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pytme 0.2.5 documentation

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Data Structures

  • Density
    • Density
      • Density.data
      • Density.empty
      • Density.metadata
      • Density.origin
      • Density.sampling_rate
      • Density.shape
      • Density.adjust_box
      • Density.center_of_mass
      • Density.centered
      • Density.copy
      • Density.core_mask
      • Density.density_boundary
      • Density.fourier_shell_correlation
      • Density.from_file
      • Density.from_structure
      • Density.match_densities
      • Density.match_structure_to_density
      • Density.minimum_enclosing_box
      • Density.normal_vectors
      • Density.pad
      • Density.resample
      • Density.rigid_transform
      • Density.surface_coordinates
      • Density.to_file
      • Density.to_memmap
      • Density.to_numpy
      • Density.to_pointcloud
      • Density.trim_box
    • Density.data
    • Density.origin
    • Density.sampling_rate
    • Density.metadata
    • Density.shape
    • Density.empty
    • Density.to_file
    • Density.from_file
    • Density.from_structure
    • Density.copy
    • Density.to_numpy
    • Density.to_memmap
    • Density.pad
    • Density.trim_box
    • Density.centered
    • Density.adjust_box
    • Density.minimum_enclosing_box
    • Density.rigid_transform
    • Density.to_pointcloud
    • Density.resample
    • Density.density_boundary
    • Density.surface_coordinates
    • Density.normal_vectors
    • Density.core_mask
    • Density.center_of_mass
    • Density.match_densities
    • Density.match_structure_to_density
    • Density.fourier_shell_correlation
  • Structure
    • Structure
      • Structure.record_type
      • Structure.atom_serial_number
      • Structure.atom_name
      • Structure.atom_coordinate
      • Structure.alternate_location_indicator
      • Structure.residue_name
      • Structure.chain_identifier
      • Structure.residue_sequence_number
      • Structure.code_for_residue_insertion
      • Structure.occupancy
      • Structure.temperature_factor
      • Structure.segment_identifier
      • Structure.element_symbol
      • Structure.charge
      • Structure.metadata
      • Structure.align_structures
      • Structure.center_of_mass
      • Structure.centered
      • Structure.compare_structures
      • Structure.copy
      • Structure.from_file
      • Structure.rigid_transform
      • Structure.subset_by_chain
      • Structure.subset_by_range
      • Structure.to_file
      • Structure.to_volume
    • Structure.record_type
    • Structure.atom_serial_number
    • Structure.atom_name
    • Structure.atom_coordinate
    • Structure.alternate_location_indicator
    • Structure.residue_name
    • Structure.chain_identifier
    • Structure.residue_sequence_number
    • Structure.code_for_residue_insertion
    • Structure.occupancy
    • Structure.temperature_factor
    • Structure.segment_identifier
    • Structure.element_symbol
    • Structure.charge
    • Structure.metadata
    • Structure.to_file
    • Structure.from_file
    • Structure.to_volume
    • Structure.copy
    • Structure.subset_by_chain
    • Structure.subset_by_range
    • Structure.rigid_transform
    • Structure.align_structures
    • Structure.compare_structures
    • Structure.center_of_mass
    • Structure.centered
  • MatchingData
    • MatchingData
      • MatchingData.rotations
      • MatchingData.target
      • MatchingData.target_filter
      • MatchingData.target_mask
      • MatchingData.template
      • MatchingData.template_filter
      • MatchingData.template_mask
      • MatchingData.fourier_padding
      • MatchingData.subset_array
      • MatchingData.subset_by_slice
      • MatchingData.target_padding
      • MatchingData.to_backend
    • MatchingData.to_backend
    • MatchingData.target
    • MatchingData.template
    • MatchingData.target_mask
    • MatchingData.template_mask
    • MatchingData.rotations
    • MatchingData.subset_array
    • MatchingData.subset_by_slice

