Index

_

_must_flush_buffer (cryolike.file_conversions.particle_stacks_converter.ParticleStackConverter attribute) _stack_absolute_index (cryolike.file_conversions.particle_stacks_converter.ParticleStackConverter attribute)

_stack_start_file (cryolike.file_conversions.particle_stacks_converter.ParticleStackConverter attribute) _translation_matrix (cryolike.stacks.image.Images attribute)

A

add_noise_fourier() (cryolike.stacks.image.Images method) add_noise_phys() (cryolike.stacks.image.Images method) aggregate_ill() (in module cryolike.likelihoods.iteration.integrated_log_likelihood_aggregation) amplitudeContrast (cryolike.metadata.lens_descriptor.LensDescriptor attribute) anglePsi (cryolike.metadata.lens_descriptor.LensDescriptor attribute) angleRotation (cryolike.metadata.lens_descriptor.LensDescriptor attribute) angleTilt (cryolike.metadata.lens_descriptor.LensDescriptor attribute) anisotropy (cryolike.microscopy.ctf.CTF attribute) apply_ctf() (cryolike.stacks.image.Images method) ArbitraryPolarQuadrature (class in cryolike.grids.polar_grid) atom_radii (cryolike.metadata.image_descriptor.ImageDescriptor attribute) (cryolike.util.atomic_model.AtomicModel attribute)

atom_selection (cryolike.metadata.image_descriptor.ImageDescriptor attribute) atom_shape (cryolike.metadata.image_descriptor.ImageDescriptor attribute) atomic_coordinates (cryolike.util.atomic_model.AtomicModel attribute) AtomicModel (class in cryolike.util.atomic_model) AtomShape (class in cryolike.util.enums) azimu_points (cryolike.grids.sphere_grid.SphereGrid attribute) (cryolike.grids.sphere_grid.SphereShell attribute) azimus (cryolike.metadata.viewing_angles.ViewingAngles attribute) azimuthal_sampling (cryolike.grids.sphere_grid.SphereGrid attribute) (cryolike.grids.sphere_grid.SphereShell attribute)

B

Basis (class in cryolike.util.enums) batch_whole() (cryolike.metadata.lens_descriptor.LensDescriptor method) box_size (cryolike.grids.cartesian_grid.CartesianGrid2D attribute) (cryolike.grids.cartesian_grid.CartesianGrid3D attribute) (cryolike.grids.volume.Volume attribute) (cryolike.microscopy.ctf.CTF attribute) (cryolike.stacks.image.Images attribute) (cryolike.stacks.template.Templates attribute) (cryolike.util.atomic_model.AtomicModel attribute)

C

cartesian_grid (cryolike.metadata.image_descriptor.ImageDescriptor attribute) cartesian_points (cryolike.grids.sphere_grid.SphereGrid attribute) (cryolike.grids.sphere_grid.SphereShell attribute) CartesianGrid2D (class in cryolike.grids.cartesian_grid) CartesianGrid3D (class in cryolike.grids.cartesian_grid) CartesianShell (class in cryolike.grids.sphere_grid) center_physical_image_signal() (cryolike.stacks.image.Images method) change_images_phys_size() (cryolike.stacks.image.Images method) check_nufft_installed() (in module cryolike.util.device_handling) compute_cross_correlation() (in module cryolike.likelihoods.kernels.cross_correlation_likelihood_kernel) compute_cross_correlation_complete() (in module cryolike.likelihoods.interface.cross_correlation_full_return) compute_image_norms() (in module cryolike.likelihoods.kernels.cross_correlation_likelihood_kernel) compute_optimal_displacement() (in module cryolike.likelihoods.interface.cross_correlation_optimal_displacement) compute_optimal_displacement_and_rotation() (in module cryolike.likelihoods.interface.cross_correlation_optimal_displacement_rotation) compute_optimal_pose() (in module cryolike.likelihoods.interface.cross_correlation_optimal_pose) compute_optimal_rotation() (in module cryolike.likelihoods.interface.cross_correlation_optimal_rotation) compute_template_norms() (in module cryolike.likelihoods.kernels.cross_correlation_likelihood_kernel) configure_displacement() (in module cryolike.run_likelihood) configure_likelihood_files() (in module cryolike.run_likelihood) convert_particle_stacks_from_cryosparc_job_directory() (in module cryolike.file_conversions.particle_stacks_wrappers) convert_particle_stacks_from_indexed_cryosparc_file() (in module cryolike.file_conversions.particle_stacks_wrappers) convert_particle_stacks_from_indexed_star_file() (in module cryolike.file_conversions.particle_stacks_wrappers) convert_particle_stacks_from_paired_star_and_mrc_files() (in module cryolike.file_conversions.particle_stacks_wrappers) convert_stacks() (cryolike.file_conversions.particle_stacks_converter.ParticleStackConverter method) cross_correlation_msdw (cryolike.likelihoods.iteration.cross_correlation_iterator_types.CrossCorrelationYieldType attribute), [1] CrossCorrelationReturnType (class in cryolike.util.enums) CrossCorrelationYieldType (class in cryolike.likelihoods.iteration.cross_correlation_iterator_types) cryolike.file_conversions.make_templates_from_inputs_api module cryolike.file_conversions.particle_stacks_converter module cryolike.file_conversions.particle_stacks_wrappers module cryolike.grids.cartesian_grid module cryolike.grids.polar_grid module cryolike.grids.sphere_grid module cryolike.grids.volume module cryolike.likelihoods.interface.cross_correlation_full_return module cryolike.likelihoods.interface.cross_correlation_optimal_displacement module cryolike.likelihoods.interface.cross_correlation_optimal_displacement_rotation module cryolike.likelihoods.interface.cross_correlation_optimal_pose module

