sdfrust 0.5.0__tar.gz

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Files changed (56) hide show
  1. sdfrust-0.5.0/.gitignore +23 -0
  2. sdfrust-0.5.0/CHANGELOG.md +62 -0
  3. sdfrust-0.5.0/Cargo.lock +1270 -0
  4. sdfrust-0.5.0/Cargo.toml +55 -0
  5. sdfrust-0.5.0/LICENSE +21 -0
  6. sdfrust-0.5.0/PKG-INFO +251 -0
  7. sdfrust-0.5.0/README.md +290 -0
  8. sdfrust-0.5.0/examples/basic_usage.rs +157 -0
  9. sdfrust-0.5.0/examples/benchmark.rs +284 -0
  10. sdfrust-0.5.0/examples/parse_molecules.rs +189 -0
  11. sdfrust-0.5.0/pyproject.toml +44 -0
  12. sdfrust-0.5.0/python/sdfrust/__init__.py +162 -0
  13. sdfrust-0.5.0/python/sdfrust/py.typed +0 -0
  14. sdfrust-0.5.0/sdfrust-python/.gitignore +35 -0
  15. sdfrust-0.5.0/sdfrust-python/Cargo.toml +26 -0
  16. sdfrust-0.5.0/sdfrust-python/LICENSE +21 -0
  17. sdfrust-0.5.0/sdfrust-python/README.md +219 -0
  18. sdfrust-0.5.0/sdfrust-python/examples/README.md +82 -0
  19. sdfrust-0.5.0/sdfrust-python/examples/basic_usage.py +531 -0
  20. sdfrust-0.5.0/sdfrust-python/src/atom.rs +184 -0
  21. sdfrust-0.5.0/sdfrust-python/src/bond.rs +487 -0
  22. sdfrust-0.5.0/sdfrust-python/src/error.rs +63 -0
  23. sdfrust-0.5.0/sdfrust-python/src/iterators.rs +273 -0
  24. sdfrust-0.5.0/sdfrust-python/src/lib.rs +150 -0
  25. sdfrust-0.5.0/sdfrust-python/src/molecule.rs +831 -0
  26. sdfrust-0.5.0/sdfrust-python/src/parsing.rs +543 -0
  27. sdfrust-0.5.0/sdfrust-python/src/writing.rs +188 -0
  28. sdfrust-0.5.0/sdfrust-python/tests/test_basic.py +483 -0
  29. sdfrust-0.5.0/sdfrust-python/tests/test_geometry.py +218 -0
  30. sdfrust-0.5.0/sdfrust-python/tests/test_gzip.py +257 -0
  31. sdfrust-0.5.0/src/atom.rs +106 -0
  32. sdfrust-0.5.0/src/bond.rs +164 -0
  33. sdfrust-0.5.0/src/collection.rs +121 -0
  34. sdfrust-0.5.0/src/descriptors/elements.rs +374 -0
  35. sdfrust-0.5.0/src/descriptors/mod.rs +42 -0
  36. sdfrust-0.5.0/src/descriptors/molecular.rs +276 -0
  37. sdfrust-0.5.0/src/descriptors/topological.rs +581 -0
  38. sdfrust-0.5.0/src/error.rs +59 -0
  39. sdfrust-0.5.0/src/geometry/distance.rs +102 -0
  40. sdfrust-0.5.0/src/geometry/mod.rs +241 -0
  41. sdfrust-0.5.0/src/geometry/rmsd.rs +161 -0
  42. sdfrust-0.5.0/src/geometry/transform.rs +291 -0
  43. sdfrust-0.5.0/src/lib.rs +482 -0
  44. sdfrust-0.5.0/src/molecule.rs +418 -0
  45. sdfrust-0.5.0/src/parser/compression.rs +124 -0
  46. sdfrust-0.5.0/src/parser/mod.rs +32 -0
  47. sdfrust-0.5.0/src/parser/mol2.rs +688 -0
  48. sdfrust-0.5.0/src/parser/sdf.rs +1070 -0
  49. sdfrust-0.5.0/src/parser/sdf_v3000.rs +1125 -0
  50. sdfrust-0.5.0/src/parser/xyz.rs +555 -0
  51. sdfrust-0.5.0/src/sgroup.rs +175 -0
  52. sdfrust-0.5.0/src/stereogroup.rs +92 -0
  53. sdfrust-0.5.0/src/writer/mod.rs +15 -0
  54. sdfrust-0.5.0/src/writer/mol2.rs +305 -0
  55. sdfrust-0.5.0/src/writer/sdf.rs +178 -0
  56. sdfrust-0.5.0/src/writer/sdf_v3000.rs +391 -0
sdfrust-0.5.0/.gitignore ADDED
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+ # Generated by Cargo
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+ /target/
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+
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+ # Cargo.lock for libraries (not binaries)
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+ Cargo.lock
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+
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+ # IDE
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+ .idea/
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+ .vscode/
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+ *.swp
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+ *.swo
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+
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+ # OS
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+ .DS_Store
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+ Thumbs.db
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+
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+ # Test artifacts
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+ *.tmp
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+
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+ # Benchmark generated data
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+ benches/data/*.sdf
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+ benches/comparison/.venv/
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+ benches/comparison/results/
sdfrust-0.5.0/CHANGELOG.md ADDED
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+ # Changelog
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+
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+ All notable changes to this project will be documented in this file.