Preprocessing

  • Preprocessor
    • Preprocessor
      • Preprocessor.apply_method
      • Preprocessor.bandpass_filter
      • Preprocessor.bandpass_mask
      • Preprocessor.blob_filter
      • Preprocessor.continuous_wedge_mask
      • Preprocessor.difference_of_gaussian_filter
      • Preprocessor.edge_gaussian_filter
      • Preprocessor.gaussian_filter
      • Preprocessor.hamming_filter
      • Preprocessor.interpolate_box
      • Preprocessor.kaiserb_filter
      • Preprocessor.local_gaussian_alignment_filter
      • Preprocessor.local_gaussian_filter
      • Preprocessor.mean_filter
      • Preprocessor.median_filter
      • Preprocessor.method_to_id
      • Preprocessor.mipmap_filter
      • Preprocessor.rank_filter
      • Preprocessor.step_wedge_mask
    • Preprocessor.continuous_wedge_mask
    • Preprocessor.step_wedge_mask
    • Preprocessor.gaussian_filter
    • Preprocessor.difference_of_gaussian_filter
    • Preprocessor.bandpass_filter
    • Preprocessor.local_gaussian_alignment_filter
    • Preprocessor.local_gaussian_filter
    • Preprocessor.edge_gaussian_filter
    • Preprocessor.mean_filter
    • Preprocessor.rank_filter
    • Preprocessor.mipmap_filter
    • Preprocessor.kaiserb_filter
    • Preprocessor.blob_filter
    • Preprocessor.hamming_filter
    • Preprocessor.interpolate_box
  • Composable Filters
    • ComposableFilter
    • Compose
    • BandPassFilter
      • BandPassFilter.discrete_bandpass
      • BandPassFilter.gaussian_bandpass
    • LinearWhiteningFilter
    • CTF
      • CTF.acceleration_voltage
      • CTF.amplitude_contrast
      • CTF.angles
      • CTF.correct_defocus_gradient
      • CTF.defocus_angle
      • CTF.defocus_y
      • CTF.flip_phase
      • CTF.opening_axis
      • CTF.phase_shift
      • CTF.return_real_fourier
      • CTF.sampling_rate
      • CTF.spherical_aberration
      • CTF.tilt_axis
      • CTF.shape
      • CTF.defocus_x
      • CTF.from_file
      • CTF.weight
    • Wedge
      • Wedge.from_file
      • Wedge.weight_angle
      • Wedge.weight_grigorieff
      • Wedge.weight_relion
    • WedgeReconstructed
      • WedgeReconstructed.continuous_wedge
      • WedgeReconstructed.step_wedge
    • ReconstructFromTilt
      • ReconstructFromTilt.angles
      • ReconstructFromTilt.interpolation_order
      • ReconstructFromTilt.opening_axis
      • ReconstructFromTilt.reconstruction_filter
      • ReconstructFromTilt.return_real_fourier
      • ReconstructFromTilt.shape
      • ReconstructFromTilt.tilt_axis
      • ReconstructFromTilt.reconstruct

