026-09` for the GCS staging copy). It performs no cloud I/O.
-
-Upload changed objects first, then the manifest, then delete removed objects,
-so clients never see a manifest that lists missing files. Cloudflare caches
-`.gz` responses by default; upload the manifest with
-`--header-upload "Cache-Control: public, max-age=60"` (rclone) so a new
-manifest is served within a minute.
-
-The current `2026-09` manifest lists 11,099 objects totaling 139,592,033,582
-bytes. Its 288,878 published bytes have SHA256
-`50640faf0eb855b9dc042a8e4c82127b54e7cc6479853966f3d4f55b3415eff9`. On
-2026-10-04, `rclone check` against the GCS staging copy found every object
-identical (MD5), and the R2 listing matched the manifest exactly.
-
-## Initial migration validation (2026-09-14, legacy `2024-06/v2`)
-
-These results record the original migration of the legacy release; that
-release's commands (e.g. `--iteration`) predate the current CLI.
-
-```bash
-python -m pytest --noconftest tests/core/test_r2.py tests/core/test_core_config.py tests/core/test_atoms.py::test_default_sequence_alignment -q -o addopts=''
-```
-
-30 focused tests passed with Python 3.12.13, cloudpathlib 0.25.0 and NumPy 2.5.3.
-They cover directory/archive access, checksums, atomic replacement, cache reuse,
-forced refresh, path containment, offline behavior, interrupted-transfer retry
-and integer gap penalties required by Biotite's sequence alignment API.
-`--noconftest` excludes repository-wide OpenStructure-dependent fixtures. These
-results do not represent full project CI or evaluation coverage.
-
-On 2026-09-14, the revised implementation downloaded the complete release with
-`plinder_download --release 2024-06 --iteration v2 --yes`: all 5,891 objects
-(219,677,619,278 bytes) passed size and MD5 checks. All 1,060 system archives and
-both linked-structure archives extracted successfully. Their contents total
-567,902,199,349 bytes, so allow roughly 788 GB plus filesystem overhead for the
-downloaded files and extracted contents together.
-
-A deliberate process interruption preserved 1,011 completed files; restarting
-the CLI reused them without changing their timestamps. A final fully cached CLI
-run exited successfully in 6.44 seconds, downloaded no dataset files and left all
-5,891 files unchanged. No unplanned transfer errors or retries occurred during
-the full download; interrupted-transfer retry was exercised by the HTTP test
-server. A separate offline reuse check passed with networking blocked.
-
-The API tutorial, index-query notebook and system-access notebook executed all
-63 code cells against the local release. A `PlinderSystem` structure smoke test
-loaded the receptor and ligand for `4agi__1__1.C__1.W` successfully.
-
-Repository-wide Ruff checks, strict typing of all 91 source files and the full
-Sphinx documentation build with warnings treated as errors passed locally.
-The manifest builder was checked with synthetic inventories for sorting,
-checksum/duplicate rejection and preservation of an existing output on those
-validation failures. These checks do not represent full evaluation coverage.
-
-No dataset copy, permission change or public GCS retirement is part of these
-commits. Existing installed clients still use GCS until upgraded.
diff --git a/docs/tutorial/dataset.md b/docs/tutorial/dataset.md
index d77a5b93..01ab2391 100644
--- a/docs/tutorial/dataset.md
+++ b/docs/tutorial/dataset.md
@@ -9,10 +9,12 @@ files, querying annotations, and reconstructing structures.
 pip install plinder
 ```
 
-Releases download from Cloudflare R2
-(`https://plinderdata.org/<release-month>/`) with checksum verification and automatic retries;
-no Google Cloud SDK is required. `PLINDER_MIRROR_URL` selects another HTTP(S)
-mirror serving the same release layout and manifest.
+Releases download directly from the Cameo file server
+(`https://cameo3d.org/plinder/PLINDER-<release-month>/`) with HTTP size validation
+and automatic retries; no Google Cloud SDK is required. Server modification
+times are checked on access so data hotfixes refresh the local cache.
+`PLINDER_MIRROR_URL` selects another HTTP(S) file-server root containing
+`PLINDER-<release-month>/` directories with browsable directory indexes.
 
 A release is identified by the month of its PDB snapshot. The current release
 (`2026-09`) is the default; select another with:
diff --git a/scripts/build_r2_manifest.py b/scripts/build_r2_manifest.py
deleted file mode 100644
index 28fba050..00000000
--- a/scripts/build_r2_manifest.py
+++ /dev/null
@@ -1,57 +0,0 @@
-"""Build the release's HTTP listing from audited GCS metadata, without cloud I/O."""
-
-import argparse
-import base64
-import gzip
-import hashlib
-import json
-from pathlib import Path
-
-
-def build(inventory: Path, destination: Path, release: str) -> int:
-    prefix = release.strip("/") + "/"
-    shards = json.loads((inventory / "manifest-files.json").read_text())
-    records = {}
-    for shard in shards:
-        path = (inventory / shard["path"]).resolve()
-        if not path.is_relative_to(inventory.resolve()):
-            raise ValueError("Invalid inventory path")
-        if hashlib.sha256(path.read_bytes()).hexdigest() != shard["sha256"]:
-            raise ValueError("Inventory checksum mismatch")
-        with gzip.open(path, "rt") as stream:
-            for line in stream:
-                r = json.loads(line)
-                if not r["name"].startswith(prefix):
-                    raise ValueError("Unexpected release")
-                key = r["name"][len(prefix) :]
-                if not key or key.endswith("/"):
-                    continue
-                if (
-                    not key
-                    or "\\" in key
-                    or any(p in {"", ".", ".."} for p in key.split("/"))
-                    or key in records
-                ):
-                    raise ValueError("Invalid or duplicate object key")
-                size = int(r["size"])
-                if size < 0 or len(base64.b64decode(r["md5Hash"], validate=True)) != 16:
-                    raise ValueError("Invalid object metadata")
-                records[key] = {"key": key, "size": size, "md5": r["md5Hash"]}
-    destination.parent.mkdir(parents=True, exist_ok=True)
-    with gzip.open(destination, "wt") as stream:
-        for key in sorted(records):
-            stream.write(json.dumps(records[key], separators=(",", ":")) + "\n")
-    return len(records)
-
-
-if __name__ == "__main__":
-    parser = argparse.ArgumentParser(description=__doc__)
-    parser.add_argument("inventory", type=Path)
-    parser.add_argument("destination", type=Path)
-    parser.add_argument(
-        "release",
-        help="object-name prefix of the release in the inventory, "
-        "e.g. 2026-09 or PLINDER-2026-09",
-    )
-    args = parser.parse_args()
-    print(build(args.inventory, args.destination, args.release))
diff --git a/src/plinder/core/__init__.py b/src/plinder/core/__init__.py
index c4b1e833..f38fbe9a 100644
--- a/src/plinder/core/__init__.py
+++ b/src/plinder/core/__init__.py
@@ -4,10 +4,11 @@
 The plinder.core package collects useful functions and classes for interacting
 with the PLINDER dataset. It manages app configuration and will automatically
 download (and / or sync) the dataset to a local cache in a lazy manner, when
-particular assets are requested. Downloads are checked against the release
-manifest for size and MD5 before replacing a local file. Cached files with the
-expected size are reused without rehashing; force a refresh to repair same-size
-local corruption.
+particular assets are requested. Downloads come directly from the Cameo file
+server and are checked against HTTP Content-Length before replacing a local
+file. Cached files with matching size and Last-Modified time are reused; server
+hotfixes are fetched on the next access. Force a refresh to repair local
+corruption that preserves both size and modification time.
