Index

_

__init__() (mkt.databases.aligners.BioAligner method), [1], [2] (mkt.databases.aligners.BL2UniProtAligner method), [1], [2] (mkt.databases.aligners.ClustalOmegaAligner method), [1], [2] (mkt.databases.aligners.CustomAligner method) (mkt.databases.aligners.Kincore2UniProtAligner method), [1], [2] (mkt.databases.alphafold.AlphaFoldPrediction method) (mkt.databases.alphafold.AlphaFoldStructure method) (mkt.databases.api_schema.APIClient method), [1], [2] (mkt.databases.api_schema.APIKeyRESTAPIClient method) (mkt.databases.api_schema.APIKeySwaggerClient method) (mkt.databases.api_schema.GraphQLClient method), [1], [2] (mkt.databases.api_schema.RESTAPIClient method) (mkt.databases.api_schema.SwaggerAPIClient method) (mkt.databases.app.properties.PropertyTables method), [1], [2] (mkt.databases.app.schema.DefaultConfig method), [1], [2] (mkt.databases.app.schema.KLIFSAdaptiveConfig method), [1], [2] (mkt.databases.app.schema.KLIFSConfig method), [1], [2] (mkt.databases.app.schema.KLIFSCustomConfig method), [1], [2] (mkt.databases.app.schema.KLIFSImportantConfig method), [1], [2] (mkt.databases.app.schema.KLIFSPathogenicConfig method), [1], [2] (mkt.databases.app.schema.KLIFSRegionLabelConfig method), [1], [2] (mkt.databases.app.schema.MutationsConfig method), [1], [2] (mkt.databases.app.schema.MutationsDefaultConfig method), [1], [2] (mkt.databases.app.schema.MutationsGroupConfig method), [1], [2] (mkt.databases.app.schema.MutationsKLIFSConfig method), [1], [2] (mkt.databases.app.schema.PhosphositesConfig method), [1], [2] (mkt.databases.app.schema.StandardConfig method) (mkt.databases.app.schema.StandardConfigChoice method) (mkt.databases.app.schema.StructureConfig method), [1], [2] (mkt.databases.app.sequences.SequenceAlignment method) (mkt.databases.app.structures.StructureVisualizer method), [1], [2] (mkt.databases.cancer_hotspots.CancerHotspots method) (mkt.databases.cancer_hotspots.CancerHotspotsQuery method) (mkt.databases.cancer_hotspots.HotspotTier method) (mkt.databases.cancer_hotspots.HotspotVersion method) (mkt.databases.cbioportal.cBioPortal method), [1], [2] (mkt.databases.cbioportal.cBioPortalQuery method), [1], [2] (mkt.databases.cbioportal.Clinical method), [1], [2] (mkt.databases.cbioportal.ClinicalPatient method), [1], [2] (mkt.databases.cbioportal.ClinicalSample method), [1], [2] (mkt.databases.cbioportal.GenePanel method), [1], [2] (mkt.databases.cbioportal.KinaseMissenseMutations method), [1], [2] (mkt.databases.cbioportal.Mutations method), [1], [2] (mkt.databases.cbioportal.PanelData method), [1], [2] (mkt.databases.cbioportal.StudyData method), [1], [2] (mkt.databases.cbioportal.Treatment method), [1], [2] (mkt.databases.chembl.ChEMBL method), [1], [2] (mkt.databases.chembl.ChEMBLMolecule method), [1], [2] (mkt.databases.chembl.ChEMBLMoleculeExact method), [1], [2] (mkt.databases.chembl.ChEMBLMoleculePreferred method), [1], [2] (mkt.databases.chembl.ChEMBLMoleculeSearch method), [1], [2] (mkt.databases.colors.AminoAcidPalette method) (mkt.databases.conservation._HandlerRoundedBox method) (mkt.databases.conservation.KLIFSConservationTreeFigure method) (mkt.databases.conservation.KLIFSDisplayLeaf method), [1], [2] (mkt.databases.conservation.KLIFSDisplaySplit method), [1], [2] (mkt.databases.conservation.KLIFSDisplayTree method), [1], [2] (mkt.databases.conservation.KLIFSHierarchicalConservation method) (mkt.databases.conservation.KLIFSResidueDotApp method) (mkt.databases.conservation.KLIFSTreeConservationApp method) (mkt.databases.datasets.discoverx.DiscoverXInfo method) (mkt.databases.datasets.discoverx.DiscoverXInfoGenerator method), [1], [2] (mkt.databases.hgnc.HGNC method), [1], [2] (mkt.databases.kinase_schema.KinaseInfoGenerator method) (mkt.databases.kinase_schema.KinaseInfoKinaseDomainGenerator method) (mkt.databases.kinase_schema.KinaseInfoUniProtGenerator method) (mkt.databases.klifs.KinaseInfo method), [1], [2] (mkt.databases.klifs.KinaseNames method), [1], [2] (mkt.databases.klifs.KLIFS method), [1], [2] (mkt.databases.klifs.KLIFSPocket method), [1], [2] (mkt.databases.ncbi.ProteinEntrez method) (mkt.databases.ncbi.ProteinNCBI method) (mkt.databases.oncokb.OncoKB method), [1], [2] (mkt.databases.oncokb.OncoKBCancerGeneList method), [1], [2] (mkt.databases.oncokb.OncoKBInfo method) (mkt.databases.oncokb.OncoKBProteinChange method), [1], [2] (mkt.databases.oncotree.OncoTree method) (mkt.databases.open_targets.OpenTargets method), [1], [2] (mkt.databases.open_targets.OpenTargetsDrugMoA method), [1], [2] (mkt.databases.pfam.Pfam method), [1], [2] (mkt.databases.plot.SequenceAlignment method) (mkt.databases.plot_config.CladeMembershipTableConfig method), [1], [2] (mkt.databases.plot_config.ColKinaseColorConfig method), [1], [2] (mkt.databases.plot_config.ConservationTreeConfig method), [1], [2] (mkt.databases.plot_config.ConservationTreeExplorerConfig method), [1], [2] (mkt.databases.plot_config.DataSourceConfig method), [1], [2] (mkt.databases.plot_config.DictKinaseFiguresConfig method), [1], [2] (mkt.databases.plot_config.DynamicRangePlotConfig method), [1], [2] (mkt.databases.plot_config.FamilyColorConfig method), [1], [2] (mkt.databases.plot_config.MatplotlibRCConfig method), [1], [2] (mkt.databases.plot_config.MetricsBoxplotConfig method), [1], [2] (mkt.databases.plot_config.OutputConfig method), [1], [2] (mkt.databases.plot_config.PlotDatasetConfig method), [1], [2] (mkt.databases.plot_config.RegionGapViolinConfig method), [1], [2] (mkt.databases.plot_config.ResidueDotConfig method), [1], [2] (mkt.databases.plot_config.ResidueDotExplorerConfig method), [1], [2] (mkt.databases.plot_config.RidgelinePlotConfig method), [1], [2] (mkt.databases.plot_config.SequenceSchematicConfig method), [1], [2] (mkt.databases.plot_config.StackedBarchartConfig method), [1], [2] (mkt.databases.plot_config.UpsetPlotConfig method), [1], [2] (mkt.databases.plot_config.VennDiagramConfig method), [1], [2] (mkt.databases.protvar.ProtvarScoreQuery method) (mkt.databases.protvar.ProtvarVariant method) (mkt.databases.protvar.ScoreDatabase method) (mkt.databases.pssm.SubstitutionPseudocounts method), [1], [2] (mkt.databases.pymol.PyMOLGenerator method), [1], [2] (mkt.databases.sasa.BaseSASAConfig method), [1], [2] (mkt.databases.sasa.BioPythonHeavyConfig method), [1], [2] (mkt.databases.sasa.BioPythonHydrogenConfig method), [1], [2] (mkt.databases.sasa.CrossValidationConfig method), [1], [2] (mkt.databases.sasa.CrossValidationHydrogenConfig method), [1], [2] (mkt.databases.sasa.PyMOLHeavyConfig method), [1], [2] (mkt.databases.sasa.PyMOLHydrogenConfig method), [1], [2] (mkt.databases.sasa.ResidueSASA method) (mkt.databases.sasa.StandardSASAConfigChoice method) (mkt.databases.sasa.StandardSASAConfigs method) (mkt.databases.three_d_hotspots.HotspotClass method) (mkt.databases.three_d_hotspots.ThreeDHotspots method) (mkt.databases.uniprot.UniProt method), [1], [2] (mkt.databases.uniprot.UniProtFASTA method), [1], [2] (mkt.databases.uniprot.UniProtJSON method), [1], [2] (mkt.databases.uniprot.UniProtRefSeqProteinGET method), [1], [2] (mkt.schema.conservation_schema.KLIFSConservationData method) (mkt.schema.kinase_schema.Family method) (mkt.schema.kinase_schema.Group method) (mkt.schema.kinase_schema.KinaseDomainName method) (mkt.schema.kinase_schema.KinaseInfo method) (mkt.schema.kinase_schema.KinaseInfoKinaseDomain method) (mkt.schema.kinase_schema.KinaseInfoUniProt method) (mkt.schema.kinase_schema.KinCore method) (mkt.schema.kinase_schema.KinCoreCIF method) (mkt.schema.kinase_schema.KinCoreFASTA method) (mkt.schema.kinase_schema.KinHub method) (mkt.schema.kinase_schema.KLIFS method) (mkt.schema.kinase_schema.MSASource method) (mkt.schema.kinase_schema.Pfam method) (mkt.schema.kinase_schema.TemplateSource method) (mkt.schema.kinase_schema.UniProt method)

_aggregate_singletons() (mkt.databases.conservation.KLIFSHierarchicalConservation method), [1] _annotate() (mkt.databases.cancer_hotspots.CancerHotspots method), [1] _annotation_callouts() (mkt.databases.conservation.KLIFSHierarchicalConservation method), [1] _annotation_lines() (mkt.databases.conservation.KLIFSHierarchicalConservation method), [1] _assemble_sasa_df() (in module mkt.databases.sasa), [1] _blosum_distance_matrix() (mkt.databases.conservation.KLIFSHierarchicalConservation method), [1] _build_align_to_klifs_mapping() (mkt.databases.app.schema.KLIFSRegionLabelConfig method), [1] _build_klifs_panel() (in module mkt.databases.conservation), [1] _build_level_code_map() (mkt.databases.oncotree.OncoTree method), [1] _build_summary_panel() (mkt.databases.conservation.KLIFSConservationTreeFigure method), [1] _build_target_probs() (mkt.databases.pssm.SubstitutionPseudocounts method), [1] _build_variants() (mkt.databases.protvar.ProtvarScoreQuery method), [1] _coerce_database() (in module mkt.databases.protvar), [1] _collect_region_gap_specs() (in module mkt.databases.plot), [1] _collect_region_map_extras() (in module mkt.databases.plot), [1] _column_stack() (mkt.databases.conservation.KLIFSResidueDotApp method), [1] _compute_kinase_sasa() (in module mkt.databases.sasa), [1] _compute_params() (mkt.databases.sasa.ResidueSASA method), [1] _conservation_cache (in module mkt.schema.io_utils) _conserved_columns() (mkt.databases.conservation.KLIFSHierarchicalConservation method), [1] _convert_color_to_hex() (mkt.databases.pymol.PyMOLGenerator method), [1] _convert_fasta2seq() (mkt.databases.uniprot.UniProtFASTA static method), [1] _convert_mmcifdict2structure() (mkt.databases.app.structures.StructureVisualizer method), [1] _convert_structure2string() (mkt.databases.app.structures.StructureVisualizer method), [1] _dominant_color() (mkt.databases.conservation.KLIFSConservationTreeFigure method), [1] _dot_style() (mkt.databases.conservation.KLIFSResidueDotApp method), [1] _download_cif() (mkt.databases.alphafold.AlphaFoldStructure method), [1] _draw_dendrogram() (mkt.databases.conservation.KLIFSConservationTreeFigure method), [1] _draw_map_block() (in module mkt.databases.plot), [1] _draw_map_connector() (in module mkt.databases.plot), [1] _draw_name_boxes() (mkt.databases.conservation.KLIFSConservationTreeFigure method), [1] _draw_region_gap_violin_panel() (in module mkt.databases.plot), [1] _draw_sequence_strip() (in module mkt.databases.plot), [1] _draw_table() (mkt.databases.conservation.KLIFSConservationTreeFigure method), [1] _draw_uniprot_klifs_map() (in module mkt.databases.plot), [1] _drop_pseudokinases() (mkt.databases.conservation.KLIFSHierarchicalConservation method), [1] _encode_pockets() (mkt.databases.conservation.KLIFSHierarchicalConservation method), [1] _extract_list_from_hgnc_response_docs() (mkt.databases.hgnc.HGNC static method), [1] _family_label() (mkt.databases.conservation.KLIFSHierarchicalConservation method), [1] _family_name() (mkt.databases.conservation.KLIFSHierarchicalConservation static method), [1] _family_types() (mkt.databases.conservation.KLIFSTreeConservationApp method), [1] _filter_mutations_to_klifs() (mkt.databases.app.schema.MutationsConfig method), [1] _flatten_on_white() (in module mkt.databases.plot), [1] _format_property_value() (mkt.databases.app.properties.PropertyTables static method), [1] _generate_highlight_idx() (mkt.databases.app.structures.StructureVisualizer method), [1] _generate_key_set_hgnc_response_docs() (mkt.databases.hgnc.HGNC static method), [1] _generate_list_idx_from_dict_align_with_attr() (mkt.databases.app.schema.StructureConfig method), [1] _get_color_and_style_mapping() (mkt.databases.pymol.PyMOLGenerator method), [1] _get_klifs_label() (mkt.databases.app.schema.MutationsConfig method), [1] _get_klifs_position_colors() (in module mkt.databases.plot), [1] _get_klifs_uniprot_mapping() (mkt.databases.app.schema.MutationsConfig static method), [1] _get_klifs_uniprot_positions() (mkt.databases.app.schema.MutationsConfig static method), [1] _get_uniprot_label() (mkt.databases.app.schema.MutationsConfig method), [1] _group_legend_handles() (mkt.databases.conservation.KLIFSConservationTreeFigure method), [1] _HandlerRoundedBox (class in mkt.databases.conservation), [1] _henikoff_weights() (mkt.databases.conservation.KLIFSHierarchicalConservation method), [1] _hover_families() (mkt.databases.conservation.KLIFSHierarchicalConservation method), [1] _identity_distance_matrix() (mkt.databases.conservation.KLIFSHierarchicalConservation method), [1] _index_mutation_region() (mkt.databases.app.schema.MutationsConfig method), [1] _index_stick_region() (mkt.databases.app.schema.KLIFSConfig method), [1] _is_kept() (mkt.databases.conservation.KLIFSHierarchicalConservation method), [1] _kinome_background() (mkt.databases.conservation.KLIFSHierarchicalConservation method), [1] _KLIFS_PANEL (in module mkt.databases.conservation) _klifs_uniprot_idx_bounds() (mkt.schema.kinase_schema.KinaseInfo method), [1] _leaf_groups() (mkt.databases.conservation.KLIFSConservationTreeFigure method), [1] _load() (mkt.databases.oncotree.OncoTree method), [1] (mkt.databases.three_d_hotspots.ThreeDHotspots method), [1] _map_aligned_to_klifs_colors() (in module mkt.databases.plot), [1] _map_group_klifs_to_uniprot() (mkt.databases.app.schema.MutationsConfig method), [1] _map_single_alignment() (mkt.databases.app.sequences.SequenceAlignment static method), [1] _member_style() (mkt.databases.conservation.KLIFSHierarchicalConservation method), [1] _nodelist() (mkt.databases.conservation.KLIFSHierarchicalConservation method), [1] _parse_ragged_tsv() (mkt.databases.oncotree.OncoTree static method), [1] _parse_start_end_values() (mkt.databases.app.sequences.SequenceAlignment method), [1] _partition_key() (mkt.databases.conservation.KLIFSConservationTreeFigure method), [1] _plot_conservation_tree() (in module mkt.databases.cli.plot_dict_kinase), [1] _plot_conservation_tree_explorer() (in module mkt.databases.cli.plot_dict_kinase), [1] _plot_region_gap_violin() (in module mkt.databases.cli.plot_dict_kinase), [1] _plot_residue_dot() (in module mkt.databases.cli.plot_dict_kinase), [1] _plot_residue_dot_explorer() (in module mkt.databases.cli.plot_dict_kinase), [1] _plot_upset() (in module mkt.databases.cli.plot_dict_kinase), [1] _precompute_aa_data() (mkt.databases.conservation.KLIFSResidueDotApp method), [1] _preprocess_mutation_dict() (mkt.databases.app.schema.MutationsConfig method), [1] _pseudocount_model() (mkt.databases.conservation.KLIFSHierarchicalConservation method), [1] _pymol_available() (mkt.databases.sasa.ResidueSASA static method), [1] _read_bytes() (mkt.databases.three_d_hotspots.ThreeDHotspots static method), [1] _read_text() (mkt.databases.oncotree.OncoTree static method), [1] _reconcile_kd_bound_with_klifs() (mkt.schema.kinase_schema.KinaseInfo method), [1] _region_map_segments() (in module mkt.databases.plot), [1] _render_panel() (mkt.databases.conservation.KLIFSConservationTreeFigure method), [1] _repair_camkk1_pocket() (in module mkt.databases.conservation), [1] _residue_sasa_biopython() (in module mkt.databases.sasa), [1] _residue_sasa_pymol() (in module mkt.databases.sasa), [1] _resolve_methods() (mkt.databases.sasa.ResidueSASA method), [1] _resolve_n_workers() (mkt.databases.sasa.ResidueSASA method), [1] _resolve_source() (mkt.databases.oncotree.OncoTree method), [1] (mkt.databases.three_d_hotspots.ThreeDHotspots method), [1] _run_tasks() (mkt.databases.sasa.ResidueSASA method), [1] _sasa_task() (in module mkt.databases.sasa), [1] _split_index() (mkt.databases.conservation.KLIFSConservationTreeFigure method), [1] _stamp_from_response() (mkt.databases.api_schema.APIClient method), [1] _stamp_now() (mkt.databases.api_schema.APIClient method), [1] _strip_hydrogens() (in module mkt.databases.sasa), [1] _table_consensus() (mkt.databases.conservation.KLIFSConservationTreeFigure method), [1] _to_dataframe() (mkt.databases.cancer_hotspots.CancerHotspotsQuery static method), [1] _uniprot_index_at() (mkt.databases.conservation.KLIFSHierarchicalConservation method), [1] _validate_config() (mkt.databases.sasa.ResidueSASA method), [1] _walk_node() (mkt.databases.conservation.KLIFSHierarchicalConservation method), [1] _write_clade_membership_table() (in module mkt.databases.cli.plot_dict_kinase), [1]