Template Matching

  • Exhaustive
    • scan
    • scan_subsets
    • cc_setup
    • lcc_setup
    • corr_setup
    • cam_setup
    • flc_setup
    • flcSphericalMask_setup
    • mcc_setup
    • corr_scoring
    • flc_scoring
    • mcc_scoring
    • register_matching_exhaustive
  • Non-exhaustive
    • FLC
      • FLC.rotate_array
      • FLC.score
      • FLC.score_angles
      • FLC.score_translation
    • CrossCorrelation
      • CrossCorrelation.grad
      • CrossCorrelation.rotate_array
      • CrossCorrelation.score
      • CrossCorrelation.score_angles
      • CrossCorrelation.score_translation
    • LaplaceCrossCorrelation
      • LaplaceCrossCorrelation.grad
      • LaplaceCrossCorrelation.rotate_array
      • LaplaceCrossCorrelation.score
      • LaplaceCrossCorrelation.score_angles
      • LaplaceCrossCorrelation.score_translation
    • NormalizedCrossCorrelation
      • NormalizedCrossCorrelation.grad
      • NormalizedCrossCorrelation.rotate_array
      • NormalizedCrossCorrelation.score
      • NormalizedCrossCorrelation.score_angles
      • NormalizedCrossCorrelation.score_translation
    • NormalizedCrossCorrelationMean
      • NormalizedCrossCorrelationMean.grad
      • NormalizedCrossCorrelationMean.rotate_array
      • NormalizedCrossCorrelationMean.score
      • NormalizedCrossCorrelationMean.score_angles
      • NormalizedCrossCorrelationMean.score_translation
    • MaskedCrossCorrelation
      • MaskedCrossCorrelation.rotate_array
      • MaskedCrossCorrelation.score
      • MaskedCrossCorrelation.score_angles
      • MaskedCrossCorrelation.score_translation
    • PartialLeastSquareDifference
      • PartialLeastSquareDifference.rotate_array
      • PartialLeastSquareDifference.score
      • PartialLeastSquareDifference.score_angles
      • PartialLeastSquareDifference.score_translation
    • Chamfer
      • Chamfer.rotate_array
      • Chamfer.score
      • Chamfer.score_angles
      • Chamfer.score_translation
    • MutualInformation
      • MutualInformation.rotate_array
      • MutualInformation.score
      • MutualInformation.score_angles
      • MutualInformation.score_translation
    • Envelope
      • Envelope.rotate_array
      • Envelope.score
      • Envelope.score_angles
      • Envelope.score_translation
    • NormalVectorScore
      • NormalVectorScore.rotate_array
      • NormalVectorScore.score
      • NormalVectorScore.score_angles
      • NormalVectorScore.score_translation
    • Chamfer
      • Chamfer.rotate_array
      • Chamfer.score
      • Chamfer.score_angles
      • Chamfer.score_translation
    • NormalVectorScore
      • NormalVectorScore.rotate_array
      • NormalVectorScore.score
      • NormalVectorScore.score_angles
      • NormalVectorScore.score_translation
    • create_score_object
    • optimize_match
  • Analyzers
    • MemmapHandler
      • MemmapHandler.merge
      • MemmapHandler.update_indices
