Index

A

accept_symbol (in module pyfurnace.design.core.symbols) add() (pyfurnace.design.core.strand.StrandsBlock method) all_pk_symbols (in module pyfurnace.design.core.symbols)

AmbiguosStructure annealing_temp() (in module pyfurnace.prepare.utils) Aptamer (class in pyfurnace.design.motifs.aptamers) auto_design_primers() (in module pyfurnace.prepare.utils)

B

base_pair_difference() (in module pyfurnace.design.core.symbols) base_pair_distance() (in module pyfurnace.design.core.symbols) base_pairing (in module pyfurnace.design.core.symbols) Biotin() (in module pyfurnace.design.motifs.aptamers)

bp_symbols (in module pyfurnace.design.core.symbols) BranchedDimer (class in pyfurnace.design.motifs.kissing_loops) BranchedKissingLoop (class in pyfurnace.design.motifs.kissing_loops) Broccoli() (in module pyfurnace.design.motifs.aptamers)

C

calculate_gc() (in module pyfurnace.prepare.utils) check_dimer() (in module pyfurnace.prepare.utils) complement() (in module pyfurnace.design.core.symbols) complementary_pk_index() (pyfurnace.design.motifs.kissing_loops.KissingLoop method)

convert_angles_to_dt() (in module pyfurnace.design.utils.origami_lib) coords (pyfurnace.design.core.strand.Strand property) copy() (pyfurnace.design.core.strand.Strand method) create_aptamer() (in module pyfurnace.design.motifs.aptamers)

D

db_pairs (in module pyfurnace.design.core.symbols) direction (pyfurnace.design.core.strand.Strand property) directionality (pyfurnace.design.core.strand.Strand property) directions (pyfurnace.design.core.strand.Strand property) dot_bracket_to_pair_map() (in module pyfurnace.design.core.symbols)

dot_bracket_to_stacks() (in module pyfurnace.design.core.symbols) dot_bracket_to_tree() (in module pyfurnace.design.core.symbols) Dovetail (class in pyfurnace.design.motifs.dovetail) down_cross (pyfurnace.design.motifs.dovetail.Dovetail property) draw() (pyfurnace.design.core.strand.Strand method)

E

end (pyfurnace.design.core.strand.Strand property) end_direction (pyfurnace.design.core.strand.Strand property)

energy (pyfurnace.design.motifs.kissing_loops.KissingLoop property) energy_tolerance (pyfurnace.design.motifs.kissing_loops.KissingLoop property) extend() (pyfurnace.design.core.strand.Strand method)

F

flip() (pyfurnace.design.core.strand.Strand method) folding_barriers() (in module pyfurnace.design.core.symbols)

from_json() (pyfurnace.design.core.strand.Strand class method) from_json_file() (pyfurnace.design.core.strand.Strand class method)

G

gc_content() (in module pyfurnace.design.core.symbols) generate_road() (in module pyfurnace.generate.road) get_base_at_pos() (pyfurnace.design.core.strand.Strand method) get_char_at_pos() (pyfurnace.design.core.strand.Strand method)

get_kissing_sequence() (pyfurnace.design.motifs.kissing_loops.BranchedKissingLoop method) (pyfurnace.design.motifs.kissing_loops.KissingLoop method) (pyfurnace.design.motifs.kissing_loops.KissingLoop180 method) get_position_map() (pyfurnace.design.core.strand.Strand method)

H

hamming_distance() (in module pyfurnace.design.core.symbols)

horiz_flip (in module pyfurnace.design.core.symbols)

I

insert() (pyfurnace.design.core.strand.Strand method) invert() (pyfurnace.design.core.strand.Strand method) ipython_clickable_txt() (in module pyfurnace.design.utils.origami_lib)

ipython_display_3d() (in module pyfurnace.design.utils.origami_lib) ipython_display_txt() (in module pyfurnace.design.utils.origami_lib) Ispinach() (in module pyfurnace.design.motifs.aptamers) iupac_code (in module pyfurnace.design.core.symbols)

J

join() (pyfurnace.design.core.strand.Strand method)

join_strands() (pyfurnace.design.core.strand.Strand static method)

