Index

A

atom_names (mdevaluate.atoms.Atoms attribute) (mdevaluate.atoms.AtomSubset attribute) (mdevaluate.coordinates.CoordinateFrame attribute) atom_subset (mdevaluate.coordinates.CoordinatesFilter attribute)

AtomMismatch Atoms (class in mdevaluate.atoms) AtomSubset (class in mdevaluate.atoms) autosave_data() (in module mdevaluate.autosave)

B

BaseReader (class in mdevaluate.reader)

box (mdevaluate.coordinates.CoordinateFrame attribute)

C

cache_info (mdevaluate.coordinates.CoordinatesKDTree attribute) (mdevaluate.reader.CachedReader attribute) CachedReader (class in mdevaluate.reader) center_of_mass() (in module mdevaluate.atoms) centers_of_mass() (in module mdevaluate.coordinates) charges (mdevaluate.coordinates.CoordinateFrame attribute) clear_cache() (mdevaluate.coordinates.Coordinates method) (mdevaluate.coordinates.CoordinatesKDTree method) (mdevaluate.reader.CachedReader method) coherent_histogram() (in module mdevaluate.utils) coherent_scattering_function() (in module mdevaluate.correlation)

coherent_sum() (in module mdevaluate.utils) cole_cole() (in module mdevaluate.functions) cole_davidson() (in module mdevaluate.functions) colen() (in module mdevaluate.functions) colenQ() (in module mdevaluate.functions) compare_regex() (in module mdevaluate.atoms) CoordinateFrame (class in mdevaluate.coordinates) Coordinates (class in mdevaluate.coordinates) CoordinatesFilter (class in mdevaluate.coordinates) CoordinatesKDTree (class in mdevaluate.coordinates) CoordinatesMap (class in mdevaluate.coordinates) correlation() (in module mdevaluate.correlation)

D

DelayedReader (class in mdevaluate.reader) description (mdevaluate.coordinates.Coordinates attribute) (mdevaluate.coordinates.CoordinatesMap attribute) disable() (in module mdevaluate.autosave)

disabled (class in mdevaluate.autosave) distance_distribution() (in module mdevaluate.distribution) distance_to_atoms() (in module mdevaluate.atoms) distance_to_atoms_cKDtree() (in module mdevaluate.atoms)

E

enable() (in module mdevaluate.autosave)

EnergyReader (class in mdevaluate.reader)

F

fast_averaged_rdf() (in module mdevaluate.distribution) filename (mdevaluate.reader.BaseReader attribute) (mdevaluate.reader.DelayedReader attribute) filon_fourier_transformation() (in module mdevaluate.utils)

five_point_stencil() (in module mdevaluate.utils) Fqt_from_Grt() (in module mdevaluate.utils) from_grofile() (in module mdevaluate.atoms) from_tprfile() (in module mdevaluate.atoms)

G

generate_nojump_matrixes() (in module mdevaluate.reader) get_directory() (in module mdevaluate.autosave) get_filename() (in module mdevaluate.autosave)

get_frame() (mdevaluate.coordinates.Coordinates method) get_mode() (mdevaluate.coordinates.Coordinates method) gyration_radius() (in module mdevaluate.atoms)

H

havriliak_negami() (in module mdevaluate.functions)

histogram() (in module mdevaluate.utils)

I

indices (mdevaluate.atoms.Atoms attribute) (mdevaluate.atoms.AtomSubset attribute) (mdevaluate.coordinates.CoordinateFrame attribute)

is_writeable() (in module mdevaluate.reader) isf() (in module mdevaluate.correlation)

K

kww() (in module mdevaluate.functions)

kww_1e() (in module mdevaluate.functions)

L

layer_of_atoms() (in module mdevaluate.atoms) len() (mdevaluate.coordinates.MeanCoordinates method)

load_data() (in module mdevaluate.autosave) load_nojump_matrixes() (in module mdevaluate.reader) log_indices() (in module mdevaluate.correlation)

M

map_coordinates() (in module mdevaluate.coordinates) mask2indices() (in module mdevaluate.utils) masses (mdevaluate.coordinates.CoordinateFrame attribute) mdevaluate (module) mdevaluate.atoms (module) mdevaluate.autosave (module) mdevaluate.coordinates (module) mdevaluate.correlation (module) mdevaluate.distribution (module)

mdevaluate.functions (module) mdevaluate.pbc (module) mdevaluate.reader (module) mdevaluate.utils (module) MeanCoordinates (class in mdevaluate.coordinates) mixing_ratio_distribution() (in module mdevaluate.distribution) mode (mdevaluate.coordinates.Coordinates attribute) moving_average() (in module mdevaluate.utils) msd() (in module mdevaluate.correlation) multi_subensemble_correlation() (in module mdevaluate.correlation)

