pdbrust 0.7.1__tar.gz

pdbrust-0.7.1/.github/ISSUE_TEMPLATE/bug_report.md

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+---
+name: Bug report
+about: Create a report to help us improve
+title: ''
+labels: 'bug'
+assignees: ''
+
+---
+
+**Describe the bug**
+A clear and concise description of what the bug is.
+
+**To Reproduce**
+Steps to reproduce the behavior:
+1. Load a PDB file with '...'
+2. Call function '....'
+3. See error
+
+**Expected behavior**
+A clear and concise description of what you expected to happen.
+
+**PDB File**
+If applicable, please share the relevant PDB file or a minimal example that reproduces the issue.
+
+**Environment:**
+ - OS: [e.g. Ubuntu 22.04]
+ - Rust version: [e.g. 1.70.0]
+ - PDBRust version: [e.g. 0.1.0]
+ - Features enabled: [e.g. parallel, geometry]
+
+**Additional context**
+Add any other context about the problem here.
+
+**Error message**
+If applicable, please share the complete error message. 

pdbrust-0.7.1/.github/ISSUE_TEMPLATE/feature_request.md

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+---
+name: Feature Request
+about: Suggest an idea for this project
+title: '[FEATURE] '
+labels: enhancement
+assignees: ''
+---
+
+**Is your feature request related to a problem? Please describe.**
+A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
+
+**Describe the solution you'd like**
+A clear and concise description of what you want to happen.
+
+**Describe alternatives you've considered**
+A clear and concise description of any alternative solutions or features you've considered.
+
+**Implementation Details**
+If you have a specific implementation in mind, please describe it here.
+
+**Additional context**
+Add any other context or screenshots about the feature request here.
+
+**Technical Considerations**
+- [ ] Does this feature require changes to the public API?
+- [ ] Does this feature require changes to the data structures?
+- [ ] Does this feature require changes to the documentation?
+- [ ] Does this feature require new dependencies?
+
+**Priority**
+Please indicate the priority of this feature:
+- [ ] High (Critical for project success)
+- [ ] Medium (Important but not blocking)
+- [ ] Low (Nice to have)
+
+**Impact**
+Please describe the impact this feature will have on:
+- Performance
+- User experience
+- Code maintainability
+- Other aspects of the project 

pdbrust-0.7.1/.github/dependabot.yml

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+version: 2
+updates:
+  # Enable version updates for Rust
+  - package-ecosystem: "cargo"
+    directory: "/"
+    schedule:
+      interval: "weekly"
+      day: "monday"
+    open-pull-requests-limit: 10
+    labels:
+      - "dependencies"
+    commit-message:
+      prefix: "chore"
+      include: "scope"
+    groups:
+      dependencies:
+        patterns:
+          - "*"
+    ignore:
+      # Ignore major version updates for now
+      - dependency-name: "*"
+        update-types: ["version-update:semver-major"] 