A

AA_MAPPING (in module mkt.databases.colors), [1] ABC1 (mkt.schema.kinase_schema.Family attribute), [1] accession (mkt.databases.datasets.discoverx.DiscoverXInfo attribute), [1] (mkt.databases.ncbi.ProteinEntrez attribute), [1] (mkt.databases.ncbi.ProteinNCBI attribute), [1] activeAF2 (mkt.schema.kinase_schema.TemplateSource attribute), [1] activePDB (mkt.schema.kinase_schema.TemplateSource attribute), [1] add_logging_flags() (in module mkt.databases.log_config), [1] add_one_hot_encoding_to_dataframe() (in module mkt.databases.utils), [1] add_retry_to_session() (in module mkt.databases.requests_wrapper), [1] adjudicate_group() (mkt.schema.kinase_schema.KinaseInfo method), [1] adjudicate_kd_end() (mkt.schema.kinase_schema.KinaseInfo method), [1] adjudicate_kd_sequence() (mkt.schema.kinase_schema.KinaseInfo method), [1] adjudicate_kd_start() (mkt.schema.kinase_schema.KinaseInfo method), [1] adjudicate_kinase_group() (in module mkt.schema.utils), [1] adjudicate_preferred_name() (mkt.databases.chembl.ChEMBLMolecule method), [1] adjudicate_prefix() (in module mkt.databases.oncokb), [1] AGC (mkt.schema.kinase_schema.Group attribute), [1] aggregate_df_by_col_set() (in module mkt.databases.utils), [1] Align (mkt.databases.aligners.BioAligner attribute), [1] align() (mkt.databases.aligners.BioAligner method), [1] (mkt.databases.aligners.ClustalOmegaAligner method), [1] (mkt.databases.aligners.CustomAligner method), [1] align_inter_intra_region() (in module mkt.databases.kinase_schema), [1] align_kincore2uniprot() (in module mkt.databases.kincore), [1] align_klifs_pocket_to_uniprot_seq() (mkt.databases.klifs.KLIFSPocket method), [1] alpha (mkt.databases.plot_config.DynamicRangePlotConfig attribute), [1]

Alpha (mkt.schema.kinase_schema.Family attribute), [1] ALPHABET_PROJECT (mkt.databases.colors.AminoAcidPalette attribute), [1] AlphaFoldPrediction (class in mkt.databases.alphafold), [1] AlphaFoldStructure (class in mkt.databases.alphafold), [1] AlphaMissense (mkt.databases.protvar.ScoreDatabase attribute), [1] alteration (mkt.databases.oncokb.OncoKBProteinChange attribute), [1] amino_acid (mkt.databases.plot_config.ResidueDotConfig attribute), [1] AminoAcidPalette (class in mkt.databases.colors), [1] analyze_nodes() (mkt.databases.conservation.KLIFSHierarchicalConservation method), [1] ancestor_code_at_level() (mkt.databases.oncotree.OncoTree method), [1] annotate_highest_level() (mkt.databases.oncokb.OncoKBProteinChange method), [1] annotate_kinase_regions() (mkt.databases.cbioportal.KinaseMissenseMutations method), [1] annotation (mkt.databases.ncbi.ProteinNCBI attribute), [1] APIClient (class in mkt.databases.api_schema), [1] APIKeyRESTAPIClient (class in mkt.databases.api_schema), [1] APIKeySwaggerClient (class in mkt.databases.api_schema), [1] apply_matplotlib_rc() (in module mkt.databases.plot), [1] ARR_SWISSPROT_BG (in module mkt.databases.pssm), [1] as_rgb_dict() (mkt.databases.plot_config.ColKinaseColorConfig method), [1] ASAP (mkt.databases.colors.AminoAcidPalette attribute), [1] assign_properties() (mkt.databases.app.properties.PropertyTables method), [1] Atypical (mkt.schema.kinase_schema.Group attribute), [1] axes_labelsize (mkt.databases.plot_config.DynamicRangePlotConfig attribute), [1] axes_titlesize (mkt.databases.plot_config.DynamicRangePlotConfig attribute), [1] axis_label_fontsize (mkt.databases.plot_config.DynamicRangePlotConfig attribute), [1] axvline_color (mkt.databases.plot_config.DynamicRangePlotConfig attribute), [1] axvline_x (mkt.databases.plot_config.DynamicRangePlotConfig attribute), [1]

B

background (mkt.databases.pssm.SubstitutionPseudocounts attribute), [1] BANDLAMUDI (mkt.databases.cancer_hotspots.HotspotTier attribute), [1] (mkt.databases.cancer_hotspots.HotspotVersion attribute), [1] bar_alpha (mkt.databases.plot_config.StackedBarchartConfig attribute), [1] bar_edgecolor (mkt.databases.plot_config.StackedBarchartConfig attribute), [1] bar_linewidth (mkt.databases.plot_config.StackedBarchartConfig attribute), [1] baseline_alpha (mkt.databases.plot_config.RidgelinePlotConfig attribute), [1] baseline_linewidth (mkt.databases.plot_config.RidgelinePlotConfig attribute), [1] BaseSASAConfig (class in mkt.databases.sasa), [1] beta (mkt.databases.pssm.SubstitutionPseudocounts attribute), [1] bins (mkt.databases.plot_config.DynamicRangePlotConfig attribute), [1] BioAligner (class in mkt.databases.aligners), [1] BIOPYTHON_HEAVY (mkt.databases.sasa.StandardSASAConfigChoice attribute), [1] (mkt.databases.sasa.StandardSASAConfigs attribute), [1] BIOPYTHON_HYDROGEN (mkt.databases.sasa.StandardSASAConfigChoice attribute), [1] (mkt.databases.sasa.StandardSASAConfigs attribute), [1] BioPythonHeavyConfig (class in mkt.databases.sasa), [1] BioPythonHydrogenConfig (class in mkt.databases.sasa), [1] BL2UniProtAligner (class in mkt.databases.aligners), [1] blosum_name (mkt.databases.conservation.KLIFSConservationTreeFigure attribute) (mkt.databases.conservation.KLIFSHierarchicalConservation attribute), [1] (mkt.databases.conservation.KLIFSResidueDotApp attribute) (mkt.databases.conservation.KLIFSTreeConservationApp attribute) (mkt.schema.conservation_schema.KLIFSConservationData attribute), [1] bool_biopython (mkt.databases.sasa.BaseSASAConfig attribute), [1] (mkt.databases.sasa.BioPythonHeavyConfig attribute), [1] (mkt.databases.sasa.BioPythonHydrogenConfig attribute), [1] (mkt.databases.sasa.CrossValidationConfig attribute), [1] (mkt.databases.sasa.CrossValidationHydrogenConfig attribute), [1] (mkt.databases.sasa.PyMOLHeavyConfig attribute), [1] (mkt.databases.sasa.PyMOLHydrogenConfig attribute), [1] (mkt.databases.sasa.ResidueSASA attribute), [1] bool_gridplot (mkt.databases.plot.SequenceAlignment attribute), [1] bool_has_kd (mkt.databases.datasets.discoverx.DiscoverXInfo attribute), [1] bool_has_klifs (mkt.databases.datasets.discoverx.DiscoverXInfo attribute), [1] bool_include_hydrogens (mkt.databases.sasa.BaseSASAConfig attribute), [1] (mkt.databases.sasa.BioPythonHydrogenConfig attribute), [1] (mkt.databases.sasa.CrossValidationHydrogenConfig attribute), [1] (mkt.databases.sasa.PyMOLHydrogenConfig attribute), [1] (mkt.databases.sasa.ResidueSASA attribute), [1] bool_klifs (mkt.databases.app.sequences.SequenceAlignment attribute), [1] bool_klifs_only (mkt.databases.app.schema.MutationsConfig attribute), [1] (mkt.databases.app.schema.MutationsDefaultConfig attribute), [1] (mkt.databases.app.schema.MutationsGroupConfig attribute), [1] (mkt.databases.app.schema.MutationsKLIFSConfig attribute), [1] bool_mismatch (mkt.databases.app.sequences.SequenceAlignment attribute), [1] bool_mutations_by_group (mkt.databases.app.schema.MutationsConfig attribute), [1] (mkt.databases.app.schema.MutationsDefaultConfig attribute), [1] (mkt.databases.app.schema.MutationsGroupConfig attribute), [1] (mkt.databases.app.schema.MutationsKLIFSConfig attribute), [1]

bool_mutations_in_kd_region (mkt.databases.datasets.discoverx.DiscoverXInfo attribute), [1] bool_mutations_in_klifs_region (mkt.databases.datasets.discoverx.DiscoverXInfo attribute), [1] bool_mutations_in_klifs_residues (mkt.databases.datasets.discoverx.DiscoverXInfo attribute), [1] bool_offset (mkt.databases.datasets.discoverx.DiscoverXInfo attribute), [1] (mkt.databases.datasets.discoverx.DiscoverXInfoGenerator attribute), [1] (mkt.databases.kinase_schema.KinaseInfoGenerator attribute), [1] bool_pdf (mkt.databases.plot_config.OutputConfig attribute), [1] bool_png (mkt.databases.plot_config.OutputConfig attribute), [1] bool_prefix (mkt.databases.cbioportal.cBioPortalQuery attribute), [1] bool_pymol (mkt.databases.sasa.BaseSASAConfig attribute), [1] (mkt.databases.sasa.BioPythonHeavyConfig attribute), [1] (mkt.databases.sasa.BioPythonHydrogenConfig attribute), [1] (mkt.databases.sasa.CrossValidationConfig attribute), [1] (mkt.databases.sasa.CrossValidationHydrogenConfig attribute), [1] (mkt.databases.sasa.PyMOLHeavyConfig attribute), [1] (mkt.databases.sasa.PyMOLHydrogenConfig attribute), [1] (mkt.databases.sasa.ResidueSASA attribute), [1] bool_relative (mkt.databases.sasa.BaseSASAConfig attribute), [1] (mkt.databases.sasa.BioPythonHydrogenConfig attribute), [1] (mkt.databases.sasa.CrossValidationHydrogenConfig attribute), [1] (mkt.databases.sasa.PyMOLHydrogenConfig attribute), [1] (mkt.databases.sasa.ResidueSASA attribute), [1] bool_reverse (mkt.databases.app.sequences.SequenceAlignment attribute), [1] (mkt.databases.plot.SequenceAlignment attribute), [1] bool_sample (mkt.databases.cbioportal.Clinical attribute), [1] (mkt.databases.cbioportal.ClinicalPatient attribute), [1] (mkt.databases.cbioportal.ClinicalSample attribute), [1] bool_show_sticks (mkt.databases.app.schema.MutationsConfig attribute), [1] (mkt.databases.app.schema.MutationsGroupConfig attribute), [1] bool_svg (mkt.databases.plot_config.OutputConfig attribute), [1] bool_top (mkt.databases.plot.SequenceAlignment attribute), [1] bool_wt (mkt.databases.datasets.discoverx.DiscoverXInfo attribute), [1] bottom_adjust (mkt.databases.plot_config.RegionGapViolinConfig attribute), [1] (mkt.databases.plot_config.StackedBarchartConfig attribute), [1] box_alpha (mkt.databases.plot_config.MetricsBoxplotConfig attribute), [1] box_widths (mkt.databases.plot_config.MetricsBoxplotConfig attribute), [1] bracket_height_pct (mkt.databases.plot_config.MetricsBoxplotConfig attribute), [1] bracket_linewidth (mkt.databases.plot_config.MetricsBoxplotConfig attribute), [1] bracket_spacing_pct (mkt.databases.plot_config.MetricsBoxplotConfig attribute), [1] bracket_start_pct (mkt.databases.plot_config.MetricsBoxplotConfig attribute), [1] build_display_tree() (mkt.databases.conservation.KLIFSHierarchicalConservation method), [1] build_figure() (mkt.databases.conservation.KLIFSConservationTreeFigure method), [1] build_layout() (mkt.databases.conservation.KLIFSResidueDotApp method), [1] (mkt.databases.conservation.KLIFSTreeConservationApp method), [1] build_residue_dot_figure() (mkt.databases.conservation.KLIFSConservationTreeFigure method), [1] build_split_figures() (mkt.databases.conservation.KLIFSConservationTreeFigure method), [1]

C

call_bravado_function() (mkt.databases.klifs.KinaseInfo method), [1] CAMK (mkt.schema.kinase_schema.Group attribute), [1] CAMK1 (mkt.schema.kinase_schema.Family attribute), [1] CAMKL (mkt.schema.kinase_schema.Family attribute), [1] CancerHotspots (class in mkt.databases.cancer_hotspots), [1] CancerHotspotsQuery (class in mkt.databases.cancer_hotspots), [1] canonical_seq (mkt.schema.kinase_schema.UniProt attribute), [1] cap_color (mkt.databases.plot_config.MetricsBoxplotConfig attribute), [1] cap_intersection_ylim (mkt.databases.plot_config.UpsetPlotConfig attribute), [1] cap_linewidth (mkt.databases.plot_config.MetricsBoxplotConfig attribute), [1] cBioPortal (class in mkt.databases.cbioportal), [1] CBIOPORTAL_INSTANCE_VAR (in module mkt.databases.config) CBIOPORTAL_TOKEN_VAR (in module mkt.databases.config) cBioPortalQuery (class in mkt.databases.cbioportal), [1] CDK (mkt.schema.kinase_schema.Family attribute), [1] CDKL (mkt.schema.kinase_schema.Family attribute), [1] CHANG (mkt.databases.cancer_hotspots.HotspotTier attribute), [1] (mkt.databases.cancer_hotspots.HotspotVersion attribute), [1] change_wrong_klifs_pocket_seq() (mkt.databases.kinase_schema.KinaseInfoKinaseDomainGenerator method), [1] check_construct_boundaries() (mkt.databases.datasets.discoverx.DiscoverXInfo static method), [1] check_deletion_boundaries() (mkt.databases.datasets.discoverx.DiscoverXInfo static method), [1] check_entity_id() (mkt.databases.cbioportal.cBioPortalQuery method), [1] (mkt.databases.cbioportal.PanelData method), [1] (mkt.databases.cbioportal.StudyData method), [1] check_if_file_exists_then_load_dataframe() (in module mkt.databases.kinase_schema), [1] check_if_job_ready() (mkt.databases.uniprot.UniProtRefSeqProteinGET method), [1] check_molecular_brake_against_canonical() (mkt.schema.kinase_schema.KinaseInfo method), [1] check_molecules() (mkt.databases.chembl.ChEMBL method), [1] check_multimatch_str() (mkt.databases.datasets.discoverx.DiscoverXInfoGenerator method), [1] check_outdir_exists() (in module mkt.databases.io_utils), [1] check_region_of_mutation() (mkt.databases.datasets.discoverx.DiscoverXInfo method), [1] check_response() (mkt.databases.api_schema.APIClient static method), [1] check_species() (mkt.databases.klifs.KinaseInfo method), [1] ChEMBL (class in mkt.databases.chembl), [1] chembl_id (mkt.databases.open_targets.OpenTargetsDrugMoA attribute), [1] ChEMBLMolecule (class in mkt.databases.chembl), [1] ChEMBLMoleculeExact (class in mkt.databases.chembl), [1] ChEMBLMoleculePreferred (class in mkt.databases.chembl), [1] ChEMBLMoleculeSearch (class in mkt.databases.chembl), [1] children (mkt.databases.conservation.KLIFSDisplaySplit attribute), [1] cif (mkt.schema.kinase_schema.KinCore attribute), [1] (mkt.schema.kinase_schema.KinCoreCIF attribute), [1] circle_alpha (mkt.databases.plot_config.VennDiagramConfig attribute), [1] CK1 (mkt.schema.kinase_schema.Family attribute), [1] (mkt.schema.kinase_schema.Group attribute), [1] clade_membership_table (mkt.databases.plot_config.DictKinaseFiguresConfig attribute), [1] CladeMembershipTableConfig (class in mkt.databases.plot_config), [1] classify_aa_change() (in module mkt.databases.properties), [1] clean_files_and_delete_directory() (in module mkt.schema.io_utils), [1] Clinical (class in mkt.databases.cbioportal), [1] ClinicalPatient (class in mkt.databases.cbioportal), [1] ClinicalSample (class in mkt.databases.cbioportal), [1] ClustalOmegaAligner (class in mkt.databases.aligners), [1] CLUSTALX (mkt.databases.colors.AminoAcidPalette attribute), [1] CLUSTER_EXCLUSIVE (mkt.databases.three_d_hotspots.HotspotClass attribute), [1] CMAP_CRITICAL_DEPTH (in module mkt.databases.colors), [1] CMGC (mkt.schema.kinase_schema.Group attribute), [1] CODE_RE (in module mkt.databases.oncotree), [1] col_kinase_colors (mkt.databases.plot_config.PlotDatasetConfig attribute), [1] ColKinaseColorConfig (class in mkt.databases.plot_config), [1] COLOR_CONSERVATION_PRIMARY (in module mkt.databases.colors), [1] COLOR_CONSERVATION_SECONDARY (in module mkt.databases.colors), [1] COLOR_CONSURF_UNGRADED (in module mkt.databases.colors), [1] COLOR_DARK_TEXT (in module mkt.databases.colors), [1] color_davis (mkt.databases.plot_config.DynamicRangePlotConfig attribute), [1] COLOR_DEPTH_NA (in module mkt.databases.colors), [1] COLOR_LOGO_BAR (in module mkt.databases.colors), [1] COLOR_LOGO_SUBTHRESHOLD (in module mkt.databases.colors), [1]

