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maltefranke
/
morph-data

Modalities:
3D
Languages:
English
ArXiv:
Tags:
chemistry
molecular-generation
3d
qm9
geom-drugs
chembl
Dataset card Files
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Document downloads, model compatibility, and data checksums

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  1. README.md +161 -0
  2. SHA256SUMS +61 -0
  3. manifest.json +371 -0
README.md ADDED
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+ ---
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+ pretty_name: Morph processed molecular datasets
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+ language:
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+ - en
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+ tags:
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+ - chemistry
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+ - molecular-generation
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+ - 3d
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+ - qm9
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+ - geom-drugs
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+ - chembl
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+ - morph
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+ - lmdb
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+ - pytorch-geometric
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+ ---
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+
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+ # Morph data
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+
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+ Ready-to-use processed QM9, GEOM-Drugs, and ChEMBL3D data for
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+ [Morph](https://huggingface.co/maltefranke/morph). Download the original processed
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+ files directly, including train/validation/test splits, ordered vocabularies,
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+ training statistics, and SMILES sidecars. No source-data download or preprocessing
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+ is needed to use these caches with Morph.
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+
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+ This dataset repository is public and supports unauthenticated downloads.
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+ It belongs to the
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+ [Morph collection](https://huggingface.co/collections/maltefranke/morph-6aca03baa0d63e6bb9baea6f).
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+
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+ ## Available datasets
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+
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+ Sizes are decimal GB. GEOM counts are conformer records; QM9 and ChEMBL3D counts
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+ are molecule records.
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+
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+ | Directory | Representation / selection | Train | Validation | Test | Size |
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+ | --- | --- | ---: | ---: | ---: | ---: |
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+ | `qm9` | Explicit H; original Morph QM9 splits | 100,000 | 20,000 | 12,947 | 0.326 GB |
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+ | `geom` | GEOM-Drugs, explicit H; at most 72 total atoms | 5,645,654 | 703,830 | 706,568 | 56.170 GB |
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+ | `chembl3d` | Explicit H; processed cache without the 100-atom cap | 1,479,308 | 184,947 | 184,960 | 14.795 GB |
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+ | `chembl3d_max100` | Explicit H; at most 100 total atoms | 1,474,008 | 184,295 | 184,242 | 14.726 GB |
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+ | `chembl3d_max100_implicit_h` | Implicit H; same capped source molecules | 1,474,008 | 184,295 | 184,242 | 9.925 GB |
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+
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+ The ChEMBL3D 100-atom cap counts hydrogens **before removal**. The implicit-H
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+ cache has its own vocabularies/statistics and includes the charge/bond
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+ normalization used for the released implicit-H models.
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+
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+ Total processed data: **95,942,750,644 bytes (95.94 GB)** in 61 files.
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+ Scaffold-decoration and protein-pocket datasets are not included in this release.
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+
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+ ## Download
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+
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+ From a Morph checkout, download a selected directory into `data/`:
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+
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+ ```bash
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+ # Choose one or more datasets:
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+ hf download maltefranke/morph-data --type dataset --include 'qm9/**' --local-dir data
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+ hf download maltefranke/morph-data --type dataset --include 'geom/**' --local-dir data
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+ hf download maltefranke/morph-data --type dataset --include 'chembl3d_max100/**' --local-dir data
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+ hf download maltefranke/morph-data --type dataset --include 'chembl3d_max100_implicit_h/**' --local-dir data
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+
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+ # Uncapped ChEMBL3D cache:
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+ hf download maltefranke/morph-data --type dataset --include 'chembl3d/**' --local-dir data
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+ ```
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+
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+ For example, QM9 will be available as `data/qm9/processed/train.pt`, and GEOM as
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+ `data/geom/processed/train_data.lmdb/data.mdb`.
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+
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+ Download everything, including the manifest and checksums:
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+
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+ ```bash
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+ hf download maltefranke/morph-data --type dataset --local-dir data
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+ (cd data && sha256sum -c SHA256SUMS)
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+ ```
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+
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+ Or use Python:
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+
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+ ```python
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+ from huggingface_hub import snapshot_download
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+
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+ snapshot_download(
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+ repo_id="maltefranke/morph-data",
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+ repo_type="dataset",
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+ allow_patterns=["qm9/**"],
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+ local_dir="data",
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+ )
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+ ```
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+
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+ For a reproducible download, pass a dataset commit hash with `--revision` in the
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+ CLI or `revision=` in Python. These are native Morph caches; load them with Morph's
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+ dataset classes rather than `datasets.load_dataset`.
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+
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+ Use a Morph checkout with support for loading processed QM9 caches without raw
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+ inputs. Older QM9 loaders, including those preserved in historical training
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+ bundles, may still fetch raw inputs during dataset initialization.
