Index

A

AbstractContinuousParticle (class in condor.particle.particle_abstract) AbstractMaterial (class in condor.utils.material) AbstractParticle (class in condor.particle.particle_abstract) add_material() (condor.particle.particle_abstract.AbstractContinuousParticle method) (condor.utils.material.MaterialMap method) angle() (in module condor.utils.linalg)

AtomDensityMaterial (class in condor.utils.material) atomic_compositions (condor.utils.material.MaterialType attribute) atomic_names (in module condor.utils.material) atomic_numbers (in module condor.utils.material)

B

bin_photons() (condor.detector.Detector method)

C

calculate_polarization_factors() (condor.detector.Detector method) clear_atomic_composition() (condor.utils.material.AtomDensityMaterial method) condor (module) condor.detector (module) condor.experiment (module) condor.particle (module), [1] condor.particle.particle_abstract (module) condor.particle.particle_atoms (module) condor.particle.particle_map (module) condor.particle.particle_sphere (module) condor.particle.particle_spheroid (module) condor.source (module) condor.utils (module) condor.utils.bodies (module) condor.utils.config (module) condor.utils.diffraction (module)

condor.utils.linalg (module) condor.utils.log (module) condor.utils.material (module) condor.utils.photon (module) condor.utils.pixelmask (module) condor.utils.profile (module) condor.utils.resample (module) condor.utils.rotation (module) condor.utils.scattering_vector (module) condor.utils.sphere_diffraction (module) condor.utils.spheroid_diffraction (module) condor.utils.testing (module) condor.utils.variation (module) crossproduct() (in module condor.utils.linalg) crystallographic_resolution() (in module condor.utils.diffraction)

D

detect_photons() (condor.detector.Detector method) Detector (class in condor.detector) diameter_mean (condor.particle.particle_atoms.ParticleAtoms attribute)

dotproduct() (in module condor.utils.linalg) downsample() (in module condor.utils.resample) downsample_pos() (in module condor.utils.resample)

E

ElectronDensityMaterial (class in condor.utils.material) euler_from_quat() (in module condor.utils.rotation) euler_to_rotmx() (in module condor.utils.rotation)

Experiment (class in condor.experiment) experiment_from_configdict() (in module condor.experiment) experiment_from_configfile() (in module condor.experiment)

F

F_sphere_diffraction() (in module condor.utils.sphere_diffraction)

F_spheroid_diffraction() (in module condor.utils.spheroid_diffraction)