K

KissingDimer (class in pyfurnace.design.motifs.kissing_loops) KissingDimer120 (class in pyfurnace.design.motifs.kissing_loops)

KissingLoop (class in pyfurnace.design.motifs.kissing_loops) KissingLoop120 (class in pyfurnace.design.motifs.kissing_loops) KissingLoop180 (class in pyfurnace.design.motifs.kissing_loops)

L

L7Ae() (in module pyfurnace.design.motifs.aptamers) length (pyfurnace.design.motifs.stem.Stem property)

log_norm() (in module pyfurnace.design.utils.origami_lib) Loop (class in pyfurnace.design.motifs.loops)

M

make_tm_calculator() (in module pyfurnace.prepare.utils) MalachiteGreen() (in module pyfurnace.design.motifs.aptamers) MalachiteGreenShort() (in module pyfurnace.design.motifs.aptamers) Mango() (in module pyfurnace.design.motifs.aptamers) max_pos (pyfurnace.design.core.strand.Strand property) min_pos (pyfurnace.design.core.strand.Strand property) minimal_dimensions (pyfurnace.design.core.strand.Strand property) module pyfurnace.design.core.strand pyfurnace.design.core.symbols pyfurnace.design.motifs.aptamers pyfurnace.design.motifs.dovetail pyfurnace.design.motifs.kissing_loops pyfurnace.design.motifs.loops pyfurnace.design.motifs.stem pyfurnace.design.utils.motif_lib pyfurnace.design.utils.origami_lib pyfurnace.generate.road pyfurnace.prepare.oxdna_sim pyfurnace.prepare.utils

MotifStructureError MS2() (in module pyfurnace.design.motifs.aptamers) mutate_nucleotide() (in module pyfurnace.design.core.symbols)

N

next_pos (pyfurnace.design.core.strand.Strand property) nucl_to_none (in module pyfurnace.design.core.symbols)

nucl_to_pair (in module pyfurnace.design.core.symbols) nucleotides (in module pyfurnace.design.core.symbols)

O

only_nucl (in module pyfurnace.design.core.symbols)

OrangeBroccoli() (in module pyfurnace.design.motifs.aptamers) oxdna_simulations() (in module pyfurnace.prepare.oxdna_sim)

P

pair_db_sym (in module pyfurnace.design.core.symbols) pair_map_to_dot_bracket() (in module pyfurnace.design.core.symbols) pair_nucleotide() (in module pyfurnace.design.core.symbols) parallel_road() (in module pyfurnace.generate.road) Pepper() (in module pyfurnace.design.motifs.aptamers) PIP3() (in module pyfurnace.design.motifs.aptamers) PIP3_mut1() (in module pyfurnace.design.motifs.aptamers) PIP3_mut3() (in module pyfurnace.design.motifs.aptamers) PIP3_mut5() (in module pyfurnace.design.motifs.aptamers) pk_index (pyfurnace.design.motifs.kissing_loops.KissingLoop property) pop() (pyfurnace.design.core.strand.Strand method) positions (pyfurnace.design.core.strand.Strand property) PP7() (in module pyfurnace.design.motifs.aptamers) prec_pos (pyfurnace.design.core.strand.Strand property) pseudo_to_dot (in module pyfurnace.design.core.symbols) pyfurnace.design.core.strand module pyfurnace.design.core.symbols module

pyfurnace.design.motifs.aptamers module pyfurnace.design.motifs.dovetail module pyfurnace.design.motifs.kissing_loops module pyfurnace.design.motifs.loops module pyfurnace.design.motifs.stem module pyfurnace.design.utils.motif_lib module pyfurnace.design.utils.origami_lib module pyfurnace.generate.road module pyfurnace.prepare.oxdna_sim module pyfurnace.prepare.utils module

R

RedBroccoli() (in module pyfurnace.design.motifs.aptamers) remove() (pyfurnace.design.core.strand.StrandsBlock method) reverse() (pyfurnace.design.core.strand.Strand method)

reverse_complement() (in module pyfurnace.design.core.symbols) rotate_90 (in module pyfurnace.design.core.symbols) rotate_dot_bracket() (in module pyfurnace.design.core.symbols)

