Index

A

ActiveWindowOverMaxStepSmooth (class in aquaduct.geom.smooth) ActiveWindowSmooth (class in aquaduct.geom.smooth) append_entry() (ManyFileEntry method) aquaduct module aquaduct.apps module aquaduct.apps.chord module aquaduct.apps.data module aquaduct.apps.valve module aquaduct.apps.valve.clusters module aquaduct.apps.valve.core module aquaduct.apps.valve.data module aquaduct.apps.valve.helpers module aquaduct.apps.valve.spath module aquaduct.apps.valve.worker module aquaduct.apps.valveconfig module aquaduct.apps.valveconfig.defaults module aquaduct.apps.valveconfig.utils module aquaduct.geom module aquaduct.geom.cluster module aquaduct.geom.cluster_available_methods module aquaduct.geom.convexhull module aquaduct.geom.hdr module aquaduct.geom.hdr_contour module aquaduct.geom.master module aquaduct.geom.pca module aquaduct.geom.pocket module aquaduct.geom.smooth module

aquaduct.geom.smooth_available_methods module aquaduct.geom.traces module aquaduct.traj module aquaduct.traj.barber module aquaduct.traj.dumps module aquaduct.traj.inlets module aquaduct.traj.paths module aquaduct.traj.sandwich module aquaduct.utils module aquaduct.utils.clui module aquaduct.utils.filecache module aquaduct.utils.helpers module aquaduct.utils.maths module aquaduct.utils.multip module aquaduct.utils.sets module aquaduct.utils.sr module aquaduct.visual module aquaduct.visual.cmaps module aquaduct.visual.helpers module aquaduct.visual.pymol_cgo module aquaduct.visual.pymol_connector module aquaduct.visual.quickplot module arrayify1() (in module aquaduct.utils.helpers) ArrayOrArray (class in aquaduct.utils.maths) Arrow (class in aquaduct.apps.chord) assign_nonsandwiched_paths (class in aquaduct.apps.valve.worker) assign_sandwiched_paths (class in aquaduct.apps.valve.worker) Auto (class in aquaduct.utils.helpers)

B

barber_with_spheres() (in module aquaduct.traj.barber) BarberCluster (class in aquaduct.geom.cluster) BarberClusterResult (class in aquaduct.geom.cluster)

beat() (CTypeSpathsCollection method) BoolEntry (class in aquaduct.apps.valveconfig.utils) Bunch (class in aquaduct.utils.helpers)

C

callback_load_dir() (DirEntry method) callback_load_file() (FileEntry method) (ManyFileEntry method) centers() (PerformClustering method) check_bounds_at_max_window_at_pos() (GeneralWindow method) chop() (in module aquaduct.utils.helpers)

chunk() (in module aquaduct.utils.helpers) combine() (in module aquaduct.utils.helpers) concatenate() (in module aquaduct.utils.helpers) coords_types_prob_widths() (CTypeSpathsCollectionWorker method) create_tmpfile() (in module aquaduct.utils.helpers) CTypeSpathsCollection (class in aquaduct.geom.master) CTypeSpathsCollectionWorker (class in aquaduct.geom.master)

D

default() (IterEncoder method) defaults (in module aquaduct.utils.maths) dictify() (in module aquaduct.utils.helpers) diff() (in module aquaduct.geom.traces) DirEntry (class in aquaduct.apps.valveconfig.utils)

dirtype (class in aquaduct.apps.valveconfig.defaults) distance_p_to_ab() (in module aquaduct.geom.traces) DistanceWindowOverMaxStepSmooth (class in aquaduct.geom.smooth) DistanceWindowSmooth (class in aquaduct.geom.smooth) distribution() (in module aquaduct.geom.pocket)

E

Entry (class in aquaduct.apps.valveconfig.utils)

entry_factory() (in module aquaduct.apps.valveconfig.utils) ETA() (SimpleProgressBar method)

F

FileEntry (class in aquaduct.apps.valveconfig.utils) filetype (class in aquaduct.apps.valveconfig.defaults) find_edges() (in module aquaduct.geom.pocket) find_minmax() (in module aquaduct.geom.pocket) find_minmax_map() (in module aquaduct.geom.pocket) finish() (SimpleProgressBar method)

fit() (BarberCluster static method) (PerformClustering method) float_default (NumpyDefaultsStorageTypes attribute) FloatWindow (class in aquaduct.geom.smooth) fractionof() (in module aquaduct.utils.helpers) full_size() (CTypeSpathsCollection method)