G

generate_absqmap() (in module condor.utils.scattering_vector) generate_qmap() (condor.detector.Detector method) (in module condor.utils.scattering_vector) generate_qmap_3d() (condor.detector.Detector method) (in module condor.utils.scattering_vector) generate_rpix_3d() (in module condor.utils.scattering_vector) generate_xypix() (condor.detector.Detector method) get() (condor.utils.variation.Variation method) get_all_pixel_solid_angles() (condor.detector.Detector method) get_all_values() (condor.utils.rotation.Rotations method) get_as_euler_angles() (condor.utils.rotation.Rotation method) get_as_quaternion() (condor.utils.rotation.Rotation method) get_as_rotation_matrix() (condor.utils.rotation.Rotation method) get_atomic_composition() (condor.utils.material.AtomDensityMaterial method) get_atomic_mass() (in module condor.utils.material) get_atomic_number() (in module condor.utils.material) get_atomic_numbers() (condor.particle.particle_atoms.ParticleAtoms method) get_atomic_positions() (condor.particle.particle_atoms.ParticleAtoms method) get_atomic_scattering_factors() (in module condor.utils.material) get_atomic_standard_weights() (condor.particle.particle_atoms.ParticleAtoms method) get_attenuation_length() (condor.utils.material.AbstractMaterial method) get_beta() (condor.utils.material.AbstractMaterial method) (condor.utils.material.MaterialMap method) get_center_of_mass() (condor.particle.particle_atoms.ParticleAtoms method) get_conf() (condor.detector.Detector method) (condor.experiment.Experiment method) (condor.particle.particle_abstract.AbstractContinuousParticle method) (condor.particle.particle_abstract.AbstractParticle method) (condor.particle.particle_atoms.ParticleAtoms method) (condor.particle.particle_map.ParticleMap method) (condor.particle.particle_sphere.ParticleSphere method) (condor.particle.particle_spheroid.ParticleSpheroid method) (condor.source.Source method) (condor.utils.material.AtomDensityMaterial method) (condor.utils.material.ElectronDensityMaterial method) (condor.utils.variation.Variation method) get_current_map() (condor.particle.particle_map.ParticleMap method) get_current_rotation() (condor.particle.particle_abstract.AbstractParticle method) (condor.utils.rotation.Rotations method) get_cx_mean_value() (condor.detector.Detector method) get_cy_mean_value() (condor.detector.Detector method) get_delta() (condor.utils.material.AbstractMaterial method) (condor.utils.material.MaterialMap method) get_dn() (condor.particle.particle_sphere.ParticleSphere method) (condor.particle.particle_spheroid.ParticleSpheroid method) (condor.utils.material.AbstractMaterial method) (condor.utils.material.MaterialMap method) get_electron_density() (condor.utils.material.AtomDensityMaterial method) (condor.utils.material.MaterialMap method) get_energy() (condor.utils.photon.Photon method) get_energy_eV() (condor.utils.photon.Photon method) get_f() (condor.utils.material.AtomDensityMaterial method) (condor.utils.material.ElectronDensityMaterial method) (condor.utils.material.MaterialMap method) get_f_element() (in module condor.utils.material) get_formalism() (condor.utils.rotation.Rotations method)

get_frequency() (condor.utils.photon.Photon method) get_fresnel_number() (condor.experiment.Experiment method) get_icosahedron_normal_vectors() (in module condor.utils.bodies) get_icosahedron_vertices() (in module condor.utils.bodies) get_intensity() (condor.source.Source method) get_linear_sampling_ratio() (condor.experiment.Experiment method) get_mask() (condor.detector.Detector method) get_max_resolution() (condor.detector.Detector method) get_mode() (condor.utils.variation.Variation method) get_model() (condor.utils.profile.Profile method) get_n() (condor.utils.material.AbstractMaterial method) (condor.utils.material.MaterialMap method) get_new_dn_map() (condor.particle.particle_map.ParticleMap method) get_new_map() (condor.particle.particle_map.ParticleMap method) get_next() (condor.detector.Detector method) (condor.particle.particle_abstract.AbstractContinuousParticle method) (condor.particle.particle_abstract.AbstractParticle method) (condor.particle.particle_atoms.ParticleAtoms method) (condor.particle.particle_map.ParticleMap method) (condor.particle.particle_sphere.ParticleSphere method) (condor.particle.particle_spheroid.ParticleSpheroid method) (condor.source.Source method) get_next_number_of_particles() (condor.particle.particle_abstract.AbstractParticle method) get_next_rotation() (condor.utils.rotation.Rotations method) get_number_of_dimensions() (condor.utils.variation.Variation method) get_original_map() (condor.particle.particle_map.ParticleMap method) get_p_max_dist() (condor.detector.Detector method) get_photoabsorption_cross_section() (condor.utils.material.AbstractMaterial method) (condor.utils.material.MaterialMap method) get_pixel_solid_angle() (condor.detector.Detector method) get_q_max() (condor.detector.Detector method) get_qmap() (condor.experiment.Experiment method) get_qmap_from_cache() (condor.experiment.Experiment method) get_radial() (condor.utils.profile.Profile method) get_radius_of_gyration() (condor.particle.particle_atoms.ParticleAtoms method) get_resolution() (condor.experiment.Experiment method) get_resolution_element_r() (condor.detector.Detector method) get_resolution_element_x() (condor.detector.Detector method) get_resolution_element_y() (condor.detector.Detector method) get_scatterer_density() (condor.utils.material.AtomDensityMaterial method) (condor.utils.material.ElectronDensityMaterial method) get_spread() (condor.utils.variation.Variation method) get_transmission() (condor.utils.material.AbstractMaterial method) get_wavelength() (condor.utils.photon.Photon method)