color_pkis2 (mkt.databases.plot_config.DynamicRangePlotConfig attribute), [1] COLOR_TREE_BREAK (in module mkt.databases.colors), [1] COLOR_TREE_FALLBACK (in module mkt.databases.colors), [1] COLOR_TREE_GUIDE (in module mkt.databases.colors), [1] COLOR_TREE_MIXED_FAMILY (in module mkt.databases.colors), [1] COLOR_TREE_NO_BREAK (in module mkt.databases.colors), [1] COLOR_TREE_PSEUDO (in module mkt.databases.colors), [1] COLOR_TREE_SPLIT_MARKER (in module mkt.databases.colors), [1] COLOR_TREE_TABLE_GAP (in module mkt.databases.colors), [1] COLOR_TREE_TABLE_NO_CONSENSUS (in module mkt.databases.colors), [1] column_conservation() (in module mkt.databases.pssm), [1] column_counts() (in module mkt.databases.pssm), [1] column_information() (mkt.databases.pssm.SubstitutionPseudocounts method), [1] column_information_content() (in module mkt.databases.pssm), [1] COLUMN_RENAME (in module mkt.databases.three_d_hotspots), [1] combine_kinaseinfo() (in module mkt.databases.kinase_schema), [1] combine_kinaseinfo_kd() (in module mkt.databases.kinase_schema), [1] combine_kinaseinfo_uniprot() (in module mkt.databases.kinase_schema), [1] compute_distance_matrix() (mkt.databases.conservation.KLIFSHierarchicalConservation method), [1] concatenate_csv_files_with_glob() (in module mkt.databases.io_utils), [1] concatenate_json_batches() (mkt.databases.uniprot.UniProtRefSeqProteinGET method), [1] configure_logging() (in module mkt.databases.log_config), [1] Conservation (mkt.databases.protvar.ScoreDatabase attribute), [1] conservation_threshold (mkt.databases.conservation.KLIFSConservationTreeFigure attribute) (mkt.databases.conservation.KLIFSHierarchicalConservation attribute), [1] (mkt.databases.conservation.KLIFSResidueDotApp attribute) (mkt.databases.conservation.KLIFSTreeConservationApp attribute) (mkt.schema.conservation_schema.KLIFSConservationData attribute), [1] conservation_tree (mkt.databases.plot_config.DictKinaseFiguresConfig attribute), [1] conservation_tree_explorer (mkt.databases.plot_config.DictKinaseFiguresConfig attribute), [1] ConservationTreeConfig (class in mkt.databases.plot_config), [1] ConservationTreeExplorerConfig (class in mkt.databases.plot_config), [1] construct_unaligned (mkt.databases.plot_config.ColKinaseColorConfig attribute), [1] consurf_grade_boundaries() (in module mkt.databases.pssm), [1] consurf_grades() (in module mkt.databases.pssm), [1] convert_api_query_to_dataframe() (mkt.databases.cbioportal.cBioPortalQuery method), [1] convert_color_to_hex() (in module mkt.databases.app.utils), [1] convert_df2dictobj() (in module mkt.databases.kinase_schema), [1] convert_from_percentile() (in module mkt.databases.plot), [1] convert_input2list() (in module mkt.databases.utils), [1] convert_log_and_truncate() (mkt.databases.cbioportal.KinaseMissenseMutations static method), [1] convert_mmcifdict2structure() (in module mkt.databases.utils), [1] convert_property2dataframe() (mkt.databases.app.properties.PropertyTables method), [1] convert_refseq2uniprot_mutations() (mkt.databases.datasets.discoverx.DiscoverXInfo method), [1] convert_str2family() (in module mkt.databases.kinase_schema), [1] convert_str2list() (in module mkt.databases.io_utils), [1] convert_structure2string() (in module mkt.databases.utils), [1] convert_to_family() (in module mkt.databases.kinase_schema), [1] convert_to_group() (in module mkt.databases.kinase_schema), [1] convert_to_percentile() (in module mkt.databases.plot), [1] convert_uniprot2refseq_klifs_residues() (mkt.databases.datasets.discoverx.DiscoverXInfo method), [1] cophenetic_correlation() (mkt.databases.conservation.KLIFSHierarchicalConservation method), [1] count_label_fontsize (mkt.databases.plot_config.UpsetPlotConfig attribute), [1] create_artists() (mkt.databases.conservation._HandlerRoundedBox method), [1] create_coldatasource() (mkt.databases.plot.SequenceAlignment method), [1] create_query_url() (mkt.databases.ncbi.ProteinNCBI method), [1] (mkt.databases.protvar.ProtvarScoreQuery method), [1] create_strsplit_list() (in module mkt.databases.utils), [1] create_structure_visualizer() (in module mkt.databases.app.utils), [1] create_tar_without_metadata() (in module mkt.databases.io_utils), [1] critical_depth() (mkt.databases.conservation.KLIFSHierarchicalConservation method), [1] CROSS_VALIDATION (mkt.databases.sasa.StandardSASAConfigChoice attribute), [1] (mkt.databases.sasa.StandardSASAConfigs attribute), [1] CROSS_VALIDATION_HYDROGEN (mkt.databases.sasa.StandardSASAConfigChoice attribute), [1] (mkt.databases.sasa.StandardSASAConfigs attribute), [1] CrossValidationConfig (class in mkt.databases.sasa), [1] CrossValidationHydrogenConfig (class in mkt.databases.sasa), [1] CustomAligner (class in mkt.databases.aligners), [1]

D

DAPK (mkt.schema.kinase_schema.Family attribute), [1] data_sources (mkt.databases.plot_config.PlotDatasetConfig attribute), [1] DataSourceConfig (class in mkt.databases.plot_config), [1] davis_csv (mkt.databases.plot_config.DataSourceConfig attribute), [1] DEFAULT (mkt.databases.app.schema.StandardConfig attribute), [1] (mkt.databases.app.schema.StandardConfigChoice attribute), [1] default_aa (mkt.databases.conservation.KLIFSResidueDotApp attribute), [1] (mkt.databases.plot_config.ResidueDotExplorerConfig attribute), [1] DEFAULT_DOT_DENSITY (in module mkt.databases.sasa), [1] DEFAULT_FILENAME (in module mkt.databases.oncotree), [1] (in module mkt.databases.three_d_hotspots), [1] DEFAULT_N_POINTS (in module mkt.databases.sasa), [1] DEFAULT_NULL_COLOR (in module mkt.databases.colors), [1] DEFAULT_PROBE_RADIUS (in module mkt.databases.sasa), [1] DEFAULT_URL (in module mkt.databases.oncotree), [1] (in module mkt.databases.three_d_hotspots), [1] DefaultConfig (class in mkt.databases.app.schema), [1] depth (mkt.databases.conservation.KLIFSDisplaySplit attribute), [1] deserialize_kinase_dict() (in module mkt.schema.io_utils), [1] df (mkt.databases.cancer_hotspots.CancerHotspots property), [1] (mkt.databases.datasets.discoverx.DiscoverXInfoGenerator attribute), [1] (mkt.databases.oncokb.OncoKBCancerGeneList property), [1] (mkt.databases.oncotree.OncoTree property), [1] (mkt.databases.sasa.ResidueSASA property), [1] (mkt.databases.three_d_hotspots.ThreeDHotspots property), [1] df_id (mkt.databases.datasets.discoverx.DiscoverXInfoGenerator attribute), [1] df_kincore (mkt.databases.app.properties.PropertyTables attribute), [1] df_kinhub (mkt.databases.app.properties.PropertyTables attribute), [1] df_klifs (mkt.databases.app.properties.PropertyTables attribute), [1] diagonal_is_similarity (mkt.schema.conservation_schema.KLIFSConservationData attribute), [1] DICT_AA20_INDEX (in module mkt.databases.pssm), [1] DICT_AA_CHANGES (in module mkt.databases.properties), [1] DICT_AA_PROPERTIES (in module mkt.databases.properties), [1] DICT_BIOCHEM_PROP_COLORS (in module mkt.databases.colors), [1] DICT_CLADE_ANCHORS (in module mkt.schema.conservation_schema), [1] DICT_CLASS_KEY (in module mkt.databases.protvar), [1] dict_code_color (mkt.databases.oncotree.OncoTree property), [1] DICT_CODE_COLOR_OVERRIDE (in module mkt.databases.oncotree), [1] dict_code_metacolor (mkt.databases.oncotree.OncoTree property), [1] dict_code_name (mkt.databases.oncotree.OncoTree property), [1] DICT_COL2OBJ_ORIG (in module mkt.databases.kinase_schema), [1] DICT_COL2OBJ_REV (in module mkt.databases.kinase_schema), [1] dict_color (mkt.databases.app.sequences.SequenceAlignment attribute), [1] DICT_COLOR_CATEGORY (in module mkt.databases.oncotree), [1] DICT_COLOR_MAP (in module mkt.databases.pymol), [1] DICT_COLORS (in module mkt.databases.colors), [1] dict_colors (mkt.databases.plot.SequenceAlignment attribute), [1] (mkt.databases.plot_config.UpsetPlotConfig attribute), [1] DICT_COLUMNS (in module mkt.databases.cancer_hotspots), [1] dict_construct_sequences (mkt.databases.datasets.discoverx.DiscoverXInfo attribute), [1] DICT_CONSURF_GRADE_BANDS (in module mkt.schema.constants), [1] DICT_CONSURF_GRADE_COLORS (in module mkt.databases.colors), [1] DICT_DAVIS_DROP (in module mkt.databases.datasets.discoverx), [1]

DICT_DAVIS_MERGE_FIX (in module mkt.databases.datasets.discoverx), [1] DICT_FILENAME_DEFAULTS (in module mkt.databases.pymol), [1] dict_filenames (mkt.databases.pymol.PyMOLGenerator attribute), [1] DICT_FUNCS (in module mkt.schema.io_utils), [1] DICT_GROUP_KINCORE (in module mkt.databases.kincore), [1] dict_highest_level (mkt.databases.oncokb.OncoKBProteinChange attribute), [1] dict_kinase (mkt.databases.sasa.ResidueSASA attribute), [1] DICT_KINASE_GROUP_COLORS (in module mkt.schema.constants), [1] DICT_KINCORE_PARAMS (in module mkt.databases.kincore), [1] DICT_MERGE_MULTIMAP (in module mkt.databases.kinase_schema), [1] DICT_MERGE_MULTIMAP_REV (in module mkt.databases.kinase_schema), [1] dict_mod_res (mkt.databases.uniprot.UniProtJSON attribute), [1] DICT_MOLECULAR_BRAKE (in module mkt.schema.constants), [1] DICT_MOLECULAR_BRAKE_OFFSET (in module mkt.schema.constants), [1] dict_mutations (mkt.databases.app.schema.MutationsConfig attribute), [1] (mkt.databases.app.schema.MutationsDefaultConfig attribute) (mkt.databases.app.schema.MutationsGroupConfig attribute) (mkt.databases.app.schema.MutationsKLIFSConfig attribute) DICT_ONCOKB_PREFIXES (in module mkt.databases.oncokb), [1] DICT_ONCOTREE_LEGACY_ALIAS (in module mkt.databases.oncotree), [1] DICT_PHOSPHO_EMPTY (in module mkt.databases.uniprot), [1] DICT_POCKET_KLIFS_REGIONS (in module mkt.databases.klifs), [1] (in module mkt.schema.constants), [1] DICT_QUARTILE_HEATMAP_COLORMAP (in module mkt.databases.colors), [1] DICT_QUARTILE_HEATMAP_COLORMAP_PLASMA (in module mkt.databases.colors), [1] DICT_QUARTILE_HEATMAP_COLORMAP_VIRIDIS (in module mkt.databases.colors), [1] dict_refseq_indices (mkt.databases.datasets.discoverx.DiscoverXInfo attribute), [1] dict_replace (mkt.databases.cbioportal.KinaseMissenseMutations attribute), [1] DICT_SCORE_KEY (in module mkt.databases.protvar), [1] DICT_TISSUE_COLOR (in module mkt.databases.oncotree), [1] DICT_UNIPROT_EVIDENCE (in module mkt.databases.uniprot), [1] DictKinaseFiguresConfig (class in mkt.databases.plot_config), [1] discoverx_gene_symbol (mkt.databases.datasets.discoverx.DiscoverXInfo attribute), [1] DiscoverXInfo (class in mkt.databases.datasets.discoverx), [1] DiscoverXInfoGenerator (class in mkt.databases.datasets.discoverx), [1] display_leaf_names() (mkt.schema.conservation_schema.KLIFSConservationData method), [1] display_leaves (mkt.schema.conservation_schema.KLIFSConservationData attribute), [1] display_order (mkt.schema.conservation_schema.KLIFSConservationData attribute), [1] distance_matrix (mkt.databases.conservation.KLIFSConservationTreeFigure attribute) (mkt.databases.conservation.KLIFSHierarchicalConservation attribute), [1] (mkt.databases.conservation.KLIFSResidueDotApp attribute) (mkt.databases.conservation.KLIFSTreeConservationApp attribute) distances_condensed (mkt.schema.conservation_schema.KLIFSConservationData attribute), [1] DMPK (mkt.schema.kinase_schema.Family attribute), [1] domain_name (mkt.schema.kinase_schema.Pfam attribute), [1] dot_density (mkt.databases.sasa.BaseSASAConfig attribute), [1] (mkt.databases.sasa.CrossValidationConfig attribute), [1] (mkt.databases.sasa.CrossValidationHydrogenConfig attribute), [1] (mkt.databases.sasa.PyMOLHeavyConfig attribute), [1] (mkt.databases.sasa.PyMOLHydrogenConfig attribute), [1] (mkt.databases.sasa.ResidueSASA attribute), [1] dynamic_range (mkt.databases.plot_config.PlotDatasetConfig attribute), [1] DynamicRangePlotConfig (class in mkt.databases.plot_config), [1] DYRK (mkt.schema.kinase_schema.Family attribute), [1]

E

edge_linewidth (mkt.databases.plot_config.RidgelinePlotConfig attribute), [1] edgecolor (mkt.databases.plot_config.RidgelinePlotConfig attribute), [1] element_size (mkt.databases.plot_config.UpsetPlotConfig attribute), [1] ellipsis_color (mkt.databases.plot_config.SequenceSchematicConfig attribute), [1] ellipsis_fontsize (mkt.databases.plot_config.SequenceSchematicConfig attribute), [1] email (mkt.databases.ncbi.ProteinEntrez attribute), [1] end (mkt.schema.kinase_schema.KinCore attribute), [1] (mkt.schema.kinase_schema.KinCoreCIF attribute), [1] (mkt.schema.kinase_schema.KinCoreFASTA attribute), [1] (mkt.schema.kinase_schema.Pfam attribute), [1] end_af2 (mkt.schema.kinase_schema.KinCoreFASTA attribute), [1] end_md (mkt.schema.kinase_schema.KinCoreFASTA attribute), [1] Eph (mkt.schema.kinase_schema.Family attribute), [1] ESM1b (mkt.databases.protvar.ScoreDatabase attribute), [1]

EVE (mkt.databases.protvar.ScoreDatabase attribute), [1] exclude_pseudokinases (mkt.databases.conservation.KLIFSConservationTreeFigure attribute) (mkt.databases.conservation.KLIFSHierarchicalConservation attribute), [1] (mkt.databases.conservation.KLIFSResidueDotApp attribute) (mkt.databases.conservation.KLIFSTreeConservationApp attribute) (mkt.schema.conservation_schema.KLIFSConservationData attribute), [1] extend_gap_score (mkt.databases.aligners.BioAligner attribute), [1] extract_level_as_int() (mkt.databases.oncokb.OncoKB static method), [1] extract_modified_residues() (mkt.databases.uniprot.UniProtJSON method), [1] extract_pk_cif_files_as_list() (in module mkt.databases.kincore), [1] extract_pk_fasta_info_as_list() (in module mkt.databases.kincore), [1] extract_region_indices() (mkt.databases.datasets.discoverx.DiscoverXInfo method), [1] extract_sequence_from_cif() (mkt.schema.kinase_schema.KinaseInfo method), [1] extract_tarfiles() (in module mkt.schema.io_utils), [1]

