Index _ | A | B | C | D | E | F | G | H | I | L | M | N | O | P | R | S | T | U | V | W | X _ _2go_checkandmove() (in module alhambra.fastreduceD) _2go_findtrialmoves() (in module alhambra.fastreduceD) _2go_moveandfill() (in module alhambra.fastreduceD) __add__() (alhambra.classes.UpdateListD method) (alhambra.seq.Seq method) __contains__() (alhambra.classes.UpdateListD method) __delitem__() (alhambra.classes.UpdateListD method) (alhambra.tiles.EdgeView method) __eq__() (alhambra.Glue method) (alhambra.glues.Glue method) __getitem__() (alhambra.classes.UpdateListD method) (alhambra.endreorder.cachedarray method) (alhambra.endreorder.FastState method) (alhambra.grid.AbstractLattice method) (alhambra.grid.Lattice method) (alhambra.grid.ScadnanoLattice method) (alhambra.seq.Seq method) (alhambra.tiles.EdgeView method) (alhambra.tiles.UseView method) __iadd__() (alhambra.classes.UpdateListD method) __ior__() (alhambra.classes.UpdateListD method) (alhambra.Glue method) (alhambra.glues.Glue method) __iter__() (alhambra.classes.UpdateListD method) (alhambra.tiles.EdgeView method) __len__() (alhambra.classes.UpdateListD method) (alhambra.fastreduceD.FTilesArray method) (alhambra.seq.Seq method) (alhambra.tiles.EdgeView method) (alhambra.tiles.UseView method) __next__() (alhambra.tiles.EdgeView method) __or__() (alhambra.classes.UpdateListD method) (alhambra.Glue method) (alhambra.glues.Glue method) (alhambra.glues.Use method) (alhambra.seq.Seq method) __radd__() (alhambra.seq.Seq method) __repr__() (alhambra.classes.UpdateListD method) (alhambra.seq.Seq method) (alhambra.tiles.BaseSSTile method) (alhambra.tiles.EdgeView method) (alhambra.tiles.UseView method) (alhambra.TileSet method) (alhambra.tilesets.TileSet method) __ror__() (alhambra.Glue method) (alhambra.glues.Glue method) (alhambra.glues.Use method) (alhambra.seq.Seq method) __setitem__() (alhambra.classes.UpdateListD method) (alhambra.grid.AbstractLattice method) (alhambra.grid.Lattice method) (alhambra.grid.ScadnanoLattice method) (alhambra.tiles.EdgeView method) (alhambra.tiles.UseView method) __slots__ (alhambra.classes.UpdateListD attribute) (alhambra.Tile attribute) (alhambra.tiles.EdgeView attribute) (alhambra.tiles.Tile attribute) (alhambra.tiles.UseView attribute) __str__() (alhambra.classes.UpdateListD method) (alhambra.glues.DXGlue method) (alhambra.seq.Seq method) (alhambra.tiles.BaseSSTile method) (alhambra.tiles.EdgeView method) (alhambra.tiles.UseView method) (alhambra.TileSet method) (alhambra.tilesets.TileSet method) __sub__() (alhambra.classes.UpdateListD method) _AMBBASES (in module alhambra.seq) _base_domains (alhambra.flatish.FlatishHDupleTile10_E attribute) (alhambra.flatish.FlatishHDupleTile9_E attribute) (alhambra.flatish.FlatishSingleTile10 attribute) (alhambra.flatish.FlatishSingleTile9 attribute) (alhambra.flatish.FlatishVDupleTile10_E2 attribute) (alhambra.flatish.FlatishVDupleTile9_E2 attribute) (alhambra.tiles.BaseSSTile property) (alhambra.tiles.SST10 attribute) (alhambra.tiles.SST10_5S attribute) (alhambra.tiles.SST11 attribute) (alhambra.tiles.SST11_5S attribute) _base_edges (alhambra.flatish.FlatishHDupleTile10_E attribute) (alhambra.flatish.FlatishHDupleTile9_E attribute) (alhambra.flatish.FlatishVDupleTile10_E2 attribute) (alhambra.flatish.FlatishVDupleTile9_E2 attribute) (alhambra.tiles.BaseSSTile property) (alhambra.tiles.BaseSSTSingle property) (alhambra.tiles.SST10_5S property) (alhambra.tiles.SST11_5S property) _baseglues (alhambra.tiles.DAOESingle3p attribute) (alhambra.tiles.DAOESingle5p attribute) _branchtiles() (in module alhambra.fastlatticedefect) _convert_adapts() (in module alhambra.seeds) _deserialize() (alhambra.classes.Serializable class method) (alhambra.TileSet class method) (alhambra.tilesets.TileSet class method) _edges (alhambra.Tile attribute) (alhambra.tiles.BaseSSTile attribute) (alhambra.tiles.BaseSSTSingle attribute) (alhambra.tiles.DAOETile attribute) (alhambra.tiles.EdgeView attribute) (alhambra.tiles.Tile attribute) _el (alhambra.drawing.Rectangle attribute) (alhambra.drawing.Text attribute) (alhambra.drawing.Use attribute) _ENDER (in module alhambra.fastlatticedefect) (in module alhambra.latticedefect) _ensure_glue_name() (in module alhambra.glues) _fakesingle() (in module alhambra.sensitivitynew) _fakesingles() (in module alhambra.sensitivitynew) _FastTileSet (class in alhambra.fastreduce) (class