    • MaxScoreOverRotations
      • MaxScoreOverRotations.shared
      • MaxScoreOverRotations.merge
    • PeakCaller
      • PeakCaller.call_peaks
      • PeakCaller.merge
      • PeakCaller.oversample_peaks
    • PeakCallerSort
      • PeakCallerSort.call_peaks
      • PeakCallerSort.merge
      • PeakCallerSort.oversample_peaks
    • PeakCallerMaximumFilter
      • PeakCallerMaximumFilter.call_peaks
      • PeakCallerMaximumFilter.merge
      • PeakCallerMaximumFilter.oversample_peaks
    • PeakCallerFast
      • PeakCallerFast.call_peaks
      • PeakCallerFast.merge
      • PeakCallerFast.oversample_peaks
    • PeakCallerRecursiveMasking
      • PeakCallerRecursiveMasking.call_peaks
      • PeakCallerRecursiveMasking.merge
      • PeakCallerRecursiveMasking.oversample_peaks
    • PeakCallerScipy
      • PeakCallerScipy.call_peaks
      • PeakCallerScipy.merge
      • PeakCallerScipy.oversample_peaks
  • Memory
    • estimate_ram_usage
    • MatchingMemoryUsage
      • MatchingMemoryUsage.base_usage
      • MatchingMemoryUsage.per_fork
    • MatchingMemoryUsage
      • MatchingMemoryUsage.base_usage
      • MatchingMemoryUsage.per_fork
    • CCMemoryUsage
      • CCMemoryUsage.base_usage
      • CCMemoryUsage.per_fork
    • LCCMemoryUsage
      • LCCMemoryUsage.base_usage
      • LCCMemoryUsage.per_fork
    • CORRMemoryUsage
      • CORRMemoryUsage.base_usage
      • CORRMemoryUsage.per_fork
    • CAMMemoryUsage
      • CAMMemoryUsage.base_usage
      • CAMMemoryUsage.per_fork
    • FLCSphericalMaskMemoryUsage
      • FLCSphericalMaskMemoryUsage.base_usage
      • FLCSphericalMaskMemoryUsage.per_fork
    • FLCMemoryUsage
      • FLCMemoryUsage.base_usage
      • FLCMemoryUsage.per_fork
    • MCCMemoryUsage
      • MCCMemoryUsage.base_usage
      • MCCMemoryUsage.per_fork
    • MaxScoreOverRotationsMemoryUsage
      • MaxScoreOverRotationsMemoryUsage.base_usage
      • MaxScoreOverRotationsMemoryUsage.per_fork
    • PeakCallerMaximumFilterMemoryUsage
      • PeakCallerMaximumFilterMemoryUsage.base_usage
      • PeakCallerMaximumFilterMemoryUsage.per_fork
    • CupyBackendMemoryUsage
      • CupyBackendMemoryUsage.base_usage
      • CupyBackendMemoryUsage.per_fork
  • Utilities
    • box_mask
    • create_mask
    • tube_mask
    • elliptical_mask
    • get_rotation_matrices
    • euler_to_rotationmatrix
    • rotation_aligning_vectors
    • euler_from_rotationmatrix
    • load_quaternions_by_angle
    • get_rotations_around_vector
    • quaternion_to_rotation_matrix
    • centered
    • split_shape
    • centered_mask
    • apply_convolution_mode
    • compute_full_convolution_index
    • compute_parallelization_schedule
    • load_pickle
    • write_pickle
    • scramble_phases
    • rigid_transform
    • array_to_memmap
    • memmap_to_array
    • normalize_template
    • conditional_execute
    • minimum_enclosing_box
    • generate_tempfile_name

