Index

_

__add__() (picometer.atom.AtomSet method) __bool__() (picometer.atom.Locator method) __delitem__() (picometer.settings.Settings method) __eq__() (picometer.instructions.Instruction method) __getitem__() (picometer.atom.AtomSet method) __len__() (picometer.atom.AtomSet method) __repr__() (picometer.instructions.Instruction method) (picometer.shapes.Shape method) __setitem__() (picometer.settings.Settings method) __version__ (in module picometer)

_angle() (picometer.atom.AtomSet method) (picometer.shapes.ExplicitShape method) (picometer.shapes.Shape method) _collect_shapes() (picometer.instructions.SerialInstructionHandler method) _distance() (picometer.atom.AtomSet method) (picometer.shapes.Line method) (picometer.shapes.Plane method) (picometer.shapes.Shape method) _get_logger() (in module picometer.logging) _load_model_state() (picometer.instructions.LoadInstructionHandler method)

A

ab_degrees (in module tests.test_shapes) add_file_handler() (in module picometer.logging) angle() (picometer.shapes.Shape method) AngleInstructionHandler (class in picometer.instructions) are_antiparallel() (in module picometer.shapes) are_parallel() (in module picometer.shapes) are_perpendicular() (in module picometer.shapes) are_synparallel() (in module picometer.shapes) as_dict() (picometer.instructions.Instruction method) (picometer.instructions.Routine method)

assertNumericallyEqual (tests.test_shapes.TestCaseExtras attribute) at (picometer.atom.Locator attribute) at() (picometer.shapes.Shape method) atoms (picometer.models.ModelState attribute) AtomSet (class in picometer.atom) (class in picometer.shapes) auto_write_unit_cell (picometer.settings.DefaultSettings attribute) axial (picometer.shapes.Shape.Kind attribute)

B

base (picometer.atom.AtomSet attribute)

BaseInstructionHandler (class in picometer.instructions) BaseInstructionHandlerType (class in picometer.instructions)

C

cart_xyz (picometer.atom.AtomSet property) (picometer.shapes.AtomSet attribute) centroid (picometer.atom.AtomSet property) CentroidInstructionHandler (class in picometer.instructions) centroids (picometer.models.ModelState attribute) clear_selection() (picometer.instructions.BaseInstructionHandler method)

clear_selection_after_use (picometer.settings.DefaultSettings attribute) clear_selection_after_use() (picometer.instructions.BaseInstructionHandler method) ClearInstructionHandler (class in picometer.instructions) complete_uiso_from_umatrix (picometer.settings.DefaultSettings attribute) complete_umatrix_from_uiso (picometer.settings.DefaultSettings attribute) concatenate() (picometer.instructions.Routine class method) CoordinatesInstructionHandler (class in picometer.instructions)

D

DefaultSettings (class in picometer.settings) degrees_between() (in module picometer.shapes) dihedral() (picometer.atom.AtomSet method) DihedralInstructionHandler (class in picometer.instructions) direction (picometer.atom.AtomSet property) (picometer.shapes.ExplicitShape property) (picometer.shapes.Shape attribute)

displacement_get_cartesian_eigenvalues (picometer.settings.DefaultSettings attribute) DisplacementInstructionHandler (class in picometer.instructions) distance() (picometer.shapes.Shape method) DistanceInstructionHandler (class in picometer.instructions)

E

emit() (picometer.logging.LogEventHandler method) evaluation_table (picometer.instructions.ProcessorProtocol attribute) (picometer.process.Processor attribute)

ExplicitShape (class in picometer.shapes)

F

formatter (in module picometer.logging) fract_uij (picometer.atom.AtomSet property) fract_xyz (picometer.atom.AtomSet property) fractionalise() (picometer.atom.AtomSet method) from_cif() (picometer.atom.AtomSet class method)

from_dict() (picometer.atom.Locator class method) (picometer.instructions.Routine class method) from_string() (picometer.instructions.Routine class method) from_yaml() (picometer.instructions.Routine class method) (picometer.settings.Settings class method)

G

get_field() (picometer.settings.DefaultSettings class method) get_yaml() (in module tests.test_instructions)

group_registry (in module picometer.atom) GroupInstructionHandler (class in picometer.instructions)