F

families (mkt.databases.plot_config.FamilyColorConfig attribute), [1] Family (class in mkt.schema.kinase_schema), [1] family (mkt.schema.kinase_schema.KinHub attribute), [1] (mkt.schema.kinase_schema.KLIFS attribute), [1] (mkt.schema.kinase_schema.MSASource attribute), [1] family_colors (mkt.databases.plot_config.PlotDatasetConfig attribute), [1] FamilyColorConfig (class in mkt.databases.plot_config), [1] fasta (mkt.schema.kinase_schema.KinCore attribute), [1] figsize (mkt.databases.plot_config.DynamicRangePlotConfig attribute), [1] (mkt.databases.plot_config.MetricsBoxplotConfig attribute), [1] (mkt.databases.plot_config.RegionGapViolinConfig attribute), [1] (mkt.databases.plot_config.RidgelinePlotConfig attribute), [1] (mkt.databases.plot_config.SequenceSchematicConfig attribute), [1] (mkt.databases.plot_config.UpsetPlotConfig attribute), [1] (mkt.databases.plot_config.VennDiagramConfig attribute), [1] figsize_height (mkt.databases.plot_config.StackedBarchartConfig attribute), [1] figsize_width_per_source (mkt.databases.plot_config.StackedBarchartConfig attribute), [1] figure_titlesize (mkt.databases.plot_config.DynamicRangePlotConfig attribute), [1] filename (mkt.databases.plot_config.CladeMembershipTableConfig attribute), [1] (mkt.databases.plot_config.ConservationTreeExplorerConfig attribute), [1] (mkt.databases.plot_config.DynamicRangePlotConfig attribute), [1] (mkt.databases.plot_config.MetricsBoxplotConfig attribute), [1] (mkt.databases.plot_config.RegionGapViolinConfig attribute), [1] (mkt.databases.plot_config.ResidueDotExplorerConfig attribute), [1] (mkt.databases.plot_config.RidgelinePlotConfig attribute), [1] (mkt.databases.plot_config.SequenceSchematicConfig attribute), [1] (mkt.databases.plot_config.StackedBarchartConfig attribute), [1] (mkt.databases.plot_config.UpsetPlotConfig attribute), [1] (mkt.databases.plot_config.VennDiagramConfig attribute), [1] filepath (mkt.databases.oncotree.OncoTree attribute), [1] (mkt.databases.three_d_hotspots.ThreeDHotspots attribute), [1] fill_alpha (mkt.databases.plot_config.RegionGapViolinConfig attribute), [1] (mkt.databases.plot_config.RidgelinePlotConfig attribute), [1] filter_single_aa_missense_mutations() (mkt.databases.cbioportal.KinaseMissenseMutations method), [1] find_alternative_hgnc() (in module mkt.databases.kinase_schema), [1] find_closest_mapping() (mkt.databases.datasets.discoverx.DiscoverXInfo method), [1] find_intra_gaps() (mkt.databases.datasets.discoverx.DiscoverXInfo method), [1] (mkt.databases.klifs.KLIFSPocket method), [1] find_pfam_domain() (in module mkt.databases.pfam), [1] find_start_or_end_idx_recursively() (mkt.databases.klifs.KLIFSPocket method), [1] first_occurrence_map() (mkt.databases.cancer_hotspots.CancerHotspots method), [1]

flatten_iterables_in_iterable() (in module mkt.databases.utils), [1] FLOAT_CONSERVATION_THRESHOLD (in module mkt.databases.conservation), [1] FLOAT_TREE_BOX_GAP_IN (in module mkt.databases.conservation), [1] FLOAT_TREE_BOX_PAD_IN (in module mkt.databases.conservation), [1] FLOAT_TREE_BRANCH_LW (in module mkt.databases.conservation), [1] FLOAT_TREE_DEPTH_STEP_IN (in module mkt.databases.conservation), [1] FLOAT_TREE_DETAIL_LEGEND_FS (in module mkt.databases.conservation), [1] FLOAT_TREE_DETAIL_LEGEND_IN (in module mkt.databases.conservation), [1] FLOAT_TREE_DETAIL_PAGE_W (in module mkt.databases.conservation), [1] FLOAT_TREE_DETAIL_ROW_IN (in module mkt.databases.conservation), [1] FLOAT_TREE_DOMINANT_FRACTION (in module mkt.databases.conservation), [1] FLOAT_TREE_FONT_SIZE (in module mkt.databases.conservation), [1] FLOAT_TREE_GUIDE_LW (in module mkt.databases.conservation), [1] FLOAT_TREE_LOGO_CUTOFF (in module mkt.databases.conservation), [1] FLOAT_TREE_LOGO_IC_FLOOR (in module mkt.databases.conservation), [1] FLOAT_TREE_LOGO_IC_MAX (in module mkt.databases.conservation), [1] FLOAT_TREE_PSEUDO_BORDER_LW (in module mkt.databases.conservation), [1] FLOAT_TREE_RIGHT_PAD_IN (in module mkt.databases.conservation), [1] FLOAT_TREE_ROW_HEIGHT (in module mkt.databases.conservation), [1] FLOAT_TREE_SPLIT_FONT_SIZE (in module mkt.databases.conservation), [1] FLOAT_TREE_SUMMARY_LEGEND_FS (in module mkt.databases.conservation), [1] FLOAT_TREE_TABLE_GAP_IN (in module mkt.databases.conservation), [1] font_size (mkt.databases.conservation.KLIFSConservationTreeFigure attribute), [1] (mkt.databases.plot.SequenceAlignment attribute), [1] (mkt.databases.plot_config.ConservationTreeConfig attribute), [1] (mkt.databases.plot_config.DynamicRangePlotConfig attribute), [1] format_property_columns() (mkt.databases.app.properties.PropertyTables method), [1] formats (mkt.databases.plot_config.ConservationTreeConfig attribute), [1] (mkt.databases.plot_config.ResidueDotConfig attribute), [1] from_cache (mkt.databases.api_schema.APIClient attribute), [1] from_conservation_data() (mkt.databases.conservation.KLIFSHierarchicalConservation class method), [1] from_csv() (mkt.databases.cancer_hotspots.CancerHotspots class method), [1] (mkt.databases.oncokb.OncoKBCancerGeneList class method), [1] (mkt.databases.three_d_hotspots.ThreeDHotspots class method), [1] from_dataclass() (mkt.databases.sasa.ResidueSASA class method), [1] from_dataframe() (mkt.databases.cancer_hotspots.CancerHotspots class method), [1] (mkt.databases.oncokb.OncoKBCancerGeneList class method), [1] (mkt.databases.three_d_hotspots.ThreeDHotspots class method), [1] from_yaml() (mkt.databases.plot_config.DictKinaseFiguresConfig class method), [1] (mkt.databases.plot_config.PlotDatasetConfig class method), [1] full_name (mkt.schema.kinase_schema.KLIFS attribute), [1]

G

gap_chars (mkt.databases.conservation.KLIFSConservationTreeFigure attribute) (mkt.databases.conservation.KLIFSHierarchicalConservation attribute), [1] (mkt.databases.conservation.KLIFSResidueDotApp attribute) (mkt.databases.conservation.KLIFSTreeConservationApp attribute) (mkt.schema.conservation_schema.KLIFSConservationData attribute), [1] gap_color (mkt.databases.plot_config.SequenceSchematicConfig attribute), [1] gap_score (mkt.databases.aligners.BioAligner attribute), [1] gather_children() (mkt.databases.conservation.KLIFSHierarchicalConservation method), [1] gene_name (mkt.databases.oncokb.OncoKBProteinChange attribute), [1] (mkt.databases.pymol.PyMOLGenerator attribute), [1] (mkt.schema.kinase_schema.KLIFS attribute), [1] GenePanel (class in mkt.databases.cbioportal), [1] generate_alignment_dict_including_gaps() (mkt.databases.datasets.discoverx.DiscoverXInfo method), [1] generate_alignment_list() (mkt.databases.klifs.KLIFSPocket method), [1] generate_alignment_list_including_gaps() (mkt.databases.klifs.KLIFSPocket method), [1] generate_alignments() (mkt.databases.app.sequences.SequenceAlignment method), [1] generate_annotated_pdb() (mkt.databases.pymol.PyMOLGenerator method), [1] generate_bottom_plot() (mkt.databases.plot.SequenceAlignment method), [1] generate_colormap_legend() (in module mkt.databases.colors), [1] generate_construct_dictionary() (mkt.databases.datasets.discoverx.DiscoverXInfo method), [1] generate_construct_sequence_dict() (mkt.databases.datasets.discoverx.DiscoverXInfo method), [1] generate_dataframes() (mkt.databases.datasets.discoverx.DiscoverXInfoGenerator method), [1] generate_dict_obj_from_api_or_scraper() (in module mkt.databases.kinase_schema), [1] generate_discoverx_info_dict() (mkt.databases.datasets.discoverx.DiscoverXInfoGenerator method), [1] generate_gridplot() (mkt.databases.plot.SequenceAlignment method), [1] generate_instructions() (mkt.databases.pymol.PyMOLGenerator method), [1] generate_kincore2uniprot_alignment() (mkt.databases.kinase_schema.KinaseInfoGenerator method), [1] generate_kincore_fasta2cif_alignment() (mkt.databases.kinase_schema.KinaseInfoKinaseDomainGenerator method), [1] generate_KLIFS2RefSeqIdx() (mkt.databases.datasets.discoverx.DiscoverXInfo method), [1] generate_klifs2uniprot_dict() (mkt.databases.kinase_schema.KinaseInfoGenerator method), [1] generate_klifs_region_seq_list_from_dict_idx() (mkt.databases.datasets.discoverx.DiscoverXInfo method), [1] generate_labels() (mkt.databases.app.schema.KLIFSCustomConfig method), [1] (mkt.databases.app.schema.KLIFSRegionLabelConfig method), [1] (mkt.databases.app.schema.MutationsConfig method), [1] (mkt.databases.app.schema.MutationsDefaultConfig method), [1] (mkt.databases.app.schema.MutationsGroupConfig method), [1] (mkt.databases.app.schema.MutationsKLIFSConfig method), [1] (mkt.databases.app.schema.StructureConfig method), [1] generate_list_idx() (mkt.databases.app.schema.DefaultConfig method), [1] (mkt.databases.app.schema.KLIFSConfig method), [1] (mkt.databases.app.schema.KLIFSCustomConfig method), [1] (mkt.databases.app.schema.MutationsConfig method), [1] (mkt.databases.app.schema.PhosphositesConfig method), [1] (mkt.databases.app.schema.StructureConfig method), [1] generate_pivot_table() (mkt.databases.cbioportal.KinaseMissenseMutations method), [1] generate_pymol_script() (mkt.databases.pymol.PyMOLGenerator method), [1] generate_style_color_lists() (mkt.databases.app.schema.DefaultConfig method), [1] (mkt.databases.app.schema.KLIFSConfig method), [1] (mkt.databases.app.schema.KLIFSCustomConfig method), [1] (mkt.databases.app.schema.KLIFSRegionLabelConfig method), [1] (mkt.databases.app.schema.MutationsConfig method), [1] (mkt.databases.app.schema.PhosphositesConfig method), [1] (mkt.databases.app.schema.StructureConfig method), [1] generate_top_plot() (mkt.databases.plot.SequenceAlignment method), [1] generate_venn_diagram_dict() (in module mkt.databases.plot), [1] get_aa_property() (in module mkt.databases.properties), [1] get_boundaries_in_key() (mkt.databases.datasets.discoverx.DiscoverXInfo method), [1] get_cached_session() (in module mkt.databases.requests_wrapper), [1] get_cbioportal() (mkt.databases.cbioportal.cBioPortal method), [1] get_cbioportal_instance() (in module mkt.databases.config)

get_chembl_id() (mkt.databases.chembl.ChEMBL method), [1] get_classification() (mkt.databases.protvar.ProtvarVariant method), [1] get_colors() (mkt.databases.plot.SequenceAlignment static method), [1] (mkt.databases.plot_config.FamilyColorConfig method), [1] get_consurf_grade_color() (in module mkt.databases.colors), [1] get_data() (mkt.databases.cbioportal.cBioPortalQuery method), [1] get_df() (mkt.databases.cbioportal.cBioPortalQuery method), [1] get_entity_id() (mkt.databases.cbioportal.cBioPortalQuery method), [1] (mkt.databases.cbioportal.PanelData method), [1] (mkt.databases.cbioportal.StudyData method), [1] get_gene() (mkt.databases.cancer_hotspots.CancerHotspots method), [1] (mkt.databases.cancer_hotspots.CancerHotspotsQuery method), [1] (mkt.databases.oncokb.OncoKBCancerGeneList method), [1] (mkt.databases.three_d_hotspots.ThreeDHotspots method), [1] get_highlight_data() (mkt.databases.app.structures.StructureVisualizer method), [1] get_instance() (mkt.databases.cbioportal.cBioPortal method), [1] get_inter_region() (mkt.databases.datasets.discoverx.DiscoverXInfo method), [1] (mkt.databases.klifs.KLIFSPocket method), [1] get_intra_region() (mkt.databases.datasets.discoverx.DiscoverXInfo method), [1] (mkt.databases.klifs.KLIFSPocket method), [1] get_kinase_info() (mkt.databases.klifs.KinaseInfo method), [1] get_kinase_missense_mutations() (mkt.databases.cbioportal.KinaseMissenseMutations method), [1] get_kinase_names() (mkt.databases.klifs.KinaseNames method), [1] get_klifs() (mkt.databases.klifs.KLIFS method), [1] get_moa() (mkt.databases.open_targets.OpenTargetsDrugMoA method), [1] get_oncokb_levels() (in module mkt.databases.oncokb), [1] get_output_dir() (in module mkt.databases.config) (in module mkt.schema.config), [1] get_parser() (in module mkt.databases.cli.extract_cbioportal_missense_kinases), [1] (in module mkt.databases.cli.generate_kinaseinfo_objects), [1] get_popeve() (mkt.databases.protvar.ProtvarVariant method), [1] get_repo_root() (in module mkt.databases.io_utils), [1] (in module mkt.schema.io_utils), [1] get_score() (mkt.databases.protvar.ProtvarVariant method), [1] get_scores() (mkt.databases.protvar.ProtvarScoreQuery method), [1] get_search_field() (mkt.databases.klifs.KinaseInfo method), [1] get_search_term() (mkt.databases.klifs.KinaseInfo method), [1] get_sequence_max_with_exception() (in module mkt.databases.kinase_schema), [1] get_species() (mkt.databases.klifs.KinaseInfo method), [1] get_status_code() (mkt.databases.klifs.KinaseInfo method), [1] get_treatments() (mkt.databases.oncokb.OncoKBProteinChange method), [1] get_url() (mkt.databases.cbioportal.cBioPortal method), [1] (mkt.databases.klifs.KLIFS method), [1] get_variant() (mkt.databases.protvar.ProtvarScoreQuery method), [1] GraphQLClient (class in mkt.databases.api_schema), [1] grid_alpha (mkt.databases.plot_config.MetricsBoxplotConfig attribute), [1] (mkt.databases.plot_config.RegionGapViolinConfig attribute), [1] (mkt.databases.plot_config.RidgelinePlotConfig attribute), [1] GRK (mkt.schema.kinase_schema.Family attribute), [1] Group (class in mkt.schema.kinase_schema), [1] group (mkt.schema.kinase_schema.KinCoreCIF attribute), [1] (mkt.schema.kinase_schema.KinCoreFASTA attribute), [1] (mkt.schema.kinase_schema.KinHub attribute), [1] (mkt.schema.kinase_schema.KLIFS attribute), [1] group_concordance() (mkt.databases.conservation.KLIFSHierarchicalConservation method), [1] group_name_homologs() (in module mkt.schema.utils), [1] groups (mkt.databases.conservation.KLIFSConservationTreeFigure attribute) (mkt.databases.conservation.KLIFSHierarchicalConservation attribute), [1] (mkt.databases.conservation.KLIFSResidueDotApp attribute) (mkt.databases.conservation.KLIFSTreeConservationApp attribute)

H

handle_page_not_found() (mkt.databases.klifs.KinaseInfo method), [1] harmonize_kincore_fasta_cif() (in module mkt.databases.kincore), [1] has_json() (mkt.databases.oncokb.OncoKB method), [1] header (mkt.databases.oncokb.OncoKB attribute), [1] (mkt.databases.oncokb.OncoKBProteinChange attribute) (mkt.databases.protvar.ProtvarScoreQuery attribute), [1] (mkt.schema.kinase_schema.UniProt attribute), [1] headers (mkt.databases.alphafold.AlphaFoldPrediction attribute), [1] (mkt.databases.ncbi.ProteinNCBI attribute), [1] (mkt.databases.uniprot.UniProtJSON attribute), [1] height_ratios (mkt.databases.plot_config.RegionGapViolinConfig attribute), [1] henikoff_weights() (in module mkt.databases.pssm), [1] HGNC (class in mkt.databases.hgnc), [1] hgnc (mkt.schema.kinase_schema.KinCoreCIF attribute), [1] (mkt.schema.kinase_schema.KinCoreFASTA attribute), [1]

hgnc_name (mkt.databases.kinase_schema.KinaseInfoGenerator attribute) (mkt.schema.kinase_schema.KinaseInfo attribute), [1] (mkt.schema.kinase_schema.KinaseInfoUniProt attribute), [1] (mkt.schema.kinase_schema.KinHub attribute), [1] highlight_cartoon_transparency (mkt.databases.app.schema.KLIFSCustomConfig attribute), [1] (mkt.databases.app.schema.StructureConfig attribute), [1] highlight_targets (mkt.databases.plot_config.ResidueDotConfig attribute), [1] HOTSPOT (mkt.databases.three_d_hotspots.HotspotClass attribute), [1] HOTSPOT_LINKED (mkt.databases.three_d_hotspots.HotspotClass attribute), [1] HotspotClass (class in mkt.databases.three_d_hotspots), [1] HotspotTier (class in mkt.databases.cancer_hotspots), [1] HotspotVersion (class in mkt.databases.cancer_hotspots), [1] hspace (mkt.databases.plot_config.RegionGapViolinConfig attribute), [1]

