pxmeter 0.1.5__tar.gz → 1.0.0__tar.gz

{pxmeter-0.1.5/pxmeter.egg-info → pxmeter-1.0.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pxmeter
-Version: 0.1.5
+Version: 1.0.0
 Summary: PXMeter is a comprehensive toolkit for evaluating the quality of         structures generated by biomolecular structure prediction models.
 Author: Bytedance Inc.
 Author-email: ai4s-bio@bytedance.com
@@ -9,7 +9,6 @@ Platform: manylinux1
 Requires-Python: >=3.11
 License-File: LICENSE
 Requires-Dist: biotite>=1.2.0
-Requires-Dist: dockq==2.1.3
 Requires-Dist: gemmi==0.7.0
 Requires-Dist: joblib
 Requires-Dist: ml_collections
@@ -22,6 +21,8 @@ Requires-Dist: scipy
 Requires-Dist: tabulate
 Requires-Dist: tqdm
 Requires-Dist: click
+Requires-Dist: pyarrow
+Requires-Dist: PyYAML
 Dynamic: author
 Dynamic: author-email
 Dynamic: license

{pxmeter-0.1.5 → pxmeter-1.0.0}/README.md

@@ -32,7 +32,7 @@ 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:
+PXMeter directly uses the Chemical Component Dictionary (CCD) bundled with Biotite. To update the CCD files:
 
 ```bash
 pxm ccd update
@@ -48,12 +48,13 @@ 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")
+- `-o` or `--output_json`: 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).
+- `--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.
+- `-C key.path=value`: Override fields in `pxmeter.configs.run_config.RUN_CONFIG` (repeatable; e.g., `-C metric.lddt.eps=1e-4 -C mapping.mapping_ligand=false`).
 
 To access the full list of parameters, use the `--help` option.
 
@@ -80,18 +81,59 @@ For detailed descriptions of additional parameters, use the `help()` function:
 help(evaluate)
 ```
 
+If you need to modify the runtime settings defined in
+`pxmeter.configs.run_config.RUN_CONFIG` (equivalent to using `-C` on the command line),
+you may directly update the values in `RUN_CONFIG` and then pass it into the evaluate() function.
+```python
+from pxmeter.configs.run_config import RUN_CONFIG
+
+RUN_CONFIG.mapping.res_id_alignments = False
+metric_result = evaluate(
+    ...,
+	run_config=RUN_CONFIG,
+)
+```
+
+For a detailed, step-by-step description of the PXMeter runtime evaluation pipeline (mapping, alignment, and metric computation), please refer to the [PXMeter evaluation pipeline details](docs/pxmeter_eval_details.md).
+
+For a comprehensive overview of the runtime configuration options, recommended defaults, and advanced usage examples, see the [PXMeter run configuration guide](docs/run_config_details.md).
+
+### Optional: Stereochemistry checks
+
+Run stereochemistry checks for a single CIF and export a CSV report:
+
+```bash
+pxm stereocheck -c examples/7rss_protenix_pred.cif -o stereochem_report.csv
+```
+**`pxm stereocheck` Parameters**:
+- `-c` or `--cif` (required): Path to the CIF file
+- `-o` or `--output-csv`: Path to the output CSV report (default: `stereochem_report.csv`)
+
+
 ## 📊 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 our paper:
+PXMeter offers a reproducible workflow covering both dataset creation and model evaluation.
+
+**Note**: The benchmarking workflow (the `benchmark/` directory) is only available in the source repository and is not shipped with the PyPI package. To run benchmarking, please clone the repository first:
+
+```bash
+git clone https://github.com/bytedance/PXMeter.git
+cd PXMeter
+```
+
+- The **[Benchmark Documentation](docs/benchmark.md)** explains how to run evaluations on model predictions and how the aggregated metrics are computed.
+- The **[Dataset Pipeline Overview](docs/datapipeline.md)** describes the complete construction of the RecentPDB low-homology dataset,
+including filtering, homology scans, clustering, and subset labeling.
+The pipeline also allows users to **rebuild the evaluation dataset from scratch using any custom time window**.
+This makes the benchmark fully flexible and adaptable to different release periods or ongoing updates from the PDB.
+- For details on the dataset used in our paper, please refer to the **[legacy dataset documentation](docs/legacy_dataset_reference.md)**, which describes the dataset version and evaluation code used at the time of the initial release.
+
+## ➡️ Preparing input files
 
-📄 <a href="https://www.biorxiv.org/content/10.1101/2025.07.17.664878v1">From Dataset Curation to Unified Evaluation: Revisiting
- Structure Prediction Benchmarks with PXMeter</a>
+When working with structural inputs—e.g., converting mmCIF, AlpahFold3, Protenix, or Boltz formats—you may find the following utility helpful:
 
+[pxm gen-input Usage Guide](docs/gen_input.md).
+ — a tool for generating and converting model input files via CLI or Python API.
 
 
 ## 💪 Contributing to PXMeter
@@ -124,7 +166,6 @@ If you use PXMeter in your research, please cite the following:
 
 
 ## 🚧 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.