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feat(algo): support guessing atom/bond properties from geometry #189

Merged
merged 49 commits into from
Feb 6, 2024
Merged

feat(algo): support guessing atom/bond properties from geometry #189

merged 49 commits into from
Feb 6, 2024

Commits on Feb 6, 2024

  1. refactor(core): move ring finding algorithms to new directory algo/

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  2. chore: allow short statements without surrounding braces

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  3. refactor(core): introduce swap_axis() to use Eigen's col-major APIs

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  4. fix(core): update ownership of substructures on copy/move of Molecule

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  5. perf(core): re-map node ids of substructures directly

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  6. refactor(core): extract conformer remapping logic

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  7. fix(core): copy/move id/props while copy/moving substructures

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  8. refactor(core): rename erase_*_of -> erase_*_if

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  9. perf(core): skip finalize if graph itself is not changed

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  10. docs(core): correct docstrings to reflect behavior change of mutator

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  11. feat(core): promote ClearablePQ to internal API

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  12. feat: add more Eigen-like type aliases

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  13. feat(core): implement octree-based nearest neighbor search

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  14. test(core): add tests for octree nn search

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  15. fix: add missing headers

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  16. feat(core): add element type and standard state

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  17. feat(core): disallow negative implicit hydrogen count

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  18. feat(core): remove bond length from BondData

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  19. build(test): create nuri_add_test function

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  20. feat(core): support direct indexing on neighbors of NodeWrapper

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  21. feat(core): add cconf() method to Molecule

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  22. feat(core): allow mutating substructures of molecule

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  23. feat(core): add static reference to the periodic table for convenience

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  24. feat(core): promote nonbonding_electrons to public API

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  25. feat: add CompactMap for bounded integer-like keys

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  26. chore: update clang-tidy config

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  27. feat(core): add primitives for angle calculation

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  28. test(core): add test for fit_plane()

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  29. feat: rename add_if -> value_if to support broader applications

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  30. feat(core): add "other" bond order for flexibility

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  31. feat(core): make most set_* methods of {Atom,Bond}Data return itself 

    Also:
- promote {Atom,Bond}Flags enum to public API.
- add {add,del}_flags() methods as a shortcut to update atom/bond flags.
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  32. style(fmt/mol2): remove most braces around single-line blocks

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  33. perf(core): use octant distance while octree traversal

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  34. feat(core): update molecule API for better usability

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  35. feat(core): remove valence warning in internal::count_pi_e function

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  36. feat(core): add steric_number function

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  37. feat(core): add find_adjacent method to NodeWrapper

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  38. feat: add more eigen typedefs

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  39. feat: add cyclic indexer for eigen types

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  40. feat: create bitmask based PowersetStream

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  41. feat: create ZippedIterator utility

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  42. feat: add more utility functions

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  43. feat: update signature of generate_index, argsort, argpartition

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  44. perf: optimize stack() function

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  45. feat(core): add utility function to use NodeWrapper as Eigen indexer

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  46. feat(algo): implement guessing algorithm based on 3D atom coordinates

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  47. test(algo): add tests for guessing algorithms

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  48. fix: update headers

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  49. feat(algo): remove unimplemented functions 

    [skip ci]
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