 
 Note
 ----
diff --git a/src/plinder/core/utils/config.py b/src/plinder/core/utils/config.py
index 058f2224..3fd74f55 100644
--- a/src/plinder/core/utils/config.py
+++ b/src/plinder/core/utils/config.py
@@ -15,7 +15,7 @@
 
 LOG = setup_logger(__name__)
 
-# Default public release: a YYYY-MM PDB snapshot stamp served flat on R2.
+# Default public release: a YYYY-MM PDB snapshot stamp on the Cameo file server.
 DEFAULT_RELEASE = "2026-09"
 
 
@@ -223,7 +223,8 @@ class DataConfig:
         set automatically
     plinder_remote : str
         set automatically; the release root under ``PLINDER_MIRROR_URL``
-        (default ``https://plinderdata.org``)
+        (default ``https://cameo3d.org/plinder``), in ``PLINDER-YYYY-MM``
+        directories
     """
 
     plinder_release: str = field(
@@ -257,8 +258,8 @@ def __post_init__(self) -> None:
         else:
             root = Path(self.plinder_mount) / self.plinder_bucket
         self.plinder_dir = (root / suffix).as_posix() if suffix else root.as_posix()
-        base = getenv("PLINDER_MIRROR_URL", "https://plinderdata.org").rstrip("/")
-        self.plinder_remote = f"{base}/{suffix}" if suffix else base
+        base = getenv("PLINDER_MIRROR_URL", "https://cameo3d.org/plinder").rstrip("/")
+        self.plinder_remote = f"{base}/PLINDER-{suffix}" if suffix else base
 
 
 @dataclass
diff --git a/src/plinder/core/utils/cpl.py b/src/plinder/core/utils/cpl.py
index 005c0d13..1b29a507 100644
--- a/src/plinder/core/utils/cpl.py
+++ b/src/plinder/core/utils/cpl.py
@@ -1,4 +1,4 @@
-"""Public dataset access with cloudpathlib and a local immutable-release cache."""
+"""Public dataset access with cloudpathlib and a local release cache."""
 
 import os
 import re
@@ -10,7 +10,7 @@
 from tqdm import tqdm
 
 from plinder.core.utils.config import get_config
-from plinder.core.utils.r2 import ReleaseClient, checked_key, manifest
+from plinder.core.utils.http import ReleaseClient, checked_key
 
 T = TypeVar("T")
 
@@ -40,12 +40,12 @@ def thread_pool(func: Callable[[T], None], items: Iterable[T]) -> None:
 
 def _get_client() -> ReleaseClient:
     cfg = get_config().data
-    if (
-        cfg.plinder_bucket != "plinder"
-        or cfg.plinder_release_number
-        or not re.fullmatch(r"\d{4}-(0[1-9]|1[0-2])", cfg.plinder_release)
+    if cfg.plinder_release_number or not re.fullmatch(
+        r"\d{4}-(0[1-9]|1[0-2])", cfg.plinder_release
     ):
-        raise ValueError("R2 downloads support only plinder/YYYY-MM releases")
+        raise ValueError(
+            "HTTP downloads support only YYYY-MM releases without a release number"
+        )
     remote = str(cfg.plinder_remote).rstrip("/")
     url = urlsplit(remote)
     if (
@@ -56,9 +56,7 @@ def _get_client() -> ReleaseClient:
         or url.username
         or url.password
     ):
-        raise ValueError("PLINDER_MIRROR_URL must be an HTTP(S) bucket URL")
-    if cfg.force_update:
-        manifest.cache_clear()
+        raise ValueError("PLINDER_MIRROR_URL must be an HTTP(S) file-server URL")
     return ReleaseClient(remote)
 
 
@@ -68,14 +66,18 @@ def _download(client: ReleaseClient, paths: list[Path], force_progress: bool) ->
 
     def fetch(path: Path) -> None:
         key = checked_key(path.resolve().relative_to(root).as_posix())
-        if key not in client.records:
-            raise FileNotFoundError(f"File absent from release manifest: {key}")
+        remote = client.path(key)
+        if not remote.exists():
+            raise FileNotFoundError(f"File absent from release: {key}")
+        metadata = client.metadata(remote)
         if (
             cfg.force_update
             or not path.is_file()
-            or path.stat().st_size != client.records[key]["size"]
+            or path.stat().st_size != metadata.size
+            or metadata.modified is None
+            or path.stat().st_mtime != metadata.modified
         ):
-            client.path(key).download_to(path)
+            remote.download_to(path)
             if path.suffix == ".zip":
                 path.with_name(path.stem + "_done").unlink(missing_ok=True)
 
@@ -106,7 +108,7 @@ def download_paths(*, paths: list[Path], force_progress: bool = False) -> None:
         _download(_get_client(), paths, force_progress)
 
 
-def _prune_unpublished(client: ReleaseClient, directory: Path) -> None:
+def _prune_unpublished(directory: Path, published: set[str]) -> None:
     """Remove cached Parquet files that the release no longer lists.
 
     Directory artifacts are read as whole Parquet datasets, so a file dropped
@@ -116,7 +118,7 @@ def _prune_unpublished(client: ReleaseClient, directory: Path) -> None:
     for path in directory.rglob("*.parquet"):
         if path.is_symlink() or not path.is_file():
             continue
-        if path.relative_to(root).as_posix() not in client.records:
+        if path.relative_to(root).as_posix() not in published:
             path.unlink()
 
 
@@ -147,14 +149,17 @@ def get_plinder_path(
     local = root / checked_key(rel)
     if is_offline() or not download:
         return local
+    local.resolve().relative_to(root.resolve())
     client = _get_client()
     remote = client.path(rel)
     if not remote.exists():
-        raise FileNotFoundError(f"Path absent from release manifest: {rel}")
+        raise FileNotFoundError(f"Path absent from release: {rel}")
     files = (
         [remote] if remote.is_file() else [p for p in remote.rglob("*") if p.is_file()]
     )
-    _download(client, [root / client.key(p) for p in files], force_progress)
+    keys = {client.key(p) for p in files}
+    _download(client, [root / key for key in sorted(keys)], force_progress)
     if not remote.is_file():
-        _prune_unpublished(client, local)
+        local.mkdir(parents=True, exist_ok=True)
+        _prune_unpublished(local, keys)
     return local
diff --git a/src/plinder/core/utils/http.py b/src/plinder/core/utils/http.py
new file mode 100644
index 00000000..4d3fa90a
--- /dev/null
+++ b/src/plinder/core/utils/http.py
@@ -0,0 +1,232 @@
+"""Directory listing and atomic downloads from the public PLINDER file server."""
+
+import os
+import shutil
+from dataclasses import dataclass
+from email.utils import parsedate_to_datetime
+from html.parser import HTMLParser
+from http.client import HTTPException
+from os import PathLike
+from pathlib import Path
+from tempfile import TemporaryDirectory
+from time import sleep
+from typing import Callable, Iterator, TypeVar, cast
+from urllib.error import HTTPError
+from urllib.parse import quote, unquote, urlsplit
+from urllib.request import BaseHandler, Request
+
+from cloudpathlib import CloudPath as BaseCloudPath
+from cloudpathlib import HttpPath, HttpsClient, HttpsPath
+
+CloudPathT = TypeVar("CloudPathT", bound=BaseCloudPath)
+T = TypeVar("T")
+
+
+def checked_key(key: str) -> str:
+    if key and ("\\" in key or any(p in {"", ".", ".."} for p in key.split("/"))):
+        raise ValueError(f"Invalid dataset path: {key!r}")
+    return key
+
+
+class _TimeoutHandler(BaseHandler):
+    def http_request(self, request: Request) -> Request:
+        # Bound connection/read inactivity without limiting total transfer time.