in alhambra.fastreduceD) _fdg() (in module alhambra.fastreduce) (in module alhambra.fastreduceD) _ffakedouble_n() (in module alhambra.fastreduce) (in module alhambra.fastreduceD) _ffakesingle() (in module alhambra.fastreduce) (in module alhambra.fastreduceD) _find_pairs_from_tile() (in module alhambra.sensitivity) _findpotentialgluemerges() (in module alhambra.fastreduce) (in module alhambra.fastreduceD) _findpotentialtilemerges() (in module alhambra.fastreduce) (in module alhambra.fastreduceD) _ft_to_fta() (in module alhambra.fastreduce) _generate_stickydesign_energetic_classes() (in module alhambra.tilesets) _generic_branch() (in module alhambra.latticedefect) _get_edge_index() (alhambra.Tile class method) (alhambra.tiles.HDupleTile class method) (alhambra.tiles.SingleTile class method) (alhambra.tiles.Tile class method) (alhambra.tiles.VDupleTile class method) _gl (in module alhambra.tilesets) _gluelocs (alhambra.tiles.DAOESingle3p attribute) (alhambra.tiles.DAOESingle5p attribute) _gluereduce() (in module alhambra.fastreduce) (in module alhambra.fastreduceD) _input_neighborhood_domains() (alhambra.flatish.FlatishHDupleTile10_E method) (alhambra.flatish.FlatishHDupleTile9_E method) (alhambra.flatish.FlatishVDupleTile10_E2 method) (alhambra.flatish.FlatishVDupleTile9_E2 method) (alhambra.tiles.BaseSSTile method) (alhambra.tiles.BaseSSTSingle method) _into_complement() (alhambra.Glue method) (alhambra.glues.DXGlue method) (alhambra.glues.Glue method) (alhambra.glues.SSGlue method) _L_TO_N (in module alhambra.seq) _latticedefect_tile() (in module alhambra.fastlatticedefect) (in module alhambra.latticedefect) _N_TO_L (in module alhambra.seq) _OE (in module alhambra.fastlatticedefect) (in module alhambra.latticedefect) _pairs_commonside() (in module alhambra.sensitivity) _ppld() (in module alhambra.latticedefect) _PUNC (in module alhambra.seq) _rebuild_map() (alhambra.util.GlueMergeSpec method) (alhambra.util.TileMergeSpec method) _recfix() (in module alhambra.fastreduce) (in module alhambra.fastreduceD) _repr_html_() (alhambra.drawing.Drawing method) _repr_svg_() (alhambra.drawing.Drawing method) _rev (in module alhambra.sensitivitynew) _scadnano_5p_offset (alhambra.flatish.FlatishHDupleTile10_E attribute) (alhambra.flatish.FlatishHDupleTile9_E attribute) (alhambra.flatish.FlatishSingleTile10 attribute) (alhambra.flatish.FlatishSingleTile9 attribute) (alhambra.flatish.FlatishVDupleTile10_E2 attribute) (alhambra.flatish.FlatishVDupleTile9_E2 attribute) (alhambra.tiles.SST10 attribute) (alhambra.tiles.SST10_5S attribute) (alhambra.tiles.SST11 attribute) (alhambra.tiles.SST11_5S attribute) (alhambra.tiles.TileSupportingScadnano property) _scadnano_color() (in module alhambra.tiles) _scadnano_offsets (alhambra.flatish.FlatishSingleTile10 attribute) (alhambra.flatish.FlatishSingleTile9 attribute) (alhambra.flatish.FlatishVDupleTile10_E2 attribute) (alhambra.flatish.FlatishVDupleTile9_E2 attribute) (alhambra.tiles.SST10 attribute) (alhambra.tiles.SST10_5S attribute) (alhambra.tiles.SST11 attribute) (alhambra.tiles.SST11_5S attribute) _second_order_type() (in module alhambra.sensitivity) _sequence (alhambra.glues.SSGlue attribute) _sequence_length (alhambra.tiles.BaseSSTile property) (alhambra.tiles.BaseSSTSingleWithExtensions property) _serialize() (alhambra.classes.Serializable method) (alhambra.TileSet method) (alhambra.tilesets.TileSet method) _shortdesc (alhambra.glues.SSGlue property) _single_reduce_ends() (in module alhambra.fastreduce) (in module alhambra.fastreduceD) _single_reduce_tiles() (in module alhambra.fastreduce) (in module alhambra.fastreduceD) _skip_polyT_and_inertname() (in module alhambra.grid) _strand_sequences (alhambra.tiles.DAOETile attribute) _tile (alhambra.tiles.EdgeView attribute) (alhambra.tiles.UseView attribute) _tilereduce() (in module alhambra.fastreduce) (in module alhambra.fastreduceD) _to_xgrow_dict() (alhambra.TileSet method) (alhambra.tilesets.TileSet method) _VALID_NTS (in module alhambra.seq) _VALID_WITH_PUNC (in module alhambra.seq) _WC (in module alhambra.seq) _WC_WITH_PUNC (in module alhambra.seq) A abstract_diagram() (alhambra.Tile method) (alhambra.tiles.HDupleTile method) (alhambra.tiles.SingleTile method) (alhambra.tiles.Tile method) (alhambra.tiles.VDupleTile method) AbstractLattice (class in alhambra.grid) AbstractLatticeSupportingScadnano (class in