Index

_

__call__() (arrayify method) (CTypeSpathsCollectionWorker method) (Center method) (ColorMapDistMap method) (LinearizeHobbit method) (LinearizeRecursive method) (MasterReader method) (Normalize method) (PCA method) (PerformClustering method) (Smooth method) (Standartize method) (fbm method) __cmp__() (InletClusterGenericType method) __del__() (ConnectToPymol method) (ReaderTraj method) (SimpleTarWriteHelper method) (TmpDumpWriterOfMDA method) (ValveDataAccessRoots method) __enter__() (fbm method) (tictoc method) __eq__() (SinglePathID method) __exit__() (fbm method) (tictoc method) __getitem__() (InletClusterGenericType method) __getstate__() (MasterReader method) __has_out (PassingPath attribute) __hash__() (InletClusterGenericType method) __init__() (ActiveWindowOverMaxStepSmooth method) (ActiveWindowSmooth method) (BarberClusterResult method) (BasicPymolCGO method) (Bunch method) (CTypeSpathsCollection method) (CTypeSpathsCollectionWorker method) (Center method) (ColorMapDistMap method) (ConnectToPymol method) (DistanceWindowOverMaxStepSmooth method) (DistanceWindowSmooth method) (FakeSingleResidueSelection method) (FloatWindow method) (FramesRangeCollection method) (GeneralWindow method) (GenericPaths method) (Inlet method) (InletClusterExtendedType method) (InletClusterGenericType method) (Inlets method) (IntWindow method) (LoadDumpWrapper method) (MacroMolPath method) (MasterPath method) (MaxStepSmooth method) (Normalize method) (PCA method) (PassingPath method) (PerformClustering method) (ReaderTraj method) (SavgolSmooth method) (Selection method) (SimpleProgressBar method) (SimpleTarWriteHelper method) (SimpleTree method) (SinglePathID method) (SinglePathPlotter method) (SingleResidueSelection method) (SmartRange method) (SmartRangeFunction method) (Smooth method) (Standartize method) (TmpDumpWriterOfMDA method) (TriangleLinearize method) (ValveConfig method) (ValveDataAccess_nc method) (VectorLinearize method) (WhereToCut method) (Window method) (WindowOverMaxStepSmooth method) (WindowSmooth method) (arrayify method) (fbm method) (tictoc method)

__iter__() (SmartRange method) __len__() (InletClusterGenericType method) (SmartRange method) (SmartRangeFunction method) __repr__() (Auto method) (InletClusterGenericType method) (MasterReader method) (ReaderTraj method) (SimpleTree method) (SmartRange method) (SmartRangeFunction method) (Window method) __setstate__() (MasterReader method) __str__() (Auto method) (InletClusterGenericType method) (PerformClustering method) (SinglePathID method) (SmartRange method) (SmartRangeFunction method) _ColorMapDistMap__do_cadex() (ColorMapDistMap method) _coords() (SingleResidueSelection method) _cut_thyself() (WhereToCut method) _edges() (in module aquaduct.geom.convexhull) _facets() (in module aquaduct.geom.convexhull) _get_noclusters() (PerformClustering method) _gpi() (GenericPaths method) _gpo() (GenericPaths method) _gpt() (GenericPaths method) _MacroMolPath__object_len_calculate() (MacroMolPath method) _make_smooth_coords() (MacroMolPath method) _PassingPath__object_len_calculate() (PassingPath method) _paths (MacroMolPath attribute) (PassingPath attribute) _point_within_convexhull() (in module aquaduct.geom.convexhull) _ValveConfig__make_options_nt() (ValveConfig method) _vertices_ids() (in module aquaduct.geom.convexhull) _vertices_points() (in module aquaduct.geom.convexhull)