Flexible Backends

  • Backends
    • BackendManager
      • BackendManager.add_backend
      • BackendManager.available_backends
      • BackendManager.change_backend
    • MatchingBackend
      • MatchingBackend.abs
      • MatchingBackend.add
      • MatchingBackend.arange
      • MatchingBackend.argsort
      • MatchingBackend.astype
      • MatchingBackend.build_fft
      • MatchingBackend.clip
      • MatchingBackend.compute_convolution_shapes
      • MatchingBackend.concatenate
      • MatchingBackend.datatype_bytes
      • MatchingBackend.device_count
      • MatchingBackend.divide
      • MatchingBackend.einsum
      • MatchingBackend.eps
      • MatchingBackend.extract_center
      • MatchingBackend.fill
      • MatchingBackend.free_cache
      • MatchingBackend.from_sharedarr
      • MatchingBackend.full
      • MatchingBackend.get_available_memory
      • MatchingBackend.get_fundamental_dtype
      • MatchingBackend.indices
      • MatchingBackend.max
      • MatchingBackend.max_filter_coordinates
      • MatchingBackend.maximum
      • MatchingBackend.mean
      • MatchingBackend.min
      • MatchingBackend.minimum
      • MatchingBackend.mod
      • MatchingBackend.multiply
      • MatchingBackend.power
      • MatchingBackend.repeat
      • MatchingBackend.reverse
      • MatchingBackend.rigid_transform
      • MatchingBackend.roll
      • MatchingBackend.set_device
      • MatchingBackend.size
      • MatchingBackend.sqrt
      • MatchingBackend.square
      • MatchingBackend.stack
      • MatchingBackend.std
      • MatchingBackend.subtract
      • MatchingBackend.sum
      • MatchingBackend.to_backend_array
      • MatchingBackend.to_cpu_array
      • MatchingBackend.to_numpy_array
      • MatchingBackend.to_sharedarr
      • MatchingBackend.tobytes
      • MatchingBackend.topk_indices
      • MatchingBackend.topleft_pad
      • MatchingBackend.transpose
      • MatchingBackend.tril_indices
      • MatchingBackend.unique
      • MatchingBackend.unravel_index
      • MatchingBackend.where
      • MatchingBackend.zeros
    • NumpyFFTWBackend
      • NumpyFFTWBackend.abs
      • NumpyFFTWBackend.add
      • NumpyFFTWBackend.arange
      • NumpyFFTWBackend.argsort
      • NumpyFFTWBackend.astype
      • NumpyFFTWBackend.build_fft
      • NumpyFFTWBackend.center_of_mass
      • NumpyFFTWBackend.clip
      • NumpyFFTWBackend.compute_convolution_shapes
      • NumpyFFTWBackend.concatenate
      • NumpyFFTWBackend.datatype_bytes
      • NumpyFFTWBackend.device_count
      • NumpyFFTWBackend.divide
      • NumpyFFTWBackend.dot
      • NumpyFFTWBackend.einsum
      • NumpyFFTWBackend.eps
      • NumpyFFTWBackend.extract_center
      • NumpyFFTWBackend.fill
      • NumpyFFTWBackend.free_cache
      • NumpyFFTWBackend.from_sharedarr
      • NumpyFFTWBackend.full
      • NumpyFFTWBackend.get_available_memory
      • NumpyFFTWBackend.get_fundamental_dtype
      • NumpyFFTWBackend.identity
      • NumpyFFTWBackend.indices
      • NumpyFFTWBackend.max
      • NumpyFFTWBackend.max_filter_coordinates
      • NumpyFFTWBackend.max_score_over_rotations
      • NumpyFFTWBackend.maximum
      • NumpyFFTWBackend.mean
      • NumpyFFTWBackend.min
      • NumpyFFTWBackend.minimum
      • NumpyFFTWBackend.mod
      • NumpyFFTWBackend.multiply
      • NumpyFFTWBackend.norm_scores
      • NumpyFFTWBackend.power
      • NumpyFFTWBackend.repeat
      • NumpyFFTWBackend.reshape
      • NumpyFFTWBackend.reverse
      • NumpyFFTWBackend.rigid_transform
      • NumpyFFTWBackend.roll
      • NumpyFFTWBackend.set_device
      • NumpyFFTWBackend.size
      • NumpyFFTWBackend.sqrt
      • NumpyFFTWBackend.square
      • NumpyFFTWBackend.stack
      • NumpyFFTWBackend.std
      • NumpyFFTWBackend.subtract
      • NumpyFFTWBackend.sum
      • NumpyFFTWBackend.to_backend_array
      • NumpyFFTWBackend.to_cpu_array
      • NumpyFFTWBackend.to_numpy_array
      • NumpyFFTWBackend.to_sharedarr
      • NumpyFFTWBackend.tobytes
      • NumpyFFTWBackend.topk_indices
      • NumpyFFTWBackend.topleft_pad
      • NumpyFFTWBackend.transpose
      • NumpyFFTWBackend.tril_indices
      • NumpyFFTWBackend.unique
      • NumpyFFTWBackend.unravel_index
      • NumpyFFTWBackend.where
      • NumpyFFTWBackend.zeros
    • PytorchBackend