I

id (mkt.databases.chembl.ChEMBL attribute), [1] (mkt.databases.chembl.ChEMBLMolecule attribute) (mkt.databases.chembl.ChEMBLMoleculeExact attribute) (mkt.databases.chembl.ChEMBLMoleculePreferred attribute) (mkt.databases.chembl.ChEMBLMoleculeSearch attribute) (mkt.databases.conservation.KLIFSDisplaySplit attribute), [1] idx_kd (mkt.databases.klifs.KLIFSPocket attribute), [1] idx_start (mkt.databases.datasets.discoverx.DiscoverXInfo attribute), [1] idx_stop (mkt.databases.datasets.discoverx.DiscoverXInfo attribute), [1] in_alphafold (mkt.schema.kinase_schema.Pfam attribute), [1] input_is_hgnc_symbol (mkt.databases.hgnc.HGNC attribute), [1] input_symbol_or_id (mkt.databases.hgnc.HGNC attribute), [1] instance (mkt.databases.cbioportal.cBioPortal attribute), [1] INT_KLIFS_POCKET_LENGTH (in module mkt.databases.conservation), [1] INT_MIN_CHILD_MEMBERS (in module mkt.databases.conservation), [1] INT_RESIDUE_DOT_MIN_ENCLOSE (in module mkt.databases.conservation), [1]

INT_RESIDUE_DOT_MIN_SHARED (in module mkt.databases.conservation), [1] INT_TREE_MIN_CLUSTER_DISPLAY (in module mkt.databases.conservation), [1] INT_TREE_NAME_TRUNC (in module mkt.databases.conservation), [1] INT_TREE_SPLIT_INDEX (in module mkt.databases.conservation), [1] inter_color (mkt.databases.plot_config.RegionGapViolinConfig attribute), [1] interpolate_color() (in module mkt.databases.colors), [1] intersection_alpha (mkt.databases.plot_config.VennDiagramConfig attribute), [1] intersection_color (mkt.databases.plot_config.VennDiagramConfig attribute), [1] intersection_plot_elements (mkt.databases.plot_config.UpsetPlotConfig attribute), [1] intra_color (mkt.databases.plot_config.RegionGapViolinConfig attribute), [1] is_lipid_kinase() (mkt.schema.kinase_schema.KinaseInfo method), [1] is_not_valid_string() (in module mkt.databases.kinase_schema), [1] is_pseudogene() (mkt.schema.kinase_schema.KinaseInfo method), [1] is_pseudokinase() (mkt.schema.kinase_schema.KinaseInfo method), [1] iterate_klifs_alignment() (mkt.databases.klifs.KLIFSPocket method), [1] iuphar (mkt.schema.kinase_schema.KLIFS attribute), [1]

J

JakA (mkt.schema.kinase_schema.Family attribute), [1] JakB (mkt.schema.kinase_schema.Family attribute), [1] jitter_alpha (mkt.databases.plot_config.MetricsBoxplotConfig attribute), [1] (mkt.databases.plot_config.RegionGapViolinConfig attribute), [1] jitter_color (mkt.databases.plot_config.MetricsBoxplotConfig attribute), [1] jitter_edgecolor (mkt.databases.plot_config.RegionGapViolinConfig attribute), [1]

jitter_linewidth (mkt.databases.plot_config.RegionGapViolinConfig attribute), [1] jitter_mixed_color (mkt.databases.plot_config.RegionGapViolinConfig attribute), [1] jitter_size (mkt.databases.plot_config.MetricsBoxplotConfig attribute), [1] (mkt.databases.plot_config.RegionGapViolinConfig attribute), [1] jitter_std (mkt.databases.plot_config.MetricsBoxplotConfig attribute), [1] (mkt.databases.plot_config.RegionGapViolinConfig attribute), [1]

K

KD1 (mkt.schema.kinase_schema.KinaseDomainName attribute), [1] KD2 (mkt.schema.kinase_schema.KinaseDomainName attribute), [1] KD3 (mkt.schema.kinase_schema.KinaseDomainName attribute), [1] key (mkt.databases.datasets.discoverx.DiscoverXInfo attribute), [1] kinase_group_legend_handles() (in module mkt.databases.plot), [1] kinase_id (mkt.schema.kinase_schema.KLIFS attribute), [1] kinase_name (mkt.schema.kinase_schema.KinHub attribute), [1] KinaseDomainName (class in mkt.schema.kinase_schema), [1] KinaseInfo (class in mkt.databases.klifs), [1] (class in mkt.schema.kinase_schema), [1] KinaseInfoGenerator (class in mkt.databases.kinase_schema), [1] KinaseInfoKinaseDomain (class in mkt.schema.kinase_schema), [1] KinaseInfoKinaseDomainGenerator (class in mkt.databases.kinase_schema), [1] KinaseInfoUniProt (class in mkt.schema.kinase_schema), [1] KinaseInfoUniProtGenerator (class in mkt.databases.kinase_schema), [1] KinaseMissenseMutations (class in mkt.databases.cbioportal), [1] KinaseNames (class in mkt.databases.klifs), [1] KinCore (class in mkt.schema.kinase_schema), [1] kincore (mkt.databases.kinase_schema.KinaseInfoGenerator attribute) (mkt.schema.kinase_schema.KinaseInfo attribute), [1] (mkt.schema.kinase_schema.KinaseInfoKinaseDomain attribute), [1] Kincore2UniProtAligner (class in mkt.databases.aligners), [1] KinCoreCIF (class in mkt.schema.kinase_schema), [1] KinCoreFASTA (class in mkt.schema.kinase_schema), [1] kind (mkt.databases.conservation.KLIFSDisplayLeaf attribute), [1] KinHub (class in mkt.schema.kinase_schema), [1] kinhub (mkt.databases.kinase_schema.KinaseInfoGenerator attribute) (mkt.schema.kinase_schema.KinaseInfo attribute), [1] (mkt.schema.kinase_schema.KinaseInfoKinaseDomain attribute), [1] kinhub() (in module mkt.databases.scrapers), [1] KLIFS (class in mkt.databases.klifs), [1] (class in mkt.schema.kinase_schema), [1] klifs (mkt.databases.kinase_schema.KinaseInfoGenerator attribute) (mkt.schema.kinase_schema.KinaseInfo attribute), [1] (mkt.schema.kinase_schema.KinaseInfoKinaseDomain attribute), [1] KLIFS2RefSeqIdx (mkt.databases.datasets.discoverx.DiscoverXInfo attribute), [1]

KLIFS2RefSeqSeq (mkt.databases.datasets.discoverx.DiscoverXInfo attribute), [1] KLIFS2UniProtIdx (mkt.databases.kinase_schema.KinaseInfoGenerator attribute) (mkt.databases.klifs.KLIFSPocket attribute), [1] (mkt.schema.kinase_schema.KinaseInfo attribute), [1] KLIFS2UniProtSeq (mkt.databases.kinase_schema.KinaseInfoGenerator attribute) (mkt.databases.klifs.KLIFSPocket attribute), [1] (mkt.schema.kinase_schema.KinaseInfo attribute), [1] KLIFS_ADAPTIVE (mkt.databases.app.schema.StandardConfig attribute), [1] (mkt.databases.app.schema.StandardConfigChoice attribute), [1] KLIFS_CUSTOM (mkt.databases.app.schema.StandardConfig attribute), [1] (mkt.databases.app.schema.StandardConfigChoice attribute), [1] KLIFS_IMPORTANT (mkt.databases.app.schema.StandardConfig attribute), [1] (mkt.databases.app.schema.StandardConfigChoice attribute), [1] KLIFS_PATHOGENIC (mkt.databases.app.schema.StandardConfig attribute), [1] (mkt.databases.app.schema.StandardConfigChoice attribute), [1] klifs_region_aligned (mkt.databases.plot_config.ColKinaseColorConfig attribute), [1] KLIFS_REGION_LABEL (mkt.databases.app.schema.StandardConfig attribute), [1] (mkt.databases.app.schema.StandardConfigChoice attribute), [1] klifs_residues_only (mkt.databases.plot_config.ColKinaseColorConfig attribute), [1] KLIFSAdaptiveConfig (class in mkt.databases.app.schema), [1] KLIFSConfig (class in mkt.databases.app.schema), [1] KLIFSConservationData (class in mkt.schema.conservation_schema), [1] KLIFSConservationTreeFigure (class in mkt.databases.conservation), [1] KLIFSCustomConfig (class in mkt.databases.app.schema), [1] KLIFSDisplayLeaf (class in mkt.databases.conservation), [1] KLIFSDisplaySplit (class in mkt.databases.conservation), [1] KLIFSDisplayTree (class in mkt.databases.conservation), [1] KLIFSHierarchicalConservation (class in mkt.databases.conservation), [1] KLIFSImportantConfig (class in mkt.databases.app.schema), [1] KLIFSPathogenicConfig (class in mkt.databases.app.schema), [1] KLIFSPocket (class in mkt.databases.klifs), [1] KLIFSRegionLabelConfig (class in mkt.databases.app.schema), [1] KLIFSResidueDotApp (class in mkt.databases.conservation), [1] klifsSeq (mkt.databases.klifs.KLIFSPocket attribute), [1] KLIFSTreeConservationApp (class in mkt.databases.conservation), [1] known_codes (mkt.databases.oncotree.OncoTree property), [1] known_effect (mkt.databases.oncokb.OncoKBProteinChange attribute), [1]

L

label_connector (mkt.databases.app.schema.KLIFSCustomConfig attribute), [1] (mkt.databases.app.schema.StructureConfig attribute), [1] label_fontsize (mkt.databases.plot_config.SequenceSchematicConfig attribute), [1] label_min_dist (mkt.databases.app.schema.KLIFSCustomConfig attribute), [1] (mkt.databases.app.schema.KLIFSRegionLabelConfig attribute), [1] (mkt.databases.app.schema.StructureConfig attribute), [1] label_offset (mkt.databases.app.schema.KLIFSCustomConfig attribute), [1] (mkt.databases.app.schema.KLIFSRegionLabelConfig attribute), [1] (mkt.databases.app.schema.StructureConfig attribute), [1] label_size (mkt.databases.app.schema.KLIFSCustomConfig attribute), [1] (mkt.databases.app.schema.StructureConfig attribute), [1] label_spring_strength (mkt.databases.app.schema.KLIFSRegionLabelConfig attribute), [1] (mkt.databases.app.schema.StructureConfig attribute), [1] layout_nrows (mkt.databases.plot_config.StackedBarchartConfig attribute), [1] leaves (mkt.databases.conservation.KLIFSDisplayTree attribute), [1] leaves_order (mkt.schema.conservation_schema.KLIFSConservationData attribute), [1] left_adjust (mkt.databases.plot_config.RegionGapViolinConfig attribute), [1] legend_bbox_y (mkt.databases.plot_config.StackedBarchartConfig attribute), [1] legend_fontsize (mkt.databases.plot_config.StackedBarchartConfig attribute), [1] legend_title_fontsize (mkt.databases.plot_config.StackedBarchartConfig attribute), [1] length_af2 (mkt.schema.kinase_schema.KinCoreFASTA attribute), [1] length_md (mkt.schema.kinase_schema.KinCoreFASTA attribute), [1] length_uniprot (mkt.schema.kinase_schema.KinCoreFASTA attribute), [1] LEVEL_PREFIX (in module mkt.databases.oncotree), [1] LICENSE_COL_PREFIX (in module mkt.databases.three_d_hotspots), [1] linkage_matrix (mkt.databases.conservation.KLIFSConservationTreeFigure attribute) (mkt.databases.conservation.KLIFSHierarchicalConservation attribute), [1] (mkt.databases.conservation.KLIFSResidueDotApp attribute) (mkt.databases.conservation.KLIFSTreeConservationApp attribute) (mkt.schema.conservation_schema.KLIFSConservationData attribute), [1] linkage_method (mkt.databases.conservation.KLIFSConservationTreeFigure attribute) (mkt.databases.conservation.KLIFSHierarchicalConservation attribute), [1] (mkt.databases.conservation.KLIFSResidueDotApp attribute) (mkt.databases.conservation.KLIFSTreeConservationApp attribute) (mkt.schema.conservation_schema.KLIFSConservationData attribute), [1] list_align (mkt.databases.klifs.KLIFSPocket attribute), [1] LIST_CIF_KEYS (in module mkt.databases.kincore), [1] list_col_explode (mkt.databases.cbioportal.cBioPortalQuery attribute), [1] list_color (mkt.databases.app.schema.DefaultConfig attribute) (mkt.databases.app.schema.KLIFSAdaptiveConfig attribute) (mkt.databases.app.schema.KLIFSConfig attribute) (mkt.databases.app.schema.KLIFSCustomConfig attribute) (mkt.databases.app.schema.KLIFSImportantConfig attribute) (mkt.databases.app.schema.KLIFSPathogenicConfig attribute) (mkt.databases.app.schema.KLIFSRegionLabelConfig attribute) (mkt.databases.app.schema.MutationsConfig attribute) (mkt.databases.app.schema.MutationsDefaultConfig attribute) (mkt.databases.app.schema.MutationsGroupConfig attribute) (mkt.databases.app.schema.MutationsKLIFSConfig attribute) (mkt.databases.app.schema.PhosphositesConfig attribute) (mkt.databases.app.schema.StructureConfig attribute), [1] LIST_COLUMNS (in module mkt.databases.oncokb), [1] list_custom_color (mkt.databases.app.schema.KLIFSCustomConfig attribute), [1] list_deletion_mutations (mkt.databases.datasets.discoverx.DiscoverXInfo attribute), [1] LIST_DOT_ALPHABET (in module mkt.databases.conservation), [1] LIST_FASTA_KEYS1 (in module mkt.databases.kincore), [1] LIST_FASTA_KEYS2 (in module mkt.databases.kincore), [1] LIST_FULL_KLIFS_REGION (in module mkt.schema.constants), [1] list_headers (mkt.databases.ncbi.ProteinNCBI attribute), [1] list_ids (mkt.databases.plot.SequenceAlignment attribute), [1] (mkt.databases.sasa.ResidueSASA attribute), [1] list_idx (mkt.databases.app.schema.DefaultConfig attribute) (mkt.databases.app.schema.KLIFSAdaptiveConfig attribute) (mkt.databases.app.schema.KLIFSConfig attribute) (mkt.databases.app.schema.KLIFSCustomConfig attribute) (mkt.databases.app.schema.KLIFSImportantConfig attribute) (mkt.databases.app.schema.KLIFSPathogenicConfig attribute) (mkt.databases.app.schema.KLIFSRegionLabelConfig attribute) (mkt.databases.app.schema.MutationsConfig attribute) (mkt.databases.app.schema.MutationsDefaultConfig attribute) (mkt.databases.app.schema.MutationsGroupConfig attribute) (mkt.databases.app.schema.MutationsKLIFSConfig attribute) (mkt.databases.app.schema.PhosphositesConfig attribute) (mkt.databases.app.schema.StructureConfig attribute), [1]

LIST_INTER_REGIONS (in module mkt.databases.klifs), [1] LIST_INTRA_REGIONS (in module mkt.databases.klifs), [1] LIST_KINASE_GROUP_ORDER (in module mkt.databases.plot), [1] LIST_KINASEINFO_KEYS (in module mkt.databases.klifs), [1] LIST_KLIFS_REGION (in module mkt.databases.klifs), [1] (in module mkt.schema.constants), [1] list_klifs_region (mkt.databases.klifs.KLIFSPocket attribute), [1] list_klifs_substr_actual (mkt.databases.klifs.KLIFSPocket attribute), [1] list_klifs_substr_match (mkt.databases.klifs.KLIFSPocket attribute), [1] list_label (mkt.databases.app.schema.DefaultConfig attribute) (mkt.databases.app.schema.KLIFSAdaptiveConfig attribute) (mkt.databases.app.schema.KLIFSConfig attribute) (mkt.databases.app.schema.KLIFSCustomConfig attribute) (mkt.databases.app.schema.KLIFSImportantConfig attribute) (mkt.databases.app.schema.KLIFSPathogenicConfig attribute) (mkt.databases.app.schema.KLIFSRegionLabelConfig attribute) (mkt.databases.app.schema.MutationsConfig attribute) (mkt.databases.app.schema.MutationsDefaultConfig attribute) (mkt.databases.app.schema.MutationsGroupConfig attribute) (mkt.databases.app.schema.MutationsKLIFSConfig attribute) (mkt.databases.app.schema.PhosphositesConfig attribute) (mkt.databases.app.schema.StructureConfig attribute), [1] list_methods (mkt.databases.sasa.ResidueSASA property), [1] list_missense_mutations (mkt.databases.datasets.discoverx.DiscoverXInfo attribute), [1] LIST_PFAM_KD (in module mkt.schema.constants), [1] LIST_PSEUDOKINASE_HEURISTIC_FALSE_POSITIVE (in module mkt.schema.constants), [1] LIST_PSEUDOKINASE_TRIAD_INTACT (in module mkt.schema.constants), [1] list_refseq2uniprot (mkt.databases.datasets.discoverx.DiscoverXInfo attribute), [1] LIST_RESIDUE_DOT_KINASES (in module mkt.databases.conservation), [1] list_seq (mkt.databases.ncbi.ProteinNCBI attribute), [1] list_sequences (mkt.databases.aligners.ClustalOmegaAligner attribute), [1] (mkt.databases.plot.SequenceAlignment attribute), [1] list_stick_positions (mkt.databases.app.schema.KLIFSAdaptiveConfig attribute), [1] (mkt.databases.app.schema.KLIFSConfig attribute), [1] (mkt.databases.app.schema.KLIFSCustomConfig attribute) (mkt.databases.app.schema.KLIFSImportantConfig attribute), [1] (mkt.databases.app.schema.KLIFSPathogenicConfig attribute), [1] (mkt.databases.app.schema.KLIFSRegionLabelConfig attribute), [1] list_style (mkt.databases.app.schema.DefaultConfig attribute) (mkt.databases.app.schema.KLIFSAdaptiveConfig attribute) (mkt.databases.app.schema.KLIFSConfig attribute) (mkt.databases.app.schema.KLIFSCustomConfig attribute) (mkt.databases.app.schema.KLIFSImportantConfig attribute) (mkt.databases.app.schema.KLIFSPathogenicConfig attribute) (mkt.databases.app.schema.KLIFSRegionLabelConfig attribute) (mkt.databases.app.schema.MutationsConfig attribute) (mkt.databases.app.schema.MutationsDefaultConfig attribute) (mkt.databases.app.schema.MutationsGroupConfig attribute) (mkt.databases.app.schema.MutationsKLIFSConfig attribute) (mkt.databases.app.schema.PhosphositesConfig attribute) (mkt.databases.app.schema.StructureConfig attribute), [1] list_substring_idxs (mkt.databases.klifs.KLIFSPocket attribute), [1] list_treatment (mkt.databases.oncokb.OncoKBProteinChange attribute), [1] list_uniprot2refseq (mkt.databases.datasets.discoverx.DiscoverXInfo attribute), [1] list_uniprot_idx (mkt.databases.app.schema.KLIFSCustomConfig attribute), [1] load_conservation_data() (in module mkt.schema.io_utils), [1] load_conservation_renderer() (in module mkt.databases.conservation), [1] load_csv_to_dataframe() (in module mkt.databases.io_utils), [1] load_from_csv() (mkt.databases.cbioportal.cBioPortalQuery method), [1] load_kinase_object() (in module mkt.databases.utils), [1] logo_cutoff (mkt.databases.conservation.KLIFSTreeConservationApp attribute), [1] (mkt.databases.plot_config.ConservationTreeExplorerConfig attribute), [1]