S

save_3d_model() (pyfurnace.design.core.strand.Strand method) save_json() (pyfurnace.design.core.strand.Strand method) seq_positions (pyfurnace.design.core.strand.Strand property) sequence (pyfurnace.design.core.strand.Strand property) sequence_list (pyfurnace.design.core.strand.Strand property) sequence_slice (pyfurnace.design.core.strand.Strand property) set_down_sequence() (pyfurnace.design.motifs.dovetail.Dovetail method) (pyfurnace.design.motifs.kissing_loops.BranchedDimer method) (pyfurnace.design.motifs.kissing_loops.KissingDimer method) (pyfurnace.design.motifs.kissing_loops.KissingDimer120 method) (pyfurnace.design.motifs.stem.Stem method) set_sequence() (pyfurnace.design.motifs.kissing_loops.KissingLoop method) (pyfurnace.design.motifs.loops.TetraLoop method) set_strong_bases() (pyfurnace.design.motifs.stem.Stem method) set_up_sequence() (pyfurnace.design.motifs.dovetail.Dovetail method) (pyfurnace.design.motifs.kissing_loops.BranchedDimer method) (pyfurnace.design.motifs.kissing_loops.KissingDimer method) (pyfurnace.design.motifs.kissing_loops.KissingDimer120 method) (pyfurnace.design.motifs.stem.Stem method)

shift() (pyfurnace.design.core.strand.Strand method) simple_origami() (in module pyfurnace.design.utils.origami_lib) single_strand() (in module pyfurnace.design.utils.motif_lib) start (pyfurnace.design.core.strand.Strand property) start_end_stem() (in module pyfurnace.design.utils.motif_lib) Stem (class in pyfurnace.design.motifs.stem) stem_cap_link() (in module pyfurnace.design.utils.motif_lib) Strand (class in pyfurnace.design.core.strand) strand (pyfurnace.design.core.strand.Strand property) strands_block (pyfurnace.design.core.strand.Strand property) StrandsBlock (class in pyfurnace.design.core.strand) Streptavidin() (in module pyfurnace.design.motifs.aptamers) symb_to_none (in module pyfurnace.design.core.symbols) symb_to_road (in module pyfurnace.design.core.symbols)

T

T7_PROMOTER (in module pyfurnace.design.core.symbols) TAR_TAT() (in module pyfurnace.design.motifs.aptamers) template_2_helix() (in module pyfurnace.design.utils.origami_lib) template_3_arms_droplet() (in module pyfurnace.design.utils.origami_lib) template_4_arms_droplet() (in module pyfurnace.design.utils.origami_lib) template_pentagon_tile() (in module pyfurnace.design.utils.origami_lib) template_rectangle_10H_3X() (in module pyfurnace.design.utils.origami_lib) template_rna_filament() (in module pyfurnace.design.utils.origami_lib)

template_rna_filament_ispinach() (in module pyfurnace.design.utils.origami_lib) TetraLoop (class in pyfurnace.design.motifs.loops) Thrombin_exosite1() (in module pyfurnace.design.motifs.aptamers) Thrombin_exosite2() (in module pyfurnace.design.motifs.aptamers) to_json() (pyfurnace.design.core.strand.Strand method) transform() (pyfurnace.design.core.strand.Strand method) (pyfurnace.design.core.strand.StrandsBlock method) tree_to_dot_bracket() (in module pyfurnace.design.core.symbols)

U

up_cross (pyfurnace.design.motifs.dovetail.Dovetail property)

update() (pyfurnace.design.core.strand.StrandsBlock method) Utils (class in pyfurnace.design.utils.motif_lib)

V

verti_flip (in module pyfurnace.design.core.symbols)

vertical_double_link() (in module pyfurnace.design.utils.motif_lib) vertical_link() (in module pyfurnace.design.utils.motif_lib)

W

wobble_insert (pyfurnace.design.motifs.stem.Stem property)

wobble_interval (pyfurnace.design.motifs.stem.Stem property) wobble_tolerance (pyfurnace.design.motifs.stem.Stem property)