+        request.timeout = 60
+        return request
+
+    https_request = http_request
+
+
+def _retry(operation: Callable[[], T]) -> T:
+    for attempt in range(3):
+        try:
+            return operation()
+        except (OSError, HTTPException) as exc:
+            if isinstance(exc, HTTPError) and exc.code not in {
+                408,
+                429,
+                500,
+                502,
+                503,
+                504,
+            }:
+                raise
+            if attempt == 2:
+                raise
+            sleep(2**attempt)
+    raise AssertionError("unreachable")
+
+
+class _DirectoryIndex(HTMLParser):
+    def __init__(self) -> None:
+        super().__init__()
+        self.links: list[str] = []
+        self.title = ""
+        self.in_title = False
+
+    def handle_starttag(self, tag: str, attrs: list[tuple[str, str | None]]) -> None:
+        if tag == "title":
+            self.in_title = True
+        if tag == "a":
+            self.links.extend(
+                value for name, value in attrs if name == "href" and value
+            )
+
+    def handle_endtag(self, tag: str) -> None:
+        if tag == "title":
+            self.in_title = False
+
+    def handle_data(self, data: str) -> None:
+        if self.in_title:
+            self.title += data
+
+
+@dataclass(frozen=True)
+class FileMetadata:
+    size: int
+    modified: float | None
+    is_dir: bool
+
+
+class ReleaseClient(HttpsClient):
+    """Read a fresh directory index and HTTP metadata for each cache access."""
+
+    def __init__(self, remote: str):
+        super().__init__(auth=_TimeoutHandler())
+        self.remote = remote.rstrip("/")
+        # These caches live only for one get_plinder_path/download_paths call.
+        self._metadata: dict[str, FileMetadata] = {}
+        self._listed: dict[str, bool] = {}
+        self.dir_matcher = self._is_directory
+
+    def CloudPath(self, path: str | CloudPathT, *parts: str) -> CloudPathT:
+        cls = HttpsPath if self.remote.startswith("https:") else HttpPath
+        return cast(CloudPathT, cls(str(path), *parts, client=self))
+
+    def path(self, key: str = "") -> HttpPath:
+        return cast(
+            HttpPath,
+            self.CloudPath(
+                self.remote + ("/" + quote(checked_key(key), safe="/") if key else "")
+            ),
+        )
+
+    def key(self, path: str | BaseCloudPath) -> str:
+        url = str(path).removesuffix("/")
+        if url == self.remote:
+            return ""
+        if not url.startswith(self.remote + "/"):
+            raise ValueError("Path is outside the release")
+        return checked_key(unquote(url[len(self.remote) + 1 :]))
+
+    def metadata(self, path: HttpPath) -> FileMetadata:
+        key = self.key(path)
+        if key not in self._metadata:
+
+            def read() -> FileMetadata:
+                request = Request(
+                    str(path), method="HEAD", headers={"Cache-Control": "no-cache"}
+                )
+                with self.opener.open(request) as response:
+                    if self.key(response.geturl()) != key:
+                        raise ValueError(
+                            "File server redirected outside the requested path"
+                        )
+                    is_dir = response.geturl().endswith("/")
+                    size = response.headers.get("Content-Length")
+                    if not is_dir and size is None:
+                        raise ValueError("File server must supply Content-Length")
+                    modified = response.headers.get("Last-Modified")
+                    return FileMetadata(
+                        int(size or 0),
+                        parsedate_to_datetime(modified).timestamp()
+                        if modified
+                        else None,
+                        is_dir,
+                    )
+
+            self._metadata[key] = _retry(read)
+        return self._metadata[key]
+
+    def _is_directory(self, url: str) -> bool:
+        key = self.key(url)
+        if key in self._listed:
+            return self._listed[key]
+        return self.metadata(self.path(key)).is_dir
+
+    def _exists(self, path: HttpPath) -> bool:
+        if self.key(path) in self._listed:
+            return True
+        try:
+            self.metadata(path)
+        except HTTPError as exc:
+            if exc.code == 404:
+                return False
+            raise
+        return True
+
+    def _list_dir(
+        self, path: HttpPath, recursive: bool
+    ) -> Iterator[tuple[HttpPath, bool]]:
+        key = self.key(path)
+        url = str(self.path(key)) + "/"
+
+        def read() -> str:
+            request = Request(url, headers={"Cache-Control": "no-cache"})
+            with self.opener.open(request) as response:
+                if self.key(response.geturl()) != key:
+                    raise ValueError(
+                        "File server redirected outside the requested directory"
+                    )
+                return cast(bytes, response.read()).decode("utf-8")
+
+        index = _DirectoryIndex()
+        index.feed(_retry(read))
+        if not index.title.startswith(("Index of ", "Directory listing for ")):
+            raise ValueError("Expected an HTTP directory index")
+        children: dict[str, bool] = {}
+        for href in index.links:
+            link = urlsplit(href)
+            if link.scheme or link.netloc or link.query or link.fragment:
+                continue
+            name = unquote(link.path.removesuffix("/"))
+            # Only immediate relative children: ignore parent/sort/navigation links.
+            if not name or name in {".", ".."} or "/" in name or "\\" in name:
+                continue
+            child = checked_key(f"{key}/{name}" if key else name)
+            children[child] = link.path.endswith("/")
+        self._listed.update(children)
+        for child, is_dir in sorted(children.items()):
+            child_path = self.path(child)
+            yield child_path, is_dir
+            if recursive and is_dir:
+                yield from self._list_dir(child_path, recursive=True)
+
+    def _download_file(self, path: HttpPath, local_path: str | PathLike[str]) -> Path:
+        destination = Path(local_path)
+        destination.parent.mkdir(parents=True, exist_ok=True)
+        with TemporaryDirectory(dir=destination.parent) as tmp:
+            temporary = Path(tmp) / "download"
+
+            def download() -> None:
+                request = Request(str(path), headers={"Cache-Control": "no-cache"})
+                with self.opener.open(request) as response:
+                    if self.key(response.geturl()) != self.key(path):
+                        raise ValueError(
+                            "File server redirected outside the requested path"
+                        )
+                    size = response.headers.get("Content-Length")
+                    if size is None:
+                        raise ValueError("File server must supply Content-Length")
+                    with temporary.open("wb") as stream:
+                        shutil.copyfileobj(response, stream)
+                    if temporary.stat().st_size != int(size):
+                        raise OSError("Incomplete dataset download")
+                    modified = response.headers.get("Last-Modified")
+                    if modified:
+                        timestamp = parsedate_to_datetime(modified).timestamp()
+                        os.utime(temporary, (timestamp, timestamp))
+
+            _retry(download)
+            temporary.replace(destination)
+        return destination
diff --git a/src/plinder/core/utils/r2.py b/src/plinder/core/utils/r2.py
deleted file mode 100644
index 57c4be58..00000000
--- a/src/plinder/core/utils/r2.py
+++ /dev/null
@@ -1,166 +0,0 @@
-"""Manifest-backed listing and verified cloudpathlib downloads for public R2."""