pdbrust-0.7.1/.github/workflows/python-publish.yml

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+name: Python Wheels
+
+on:
+  push:
+    tags:
+      - 'v*'
+  pull_request:
+    paths:
+      - 'pdbrust-python/**'
+      - '.github/workflows/python-publish.yml'
+  workflow_dispatch:
+
+permissions:
+  contents: read
+
+jobs:
+  # Build wheels for Linux
+  linux:
+    runs-on: ${{ matrix.runner }}
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+          - target: x86_64
+            runner: ubuntu-latest
+          # Built natively: the manylinux2014 cross-compiler for aarch64 cannot
+          # assemble ring's ARM code (needed for rustls).
+          - target: aarch64
+            runner: ubuntu-24.04-arm
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: '3.12'
+
+      - name: Build wheels
+        uses: PyO3/maturin-action@v1
+        with:
+          target: ${{ matrix.target }}
+          args: --release --out dist -i 3.10 3.11 3.12 3.13 3.14 --manifest-path pdbrust-python/Cargo.toml --features full
+          sccache: 'true'
+          manylinux: auto
+
+      # Wheels must install only the pdbrust package (no stray top-level files
+      # in site-packages).
+      - name: Check wheel contents
+        shell: bash
+        run: |
+          python - <<'EOF'
+          import glob, sys, zipfile
+          wheels = glob.glob("dist/*.whl")
+          if not wheels:
+              sys.exit("no wheels found in dist/")
+          for wheel in wheels:
+              names = zipfile.ZipFile(wheel).namelist()
+              stray = [n for n in names if not n.startswith(("pdbrust/", "pdbrust-"))]
+              if stray:
+                  sys.exit(f"{wheel} installs files outside the pdbrust package: {stray}")
+          print(f"{len(wheels)} wheel(s) contain only the pdbrust package")
+          EOF
+
+      - name: Upload wheels
+        uses: actions/upload-artifact@v4
+        with:
+          name: wheels-linux-${{ matrix.target }}
+          path: dist
+
+  # Build wheels for macOS (full features including RCSB)
+  macos:
+    runs-on: macos-latest
+    strategy:
+      matrix:
+        target: [x86_64, aarch64]
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: '3.12'
+
+      - name: Build wheels
+        uses: PyO3/maturin-action@v1
+        with:
+          target: ${{ matrix.target }}
+          args: --release --out dist -i 3.10 3.11 3.12 3.13 3.14 --manifest-path pdbrust-python/Cargo.toml --features full
+          sccache: 'true'
+
+      # Wheels must install only the pdbrust package (no stray top-level files
+      # in site-packages).
+      - name: Check wheel contents
+        shell: bash
+        run: |
+          python - <<'EOF'
+          import glob, sys, zipfile
+          wheels = glob.glob("dist/*.whl")
+          if not wheels:
+              sys.exit("no wheels found in dist/")
+          for wheel in wheels:
+              names = zipfile.ZipFile(wheel).namelist()
+              stray = [n for n in names if not n.startswith(("pdbrust/", "pdbrust-"))]
+              if stray:
+                  sys.exit(f"{wheel} installs files outside the pdbrust package: {stray}")
+          print(f"{len(wheels)} wheel(s) contain only the pdbrust package")
+          EOF
+
+      - name: Upload wheels
+        uses: actions/upload-artifact@v4
+        with:
+          name: wheels-macos-${{ matrix.target }}
+          path: dist
+
+  # Build wheels for Windows (full features including RCSB)
+  windows:
+    runs-on: windows-latest
+    strategy:
+      matrix:
+        target: [x64]
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: '3.12'
+          architecture: ${{ matrix.target }}
+
+      - name: Build wheels
+        uses: PyO3/maturin-action@v1
+        with:
+          target: ${{ matrix.target }}
+          args: --release --out dist -i 3.10 3.11 3.12 3.13 3.14 --manifest-path pdbrust-python/Cargo.toml --features full
+          sccache: 'true'
+
+      # Wheels must install only the pdbrust package (no stray top-level files
+      # in site-packages).
+      - name: Check wheel contents
+        shell: bash
+        run: |
+          python - <<'EOF'
+          import glob, sys, zipfile
+          wheels = glob.glob("dist/*.whl")
+          if not wheels:
+              sys.exit("no wheels found in dist/")
+          for wheel in wheels:
+              names = zipfile.ZipFile(wheel).namelist()
+              stray = [n for n in names if not n.startswith(("pdbrust/", "pdbrust-"))]
+              if stray:
+                  sys.exit(f"{wheel} installs files outside the pdbrust package: {stray}")
+          print(f"{len(wheels)} wheel(s) contain only the pdbrust package")
+          EOF
+
+      - name: Upload wheels
+        uses: actions/upload-artifact@v4
+        with:
+          name: wheels-windows-${{ matrix.target }}
+          path: dist
+
+  # Build source distribution
+  sdist:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Build sdist
+        uses: PyO3/maturin-action@v1
+        with:
+          command: sdist
+          args: --out dist --manifest-path pdbrust-python/Cargo.toml
+
+      # Users on platforms without a pre-built wheel install from the sdist,
+      # so make sure it builds and imports.
+      - uses: actions/setup-python@v5
+        with:
+          python-version: '3.12'
+
+      - name: Install from the sdist and smoke-test
+        run: |
+          python -m pip install dist/*.tar.gz
+          python -c "import pdbrust; s = pdbrust.parse_pdb_file('examples/pdb_files/1UBQ.pdb'); assert s.num_atoms == 660; print('sdist OK:', s.num_atoms, 'atoms')"
+
+      - name: Upload sdist
+        uses: actions/upload-artifact@v4
+        with:
+          name: wheels-sdist
+          path: dist
+        if: success()
+
+  # Publish to PyPI on tag push
+  publish:
+    name: Publish to PyPI
+    runs-on: ubuntu-latest
+    if: startsWith(github.ref, 'refs/tags/v')
+    # Wait for the sdist too, so it is always uploaded together with the wheels.
+    needs: [linux, macos, windows, sdist]
+    permissions:
+      id-token: write  # For trusted publishing
+    steps:
+      - name: Download all wheels
+        uses: actions/download-artifact@v4
+        with:
+          pattern: wheels-*
+          path: dist
+          merge-multiple: true
+
+      - name: List wheels
+        run: ls -la dist/
+
+      - name: Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          verbose: true