94
+
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+ ## Matching the released checkpoints
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+
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+ | Model subfolder in `maltefranke/morph` | Dataset directory here |
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+ | --- | --- |
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+ | `qm9/explicit_h` | `qm9` |
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+ | `geom/explicit_h` | `geom` |
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+ | `chembl3d/explicit_h` | `chembl3d_max100` |
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+ | `chembl3d/implicit_h` | `chembl3d_max100_implicit_h` |
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+
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+ When using a model's training bundle, point `MORPH_DATASET_ROOT` to the downloaded
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+ dataset directory that contains `processed/`. For example:
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+
107
+ ```bash
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+ export MORPH_DATASET_ROOT="$PWD/data/chembl3d_max100_implicit_h"
109
+ ```
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+
111
+ Vocabulary/statistics SHA-256 hashes and split-file sizes were checked against
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+ the dataset references in the published training bundles. Those historical
113
+ references contain split sizes, not split content hashes. This dataset snapshot
114
+ adds full SHA-256 checksums for every distributed data file in `SHA256SUMS` and
115
+ `manifest.json`.
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+
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+ ## File layout
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+
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+ Each dataset directory contains a `processed/` subdirectory with:
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+
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+ - **QM9:** `train.pt`, `val.pt`, `test.pt`, plus PyG preprocessing metadata.
122
+ - **GEOM and ChEMBL3D:** `train_data.lmdb/data.mdb`, `val_data.lmdb/data.mdb`,
123
+ `test_data.lmdb/data.mdb`.
124
+ - **All datasets:** `atom_tokens.txt`, `edge_tokens.txt`, `charge_tokens.txt`,
125
+ `distributions.pt`, and `train_smiles.txt`, `val_smiles.txt`, `test_smiles.txt`.
126
+ - **ChEMBL3D:** original `preprocessing_summary.json`; the capped variants also
127
+ contain `*_source_indices.npy` mappings to their source-cache records.
128
+
129
+ LMDB records contain atomic numbers (`z`), coordinates (`pos`), charges,
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+ `edge_index`, `edge_attr`, and SMILES. Coordinates are stored in physical Angstroms;
131
+ Morph applies the supplied training statistics when constructing model inputs.
132
+ SMILES sidecars contain unique split SMILES and are not per-record index maps.
133
+ Keep each cache's split files, vocabularies, and statistics together.
134
+
135
+ Only the LMDB `data.mdb` files are distributed; the Morph reader uses read-only
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+ LMDB access without lock files. Raw inputs, alternative statistics backups,
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+ scaffold caches, and temporary files are omitted.
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+
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+ ## Sources and citation
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+
141
+ These are processed snapshots of existing molecular datasets. Upstream sources
142
+ used by Morph's preprocessing include the
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+ [corrected QM9 structures](https://zenodo.org/records/15700961), the
144
+ [GEOM-Drugs Revisited split files](https://bits.csb.pitt.edu/files/geom_raw/), and
145
+ LoQI's ChEMBL3D processed release (Figshare file IDs 62280814, 62280805, 62280802).
146
+ Consult the upstream releases for their dataset licenses and citation details.
147
+
148
+ For Morph, please cite
149
+ [Generative Molecular Morphing for Flexible-Size Design via Unbalanced Optimal Transport](https://arxiv.org/abs/2606.07239):
150
+
151
+ ```bibtex
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+ @misc{franke2026generativemolecularmorphingflexiblesize,
153
+ title={Generative Molecular Morphing for Flexible-Size Design via Unbalanced Optimal Transport},
154
+ author={Malte Franke and Stefan P. Schmid and Zarko Ivkovic and Kjell Jorner and Andreas Krause},
155
+ year={2026},
156
+ eprint={2606.07239},
157
+ archivePrefix={arXiv},
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+ primaryClass={cs.LG},
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+ url={https://arxiv.org/abs/2606.07239},
160
+ }
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+ ```
SHA256SUMS ADDED
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+ e4a51269bb7c838d1f85704f031cb2a013b39520a9692763d5d85bf22e553f09 chembl3d/processed/preprocessing_summary.json
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+ 71cbe3ea2ef59215ec5608e1d2f1392c54f5df2fa590f4f25a836087a86ccbe6 chembl3d_max100/processed/atom_tokens.txt
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+ f5d5fb17b30809b00de20eeb6fe7b0d93a2a60ffd36339e06e875f5ba882de0c qm9/processed/atom_tokens.txt
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+ 3da517eb4dce07d46c58255935020d0f2923a8c0900feebf68434b67285b4fbc qm9/processed/val_smiles.txt
manifest.json ADDED
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1
+ {
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+ "schema_version": 1,
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+ "repository": "maltefranke/morph-data",
4
+ "created_date": "2026-10-12",
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+ "model_repository": "maltefranke/morph",
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+ "datasets": [
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+ {
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+ "directory": "qm9",
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+ },
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+ "hydrogen_mode": "explicit",
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+ "model_subfolder": "geom/explicit_h"
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+ },
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+ }
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+ ],
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+ "total_data_bytes": 95942750644,
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+ "files": [
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