alhambra.grid) abstractstrength (alhambra.Glue attribute) (alhambra.glues.Glue attribute) adapter_tiles (alhambra.flatish.FlatishHSeed9 attribute) (alhambra.flatish.FlatishVSeed9 attribute) adapters (alhambra.seeds.DiagonalSESeed attribute) (alhambra.seeds.DXOrigamiSeed attribute) add() (alhambra.classes.UpdateListD method) (alhambra.sensitivitynew.CounterSet method) (alhambra.sensitivitynew.PathSet method) (alhambra.sensitivitynew.SetSet method) (alhambra.util.GlueMergeSpec method) (alhambra.util.TileMergeSpec method) AL (in module alhambra.grid) alhambra module alhambra._tilesets_dx module alhambra._version module alhambra.anneal module alhambra.classes module alhambra.drawing module alhambra.edotparen module alhambra.endreorder module alhambra.fastlatticedefect module alhambra.fastreduce module alhambra.fastreduceD module alhambra.flatish module alhambra.glues module alhambra.grid module alhambra.latticedefect module alhambra.mixes module alhambra.nuad module alhambra.quantitate module alhambra.seeds module alhambra.sensitivity module alhambra.sensitivitynew module alhambra.seq module alhambra.tiles module alhambra.tilesets module alhambra.util module alldomains (alhambra.TileSet property) (alhambra.tilesets.TileSet property) allglues (alhambra.TileSet property) (alhambra.tilesets.TileSet property) alpha (alhambra.tilesets.GrowFullGlues attribute) (alhambra.tilesets.GrowOrthogonalGlues attribute) anneal() (alhambra.anneal.Annealer method) Annealer (class in alhambra.anneal) append() (alhambra.drawing.Group method) apply_equiv() (alhambra.TileSet method) (alhambra.tilesets.TileSet method) applyequiv() (alhambra.fastreduce._FastTileSet method) (alhambra.fastreduceD._FastTileSet method) asdict() (alhambra.classes.UpdateListD method) (alhambra.grid.AbstractLattice method) (alhambra.grid.Lattice method) (alhambra.grid.ScadnanoLattice method) aslist() (alhambra.classes.UpdateListD method) auto() (alhambra.anneal.Annealer method) B base() (in module alhambra.util) base_str (alhambra.seq.Seq property) basename() (alhambra.Glue method) (alhambra.glues.Glue method) BaseSSTile (class in alhambra.tiles) BaseSSTSingle (class in alhambra.tiles) BaseSSTSingleWithExtensions (class in alhambra.tiles) blankequiv() (alhambra.fastreduce.FGlueList method) (alhambra.fastreduceD.FGlueList method) BOTH (alhambra.glues.Use attribute) C cachedarray (class in alhambra.endreorder) calculate_gses() (alhambra.tilesets.GrowFullGlues method) (alhambra.tilesets.GrowOrthogonalGlues method) (alhambra.tilesets.GrowPerfectGlues method) (alhambra.tilesets.GrowSelfComplementaryGlues method) (alhambra.tilesets.XgrowGlueOpts method) check_consistent() (alhambra.TileSet method) (alhambra.tilesets.TileSet method) check_edotparen_consistency() (in module alhambra.edotparen) check_edotparen_sequence() (in module alhambra.edotparen) check_seq() (in module alhambra.seq) color (alhambra.fastreduceD.FTile attribute) (alhambra.fastreduceD.FTilesArray attribute) (alhambra.Tile attribute) (alhambra.tiles.Tile attribute) Color (in module alhambra.tiles) comp (alhambra.glues.DXGlue property) comp() (in module alhambra.sensitivity) (in module alhambra.util) complement (alhambra.Glue property) (alhambra.glues.Glue property) (alhambra.tiles.D property) consolidate_pairs() (in module alhambra.sensitivity) copy() (alhambra.classes.IdentMergeableItem method) (alhambra.classes.UpdateListD method) (alhambra.endreorder.FastState method) (alhambra.endreorder.FseqState method) (alhambra.Glue method) (alhambra.glues.Glue method) (alhambra.Tile method) (alhambra.tiles.Tile method) (alhambra.TileSet method) (alhambra.tilesets.TileSet method) copyadd() (alhambra.util.GlueMergeSpec method) (alhambra.util.TileMergeSpec method) count_ambiguous() (in module alhambra.seq) CounterSet (class in alhambra.sensitivitynew) create_abstract_diagram() (alhambra.TileSet method) (alhambra.tilesets.TileSet method) create_guards() (alhambra.tiles.BaseSSTile method) (alhambra.tiles.SupportsGuards method) create_guards_square() (alhambra.TileSet method) (alhambra.tilesets.TileSet method) D D (class in alhambra.tiles) DAOEHDouble3p (class in alhambra.tiles) DAOEHDouble5p (class in alhambra.tiles) DAOESingle (class in alhambra.tiles) DAOESingle3p (class in alhambra.tiles) DAOESingle5p (class in alhambra.tiles) DAOETile (class in alhambra.tiles) DAOEVDouble3p (class in alhambra.tiles) DAOEVDouble5p (class