Index Symbols | A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | Q | R | S | T | U | V | W | Z Symbols |project| module A abs() (CupyBackend method) (JaxBackend method) (MatchingBackend method) (MLXBackend method) (NumpyFFTWBackend method) (PytorchBackend method) absolute_minimum_deviation() (in module tme.extensions) acceleration_voltage (CTF attribute) add() (CupyBackend method) (JaxBackend method) (MatchingBackend method) (MLXBackend method) (NumpyFFTWBackend method) (PytorchBackend method) add_backend() (BackendManager method) adjust_box() (Density method) align_structures() (Structure class method) alternate_location_indicator (Structure attribute) amplitude_contrast (CTF attribute) angles (CTF attribute) (ReconstructFromTilt attribute) apply_convolution_mode() (in module tme.matching_utils) apply_method() (Preprocessor method) arange() (CupyBackend method) (JaxBackend method) (MatchingBackend method) (MLXBackend method) (NumpyFFTWBackend method) (PytorchBackend method) argsort() (CupyBackend method) (JaxBackend method) (MatchingBackend method) (MLXBackend method) (NumpyFFTWBackend method) (PytorchBackend method) array_to_memmap() (in module tme.matching_utils) astype() (CupyBackend static method) (JaxBackend static method) (MatchingBackend method) (MLXBackend static method) (NumpyFFTWBackend static method) (PytorchBackend method) atom_coordinate (Structure attribute) atom_name (Structure attribute) atom_serial_number (Structure attribute) available_backends() (BackendManager method) B BackendManager (class in tme.backends) bandpass_filter() (Preprocessor method) bandpass_mask() (Preprocessor method) BandPassFilter (class in tme.preprocessing.frequency_filters) base_usage() (CAMMemoryUsage method) (CCMemoryUsage method) (CORRMemoryUsage method) (CupyBackendMemoryUsage method) (FLCMemoryUsage method) (FLCSphericalMaskMemoryUsage method) (LCCMemoryUsage method) (MatchingMemoryUsage method) (MaxScoreOverRotationsMemoryUsage method) (MCCMemoryUsage method) (PeakCallerMaximumFilterMemoryUsage method) blob_filter() (Preprocessor method) box_mask() (in module tme.matching_utils) build_fft() (CupyBackend method) (JaxBackend method) (MatchingBackend method) (MLXBackend method) (NumpyFFTWBackend method) (PytorchBackend method) C call_peaks() (PeakCaller method) (PeakCallerFast method) (PeakCallerMaximumFilter method) (PeakCallerRecursiveMasking method) (PeakCallerScipy method) (PeakCallerSort method) cam_setup() (in module tme.matching_scores) CAMMemoryUsage (class in tme.memory) cc_setup() (in module tme.matching_scores) CCMemoryUsage (class in tme.memory) center_of_mass() (CupyBackend method) (Density static method) (JaxBackend method) (MLXBackend method) (NumpyFFTWBackend method) (PytorchBackend method) (Structure method) centered() (Density method) (in module tme.matching_utils) (Structure method) centered_mask() (in module tme.matching_utils) chain_identifier (Structure attribute) Chamfer (class in tme.matching_optimization) change_backend() (BackendManager method) charge (Structure attribute) clip() (CupyBackend method) (JaxBackend method) (MatchingBackend method) (MLXBackend method) (NumpyFFTWBackend method) (PytorchBackend method) code_for_residue_insertion (Structure attribute) compare_structures() (Structure class method) ComposableFilter (class in tme.preprocessing.composable_filter) Compose (class in tme.preprocessing.compose) compute_convolution_shapes() (CupyBackend method) (JaxBackend method) (MatchingBackend method) (MLXBackend method) (NumpyFFTWBackend method) (PytorchBackend method) compute_full_convolution_index() (in module tme.matching_utils) compute_parallelization_schedule() (in