pdbrust-0.7.1/.github/workflows/rust.yml

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+name: Rust CI/CD
+
+on:
+  push:
+    branches: [ "main" ]
+  pull_request:
+    branches: [ "main" ]
+
+env:
+  CARGO_TERM_COLOR: always
+  RUSTFLAGS: "-D warnings"
+
+jobs:
+  test:
+    name: Test
+    runs-on: ${{ matrix.os }}
+    strategy:
+      # Let every OS/toolchain combination finish so one failure (or a flaky
+      # runner) doesn't hide the results of the others.
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, windows-latest, macos-latest]
+        rust: [stable, 1.85.0]  # Test on both stable and MSRV
+        include:
+          - os: ubuntu-latest
+            rust: stable
+            run-coverage: true
+    steps:
+      - uses: actions/checkout@v5
+      
+      - name: Install Rust toolchain
+        uses: dtolnay/rust-toolchain@master
+        with:
+          toolchain: ${{ matrix.rust }}
+      
+      - name: Cache dependencies
+        uses: actions/cache@v5
+        with:
+          path: |
+            ~/.cargo/registry
+            ~/.cargo/git
+            target
+          key: ${{ runner.os }}-cargo-${{ matrix.rust }}-${{ hashFiles('**/Cargo.lock') }}
+      
+      - name: Run tests
+        run: cargo test --lib --tests --verbose --package pdbrust
+
+      - name: Run tests with all features
+        run: cargo test --all-features --verbose --package pdbrust
+
+  lint:
+    name: Lint
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v5
+      
+      - name: Install Rust toolchain
+        uses: dtolnay/rust-toolchain@stable
+        with:
+          components: clippy, rustfmt
+      
+      - name: Cache dependencies
+        uses: actions/cache@v5
+        with:
+          path: |
+            ~/.cargo/registry
+            ~/.cargo/git
+            target
+          key: ${{ runner.os }}-cargo-lint-${{ hashFiles('**/Cargo.lock') }}
+      
+      - name: Clippy check
+        run: cargo clippy --all-targets --all-features --package pdbrust
+      
+      - name: Check formatting
+        run: cargo fmt --all -- --check
+
+  features:
+    name: Feature combinations
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v5
+
+      - name: Install Rust toolchain
+        uses: dtolnay/rust-toolchain@stable
+
+      - name: Install cargo-hack
+        uses: taiki-e/install-action@cargo-hack
+
+      # Users often enable a single feature (e.g. `features = ["geometry"]`);
+      # make sure each one compiles on its own without warnings.
+      - name: Check each feature individually
+        run: cargo hack check --each-feature --package pdbrust
+
+  python:
+    name: Python bindings (${{ matrix.python-version }})
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        # Oldest and newest supported Python versions
+        python-version: ["3.10", "3.14"]
+    env:
+      # Build the bindings the same way the release wheels are built
+      # (python-publish.yml does not use -D warnings).
+      RUSTFLAGS: ""
+    steps:
+      - uses: actions/checkout@v5
+
+      - uses: actions/setup-python@v6
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install Rust toolchain
+        uses: dtolnay/rust-toolchain@stable
+
+      - name: Compile-check all binding features
+        run: cargo check --package pdbrust-python --all-features
+
+      # Same features as the Linux release wheels (see python-publish.yml).
+      - name: Build and install the Python package
+        run: |
+          python -m pip install --upgrade pip maturin
+          maturin build --manifest-path pdbrust-python/Cargo.toml --interpreter python --features full --out dist
+          python -m pip install dist/*.whl numpy
+
+      - name: Smoke-test the Python package
+        run: |
+          python - <<'EOF'
+          import pdbrust
+
+          pdb = pdbrust.parse_pdb_file("examples/pdb_files/1UBQ.pdb")
+          cif = pdbrust.parse_mmcif_file("examples/pdb_files/1CRN.cif")
+          for s in (pdb, cif):
+              assert s.num_atoms > 0
+              assert s.get_coords_array().shape == (s.num_atoms, 3)
+
+          print(f"1UBQ: {pdb.num_atoms} atoms, {pdb.num_chains} chain(s)")
+          print(f"1CRN: {cif.num_atoms} atoms")
+          print(f"Radius of gyration: {pdb.radius_of_gyration():.2f}")
+          print(f"Secondary structure: {pdb.secondary_structure_string()[:40]}")
+          EOF
+
+      # Includes checks that files written by pdbrust are read correctly by gemmi.
+      - name: Run the Python tests
+        run: |
+          python -m pip install pytest gemmi==0.7.5
+          python -m pytest pdbrust-python/tests -q
+
+  coverage:
+    name: Code coverage
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v5
+      
+      - name: Install Rust toolchain
+        uses: dtolnay/rust-toolchain@stable
+        with:
+          components: llvm-tools-preview
+      
+      - name: Install cargo-llvm-cov
+        uses: taiki-e/install-action@cargo-llvm-cov
+      
+      - name: Generate code coverage
+        run: cargo llvm-cov --all-features --package pdbrust --lcov --output-path lcov.info
+      
+      - name: Upload coverage to Codecov
+        uses: codecov/codecov-action@v6
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          files: lcov.info
+          # Dependabot and fork PRs have no access to the token; an upload
+          # failure there says nothing about the code, so don't fail CI on it.
+          fail_ci_if_error: false
+
+  doc:
+    name: Documentation
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v5
+      
+      - name: Install Rust toolchain
+        uses: dtolnay/rust-toolchain@stable
+      
+      - name: Check documentation
+        env:
+          RUSTDOCFLAGS: "-D warnings"
+        run: cargo doc --no-deps --all-features --package pdbrust
+
+  security:
+    name: Security
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v5
+      
+      - name: Install Rust toolchain
+        uses: dtolnay/rust-toolchain@stable
+      
+      - name: Install cargo-audit
+        run: cargo install cargo-audit
+      
+      - name: Run security audit
+        run: cargo audit
+        continue-on-error: true  # Advisory - don't block on security for now
+
+  release:
+    name: Release
+    needs: [test, lint, security]
+    runs-on: ubuntu-latest
+    if: startsWith(github.ref, 'refs/tags/')
+    steps:
+      - uses: actions/checkout@v5
+      
+      - name: Install Rust toolchain
+        uses: dtolnay/rust-toolchain@stable
+      
+      - name: Publish to crates.io
+        run: cargo publish --token ${{ secrets.CRATES_IO_TOKEN }}