I

I_sphere_diffraction() (in module condor.utils.sphere_diffraction) I_spheroid_diffraction() (in module condor.utils.spheroid_diffraction)

invert() (condor.utils.rotation.Rotation method) is_similar() (condor.utils.rotation.Rotation method)

L

length() (in module condor.utils.linalg) log() (in module condor.utils.log) log_and_raise_error() (in module condor.utils.log) log_debug() (in module condor.utils.log)

log_execution_time() (in module condor.utils.log) log_info() (in module condor.utils.log) log_warning() (in module condor.utils.log)

M

make_euler_unique_repax() (in module condor.utils.rotation) make_icosahedron_map() (in module condor.utils.bodies) make_icosahedron_map_slow() (in module condor.utils.bodies) make_sphere_map() (in module condor.utils.bodies)

make_spheroid_map() (in module condor.utils.bodies) mass_densities (condor.utils.material.MaterialType attribute) MaterialMap (class in condor.utils.material) MaterialType (class in condor.utils.material)

N

norm_quat() (in module condor.utils.rotation)

nyquist_pixel_size() (in module condor.utils.diffraction)

P

ParticleAtoms (class in condor.particle.particle_atoms) ParticleMap (class in condor.particle.particle_map) ParticleSphere (class in condor.particle.particle_sphere) ParticleSpheroid (class in condor.particle.particle_spheroid) Photon (class in condor.utils.photon) PIXEL_FAILED_ARTIFACT_CORRECTION (condor.utils.pixelmask.PixelMask attribute) PIXEL_IS_ARTIFACT_CORRECTED (condor.utils.pixelmask.PixelMask attribute) PIXEL_IS_BAD (condor.utils.pixelmask.PixelMask attribute) PIXEL_IS_DEAD (condor.utils.pixelmask.PixelMask attribute) PIXEL_IS_HOT (condor.utils.pixelmask.PixelMask attribute) PIXEL_IS_IN_MASK (condor.utils.pixelmask.PixelMask attribute) PIXEL_IS_IN_PEAKMASK (condor.utils.pixelmask.PixelMask attribute) PIXEL_IS_INVALID (condor.utils.pixelmask.PixelMask attribute) PIXEL_IS_MISSING (condor.utils.pixelmask.PixelMask attribute)

PIXEL_IS_NOISY (condor.utils.pixelmask.PixelMask attribute) PIXEL_IS_OUT_OF_RESOLUTION_LIMITS (condor.utils.pixelmask.PixelMask attribute) PIXEL_IS_PEAK_FOR_HITFINDER (condor.utils.pixelmask.PixelMask attribute) PIXEL_IS_PERFECT (condor.utils.pixelmask.PixelMask attribute) PIXEL_IS_PHOTON_BACKGROUND_CORRECTED (condor.utils.pixelmask.PixelMask attribute) PIXEL_IS_SATURATED (condor.utils.pixelmask.PixelMask attribute) PIXEL_IS_SHADOWED (condor.utils.pixelmask.PixelMask attribute) PIXEL_IS_TO_BE_IGNORED (condor.utils.pixelmask.PixelMask attribute) PixelMask (class in condor.utils.pixelmask) polarization_factor() (in module condor.utils.diffraction) Profile (class in condor.utils.profile) propagate() (condor.experiment.Experiment method) propagate3d() (condor.experiment.Experiment method)