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+
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+ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
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+ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
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+
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+ ## [Unreleased]
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+
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+ ## [0.5.0] - 2026-02-17
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+
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+ ### Added
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+
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+ - Transparent gzip decompression for all file parsers (optional `gzip` feature)
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+ - XYZ format parser with streaming support, atomic number input, and case normalization
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+ - XYZ auto-detection in `parse_auto_*()` and `iter_auto_file()`
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+ - Python bindings for XYZ parsing and gzip support
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+ - PDBbind 2024 large-scale SDF benchmark test (27,670 files, 100% success rate, ~14k files/sec)
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+
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+ ## [0.4.0] - 2026-01-30
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+
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+ ### Added
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+
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+ - Python bindings via PyO3 (`sdfrust-python/` crate) with full API coverage
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+ - NumPy integration for coordinate and atomic number arrays
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+ - Streaming iterators for Python (`iter_sdf_file`, `iter_mol2_file`)
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+ - Workspace configuration for multi-crate build
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+
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+ ## [0.3.0] - 2026-01-30
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+
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+ ### Added
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+
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+ - Molecular descriptors module: molecular weight, exact mass, heavy atom count, bond type counts
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+ - Topological descriptors: ring count, ring atoms/bonds detection, rotatable bond count
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+ - Element data table (~30 elements with IUPAC 2021 atomic weights)
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+ - Convenience descriptor methods on `Molecule`
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+
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+ ## [0.2.0] - 2025-01-29
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+
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+ ### Added
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+
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+ - SDF V3000 parser and writer with stereogroups, SGroups, and collections
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+ - Automatic V2000/V3000 format detection and auto-format writing
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+ - MOL2 (TRIPOS) parser with streaming support
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+ - Performance benchmarks (~220k mol/s, 4-7x faster than RDKit)
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+
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+ ## [0.1.0] - 2025-01-25
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+
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+ ### Added
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+
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+ - SDF V2000 parser with atom/bond/property blocks and M CHG/M ISO lines
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+ - SDF V2000 writer with property preservation and multi-molecule output
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+ - Core types: `Molecule`, `Atom`, `Bond`, `BondOrder`, `BondStereo`
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+ - Molecule methods: `formula()`, `centroid()`, `translate()`, `neighbors()`, `element_counts()`
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+ - Memory-efficient streaming iterator for large multi-molecule files
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+
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+ [Unreleased]: https://github.com/HFooladi/sdfrust/compare/v0.5.0...HEAD
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+ [0.5.0]: https://github.com/HFooladi/sdfrust/compare/v0.4.0...v0.5.0
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+ [0.4.0]: https://github.com/HFooladi/sdfrust/compare/v0.3.0...v0.4.0
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+ [0.3.0]: https://github.com/HFooladi/sdfrust/compare/v0.2.0...v0.3.0
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+ [0.2.0]: https://github.com/HFooladi/sdfrust/compare/v0.1.0...v0.2.0
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+ [0.1.0]: https://github.com/HFooladi/sdfrust/releases/tag/v0.1.0