module tme.matching_utils) concatenate() (CupyBackend method) (JaxBackend method) (MatchingBackend method) (MLXBackend method) (NumpyFFTWBackend method) (PytorchBackend method) conditional_execute() (in module tme.matching_utils) continuous_wedge() (WedgeReconstructed static method) continuous_wedge_mask() (Preprocessor method) copy() (Density method) (Orientations method) (Structure method) core_mask() (Density method) corr_scoring() (in module tme.matching_scores) corr_setup() (in module tme.matching_scores) correct_defocus_gradient (CTF attribute) CORRMemoryUsage (class in tme.memory) create_mask() (in module tme.matching_utils) create_score_object() (in module tme.matching_optimization) CrossCorrelation (class in tme.matching_optimization) CTF (class in tme.preprocessing.tilt_series) CupyBackend (class in tme.backends) CupyBackendMemoryUsage (class in tme.memory) D data (Density property) datatype_bytes() (CupyBackend method) (JaxBackend method) (MatchingBackend method) (MLXBackend method) (NumpyFFTWBackend method) (PytorchBackend method) defocus_angle (CTF attribute) defocus_x (CTF attribute) defocus_y (CTF attribute) Density (class in tme.density) density_boundary() (Density method) details (Orientations attribute) device_count() (CupyBackend method) (JaxBackend method) (MatchingBackend method) (MLXBackend method) (NumpyFFTWBackend method) (PytorchBackend method) difference_of_gaussian_filter() (Preprocessor method) discrete_bandpass() (BandPassFilter static method) divide() (CupyBackend method) (JaxBackend method) (MatchingBackend method) (MLXBackend method) (NumpyFFTWBackend method) (PytorchBackend method) dot() (CupyBackend method) (JaxBackend method) (MLXBackend method) (NumpyFFTWBackend method) (PytorchBackend method) E edge_gaussian_filter() (Preprocessor method) einsum() (CupyBackend method) (JaxBackend method) (MatchingBackend method) (MLXBackend method) (NumpyFFTWBackend method) (PytorchBackend method) element_symbol (Structure attribute) elliptical_mask() (in module tme.matching_utils) empty (Density property) Envelope (class in tme.matching_optimization) eps() (CupyBackend method) (JaxBackend method) (MatchingBackend method) (MLXBackend method) (NumpyFFTWBackend method) (PytorchBackend method) estimate_ram_usage() (in module tme.memory) euler_from_rotationmatrix() (in module tme.matching_utils) euler_to_rotationmatrix() (in module tme.matching_utils) extract_center() (CupyBackend method) (JaxBackend method) (MatchingBackend method) (MLXBackend method) (NumpyFFTWBackend method) (PytorchBackend method) F fill() (CupyBackend method) (JaxBackend method) (MatchingBackend method) (MLXBackend method) (NumpyFFTWBackend method) (PytorchBackend method) find_candidate_coordinates() (in module tme.extensions) find_candidate_indices() (in module tme.extensions) FLC (class in tme.matching_optimization) flc_scoring() (in module tme.matching_scores) flc_setup() (in module tme.matching_scores) FLCMemoryUsage (class in tme.memory) flcSphericalMask_setup() (in module tme.matching_scores) FLCSphericalMaskMemoryUsage (class in tme.memory) flip() (PytorchBackend method) flip_phase (CTF attribute) fourier_padding() (MatchingData method) fourier_shell_correlation() (Density static method) free_cache() (CupyBackend method) (JaxBackend method) (MatchingBackend method) (MLXBackend method) (NumpyFFTWBackend method) (PytorchBackend method) from_file() (CTF class method) (Density class method) (Orientations class method) (Structure class method) (Wedge class method) from_sharedarr() (CupyBackend method) (JaxBackend method) (MatchingBackend method) (MLXBackend method) (NumpyFFTWBackend