G

GeneralWindow (class in aquaduct.geom.smooth) generate_arc() (in module aquaduct.apps.chord) get() (BoolEntry method) (DirEntry method) (Entry method) (FileEntry method) (ManyFileEntry method) (ParenthesedEntry method) (StandardEntry method)

get_default_entry() (in module aquaduct.apps.valveconfig.defaults) get_default_section() (in module aquaduct.apps.valveconfig.defaults) get_master_path() (CTypeSpathsCollection method) get_spc() (in module aquaduct.geom.pocket) get_widget_bg() (in module aquaduct.apps.valveconfig.utils) glind() (in module aquaduct.utils.helpers) greetings() (in module aquaduct) gregorian_year_in_days (in module aquaduct.utils.clui) gsep() (in module aquaduct.utils.clui)

H

here() (LinearizeRecursive method) hex2rgb() (in module aquaduct.apps.chord)

HidingFrame (class in aquaduct.apps.valveconfig.utils) highlight() (Entry method) (ManyFileEntry method)

I

InfoIconWidget (class in aquaduct.apps.valveconfig.utils) int2range() (in module aquaduct.utils.helpers) int_default (NumpyDefaultsStorageTypes attribute) int_type (NumpyDefaultsStorageTypes attribute) IntWindow (class in aquaduct.geom.smooth) is_iterable() (in module aquaduct.utils.helpers)

is_linear() (VectorLinearize method) is_linear_core() (VectorLinearize method) is_menu() (in module aquaduct.apps.valveconfig.defaults) is_p_above_vp0_plane() (in module aquaduct.geom.traces) iskeyword() (in module aquaduct.apps.valve) isndarray() (ArrayOrArray property) IterEncoder (class in aquaduct.apps.data)

L

length_step_std() (in module aquaduct.geom.traces) lens() (CTypeSpathsCollection method) lens_norm() (CTypeSpathsCollection method) lens_real() (CTypeSpathsCollection method) lind() (in module aquaduct.utils.helpers) LinearizeHobbitTriangle (class in aquaduct.geom.traces) LinearizeHobbitVector (class in aquaduct.geom.traces) LinearizeOneWayTriangle (class in aquaduct.geom.traces)

LinearizeOneWayVector (class in aquaduct.geom.traces) LinearizeRecursive (class in aquaduct.geom.traces) LinearizeRecursiveTriangle (class in aquaduct.geom.traces) LinearizeRecursiveVector (class in aquaduct.geom.traces) Link (class in aquaduct.apps.chord) list_blocks_to_slices() (in module aquaduct.utils.helpers) listify() (in module aquaduct.utils.helpers) longstr (class in aquaduct.apps.valveconfig.defaults)

M

make_default_array() (in module aquaduct.utils.maths) make_fraction() (in module aquaduct.utils.helpers) make_fractionof() (in module aquaduct.utils.helpers) make_iterable() (in module aquaduct.utils.helpers) ManyFileEntry (class in aquaduct.apps.valveconfig.utils) manyfiletype (class in aquaduct.apps.valveconfig.defaults) max_window_at_pos() (GeneralWindow static method) MaxStepSmooth (class in aquaduct.geom.smooth) MeanShiftBandwidth() (in module aquaduct.geom.cluster) MemMap (class in aquaduct.utils.maths) message() (in module aquaduct.utils.clui) midpoints() (in module aquaduct.geom.traces) module aquaduct aquaduct.apps aquaduct.apps.chord aquaduct.apps.data aquaduct.apps.valve aquaduct.apps.valve.clusters aquaduct.apps.valve.core aquaduct.apps.valve.data aquaduct.apps.valve.helpers aquaduct.apps.valve.spath aquaduct.apps.valve.worker aquaduct.apps.valveconfig aquaduct.apps.valveconfig.defaults aquaduct.apps.valveconfig.utils aquaduct.geom aquaduct.geom.cluster aquaduct.geom.cluster_available_methods aquaduct.geom.convexhull aquaduct.geom.hdr aquaduct.geom.hdr_contour aquaduct.geom.master aquaduct.geom.pca aquaduct.geom.pocket aquaduct.geom.smooth aquaduct.geom.smooth_available_methods aquaduct.geom.traces aquaduct.traj aquaduct.traj.barber aquaduct.traj.dumps aquaduct.traj.inlets aquaduct.traj.paths aquaduct.traj.sandwich aquaduct.utils aquaduct.utils.clui aquaduct.utils.filecache aquaduct.utils.helpers aquaduct.utils.maths aquaduct.utils.multip aquaduct.utils.sets aquaduct.utils.sr aquaduct.visual aquaduct.visual.cmaps aquaduct.visual.helpers aquaduct.visual.pymol_cgo aquaduct.visual.pymol_connector aquaduct.visual.quickplot