in alhambra.tiles) data (alhambra.classes.UpdateListD attribute) DEFAULT_ENERGETICS (in module alhambra.util) DEFAULT_MM_ENERGETICS_NAMES (in module alhambra.util) DEFAULT_MULTIMODEL_ENERGETICS (in module alhambra.util) DEFAULT_REGION_ENERGETICS (in module alhambra.util) DEFAULT_SD2_MULTIMODEL_ENERGETICS (in module alhambra.util) defs (alhambra.drawing.Drawing attribute) dfake (alhambra.fastreduceD.FTile attribute) (alhambra.fastreduceD.FTilesArray attribute) DiagonalSESeed (class in alhambra.seeds) direction (alhambra.tiles.EdgeLoc attribute) directions (in module alhambra.fastreduceD) dna_length (alhambra.glues.SSGlue property) (alhambra.seq.Seq property) dna_length() (in module alhambra.seq) Domain (in module alhambra.tiles) domains (alhambra.flatish.FlatishHDupleTile10_E property) (alhambra.flatish.FlatishHDupleTile9_E property) (alhambra.flatish.FlatishVDupleTile10_E2 property) (alhambra.flatish.FlatishVDupleTile9_E2 property) (alhambra.tiles.BaseSSTile property) (alhambra.tiles.BaseSSTSingle property) (alhambra.tiles.BaseSSTSingleWithExtensions property) (alhambra.tiles.SST10_5S property) (alhambra.tiles.SST11_5S property) domains_from_tiles() (alhambra.TileList method) (alhambra.tiles.TileList method) domerge() (alhambra.fastreduce.FGlueList method) (alhambra.fastreduceD.FGlueList method) Drawing (class in alhambra.drawing) DrawingElement (class in alhambra.drawing) dx_plot_adjacent_regions() (in module alhambra._tilesets_dx) dx_plot_se_hists() (in module alhambra._tilesets_dx) dx_plot_se_lv() (in module alhambra._tilesets_dx) dx_plot_side_strands() (in module alhambra._tilesets_dx) DXAdapter (class in alhambra.seeds) DXGlue (class in alhambra.glues) DXOrigamiSeed (class in alhambra.seeds) E E (alhambra.tiles.D attribute) ecomp() (in module alhambra.endreorder) edge_directions (alhambra.Tile property) (alhambra.tiles.BaseSSTile property) (alhambra.tiles.HDupleTile property) (alhambra.tiles.SingleTile property) (alhambra.tiles.Tile property) (alhambra.tiles.VDupleTile property) edge_locations (alhambra.Tile property) (alhambra.tiles.HDupleTile property) (alhambra.tiles.SingleTile property) (alhambra.tiles.Tile property) (alhambra.tiles.VDupleTile property) EdgeLoc (class in alhambra.tiles) edges (alhambra.seeds.DXAdapter attribute) (alhambra.Tile property) (alhambra.tiles.BaseSSTile property) (alhambra.tiles.Tile property) EdgeView (class in alhambra.tiles) edp_closetoopen (in module alhambra.edotparen) EL (in module alhambra.tiles) elements (alhambra.drawing.Drawing attribute) (alhambra.drawing.Group attribute) empty() (alhambra.grid.AbstractLattice class method) EndSystemFseq (class in alhambra.endreorder) eq() (alhambra.util.GlueMergeSpec method) (alhambra.util.TileMergeSpec method) Equiv (in module alhambra.fastreduceD) etype (alhambra.Glue property) (alhambra.glues.DXGlue attribute) (alhambra.glues.Glue property) (alhambra.glues.SSGlue attribute) expand_compact_edotparen() (in module alhambra.edotparen) F fake (alhambra.Tile attribute) (alhambra.tiles.Tile attribute) FakeSingle (class in alhambra.sensitivitynew) FastState (class in alhambra.endreorder) FGlueList (class in alhambra.fastreduce) (class in alhambra.fastreduceD) findmovetiles() (in module alhambra.fastreduceD) findtile() (alhambra.grid.ScadnanoLattice method) firstsortorder (in module alhambra.sensitivity) FlatishHDupleTile10_E (class in alhambra.flatish) FlatishHDupleTile9_E (class in alhambra.flatish) FlatishHSeed9 (class in alhambra.flatish) FlatishSingleTile10 (class in alhambra.flatish) FlatishSingleTile9 (class in alhambra.flatish) FlatishVDupleTile10_E2 (class in alhambra.flatish) FlatishVDupleTile9_E2 (class in alhambra.flatish) FlatishVSeed9 (class in alhambra.flatish) flatten() (in module alhambra.endreorder) flipdir (in module alhambra.sensitivity) from_any() (alhambra.glues.Use class method) from_dict() (alhambra.flatish.FlatishHSeed9 class method) (alhambra.flatish.FlatishVSeed9 class method) (alhambra.Glue static method) (alhambra.glues.Glue static method) (alhambra.glues.GlueFactory method) (alhambra.grid.LatticeFactory method) (alhambra.seeds.DiagonalSESeed class method) (alhambra.seeds.DXAdapter class method) (alhambra.seeds.DXOrigamiSeed class method) (alhambra.seeds.Seed class method) (alhambra.seeds.SeedFactory method) (alhambra.Tile static method) (alhambra.tiles.Tile static method) (alhambra.tiles.TileFactory