method) (PytorchBackend method) from_structure() (Density class method) full() (CupyBackend method) (JaxBackend method) (MatchingBackend method) (MLXBackend method) (NumpyFFTWBackend method) (PytorchBackend method) G gaussian_bandpass() (BandPassFilter static method) gaussian_filter() (Preprocessor method) generate_tempfile_name() (in module tme.matching_utils) get() (MMCIFParser method) (Parser method) (PDBParser method) get_available_memory() (CupyBackend method) (JaxBackend method) (MatchingBackend method) (MLXBackend method) (NumpyFFTWBackend method) (PytorchBackend method) get_extraction_slices() (Orientations method) get_fundamental_dtype() (CupyBackend method) (JaxBackend method) (MatchingBackend method) (MLXBackend method) (NumpyFFTWBackend method) (PytorchBackend method) get_rotation_matrices() (in module tme.matching_utils) get_rotations_around_vector() (in module tme.matching_utils) grad() (CrossCorrelation method) (LaplaceCrossCorrelation method) (NormalizedCrossCorrelation method) (NormalizedCrossCorrelationMean method) H hamming_filter() (Preprocessor method) I identity() (CupyBackend method) (JaxBackend method) (MLXBackend method) (NumpyFFTWBackend method) (PytorchBackend method) indices() (CupyBackend method) (JaxBackend method) (MatchingBackend method) (MLXBackend method) (NumpyFFTWBackend method) (PytorchBackend method) interpolate_box() (Preprocessor method) interpolation_order (ReconstructFromTilt attribute) items() (MMCIFParser method) (Parser method) (PDBParser method) J JaxBackend (class in tme.backends) K kaiserb_filter() (Preprocessor method) keys() (MMCIFParser method) (Parser method) (PDBParser method) L LaplaceCrossCorrelation (class in tme.matching_optimization) lcc_setup() (in module tme.matching_scores) LCCMemoryUsage (class in tme.memory) LinearWhiteningFilter (class in tme.preprocessing.frequency_filters) load_pickle() (in module tme.matching_utils) load_quaternions_by_angle() (in module tme.matching_utils) local_gaussian_alignment_filter() (Preprocessor method) local_gaussian_filter() (Preprocessor method) M MaskedCrossCorrelation (class in tme.matching_optimization) match_densities() (Density class method) match_structure_to_density() (Density class method) MatchingBackend (class in tme.backends) MatchingData (class in tme.matching_data) MatchingMemoryUsage (class in tme.memory) max() (CupyBackend method) (JaxBackend method) (MatchingBackend method) (MLXBackend method) (NumpyFFTWBackend method) (PytorchBackend method) max_euclidean_distance() (in module tme.extensions) max_filter_coordinates() (CupyBackend method) (JaxBackend method) (MatchingBackend method) (MLXBackend method) (NumpyFFTWBackend method) (PytorchBackend method) max_index_by_label() (in module tme.extensions) max_score_over_rotations() (CupyBackend method) (JaxBackend method) (MLXBackend method) (NumpyFFTWBackend method) (PytorchBackend method) maximum() (CupyBackend method) (JaxBackend method) (MatchingBackend method) (MLXBackend method) (NumpyFFTWBackend method) (PytorchBackend method) MaxScoreOverRotations (class in tme.analyzer) MaxScoreOverRotationsMemoryUsage (class in tme.memory) mcc_scoring() (in module tme.matching_scores) mcc_setup() (in module tme.matching_scores) MCCMemoryUsage (class in tme.memory) mean() (CupyBackend method) (JaxBackend method) (MatchingBackend method) (MLXBackend method) (NumpyFFTWBackend method) (PytorchBackend method) mean_filter() (Preprocessor method) median_filter() (Preprocessor method) memmap_to_array() (in module tme.matching_utils) MemmapHandler (class in tme.analyzer) merge() (MaxScoreOverRotations class method) (MemmapHandler class method) (PeakCaller