Index

_

__call__() (Center method) (CTypeSpathsCollectionWorker method) (ColorMapDistMap method) (LinearizeHobbit method) (LinearizeRecursive method) (Normalize method) (PCA method) (Standartize method) (fbm method) __cmp__() (InletClusterGenericType method) __del__() (ConnectToPymol method) (SimpleTarWriteHelper method) (TmpDumpWriterOfMDA method) __enter__() (fbm method) (tictoc method) __eq__() (SinglePathID method) __exit__() (fbm method) (tictoc method) __getitem__() (InletClusterGenericType method) __hash__() (InletClusterGenericType method) __init__() (BasicPymolCGO method) (Bunch method) (CTypeSpathsCollection method) (CTypeSpathsCollectionWorker method) (Center method) (ColorMapDistMap method) (ConnectToPymol method) (GenericPaths method) (Inlet method) (InletClusterExtendedType method) (InletClusterGenericType method) (Inlets method) (MacroMolPath method) (MasterPath method) (Normalize method) (PCA method) (PassingPath method) (SimpleProgressBar method) (SimpleTarWriteHelper method) (SimpleTree method) (SinglePathID method) (SinglePathPlotter method) (SmartRange method) (SmartRangeFunction method) (Standartize method) (TmpDumpWriterOfMDA method) (TriangleLinearize method) (VectorLinearize method) (fbm method) (tictoc method)

__len__() (InletClusterGenericType method) (SmartRange method) __repr__() (Auto method) (InletClusterGenericType method) (SimpleTree method) (SmartRangeFunction method) __str__() (Auto method) (InletClusterGenericType method) (SinglePathID method) _ColorMapDistMap__do_cadex() (ColorMapDistMap method) _edges() (in module aquaduct.geom.convexhull) _facets() (in module aquaduct.geom.convexhull) _gpi() (GenericPaths method) _gpo() (GenericPaths method) _gpt() (GenericPaths method) _make_smooth_coords() (MacroMolPath method) _paths (MacroMolPath attribute) (PassingPath attribute) _point_within_convexhull() (in module aquaduct.geom.convexhull) _vertices_ids() (in module aquaduct.geom.convexhull) _vertices_points() (in module aquaduct.geom.convexhull)

A

add() (BasicPymolCGOLines method) (BasicPymolCGOSpheres method) add_cgo_object() (ConnectToPymol method) add_cluster_annotations() (Inlets method) add_cone() (BasicPymolCGOPointers method) add_coord() (GenericPaths method) add_leaf() (SimpleTree method) add_leaf_to_leaf() (SimpleTree method) add_leaf_wrapper() (Inlets method) add_message() (SimpleTree method) add_message_to_leaf() (SimpleTree method) add_message_wrapper() (Inlets method) add_object() (GenericPaths method) add_outliers_annotations() (Inlets method) add_pointer() (BasicPymolCGOPointers method) add_scope() (GenericPaths method) add_single_path_continous_trace() (SinglePathPlotter method) add_spheres() (Inlets method) add_type() (GenericPaths method) add_width() (MasterPath method) all_incoming (InletTypeCodes attribute) all_internal (InletTypeCodes attribute) all_outgoing (InletTypeCodes attribute) all_surface (InletTypeCodes attribute) and_back_again() (LinearizeHobbit method) append() (SmartRange method)

apply_smoothing() (MacroMolPath method) aquaduct (module) aquaduct.apps (module) aquaduct.geom (module) aquaduct.geom.convexhull (module) aquaduct.geom.master (module) aquaduct.geom.pca (module) aquaduct.geom.traces (module) aquaduct.traj (module) aquaduct.traj.dumps (module) aquaduct.traj.inlets (module) aquaduct.traj.paths (module) aquaduct.utils (module) aquaduct.utils.clui (module) aquaduct.utils.helpers (module) aquaduct.utils.maths (module) aquaduct.utils.multip (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) are_rows_uniq() (in module aquaduct.utils.helpers) arrayify() (in module aquaduct.utils.helpers) arrayify1() (in module aquaduct.utils.helpers) Auto (class in aquaduct.utils.helpers)