M

main() (in module mkt.databases.cli.extract_cbioportal_missense_kinases), [1] (in module mkt.databases.cli.generate_conservation_data), [1] (in module mkt.databases.cli.generate_kinaseinfo_objects), [1] (in module mkt.databases.cli.generate_pymol_files), [1] (in module mkt.databases.cli.plot_dict_kinase), [1] manning_name (mkt.schema.kinase_schema.KinHub attribute), [1] map_aa_to_single_letter_code() (in module mkt.databases.colors), [1] map_ellipsis_fontsize (mkt.databases.plot_config.RegionGapViolinConfig attribute), [1] map_legend_fontsize (mkt.databases.plot_config.RegionGapViolinConfig attribute), [1] map_name_fontsize (mkt.databases.plot_config.RegionGapViolinConfig attribute), [1] map_range_fontsize (mkt.databases.plot_config.RegionGapViolinConfig attribute), [1] map_region_fontsize (mkt.databases.plot_config.RegionGapViolinConfig attribute), [1] map_single_letter_aa_to_color() (in module mkt.databases.colors), [1] map_track_fontsize (mkt.databases.plot_config.RegionGapViolinConfig attribute), [1] MAPK (mkt.schema.kinase_schema.Family attribute), [1] MAPKAPK (mkt.schema.kinase_schema.Family attribute), [1] MAST (mkt.schema.kinase_schema.Family attribute), [1] matplotlib_rc (mkt.databases.plot_config.DictKinaseFiguresConfig attribute), [1] (mkt.databases.plot_config.PlotDatasetConfig attribute), [1] MatplotlibRCConfig (class in mkt.databases.plot_config), [1] matrix (mkt.databases.pssm.SubstitutionPseudocounts attribute), [1] MAX_ASA_TIEN_2013 (in module mkt.databases.sasa), [1] maybe_get_cbioportal_token() (in module mkt.databases.config) maybe_get_gene_names() (mkt.databases.uniprot.UniProtRefSeqProteinGET method), [1] maybe_get_info_from_hgnc_fetch() (mkt.databases.hgnc.HGNC method), [1] maybe_get_oncokb_token() (in module mkt.databases.config) maybe_get_request_cache() (in module mkt.databases.config) maybe_get_symbol_from_hgnc_search() (mkt.databases.hgnc.HGNC method), [1] maybe_get_token() (mkt.databases.api_schema.APIKeyRESTAPIClient method), [1] (mkt.databases.api_schema.APIKeySwaggerClient method), [1] (mkt.databases.cbioportal.cBioPortal method), [1] (mkt.databases.oncokb.OncoKB method), [1] median_color (mkt.databases.plot_config.MetricsBoxplotConfig attribute), [1] median_linewidth (mkt.databases.plot_config.MetricsBoxplotConfig attribute), [1] members (mkt.databases.conservation.KLIFSDisplayLeaf attribute), [1] (mkt.databases.conservation.KLIFSDisplaySplit attribute), [1] members_consensus() (mkt.databases.conservation.KLIFSHierarchicalConservation method), [1] META_COLS (in module mkt.databases.oncotree), [1] metric (mkt.databases.conservation.KLIFSConservationTreeFigure attribute) (mkt.databases.conservation.KLIFSHierarchicalConservation attribute), [1] (mkt.databases.conservation.KLIFSResidueDotApp attribute) (mkt.databases.conservation.KLIFSTreeConservationApp attribute) (mkt.schema.conservation_schema.KLIFSConservationData attribute), [1] metrics_boxplot (mkt.databases.plot_config.PlotDatasetConfig attribute), [1] metrics_csv (mkt.databases.plot_config.DataSourceConfig attribute), [1] MetricsBoxplotConfig (class in mkt.databases.plot_config), [1] min_aloop_pLDDT (mkt.schema.kinase_schema.KinCoreCIF attribute), [1] min_child_members (mkt.databases.conservation.KLIFSConservationTreeFigure attribute) (mkt.databases.conservation.KLIFSHierarchicalConservation attribute), [1] (mkt.databases.conservation.KLIFSResidueDotApp attribute) (mkt.databases.conservation.KLIFSTreeConservationApp attribute) min_cluster_size (mkt.databases.conservation.KLIFSConservationTreeFigure attribute), [1] (mkt.databases.conservation.KLIFSResidueDotApp attribute), [1] (mkt.databases.conservation.KLIFSTreeConservationApp attribute), [1] (mkt.databases.plot_config.ConservationTreeConfig attribute), [1] (mkt.databases.plot_config.ConservationTreeExplorerConfig attribute), [1] (mkt.databases.plot_config.ResidueDotConfig attribute), [1] (mkt.databases.plot_config.ResidueDotExplorerConfig attribute), [1] mismatch (mkt.schema.kinase_schema.KinCore attribute), [1] (mkt.schema.kinase_schema.KinCoreCIF attribute), [1] (mkt.schema.kinase_schema.KinCoreFASTA attribute), [1] mkt.databases module mkt.databases.aligners module mkt.databases.alphafold module mkt.databases.api_schema module mkt.databases.app module mkt.databases.app.properties module mkt.databases.app.schema module mkt.databases.app.sequences module mkt.databases.app.structures module mkt.databases.app.utils module mkt.databases.cancer_hotspots module mkt.databases.cbioportal module mkt.databases.chembl module mkt.databases.cli module mkt.databases.cli.extract_cbioportal_missense_kinases module mkt.databases.cli.generate_conservation_data module mkt.databases.cli.generate_kinaseinfo_objects module mkt.databases.cli.generate_pymol_files module mkt.databases.cli.plot_dict_kinase module mkt.databases.colors module mkt.databases.config module mkt.databases.conservation module mkt.databases.datasets module mkt.databases.datasets.discoverx module mkt.databases.hgnc module mkt.databases.io_utils module mkt.databases.kinase_schema module mkt.databases.kincore module mkt.databases.klifs module mkt.databases.log_config module mkt.databases.ncbi module mkt.databases.oncokb module

mkt.databases.oncotree module mkt.databases.open_targets module mkt.databases.pfam module mkt.databases.plot module mkt.databases.plot_config module mkt.databases.properties module mkt.databases.protvar module mkt.databases.pssm module mkt.databases.pymol module mkt.databases.requests_wrapper module mkt.databases.sasa module mkt.databases.scrapers module mkt.databases.three_d_hotspots module mkt.databases.uniprot module mkt.databases.utils module mkt.databases.utils_requests module mkt.schema module mkt.schema.config module mkt.schema.conservation_schema module mkt.schema.constants module mkt.schema.io_utils module mkt.schema.kinase_schema module mkt.schema.utils module MLCK (mkt.schema.kinase_schema.Family attribute), [1] MLK (mkt.schema.kinase_schema.Family attribute), [1] mode (mkt.databases.aligners.BioAligner attribute), [1] (mkt.databases.aligners.BL2UniProtAligner attribute), [1] (mkt.databases.aligners.Kincore2UniProtAligner attribute), [1] model_no (mkt.schema.kinase_schema.KinCoreCIF attribute), [1] model_post_init() (mkt.databases.datasets.discoverx.DiscoverXInfo method), [1] module mkt.databases mkt.databases.aligners mkt.databases.alphafold mkt.databases.api_schema mkt.databases.app mkt.databases.app.properties mkt.databases.app.schema mkt.databases.app.sequences mkt.databases.app.structures mkt.databases.app.utils mkt.databases.cancer_hotspots mkt.databases.cbioportal mkt.databases.chembl mkt.databases.cli mkt.databases.cli.extract_cbioportal_missense_kinases mkt.databases.cli.generate_conservation_data mkt.databases.cli.generate_kinaseinfo_objects mkt.databases.cli.generate_pymol_files mkt.databases.cli.plot_dict_kinase mkt.databases.colors mkt.databases.config mkt.databases.conservation mkt.databases.datasets mkt.databases.datasets.discoverx mkt.databases.hgnc mkt.databases.io_utils mkt.databases.kinase_schema mkt.databases.kincore mkt.databases.klifs mkt.databases.log_config mkt.databases.ncbi mkt.databases.oncokb mkt.databases.oncotree mkt.databases.open_targets mkt.databases.pfam mkt.databases.plot mkt.databases.plot_config mkt.databases.properties mkt.databases.protvar mkt.databases.pssm mkt.databases.pymol mkt.databases.requests_wrapper mkt.databases.sasa mkt.databases.scrapers mkt.databases.three_d_hotspots mkt.databases.uniprot mkt.databases.utils mkt.databases.utils_requests mkt.schema mkt.schema.config mkt.schema.conservation_schema mkt.schema.constants mkt.schema.io_utils mkt.schema.kinase_schema mkt.schema.utils msa_size (mkt.schema.kinase_schema.KinCoreCIF attribute), [1] msa_source (mkt.schema.kinase_schema.KinCoreCIF attribute), [1] MSASource (class in mkt.schema.kinase_schema), [1] mt (mkt.databases.protvar.ProtvarVariant attribute), [1] mut (mkt.databases.protvar.ProtvarScoreQuery attribute), [1] Mutations (class in mkt.databases.cbioportal), [1] MUTATIONS_DEFAULT (mkt.databases.app.schema.StandardConfig attribute), [1] (mkt.databases.app.schema.StandardConfigChoice attribute), [1] MUTATIONS_GROUP (mkt.databases.app.schema.StandardConfig attribute), [1] (mkt.databases.app.schema.StandardConfigChoice attribute), [1] MUTATIONS_KLIFS (mkt.databases.app.schema.StandardConfig attribute), [1] (mkt.databases.app.schema.StandardConfigChoice attribute), [1] MutationsConfig (class in mkt.databases.app.schema), [1] MutationsDefaultConfig (class in mkt.databases.app.schema), [1] MutationsGroupConfig (class in mkt.databases.app.schema), [1] MutationsKLIFSConfig (class in mkt.databases.app.schema), [1]

N

n_ellipsis (mkt.databases.plot_config.SequenceSchematicConfig attribute), [1] n_jobs (mkt.databases.sasa.ResidueSASA attribute), [1] n_kinases (mkt.schema.conservation_schema.KLIFSConservationData attribute), [1] n_points (mkt.databases.sasa.BaseSASAConfig attribute), [1] (mkt.databases.sasa.BioPythonHeavyConfig attribute), [1] (mkt.databases.sasa.BioPythonHydrogenConfig attribute), [1] (mkt.databases.sasa.CrossValidationConfig attribute), [1] (mkt.databases.sasa.CrossValidationHydrogenConfig attribute), [1] (mkt.databases.sasa.ResidueSASA attribute), [1] n_show_end (mkt.databases.plot_config.SequenceSchematicConfig attribute), [1] n_show_start (mkt.databases.plot_config.SequenceSchematicConfig attribute), [1] name (mkt.schema.kinase_schema.KLIFS attribute), [1] name_for_members() (mkt.schema.conservation_schema.KLIFSConservationData method), [1] name_trunc (mkt.databases.conservation.KLIFSTreeConservationApp attribute), [1] (mkt.databases.plot_config.ConservationTreeExplorerConfig attribute), [1]

names (mkt.databases.conservation.KLIFSConservationTreeFigure attribute) (mkt.databases.conservation.KLIFSHierarchicalConservation attribute), [1] (mkt.databases.conservation.KLIFSResidueDotApp attribute) (mkt.databases.conservation.KLIFSTreeConservationApp attribute) (mkt.schema.conservation_schema.KLIFSConservationData attribute), [1] NEK (mkt.schema.kinase_schema.Family attribute), [1] (mkt.schema.kinase_schema.Group attribute), [1] node_conservation() (mkt.databases.conservation.KLIFSHierarchicalConservation method), [1] node_id (mkt.databases.conservation.KLIFSDisplaySplit attribute), [1] node_information() (mkt.databases.conservation.KLIFSHierarchicalConservation method), [1] nodes_summary() (mkt.databases.conservation.KLIFSHierarchicalConservation method), [1] none (mkt.schema.kinase_schema.TemplateSource attribute), [1] Null (mkt.schema.kinase_schema.Family attribute), [1]

O

obj_kinase (mkt.databases.app.properties.PropertyTables attribute), [1] (mkt.databases.app.sequences.SequenceAlignment attribute), [1] offset_bool (mkt.databases.klifs.KLIFSPocket attribute), [1] oncogenic (mkt.databases.oncokb.OncoKBProteinChange attribute), [1] OncoKB (class in mkt.databases.oncokb), [1] ONCOKB_TOKEN_VAR (in module mkt.databases.config) OncoKBCancerGeneList (class in mkt.databases.oncokb), [1] OncoKBInfo (class in mkt.databases.oncokb), [1] OncoKBProteinChange (class in mkt.databases.oncokb), [1] OncoTree (class in mkt.databases.oncotree), [1] OpenTargets (class in mkt.databases.open_targets), [1]

OpenTargetsDrugMoA (class in mkt.databases.open_targets), [1] order (mkt.databases.conservation.KLIFSDisplayTree attribute), [1] order_kinase_groups() (in module mkt.databases.plot), [1] ortholog (mkt.schema.kinase_schema.MSASource attribute), [1] Other (mkt.schema.kinase_schema.Family attribute), [1] (mkt.schema.kinase_schema.Group attribute), [1] other_color (mkt.databases.plot_config.FamilyColorConfig attribute), [1] output (mkt.databases.plot_config.DictKinaseFiguresConfig attribute), [1] (mkt.databases.plot_config.PlotDatasetConfig attribute), [1] OUTPUT_DIR_VAR (in module mkt.schema.config), [1] OutputConfig (class in mkt.databases.plot_config), [1] overlap (mkt.databases.plot_config.RidgelinePlotConfig attribute), [1]

P

palette_n_colors (mkt.databases.plot_config.FamilyColorConfig attribute), [1] palette_name (mkt.databases.plot_config.FamilyColorConfig attribute), [1] panel_id (mkt.databases.cbioportal.PanelData attribute), [1] panel_title_fontsize (mkt.databases.plot_config.SequenceSchematicConfig attribute), [1] panel_title_fontweight (mkt.databases.plot_config.SequenceSchematicConfig attribute), [1] PanelData (class in mkt.databases.cbioportal), [1] params (mkt.databases.chembl.ChEMBL attribute), [1] (mkt.databases.chembl.ChEMBLMolecule attribute), [1] (mkt.databases.chembl.ChEMBLMoleculeExact attribute), [1] (mkt.databases.chembl.ChEMBLMoleculePreferred attribute), [1] (mkt.databases.chembl.ChEMBLMoleculeSearch attribute) parse_fasta_description() (in module mkt.databases.kincore), [1] parse_iterabc2dataframe() (in module mkt.databases.io_utils), [1] parse_mutation_info() (mkt.databases.datasets.discoverx.DiscoverXInfoGenerator method), [1] parse_pdb_line() (mkt.databases.app.structures.StructureVisualizer static method), [1] path_bin (mkt.databases.aligners.ClustalOmegaAligner attribute), [1] pathfile (mkt.databases.cbioportal.cBioPortalQuery attribute), [1] pathfile_filter (mkt.databases.cbioportal.KinaseMissenseMutations attribute), [1] pct_label_fontsize (mkt.databases.plot_config.StackedBarchartConfig attribute), [1] (mkt.databases.plot_config.UpsetPlotConfig attribute), [1] pct_label_fontweight (mkt.databases.plot_config.StackedBarchartConfig attribute), [1] pct_label_min_threshold (mkt.databases.plot_config.StackedBarchartConfig attribute), [1] PDB70 (mkt.schema.kinase_schema.TemplateSource attribute), [1] pdf_fonttype (mkt.databases.plot_config.MatplotlibRCConfig attribute), [1] PDGFR (mkt.schema.kinase_schema.Family attribute), [1] PDHK (mkt.schema.kinase_schema.Family attribute), [1] percentile_colormap() (in module mkt.databases.colors), [1] Pfam (class in mkt.databases.pfam), [1] (class in mkt.schema.kinase_schema), [1] pfam (mkt.databases.kinase_schema.KinaseInfoGenerator attribute) (mkt.schema.kinase_schema.KinaseInfo attribute), [1] (mkt.schema.kinase_schema.KinaseInfoUniProt attribute), [1] pfam_accession (mkt.schema.kinase_schema.Pfam attribute), [1] phospho_description (mkt.schema.kinase_schema.UniProt attribute), [1] phospho_evidence (mkt.schema.kinase_schema.UniProt attribute), [1] phospho_sites (mkt.schema.kinase_schema.UniProt attribute), [1] PHOSPHOSITES (mkt.databases.app.schema.StandardConfig attribute), [1] (mkt.databases.app.schema.StandardConfigChoice attribute), [1] PhosphositesConfig (class in mkt.databases.app.schema), [1] PIK (mkt.schema.kinase_schema.Family attribute), [1] PIKK (mkt.schema.kinase_schema.Family attribute), [1] PIPK (mkt.schema.kinase_schema.Family attribute), [1] PKA (mkt.schema.kinase_schema.Family attribute), [1] PKC (mkt.schema.kinase_schema.Family attribute), [1] pkis2_csv (mkt.databases.plot_config.DataSourceConfig attribute), [1] PLK (mkt.schema.kinase_schema.Family attribute), [1] plot() (mkt.databases.conservation.KLIFSConservationTreeFigure method), [1] plot_critical_depth() (mkt.databases.conservation.KLIFSHierarchicalConservation method), [1]

