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todo.md

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General TODO:

Primary TODO:

  • I/O:

    • Add option to guess the charge with RDKit if not set
    • Add support for writing complex trees to ASE (currently only stackable trees supported)

  • Tree improvement

    • Tree function wrappers with tree parameters for non-tree parameters in unwrapped function
    • Renaming/restructuring support of tree structure
    • Selection functions on the tree (compound=?, group=?, <grouping_param>=?)
      • Added stubs for .sel() and .isel()
      • Add implementation capturing appropriate dimensions/indexes.
      • Propagate remaining indexers to data entries.
    • Pattern matching in the getitem() method, i.e. db['/I01/**/data'] db["/I01/*/{1-20}"]

  • (De)serialization:

    • Implementation of Supports(To/From)XrConversion for various (wrapper) types
    • Tutorial on how to add own types

  • Wrapper types:

    • Add supported Shnitsel-tools functions as direct methods on wrapper types
    • Improve Visualization/helper text
    • Add DataArray wrapper
      • Add specifically an AtXYZ/Positions Wrapper type.
    • Add more wrapper types for support function returns

  • StructureSelection

    • Options in function signatures (provide directly a SMARTs string, deal with trees, etc.)
      • On-the-go construction added to geo._get_default_selection()
      • Patch existing functions to express support for descriptors
    • Add merge/subtract/intersect operations
    • Add 'BLA' and 'pwdist' feature descriptors.
    • Fix non-redundant coordinates
    • Structure selection (raise error if empty/warning if empty)
    • draw: Draw grid of highlighted feature levels

  • Analogs tree, structure selection, warning if no match for compounds

    • Adapted to tree support
    • Copy if multiple matches
    • For now: error if multiple matches

  • StateSelection

    • Add Support for textual representation of state selection
    • Add merge/subtract/intersect operations

  • biplot_kde needs to be fixed to use the descriptors of the PCA in the side plots.

    • Fix PCA loadings main contribution plot not being the same as the explained PCA.

  • Visualization support

    • Add generic plot() function to various types
    • Add option for plots from tree hierarchies

  • Add tutorial for further CLI tools

  • Dimension reduction:

    • Refactor PLS
    • Refactor LDA

  • Clustering support

    • DBSCAN sounds like a good option to support

  • Datasheet

    • Improve documentation
      • Refactor documentation
      • Make docstrings more detailed
    • DatasheetPage:
      • Improve PCA Page
      • Improve default settings for datasheet and pages.

  • CLI tutorial/SI

  • Full tutorial retinal with direct link for reviewers

    • Retinal BLA/HOOP/Dihedrals (Put all dihedrals in), 3->2 Dimension reduction
    • Retinal PCA biplot to show we can find the right parameters
    • Length threshold statistics plot
    • Datasheet (note, that generation takes somewhat longer)
    • add one more cool plot from retinal tutorial: The hop-time alignment would be perfect

Secondary TODO:

  • Add tests for conversion

  • Mask array to only consider relevant data. Would allow us to limit atom, timestep, etc. Should probably be generated at loading time and not really stored.

  • Make it possible to merge a trajectory into an already multi-trajectory. May be necessary for some users or for us extending datasets in the future.

  • Do NewtonX/PyrAI2md have charge information? SHARC 4.0 has charge info. -> Not that we know of. Probably hidden in QM interface.

  • Add command line tools for annotation and inspection of trajectories/netcdf files

  • Add tox for testing shnitsel with different python versions

Tertiary TODO:

  • Profiling of key functions like get_bats()
  • FIXME: Shape mismatch between DCM in PyRAI2md and default trajectory setup
  • Support reading SHARC netcdf output files

Profiling notes:

python -m cProfile ./shnitsel/cli/convert_to_shnitsel.py tutorials/test_data/sharc/iconds_butene/ -o tutorials/test_data/playground/iconds_butene.nc -c butene -est bravo -basis gulasch -log debug > tutorials/test_data/playground/iconds_butene.profile.log python -m cProfile ./shnitsel/cli/convert_to_shnitsel.py tutorials/test_data/playground/C02_sc-mCy_C4N2H9/init -o tutorials/test_data/playground/C02_sc-mCy_C4N2H9.nc -c C02 -est bravo -basis gulasch -log debug > tutorials/test_data/playground/C02.profile.log python -m cProfile ./shnitsel/cli/convert_to_shnitsel.py tutorials/test_data/playground/C01_sc-Cy_C3N2H7/init -o tutorials/test_data/playground/C01_sc-Cy_C3N2H7.nc -c C01 -est bravo -basis gulasch -log debug > tutorials/test_data/playground/C02.profile.log