B

bar() (SimpleProgressBar method) barber_with_spheres() (GenericPaths method) barlenght (SimpleProgressBar attribute) BasicPymolCGO (class in aquaduct.visual.pymol_connector) BasicPymolCGOLines (class in aquaduct.visual.pymol_connector)

BasicPymolCGOPointers (class in aquaduct.visual.pymol_connector) BasicPymolCGOSpheres (class in aquaduct.visual.pymol_connector) beat() (CTypeSpathsCollection method) begins (MacroMolPath attribute) Bunch (class in aquaduct.utils.helpers)

C

call_clusterization_method() (Inlets method) cc() (in module aquaduct.visual.helpers) cc_safe() (in module aquaduct.visual.helpers) Center (class in aquaduct.geom.pca) cgo_entity_begin (BasicPymolCGO attribute) (BasicPymolCGOLines attribute) (BasicPymolCGOPointers attribute) (BasicPymolCGOSpheres attribute) cgo_entity_end (BasicPymolCGO attribute) (BasicPymolCGOLines attribute) (BasicPymolCGOPointers attribute) (BasicPymolCGOSpheres attribute) cgo_line_width (ConnectToPymol attribute) cityblock() (in module aquaduct.visual.helpers) clean() (BasicPymolCGO method) close() (TmpDumpWriterOfMDA method) cluster2str() (InletClusterGenericType static method) clusters_centers (Inlets attribute) clusters_list (Inlets attribute) clusters_size (Inlets attribute) clusters_std (Inlets attribute) color_codes() (in module aquaduct.visual.helpers) color_distance() (ColorMapDistMap static method)

ColorMapDistMap (class in aquaduct.visual.helpers) combine() (in module aquaduct.utils.helpers) compress_zip() (in module aquaduct.utils.helpers) concatenate() (in module aquaduct.utils.helpers) ConnectToPymol (class in aquaduct.visual.pymol_connector) convexhull() (SinglePathPlotter method) coords (Inlets attribute) (MacroMolPath attribute) (PassingPath attribute) coords_cont (MacroMolPath attribute) coords_filo (MacroMolPath attribute) coords_first_in (MacroMolPath attribute) (PassingPath attribute) coords_last_out (MacroMolPath attribute) (PassingPath attribute) coords_types_prob_widths() (CTypeSpathsCollectionWorker method) cpu_count (CpuThreadsCount attribute) CpuThreadsCount (class in aquaduct.utils.multip) create_tmpfile() (in module aquaduct.utils.helpers) ct_file (ConnectToPymol attribute) ct_pymol (ConnectToPymol attribute) CTypeSpathsCollection (class in aquaduct.geom.master) CTypeSpathsCollectionWorker (class in aquaduct.geom.master)

D

decode_color() (ConnectToPymol method) del_cgo_object() (ConnectToPymol method) derrivative() (in module aquaduct.geom.traces)

diff() (in module aquaduct.geom.traces) distance() (ColorMapDistMap method) dump_frames() (TmpDumpWriterOfMDA method)

E

emit_message_to_file_in_root_logger() (in module aquaduct.utils.clui) empty_coords (MacroMolPath attribute) ends (MacroMolPath attribute) ETA() (SimpleProgressBar method)

etypes (MacroMolPath attribute) etypes_cont (MacroMolPath attribute) euclidean() (in module aquaduct.visual.helpers) extend_inlets() (Inlets method)

F

f_like() (in module aquaduct.visual.helpers) fbm (class in aquaduct.utils.clui) find_paths() (GenericPaths method) find_paths_coords_types() (GenericPaths method)

finish() (SimpleProgressBar method) float_default (NumpyDefaultsStorageTypes attribute) frames (GenericPaths attribute) full_size() (CTypeSpathsCollection method)