class method) (PeakCallerFast class method) (PeakCallerMaximumFilter class method) (PeakCallerRecursiveMasking class method) (PeakCallerScipy class method) (PeakCallerSort class method) metadata (Density property) (Structure attribute) method_to_id() (Preprocessor method) min() (CupyBackend method) (JaxBackend method) (MatchingBackend method) (MLXBackend method) (NumpyFFTWBackend method) (PytorchBackend method) minimum() (CupyBackend method) (JaxBackend method) (MatchingBackend method) (MLXBackend method) (NumpyFFTWBackend method) (PytorchBackend method) minimum_enclosing_box() (Density method) (in module tme.matching_utils) mipmap_filter() (Preprocessor method) MLXBackend (class in tme.backends) MMCIFParser (class in tme.parser) mod() (CupyBackend method) (JaxBackend method) (MatchingBackend method) (MLXBackend method) (NumpyFFTWBackend method) (PytorchBackend method) module |project| tme.extensions multiply() (CupyBackend method) (JaxBackend method) (MatchingBackend method) (MLXBackend method) (NumpyFFTWBackend method) (PytorchBackend method) MutualInformation (class in tme.matching_optimization) N norm_scores() (CupyBackend method) (JaxBackend method) (MLXBackend method) (NumpyFFTWBackend method) (PytorchBackend method) normal_vectors() (Density method) normalize_template() (in module tme.matching_utils) NormalizedCrossCorrelation (class in tme.matching_optimization) NormalizedCrossCorrelationMean (class in tme.matching_optimization) NormalVectorScore (class in tme.matching_optimization) NumpyFFTWBackend (class in tme.backends) O occupancy (Structure attribute) online_statistics() (in module tme.extensions) opening_axis (CTF attribute) (ReconstructFromTilt attribute) optimize_match() (in module tme.matching_optimization) Orientations (class in tme.orientations) origin (Density property) oversample_peaks() (PeakCaller static method) (PeakCallerFast static method) (PeakCallerMaximumFilter static method) (PeakCallerRecursiveMasking static method) (PeakCallerScipy static method) (PeakCallerSort static method) P pad() (Density method) parse_input() (MMCIFParser method) (Parser method) (PDBParser method) Parser (class in tme.parser) PartialLeastSquareDifference (class in tme.matching_optimization) PDBParser (class in tme.parser) PeakCaller (class in tme.analyzer) PeakCallerFast (class in tme.analyzer) PeakCallerMaximumFilter (class in tme.analyzer) PeakCallerMaximumFilterMemoryUsage (class in tme.memory) PeakCallerRecursiveMasking (class in tme.analyzer) PeakCallerScipy (class in tme.analyzer) PeakCallerSort (class in tme.analyzer) per_fork() (CAMMemoryUsage method) (CCMemoryUsage method) (CORRMemoryUsage method) (CupyBackendMemoryUsage method) (FLCMemoryUsage method) (FLCSphericalMaskMemoryUsage method) (LCCMemoryUsage method) (MatchingMemoryUsage method) (MaxScoreOverRotationsMemoryUsage method) (MCCMemoryUsage method) (PeakCallerMaximumFilterMemoryUsage method) phase_shift (CTF attribute) power() (CupyBackend method) (JaxBackend method) (MatchingBackend method) (MLXBackend method) (NumpyFFTWBackend method) (PytorchBackend method) Preprocessor (class in tme.preprocessor) PytorchBackend (class in tme.backends) Q quaternion_to_rotation_matrix() (in module tme.matching_utils) R rank_filter() (Preprocessor method) reconstruct() (ReconstructFromTilt static method) ReconstructFromTilt (class in tme.preprocessing.tilt_series) reconstruction_filter (ReconstructFromTilt attribute) record_type (Structure attribute) register_matching_exhaustive() (in module tme.matching_exhaustive) repeat() (CupyBackend method) (JaxBackend method) (MatchingBackend method) (MLXBackend method) (NumpyFFTWBackend