-
-import base64
-import gzip
-import hashlib
-import json
-from functools import lru_cache
-from http.client import HTTPException
-from os import PathLike
-from pathlib import Path
-from tempfile import TemporaryDirectory
-from time import sleep
-from typing import Iterator, TypedDict, TypeVar, cast
-from urllib.error import HTTPError
-from urllib.parse import quote, unquote
-from urllib.request import BaseHandler, Request
-
-from cloudpathlib import CloudPath as BaseCloudPath
-from cloudpathlib import HttpPath, HttpsClient, HttpsPath
-
-CloudPathT = TypeVar("CloudPathT", bound=BaseCloudPath)
-
-
-class ManifestRecord(TypedDict):
-    key: str
-    size: int
-    md5: str
-
-
-def checked_key(key: str) -> str:
-    if key and ("\\" in key or any(p in {"", ".", ".."} for p in key.split("/"))):
-        raise ValueError(f"Invalid dataset path: {key!r}")
-    return key
-
-
-class _TimeoutHandler(BaseHandler):
-    def http_request(self, request: Request) -> Request:
-        # Bound connection/read inactivity without limiting total transfer time.
-        request.timeout = 60
-        return request
-
-    https_request = http_request
-
-
-class _DownloadClient(HttpsClient):
-    def __init__(self) -> None:
-        super().__init__(auth=_TimeoutHandler())
-
-    def _download(
-        self,
-        path: HttpPath,
-        local_path: str | PathLike[str],
-        expected_size: int | None = None,
-    ) -> Path:
-        destination = Path(local_path)
-        for attempt in range(3):
-            try:
-                super()._download_file(path, destination)
-                if (
-                    expected_size is not None
-                    and destination.stat().st_size != expected_size
-                ):
-                    raise OSError("Incomplete dataset download")
-                break
-            except (OSError, HTTPException) as exc:
-                if isinstance(exc, HTTPError) and exc.code not in {
-                    408,
-                    429,
-                    500,
-                    502,
-                    503,
-                    504,
-                }:
-                    raise
-                if attempt == 2:
-                    raise
-                sleep(2**attempt)
-        return destination
-
-
-@lru_cache(maxsize=4)
-def manifest(remote: str) -> dict[str, ManifestRecord]:
-    with TemporaryDirectory() as tmp:
-        path = Path(tmp) / "manifest.jsonl.gz"
-        path_class = HttpsPath if remote.startswith("https:") else HttpPath
-        client = _DownloadClient()
-        source = path_class(remote + "/manifest.jsonl.gz", client=client)
-        # A direct GET preserves transient errors hidden by cloudpathlib's HEAD check.
-        client._download(source, path)
-        data = path.read_bytes()
-    records: dict[str, ManifestRecord] = {}
-    for line in gzip.decompress(data).splitlines():
-        row = json.loads(line)
-        key = checked_key(row["key"])
-        if not key or key in records or type(row["size"]) is not int or row["size"] < 0:
-            raise ValueError("Invalid or duplicate manifest record")
-        if len(base64.b64decode(row["md5"], validate=True)) != 16:
-            raise ValueError("Invalid manifest MD5")
-        records[key] = row
-    return records
-
-
-class ReleaseClient(_DownloadClient):
-    """Use the manifest where public HTTP lacks object listing; delegate transfers."""
-
-    def __init__(self, remote: str):
-        super().__init__()
-        self.remote = remote
-        self.records = manifest(remote)
-        self.dir_matcher = lambda url: self.key(url) not in self.records
-
-    def CloudPath(self, path: str | CloudPathT, *parts: str) -> CloudPathT:
-        cls = HttpsPath if self.remote.startswith("https:") else HttpPath
-        return cast(CloudPathT, cls(str(path), *parts, client=self))
-
-    def path(self, key: str = "") -> HttpPath:
-        return cast(
-            HttpPath,
-            self.CloudPath(
-                self.remote + ("/" + quote(checked_key(key), safe="/") if key else "")
-            ),
-        )
-
-    def key(self, path: str | BaseCloudPath) -> str:
-        url = str(path)
-        if url == self.remote:
-            return ""
-        if not url.startswith(self.remote + "/"):
-            raise ValueError("Path is outside the release")
-        return checked_key(unquote(url[len(self.remote) + 1 :]))
-
-    def _exists(self, path: HttpPath) -> bool:
-        key = self.key(path)
-        return key in self.records or any(
-            not key or k.startswith(key + "/") for k in self.records
-        )
-
-    def _list_dir(
-        self, path: HttpPath, recursive: bool
-    ) -> Iterator[tuple[HttpPath, bool]]:
-        key = self.key(path)
-        prefix = key + "/" if key else ""
-        children = {}
-        for name in self.records:
-            if name.startswith(prefix):
-                parts = name[len(prefix) :].split("/")
-                for i in range(1, len(parts) + 1 if recursive else 2):
-                    children[prefix + "/".join(parts[:i])] = i < len(parts)
-        for name, is_dir in sorted(children.items()):
-            yield self.path(name), is_dir
-
-    def _download_file(self, path: HttpPath, local_path: str | PathLike[str]) -> Path:
-        destination = Path(local_path)
-        destination.parent.mkdir(parents=True, exist_ok=True)
-        record = self.records[self.key(path)]
-        with TemporaryDirectory(dir=destination.parent) as tmp:
-            temporary = Path(tmp) / "download"
-            self._download(path, temporary, expected_size=record["size"])
-            digest = hashlib.md5()
-            with temporary.open("rb") as stream:
-                for chunk in iter(lambda: stream.read(1024 * 1024), b""):
-                    digest.update(chunk)
-            if base64.b64encode(digest.digest()).decode() != record["md5"]:
-                raise ValueError("Dataset checksum mismatch")
-            temporary.replace(destination)
-        return destination
diff --git a/tests/core/test_core_config.py b/tests/core/test_core_config.py
index 5ebeb386..95b046de 100644
--- a/tests/core/test_core_config.py
+++ b/tests/core/test_core_config.py
@@ -14,7 +14,8 @@ def test_get_config():
     assert cfg == {"data": asdict(ocfg), "context": asdict(ccfg)}
 
 
-def test_release_identifier_sets_local_and_remote_roots():
+def test_release_identifier_sets_local_and_remote_roots(monkeypatch):
+    monkeypatch.delenv("PLINDER_MIRROR_URL", raising=False)
     cfg = config.DataConfig(
         plinder_release="2026-07",
         plinder_release_number="1",
@@ -23,7 +24,23 @@ def test_release_identifier_sets_local_and_remote_roots():
     )
 
     assert cfg.plinder_dir == "/cache/plinder/2026-07/1"
-    assert cfg.plinder_remote == "https://plinderdata.org/2026-07/1"
+    assert cfg.plinder_remote == "https://cameo3d.org/plinder/PLINDER-2026-07/1"
+
+
+def test_default_release_uses_cameo_without_environment_overrides(monkeypatch):
+    for key in ["PLINDER_RELEASE", "PLINDER_RELEASE_NUMBER", "PLINDER_MIRROR_URL"]:
+        monkeypatch.delenv(key, raising=False)
+    cfg = config.DataConfig(plinder_mount="/cache")
+
+    assert cfg.plinder_dir == "/cache/plinder/2026-09"
+    assert cfg.plinder_remote == "https://cameo3d.org/plinder/PLINDER-2026-09"
+
+
+def test_mirror_override_uses_the_file_server_layout(monkeypatch):