H

handle() (picometer.instructions.BaseInstructionHandler method) (picometer.instructions.ClearInstructionHandler method) (picometer.instructions.GroupInstructionHandler method) (picometer.instructions.LoadInstructionHandler method) (picometer.instructions.RecenterInstructionHandler method) (picometer.instructions.SelectInstructionHandler method) (picometer.instructions.SerialInstructionHandler method) (picometer.instructions.SetInstructionHandler method) (picometer.instructions.WriteInstructionHandler method) handle_one() (picometer.instructions.AngleInstructionHandler method) (picometer.instructions.CentroidInstructionHandler method) (picometer.instructions.CoordinatesInstructionHandler method) (picometer.instructions.DihedralInstructionHandler method) (picometer.instructions.DisplacementInstructionHandler method) (picometer.instructions.DistanceInstructionHandler method) (picometer.instructions.LineInstructionHandler method) (picometer.instructions.PlaneInstructionsHandler method) (picometer.instructions.SerialInstructionHandler method)

handler (picometer.instructions.Instruction property) history (picometer.instructions.ProcessorProtocol attribute) (picometer.process.Processor attribute)

I

Instruction (class in picometer.instructions)

instructions (picometer.process.Processor attribute)

K

keyword (picometer.instructions.Instruction attribute) kind (picometer.atom.AtomSet attribute) (picometer.shapes.Line attribute) (picometer.shapes.Plane attribute) (picometer.shapes.Shape attribute) kwargs (picometer.instructions.AngleInstructionHandler attribute) (picometer.instructions.BaseInstructionHandler attribute) (picometer.instructions.CentroidInstructionHandler attribute) (picometer.instructions.ClearInstructionHandler attribute) (picometer.instructions.CoordinatesInstructionHandler attribute) (picometer.instructions.DihedralInstructionHandler attribute) (picometer.instructions.DisplacementInstructionHandler attribute) (picometer.instructions.DistanceInstructionHandler attribute) (picometer.instructions.GroupInstructionHandler attribute) (picometer.instructions.Instruction property) (picometer.instructions.LineInstructionHandler attribute) (picometer.instructions.LoadInstructionHandler attribute) (picometer.instructions.PlaneInstructionsHandler attribute) (picometer.instructions.RecenterInstructionHandler attribute) (picometer.instructions.SelectInstructionHandler attribute) (picometer.instructions.SetInstructionHandler attribute) (picometer.instructions.WriteInstructionHandler attribute)

L

label (picometer.atom.Locator attribute) Line (class in picometer.shapes) line (picometer.atom.AtomSet property) LineInstructionHandler (class in picometer.instructions) LoadInstructionHandler (class in picometer.instructions) locate() (picometer.atom.AtomSet method) Locator (class in picometer.atom) log_callback (picometer.logging.LogEventHandler attribute)

LogEventHandler (class in picometer.logging) logger (in module picometer.atom) (in module picometer.instructions) (in module picometer.logging) (in module picometer.models) (in module picometer.process) (in module picometer.settings) (in module picometer.shapes)

M

main() (in module picometer.__main__) model_states (picometer.instructions.ProcessorProtocol attribute) (picometer.process.Processor attribute) ModelState (class in picometer.models) ModelStates (class in picometer.models) module picometer picometer.__main__ picometer.atom picometer.instructions picometer.logging picometer.models picometer.process picometer.settings picometer.shapes picometer.utility tests tests.test_instructions tests.test_logging tests.test_settings tests.test_shapes tests.test_transformations

N

name (picometer.instructions.AngleInstructionHandler attribute) (picometer.instructions.BaseInstructionHandler attribute) (picometer.instructions.CentroidInstructionHandler attribute) (picometer.instructions.ClearInstructionHandler attribute) (picometer.instructions.CoordinatesInstructionHandler attribute) (picometer.instructions.DihedralInstructionHandler attribute) (picometer.instructions.DisplacementInstructionHandler attribute) (picometer.instructions.DistanceInstructionHandler attribute) (picometer.instructions.GroupInstructionHandler attribute) (picometer.instructions.LineInstructionHandler attribute) (picometer.instructions.LoadInstructionHandler attribute) (picometer.instructions.PlaneInstructionsHandler attribute) (picometer.instructions.RecenterInstructionHandler attribute) (picometer.instructions.SelectInstructionHandler attribute) (picometer.instructions.SetInstructionHandler attribute) (picometer.instructions.WriteInstructionHandler attribute)

nodes (picometer.models.ModelState property)

