pxmeter 0.0.1__tar.gz

pxmeter-0.0.1/LICENSE

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pxmeter-0.0.1/MANIFEST.in

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+include requirements.txt

pxmeter-0.0.1/PKG-INFO

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+Metadata-Version: 2.1
+Name: pxmeter
+Version: 0.0.1
+Summary: PXMeter is a tool crafted to assess the structural quality derived from Biomolecular Folding Models
+Author: Bytedance Inc.
+Author-email: ai4s-bio@bytedance.com
+License: Apache 2.0 License
+Platform: manylinux1
+Requires-Python: >=3.11
+License-File: LICENSE

pxmeter-0.0.1/README.md

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+# PXMeter - Structural Quality Assessment for Biomolecular Structure Prediction Models
+
+[![License](https://img.shields.io/badge/License-Apache%202.0-blue.svg)](https://opensource.org/licenses/Apache-2.0)
+[![Python 3.11+](https://img.shields.io/badge/python-3.11%2B-blue.svg)](https://www.python.org/downloads/)
+
+<div align="left" style="margin: 20px 0;">
+<span style="margin: 0 10px;">📄 <a href="URL">From Dataset Diagnostics to Evaluation: Revisiting
+Structure Prediction Benchmarks with PXMeter</a></span>
+</div>
+
+PXMeter is a comprehensive toolkit for evaluating the quality of structures generated by biomolecular structure prediction models, with support for proteins, nucleic acids, and small molecules.
+
+## 🌟 Features
+- **Full-Atom Matching Between Reference and Model Structures**: Automatically matches entities, aligns sequences, and permutes chains and atoms to establish one-to-one correspondence.
+- **Multi-metric Evaluation**:
+  - Local Distance Difference Test (LDDT) - A local superposition-free score for comparing reference and model structures.
+  - DockQ - Interface interaction quality.
+  - Pocket-aligned Root Mean Squared Deviation (RMSD) - Ligand pose quality.
+  - PoseBusters Validity Checks - Plausibility checks for generated molecule poses.
+- **Dual Interfaces**: CLI & Python API
+
+## 🛠️ Installation
+
+```bash
+# Install from PyPI
+pip install pxmeter
+
+# Install from source
+git clone https://github.com/bytedance/PXMeter.git
+cd PXMeter
+pip install -r requirements.txt
+pip install -e .
+```
+
+PXMeter will automatically download the Chemical Component Dictionary (CCD) upon its first run. To update the CCD files:
+
+```bash
+pxm ccd update
+```
+
+## 🚀 Quick Start
+
+### Command Line Interface
+```bash
+pxm -r examples/7rss.cif -m examples/7rss_protenix_pred.cif -o pxm_output.json
+```
+
+**Key Parameters**:
+- `-r` or `--ref_cif`: Path to reference CIF file
+- `-m` or `--model_cif`: Path to model CIF file
+- `-o` or `--output`: Path to save evaluation results (default: "pxm_output.json")
+- `--ref_model`: Specify model number of reference CIF (default: 1)
+- `--ref_assembly_id`: Specify the assembly ID for the reference CIF (default: None; uses the Asymmetric Unit for evaluation)
+- `ref_altloc`: Specify the alternative location identifier for the reference CIF (default: "first", uses the first alternative location code for each residue).
+- `--chain_id_to_mol_json`: JSON file defining custom ligands, where keys are chain IDs (label_asym_id) and values are the corresponding ligand SMILES strings.
+- `-l` or `--interested_lig_label_asym_id`: Indicate the `label_asym_id` of ligands for metrics like pocket-aligned RMSD. Multiple ligands should be comma-separated.
+
+To access the full list of parameters, use the `--help` option.
+
+### Python API
+**Note**: For batch evaluation of multiple structures, the Python API is highly recommended. This approach is more efficient than repeated command line calls because it caches CCD CIF files in memory and thus avoids redundant disk I/O.
+
+
+```python
+from pxmeter.eval import evaluate
+
+ref_cif = "examples/7rss.cif"
+model_cif = "examples/7rss_protenix_pred.cif"
+metric_result = evaluate(
+    ref_cif=ref_cif,
+    model_cif=model_cif,
+)
+
+json_dict = metric_result.to_json_dict()
+print(json_dict)
+```
+
+For detailed descriptions of additional parameters, use the `help()` function:
+```python
+help(evaluate)
+```
+
+## 📊 Benchmarking
+Refer to [benchmark/README.md](./benchmark/README.md) for evaluation protocols on:
+- RecentPDB dataset
+- PoseBusters V2
+
+The benchmark data is released under the CC0 license.
+We include code in the `benchmark` directory that evaluates various models using PXMeter and aggregates their metrics. This serves as an example of best practices for using the tool. For more details, please refer to the [Technical Report URL].
+
+
+## 💪 Contributing to PXMeter
+We welcome contributions from the community to help improve PXMeter!
+
+Check out the [Contributing Guide](CONTRIBUTING.md) to get started.
+
+Code Quality: We use `pre-commit` hooks to maintain consistent programming style and code quality. Please install them before committing.
+
+```bash
+pip install pre-commit
+pre-commit install
+```
+
+
+## 🚧 Limitations
+- PXMeter supports chain/atom permutations but not residue-level permutations. As a result, the accuracy of evaluation for branched chains, such as glycans, cannot be fully guaranteed.
+- It is recommended to use CIF files from the RCSB PDB as references, as they ensure content accuracy. All development and testing were conducted exclusively on CIF files from this source.
+
+
+## ✍️ Citing PXMeter
+```bibtex
+@software{pxmeter,
+  title = {PXMeter: Biomolecular Structure Quality Assessment Toolkit},
+  author = {Bytedance AI for Science Team},
+  year = {2024},
+  url = {https://github.com/your-org/pxmeter},
+}
+```
+
+## 🛡️ Security
+If you discover a potential security issue in this project, or think you may
+have discovered a security issue, we ask that you notify Bytedance Security via our [security center](https://security.bytedance.com/src) or [vulnerability reporting email](sec@bytedance.com).
+
+Please do **not** create a public GitHub issue.
+
+## ⚖️ License
+The PXMeter project is made available under the [Apache 2.0 License](./LICENSE), it is free for both academic research and commercial use.