+    monkeypatch.setenv("PLINDER_MIRROR_URL", "https://mirror.example/datasets/")
+    cfg = config.DataConfig(plinder_release="2026-09", plinder_release_number="")
+
+    assert cfg.plinder_remote == "https://mirror.example/datasets/PLINDER-2026-09"
 
 
 def test_get_config_passed():
diff --git a/tests/core/test_r2.py b/tests/core/test_http.py
similarity index 58%
rename from tests/core/test_r2.py
rename to tests/core/test_http.py
index 49a896ca..9320c22a 100644
--- a/tests/core/test_r2.py
+++ b/tests/core/test_http.py
@@ -1,7 +1,4 @@
-import base64
-import gzip
-import hashlib
-import json
+import os
 from functools import partial
 from http.server import SimpleHTTPRequestHandler, ThreadingHTTPServer
 from pathlib import Path
@@ -11,15 +8,14 @@
 import pytest
 
 from plinder.core.utils import cpl
-from plinder.core.utils import r2 as dataset
+from plinder.core.utils import http as dataset
 
 
 @pytest.fixture
 def mirror(tmp_path, monkeypatch):
     origin = tmp_path / "origin"
-    release = origin / "2026-09"
+    release = origin / "PLINDER-2026-09"
     release.mkdir(parents=True)
-    records = []
     for key, data in [
         ("systems/ab.zip", b"archive"),
         ("scores/a.parquet", b"one"),
@@ -28,18 +24,23 @@ def mirror(tmp_path, monkeypatch):
         path = release / key
         path.parent.mkdir(exist_ok=True)
         path.write_bytes(data)
-        records.append(
-            {
-                "key": key,
-                "size": len(data),
-                "md5": base64.b64encode(hashlib.md5(data).digest()).decode(),
-            }
-        )
-    (release / "manifest.jsonl.gz").write_bytes(
-        gzip.compress(("\n".join(map(json.dumps, records))).encode())
-    )
+        os.utime(path, (1700000000, 1700000000))
+    requests = []
+
+    class Handler(SimpleHTTPRequestHandler):
+        def log_message(self, *args):
+            pass
+
+        def do_HEAD(self):
+            requests.append(("HEAD", self.path))
+            super().do_HEAD()
+
+        def do_GET(self):
+            requests.append(("GET", self.path))
+            super().do_GET()
+
     server = ThreadingHTTPServer(
-        ("127.0.0.1", 0), partial(SimpleHTTPRequestHandler, directory=str(origin))
+        ("127.0.0.1", 0), partial(Handler, directory=str(origin))
     )
     thread = Thread(target=server.serve_forever, daemon=True)
     thread.start()
@@ -49,18 +50,18 @@ def mirror(tmp_path, monkeypatch):
             plinder_release="2026-09",
             plinder_release_number="",
             plinder_dir=str(tmp_path / "cache"),
-            plinder_remote=f"http://127.0.0.1:{server.server_port}/2026-09",
+            plinder_remote=f"http://127.0.0.1:{server.server_port}/PLINDER-2026-09",
             force_update=False,
         )
     )
     monkeypatch.setattr(cpl, "get_config", lambda: cfg)
     monkeypatch.delenv("PLINDER_OFFLINE", raising=False)
-    cpl.manifest.cache_clear()
+    cfg.requests = requests
+    monkeypatch.delenv("PLINDER_OFFLINE_MODE", raising=False)
     yield cfg, release
     server.shutdown()
     server.server_close()
     thread.join()
-    cpl.manifest.cache_clear()
 
 
 def test_directory_download_and_truncated_cache_repair(mirror):
@@ -92,10 +93,9 @@ def test_directory_download_prunes_parquet_files_the_release_dropped(mirror):
 
 
 def test_small_batch_failure_propagates(mirror):
-    cfg, origin = mirror
-    (origin / "systems/ab.zip").write_bytes(b"corrupt")
-    with pytest.raises(ValueError, match="checksum"):
-        cpl.get_plinder_path(rel="systems/ab.zip")
+    cfg, _ = mirror
+    with pytest.raises(FileNotFoundError):
+        cpl.download_paths(paths=[Path(cfg.data.plinder_dir) / "systems/missing.zip"])
     assert not (Path(cfg.data.plinder_dir) / "systems/ab.zip").exists()
 
 
@@ -128,24 +128,50 @@ def test_missing_file_fails(mirror):
         cpl.get_plinder_path(rel="missing")
 
 
-def test_cached_same_size_edit_requires_force_update(mirror, monkeypatch):
+def test_same_size_local_edit_preserving_mtime_requires_force_update(mirror):
     cfg, _ = mirror
     path = cpl.get_plinder_path(rel="scores/a.parquet")
     path.write_bytes(b"bad")
+    os.utime(path, (1700000000, 1700000000))
     assert cpl.get_plinder_path(rel="scores/a.parquet").read_bytes() == b"bad"
     cfg.data.force_update = True
     assert cpl.get_plinder_path(rel="scores/a.parquet").read_bytes() == b"one"
 
 
-def test_failed_checksum_preserves_existing_cache(mirror):
+def test_same_size_server_hotfix_is_fetched_without_force_update(mirror):
     cfg, origin = mirror
     path = cpl.get_plinder_path(rel="scores/a.parquet")
-    (origin / "scores/a.parquet").write_bytes(b"bad")
-    cfg.data.force_update = True
-    with pytest.raises(ValueError, match="checksum"):
-        cpl.get_plinder_path(rel="scores/a.parquet")
-    assert path.read_bytes() == b"one"
-    assert list(path.parent.iterdir()) == [path]
+    source = origin / "scores/a.parquet"
+    source.write_bytes(b"new")
+    os.utime(source, (1700000010, 1700000010))
+
+    assert not cfg.data.force_update
+    assert cpl.get_plinder_path(rel="scores/a.parquet").read_bytes() == b"new"
+    assert path.stat().st_mtime == source.stat().st_mtime
+
+
+def test_directory_listing_refreshes_added_and_removed_files(mirror):
+    _, origin = mirror
+    path = cpl.get_plinder_path(rel="scores")
+    (origin / "scores/a.parquet").unlink()
+    (origin / "scores/c.parquet").write_bytes(b"new")
+
+    assert cpl.get_plinder_path(rel="scores") == path
+    assert sorted(p.name for p in path.glob("*.parquet")) == ["b.parquet", "c.parquet"]
+
+
+def test_encoded_nested_paths_and_empty_directory(mirror):
+    _, origin = mirror
+    shard = origin / "alignments" / "alignment_type=mmseqs" / "shard=a b%.parquet"
+    shard.parent.mkdir(parents=True)
+    shard.write_bytes(b"data")
+    (origin / "empty").mkdir()
+
+    assert (
+        cpl.get_plinder_path(rel="alignments")
+        / shard.relative_to(origin / "alignments")
+    ).read_bytes() == b"data"
+    assert cpl.get_plinder_path(rel="empty").is_dir()
 
 
 def test_native_cloudpath_listing_and_download(mirror, tmp_path):
@@ -175,19 +201,15 @@ def test_cache_symlink_escape_is_rejected(mirror, tmp_path):
     assert not (outside / "a.parquet").exists()
 
 
-def test_force_update_fetches_manifest_once(mirror, monkeypatch):
+def test_force_update_fetches_metadata_once_per_file(mirror):
     cfg, _ = mirror
-    actual = dataset.manifest.__wrapped__
-    calls = []
-
-    def tracked(remote):
-        calls.append(remote)
-        return actual(remote)
-
-    monkeypatch.setattr(dataset, "manifest", tracked)
     cfg.data.force_update = True
     cpl.get_plinder_path(rel="scores")
-    assert len(calls) == 1
+    for name in ["a", "b"]:
+        assert (
+            cfg.requests.count(("HEAD", f"/PLINDER-2026-09/scores/{name}.parquet")) == 1
+        )
+    assert all("manifest" not in url for _, url in cfg.requests)
 
 
 def test_cached_file_is_not_read_or_transferred(mirror, monkeypatch):
@@ -211,12 +233,6 @@ def test_interrupted_native_transfer_restarts(tmp_path, monkeypatch):
     from http.server import BaseHTTPRequestHandler
 
     payload = b"abcdef" * 500000
-    row = {
-        "key": "archive.zip",
-        "size": len(payload),
-        "md5": base64.b64encode(hashlib.md5(payload).digest()).decode(),
-    }
-    listing = gzip.compress(json.dumps(row).encode())
     requests = []
 
     class Handler(BaseHTTPRequestHandler):