G

generic (InletClusterExtendedType attribute) GenericPaths (class in aquaduct.traj.paths) GenericPathTypeCodes (class in aquaduct.traj.paths) get() (BasicPymolCGO method) (SmartRange method) (SmartRangeDecrement method) (SmartRangeEqual method) (SmartRangeFunction method) (SmartRangeIncrement method) get_acceleration_cont() (MacroMolPath method) get_ax3d() (in module aquaduct.visual.quickplot) get_chull() (Inlets method) get_cmap() (in module aquaduct.visual.helpers) get_coords() (MacroMolPath method) (PassingPath method) get_coords_cont() (MacroMolPath method) get_distance_both_cont() (MacroMolPath method) get_distance_cont() (MacroMolPath method) get_distance_rev_cont() (MacroMolPath method)

get_flat_tree() (Inlets method) get_inlets() (MacroMolPath method) (PassingPath method) get_inlets_references() (Inlets method) get_leaf() (SimpleTree method) get_master_path() (CTypeSpathsCollection method) get_paths_in() (GenericPaths method) get_paths_out() (GenericPaths method) get_single_path_coords_types() (GenericPaths method) get_str_timestamp() (in module aquaduct.utils.clui) get_velocity_cont() (MacroMolPath method) glue() (in module aquaduct.traj.paths) greetings() (in module aquaduct) gregorian_year_in_days (in module aquaduct.utils.clui) grey (ColorMapDistMap attribute) gsep() (in module aquaduct.utils.clui) gtypes (MacroMolPath attribute) (PassingPath attribute) gtypes_cont (MacroMolPath attribute)

H

has_in (MacroMolPath attribute) (PassingPath attribute) has_object (MacroMolPath attribute) has_out (MacroMolPath attribute) (PassingPath attribute)

heartbeat() (SimpleProgressBar method) here() (LinearizeOneWay method) (LinearizeRecursive method)

I

incoming (ProtoInletTypeCodes attribute) init_ax() (MPLTracePlotter method) init_pymol() (ConnectToPymol method) init_script() (ConnectToPymol method) Inlet (class in aquaduct.traj.inlets) InletClusterExtendedType (class in aquaduct.traj.inlets) InletClusterGenericType (class in aquaduct.traj.inlets) Inlets (class in aquaduct.traj.inlets) InletTypeCodes (class in aquaduct.traj.inlets) input (InletClusterGenericType attribute) int2range() (in module aquaduct.utils.helpers) int_default (NumpyDefaultsStorageTypes attribute) internal (ProtoInletTypeCodes attribute) internal_incoming (InletTypeCodes attribute) internal_outgoing (InletTypeCodes attribute) is_frame_in() (MacroMolPath method) is_frame_object() (MacroMolPath method) is_frame_out() (MacroMolPath method) is_frame_walk() (MacroMolPath method) (PassingPath method)

is_iterable() (in module aquaduct.utils.helpers) is_leaf() (SimpleTree method) is_linear() (TriangleLinearize method) (VectorLinearize method) is_linear_core() (VectorLinearize method) is_number() (in module aquaduct.utils.helpers) is_passing() (MacroMolPath method) (PassingPath method) (SinglePath method) is_point_within_convexhull() (in module aquaduct.geom.convexhull) is_single() (MacroMolPath method) (PassingPath method) (SinglePath method) isin() (SmartRange method) (SmartRangeDecrement method) (SmartRangeEqual method) (SmartRangeFunction method) (SmartRangeIncrement method) itype (InletTypeCodes attribute)

L

last_element() (SmartRange method) last_times() (SmartRange method) leafs_names (SimpleTree attribute) left() (in module aquaduct.traj.paths) length_step_std() (in module aquaduct.geom.traces) lens() (CTypeSpathsCollection method) lens_norm() (CTypeSpathsCollection method) lens_real() (CTypeSpathsCollection method) lim2clusters() (Inlets method) lim2rnames() (Inlets method) lim2spaths() (Inlets method) lim2types() (Inlets method) lim_to() (Inlets method)

limspaths2() (Inlets method) lind() (in module aquaduct.utils.helpers) LinearizeHobbit (class in aquaduct.geom.traces) LinearizeHobbitTriangle (class in aquaduct.geom.traces) LinearizeHobbitVector (class in aquaduct.geom.traces) LinearizeOneWay (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) list_blocks_to_slices() (in module aquaduct.utils.helpers) listify() (in module aquaduct.utils.helpers) load_pdb() (ConnectToPymol method)

