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Kaipengm2
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CrystalX-dataset

Size:
10K<n<100K
Tags:
crystallography
x-ray-diffraction
materials-science
computational-chemistry
deep-learning
License:
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  1. LICENSE +25 -0
  2. README.md +76 -0
  3. equiv_pt/equiv_1100908.pt +3 -0
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LICENSE ADDED
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+ CrystalX Dataset Notice
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+
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+ This release contains preprocessed records derived from the open-access
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+ Crystallography Open Database (COD) together with CrystalX project
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+ preprocessing outputs.
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+
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+ Use of this dataset release must comply with:
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+
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+ 1. the terms and attribution requirements applicable to the original COD data;
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+ 2. any third-party rights attached to individual source structures; and
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+ 3. applicable law, institutional policy, and publication policy.
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+
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+ This repository does not grant additional rights beyond those already attached
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+ to the underlying source data and the CrystalX preprocessing artifacts.
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+
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+ Recommended use:
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+
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+ - research
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+ - benchmarking
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+ - reproducibility of the CrystalX paper
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+
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+ If you redistribute this package or publish results derived from it, cite both
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+ the CrystalX paper and the COD.
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+
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+ This dataset is provided "as is", without warranty of any kind.
README.md ADDED
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+ ---
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+ pretty_name: CrystalX Dataset
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+ license: other
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+ size_categories:
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+ - 10K<n<100K
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+ tags:
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+ - crystallography
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+ - x-ray-diffraction
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+ - materials-science
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+ - computational-chemistry
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+ - deep-learning
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+ ---
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+
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+ # CrystalX Dataset
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+
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+ This repository provides the preprocessed CrystalX dataset for training and dataset-level evaluation.
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+
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+ ## Files
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+
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+ - `equiv_pt/`: preprocessed `equiv_*.pt` files
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+ - `splits/sorted_by_journal_year.txt`: publication-year metadata used for splitting
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+ - `LICENSE`
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+
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+ The year metadata covers `1994-2024`.
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+
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+ ## Data Format
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+
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+ Each `equiv_*.pt` file is a Python dictionary saved with `torch.save`.
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+
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+ Main fields:
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+
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+ - `z`: input heavy-atom element symbols
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+ - `equiv_gt`: heavy atoms with symmetry-expanded context
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+ - `gt`: heavy-atom labels
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+ - `hydro_gt`: hydrogen-count labels
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+ - `pos`: Cartesian coordinates with shape `[N, 3]` in angstrom
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+
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+ Other auxiliary fields may also be present.
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+
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+ ## Split File
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+
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+ Each line in `splits/sorted_by_journal_year.txt` has this format:
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+
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+ ```text
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+ year timestamp cif_name
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+ ```
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+
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+ The current CrystalX code uses:
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+
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+ - column 1 as the publication year
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+ - column 3 as the CIF stem
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+
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+ ## Usage
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+
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+ ```bash
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+ python -m crystalx_train.trainers.trainer_heavy \
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+ --pt_dir equiv_pt \
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+ --txt_path splits/sorted_by_journal_year.txt
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+ ```
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+
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+ ## Source
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+
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+ The dataset is derived from the open-access Crystallography Open Database (COD) and CrystalX preprocessing.
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+
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+ ## Citation
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+
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+ If you use this dataset, please cite the CrystalX paper and the COD.
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+
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+ ```bibtex
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+ @article{doi:10.1021/jacs.5c21832,
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+ author = {Zheng, Kaipeng and Huang, Weiran and Ouyang, Wanli and Zhong, Han-Sen and Li, Yuqiang},
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+ title = {CrystalX: High-Accuracy Crystal Structure Analysis Using Deep Learning},
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+ journal = {Journal of the American Chemical Society},
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+ doi = {10.1021/jacs.5c21832}
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+ }
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+ ```
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