A

ActiveWindowOverMaxStepSmooth (class in aquaduct.geom.smooth) ActiveWindowSmooth (class in aquaduct.geom.smooth) add() (BasicPymolCGOLines method) (BasicPymolCGOSpheres method) (Selection method) add_012() (GenericPaths method) add_cgo_object() (ConnectToPymol method) add_cluster_annotations() (Inlets method) add_cone() (BasicPymolCGOPointers 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_spheres_from_inlets() (WhereToCut method) add_spheres_from_spaths() (WhereToCut 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() (FramesRangeCollection method) (SmartRange method) aquaduct (module) aquaduct.apps (module) aquaduct.apps.data (module) aquaduct.apps.valvecore (module) aquaduct.geom (module)

aquaduct.geom.cluster (module) aquaduct.geom.convexhull (module) aquaduct.geom.master (module) aquaduct.geom.pca (module) aquaduct.geom.smooth (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.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) aquaduct_version_nice() (in module aquaduct.apps.valvecore) are_rows_uniq() (in module aquaduct.utils.helpers) arrayify (class in aquaduct.utils.helpers) arrayify1() (in module aquaduct.utils.helpers) arrays2dict() (IdsOverIds static method) atom2residue() (ReaderTraj method) (ReaderTrajViaMDA method) atom_vdw() (ReaderTraj method) (ReaderTrajViaMDA method) atoms_masses() (ReaderTraj method) (ReaderTrajViaMDA method) atoms_positions() (ReaderTraj method) (ReaderTrajViaMDA method) AtomSelection (class in aquaduct.traj.sandwich) Auto (class in aquaduct.utils.helpers)

B

baguette() (MasterReader method) bar() (SimpleProgressBar method) barber_with_spheres() (GenericPaths method) BarberCluster (class in aquaduct.geom.cluster) BarberClusterResult (class in aquaduct.geom.cluster) 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

cache (CoordsRangeIndexCache attribute) cachedir (GlobalConfigStore attribute) cachemem (GlobalConfigStore attribute) call_clusterization_method() (Inlets method) cc() (in module aquaduct.visual.helpers) cc_safe() (in module aquaduct.visual.helpers) Center (class in aquaduct.geom.pca) center_of_mass() (AtomSelection method) (Selection method) centers() (PerformClustering method) 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) check_bounds_at_max_window_at_pos() (GeneralWindow method) check_minmaxcuts() (WhereToCut method) check_version_compliance() (in module aquaduct.apps.data) check_versions() (in module aquaduct.apps.data) chull() (AtomSelection method) cityblock() (in module aquaduct.visual.helpers) clean() (BasicPymolCGO method) close() (TmpDumpWriterOfMDA method) (ValveDataAccess_pickle method) close_all() (ValveDataAccessRoots method) close_trajectory() (ReaderTraj method) (ReaderTrajViaMDA method) cloud_groups() (WhereToCut method) cluster2str() (InletClusterGenericType static method) cluster_name() (ValveConfig 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)

common_config_names() (ValveConfig static method) common_traj_data_config_names() (ValveConfig static method) compress_zip() (in module aquaduct.utils.helpers) concatenate() (in module aquaduct.utils.helpers) ConnectToPymol (class in aquaduct.visual.pymol_connector) containing_residues() (AtomSelection method) contains() (SmartRangeFunction method) contains_residues() (AtomSelection method) convert() (LoadDumpWrapper method) convexhull() (SinglePathPlotter method) coords (GenericPaths attribute) (Inlets attribute) (MacroMolPath attribute) (PassingPath attribute) coords() (AtomSelection method) (FakeSingleResidueSelection method) (ResidueSelection method) (Selection method) (SingleResidueSelection method) coords_cont (MacroMolPath attribute) coords_filo (MacroMolPath attribute) coords_first_in (MacroMolPath attribute) (PassingPath attribute) coords_in (MacroMolPath attribute) coords_last_out (MacroMolPath attribute) (PassingPath attribute) coords_object (MacroMolPath attribute) coords_out (MacroMolPath attribute) coords_range() (in module aquaduct.traj.sandwich) coords_range_core() (in module aquaduct.traj.sandwich) coords_smooth() (FakeSingleResidueSelection method) (SingleResidueSelection method) coords_types_prob_widths() (CTypeSpathsCollectionWorker method) CoordsRangeIndexCache (class in aquaduct.apps.data) correct_window() (MasterReader 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) cut_thyself() (WhereToCut method)

