shape-complementarity 0.1.0__tar.gz
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- shape_complementarity-0.1.0/.github/workflows/CI.yml +38 -0
- shape_complementarity-0.1.0/.github/workflows/release.yml +96 -0
- shape_complementarity-0.1.0/.gitignore +24 -0
- shape_complementarity-0.1.0/CHANGELOG.md +19 -0
- shape_complementarity-0.1.0/Cargo.lock +331 -0
- shape_complementarity-0.1.0/Cargo.toml +13 -0
- shape_complementarity-0.1.0/LICENSE +21 -0
- shape_complementarity-0.1.0/PKG-INFO +12 -0
- shape_complementarity-0.1.0/README.md +261 -0
- shape_complementarity-0.1.0/benchmark/speed.py +383 -0
- shape_complementarity-0.1.0/pyproject.toml +24 -0
- shape_complementarity-0.1.0/python/shape_complementarity/__init__.py +20 -0
- shape_complementarity-0.1.0/python/shape_complementarity/batch.py +80 -0
- shape_complementarity-0.1.0/python/shape_complementarity/io.py +402 -0
- shape_complementarity-0.1.0/src/lib.rs +110 -0
- shape_complementarity-0.1.0/tests/conftest.py +22 -0
- shape_complementarity-0.1.0/tests/data/1fyt.pdb +7310 -0
- shape_complementarity-0.1.0/tests/data/nb_ag_test.pdb +2496 -0
- shape_complementarity-0.1.0/tests/test_boltzgen.py +355 -0
- shape_complementarity-0.1.0/tests/test_core.py +87 -0
- shape_complementarity-0.1.0/tests/test_io.py +83 -0
- shape_complementarity-0.1.0/tests/test_parity.py +118 -0
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test:
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name: test (py${{ matrix.python-version }}, ${{ matrix.os }})
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python-version: ["3.10", "3.11", "3.12", "3.13"]
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run: .venv/bin/pip install pytest biopython numpy
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# parity tests skip automatically when `sc` binary is not in PATH
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run: .venv/bin/pytest tests/ -v
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# Triggered by pushing a version tag: git tag v0.1.0 && git push --tags
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# ── Build binary wheels (abi3: one wheel per platform/arch, Python 3.10+) ──
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# ── Source distribution (for platforms without pre-built wheels) ─────────
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url: https://pypi.org/p/shape-complementarity
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permissions:
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id-token: write # required for OIDC trusted publishing
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# Rust
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/target/
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# Python
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.venv/
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__pycache__/
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*.py[cod]
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*.egg-info/
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dist/
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build/
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.pytest_cache/
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# maturin compiled extensions (generated by `maturin develop`)
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*.so
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*.pyd
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# Downloaded benchmark fixtures (auto-fetched at runtime)
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tests/data/*.cif
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# IDE / OS
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*.swp
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# Changelog
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## [0.1.0] — 2026-05-25
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### Added
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- `compute_sc()`: low-level PyO3 binding to `sc-rs`'s `ScCalculator`, accepting
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pre-parsed atom coordinate arrays.
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- `ScResult`: read-only Python class exposing `sc`, `median_distance`,
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`trimmed_area`, `atoms_a`, `atoms_b`.
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- `from_pdb()` / `from_structure()`: biopython-based PDB/mmCIF parsing that
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mirrors the filtering logic of the `sc-rs` CLI exactly (ATOM-only, altloc A/'
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' , heavy atoms only by default).
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- `score_many()`: multiprocessing batch scorer returning a `pd.DataFrame`;
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per-file exceptions are caught and reported in a `status`/`error` column.
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- Full test suite: unit tests for the Rust core, IO layer, and parity tests
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comparing `shape_complementarity` output against the `sc-rs` CLI binary.
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- Benchmark script (`benchmark/speed.py`).
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- Pinned to `sc-rs` v1.0.0 via git tag.
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# This file is automatically @generated by Cargo.
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# It is not intended for manual editing.
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version = 4
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name = "anyhow"
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version = "1.0.102"
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@@ -0,0 +1,13 @@
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[package]
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name = "shape-complementarity"
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version = "0.1.0"
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edition = "2021"
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readme = "README.md"
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[lib]
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name = "_core"
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crate-type = ["cdylib"]
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[dependencies]
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|
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pyo3 = { version = "0.22", features = ["extension-module", "abi3-py310"] }
|
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|
+
sc_rs = { git = "https://github.com/cytokineking/sc-rs", tag = "v1.0.0", package = "sc-rs" }
|
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@@ -0,0 +1,21 @@
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MIT License
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3
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Copyright (c) 2026
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Permission is hereby granted, free of charge, to any person obtaining a copy
|
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|
+
of this software and associated documentation files (the "Software"), to deal
|
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7
|
+
in the Software without restriction, including without limitation the rights
|
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|
+
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
|
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|
+
copies of the Software, and to permit persons to whom the Software is
|
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|
+
furnished to do so, subject to the following conditions:
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+
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The above copyright notice and this permission notice shall be included in all
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|
+
copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
|
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|
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IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
|
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+
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
|
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+
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
|
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|
+
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
|
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|
+
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
|
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|
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SOFTWARE.
|
|
@@ -0,0 +1,12 @@
|
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Metadata-Version: 2.4
|
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+
Name: shape-complementarity
|
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3
|
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Version: 0.1.0
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|
+
Requires-Dist: numpy>=1.24
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|
+
Requires-Dist: biopython>=1.83
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|
+
License-File: LICENSE
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|
+
Summary: PyO3 bindings to sc-rs for Lawrence-Colman Shape Complementarity
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|
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License: MIT
|
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|
+
Requires-Python: >=3.10
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+
Project-URL: Bug Tracker, https://github.com/aarteixeira/shape-complementarity/issues
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Project-URL: Homepage, https://github.com/aarteixeira/shape-complementarity
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|
+
Project-URL: Repository, https://github.com/aarteixeira/shape-complementarity
|