@@ -225,23 +241,20 @@ def log_message(self, *args):
 
         def do_HEAD(self):
             self.send_response(200)
+            self.send_header("Content-Length", str(len(payload)))
             self.end_headers()
 
         def do_GET(self):
-            if self.path.endswith("manifest.jsonl.gz"):
-                data = listing
-            else:
-                requests.append(self.headers.get("Range"))
-                data = payload
+            requests.append(self.headers.get("Range"))
             self.send_response(200)
-            self.send_header("Content-Length", str(len(data)))
+            self.send_header("Content-Length", str(len(payload)))
             self.end_headers()
-            if data is payload and len(requests) == 1:
-                self.wfile.write(data[:1500000])
+            if len(requests) == 1:
+                self.wfile.write(payload[:1500000])
                 self.wfile.flush()
                 self.connection.shutdown(socket.SHUT_WR)
             else:
-                self.wfile.write(data)
+                self.wfile.write(payload)
 
     server = ThreadingHTTPServer(("127.0.0.1", 0), Handler)
     thread = Thread(target=server.serve_forever, daemon=True)
@@ -258,25 +271,28 @@ def do_GET(self):
         server.server_close()
 
 
-@pytest.mark.parametrize("resource", ["manifest", "object"])
 @pytest.mark.parametrize(
-    "failure", ["503", "stall_headers", "stall_body", "exhausted", "404", "malformed"]
+    "resource,failure",
+    [
+        (resource, failure)
+        for resource in ["metadata", "listing", "object"]
+        for failure in [
+            "503",
+            "stall_headers",
+            "stall_body",
+            "exhausted",
+            "404",
+            "truncated",
+        ]
+        if resource != "metadata" or failure not in {"stall_body", "truncated"}
+    ],
 )
 def test_download_recovery(tmp_path, monkeypatch, resource, failure):
     from http.server import BaseHTTPRequestHandler
     from threading import Event
-    from urllib.error import HTTPError
 
     payload = b"dataset"
-    listing = gzip.compress(
-        json.dumps(
-            {
-                "key": "data",
-                "size": len(payload),
-                "md5": base64.b64encode(hashlib.md5(payload).digest()).decode(),
-            }
-        ).encode()
-    )
+    listing = b'<title>Index of /</title><a href="data">data</a>'
     release_stall = Event()
     requests = []
     original_timeout = dataset._TimeoutHandler.http_request
@@ -294,31 +310,40 @@ class Handler(BaseHTTPRequestHandler):
         def log_message(self, *args):
             pass
 
-        def do_HEAD(self):
-            self.send_error(503)  # Bootstrap must use GET, not hide this as missing.
-
-        def do_GET(self):
-            is_manifest = self.path.endswith("manifest.jsonl.gz")
-            selected = is_manifest == (resource == "manifest")
+        def respond(self, head=False):
+            is_listing = self.path == "/"
+            selected = (
+                head
+                if resource == "metadata"
+                else not head and is_listing == (resource == "listing")
+            )
             if selected:
                 requests.append(self.path)
-            fail = selected and (len(requests) == 1 or failure in {"404", "exhausted"})
+            fail = selected and (
+                len(requests) == 1 or failure in {"404", "exhausted", "truncated"}
+            )
             if fail and failure in {"503", "404", "exhausted"}:
                 self.send_error(503 if failure == "exhausted" else int(failure))
                 return
             if fail and failure == "stall_headers":
                 release_stall.wait(5)
                 return
-            data = listing if is_manifest else payload
-            if fail and failure == "malformed":
-                data = b"invalid"  # Same length as the object: checksum must reject it.
+            data = listing if is_listing else payload
             self.send_response(200)
             self.send_header("Content-Length", str(len(data)))
             self.end_headers()
+            if head:
+                return
             if fail and failure == "stall_body":
                 release_stall.wait(5)
                 return
-            self.wfile.write(data)
+            self.wfile.write(data[:-1] if fail and failure == "truncated" else data)
+
+        def do_HEAD(self):
+            self.respond(head=True)
+
+        def do_GET(self):
+            self.respond()
 
     server = ThreadingHTTPServer(("127.0.0.1", 0), Handler)
     thread = Thread(target=server.serve_forever, daemon=True)
@@ -328,17 +353,20 @@ def do_GET(self):
 
     def download():
         client = dataset.ReleaseClient(f"http://127.0.0.1:{server.server_port}")
+        if resource == "listing":
+            list(client.path().iterdir())
         client.path("data").download_to(destination)
 
     try:
-        if failure in {"404", "malformed", "exhausted"}:
-            error = (
-                (ValueError, gzip.BadGzipFile) if failure == "malformed" else HTTPError
-            )
+        if failure in {"404", "exhausted", "truncated"}:
+            from cloudpathlib.exceptions import CloudPathNotExistsError
+
+            error = (OSError, dataset.HTTPException, CloudPathNotExistsError)
             with pytest.raises(error):
                 download()
-            assert len(requests) == (3 if failure == "exhausted" else 1)
+            assert len(requests) == (1 if failure == "404" else 3)
             assert destination.read_bytes() == b"existing"
+            assert list(tmp_path.iterdir()) == [destination]
         else:
             download()
             assert len(requests) == 2
@@ -348,4 +376,57 @@ def download():
         server.shutdown()
         server.server_close()
         thread.join()
-        dataset.manifest.cache_clear()
+
+
+def test_listing_ignores_navigation_and_escaping_links(mirror, monkeypatch):
+    cfg, _ = mirror
+    client = cpl._get_client()
+    original_open = client.opener.open
+
+    def open_index(request):
+        response = original_open(request)
+        if request.full_url.endswith("/scores/"):
+            from io import BytesIO
+
+            response.read = BytesIO(
+                b"<title>Index of /scores/</title>"
+                b'<a href="../">parent</a><a href="?C=N;O=D">sort</a>'
+                b'<a href="https://example.com/file">external</a>'
+                b'<a href="/file">absolute</a><a href="%2e%2e/escape">escape</a>'
+                b'<a href="nested%2fescape">encoded escape</a>'
+                b'<a href="a.parquet">a</a><a href="b.parquet">b</a>'
+            ).read
+        return response
+
+    monkeypatch.setattr(client.opener, "open", open_index)
+    assert {p.name for p in client.path("scores").iterdir()} == {
+        "a.parquet",
+        "b.parquet",
+    }
+    assert all(
+        "escape" not in url and "example.com" not in url for _, url in cfg.requests
+    )
+
+
+def test_invalid_listing_preserves_cached_parquet(mirror, monkeypatch):
+    cfg, _ = mirror
+    path = cpl.get_plinder_path(rel="scores")
+    monkeypatch.setattr(dataset._DirectoryIndex, "handle_data", lambda *args: None)
+    with pytest.raises(ValueError, match="directory index"):
+        cpl.get_plinder_path(rel="scores")
+    assert (path / "a.parquet").read_bytes() == b"one"