M

MacroMolPath (class in aquaduct.traj.paths) make_color_triple() (BasicPymolCGO static method) make_default_array() (in module aquaduct.utils.maths) make_iterable() (in module aquaduct.utils.helpers) make_val() (InletClusterGenericType method) MasterPath (class in aquaduct.traj.paths) max() (SmartRange method)

max_frame (GenericPaths attribute) message() (in module aquaduct.utils.clui) message_special() (in module aquaduct.utils.clui) midpoints() (in module aquaduct.geom.traces) min() (SmartRange method) min_frame (GenericPaths attribute) MPLTracePlotter (class in aquaduct.visual.quickplot)

N

new() (BasicPymolCGO method) next() (SimpleProgressBar method)

Normalize (class in aquaduct.geom.pca) NumpyDefaultsStorageTypes (class in aquaduct.utils.maths)

O

object_name (GenericPathTypeCodes attribute) open() (SimpleTarWriteHelper method) orient_on() (ConnectToPymol method)

out_name (GenericPathTypeCodes attribute) outgoing (ProtoInletTypeCodes attribute) output (InletClusterGenericType attribute)

P

P (PCA attribute) part2type_dict (in module aquaduct.geom.master) parts (CTypeSpathsCollection attribute) (in module aquaduct.geom.master) PassingPath (class in aquaduct.traj.paths) path (PassingPath attribute) path_in (MacroMolPath attribute) path_in_code (PathTypesCodes attribute) path_object (MacroMolPath attribute) path_object_code (PathTypesCodes attribute) path_out (MacroMolPath attribute) path_out_code (PathTypesCodes attribute) path_trace() (SimpleTracePlotter method) path_walk_code (PathTypesCodes attribute) paths (MacroMolPath attribute) (PassingPath attribute) paths_cont (MacroMolPath attribute) paths_first_in (MacroMolPath attribute) (PassingPath attribute)

paths_inlets() (SinglePathPlotter method) paths_last_out (MacroMolPath attribute) (PassingPath attribute) paths_trace() (SinglePathPlotter method) PathTypesCodes (class in aquaduct.traj.paths) pbar (in module aquaduct.utils.clui) PCA (class in aquaduct.geom.pca) percent() (SimpleProgressBar method) perform_clustering() (Inlets method) perform_reclustering() (Inlets method) plot_colorful_lines() (in module aquaduct.visual.quickplot) plot_line() (MPLTracePlotter method) (SimpleTracePlotter method) plot_spath_spectrum() (in module aquaduct.visual.quickplot) preprocess() (PCA method) preprocess_undo() (PCA method) print_simple_tree() (in module aquaduct.utils.clui) protein_trace() (SimpleProteinPlotter method) ProtoInletTypeCodes (class in aquaduct.traj.inlets)

R

range2int() (in module aquaduct.utils.helpers) raw (SmartRange attribute) recluster_cluster() (Inlets method) recluster_outliers() (Inlets method) refs (Inlets attribute) refs_names (Inlets attribute) renumber_clusters() (Inlets method)

resize_leaf_0() (Inlets method) rev() (SmartRange method) (SmartRangeDecrement method) (SmartRangeEqual method) (SmartRangeFunction method) (SmartRangeIncrement method) right() (in module aquaduct.traj.paths) rotate (SimpleProgressBar attribute)