cryolike.likelihoods.interface.cross_correlation_optimal_rotation module cryolike.likelihoods.iteration.cross_correlation_iterator_types module cryolike.likelihoods.iteration.integrated_log_likelihood_aggregation module cryolike.likelihoods.iteration.template_image_comparator module cryolike.likelihoods.kernels module cryolike.likelihoods.kernels.cross_correlation_likelihood_kernel module cryolike.likelihoods.kernels.integrated_log_likelihood_kernel module cryolike.metadata.image_descriptor module cryolike.metadata.lens_descriptor module cryolike.metadata.viewing_angles module cryolike.microscopy.ctf module cryolike.plot module cryolike.run_likelihood module cryolike.stacks.image module cryolike.stacks.template module cryolike.util.atomic_model module cryolike.util.device_handling module cryolike.util.enums module cryolike.util.post_process_output module cryolike.util.types module cs_corrected (cryolike.microscopy.ctf.CTF attribute) CTF (class in cryolike.microscopy.ctf) ctf (cryolike.microscopy.ctf.CTF attribute) (cryolike.stacks.image.Images attribute) (cryolike.stacks.template.Templates attribute) ctfBfactor (cryolike.metadata.lens_descriptor.LensDescriptor attribute) ctfScalefactor (cryolike.metadata.lens_descriptor.LensDescriptor attribute)

D

defocusAngle (cryolike.metadata.lens_descriptor.LensDescriptor attribute) defocusU (cryolike.metadata.lens_descriptor.LensDescriptor attribute) defocusV (cryolike.metadata.lens_descriptor.LensDescriptor attribute) density_fourier (cryolike.grids.volume.Volume attribute) density_physical (cryolike.grids.volume.Volume attribute) device (cryolike.file_conversions.particle_stacks_converter.ParticleStackConverter attribute) displace_fourier_images() (cryolike.stacks.image.Images method) displacement_count (cryolike.stacks.image.Images attribute)

displacement_grid_angstrom (cryolike.stacks.image.Images attribute) dist_eq (cryolike.grids.sphere_grid.SphereGrid attribute) (cryolike.grids.sphere_grid.SphereShell attribute) dist_radii (cryolike.grids.polar_grid.PolarGrid attribute) dist_type (cryolike.grids.sphere_grid.SphereGrid attribute) downsample_factor (cryolike.file_conversions.particle_stacks_converter.ParticleStackConverter attribute) downsample_images_phys() (cryolike.stacks.image.Images method) downsample_type (cryolike.file_conversions.particle_stacks_converter.ParticleStackConverter attribute)

E

equal_shell (cryolike.grids.sphere_grid.SphereGrid attribute)

F

filename (cryolike.stacks.image.Images attribute) (cryolike.stacks.template.Templates attribute) files (cryolike.metadata.lens_descriptor.LensDescriptor attribute) filter_padded_images() (cryolike.stacks.image.Images method) from_cryosparc_file() (cryolike.metadata.lens_descriptor.LensDescriptor class method) from_individual_values() (cryolike.metadata.image_descriptor.ImageDescriptor class method)

from_mrc() (cryolike.grids.volume.Volume class method) (cryolike.stacks.image.Images class method) from_starfile() (cryolike.metadata.lens_descriptor.LensDescriptor class method) from_tensor_fourier() (cryolike.grids.volume.Volume class method) from_tensor_physical() (cryolike.grids.volume.Volume class method) from_viewing_distance() (cryolike.metadata.viewing_angles.ViewingAngles class method)