method) (PytorchBackend method) resample() (Density method) reshape() (CupyBackend method) (JaxBackend method) (MLXBackend method) (NumpyFFTWBackend method) (PytorchBackend method) residue_name (Structure attribute) residue_sequence_number (Structure attribute) return_real_fourier (CTF attribute) (ReconstructFromTilt attribute) reverse() (CupyBackend static method) (JaxBackend static method) (MatchingBackend method) (MLXBackend static method) (NumpyFFTWBackend static method) (PytorchBackend method) rigid_transform() (CupyBackend method) (Density method) (in module tme.matching_utils) (JaxBackend method) (MatchingBackend method) (MLXBackend method) (NumpyFFTWBackend method) (PytorchBackend method) (Structure method) roll() (CupyBackend method) (JaxBackend method) (MatchingBackend method) (MLXBackend method) (NumpyFFTWBackend method) (PytorchBackend method) rotate_array() (Chamfer method) (CrossCorrelation method) (Envelope method) (FLC method) (LaplaceCrossCorrelation method) (MaskedCrossCorrelation method) (MutualInformation method) (NormalizedCrossCorrelation method) (NormalizedCrossCorrelationMean method) (NormalVectorScore method) (PartialLeastSquareDifference method) rotation_aligning_vectors() (in module tme.matching_utils) rotations (MatchingData property) (Orientations attribute) S sampling_rate (CTF attribute) (Density property) scan() (in module tme.matching_exhaustive) scan_subsets() (in module tme.matching_exhaustive) score() (Chamfer method) (CrossCorrelation method) (Envelope method) (FLC method) (LaplaceCrossCorrelation method) (MaskedCrossCorrelation method) (MutualInformation method) (NormalizedCrossCorrelation method) (NormalizedCrossCorrelationMean method) (NormalVectorScore method) (PartialLeastSquareDifference method) score_angles() (Chamfer method) (CrossCorrelation method) (Envelope method) (FLC method) (LaplaceCrossCorrelation method) (MaskedCrossCorrelation method) (MutualInformation method) (NormalizedCrossCorrelation method) (NormalizedCrossCorrelationMean method) (NormalVectorScore method) (PartialLeastSquareDifference method) score_translation() (Chamfer method) (CrossCorrelation method) (Envelope method) (FLC method) (LaplaceCrossCorrelation method) (MaskedCrossCorrelation method) (MutualInformation method) (NormalizedCrossCorrelation method) (NormalizedCrossCorrelationMean method) (NormalVectorScore method) (PartialLeastSquareDifference method) scores (Orientations attribute) scramble_phases() (in module tme.matching_utils) segment_identifier (Structure attribute) set_device() (CupyBackend method) (JaxBackend method) (MatchingBackend method) (MLXBackend method) (NumpyFFTWBackend method) (PytorchBackend method) shape (CTF attribute) (Density property) (ReconstructFromTilt attribute) shared (MaxScoreOverRotations property) size() (CupyBackend method) (JaxBackend method) (MatchingBackend method) (MLXBackend method) (NumpyFFTWBackend method) (PytorchBackend method) spherical_aberration (CTF attribute) split_shape() (in module tme.matching_utils) sqrt() (CupyBackend method) (JaxBackend method) (MatchingBackend method) (MLXBackend method) (NumpyFFTWBackend method) (PytorchBackend method) square() (CupyBackend method) (JaxBackend method) (MatchingBackend method) (MLXBackend method) (NumpyFFTWBackend method) (PytorchBackend method) stack() (CupyBackend method) (JaxBackend method) (MatchingBackend method) (MLXBackend method) (NumpyFFTWBackend method) (PytorchBackend method) std() (CupyBackend method) (JaxBackend method) (MatchingBackend method) (MLXBackend method) (NumpyFFTWBackend method) (PytorchBackend method) step_wedge() (WedgeReconstructed static