Index

_

__init__() (parakeet.beam.Beam method) (parakeet.detector.Detector method) (parakeet.lens.Lens method) (parakeet.microscope.Microscope method) (parakeet.sample.Sample method) (parakeet.scan.Scan method)

A

acceleration_voltage_spread (parakeet.beam.Beam property) add_atoms() (parakeet.sample.Sample method) add_molecule() (parakeet.sample.Sample method) add_molecules() (in module parakeet.sample) angles (parakeet.scan.Scan property)

atoms_dataset_name() (parakeet.sample.Sample method) atoms_dataset_range() (parakeet.sample.Sample method) atoms_dataset_range_3d() (parakeet.sample.Sample method) average_all_particles() (in module parakeet.analyse) average_particles() (in module parakeet.analyse) axes (parakeet.scan.Scan property)

B

Beam (class in parakeet.beam) beam (parakeet.microscope.Microscope property)

beam_tilt_phi (parakeet.scan.Scan property) beam_tilt_theta (parakeet.scan.Scan property) bounding_box (parakeet.sample.Sample property)

C

centre (parakeet.sample.Sample property) close() (parakeet.sample.Sample method)

containing_box (parakeet.sample.Sample property) correct() (in module parakeet.analyse) ctf() (in module parakeet.simulate)

D

defocus_offset (parakeet.scan.Scan property) del_atoms() (parakeet.sample.Sample method)

Detector (class in parakeet.detector) detector (parakeet.microscope.Microscope property) dimensions (parakeet.sample.Sample property)

E

electrons_per_angstrom (parakeet.beam.Beam property) (parakeet.scan.Scan property) energy (parakeet.beam.Beam property) energy_spread (parakeet.beam.Beam property)

euler_angles (parakeet.scan.Scan property) exit_wave() (in module parakeet.simulate) exposure_time (parakeet.scan.Scan property) extract() (in module parakeet.analyse)

F

fraction_number (parakeet.scan.Scan property)

G

get_atoms() (parakeet.sample.Sample method) get_atoms_in_fov() (parakeet.sample.Sample method) get_atoms_in_group() (parakeet.sample.Sample method)

get_atoms_in_range() (parakeet.sample.Sample method) get_molecule() (parakeet.sample.Sample method) get_pdb() (in module parakeet.data)

I

identifier() (parakeet.sample.Sample method) illumination_semiangle (parakeet.beam.Beam property) image() (in module parakeet.simulate) image_number (parakeet.scan.Scan property)

info() (parakeet.sample.Sample method) iter_atom_groups() (parakeet.sample.Sample method) iter_atoms() (parakeet.sample.Sample method) iter_molecules() (parakeet.sample.Sample method)

L

Lens (class in parakeet.lens)

lens (parakeet.microscope.Microscope property)

M

Microscope (class in parakeet.microscope) mill() (in module parakeet.sample)

model (parakeet.microscope.Microscope property) molecules (parakeet.sample.Sample property)

N

new() (in module parakeet.config) (in module parakeet.io) (in module parakeet.sample)

number_of_atoms (parakeet.sample.Sample property) number_of_molecular_models (parakeet.sample.Sample property) number_of_molecules (parakeet.sample.Sample property)

O

open() (in module parakeet.io)

optics() (in module parakeet.simulate) orientation (parakeet.scan.Scan property)

P

phase_plate (parakeet.microscope.Microscope property) phi (parakeet.beam.Beam property)

position (parakeet.scan.Scan property) potential() (in module parakeet.simulate)

R

reconstruct() (in module parakeet.analyse)

refine() (in module parakeet.analyse) run() (in module parakeet)

S

Sample (class in parakeet.sample) Scan (class in parakeet.scan) shape (parakeet.sample.Sample property) shape_box (parakeet.sample.Sample property)

shape_radius (parakeet.sample.Sample property) shift (parakeet.scan.Scan property) shift_delta (parakeet.scan.Scan property) sputter() (in module parakeet.sample)

T

theta (parakeet.beam.Beam property)