G

gammas (cryolike.metadata.viewing_angles.ViewingAngles attribute) get_device() (in module cryolike.util.device_handling) get_dtypes() (cryolike.util.enums.Precision method) get_fourier_translation_kernel() (cryolike.grids.polar_grid.PolarGrid method)

get_item_size() (cryolike.stacks.image.Images method) get_power_spectrum() (cryolike.stacks.image.Images method) get_selections() (cryolike.metadata.lens_descriptor.LensDescriptor method) get_slice() (cryolike.metadata.lens_descriptor.LensDescriptor method)

I

i_end (cryolike.likelihoods.iteration.cross_correlation_iterator_types.CrossCorrelationYieldType attribute), [1] i_stacks (cryolike.file_conversions.particle_stacks_converter.ParticleStackConverter attribute) i_start (cryolike.likelihoods.iteration.cross_correlation_iterator_types.CrossCorrelationYieldType attribute), [1] idxs (cryolike.metadata.lens_descriptor.LensDescriptor attribute) ill_kernel() (in module cryolike.likelihoods.kernels.integrated_log_likelihood_kernel) ImageDescriptor (class in cryolike.metadata.image_descriptor) Images (class in cryolike.stacks.image)

images_buffer (cryolike.file_conversions.particle_stacks_converter.ParticleStackConverter attribute) images_fourier (cryolike.stacks.image.Images attribute) images_phys (cryolike.stacks.image.Images attribute) img_desc (cryolike.file_conversions.particle_stacks_converter.ParticleStackConverter attribute) InputFileType (class in cryolike.util.enums) inputs_buffer (cryolike.file_conversions.particle_stacks_converter.ParticleStackConverter attribute) integration_weight_points (cryolike.grids.polar_grid.PolarGrid attribute)

L

lens_desc (cryolike.file_conversions.particle_stacks_converter.ParticleStackConverter attribute) lens_desc_buffer (cryolike.file_conversions.particle_stacks_converter.ParticleStackConverter attribute)

lens_descriptor (cryolike.microscopy.ctf.CTF attribute) LensDescriptor (class in cryolike.metadata.lens_descriptor) log_likelihood_ms (cryolike.likelihoods.iteration.cross_correlation_iterator_types.CrossCorrelationYieldType attribute), [1]

M

make_templates_from_inputs() (in module cryolike.file_conversions.make_templates_from_inputs_api) mask_integral (cryolike.grids.polar_grid.PolarGrid attribute) mask_points (cryolike.grids.polar_grid.PolarGrid attribute) max_imgs_to_plot (cryolike.file_conversions.particle_stacks_converter.ParticleStackConverter attribute) max_stacks (cryolike.file_conversions.particle_stacks_converter.ParticleStackConverter attribute) modify_pixel_size() (cryolike.stacks.image.Images method) module cryolike.file_conversions.make_templates_from_inputs_api cryolike.file_conversions.particle_stacks_converter cryolike.file_conversions.particle_stacks_wrappers cryolike.grids.cartesian_grid cryolike.grids.polar_grid cryolike.grids.sphere_grid cryolike.grids.volume cryolike.likelihoods.interface.cross_correlation_full_return cryolike.likelihoods.interface.cross_correlation_optimal_displacement cryolike.likelihoods.interface.cross_correlation_optimal_displacement_rotation cryolike.likelihoods.interface.cross_correlation_optimal_pose cryolike.likelihoods.interface.cross_correlation_optimal_rotation cryolike.likelihoods.iteration.cross_correlation_iterator_types cryolike.likelihoods.iteration.integrated_log_likelihood_aggregation cryolike.likelihoods.iteration.template_image_comparator cryolike.likelihoods.kernels cryolike.likelihoods.kernels.cross_correlation_likelihood_kernel cryolike.likelihoods.kernels.integrated_log_likelihood_kernel cryolike.metadata.image_descriptor cryolike.metadata.lens_descriptor cryolike.metadata.viewing_angles cryolike.microscopy.ctf cryolike.plot cryolike.run_likelihood cryolike.stacks.image cryolike.stacks.template cryolike.util.atomic_model cryolike.util.device_handling cryolike.util.enums cryolike.util.post_process_output cryolike.util.types