Q

q_from_p() (in module condor.utils.scattering_vector) quat() (in module condor.utils.rotation) quat_conj() (in module condor.utils.rotation) quat_from_rotmx() (in module condor.utils.rotation) quat_mult() (in module condor.utils.rotation)

quat_vec_mult() (in module condor.utils.rotation) quat_x() (in module condor.utils.rotation) quat_y() (in module condor.utils.rotation) quat_z() (in module condor.utils.rotation)

R

R_x() (in module condor.utils.rotation) R_y() (in module condor.utils.rotation) R_z() (in module condor.utils.rotation) rand_quat() (in module condor.utils.rotation) read_configdict() (in module condor.utils.config) read_configfile() (in module condor.utils.config) remove_from_dict() (in module condor.experiment) reset_counter() (condor.utils.variation.Variation method) resolution_element() (in module condor.utils.diffraction)

rot_x() (in module condor.utils.rotation) rot_y() (in module condor.utils.rotation) rot_z() (in module condor.utils.rotation) rotate_quat() (in module condor.utils.rotation) rotate_vector() (condor.utils.rotation.Rotation method) rotate_vectors() (condor.utils.rotation.Rotation method) Rotation (class in condor.utils.rotation) Rotations (class in condor.utils.rotation) rotmx_from_quat() (in module condor.utils.rotation)

S

same_shape() (in module condor.utils.testing) set_alignment() (condor.particle.particle_abstract.AbstractParticle method) set_as_random() (condor.utils.rotation.Rotation method) set_as_random_x() (condor.utils.rotation.Rotation method) set_as_random_y() (condor.utils.rotation.Rotation method) set_as_random_z() (condor.utils.rotation.Rotation method) set_atomic_concentration() (condor.utils.material.AtomDensityMaterial method) set_atoms_from_arrays() (condor.particle.particle_atoms.ParticleAtoms method) set_atoms_from_pdb_file() (condor.particle.particle_atoms.ParticleAtoms method) set_atoms_from_pdb_id() (condor.particle.particle_atoms.ParticleAtoms method) set_center_variation() (condor.detector.Detector method) set_custom_geometry_by_array() (condor.particle.particle_map.ParticleMap method) set_custom_geometry_by_emd_id() (condor.particle.particle_map.ParticleMap method) set_custom_geometry_by_h5file() (condor.particle.particle_map.ParticleMap method) set_custom_geometry_by_mrcfile() (condor.particle.particle_map.ParticleMap method) set_diameter_variation() (condor.particle.particle_abstract.AbstractContinuousParticle method) set_energy() (condor.utils.photon.Photon method)

set_energy_eV() (condor.utils.photon.Photon method) set_flattening_variation() (condor.particle.particle_spheroid.ParticleSpheroid method) set_frequency() (condor.utils.photon.Photon method) set_material() (condor.particle.particle_abstract.AbstractContinuousParticle method) set_mode() (condor.utils.variation.Variation method) set_model() (condor.utils.profile.Profile method) set_noise() (condor.detector.Detector method) set_number_of_dimensions() (condor.utils.variation.Variation method) set_position_variation() (condor.particle.particle_abstract.AbstractParticle method) set_pulse_energy_variation() (condor.source.Source method) set_spread() (condor.utils.variation.Variation method) set_wavelength() (condor.utils.photon.Photon method) set_with_euler_angles() (condor.utils.rotation.Rotation method) set_with_quaternion() (condor.utils.rotation.Rotation method) set_with_rotation_matrix() (condor.utils.rotation.Rotation method) Source (class in condor.source)

T

to_spheroid_diameter() (in module condor.utils.spheroid_diffraction) to_spheroid_flattening() (in module condor.utils.spheroid_diffraction)

to_spheroid_semi_diameter_a() (in module condor.utils.spheroid_diffraction) to_spheroid_semi_diameter_c() (in module condor.utils.spheroid_diffraction)

U

unique_representation_quat() (in module condor.utils.rotation)

upsample_pos() (in module condor.utils.resample)

V

validate() (condor.utils.variation.Variation method)

Variation (class in condor.utils.variation)

W

write_configfile() (in module condor.utils.config)