O

origin (picometer.atom.AtomSet property) (picometer.shapes.ExplicitShape attribute) (picometer.shapes.Shape attribute)

orthogonalise() (picometer.atom.AtomSet method)

P

parse_args() (in module picometer.__main__) picometer module picometer.__main__ module picometer.atom module picometer.instructions module picometer.logging module picometer.models module picometer.process module

picometer.settings module picometer.shapes module picometer.utility module planar (picometer.shapes.Shape.Kind attribute) Plane (class in picometer.shapes) plane (picometer.atom.AtomSet property) PlaneInstructionsHandler (class in picometer.instructions) process() (in module picometer.process) (picometer.process.Processor method) Processor (class in picometer.process) processor (picometer.instructions.BaseInstructionHandler attribute) ProcessorProtocol (class in picometer.instructions)

R

raw_kwargs (picometer.instructions.Instruction attribute) RecenterInstructionHandler (class in picometer.instructions) register_log_listener() (in module picometer.logging) REGISTRY (picometer.instructions.BaseInstructionHandlerType attribute)

rot3_at_cobalt_code (tests.test_transformations.TestTransformations attribute) rot6_at_origin_code (tests.test_transformations.TestTransformations attribute) Routine (class in picometer.instructions) routine_prefix (tests.test_instructions.TestMeasuringInstructions attribute) (tests.test_instructions.TestSettingInstructions attribute)

S

select_atom() (picometer.atom.AtomSet method) SelectInstructionHandler (class in picometer.instructions) selection (picometer.instructions.ProcessorProtocol attribute) (picometer.process.Processor attribute) SerialInstructionHandler (class in picometer.instructions) SetInstructionHandler (class in picometer.instructions) Settings (class in picometer.settings) settings (picometer.instructions.ProcessorProtocol attribute) (picometer.process.Processor attribute) SettingsError

setUp() (tests.test_instructions.TestMeasuringInstructions method) (tests.test_instructions.TestSettingInstructions method) (tests.test_logging.TestLogging method) (tests.test_settings.TestSettings method) setUpClass() (tests.test_transformations.TestTransformations class method) Shape (class in picometer.shapes) Shape.Kind (class in picometer.shapes) shapes (picometer.models.ModelState attribute) spatial (picometer.shapes.Shape.Kind attribute) symm (picometer.atom.Locator attribute)

T

table (picometer.atom.AtomSet attribute) test_access_group() (tests.test_instructions.TestSettingInstructions method) test_angle_fails_on_4_atoms() (tests.test_instructions.TestMeasuringInstructions method) test_angle_line_line() (tests.test_instructions.TestMeasuringInstructions method) test_angle_nodes() (tests.test_instructions.TestMeasuringInstructions method) test_angle_plane_line() (tests.test_instructions.TestMeasuringInstructions method) test_angle_plane_plane() (tests.test_instructions.TestMeasuringInstructions method) test_are_antiparallel() (tests.test_shapes.TestVectorTools method) test_are_parallel() (tests.test_shapes.TestVectorTools method) test_are_perpendicular() (tests.test_shapes.TestVectorTools method) test_are_synparallel() (tests.test_shapes.TestVectorTools method) test_as_dict() (tests.test_instructions.TestBasicsInstructions method) test_centroid() (tests.test_instructions.TestSettingInstructions method) test_coordinates() (tests.test_instructions.TestMeasuringInstructions method) test_coordinates2() (tests.test_instructions.TestMeasuringInstructions method) test_degrees_between() (tests.test_shapes.TestVectorTools method) test_deleting_reverts_to_defaults() (tests.test_settings.TestSettings method) test_dihedral_fails_on_3_atoms() (tests.test_instructions.TestMeasuringInstructions method) test_dihedral_mixed() (tests.test_instructions.TestMeasuringInstructions method) test_dihedral_positive() (tests.test_instructions.TestMeasuringInstructions method) test_displacement() (tests.test_instructions.TestMeasuringInstructions method) test_displacement_complete_uiso_from_umatrix() (tests.test_instructions.TestMeasuringInstructions method) test_displacement_complete_umatrix_from_Uiso() (tests.test_instructions.TestMeasuringInstructions method) test_displacement_displacement_get_cartesian_eigenvalues() (tests.test_instructions.TestMeasuringInstructions method) test_distance_line_line() (tests.test_instructions.TestMeasuringInstructions method) test_distance_line_plane() (tests.test_instructions.TestMeasuringInstructions method) test_distance_nodes_line() (tests.test_instructions.TestMeasuringInstructions method) test_distance_nodes_nodes() (tests.test_instructions.TestMeasuringInstructions method) test_distance_nodes_plane() (tests.test_instructions.TestMeasuringInstructions method) test_distance_plane_plane() (tests.test_instructions.TestMeasuringInstructions method) test_document_history() (tests.test_instructions.TestMeasuringInstructions method) test_equal() (tests.test_instructions.TestBasicsInstructions method) test_file_handler() (tests.test_logging.TestLogging method) test_getting_unknown_raises() (tests.test_settings.TestSettings method) test_group_at_group() (tests.test_instructions.TestSettingInstructions method) test_init() (tests.test_instructions.TestBasicsInstructions method) test_line() (tests.test_instructions.TestSettingInstructions method) test_line_at_symm() (tests.test_instructions.TestSettingInstructions method) test_line_line_metrics() (tests.test_shapes.TestExplicitShapes method) test_line_plane_at() (tests.test_shapes.TestExplicitShapes method) test_line_plane_metrics() (tests.test_shapes.TestExplicitShapes method) test_load_grep() (tests.test_instructions.TestSettingInstructions method) test_load_single() (tests.test_instructions.TestSettingInstructions method) test_log_listener() (tests.test_logging.TestLogging method)