method) (alhambra.TileSet class method) (alhambra.tilesets.TileSet class method) from_file() (alhambra.TileSet class method) (alhambra.tilesets.TileSet class method) from_ftiles() (alhambra.fastreduceD.FTilesArray class method) from_json() (alhambra.classes.Serializable class method) from_mix() (alhambra.TileSet class method) (alhambra.tilesets.TileSet class method) from_scadnano() (alhambra.tiles.TileFactory method) (alhambra.TileSet class method) (alhambra.tilesets.TileSet class method) from_str() (alhambra.tilesets.XgrowGlueOpts class method) from_toml() (alhambra.classes.Serializable class method) from_yaml() (alhambra.classes.Serializable class method) fromdict() (alhambra.grid.AbstractLattice class method) (alhambra.grid.Lattice class method) (alhambra.grid.ScadnanoLattice class method) fseq (alhambra.glues.DXGlue property) FseqState (class in alhambra.endreorder) fta_to_ft() (in module alhambra.fastreduce) (in module alhambra.fastreduceD) FTI (in module alhambra.fastreduce) (in module alhambra.fastreduceD) FTile (class in alhambra.fastreduceD) (in module alhambra.fastreduce) FTileList (class in alhambra.fastreduce) (class in alhambra.fastreduceD) FTilesArray (class in alhambra.fastreduceD) (in module alhambra.fastreduce) FTS (in module alhambra.fastreduceD) fullseq (alhambra.glues.DXGlue attribute) G gcomp() (in module alhambra.fastreduceD) gen_2go_maps() (in module alhambra.fastreduceD) gen_2go_profile() (in module alhambra.fastreduce) (in module alhambra.fastreduceD) gen_2go_single_ins() (in module alhambra.fastreduce) get_concentration() (alhambra.Tile method) (alhambra.tiles.Tile method) get_stoic() (alhambra.Tile method) (alhambra.tiles.Tile method) get_xgrow_gse() (alhambra.tilesets.GrowFullGlues method) (alhambra.tilesets.GrowOrthogonalGlues method) (alhambra.tilesets.GrowPerfectGlues method) (alhambra.tilesets.GrowSelfComplementaryGlues method) (alhambra.tilesets.XgrowGlueOpts method) Glue (class in alhambra) (class in alhambra.glues) glue_factory (in module alhambra.glues) glue_name_map() (alhambra.tilesets.GrowSelfComplementaryGlues method) (alhambra.tilesets.XgrowGlueOpts method) GlueA (in module alhambra.glues) GlueB (in module alhambra.glues) GlueFactory (class in alhambra.glues) gluelist (alhambra.fastreduceD._FastTileSet attribute) GlueList (class in alhambra) (class in alhambra.glues) GlueMergeSpec (class in alhambra.util) glues (alhambra.fastreduceD.FTile attribute) (alhambra.fastreduceD.FTilesArray attribute) (alhambra.TileSet attribute) (alhambra.tilesets.TileSet attribute) glues_from_tiles() (alhambra.TileList method) (alhambra.tiles.TileList method) gmatch() (in module alhambra.fastreduceD) grid (alhambra.grid.AbstractLattice attribute) Group (class in alhambra.drawing) group_strand_pairs_by_groups_and_complementary_domains() (in module alhambra.nuad) GrowFullGlues (class in alhambra.tilesets) GrowOrthogonalGlues (class in alhambra.tilesets) GrowPerfectGlues (class in alhambra.tilesets) GrowSelfComplementaryGlues (class in alhambra.tilesets) guards (alhambra.TileSet attribute) (alhambra.tilesets.TileSet attribute) H HAS_SD_ACCEL (in module alhambra.tilesets) HDupleTile (class in alhambra.tiles) height (alhambra.drawing.Drawing attribute) ho_from_seed_offset() (alhambra.seeds.SeedSupportingScadnano method) HSEL (in module alhambra.fastreduce) (in module alhambra.fastreduceD) htiles (alhambra.fastreduceD.FTileList attribute) I id (alhambra.drawing.Group attribute) ident() (alhambra.classes.IdentMergeableItem method) (alhambra.Glue method) (alhambra.glues.Glue method) (alhambra.glues.SSGlue method) (alhambra.Tile method) (alhambra.tiles.Tile method) IdentMergeableItem (class in alhambra.classes) INPUT (alhambra.glues.Use attribute) insert() (alhambra.tiles.EdgeView method) (alhambra.tiles.UseView method) invalids (alhambra.seq.InvalidSequence attribute) InvalidSequence invert() (alhambra.glues.Use method) invertuse (in module alhambra.fastreduceD) is_22go_equiv() (in module alhambra.fastreduce) (in module alhambra.fastreduceD) is_2go_equiv() (in module alhambra.fastreduce) (in module alhambra.fastreduceD) is_2go_nn() (in module alhambra.fastreduceD) is_2go_single_nn() (in module alhambra.fastreduce) is_complement (alhambra.Glue property) (alhambra.glues.Glue property) is_definite (alhambra.seq.Seq property) is_definite() (in module alhambra.seq) is_fake (alhambra.Tile property) (alhambra.tiles.Tile