N

Node (class in aquaduct.apps.chord)

NumpyDefaultsStorageTypes (class in aquaduct.utils.maths)

O

OpenReaderTraj (class in aquaduct.traj.sandwich)

outer_inner() (in module aquaduct.geom.pocket)

P

ParenthesedEntry (class in aquaduct.apps.valveconfig.utils) part2type_dict (in module aquaduct.geom.master) parts (CTypeSpathsCollection attribute) (in module aquaduct.geom.master)

pbar (in module aquaduct.utils.clui) percent() (SimpleProgressBar method) PerformClustering (class in aquaduct.geom.cluster) polar2point() (in module aquaduct.apps.chord) project_p_on_ab() (in module aquaduct.geom.traces)

R

range2int() (in module aquaduct.utils.helpers) readonly() (ArrayOrArray method) (MemMap method)

readwrite() (ArrayOrArray method) (MemMap method)

S

SavgolSmooth (class in aquaduct.geom.smooth) SciPyConvexHull (class in aquaduct.geom.convexhull) set() (BoolEntry method) (DirEntry method) (Entry method) (FileEntry method) (ManyFileEntry method) (ParenthesedEntry method) (StandardEntry method) show() (HidingFrame method) (SimpleProgressBar method) simple_types_distribution() (CTypeSpathsCollection static method) SimpleProgressBar (class in aquaduct.utils.clui) smart_time_string() (in module aquaduct.utils.clui) SmartRangeDecrement (class in aquaduct.utils.helpers) SmartRangeEqual (class in aquaduct.utils.helpers)

SmartRangeFunction (class in aquaduct.utils.helpers) SmartRangeIncrement (class in aquaduct.utils.helpers) Smooth (class in aquaduct.geom.smooth) smooth() (ActiveWindowOverMaxStepSmooth method) (ActiveWindowSmooth method) (DistanceWindowOverMaxStepSmooth method) (DistanceWindowSmooth method) (MaxStepSmooth method) (SavgolSmooth method) (Smooth method) (WindowOverMaxStepSmooth method) (WindowSmooth method) sortify() (in module aquaduct.utils.helpers) Sphere (class in aquaduct.geom) sphere_density_raw() (in module aquaduct.geom.pocket) square_area() (in module aquaduct.geom.traces) StandardEntry (class in aquaduct.apps.valveconfig.utils)

T

Text (class in aquaduct.apps.valveconfig.utils) thead() (in module aquaduct.utils.clui) ToolTip (class in aquaduct.apps.valveconfig.utils) tracepoints() (in module aquaduct.geom.traces) triangle_angles() (in module aquaduct.geom.traces) triangle_angles_last() (in module aquaduct.geom.traces)

triangle_area() (in module aquaduct.geom.traces) triangle_height() (in module aquaduct.geom.traces) tsep() (in module aquaduct.utils.clui) ttime() (SimpleProgressBar method) tupleify() (in module aquaduct.utils.helpers) types_distribution() (CTypeSpathsCollection method) types_prob_to_types() (CTypeSpathsCollection method)

U

underline() (in module aquaduct.utils.clui) unhighlight() (Entry method) (ManyFileEntry method)

uniqify() (in module aquaduct.utils.helpers) update() (CTypeSpathsCollection method) (SimpleProgressBar method)

V

ValveDataCodec (class in aquaduct.apps.valve.data) varname() (ValveDataCodec static method) VdW_radii (in module aquaduct.traj.sandwich) vector_change_len() (in module aquaduct.geom.traces) vector_norm() (in module aquaduct.geom.traces) vector_one() (in module aquaduct.geom.traces) VectorLinearize (class in aquaduct.geom.traces)

vectors_angle() (in module aquaduct.geom.traces) vectors_angle_alt() (in module aquaduct.geom.traces) vectors_angle_alt_anorm() (in module aquaduct.geom.traces) vectors_angle_anorm() (in module aquaduct.geom.traces) version (ValveDataCodec attribute) version() (in module aquaduct) version_nice() (in module aquaduct) VerticalScrolledFrame (class in aquaduct.apps.valveconfig.utils)

W

WarningIconWidget (class in aquaduct.apps.valveconfig.utils) what2what() (in module aquaduct.utils.helpers) WhereToCut (class in aquaduct.traj.barber)

widget_factory() (in module aquaduct.apps.valveconfig.utils) WindowOverMaxStepSmooth (class in aquaduct.geom.smooth) WindowSmooth (class in aquaduct.geom.smooth)