pdbrust-0.7.1/.gitignore

@@ -0,0 +1,21 @@
+/target
+**/*.rs.bk
+.idea/
+.vscode/
+*.swp
+*.swo
+libraryPDB/
+
+# Paper sources are kept private until a preprint is posted
+/docs/paper/
+/docs/*overleaf*.zip
+
+# Python
+__pycache__/
+*.py[cod]
+*.so
+*.egg-info/
+dist/
+build/
+.eggs/
+.venv/

pdbrust-0.7.1/.zenodo.json

@@ -0,0 +1,53 @@
+{
+  "title": "PDBRust: A High-Performance Rust Library for PDB/mmCIF Parsing and Analysis",
+  "description": "<p>PDBRust is a fast Rust library for parsing and analyzing Protein Data Bank (PDB) and mmCIF protein structure files. It provides comprehensive support for molecular structure data with robust error handling, structural analysis, quality assessment, and RCSB PDB integration.</p><p>Key features:</p><ul><li>Dual format support: PDB and mmCIF with automatic format detection</li><li>40-260x faster than equivalent Python implementations</li><li>Validated against the entire PDB archive (230,655 structures, 100% success rate)</li><li>Python bindings available via PyPI</li><li>Feature-gated modules for minimal compile times</li></ul>",
+  "creators": [
+    {
+      "name": "Fooladi, Hosein",
+      "orcid": "0000-0002-3124-2761",
+      "affiliation": "Department of Pharmaceutical Sciences, Division of Pharmaceutical Chemistry, Faculty of Life Sciences, University of Vienna, Josef-Holaubek-Platz 2, 1090 Vienna, Austria"
+    }
+  ],
+  "keywords": [
+    "bioinformatics",
+    "protein structure",
+    "PDB",
+    "mmCIF",
+    "structural biology",
+    "Rust",
+    "Python",
+    "molecular structure",
+    "protein analysis",
+    "computational biology"
+  ],
+  "license": "MIT",
+  "upload_type": "software",
+  "access_right": "open",
+  "programming_language": ["Rust", "Python"],
+  "related_identifiers": [
+    {
+      "identifier": "https://github.com/HFooladi/pdbrust",
+      "relation": "isSupplementTo",
+      "resource_type": "software",
+      "scheme": "url"
+    },
+    {
+      "identifier": "https://crates.io/crates/pdbrust",
+      "relation": "isIdenticalTo",
+      "resource_type": "software",
+      "scheme": "url"
+    },
+    {
+      "identifier": "https://pypi.org/project/pdbrust/",
+      "relation": "isIdenticalTo",
+      "resource_type": "software",
+      "scheme": "url"
+    },
+    {
+      "identifier": "https://docs.rs/pdbrust",
+      "relation": "isDocumentedBy",
+      "resource_type": "publication-other",
+      "scheme": "url"
+    }
+  ]
+}