D

decode_color() (ConnectToPymol method) del_cgo_object() (ConnectToPymol method) derrivative() (in module aquaduct.geom.traces) dict2arrays() (IdsOverIds static method) diff() (in module aquaduct.geom.traces) distance() (ColorMapDistMap method) DistanceWindowOverMaxStepSmooth (class in aquaduct.geom.smooth)

DistanceWindowSmooth (class in aquaduct.geom.smooth) dump() (ValveDataAccess_pickle method) dump_config() (ValveConfig method) dump_frames() (ReaderTraj method) (TmpDumpWriterOfMDA method) dump_frames_to_file() (ReaderTraj method) (ReaderTrajViaMDA method)

E

emit_message_to_file_in_root_logger() (in module aquaduct.utils.clui) empty_coords (MacroMolPath attribute) ends (MacroMolPath attribute) engine (MasterReader attribute) engine_name (MasterReader 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) FakeSingleResidueSelection (class in aquaduct.geom.master) fbm (class in aquaduct.utils.clui) find_paths() (GenericPaths method) find_paths_types() (GenericPaths method) finish() (SimpleProgressBar method) first_element() (SmartRange method) (SmartRangeFunction method)

fit() (BarberCluster method) (PerformClustering method) float_default (NumpyDefaultsStorageTypes attribute) FloatWindow (class in aquaduct.geom.smooth) frames (GenericPaths attribute) FramesRangeCollection (class in aquaduct.traj.sandwich) full_size() (CTypeSpathsCollection method)

G

GeneralWindow (class in aquaduct.geom.smooth) 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_cluster_options() (ValveConfig method) get_cmap() (in module aquaduct.visual.helpers) get_common_traj_data() (ValveConfig method) get_coords() (MacroMolPath method) (PassingPath method) get_coords_cont() (MacroMolPath method) get_cric_reader() (in module aquaduct.apps.data) get_current_nr() (WhereToCut method) get_default_config() (ValveConfig method) get_distance_both_cont() (MacroMolPath method) get_distance_cont() (MacroMolPath method) get_distance_rev_cont() (MacroMolPath method) get_flat_tree() (Inlets method) get_general_comment() (ValveConfig method) get_global_options() (ValveConfig method) get_inlets() (MacroMolPath method) (PassingPath method) get_inlets_references() (Inlets method)

get_leaf() (SimpleTree method) get_master_path() (CTypeSpathsCollection method) get_object_from_name() (in module aquaduct.apps.data) get_object_name() (in module aquaduct.apps.data) get_paths_in() (GenericPaths method) get_paths_out() (GenericPaths method) get_ranges() (FramesRangeCollection method) get_reader() (Selection method) (SingleResidueSelection method) get_reader_by_id() (MasterReader method) get_real() (Window method) get_recluster_options() (ValveConfig method) get_required_params() (in module aquaduct.geom.cluster) get_single_path_types() (GenericPaths method) get_single_reader() (MasterReader method) get_smooth_options() (ValveConfig method) get_stage_options() (ValveConfig method) get_str_timestamp() (in module aquaduct.utils.clui) get_variable() (ValveDataAccess_pickle method) get_vda_reader() (in module aquaduct.apps.data) get_velocity_cont() (MacroMolPath method) global_name() (ValveConfig static method) GlobalConfigStore (class in aquaduct.apps.data) 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