N

n_angles (cryolike.metadata.viewing_angles.ViewingAngles attribute) n_azimus_each_circle (cryolike.grids.sphere_grid.SphereShell attribute) n_CTF (cryolike.microscopy.ctf.CTF attribute) n_images (cryolike.stacks.image.Images attribute) n_inplane_shells (cryolike.grids.polar_grid.PolarGrid attribute) n_inplanes (cryolike.grids.polar_grid.PolarGrid attribute) n_pixels (cryolike.grids.cartesian_grid.CartesianGrid2D attribute) n_pixels_total (cryolike.grids.cartesian_grid.CartesianGrid2D attribute) (cryolike.grids.cartesian_grid.CartesianGrid3D attribute) n_points (cryolike.grids.polar_grid.PolarGrid attribute) (cryolike.grids.sphere_grid.SphereGrid attribute) (cryolike.grids.sphere_grid.SphereShell attribute)

n_polar_circles (cryolike.grids.sphere_grid.SphereShell attribute) n_shells (cryolike.grids.polar_grid.PolarGrid attribute) (cryolike.grids.sphere_grid.SphereGrid attribute) n_templates (cryolike.stacks.template.Templates attribute) n_voxels (cryolike.grids.cartesian_grid.CartesianGrid3D attribute) normalize_images_fourier() (cryolike.stacks.image.Images method) normalize_images_phys() (cryolike.stacks.image.Images method) NormType (class in cryolike.util.enums)

O

output_plots (cryolike.file_conversions.particle_stacks_converter.ParticleStackConverter attribute)

P

ParticleStackConverter (class in cryolike.file_conversions.particle_stacks_converter) pdb_file (cryolike.util.atomic_model.AtomicModel attribute) phaseShift (cryolike.metadata.lens_descriptor.LensDescriptor attribute) phys_grid (cryolike.stacks.image.Images attribute) (cryolike.stacks.template.Templates attribute) pixel_size (cryolike.file_conversions.particle_stacks_converter.ParticleStackConverter attribute) (cryolike.grids.cartesian_grid.CartesianGrid2D attribute) point_shell_start_indices (cryolike.grids.sphere_grid.SphereGrid attribute) polar_circles (cryolike.grids.sphere_grid.SphereShell attribute) polar_grid (cryolike.metadata.image_descriptor.ImageDescriptor attribute) (cryolike.stacks.image.Images attribute) (cryolike.stacks.template.Templates attribute)

polar_points (cryolike.grids.sphere_grid.SphereGrid attribute) (cryolike.grids.sphere_grid.SphereShell attribute) PolarGrid (class in cryolike.grids.polar_grid) polars (cryolike.metadata.viewing_angles.ViewingAngles attribute) Precision (class in cryolike.util.enums) precision (cryolike.metadata.image_descriptor.ImageDescriptor attribute) prepare_indexed_file() (cryolike.file_conversions.particle_stacks_converter.ParticleStackConverter method) prepare_sequential_cryosparc() (cryolike.file_conversions.particle_stacks_converter.ParticleStackConverter method) prepare_star_files() (cryolike.file_conversions.particle_stacks_converter.ParticleStackConverter method) print() (cryolike.metadata.image_descriptor.ImageDescriptor method) project_images_over_displacements() (cryolike.stacks.image.Images method)

Q

QuadratureType (class in cryolike.util.enums)

R

radius (cryolike.grids.cartesian_grid.CartesianGrid2D attribute) (cryolike.grids.cartesian_grid.CartesianGrid3D attribute) (cryolike.grids.sphere_grid.SphereShell attribute) radius_max (cryolike.grids.polar_grid.PolarGrid attribute) (cryolike.grids.sphere_grid.SphereGrid attribute) radius_points (cryolike.grids.polar_grid.PolarGrid attribute) (cryolike.grids.sphere_grid.SphereGrid attribute)

radius_shells (cryolike.grids.polar_grid.PolarGrid attribute) (cryolike.grids.sphere_grid.SphereGrid attribute) read_from_pdb() (cryolike.util.atomic_model.AtomicModel class method) ref_pixel_size (cryolike.metadata.lens_descriptor.LensDescriptor attribute) rotate_images_fourier_discrete() (cryolike.stacks.image.Images method) run_likelihood_full_cross_correlation() (in module cryolike.run_likelihood) run_likelihood_optimal_pose() (in module cryolike.run_likelihood)