property) is_null (alhambra.seq.Seq property) is_null() (in module alhambra.seq) isatamequiv() (in module alhambra.fastreduce) (in module alhambra.fastreduceD) iseq() (alhambra.fastreduce.FGlueList method) (alhambra.fastreduceD.FGlueList method) item1 (alhambra.seq.MergeConflictError attribute) item2 (alhambra.seq.MergeConflictError attribute) L Lattice (class in alhambra.grid) lattice_factory (in module alhambra.grid) lattice_tiles() (alhambra.TileSet method) (alhambra.tilesets.TileSet method) latticedefects() (alhambra.TileSet method) (alhambra.tilesets.TileSet method) (in module alhambra.fastlatticedefect) (in module alhambra.latticedefect) LatticeFactory (class in alhambra.grid) lattices (alhambra.TileSet attribute) (alhambra.tilesets.TileSet attribute) LatticeSupportingScadnano (class in alhambra.grid) load_nuad_design() (in module alhambra.nuad) loc (alhambra.seeds.DXAdapter attribute) location (alhambra.seq.MergeConflictError attribute) log (in module alhambra.nuad) (in module alhambra.tiles) (in module alhambra.tilesets) M MAPPER (in module alhambra.util) merge() (alhambra.classes.IdentMergeableItem method) (alhambra.Glue method) (alhambra.glues.DXGlue method) (alhambra.glues.Glue method) (alhambra.glues.SSGlue method) (alhambra.glues.Use method) (alhambra.seq.Seq method) (alhambra.Tile method) (alhambra.tiles.Tile method) (in module alhambra.seq) merge_complements() (alhambra.GlueList method) (alhambra.glues.GlueList method) merge_glue() (alhambra.GlueList method) (alhambra.glues.GlueList method) merge_glue_and_update_list() (alhambra.GlueList method) (alhambra.glues.GlueList method) merge_items() (in module alhambra.glues) MergeConflictError MergeConflictsError mod3 (alhambra.tiles.BaseSSTSingleWithExtensions attribute) mod5 (alhambra.tiles.BaseSSTSingleWithExtensions attribute) module alhambra alhambra._tilesets_dx alhambra._version alhambra.anneal alhambra.classes alhambra.drawing alhambra.edotparen alhambra.endreorder alhambra.fastlatticedefect alhambra.fastreduce alhambra.fastreduceD alhambra.flatish alhambra.glues alhambra.grid alhambra.latticedefect alhambra.mixes alhambra.nuad alhambra.quantitate alhambra.seeds alhambra.sensitivity alhambra.sensitivitynew alhambra.seq alhambra.tiles alhambra.tilesets alhambra.util MPOBJECT (in module alhambra.util) multimap() (in module alhambra.util) mutate() (alhambra.endreorder.EndSystemFseq method) N N (alhambra.tiles.D attribute) n_ambiguous (alhambra.seq.Seq property) name (alhambra.fastreduceD.FTile attribute) (alhambra.fastreduceD.FTilesArray attribute) (alhambra.Glue attribute) (alhambra.glues.Glue attribute) (alhambra.seeds.DXAdapter attribute) (alhambra.Tile attribute) (alhambra.tiles.Tile attribute) note (alhambra.Glue attribute) (alhambra.glues.Glue attribute) (alhambra.Tile attribute) (alhambra.tiles.Tile attribute) NULL (alhambra.glues.Use attribute) Number (in module alhambra.drawing) O Offset (in module alhambra.tiles) other (in module alhambra.fastreduceD) OUTPUT (alhambra.glues.Use attribute) P params (alhambra.TileSet attribute) (alhambra.tilesets.TileSet attribute) PathSet (class in alhambra.sensitivitynew) PERMANENT (alhambra.glues.Use attribute) position (alhambra.tiles.EdgeLoc attribute) positions (alhambra.grid.ScadnanoLattice attribute) prettify_edotparen() (in module alhambra.edotparen) ProgressLogger (class in alhambra.util) ptins() (in module alhambra.fastreduce) (in module alhambra.fastreduceD) R Rectangle (class in alhambra.drawing) reduce_ends() (alhambra.TileSet method) (alhambra.tilesets.TileSet method) (in module alhambra.fastreduce) (in module alhambra.fastreduceD) reduce_tiles() (alhambra.TileSet method) (alhambra.tilesets.TileSet method) (in module alhambra.fastreduce) (in module alhambra.fastreduceD) refreshnames() (alhambra.classes.UpdateListD method) register() (alhambra.glues.GlueFactory method) (alhambra.grid.LatticeFactory method) (alhambra.seeds.SeedFactory method) (alhambra.tiles.TileFactory method) revcomp (alhambra.seq.Seq property) revcomp() (in module alhambra.seq) rotations (alhambra.Tile property) (alhambra.tiles.Tile property) round_figures() (in module alhambra.anneal) RSEL (in module alhambra.fastreduce) (in module alhambra.fastreduceD) run_xgrow() (alhambra.TileSet method) (alhambra.tilesets.TileSet method) S S (alhambra.tiles.D attribute) save_svg() (alhambra.drawing.Drawing method) saveSvg (alhambra.drawing.Drawing attribute) ScadnanoLattice (class in alhambra.grid) score() (alhambra.endreorder.EndSystemFseq method) SD_ENERGETICS_CLASSES (in module alhambra.tilesets) search() (alhambra.classes.UpdateListD method) secondclasses (in module alhambra.sensitivity) secondsortorder (in module alhambra.sensitivity) seed (alhambra.grid.AbstractLattice attribute) (alhambra.grid.AbstractLatticeSupportingScadnano attribute) (alhambra.grid.Lattice property) (alhambra.grid.LatticeSupportingScadnano attribute) (alhambra.grid.ScadnanoLattice attribute) Seed (class in alhambra.seeds) seed_factory (in module alhambra.seeds) seed_offset (alhambra.grid.AbstractLattice attribute) seed_position (alhambra.grid.ScadnanoLattice attribute) SeedFactory (class in alhambra.seeds) seeds (alhambra.TileSet attribute) (alhambra.tilesets.TileSet attribute) SeedSupportingScadnano (class in alhambra.seeds) SELOGGER (in module alhambra._tilesets_dx) sensitivity_classes() (in module alhambra.sensitivitynew) senspairs() (in module alhambra.sensitivity) seq (alhambra.glues.DXGlue property) Seq (class in alhambra.seq) seq_str (alhambra.seq.Seq attribute) sequence (alhambra.glues.SSGlue property) (alhambra.seq.InvalidSequence attribute) (alhambra.tiles.BaseSSTile property) (alhambra.tiles.BaseSSTSingleWithExtensions property) sequences (alhambra.seeds.DXAdapter attribute) Serializable (class in alhambra.classes) set_edge() (alhambra.Tile method) (alhambra.tiles.BaseSSTile method) (alhambra.tiles.Tile method) SetSet (class in alhambra.sensitivitynew) setup_multi() (in module alhambra.util) sfake (alhambra.fastreduceD.FTile attribute) (alhambra.fastreduceD.FTilesArray attribute) SingleTile (class in alhambra.tiles) slowseqs() (alhambra.endreorder.EndSystemFseq method) SomeTile (in module alhambra.tiles) SSGlue (class in alhambra.glues) SST10 (class in alhambra.tiles) SST10_5S (class in alhambra.tiles) SST11 (class in alhambra.tiles) SST11_5S (class in alhambra.tiles) sst_10_11_hofromxy() (in module alhambra.grid) SSTLattice (class in alhambra.grid) stickydesign_create_dx_glue_sequences() (in module alhambra._tilesets_dx) stiles (alhambra.fastreduceD.FTileList attribute) stoic (alhambra.Tile attribute) (alhambra.tiles.Tile attribute) structure (alhambra.fastreduceD.FTile attribute) (alhambra.fastreduceD.FTilesArray attribute) (alhambra.Tile property) (alhambra.tiles.Tile property) summary() (alhambra.TileSet method) (alhambra.tilesets.TileSet method) SupportsGuards (class in alhambra.tiles) T T (in module alhambra.classes) (in module alhambra.glues) (in module alhambra.seeds) (in module alhambra.tiles) (in module alhambra.tilesets) T_NMI (in module alhambra.classes) TAU (in module alhambra.fastreduce) (in module alhambra.fastreduceD) temperature (alhambra.tilesets.GrowFullGlues attribute) (alhambra.tilesets.GrowOrthogonalGlues attribute) Text (class in alhambra.drawing) threshold (alhambra.tilesets.GrowFullGlues attribute) Tile (class in alhambra) (class in alhambra.tiles) tile_factory (in module alhambra.tiles) tilebase (alhambra.seeds.DXAdapter attribute) TileFactory (class in alhambra.tiles) tilelist (alhambra.fastreduceD._FastTileSet attribute) TileList (class in alhambra) (class in alhambra.tiles) tilemerge() (in module alhambra.fastreduce) (in module alhambra.fastreduceD) TileMergeSpec (class in alhambra.util) tilenames (alhambra.grid.AbstractLattice property) tiles (alhambra.TileSet attribute) (alhambra.tilesets.TileSet attribute) TileSet (class in alhambra) (class in alhambra.tilesets) tileset_to_nuad_design() (in module alhambra.nuad) TileSupportingScadnano (class in alhambra.tiles) TileWithUse (class in alhambra.fastreduceD) time_string() (in module alhambra.anneal) TMap (in module alhambra.fastreduceD) to_bytes() (alhambra.drawing.Drawing method) to_dict() (alhambra.flatish.FlatishHSeed9 method) (alhambra.flatish.FlatishVSeed9 method) (alhambra.Glue method) (alhambra.glues.Glue method) (alhambra.glues.SSGlue method) (alhambra.seeds.DiagonalSESeed method) (alhambra.seeds.DXAdapter method) (alhambra.seeds.DXOrigamiSeed method) (alhambra.seeds.Seed method) (alhambra.Tile method) (alhambra.tiles.BaseSSTile method) (alhambra.tiles.BaseSSTSingleWithExtensions method) (alhambra.tiles.DAOETile method) (alhambra.tiles.Tile method) (alhambra.TileSet method) (alhambra.tilesets.TileSet method) to_endarrays() (alhambra.GlueList