ids() (Selection method) IdsOverIds (class in aquaduct.apps.data) incoming (ProtoInletTypeCodes attribute) init_ax() (MPLTracePlotter method) init_pymol() (ConnectToPymol method) init_script() (ConnectToPymol method) Inlet (class in aquaduct.traj.inlets) inlet2sphere() (WhereToCut method) 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) IntWindow (class in aquaduct.geom.smooth) 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_overlaping_with_cloud() (WhereToCut method) is_passing() (MacroMolPath method) (PassingPath method) (SinglePath method) is_point_within() (Sphere method) is_point_within_convexhull() (in module aquaduct.geom.convexhull) is_single() (MacroMolPath method) (PassingPath method) (SinglePath method) is_sphere_cloud() (Sphere method) is_sphere_within() (Sphere method) isin() (SmartRange method) (SmartRangeDecrement method) (SmartRangeEqual method) (SmartRangeFunction method) (SmartRangeIncrement method) iterate() (MasterReader method) iterate_or_die() (in module aquaduct.utils.helpers) iterate_over_frames() (ReaderTraj method) itype (InletTypeCodes attribute) ix() (Selection method)

L

last_element() (SmartRange method) (SmartRangeDecrement method) (SmartRangeEqual method) (SmartRangeFunction method) (SmartRangeIncrement method) last_times() (SmartRange method) layer() (Selection method) leafs_names (SimpleTree attribute) left() (in module aquaduct.traj.paths) len() (Selection method) (Window method) 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() (ValveDataAccess_pickle method) load_config() (ValveConfig method) load_cric() (in module aquaduct.apps.data) load_pdb() (ConnectToPymol method) LoadDumpWrapper (class in aquaduct.apps.data)

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) MasterReader (class in aquaduct.traj.sandwich) max() (SmartRange method) max_frame (GenericPaths attribute)

max_window_at_pos() (GeneralWindow static method) MaxStepSmooth (class in aquaduct.geom.smooth) MeanShiftBandwidth() (in module aquaduct.geom.cluster) message() (in module aquaduct.utils.clui) message_special() (in module aquaduct.utils.clui) midpoints() (in module aquaduct.geom.traces) mimic_old_var_name (ValveDataAccess_pickle attribute) min() (SmartRange method) min_frame (GenericPaths attribute) MPLTracePlotter (class in aquaduct.visual.quickplot)

N

names() (ResidueSelection method) new() (BasicPymolCGO method) next() (SimpleProgressBar method) noaction() (in module aquaduct.utils.helpers)

Normalize (class in aquaduct.geom.pca) number_of_frames() (MasterReader method) number_of_layers() (MasterReader method) numbers() (Selection method) NumpyDefaultsStorageTypes (class in aquaduct.utils.maths)

O

object_len (MacroMolPath attribute) (PassingPath attribute) object_name (GenericPathTypeCodes attribute) open() (SimpleTarWriteHelper method) (ValveDataAccessRoots method) (ValveDataAccess_nc method) (ValveDataAccess_pickle method) open_reader_traj (MasterReader attribute)

open_trajectory() (ReaderTraj method) (ReaderTrajViaMDA method) orient_on() (ConnectToPymol method) out_name (GenericPathTypeCodes attribute) outgoing (ProtoInletTypeCodes attribute) output (InletClusterGenericType attribute) overlaps() (SmartRangeFunction method) overlaps_mutual() (SmartRangeFunction method)

P

P (PCA attribute) parse_selection() (ReaderTraj method) (ReaderTrajViaMDA method) 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) PerformClustering (class in aquaduct.geom.cluster) 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

range() (Window method) range2int() (in module aquaduct.utils.helpers) raw (SmartRange attribute) read() (LoadDumpWrapper method) reader (ReaderAccess attribute) ReaderAccess (class in aquaduct.traj.sandwich) ReaderTraj (class in aquaduct.traj.sandwich) ReaderTrajViaMDA (class in aquaduct.traj.sandwich) readline() (LoadDumpWrapper method) real_number_of_frames() (MasterReader method) (ReaderTraj method) (ReaderTrajViaMDA method) recluster_cluster() (Inlets method) recluster_name() (ValveConfig static method) recluster_outliers() (Inlets method) recursive_clusterization_name() (ValveConfig static method) recursive_threshold_name() (ValveConfig static method) refs (Inlets attribute) refs_names (Inlets attribute)