N

next_neighbor_distribution() (in module mdevaluate.distribution) next_neighbors() (in module mdevaluate.atoms) nojump (mdevaluate.coordinates.CoordinateFrame attribute) (mdevaluate.coordinates.Coordinates attribute) (mdevaluate.coordinates.CoordinatesMap attribute) nojump() (in module mdevaluate.pbc)

nojump_filename() (in module mdevaluate.reader) nojump_matrixes (mdevaluate.reader.BaseReader attribute) NojumpError non_gaussian() (in module mdevaluate.correlation) NoReaderAvailabelError norm (in module mdevaluate.utils) notify() (in module mdevaluate.autosave)

O

open() (in module mdevaluate) (in module mdevaluate.reader) open_energy() (in module mdevaluate)

open_with_mdanalysis() (in module mdevaluate.reader) open_with_pygmx() (in module mdevaluate.reader) overlap() (in module mdevaluate.correlation)

P

parse_jumps() (in module mdevaluate.reader) pbc (mdevaluate.coordinates.CoordinateFrame attribute) (mdevaluate.coordinates.Coordinates attribute) (mdevaluate.coordinates.CoordinatesMap attribute) pbc_backfold_compact() (in module mdevaluate.pbc) pbc_backfold_rect() (in module mdevaluate.pbc) pbc_diff() (in module mdevaluate.pbc) pbc_diff_numba (in module mdevaluate.pbc) pbc_diff_old() (in module mdevaluate.pbc) pbc_diff_rect() (in module mdevaluate.pbc)

pbc_diff_tric() (in module mdevaluate.pbc) pbc_dist() (in module mdevaluate.pbc) pbc_extend() (in module mdevaluate.pbc) pbc_kdtree() (in module mdevaluate.pbc) pbc_kdtree_query() (in module mdevaluate.pbc) pbc_points() (in module mdevaluate.pbc) pbc_spm_rdf() (in module mdevaluate.distribution) pbc_tree_rdf() (in module mdevaluate.distribution) polar_coordinates() (in module mdevaluate.coordinates) pore_coordinates() (in module mdevaluate.coordinates)

Q

quick1etau() (in module mdevaluate.utils)

R

radial_density() (in module mdevaluate.distribution) radial_selector() (in module mdevaluate.coordinates) rdf() (in module mdevaluate.distribution) residue_ids (mdevaluate.atoms.Atoms attribute) (mdevaluate.atoms.AtomSubset attribute) (mdevaluate.coordinates.CoordinateFrame attribute)

residue_names (mdevaluate.atoms.Atoms attribute) (mdevaluate.atoms.AtomSubset attribute) (mdevaluate.coordinates.CoordinateFrame attribute) rotate_axis() (in module mdevaluate.coordinates) rotational_autocorrelation() (in module mdevaluate.correlation) runningmean() (in module mdevaluate.utils)

S

save_data() (in module mdevaluate.autosave) save_nojump_matrixes() (in module mdevaluate.reader) selection (mdevaluate.coordinates.CoordinateFrame attribute) set_has_counter() (in module mdevaluate.correlation) shell_density() (in module mdevaluate.distribution) shifted_correlation() (in module mdevaluate.correlation) singledispatchmethod() (in module mdevaluate.utils) spatial_density() (in module mdevaluate.distribution) spatial_selector() (in module mdevaluate.coordinates) spherical_coordinates() (in module mdevaluate.coordinates)

spherical_radius() (in module mdevaluate.coordinates) Sq_from_gr() (in module mdevaluate.utils) subensemble_correlation() (in module mdevaluate.correlation) subset() (mdevaluate.atoms.Atoms method) (mdevaluate.atoms.AtomSubset method) (mdevaluate.coordinates.Coordinates method) (mdevaluate.coordinates.CoordinatesMap method) summary (mdevaluate.atoms.AtomSubset attribute) superpose() (in module mdevaluate.utils) susceptibility() (in module mdevaluate.correlation)

T

tetrahedral_order() (in module mdevaluate.distribution) tetrahedral_order_distribution() (in module mdevaluate.distribution)

time (mdevaluate.coordinates.CoordinateFrame attribute) time_average() (in module mdevaluate.distribution) time_histogram() (in module mdevaluate.distribution)

U

UnknownCoordinatesMode

V

van_hove_distinct() (in module mdevaluate.correlation) van_hove_self() (in module mdevaluate.correlation)

vectors() (in module mdevaluate.coordinates) verify_file() (in module mdevaluate.autosave) volume (mdevaluate.coordinates.CoordinateFrame attribute)

W

whole (mdevaluate.coordinates.CoordinateFrame attribute) (mdevaluate.coordinates.Coordinates attribute) (mdevaluate.coordinates.CoordinatesMap attribute)

whole() (in module mdevaluate.pbc)