+    assert (path / "b.parquet").read_bytes() == b"two"
+
+
+def test_empty_directory_cannot_prune_through_a_cache_symlink(mirror, tmp_path):
+    cfg, origin = mirror
+    (origin / "empty").mkdir()
+    root = Path(cfg.data.plinder_dir)
+    root.mkdir()
+    outside = tmp_path / "outside"
+    outside.mkdir()
+    (outside / "kept.parquet").write_bytes(b"kept")
+    (root / "empty").symlink_to(outside, target_is_directory=True)
+    with pytest.raises(ValueError):
+        cpl.get_plinder_path(rel="empty")
+    assert (outside / "kept.parquet").read_bytes() == b"kept"

From facb93988c3ebd9189a3a3e8315ff56f5ff6776b Mon Sep 17 00:00:00 2001
From: Ninjani <janani.durairaj@gmail.com>
Date: Fri, 9 Oct 2026 15:55:55 +0200
Subject: [PATCH 26/26] update docs

---
 docs/conf.py                                  |  1 +
 docs/examples/1_download.ipynb                | 88 ++++++-------------
 docs/examples/index.md                        | 11 ++-
 .../similarity_and_representatives.ipynb      |  6 +-
 docs/index.md                                 |  5 +-
 docs/migration/http.md                        | 62 -------------
 docs/tutorial/dataset.md                      | 15 ++--
 7 files changed, 49 insertions(+), 139 deletions(-)
 delete mode 100644 docs/migration/http.md

diff --git a/docs/conf.py b/docs/conf.py
index 19c80b83..c425beb2 100644
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -149,6 +149,7 @@
 }
 html_sidebars = {
     # No primary sidebar for these pages
+    "tutorial/**": [],
     "dataset": [],
     "evaluation": [],
     "citation": [],
diff --git a/docs/examples/1_download.ipynb b/docs/examples/1_download.ipynb
index 938dcadb..6c6283b3 100644
--- a/docs/examples/1_download.ipynb
+++ b/docs/examples/1_download.ipynb
@@ -4,57 +4,39 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "# Downloading the dataset\n",
+    "# Download the full dataset\n",
     "\n",
-    "The default location for the dataset is `~/.local/share/plinder/<PLINDER_RELEASE>`, where `<PLINDER_RELEASE>` is the month of the PDB snapshot, formatted as `YYYY-MM` (currently `2026-09`).\n",
-    "\n",
-    "Set the `PLINDER_MOUNT` environment variable to use a different location."
+    "Use `plinder_download` when you need a local copy, for example on a compute node without internet access."
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
+    "## Choose a local directory\n",
     "\n",
-    "## Use `plinder_download` to download the complete dataset\n",
-    "\n",
-    "```bash\n",
-    "plinder_download --help\n",
-    "usage:\n",
-    "    Download the full plinder dataset for the current configuration.\n",
-    "    Note that even though this is wrapped in a progress bar, the estimated\n",
-    "    completion time can vary wildly as it iterates over larger files vs.\n",
-    "    smaller ones.\n",
-    "    \n",
-    "\n",
-    "optional arguments:\n",
-    "  -h, --help            show this help message and exit\n",
-    "  --release RELEASE     plinder release\n",
-    "  --release-number RELEASE_NUMBER\n",
-    "                        plinder release number\n",
-    "  -y, --yes             skip confirmation\n",
-    "```\n",
-    "\n",
-    ":::{note} The public `2026-09` release is served directly from the [Cameo file server](https://cameo3d.org/plinder/PLINDER-2026-09/) and contains about 140 GB of downloadable files. Allow additional space for extracted archives; download time depends on your connection. Completed files are reused when their size and server modification time match; data hotfixes are fetched on the next access. Set `PLINDER_OFFLINE=true` to use the cache without network requests. :::"
+    "Files are cached in `~/.local/share/plinder/<release-month>` by default. Set `PLINDER_MOUNT` before importing PLINDER to choose another location. Inspect the configured directory with:"
    ]
   },
   {
-   "cell_type": "markdown",
+   "cell_type": "code",
+   "execution_count": null,
    "metadata": {},
+   "outputs": [],
    "source": [
-    "## Use the `plinder` Python package to lazily access the dataset\n",
+    "from plinder.core import get_config\n",
     "\n",
-    "Alternatively, if the `PLINDER_OFFLINE` environment variable **unset** (which is the default empty), the dataset will be downloaded on lazily and on the fly as you access the data. This is preferred for exploration and prototyping as you don't need to download the entire dataset at once and can just work with the assets you need for your use-case."
+    "cfg = get_config()\n",
+    "print(cfg.data.plinder_dir)"
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "## Use `plinder_download` to select release files\n",
+    "## Download release files\n",
     "\n",
-    "The command describes the available release and confirmation options:\n",
-    ""
+    "`plinder_download` downloads the index and representative-cover tables, then asks which larger groups to include. The [dataset reference](../dataset.md) lists these groups."
    ]
   },
   {
@@ -70,29 +52,21 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "The [dataset reference](../dataset.md) lists the default and optional download groups. After preparing the required files, set `PLINDER_OFFLINE=true` to prevent network access."
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "## Access release files from Python\n",
+    "Run this in a terminal to include every group without confirmation:\n",
     "\n",
-    "Alternatively, when `PLINDER_OFFLINE` is unset, API calls fetch missing release files as they are requested. This is useful for exploration because only the files needed by the current query or reconstruction are cached."
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "from plinder.core import get_config\n",
+    "```bash\n",
+    "plinder_download --yes\n",
+    "```\n",
     "\n",
-    "cfg = get_config()\n",
-    "print(f\"local directory: {cfg.data.plinder_dir}\")\n",
-    "print(f\"remote data directory: {cfg.data.plinder_remote}\")"
+    "Rerun the same command after an interruption; completed files are reused. Source PDB mmCIFs are fetched separately when reconstructing structures. For offline reconstruction, first cache the entries you need with `download_pdb_mmcifs()`, described in the {ref}`structure reference <structure-asset-reference>`.\n",
+    "\n",
+    "## Work offline\n",
+    "\n",
+    "After the files you need are available locally, set this before starting Python:\n",
+    "\n",
+    "```bash\n",
+    "export PLINDER_OFFLINE=true\n",
+    "```"
    ]
   }
  ],
@@ -103,18 +77,10 @@
    "name": "python3"
   },
   "language_info": {
-   "codemirror_mode": {
-    "name": "ipython",
-    "version": 3
-   },
-   "file_extension": ".py",
-   "mimetype": "text/x-python",
    "name": "python",
-   "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3",
-   "version": "3.10.14"
+   "version": "3.12"
   }
  },
  "nbformat": 4,
- "nbformat_minor": 2
+ "nbformat_minor": 4
 }
diff --git a/docs/examples/index.md b/docs/examples/index.md
index 561eb873..9555b3e2 100644
--- a/docs/examples/index.md
+++ b/docs/examples/index.md
@@ -10,7 +10,6 @@ Start here when working directly with the release tables and files.
 ```{toctree}
 :maxdepth: 1
 
-1_download
 2_query_filter_index
 ```
 
@@ -48,3 +47,13 @@ Compare predicted ligand poses and protein interfaces with known references.
 
 evaluation
 ```
+
+## Offline access
+
+Download a local copy when you need to work without internet access.