method) (alhambra.glues.GlueList method) to_et() (alhambra.drawing.Drawing method) to_file() (alhambra.TileSet method) (alhambra.tilesets.TileSet method) to_json() (alhambra.classes.Serializable method) to_rgrow() (alhambra.TileSet method) (alhambra.tilesets.TileSet method) to_rgrow_dict() (alhambra.TileSet method) (alhambra.tilesets.TileSet method) to_scadnano() (alhambra.flatish.FlatishHDupleTile10_E method) (alhambra.flatish.FlatishHDupleTile9_E method) (alhambra.flatish.FlatishVDupleTile10_E2 method) (alhambra.flatish.FlatishVDupleTile9_E2 method) (alhambra.grid.AbstractLatticeSupportingScadnano method) (alhambra.grid.LatticeSupportingScadnano method) (alhambra.seeds.SeedSupportingScadnano method) (alhambra.tiles.BaseSSTSingle method) (alhambra.tiles.TileSupportingScadnano method) (alhambra.TileSet method) (alhambra.tilesets.TileSet method) to_scadnano_lattice() (alhambra.grid.AbstractLatticeSupportingScadnano method) (alhambra.grid.LatticeSupportingScadnano method) (alhambra.grid.ScadnanoLattice method) (alhambra.grid.SSTLattice method) to_string() (alhambra.drawing.Drawing method) to_toml() (alhambra.classes.Serializable method) to_xgrow() (alhambra.flatish.FlatishHSeed9 method) (alhambra.flatish.FlatishVSeed9 method) (alhambra.seeds.DiagonalSESeed method) (alhambra.seeds.DXOrigamiSeed method) (alhambra.seeds.Seed method) (alhambra.Tile method) (alhambra.tiles.HDupleTile method) (alhambra.tiles.Tile method) (alhambra.tiles.VDupleTile method) (alhambra.TileSet method) (alhambra.tilesets.TileSet method) to_xml() (alhambra.drawing.Drawing method) (alhambra.drawing.DrawingElement method) (alhambra.drawing.Group method) (alhambra.drawing.Rectangle method) (alhambra.drawing.Text method) (alhambra.drawing.Use method) (alhambra.drawing.XMLElement method) to_yaml() (alhambra.classes.Serializable method) togluemergespec() (alhambra.fastreduce._FastTileSet method) (alhambra.fastreduceD._FastTileSet method) TS (in module alhambra.classes) type (alhambra.Glue property) (alhambra.glues.Glue property) types (alhambra.glues.GlueFactory attribute) (alhambra.grid.LatticeFactory attribute) (alhambra.seeds.SeedFactory attribute) (alhambra.tiles.TileFactory attribute) U U_INPUT (in module alhambra.fastreduce) U_OUTPUT (in module alhambra.fastreduce) U_UNUSED (in module alhambra.fastreduce) uB (in module alhambra.fastreduce) (in module alhambra.fastreduceD) uI (in module alhambra.fastreduce) (in module alhambra.fastreduceD) uN (in module alhambra.fastreduce) (in module alhambra.fastreduceD) UNSET (alhambra.glues.Use attribute) UNUSED (alhambra.glues.Use attribute) uO (in module alhambra.fastreduce) (in module alhambra.fastreduceD) uP (in module alhambra.fastreduce) (in module alhambra.fastreduceD) update() (alhambra.classes.UpdateListD method) (alhambra.Glue method) (alhambra.glues.Glue method) (alhambra.glues.SSGlue method) (alhambra.util.ProgressLogger method) update_glues() (alhambra.Tile method) (alhambra.tiles.Tile method) update_glues_and_list() (alhambra.Tile method) (alhambra.tiles.Tile method) update_nuad_design() (in module alhambra.nuad) UpdateListD (class in alhambra.classes) use (alhambra.fastreduceD.FTile attribute) (alhambra.fastreduceD.FTilesArray attribute) (alhambra.fastreduceD.TileWithUse property) (alhambra.Glue attribute) (alhambra.glues.Glue attribute) (alhambra.Tile property) (alhambra.tiles.Tile property) Use (class in alhambra.drawing) (class in alhambra.glues) use_adapters (alhambra.seeds.DXOrigamiSeed attribute) used (alhambra.fastreduceD.FTile attribute) (alhambra.fastreduceD.FTilesArray attribute) usedict (in module alhambra.fastreduceD) uses (alhambra.Tile attribute) (alhambra.tiles.Tile attribute) UseView (class in alhambra.tiles) uU (in module alhambra.fastreduceD) V value1 (alhambra.seq.MergeConflictError attribute) value2 (alhambra.seq.MergeConflictError attribute) VDupleTile (class in alhambra.tiles) viewBox (alhambra.drawing.Drawing attribute) VSEL (in module alhambra.fastreduce) (in module alhambra.fastreduceD) vtiles (alhambra.fastreduceD.FTileList attribute) W W (alhambra.tiles.D attribute) wc() (in module alhambra.endreorder) wcd (in module alhambra.endreorder) width (alhambra.drawing.Drawing attribute) X xgname (alhambra.Tile property) (alhambra.tiles.Tile property) xgrow_edges() (alhambra.seeds.DXAdapter method) XgrowGlueOpts (class in alhambra.tilesets) XMLElement (class in alhambra.drawing)