test_make_group() (tests.test_instructions.TestSettingInstructions method) test_plane() (tests.test_instructions.TestSettingInstructions method) test_plane_at_group() (tests.test_instructions.TestSettingInstructions method) test_plane_plane_metrics() (tests.test_shapes.TestExplicitShapes method) test_regex_group() (tests.test_instructions.TestSettingInstructions method) test_routine_concatenate() (tests.test_instructions.TestRoutine method) test_routine_from_dict() (tests.test_instructions.TestRoutine method) test_routine_from_string() (tests.test_instructions.TestRoutine method) test_routine_from_yaml() (tests.test_instructions.TestRoutine method) test_routine_init() (tests.test_instructions.TestRoutine method) test_routine_to_yaml() (tests.test_instructions.TestRoutine method) test_select_atom() (tests.test_instructions.TestSettingInstructions method) test_select_none() (tests.test_instructions.TestSettingInstructions method) test_setting_unknown_raises() (tests.test_settings.TestSettings method) test_settings_change() (tests.test_settings.TestSettings method) test_settings_pull_defaults() (tests.test_settings.TestSettings method) test_transform_coordinates() (tests.test_transformations.TestTransformations method) test_transform_u_matrix() (tests.test_transformations.TestTransformations method) test_transformed_group() (tests.test_instructions.TestSettingInstructions method) test_write() (tests.test_instructions.TestMeasuringInstructions method) TestBasicsInstructions (class in tests.test_instructions) TestCaseExtras (class in tests.test_shapes) TestExplicitShapes (class in tests.test_shapes) TestLogging (class in tests.test_logging) TestMeasuringInstructions (class in tests.test_instructions) TestRoutine (class in tests.test_instructions) tests module tests.test_instructions module tests.test_logging module tests.test_settings module tests.test_shapes module tests.test_transformations module TestSettingInstructions (class in tests.test_instructions) TestSettings (class in tests.test_settings) TestTransformations (class in tests.test_transformations) TestVectorTools (class in tests.test_shapes) to_yaml() (picometer.instructions.Routine method) transform() (picometer.atom.AtomSet method)

U

u_cartesian_eigenvalues (picometer.atom.AtomSet property) update() (picometer.settings.Settings method)

ustr2float() (in module picometer.utility) ustr2floats() (in module picometer.utility)

V

v_a (in module tests.test_shapes) v_b (in module tests.test_shapes) v_c (in module tests.test_shapes)

v_d (in module tests.test_shapes) Vector3 (in module picometer.shapes) Versor3 (in module picometer.shapes) versorize() (in module picometer.shapes)

W

WriteInstructionHandler (class in picometer.instructions)

Z

zero3 (in module picometer.shapes)