useful_rdkit_utils 2.0.1 Documentation

A motley collection of useful RDKit functions.

Getting Started

• Installation
  • Extras
  • Running the tests
• Command Line Tools
  • build_ring_dictionary
  • silly_walks

API Reference

• REOS
  • REOS
• Ring Systems
  • RingSystemFinder
  • RingSystemLookup
  • test_ring_system_finder()
  • create_ring_dictionary()
  • build_ring_systems_dataframe()
  • test_ring_system_lookup()
  • get_min_ring_frequency()
  • get_spiro_atoms()
  • max_ring_size()
  • ring_stats()
• Fingerprints and Descriptors
  • Smi2Fp
  • mol2morgan_fp()
  • smi2morgan_fp()
  • mol2numpy_fp()
  • smi2numpy_fp()
  • RDKitDescriptors
  • clean_descriptors()
  • scale_descriptors()
  • clean_and_scale_descriptors()
  • RDKitProperties
  • Ro5Calculator
  • plot_properties()
  • compare_datasets()
• Descriptor Preprocessor
  • DescriptorPreprocessor
• Scaffold Finder
  • cleanup_fragment()
  • generate_fragments()
  • find_scaffolds()
  • get_molecules_with_scaffold()
• Silly Walks
• Cross-validation and data splitting
  • GroupKFoldShuffle
  • get_scaffold()
  • get_random_clusters()
  • get_butina_clusters()
  • get_bemis_murcko_clusters()
  • get_kmeans_clusters()
  • cross_validate()
• Reactions
  • enumerate_library()
  • enumerate_library_sample()
• Molecular Geometry
  • get_center()
  • get_shape_moments()
  • gen_3d()
  • gen_conformers()
  • refine_conformers()
  • get_conformer_energies()
  • mcs_rmsd()
  • mol_to_3D_view()
• Miscellaneous Utilities
  • smi2mol_with_errors()
  • count_fragments()
  • get_largest_fragment()
  • taylor_butina_clustering()
  • label_atoms()
  • tag_atoms()
  • rd_shut_the_hell_up()
  • demo_block_logs()
  • boxplot_base64_image()
  • mol_to_base64_image()
  • smi_to_base64_image()
  • remove_dummy_atoms()
  • align_mols_to_template()
  • mcs_align()
• Jupyter
  • rd_setup_jupyter()
  • rd_enable_svg()
  • rd_enable_png()
  • rd_set_image_size()
  • rd_make_structures_pretty()
  • rd_show_cip_stereo()
  • rd_show_atom_indices()
• Pandas
  • value_counts_df()
  • add_molecule_and_errors()
  • split_dataframe()
• Seaborn
  • set_sns_defaults()
  • set_sns_size()
• Stats
  • bootstrap_confidence_interval()
  • pearson_confidence()
  • max_possible_correlation()
• Units
  • get_unit_multiplier()
  • ki_to_kcal()
  • kcal_to_ki()
  • ug_ml_to_uM()
• SALI
  • calculate_sali()
  • plot_sali_pairs()
• Model Comparison
  • WrapperFactory
  • get_performance_stats()
  • make_tukey_plot()
  • plot_r2_mae()
  • plot_tukey_stats()
• Optional
  • get_t_sne_clusters()
  • get_umap_clusters()

Indices and Tables

• Index

• Module Index

• Search Page