S

save_file2tar() (SimpleTarWriteHelper method) save_object2tar() (SimpleTarWriteHelper method) scatter() (MPLTracePlotter method) (SinglePathPlotter method) scope_name (GenericPathTypeCodes attribute) show() (SimpleProgressBar method) showit() (in module aquaduct.visual.quickplot) simple_types_distribution() (CTypeSpathsCollection static method) SimplePathPlotter (class in aquaduct.visual.quickplot) SimpleProgressBar (class in aquaduct.utils.clui) SimpleProteinPlotter (class in aquaduct.visual.quickplot) SimpleTarWriteHelper (class in aquaduct.visual.pymol_connector) SimpleTracePlotter (class in aquaduct.visual.quickplot) SimpleTree (class in aquaduct.utils.clui) single_path_traces() (SimplePathPlotter method) single_trace() (SimpleTracePlotter method) SinglePath (class in aquaduct.traj.paths) SinglePathID (class in aquaduct.traj.paths) SinglePathPlotter (class in aquaduct.visual.pymol_connector) size (Inlets attribute) (MacroMolPath attribute)

sizes (MacroMolPath attribute) (PassingPath attribute) small_clusters_to_outliers() (Inlets method) smart_time_string() (in module aquaduct.utils.clui) SmartRange (class in aquaduct.utils.helpers) SmartRangeDecrement (class in aquaduct.utils.helpers) SmartRangeEqual (class in aquaduct.utils.helpers) SmartRangeFunction (class in aquaduct.utils.helpers) SmartRangeIncrement (class in aquaduct.utils.helpers) sort_clusters() (Inlets method) sortify() (in module aquaduct.utils.helpers) spath2ctype() (Inlets method) spath_spectrum() (in module aquaduct.visual.quickplot) spaths2ctypes() (Inlets method) spaths_spectra() (in module aquaduct.visual.quickplot) split_list() (in module aquaduct.utils.helpers) Standartize (class in aquaduct.geom.pca) strech_zip() (in module aquaduct.utils.helpers) surface (ProtoInletTypeCodes attribute) surface_incoming (InletTypeCodes attribute) surface_outgoing (InletTypeCodes attribute)

T

thead() (in module aquaduct.utils.clui) threads_count (CpuThreadsCount attribute) tictoc (class in aquaduct.utils.clui) TmpDumpWriterOfMDA (class in aquaduct.traj.dumps) tracepoints() (in module aquaduct.geom.traces) triangle_angles() (in module aquaduct.geom.traces) triangle_angles_last() (in module aquaduct.geom.traces) triangle_height() (in module aquaduct.geom.traces) TriangleLinearize (class in aquaduct.geom.traces) tsep() (in module aquaduct.utils.clui) ttime() (SimpleProgressBar method) tupleify() (in module aquaduct.utils.helpers)

type (SmartRangeDecrement attribute) (SmartRangeEqual attribute) (SmartRangeIncrement attribute) types (GenericPaths attribute) (Inlets attribute) (MacroMolPath attribute) (PassingPath attribute) types_cont (MacroMolPath attribute) types_distribution() (CTypeSpathsCollection method) types_in (MacroMolPath attribute) types_object (MacroMolPath attribute) types_out (MacroMolPath attribute) types_prob_to_types() (CTypeSpathsCollection method)

U

underline() (in module aquaduct.utils.clui) undo() (Center method) (Normalize method) (PCA method) (Standartize method)

union() (in module aquaduct.traj.paths) union_full() (in module aquaduct.traj.paths) union_smartr() (in module aquaduct.traj.paths) uniqify() (in module aquaduct.utils.helpers) update() (CTypeSpathsCollection method) (SimpleProgressBar method)

V

vector_norm() (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() (in module aquaduct) version_nice() (in module aquaduct)

W

what2what() (in module aquaduct.utils.helpers)

X

xor() (in module aquaduct.traj.paths) xor_full() (in module aquaduct.traj.paths)

xor_smartr() (in module aquaduct.traj.paths) xzip_xzip() (in module aquaduct.utils.helpers)

Y

yield_single_paths() (in module aquaduct.traj.paths)

yield_spath_len_and_smooth_diff_in_types_slices() (in module aquaduct.visual.quickplot)

Z

zip_zip() (in module aquaduct.utils.helpers)