plot_dict_kinase_upset() (in module mkt.databases.plot), [1] plot_dynamic_range() (in module mkt.databases.plot), [1] plot_height (mkt.databases.plot.SequenceAlignment attribute), [1] plot_metrics_boxplot() (in module mkt.databases.plot), [1] plot_region_gap_violin() (in module mkt.databases.plot), [1] plot_residue_dot() (mkt.databases.conservation.KLIFSConservationTreeFigure method), [1] plot_ridgeline() (in module mkt.databases.plot), [1] plot_sequence_input_schematic() (in module mkt.databases.plot), [1] plot_split() (mkt.databases.conservation.KLIFSConservationTreeFigure method), [1] plot_stacked_barchart() (in module mkt.databases.plot), [1] plot_venn_diagram() (in module mkt.databases.plot), [1] plot_width (mkt.databases.plot.SequenceAlignment attribute), [1] PlotDatasetConfig (class in mkt.databases.plot_config), [1] pocket_length (mkt.schema.conservation_schema.KLIFSConservationData attribute), [1] pocket_seq (mkt.schema.kinase_schema.KLIFS attribute), [1] pockets (mkt.databases.conservation.KLIFSConservationTreeFigure attribute) (mkt.databases.conservation.KLIFSHierarchicalConservation attribute), [1] (mkt.databases.conservation.KLIFSResidueDotApp attribute) (mkt.databases.conservation.KLIFSTreeConservationApp attribute) popEVE (mkt.databases.protvar.ScoreDatabase attribute), [1] pos (mkt.databases.protvar.ProtvarScoreQuery attribute), [1] position_labels (mkt.databases.conservation.KLIFSConservationTreeFigure attribute) (mkt.databases.conservation.KLIFSHierarchicalConservation attribute), [1] (mkt.databases.conservation.KLIFSResidueDotApp attribute) (mkt.databases.conservation.KLIFSTreeConservationApp attribute) (mkt.schema.conservation_schema.KLIFSConservationData attribute), [1] preprint_2026() (mkt.databases.plot_config.RegionGapViolinConfig class method), [1] (mkt.databases.plot_config.UpsetPlotConfig class method), [1] print_status_code_if_res_not_ok() (in module mkt.databases.utils_requests), [1] probe_radius (mkt.databases.sasa.BaseSASAConfig attribute), [1] (mkt.databases.sasa.ResidueSASA attribute), [1] process_fasta() (mkt.databases.ncbi.ProteinNCBI static method), [1] process_keys_dict() (in module mkt.databases.kinase_schema), [1] PropertyTables (class in mkt.databases.app.properties), [1] protein_length (mkt.schema.kinase_schema.Pfam attribute), [1] ProteinEntrez (class in mkt.databases.ncbi), [1] ProteinNCBI (class in mkt.databases.ncbi), [1] ProtvarScoreQuery (class in mkt.databases.protvar), [1] ProtvarVariant (class in mkt.databases.protvar), [1] pseudocounts() (mkt.databases.pssm.SubstitutionPseudocounts method), [1] pvalue_fontsize (mkt.databases.plot_config.MetricsBoxplotConfig attribute), [1] pvalue_fontweight (mkt.databases.plot_config.MetricsBoxplotConfig attribute), [1] PYMOL_HEAVY (mkt.databases.sasa.StandardSASAConfigChoice attribute), [1] (mkt.databases.sasa.StandardSASAConfigs attribute), [1] PYMOL_HYDROGEN (mkt.databases.sasa.StandardSASAConfigChoice attribute), [1] (mkt.databases.sasa.StandardSASAConfigs attribute), [1] PyMOLGenerator (class in mkt.databases.pymol), [1] PyMOLHeavyConfig (class in mkt.databases.sasa), [1] PyMOLHydrogenConfig (class in mkt.databases.sasa), [1]

Q

query_api() (mkt.databases.alphafold.AlphaFoldPrediction method), [1] (mkt.databases.api_schema.GraphQLClient method), [1] (mkt.databases.api_schema.RESTAPIClient method), [1] (mkt.databases.api_schema.SwaggerAPIClient method), [1] (mkt.databases.cancer_hotspots.CancerHotspotsQuery method), [1] (mkt.databases.cbioportal.cBioPortal method), [1] (mkt.databases.chembl.ChEMBL method), [1] (mkt.databases.hgnc.HGNC method), [1] (mkt.databases.klifs.KLIFS method), [1] (mkt.databases.ncbi.ProteinNCBI method), [1] (mkt.databases.oncokb.OncoKB method), [1] (mkt.databases.oncokb.OncoKBCancerGeneList method), [1] (mkt.databases.pfam.Pfam method), [1] (mkt.databases.protvar.ProtvarScoreQuery method), [1] (mkt.databases.uniprot.UniProtFASTA method), [1] (mkt.databases.uniprot.UniProtJSON method), [1]

query_datetime (mkt.databases.api_schema.APIClient attribute), [1] query_hgnc_gene_names() (mkt.databases.cbioportal.KinaseMissenseMutations method), [1] query_kinase_info() (mkt.databases.klifs.KinaseInfo method), [1] query_kinase_names() (mkt.databases.klifs.KinaseNames method), [1] query_string (mkt.databases.api_schema.GraphQLClient attribute), [1] (mkt.databases.open_targets.OpenTargetsDrugMoA attribute), [1] query_sub_api() (mkt.databases.cbioportal.cBioPortalQuery method), [1] (mkt.databases.cbioportal.Clinical method), [1] (mkt.databases.cbioportal.GenePanel method), [1] (mkt.databases.cbioportal.Mutations method), [1] (mkt.databases.cbioportal.Treatment method), [1] query_uniprotbulk_api() (in module mkt.databases.uniprot), [1]

R

RAF (mkt.schema.kinase_schema.Family attribute), [1] random_uuid() (in module mkt.schema.utils), [1] RASMOL (mkt.databases.colors.AminoAcidPalette attribute), [1] read_csv() (mkt.databases.cancer_hotspots.CancerHotspots static method), [1] (mkt.databases.oncokb.OncoKBCancerGeneList static method), [1] (mkt.databases.three_d_hotspots.ThreeDHotspots static method), [1] readable_text_color() (in module mkt.databases.colors), [1] rebuild_square() (mkt.schema.conservation_schema.KLIFSConservationData method), [1] rebuild_tree_from_data() (in module mkt.databases.conservation), [1] rect_height (mkt.databases.plot_config.SequenceSchematicConfig attribute), [1] recursive_idx_search() (mkt.databases.datasets.discoverx.DiscoverXInfo method), [1] (mkt.databases.klifs.KLIFSPocket method), [1] regenerate_dataframe() (mkt.databases.cbioportal.cBioPortalQuery method), [1] region_gap_violin (mkt.databases.plot_config.DictKinaseFiguresConfig attribute), [1] RegionGapViolinConfig (class in mkt.databases.plot_config), [1] remove_gaps_from_klifs() (mkt.databases.klifs.KLIFSPocket static method), [1] remove_mismatched_uniprot_mutations() (mkt.databases.cbioportal.KinaseMissenseMutations method), [1] remove_spines() (in module mkt.databases.plot), [1] replace_multi_mapping_keys() (mkt.databases.datasets.discoverx.DiscoverXInfoGenerator method), [1] replace_mutations_in_sequences() (mkt.databases.datasets.discoverx.DiscoverXInfo method), [1] replace_none_with_max_len() (in module mkt.databases.kinase_schema), [1] replace_string_using_dict() (in module mkt.databases.utils), [1] REQUESTS_CACHE_VAR (in module mkt.databases.config) residue_dot (mkt.databases.plot_config.DictKinaseFiguresConfig attribute), [1] residue_dot_explorer (mkt.databases.plot_config.DictKinaseFiguresConfig attribute), [1] residue_dot_layout() (mkt.databases.conservation.KLIFSHierarchicalConservation method), [1] RESIDUE_RE (in module mkt.databases.three_d_hotspots), [1] RESIDUE_SHEET (in module mkt.databases.three_d_hotspots), [1] ResidueDotConfig (class in mkt.databases.plot_config), [1] ResidueDotExplorerConfig (class in mkt.databases.plot_config), [1] ResidueSASA (class in mkt.databases.sasa), [1] resolve_code() (mkt.databases.oncotree.OncoTree method), [1] response (mkt.databases.api_schema.GraphQLClient attribute), [1] RESTAPIClient (class in mkt.databases.api_schema), [1] return_adjusted_colname() (mkt.databases.cbioportal.cBioPortalQuery method), [1] return_bool_at_index() (in module mkt.databases.utils), [1] return_chembl_id() (in module mkt.databases.chembl), [1] return_construct_boundaries() (mkt.databases.datasets.discoverx.DiscoverXInfoGenerator static method), [1]

return_deletion_mutation() (mkt.databases.datasets.discoverx.DiscoverXInfoGenerator static method), [1] return_df_tissue_drop() (mkt.databases.oncotree.OncoTree method), [1] return_fasta_contents() (in module mkt.databases.kincore), [1] return_filenotfound_error_if_empty_or_missing() (in module mkt.schema.io_utils), [1] return_filepath_dict() (mkt.databases.pymol.PyMOLGenerator method), [1] return_idx_of_alignment_match() (mkt.databases.klifs.KLIFSPocket static method), [1] return_idx_of_substring_in_superstring() (mkt.databases.klifs.KLIFSPocket static method), [1] return_index() (mkt.databases.datasets.discoverx.DiscoverXInfo method), [1] return_intra_gap_substr() (mkt.databases.datasets.discoverx.DiscoverXInfo method), [1] (mkt.databases.klifs.KLIFSPocket method), [1] return_kinase_dict() (in module mkt.databases.io_utils), [1] return_kinase_gene_set() (in module mkt.schema.utils), [1] return_list_cif_idx() (mkt.databases.app.schema.StructureConfig method), [1] return_list_idx_intersect() (mkt.databases.app.schema.StructureConfig method), [1] return_list_intersect_color_style() (mkt.databases.app.schema.StructureConfig method), [1] return_list_match_indices() (in module mkt.databases.utils), [1] return_list_out() (in module mkt.databases.utils), [1] return_missense_mutation() (mkt.databases.datasets.discoverx.DiscoverXInfoGenerator static method), [1] return_molecular_brake_residues() (mkt.schema.kinase_schema.KinaseInfo method), [1] return_none_if_not_valid_string() (in module mkt.databases.kinase_schema), [1] return_partial_alignments() (mkt.databases.klifs.KLIFSPocket method), [1] return_preferred_name() (mkt.databases.chembl.ChEMBLMolecule method), [1] return_refseq2uniprot_mapping() (mkt.databases.datasets.discoverx.DiscoverXInfo method), [1] return_smiles() (mkt.databases.chembl.ChEMBLMolecule method), [1] return_str_path_from_pkg_data() (in module mkt.schema.io_utils), [1] reverse_order_dict_of_dict() (in module mkt.databases.kinase_schema), [1] RGC (mkt.schema.kinase_schema.Family attribute), [1] (mkt.schema.kinase_schema.Group attribute), [1] rgetattr() (in module mkt.schema.utils), [1] ribbon_alpha (mkt.databases.plot_config.RegionGapViolinConfig attribute), [1] ridgeline (mkt.databases.plot_config.PlotDatasetConfig attribute), [1] RidgelinePlotConfig (class in mkt.databases.plot_config), [1] right_adjust (mkt.databases.plot_config.RegionGapViolinConfig attribute), [1] RIPK (mkt.schema.kinase_schema.Family attribute), [1] roll_up_map() (mkt.databases.oncotree.OncoTree method), [1] rsetattr() (in module mkt.schema.utils), [1] RSK (mkt.schema.kinase_schema.Family attribute), [1] RSKb (mkt.schema.kinase_schema.Family attribute), [1] run() (mkt.databases.sasa.ResidueSASA method), [1]

S

save_app() (mkt.databases.conservation.KLIFSResidueDotApp method), [1] (mkt.databases.conservation.KLIFSTreeConservationApp method), [1] save_dataframe_to_csv() (in module mkt.databases.io_utils), [1] save_plot() (in module mkt.schema.io_utils), [1] save_pymol_files() (mkt.databases.pymol.PyMOLGenerator method), [1] scale (mkt.databases.plot_config.RidgelinePlotConfig attribute), [1] ScoreDatabase (class in mkt.databases.protvar), [1] scores (mkt.databases.protvar.ProtvarVariant attribute), [1] select_correct_alignment() (mkt.databases.klifs.KLIFSPocket method), [1] seq (mkt.schema.kinase_schema.KinCoreFASTA attribute), [1] seq_align (mkt.databases.app.schema.DefaultConfig attribute) (mkt.databases.app.schema.KLIFSAdaptiveConfig attribute) (mkt.databases.app.schema.KLIFSConfig attribute) (mkt.databases.app.schema.KLIFSCustomConfig attribute) (mkt.databases.app.schema.KLIFSImportantConfig attribute) (mkt.databases.app.schema.KLIFSPathogenicConfig attribute) (mkt.databases.app.schema.KLIFSRegionLabelConfig attribute) (mkt.databases.app.schema.MutationsConfig attribute) (mkt.databases.app.schema.MutationsDefaultConfig attribute) (mkt.databases.app.schema.MutationsGroupConfig attribute) (mkt.databases.app.schema.MutationsKLIFSConfig attribute) (mkt.databases.app.schema.PhosphositesConfig attribute) (mkt.databases.app.schema.StructureConfig attribute), [1] seq_refseq (mkt.databases.datasets.discoverx.DiscoverXInfo attribute), [1] seq_uniprot (mkt.databases.datasets.discoverx.DiscoverXInfo attribute), [1] sequence_schematic (mkt.databases.plot_config.PlotDatasetConfig attribute), [1] SequenceAlignment (class in mkt.databases.app.sequences), [1] (class in mkt.databases.plot), [1] SequenceSchematicConfig (class in mkt.databases.plot_config), [1] serialize_conservation_data() (in module mkt.schema.io_utils), [1] serialize_kinase_dict() (in module mkt.schema.io_utils), [1] set_api_key() (mkt.databases.api_schema.APIKeyRESTAPIClient method), [1] (mkt.databases.api_schema.APIKeySwaggerClient method), [1] set_cbioportal_instance() (in module mkt.databases.config) set_cbioportal_token() (in module mkt.databases.config) SET_HOMOLOG_DO_NOT_MERGE (in module mkt.schema.utils), [1] set_label_fontsize (mkt.databases.plot_config.VennDiagramConfig attribute), [1] set_label_fontweight (mkt.databases.plot_config.VennDiagramConfig attribute), [1] set_oncokb_token() (in module mkt.databases.config) set_output_dir() (in module mkt.databases.config) (in module mkt.schema.config), [1] set_request_cache() (in module mkt.databases.config) set_url() (mkt.databases.uniprot.UniProtFASTA method), [1] SHAPELY (mkt.databases.colors.AminoAcidPalette attribute), [1] show_plot() (mkt.databases.plot.SequenceAlignment method), [1] smoothed_freqs() (mkt.databases.pssm.SubstitutionPseudocounts method), [1] source_file (mkt.schema.kinase_schema.KinCoreFASTA attribute), [1] split_domain_suffix() (in module mkt.schema.utils), [1] split_index (mkt.databases.conservation.KLIFSConservationTreeFigure attribute), [1] (mkt.databases.plot_config.ConservationTreeConfig attribute), [1] split_on_first_only() (in module mkt.databases.utils), [1] splits (mkt.databases.conservation.KLIFSDisplayTree attribute), [1] Src (mkt.schema.kinase_schema.Family attribute), [1] stack_color_false (mkt.databases.plot_config.StackedBarchartConfig attribute), [1] stack_color_true (mkt.databases.plot_config.StackedBarchartConfig attribute), [1] stacked_barchart (mkt.databases.plot_config.PlotDatasetConfig attribute), [1] StackedBarchartConfig (class in mkt.databases.plot_config), [1] StandardConfig (class in mkt.databases.app.schema), [1] StandardConfigChoice (class in mkt.databases.app.schema), [1] standardize_offset() (mkt.databases.kinase_schema.KinaseInfoGenerator method), [1] StandardSASAConfigChoice (class in mkt.databases.sasa), [1] StandardSASAConfigs (class in mkt.databases.sasa), [1] start (mkt.schema.kinase_schema.KinCore attribute), [1] (mkt.schema.kinase_schema.KinCoreCIF attribute), [1] (mkt.schema.kinase_schema.KinCoreFASTA attribute), [1] (mkt.schema.kinase_schema.Pfam attribute), [1]

