migrate python scripts #59
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This was referenced Dec 22, 2023
lpardey
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lpardey
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ggutierrez-sunbright
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* add numpy and openbabel as requirements * add files to ignore * refactor to python3 and add typing for superpose3D, squared_distance and rmsd functions * add typing for coordinates add and refactor map_to_crystal function * add parseArguments function with type annotations * update variable and function names add update_coordinates function with type annotations * add get_automorphism_RMSD function with type annotations * add save_molecule_with_RMSD function with type annotation * refactor superpose_3D function * update save_molecule_with_rmsd: remove unnecessary condition add main function * add aligned-fit sdf test file * add aligned-nofit sdf test file * add input sdf test file * add ref sdf test file * add conftest with fixtures folder path as constant * add sdrms conftest file * add aligned molecules raw data fixture * add aligned fit molecule raw data fixture * add integration tests * code formatting * add aligned_nofit_filename and aligned_fit_filename fixtures * add testing comparison functions for molecules: - atoms_are_equal - molecules_are_equal - compare_sdf_files * extract parser to its own file * add sdrmsd script package to pyproject.toml * update github actions workflow for rdock-utils - add ruff - remove flake, black, isort - add pytest * add dynamic dependencies to pyproject.toml * remove unnecessary docstrings * add old sdrmrsd to be execute as script * lint and typing
ggutierrez-sunbright
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Jan 25, 2024
ggutierrez-sunbright
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* add numpy and openbabel as requirements * add files to ignore * refactor to python3 and add typing for superpose3D, squared_distance and rmsd functions * add typing for coordinates add and refactor map_to_crystal function * add parseArguments function with type annotations * update variable and function names add update_coordinates function with type annotations * add get_automorphism_RMSD function with type annotations * add save_molecule_with_RMSD function with type annotation * refactor superpose_3D function * update save_molecule_with_rmsd: remove unnecessary condition add main function * add aligned-fit sdf test file * add aligned-nofit sdf test file * add input sdf test file * add ref sdf test file * add conftest with fixtures folder path as constant * add sdrms conftest file * add aligned molecules raw data fixture * add aligned fit molecule raw data fixture * add integration tests * code formatting * add aligned_nofit_filename and aligned_fit_filename fixtures * add testing comparison functions for molecules: - atoms_are_equal - molecules_are_equal - compare_sdf_files * extract parser to its own file * add sdrmsd script package to pyproject.toml * update github actions workflow for rdock-utils - add ruff - remove flake, black, isort - add pytest * add dynamic dependencies to pyproject.toml * remove unnecessary docstrings * add old sdrmrsd to be execute as script * lint and typing
ggutierrez-sunbright
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Jan 27, 2024
lpardey
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ggutierrez-sunbright
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* extract superpose3d and type modules to a common package * add sdtether to project scritps * add parser module * add sdtether * add main file * migrate update_coordinates method to common package * add fixture data for testing sdtether * fix sdtether original argument parsing * add basic test for sdtether * refactor rmsd method update typing squared_distance method is not necessary anymore * refactor superpose3d: modified the class interface and fix several bugs class works with sdrmsd and sdtether as well * refactor: - remove _get_ref_matches_align_data, match_to_mask and get_matches functions. - add show_matches_info function - add ref_mol, ref_matches and ref_align_data as instance attributes - update run, process_molecule and write_aligned_molecule functions * add test_get_centroid for superposer3d module * fix mypy * add show_mol_mathches_info feature * add skipped molecule logger info on process_molecule method --------- Co-authored-by: ggutierrez-sunbright <94693768+ggutierrez-sunbright@users.noreply.github.com>
lpardey
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