S

SamplingStrategy (class in cryolike.util.enums) save() (cryolike.metadata.image_descriptor.ImageDescriptor method) save_to_mrc() (cryolike.stacks.image.Images method) select_images() (cryolike.stacks.image.Images method) set_displacement_grid() (cryolike.stacks.image.Images method) set_epsilon() (cryolike.util.enums.Precision method) set_mask_points() (cryolike.grids.polar_grid.PolarGrid method)

shell_indices (cryolike.grids.polar_grid.PolarGrid attribute) shells (cryolike.grids.sphere_grid.SphereGrid attribute) skip_exist (cryolike.file_conversions.particle_stacks_converter.ParticleStackConverter attribute) sphere_grid (cryolike.grids.volume.Volume attribute) SphereGrid (class in cryolike.grids.sphere_grid) SphereShell (class in cryolike.grids.sphere_grid) sphericalAberration (cryolike.metadata.lens_descriptor.LensDescriptor attribute)

T

t_end (cryolike.likelihoods.iteration.cross_correlation_iterator_types.CrossCorrelationYieldType attribute), [1] t_start (cryolike.likelihoods.iteration.cross_correlation_iterator_types.CrossCorrelationYieldType attribute), [1] template_first_comparator() (in module cryolike.likelihoods.iteration.template_image_comparator) Templates (class in cryolike.stacks.template) templates_fourier (cryolike.stacks.template.Templates attribute)

templates_phys (cryolike.stacks.template.Templates attribute) theta_points (cryolike.grids.polar_grid.PolarGrid attribute) theta_shell (cryolike.grids.polar_grid.PolarGrid attribute) theta_shells (cryolike.grids.polar_grid.PolarGrid attribute) transform_to_fourier() (cryolike.stacks.image.Images method) transform_to_spatial() (cryolike.stacks.image.Images method)

U

uniform (cryolike.grids.polar_grid.PolarGrid attribute)

use_protein_residue_model (cryolike.metadata.image_descriptor.ImageDescriptor attribute)

V

viewing_angles (cryolike.metadata.image_descriptor.ImageDescriptor attribute) (cryolike.stacks.image.Images attribute) (cryolike.stacks.template.Templates attribute) viewing_distance (cryolike.metadata.image_descriptor.ImageDescriptor attribute)

ViewingAngles (class in cryolike.metadata.viewing_angles) voltage (cryolike.metadata.lens_descriptor.LensDescriptor attribute) Volume (class in cryolike.grids.volume) voxel_grid (cryolike.grids.volume.Volume attribute) voxel_size (cryolike.grids.cartesian_grid.CartesianGrid3D attribute)

W

weight_points (cryolike.grids.polar_grid.PolarGrid attribute) (cryolike.grids.sphere_grid.SphereGrid attribute) (cryolike.grids.sphere_grid.SphereShell attribute)

weight_shells (cryolike.grids.polar_grid.PolarGrid attribute) weights_polar (cryolike.grids.sphere_grid.SphereShell attribute) weights_radius_shells (cryolike.grids.sphere_grid.SphereGrid attribute) weights_viewing (cryolike.metadata.viewing_angles.ViewingAngles attribute)

X

x_axis (cryolike.grids.cartesian_grid.CartesianGrid2D attribute) (cryolike.grids.cartesian_grid.CartesianGrid3D attribute) x_pixels (cryolike.grids.cartesian_grid.CartesianGrid2D attribute)

x_points (cryolike.grids.polar_grid.PolarGrid attribute) (cryolike.grids.sphere_grid.CartesianShell attribute), [1] x_voxels (cryolike.grids.cartesian_grid.CartesianGrid3D attribute) xyz_points (cryolike.grids.sphere_grid.CartesianShell attribute), [1]

Y

y_axis (cryolike.grids.cartesian_grid.CartesianGrid2D attribute) (cryolike.grids.cartesian_grid.CartesianGrid3D attribute) y_pixels (cryolike.grids.cartesian_grid.CartesianGrid2D attribute)

y_points (cryolike.grids.polar_grid.PolarGrid attribute) (cryolike.grids.sphere_grid.CartesianShell attribute), [1] y_voxels (cryolike.grids.cartesian_grid.CartesianGrid3D attribute)

Z

z_axis (cryolike.grids.cartesian_grid.CartesianGrid3D attribute)

z_points (cryolike.grids.sphere_grid.CartesianShell attribute), [1] z_voxels (cryolike.grids.cartesian_grid.CartesianGrid3D attribute)