start_af2 (mkt.schema.kinase_schema.KinCoreFASTA attribute), [1] start_md (mkt.schema.kinase_schema.KinCoreFASTA attribute), [1] STE (mkt.schema.kinase_schema.Group attribute), [1] STE11 (mkt.schema.kinase_schema.Family attribute), [1] STE20 (mkt.schema.kinase_schema.Family attribute), [1] STE7 (mkt.schema.kinase_schema.Family attribute), [1] STKR (mkt.schema.kinase_schema.Family attribute), [1] STR_AA20 (in module mkt.databases.pssm), [1] str_attr (mkt.databases.app.schema.DefaultConfig attribute), [1] (mkt.databases.app.schema.KLIFSConfig attribute), [1] (mkt.databases.app.schema.MutationsConfig attribute), [1] (mkt.databases.app.schema.PhosphositesConfig attribute), [1] (mkt.databases.app.schema.StructureConfig attribute), [1] (mkt.databases.pymol.PyMOLGenerator attribute), [1] str_blosom (mkt.databases.cbioportal.KinaseMissenseMutations attribute), [1] STR_BLOSUM_MATRIX (in module mkt.databases.conservation), [1] STR_CONSERVATION_FILENAME (in module mkt.schema.io_utils), [1] str_fasta (mkt.databases.ncbi.ProteinNCBI attribute), [1] STR_FILE_CONSERVATION_TREE (in module mkt.databases.conservation), [1] STR_FILE_CONSERVATION_TREE_BOTTOM (in module mkt.databases.conservation), [1] STR_FILE_CONSERVATION_TREE_SUMMARY (in module mkt.databases.conservation), [1] STR_FILE_CONSERVATION_TREE_TOP (in module mkt.databases.conservation), [1] STR_FILE_RESIDUE_DOT (in module mkt.databases.conservation), [1] STR_FILE_RESIDUE_DOT_APP (in module mkt.databases.conservation), [1] STR_FILE_TREE_APP (in module mkt.databases.conservation), [1] str_filepath_json (mkt.databases.app.schema.MutationsConfig attribute), [1] (mkt.databases.app.schema.MutationsDefaultConfig attribute) (mkt.databases.app.schema.MutationsGroupConfig attribute) (mkt.databases.app.schema.MutationsKLIFSConfig attribute) STR_GAP_CHARS (in module mkt.databases.pssm), [1] str_group (mkt.databases.plot_config.CladeMembershipTableConfig attribute), [1] str_kinase (mkt.databases.app.sequences.SequenceAlignment attribute), [1] STR_KLIFS_BETA2_LYSINE (in module mkt.schema.constants), [1] STR_KLIFS_BETA3_LYSINE (in module mkt.schema.constants), [1] STR_KLIFS_CATALYTIC_ASP (in module mkt.schema.constants), [1] STR_KLIFS_DFG_ASP (in module mkt.schema.constants), [1] STR_LINKAGE_AVERAGE (in module mkt.databases.conservation), [1] STR_LINKAGE_COMPLETE (in module mkt.databases.conservation), [1] STR_METRIC_BLOSUM (in module mkt.databases.conservation), [1] STR_METRIC_IDENTITY (in module mkt.databases.conservation), [1] STR_RESIDUE_DOT_DEFAULT_AA (in module mkt.databases.conservation), [1] str_start (mkt.databases.datasets.discoverx.DiscoverXInfo attribute), [1] str_stop (mkt.databases.datasets.discoverx.DiscoverXInfo attribute), [1] str_url (mkt.databases.datasets.discoverx.DiscoverXInfoGenerator attribute), [1] STR_WEIGHTING_HENIKOFF (in module mkt.databases.conservation), [1] STR_WEIGHTING_NONE (in module mkt.databases.conservation), [1] StructureConfig (class in mkt.databases.app.schema), [1] StructureVisualizer (class in mkt.databases.app.structures), [1] study_id (mkt.databases.cbioportal.Clinical attribute) (mkt.databases.cbioportal.ClinicalPatient attribute) (mkt.databases.cbioportal.ClinicalSample attribute) (mkt.databases.cbioportal.KinaseMissenseMutations attribute) (mkt.databases.cbioportal.StudyData attribute), [1] StudyData (class in mkt.databases.cbioportal), [1] subdir (mkt.databases.plot_config.OutputConfig attribute), [1] subset_label_fontsize (mkt.databases.plot_config.VennDiagramConfig attribute), [1] substitution_matrix (mkt.databases.aligners.BioAligner attribute), [1] (mkt.databases.aligners.ClustalOmegaAligner attribute), [1] SubstitutionPseudocounts (class in mkt.databases.pssm), [1] subtitle_alpha (mkt.databases.plot_config.DynamicRangePlotConfig attribute), [1] subtitle_fontsize (mkt.databases.plot_config.DynamicRangePlotConfig attribute), [1] subtitle_y (mkt.databases.plot_config.DynamicRangePlotConfig attribute), [1] svg_fonttype (mkt.databases.plot_config.MatplotlibRCConfig attribute), [1] SwaggerAPIClient (class in mkt.databases.api_schema), [1] swissprot (mkt.schema.kinase_schema.KinCoreFASTA attribute), [1] SwissProtPattern (in module mkt.schema.kinase_schema), [1] SwissProtPatternSuffix (in module mkt.schema.kinase_schema), [1]

T

target_probs (mkt.databases.pssm.SubstitutionPseudocounts property), [1] Tec (mkt.schema.kinase_schema.Family attribute), [1] template_source (mkt.schema.kinase_schema.KinCoreCIF attribute), [1] TemplateSource (class in mkt.schema.kinase_schema), [1] text_color (mkt.databases.plot_config.RegionGapViolinConfig attribute), [1] text_usetex (mkt.databases.plot_config.MatplotlibRCConfig attribute), [1] ThreeDHotspots (class in mkt.databases.three_d_hotspots), [1] tick_labelsize (mkt.databases.plot_config.DynamicRangePlotConfig attribute), [1] TIER_COLUMN (in module mkt.databases.cancer_hotspots), [1] tighten_totals_gap (mkt.databases.plot_config.UpsetPlotConfig attribute), [1] title_color_davis (mkt.databases.plot_config.MetricsBoxplotConfig attribute), [1] (mkt.databases.plot_config.RidgelinePlotConfig attribute), [1] (mkt.databases.plot_config.StackedBarchartConfig attribute), [1] title_color_pkis2 (mkt.databases.plot_config.MetricsBoxplotConfig attribute), [1] (mkt.databases.plot_config.RidgelinePlotConfig attribute), [1] (mkt.databases.plot_config.StackedBarchartConfig attribute), [1] title_fontsize (mkt.databases.plot_config.DynamicRangePlotConfig attribute), [1] (mkt.databases.plot_config.MetricsBoxplotConfig attribute), [1] (mkt.databases.plot_config.RidgelinePlotConfig attribute), [1] (mkt.databases.plot_config.SequenceSchematicConfig attribute), [1] (mkt.databases.plot_config.StackedBarchartConfig attribute), [1] (mkt.databases.plot_config.VennDiagramConfig attribute), [1] title_fontweight (mkt.databases.plot_config.DynamicRangePlotConfig attribute), [1] (mkt.databases.plot_config.MetricsBoxplotConfig attribute), [1] (mkt.databases.plot_config.RidgelinePlotConfig attribute), [1] (mkt.databases.plot_config.SequenceSchematicConfig attribute), [1] (mkt.databases.plot_config.StackedBarchartConfig attribute), [1] (mkt.databases.plot_config.VennDiagramConfig attribute), [1] title_y (mkt.databases.plot_config.DynamicRangePlotConfig attribute), [1]

TK (mkt.schema.kinase_schema.Group attribute), [1] TKL (mkt.schema.kinase_schema.Group attribute), [1] to_conservation_data() (mkt.databases.conservation.KLIFSHierarchicalConservation method), [1] to_csv() (mkt.databases.cancer_hotspots.CancerHotspots method), [1] (mkt.databases.oncokb.OncoKBCancerGeneList method), [1] (mkt.databases.three_d_hotspots.ThreeDHotspots method), [1] to_long_form() (mkt.schema.conservation_schema.KLIFSConservationData method), [1] top_adjust (mkt.databases.plot_config.RegionGapViolinConfig attribute), [1] totals_gap_margin (mkt.databases.plot_config.UpsetPlotConfig attribute), [1] totals_plot_elements (mkt.databases.plot_config.UpsetPlotConfig attribute), [1] TQDM_BAR_FORMAT (in module mkt.schema.utils), [1] Treatment (class in mkt.databases.cbioportal), [1] tree (mkt.databases.conservation.KLIFSConservationTreeFigure attribute) (mkt.databases.conservation.KLIFSHierarchicalConservation attribute), [1] (mkt.databases.conservation.KLIFSResidueDotApp attribute) (mkt.databases.conservation.KLIFSTreeConservationApp attribute) tree_children() (mkt.databases.conservation.KLIFSHierarchicalConservation method), [1] tree_count() (mkt.databases.conservation.KLIFSHierarchicalConservation method), [1] tree_members() (mkt.databases.conservation.KLIFSHierarchicalConservation method), [1] TrEMBLPattern (in module mkt.schema.kinase_schema), [1] TrEMBLPatternSuffix (in module mkt.schema.kinase_schema), [1] try_except_convert_str2int() (in module mkt.databases.utils), [1] try_except_match_str2dict() (in module mkt.databases.utils), [1] try_except_middle_int() (mkt.databases.cbioportal.KinaseMissenseMutations static method), [1] try_except_split_concat_str() (in module mkt.databases.utils), [1] try_except_substraction() (in module mkt.databases.utils), [1] TSSK (mkt.schema.kinase_schema.Family attribute), [1] TUP_TREE_PAGE (in module mkt.databases.conservation), [1] TUP_TREE_SUMMARY_PAGE (in module mkt.databases.conservation), [1] TUPLE_VARIANT_DATABASES (in module mkt.databases.protvar), [1]

U

ULK (mkt.schema.kinase_schema.Family attribute), [1] UniProt (class in mkt.databases.uniprot), [1] (class in mkt.schema.kinase_schema), [1] uniprot (mkt.databases.kinase_schema.KinaseInfoGenerator attribute) (mkt.schema.kinase_schema.KinaseInfo attribute), [1] (mkt.schema.kinase_schema.KinaseInfoUniProt attribute), [1] (mkt.schema.kinase_schema.KinCoreFASTA attribute), [1] uniprot_id (mkt.databases.alphafold.AlphaFoldPrediction attribute), [1] (mkt.databases.datasets.discoverx.DiscoverXInfo attribute), [1] (mkt.databases.kinase_schema.KinaseInfoGenerator attribute) (mkt.databases.pfam.Pfam attribute), [1] (mkt.databases.protvar.ProtvarScoreQuery attribute), [1] (mkt.databases.uniprot.UniProt attribute), [1] (mkt.databases.uniprot.UniProtFASTA attribute) (mkt.databases.uniprot.UniProtJSON attribute) (mkt.schema.kinase_schema.KinaseInfo attribute), [1] (mkt.schema.kinase_schema.KinaseInfoKinaseDomain attribute), [1] (mkt.schema.kinase_schema.KinaseInfoUniProt attribute), [1] UniProtFASTA (class in mkt.databases.uniprot), [1] UniProtJSON (class in mkt.databases.uniprot), [1] UniProtRefSeqProteinGET (class in mkt.databases.uniprot), [1] uniprotSeq (mkt.databases.klifs.KLIFSPocket attribute), [1] uniref90 (mkt.schema.kinase_schema.MSASource attribute), [1] untar_files_in_memory() (in module mkt.schema.io_utils), [1] untar_if_neeeded() (in module mkt.schema.io_utils), [1] update_original_cif_with_new_coords() (in module mkt.databases.kincore), [1] update_params() (mkt.databases.chembl.ChEMBL method), [1] update_url() (mkt.databases.chembl.ChEMBL method), [1] (mkt.databases.oncokb.OncoKB method), [1] (mkt.databases.oncokb.OncoKBInfo method), [1] (mkt.databases.oncokb.OncoKBProteinChange method), [1]

upset_plot (mkt.databases.plot_config.DictKinaseFiguresConfig attribute), [1] UpsetPlotConfig (class in mkt.databases.plot_config), [1] url (mkt.databases.alphafold.AlphaFoldPrediction attribute), [1] (mkt.databases.api_schema.GraphQLClient attribute), [1] (mkt.databases.cancer_hotspots.CancerHotspotsQuery attribute), [1] (mkt.databases.cbioportal.cBioPortal attribute), [1] (mkt.databases.hgnc.HGNC attribute), [1] (mkt.databases.ncbi.ProteinNCBI attribute), [1] (mkt.databases.oncokb.OncoKB attribute), [1] (mkt.databases.oncokb.OncoKBCancerGeneList attribute), [1] (mkt.databases.open_targets.OpenTargets attribute), [1] (mkt.databases.pfam.Pfam attribute), [1] (mkt.databases.protvar.ProtvarScoreQuery attribute), [1] (mkt.databases.uniprot.UniProt attribute), [1] url_base (mkt.databases.chembl.ChEMBL attribute), [1] url_fasta (mkt.databases.uniprot.UniProtFASTA attribute), [1] url_query (mkt.databases.chembl.ChEMBL attribute), [1] (mkt.databases.oncokb.OncoKB attribute), [1] url_suffix (mkt.databases.chembl.ChEMBL attribute), [1] (mkt.databases.chembl.ChEMBLMolecule attribute), [1] (mkt.databases.chembl.ChEMBLMoleculeExact attribute), [1] (mkt.databases.chembl.ChEMBLMoleculePreferred attribute), [1] (mkt.databases.chembl.ChEMBLMoleculeSearch attribute), [1] use_kinase_group_colors (mkt.databases.plot_config.FamilyColorConfig attribute), [1] use_ribbon (mkt.databases.plot_config.RegionGapViolinConfig attribute), [1]

V

validate_construct_boundaries() (mkt.databases.datasets.discoverx.DiscoverXInfo class method), [1] validate_deletions() (mkt.databases.datasets.discoverx.DiscoverXInfo class method), [1] validate_klifs2uniprotidx() (mkt.schema.kinase_schema.KinaseInfo class method), [1] validate_klifs2uniprotseq() (mkt.schema.kinase_schema.KinaseInfo class method), [1] validate_missense_mutations() (mkt.databases.datasets.discoverx.DiscoverXInfo class method), [1] validate_phosphosites2canonicalseq() (mkt.databases.kinase_schema.KinaseInfoUniProtGenerator method), [1] validate_uniprot_indices() (in module mkt.databases.app.utils), [1] validate_uniprot_length() (mkt.databases.kinase_schema.KinaseInfoUniProtGenerator method), [1] variables (mkt.databases.api_schema.GraphQLClient attribute), [1] (mkt.databases.open_targets.OpenTargets attribute) (mkt.databases.open_targets.OpenTargetsDrugMoA attribute), [1]

venn_diagram (mkt.databases.plot_config.PlotDatasetConfig attribute), [1] VennDiagramConfig (class in mkt.databases.plot_config), [1] verbose (mkt.databases.chembl.ChEMBL attribute), [1] (mkt.databases.oncokb.OncoKBProteinChange attribute), [1] version (mkt.databases.cancer_hotspots.CancerHotspotsQuery attribute), [1] violin_edgecolor (mkt.databases.plot_config.RegionGapViolinConfig attribute), [1] violin_fontsize (mkt.databases.plot_config.RegionGapViolinConfig attribute), [1] violin_linewidth (mkt.databases.plot_config.RegionGapViolinConfig attribute), [1] violin_width (mkt.databases.plot_config.RegionGapViolinConfig attribute), [1] viz (mkt.databases.pymol.PyMOLGenerator attribute), [1] vus (mkt.databases.oncokb.OncoKBProteinChange attribute), [1]

W

weighting (mkt.databases.conservation.KLIFSConservationTreeFigure attribute) (mkt.databases.conservation.KLIFSHierarchicalConservation attribute), [1] (mkt.databases.conservation.KLIFSResidueDotApp attribute) (mkt.databases.conservation.KLIFSTreeConservationApp attribute) (mkt.schema.conservation_schema.KLIFSConservationData attribute), [1]

whisker_color (mkt.databases.plot_config.MetricsBoxplotConfig attribute), [1] whisker_linewidth (mkt.databases.plot_config.MetricsBoxplotConfig attribute), [1] width_ratios (mkt.databases.plot_config.RegionGapViolinConfig attribute), [1] write_clade_membership_table() (in module mkt.databases.plot), [1] wspace (mkt.databases.plot_config.RegionGapViolinConfig attribute), [1]

X

xlabel_fontsize (mkt.databases.plot_config.RidgelinePlotConfig attribute), [1] (mkt.databases.plot_config.StackedBarchartConfig attribute), [1] xlabel_text (mkt.databases.plot_config.RidgelinePlotConfig attribute), [1]

xname (mkt.schema.kinase_schema.KinHub attribute), [1] xtick_fontsize (mkt.databases.plot_config.MetricsBoxplotConfig attribute), [1] (mkt.databases.plot_config.RidgelinePlotConfig attribute), [1] (mkt.databases.plot_config.StackedBarchartConfig attribute), [1]

Y

ylabel_fontsize (mkt.databases.plot_config.MetricsBoxplotConfig attribute), [1] (mkt.databases.plot_config.StackedBarchartConfig attribute), [1] ylabel_text (mkt.databases.plot_config.MetricsBoxplotConfig attribute), [1] (mkt.databases.plot_config.RegionGapViolinConfig attribute), [1]

ylim_max (mkt.databases.plot_config.StackedBarchartConfig attribute), [1] ytick_fontsize (mkt.databases.plot_config.MetricsBoxplotConfig attribute), [1] (mkt.databases.plot_config.RidgelinePlotConfig attribute), [1] (mkt.databases.plot_config.StackedBarchartConfig attribute), [1]

Z

ZAPPO (mkt.databases.colors.AminoAcidPalette attribute), [1]