method) step_wedge_mask() (Preprocessor method) Structure (class in tme.structure) subset_array() (MatchingData method) subset_by_chain() (Structure method) subset_by_range() (Structure method) subset_by_slice() (MatchingData method) subtract() (CupyBackend method) (JaxBackend method) (MatchingBackend method) (MLXBackend method) (NumpyFFTWBackend method) (PytorchBackend method) sum() (CupyBackend method) (JaxBackend method) (MatchingBackend method) (MLXBackend method) (NumpyFFTWBackend method) (PytorchBackend method) surface_coordinates() (Density method) T target (MatchingData property) target_filter (MatchingData property) target_mask (MatchingData property) target_padding() (MatchingData method) temperature_factor (Structure attribute) template (MatchingData property) template_filter (MatchingData property) template_mask (MatchingData property) tilt_axis (CTF attribute) (ReconstructFromTilt attribute) tme.extensions module to_backend() (MatchingData method) to_backend_array() (CupyBackend method) (JaxBackend method) (MatchingBackend method) (MLXBackend method) (NumpyFFTWBackend method) (PytorchBackend method) to_cpu_array() (CupyBackend method) (JaxBackend method) (MatchingBackend method) (MLXBackend method) (NumpyFFTWBackend method) (PytorchBackend method) to_file() (Density method) (Orientations method) (Structure method) to_memmap() (Density method) to_numpy() (Density method) to_numpy_array() (CupyBackend method) (JaxBackend method) (MatchingBackend method) (MLXBackend method) (NumpyFFTWBackend method) (PytorchBackend method) to_pointcloud() (Density method) to_sharedarr() (CupyBackend static method) (JaxBackend static method) (MatchingBackend method) (MLXBackend static method) (NumpyFFTWBackend method) (PytorchBackend method) to_volume() (Structure method) tobytes() (CupyBackend method) (JaxBackend method) (MatchingBackend method) (MLXBackend method) (NumpyFFTWBackend method) (PytorchBackend method) topk_indices() (CupyBackend method) (JaxBackend method) (MatchingBackend method) (MLXBackend method) (NumpyFFTWBackend method) (PytorchBackend method) topleft_pad() (CupyBackend method) (JaxBackend method) (MatchingBackend method) (MLXBackend method) (NumpyFFTWBackend method) (PytorchBackend method) translations (Orientations attribute) transpose() (CupyBackend method) (JaxBackend method) (MatchingBackend method) (MLXBackend method) (NumpyFFTWBackend method) (PytorchBackend method) tril_indices() (CupyBackend method) (JaxBackend method) (MatchingBackend method) (MLXBackend method) (NumpyFFTWBackend method) (PytorchBackend method) trim_box() (Density method) tube_mask() (in module tme.matching_utils) U unique() (CupyBackend method) (JaxBackend method) (MatchingBackend method) (MLXBackend method) (NumpyFFTWBackend method) (PytorchBackend method) unravel_index() (CupyBackend method) (JaxBackend method) (MatchingBackend method) (MLXBackend method) (NumpyFFTWBackend method) (PytorchBackend method) update_indices() (MemmapHandler method) V values() (MMCIFParser method) (Parser method) (PDBParser method) var() (CupyBackend method) W Wedge (class in tme.preprocessing.tilt_series) WedgeReconstructed (class in tme.preprocessing.tilt_series) weight() (CTF method) weight_angle() (Wedge static method) weight_grigorieff() (Wedge method) weight_relion() (Wedge method) where() (CupyBackend method) (JaxBackend method) (MatchingBackend method) (MLXBackend method) (NumpyFFTWBackend method) (PytorchBackend method) write_pickle() (in module tme.matching_utils) Z zeros() (CupyBackend method) (JaxBackend static method) (MatchingBackend method) (MLXBackend method) (NumpyFFTWBackend static method) (PytorchBackend method)