      • PytorchBackend.abs
      • PytorchBackend.add
      • PytorchBackend.arange
      • PytorchBackend.argsort
      • PytorchBackend.astype
      • PytorchBackend.build_fft
      • PytorchBackend.center_of_mass
      • PytorchBackend.clip
      • PytorchBackend.compute_convolution_shapes
      • PytorchBackend.concatenate
      • PytorchBackend.datatype_bytes
      • PytorchBackend.device_count
      • PytorchBackend.divide
      • PytorchBackend.dot
      • PytorchBackend.einsum
      • PytorchBackend.eps
      • PytorchBackend.extract_center
      • PytorchBackend.fill
      • PytorchBackend.flip
      • PytorchBackend.free_cache
      • PytorchBackend.from_sharedarr
      • PytorchBackend.full
      • PytorchBackend.get_available_memory
      • PytorchBackend.get_fundamental_dtype
      • PytorchBackend.identity
      • PytorchBackend.indices
      • PytorchBackend.max
      • PytorchBackend.max_filter_coordinates
      • PytorchBackend.max_score_over_rotations
      • PytorchBackend.maximum
      • PytorchBackend.mean
      • PytorchBackend.min
      • PytorchBackend.minimum
      • PytorchBackend.mod
      • PytorchBackend.multiply
      • PytorchBackend.norm_scores
      • PytorchBackend.power
      • PytorchBackend.repeat
      • PytorchBackend.reshape
      • PytorchBackend.reverse
      • PytorchBackend.rigid_transform
      • PytorchBackend.roll
      • PytorchBackend.set_device
      • PytorchBackend.size
      • PytorchBackend.sqrt
      • PytorchBackend.square
      • PytorchBackend.stack
      • PytorchBackend.std
      • PytorchBackend.subtract
      • PytorchBackend.sum
      • PytorchBackend.to_backend_array
      • PytorchBackend.to_cpu_array
      • PytorchBackend.to_numpy_array
      • PytorchBackend.to_sharedarr
      • PytorchBackend.tobytes
      • PytorchBackend.topk_indices
      • PytorchBackend.topleft_pad
      • PytorchBackend.transpose
      • PytorchBackend.tril_indices
      • PytorchBackend.unique
      • PytorchBackend.unravel_index
      • PytorchBackend.where
      • PytorchBackend.zeros
    • CupyBackend
      • CupyBackend.abs
      • CupyBackend.add
      • CupyBackend.arange
      • CupyBackend.argsort
      • CupyBackend.astype
      • CupyBackend.build_fft
      • CupyBackend.center_of_mass
      • CupyBackend.clip
      • CupyBackend.compute_convolution_shapes
      • CupyBackend.concatenate
      • CupyBackend.datatype_bytes
      • CupyBackend.device_count
      • CupyBackend.divide
      • CupyBackend.dot
      • CupyBackend.einsum
      • CupyBackend.eps
      • CupyBackend.extract_center
      • CupyBackend.fill
      • CupyBackend.free_cache
      • CupyBackend.from_sharedarr
      • CupyBackend.full
      • CupyBackend.get_available_memory
      • CupyBackend.get_fundamental_dtype
      • CupyBackend.identity
      • CupyBackend.indices
      • CupyBackend.max
      • CupyBackend.max_filter_coordinates
      • CupyBackend.max_score_over_rotations
      • CupyBackend.maximum
      • CupyBackend.mean
      • CupyBackend.min
      • CupyBackend.minimum
      • CupyBackend.mod
      • CupyBackend.multiply
      • CupyBackend.norm_scores
      • CupyBackend.power
      • CupyBackend.repeat
      • CupyBackend.reshape
      • CupyBackend.reverse
      • CupyBackend.rigid_transform
      • CupyBackend.roll
      • CupyBackend.set_device
      • CupyBackend.size
      • CupyBackend.sqrt
      • CupyBackend.square
      • CupyBackend.stack
      • CupyBackend.std
      • CupyBackend.subtract
      • CupyBackend.sum
      • CupyBackend.to_backend_array
      • CupyBackend.to_cpu_array
      • CupyBackend.to_numpy_array
      • CupyBackend.to_sharedarr
      • CupyBackend.tobytes
      • CupyBackend.topk_indices
      • CupyBackend.topleft_pad
      • CupyBackend.transpose
      • CupyBackend.tril_indices
      • CupyBackend.unique
      • CupyBackend.unravel_index
      • CupyBackend.var
      • CupyBackend.where
      • CupyBackend.zeros
    • MLXBackend
      • MLXBackend.abs
      • MLXBackend.add
      • MLXBackend.arange
      • MLXBackend.argsort
      • MLXBackend.astype
      • MLXBackend.build_fft
      • MLXBackend.center_of_mass
      • MLXBackend.clip
      • MLXBackend.compute_convolution_shapes
      • MLXBackend.concatenate
      • MLXBackend.datatype_bytes