renumber_clusters() (Inlets method) residues() (AtomSelection method) residues_names() (ReaderTraj method) (ReaderTrajViaMDA method) residues_positions() (ReaderTraj method) (ReaderTrajViaMDA method) ResidueSelection (class in aquaduct.traj.sandwich) resize_leaf_0() (Inlets method) rev() (SmartRange method) (SmartRangeDecrement method) (SmartRangeEqual method) (SmartRangeFunction method) (SmartRangeIncrement method) right() (in module aquaduct.traj.paths) robust_and() (in module aquaduct.utils.helpers) robust_or() (in module aquaduct.utils.helpers) roman_emulation (class in aquaduct.utils.clui) roots (ValveDataAccessRoots attribute) rotate (SimpleProgressBar attribute)

S

sandwich() (MasterReader method) sandwich_mode (MasterReader attribute) save_config() (ValveConfig method) save_config_stream() (ValveConfig method) save_cric() (in module aquaduct.apps.data) save_file2tar() (SimpleTarWriteHelper method) save_object2tar() (SimpleTarWriteHelper method) SavgolSmooth (class in aquaduct.geom.smooth) scatter() (MPLTracePlotter method) (SinglePathPlotter method) scope_name (GenericPathTypeCodes attribute) Selection (class in aquaduct.traj.sandwich) set_frame() (ReaderTraj method) set_real_frame() (ReaderTraj method) (ReaderTrajViaMDA method) set_savgol_function() (SavgolSmooth method) set_variable() (ValveDataAccess_pickle method) 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_residues() (ResidueSelection method) single_trace() (SimpleTracePlotter method) SinglePath (class in aquaduct.traj.paths) SinglePathID (class in aquaduct.traj.paths) SinglePathPlotter (class in aquaduct.visual.pymol_connector) SingleResidueSelection (class in aquaduct.traj.sandwich) 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) 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) smooth_coords_ranges() (in module aquaduct.traj.sandwich) smooth_name() (ValveConfig static method) sort_clusters() (Inlets method) sortify() (in module aquaduct.utils.helpers) spath2ctype() (Inlets method) spath2spheres() (WhereToCut method) spath_spectrum() (in module aquaduct.visual.quickplot) spaths2ctypes() (Inlets method) spaths_spectra() (in module aquaduct.visual.quickplot) Sphere (class in aquaduct.traj.barber) split_list() (in module aquaduct.utils.helpers) stage_I_run() (in module aquaduct.apps.valvecore) stage_II_run() (in module aquaduct.apps.valvecore) stage_III_run() (in module aquaduct.apps.valvecore) stage_IV_run() (in module aquaduct.apps.valvecore) stage_names() (ValveConfig method) stage_V_run() (in module aquaduct.apps.valvecore) stage_VI_run() (in module aquaduct.apps.valvecore) 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) topology (MasterReader attribute) toRoman() (roman_emulation method) tracepoints() (in module aquaduct.geom.traces) trajectory (MasterReader attribute) 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) uniquify() (Selection method) unknown_names (ValveDataAccess_pickle attribute) update() (CTypeSpathsCollection method) (SimpleProgressBar method)

V

valve_begin() (in module aquaduct.apps.valvecore) valve_end() (in module aquaduct.apps.valvecore) valve_exec_stage() (in module aquaduct.apps.valvecore) valve_load_config() (in module aquaduct.apps.valvecore) ValveConfig (class in aquaduct.apps.valvecore) ValveDataAccess (in module aquaduct.apps.data) ValveDataAccess_nc (class in aquaduct.apps.data) ValveDataAccess_pickle (class in aquaduct.apps.data) ValveDataAccessRoots (class in aquaduct.apps.data)

vdw() (AtomSelection method) VdW_radii (in module aquaduct.traj.sandwich) 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) WhereToCut (class in aquaduct.traj.barber) Window (class in aquaduct.traj.sandwich)

window (MasterReader attribute) WindowOverMaxStepSmooth (class in aquaduct.geom.smooth) WindowSmooth (class in aquaduct.geom.smooth)

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

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)