+
+```{toctree}
+:maxdepth: 1
+
+1_download
+```
diff --git a/docs/examples/similarity_and_representatives.ipynb b/docs/examples/similarity_and_representatives.ipynb
index c9f7a503..b52decf4 100644
--- a/docs/examples/similarity_and_representatives.ipynb
+++ b/docs/examples/similarity_and_representatives.ipynb
@@ -6,7 +6,7 @@
    "source": [
     "# Similarity scores and representative covers\n",
     "\n",
-    "Reconstruct selected pairwise scores, read part of a complete score table, and query representative assignments. {ref}`Similarity scores <similarity-score-reference>` defines the metrics and files."
+    "Compare ligands and protein interfaces, explore similarity scores, and find representative clusters. {ref}`Similarity scores <similarity-score-reference>` defines the metrics and files."
    ]
   },
   {
@@ -41,7 +41,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "## Reconstruct ligand similarities\n",
+    "## Compare ligand similarities\n",
     "\n",
     "`reconstruct_similarity_scores()` reads the files needed for the requested query and target IDs. This example uses a one-pair self-comparison to keep execution small."
    ]
@@ -98,7 +98,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "## Reconstruct protein-interface similarities\n",
+    "## Compare protein-interface similarities\n",
     "\n",
     "The interface API likewise accepts selected query and target IDs."
    ]
diff --git a/docs/index.md b/docs/index.md
index 8072a735..ee8714b4 100644
--- a/docs/index.md
+++ b/docs/index.md
@@ -11,7 +11,7 @@ html_theme.sidebar_secondary.remove: true
 Resource**: a comprehensive, annotated, high-quality resource for training and
 evaluating protein-ligand and protein-protein structure models.
 
-- \> 400k PLI systems across > 11k SCOP domains and > 50k unique small molecules
+- 611,930 protein–ligand systems, 803,190 proper ligands, and 3,811,623 protein–protein interfaces
 - Ligand and protein-interface annotations plus compact entry, chain, and representative tables
 - Automated curation pipeline to keep up with the PDB
 - Reusable ligand, pocket, and protein-interface similarities and representative assignments
@@ -37,7 +37,7 @@ Install PLINDER, select a release, and continue to the runnable guides.
 
 <div class="home-card-icon" aria-hidden="true"><i class="fa-solid fa-database"></i></div>
 
-Download release files and query columns across the ligand, interface,
+Query columns across the ligand, interface,
 entry, chain, and representative tables.
 :::::
 
@@ -86,6 +86,5 @@ dataset
 evaluation
 api/index
 contribution/index
-migration/http
 citation
 :::
diff --git a/docs/migration/http.md b/docs/migration/http.md
deleted file mode 100644
index 62e48a27..00000000
--- a/docs/migration/http.md
+++ /dev/null
@@ -1,62 +0,0 @@
-# Release downloads from the Cameo file server
-
-Public dataset reads for `YYYY-MM` releases (currently `2026-09`) use
-[the Cameo file server](https://cameo3d.org/plinder/PLINDER-2026-09/) directly.
-No S3 keys, Google credentials, or separately published manifest are required.
-Releases with a release number, such as the legacy `2024-06/v2`, are rejected;
-use an earlier `plinder` version for them.
-
-`PLINDER_MIRROR_URL` may select another HTTP(S) file-server root containing
-`PLINDER-<YYYY-MM>/` directories with nginx or Python-style directory indexes.
-For example, setting it to `https://mirror.example/datasets` selects
-`https://mirror.example/datasets/PLINDER-2026-09/` for the default release.
-The local cache remains `<PLINDER_MOUNT>/<PLINDER_BUCKET>/<YYYY-MM>/`.
-
-## Download and cache behavior
-
-The consumer uses cloudpathlib HTTP paths. Directory indexes provide file
-listings; HEAD responses provide exact sizes and Last-Modified times. Listings
-and metadata are fetched afresh for each API download call, so additions,
-removals, and hotfixes are visible without restarting Python. Directory links
-are restricted to immediate children within the release.
-
-Transfers stream into temporary files, validate HTTP Content-Length, and
-atomically replace the destination. Interrupted transfers retry from the start,
-with up to three attempts. They do not resume at a byte offset. Failed transfers
-preserve an existing destination. Metadata and directory requests use the same
-retry policy. Parallel download batches use eight workers and propagate errors.
-
-The file server does not publish per-file checksums. Content-Length validation
-detects truncated transfers; it does not detect same-size content corruption.
-
-Downloaded files retain the server's Last-Modified time. Cached files are reused
-when both size and modification time match. A changed server timestamp triggers
-a new download even for a same-size hotfix. Files without Last-Modified are
-fetched again on access. Publishers must update Last-Modified when changing a
-file; a same-size edit preserving that timestamp requires a forced refresh
-(`data.force_update=true`) or deletion of the affected cached file.
-Refreshing a ZIP clears its extraction marker.
-
-When a published release is updated in place, a directory download also removes
-cached Parquet files under that directory that the server no longer lists.
-Pruning happens only after the complete listing and all downloads succeed, so
-readers do not mix removed fragments with their replacements.
-
-`PLINDER_OFFLINE=true` bypasses all network access; unset it to return online.
-`PLINDER_OFFLINE_MODE` is also accepted. Empty values and `0`, `false`, `no`,
-and `off` leave networking enabled. Google libraries are optional for consumers
-and available through `plinder[data]` for data generation.
-
-## Focused validation
-
-```bash
-python -m pytest --noconftest tests/core/test_http.py tests/core/test_core_config.py -q -o addopts=''
-```
-
-The local HTTP-server tests exercise directory and direct-file access without a
-manifest, encoded and nested paths, cache reuse, same-size server hotfixes,
-forced refresh, removed Parquet fragments, offline behavior, path containment,
-atomic replacement, and recovery from interrupted transfers and HTTP errors.
-`--noconftest` excludes the repository-wide fixtures; full project CI also runs
-the release APIs and executes all documentation notebooks against the default
-public server.
diff --git a/docs/tutorial/dataset.md b/docs/tutorial/dataset.md
index 01ab2391..514a4407 100644
--- a/docs/tutorial/dataset.md
+++ b/docs/tutorial/dataset.md
@@ -3,19 +3,15 @@
 The `plinder` Python package is the main entry point for downloading release
 files, querying annotations, and reconstructing structures.
 
+PLINDER downloads the files needed by each API call automatically and reuses
+them on subsequent calls. You can start exploring straight away.
+
 ## Install PLINDER
 
 ```bash
 pip install plinder
 ```
 
-Releases download directly from the Cameo file server
-(`https://cameo3d.org/plinder/PLINDER-<release-month>/`) with HTTP size validation
-and automatic retries; no Google Cloud SDK is required. Server modification
-times are checked on access so data hotfixes refresh the local cache.
-`PLINDER_MIRROR_URL` selects another HTTP(S) file-server root containing
-`PLINDER-<release-month>/` directories with browsable directory indexes.
-
 A release is identified by the month of its PDB snapshot. The current release
 (`2026-09`) is the default; select another with:
 
@@ -25,10 +21,11 @@ export PLINDER_RELEASE=2026-09
 
 ## Continue with a runnable guide
 
-Start with {doc}`/examples/1_download`, then use
-{doc}`/examples/2_query_filter_index` to select ligand or protein-interface
+Start with {doc}`/examples/2_query_filter_index` to select ligand or protein-interface
 records. The remaining {doc}`/examples/index` guides cover coordinate access,
 similarity analysis, and custom scoring.
 
+For a local copy to use offline, see {doc}`/examples/1_download`.
+
 Use the {doc}`/dataset` page as the release and table reference, and
 {doc}`/api/index` for individual Python signatures.