      • MLXBackend.device_count
      • MLXBackend.divide
      • MLXBackend.dot
      • MLXBackend.einsum
      • MLXBackend.eps
      • MLXBackend.extract_center
      • MLXBackend.fill
      • MLXBackend.free_cache
      • MLXBackend.from_sharedarr
      • MLXBackend.full
      • MLXBackend.get_available_memory
      • MLXBackend.get_fundamental_dtype
      • MLXBackend.identity
      • MLXBackend.indices
      • MLXBackend.max
      • MLXBackend.max_filter_coordinates
      • MLXBackend.max_score_over_rotations
      • MLXBackend.maximum
      • MLXBackend.mean
      • MLXBackend.min
      • MLXBackend.minimum
      • MLXBackend.mod
      • MLXBackend.multiply
      • MLXBackend.norm_scores
      • MLXBackend.power
      • MLXBackend.repeat
      • MLXBackend.reshape
      • MLXBackend.reverse
      • MLXBackend.rigid_transform
      • MLXBackend.roll
      • MLXBackend.set_device
      • MLXBackend.size
      • MLXBackend.sqrt
      • MLXBackend.square
      • MLXBackend.stack
      • MLXBackend.std
      • MLXBackend.subtract
      • MLXBackend.sum
      • MLXBackend.to_backend_array
      • MLXBackend.to_cpu_array
      • MLXBackend.to_numpy_array
      • MLXBackend.to_sharedarr
      • MLXBackend.tobytes
      • MLXBackend.topk_indices
      • MLXBackend.topleft_pad
      • MLXBackend.transpose
      • MLXBackend.tril_indices
      • MLXBackend.unique
      • MLXBackend.unravel_index
      • MLXBackend.where
      • MLXBackend.zeros
    • JaxBackend
      • JaxBackend.abs
      • JaxBackend.add
      • JaxBackend.arange
      • JaxBackend.argsort
      • JaxBackend.astype
      • JaxBackend.build_fft
      • JaxBackend.center_of_mass
      • JaxBackend.clip
      • JaxBackend.compute_convolution_shapes
      • JaxBackend.concatenate
      • JaxBackend.datatype_bytes
      • JaxBackend.device_count
      • JaxBackend.divide
      • JaxBackend.dot
      • JaxBackend.einsum
      • JaxBackend.eps
      • JaxBackend.extract_center
      • JaxBackend.fill
      • JaxBackend.free_cache
      • JaxBackend.from_sharedarr
      • JaxBackend.full
      • JaxBackend.get_available_memory
      • JaxBackend.get_fundamental_dtype
      • JaxBackend.identity
      • JaxBackend.indices
      • JaxBackend.max
      • JaxBackend.max_filter_coordinates
      • JaxBackend.max_score_over_rotations
      • JaxBackend.maximum
      • JaxBackend.mean
      • JaxBackend.min
      • JaxBackend.minimum
      • JaxBackend.mod
      • JaxBackend.multiply
      • JaxBackend.norm_scores
      • JaxBackend.power
      • JaxBackend.repeat
      • JaxBackend.reshape
      • JaxBackend.reverse
      • JaxBackend.rigid_transform
      • JaxBackend.roll
      • JaxBackend.set_device
      • JaxBackend.size
      • JaxBackend.sqrt
      • JaxBackend.square
      • JaxBackend.stack
      • JaxBackend.std
      • JaxBackend.subtract
      • JaxBackend.sum
      • JaxBackend.to_backend_array
      • JaxBackend.to_cpu_array
      • JaxBackend.to_numpy_array
      • JaxBackend.to_sharedarr
      • JaxBackend.tobytes
      • JaxBackend.topk_indices
      • JaxBackend.topleft_pad
      • JaxBackend.transpose
      • JaxBackend.tril_indices
      • JaxBackend.unique
      • JaxBackend.unravel_index
      • JaxBackend.where
      • JaxBackend.zeros

Miscellaneous

  • Orientations
    • Orientations
      • Orientations.translations
      • Orientations.rotations
      • Orientations.scores
      • Orientations.details
      • Orientations.copy
      • Orientations.from_file
      • Orientations.get_extraction_slices
      • Orientations.to_file
  • Utilities
    • Extensions
    • Parser
      • Parser
      • Parser.get
      • Parser.keys
      • Parser.values
      • Parser.items
      • Parser.parse_input
      • PDBParser
      • MMCIFParser
  • API
  • JaxBackend
  • JaxBackend.t...

JaxBackend.to_backend_array#

JaxBackend.to_backend_array(arr)#

Convert a numpy array instance to backend array type.

Parameters:
arrNDArray

The numpy array instance to be converted.

Returns:
BackendArray

An array of the specified backend.

See also

MatchingBackend.to_cpu_array()
MatchingBackend.to_numpy_array()

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JaxBackend.sum

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