Index

A

add_nucleotide() (base.Strand method) add_strand() (base.System method) add_strands() (base.System method)

angle_sense() (in module origami_utils) append() (base.Strand method) array_index() (in module origami_utils)

B

base (module)

base_to_vbase() (origami_utils.Origami method) bring_in_box_nucleotides() (base.Strand method)

C

check_branch_migration_strict() (origami_utils.Origami method) cm_pos (base.Nucleotide attribute) (base.Strand attribute) compute_vh_midpoints() (origami_utils.Origami method) contains_overlaps() (base.System method)

copy() (base.Nucleotide method) (base.Strand method) (base.System method) corrug_angle() (origami_utils.Origami method) corrugation() (origami_utils.Origami method)

D

dihedral_angle_sense() (in module origami_utils)

distance() (base.Nucleotide method)

E

E_kin (base.System attribute)

E_pot (base.System attribute) E_tot (base.System attribute)

G

generate() (generators.StrandGenerator method) generators (module) get_1d_vecs() (origami_utils.Origami method) get_3d_twist() (origami_utils.Origami method) get_3d_vecs() (origami_utils.Origami method) get_alignment() (origami_utils.Origami method) get_arm_vec() (origami_utils.Origami method) get_av_helix_axis() (origami_utils.Origami method) get_backback_midpoint() (origami_utils.Origami method) get_backback_vec() (origami_utils.Origami method) get_base() (base.Nucleotide method) get_base_spline() (in module origami_utils) get_bb_midpoint() (in module origami_utils) (origami_utils.Origami method) get_bb_vec() (origami_utils.Origami method) get_bpwise_weave() (origami_utils.Origami method) get_cad2cudadna() (origami_utils.Origami method) get_com() (origami_utils.Origami method) get_corners() (origami_utils.Origami method) get_flat_nucs() (origami_utils.Origami method) get_flat_units() (origami_utils.Origami method) get_h_bond_list() (origami_utils.Origami method) get_h_bond_list_output_bonds() (origami_utils.Origami method) get_hj_alignment() (origami_utils.Origami method) get_holliday_junctions() (origami_utils.Origami method) get_junction_normal() (origami_utils.Origami method) get_junction_normal2() (origami_utils.Origami method)

get_local_twist() (origami_utils.Origami method) get_n_bp() (origami_utils.Origami method) get_n_nicks() (origami_utils.Origami method) get_nearest_native_bonded() (origami_utils.Origami method) get_nicks() (origami_utils.Origami method) get_nucleotide() (in module origami_utils) get_nucleotide_list() (base.System method) get_nucleotides() (origami_utils.Origami method) get_plane_vecs() (origami_utils.Origami method) get_pos_back_rel() (base.Nucleotide method) get_pos_midpoint() (in module origami_utils) get_principal_axes() (origami_utils.Origami method) get_radius() (origami_utils.Origami method) get_reduced() (base.System method) get_rise() (origami_utils.Origami method) get_sayar_twist() (in module origami_utils) get_sayar_writhe() (in module origami_utils) get_scaffold_index() (in module origami_utils) get_sequences() (base.System method) get_slice() (base.Strand method) get_system() (readers.LorenzoReader method) get_unique_seq() (base.System method) get_vh_midpoints() (origami_utils.Origami method) get_vh_spline() (origami_utils.Origami method) get_vhelix_ds_length() (origami_utils.Origami method) get_vhelix_neighbours() (origami_utils.Origami method) get_vhelix_vis() (in module origami_utils) get_weave() (origami_utils.Origami method)

H

has_full_hbond() (origami_utils.Origami method)

I

index (base.Nucleotide attribute) (base.Strand attribute) intra_helix_autocorr() (origami_utils.Origami method)

is_crossover() (origami_utils.Origami method) is_junction() (origami_utils.Origami method) is_nicked() (origami_utils.Origami method) is_strand_end() (origami_utils.Origami method)

J

join() (base.System method)

L

LorenzoReader (class in readers)

M

make_circular() (base.Strand method) make_noncircular() (base.Strand method) map_base_to_vbase() (origami_utils.Origami method)

map_nucleotides_to_strands() (base.System method) min_distance() (in module origami_utils) (origami_utils.Origami method)

N

N (base.Strand attribute) (base.System attribute)

N_strands (base.System attribute) norm() (in module origami_utils) Nucleotide (class in base)

O

old_get_corrug_weave() (origami_utils.Origami method) open_arrow_debug_file() (in module origami_utils) open_box_debug_file() (in module origami_utils)

Origami (class in origami_utils) origami_utils (module) overlaps_with() (base.Strand method)

P

parse_scanfile() (in module origami_utils) parse_vh_data() (in module origami_utils) parse_vh_edge() (origami_utils.Origami method) parse_vhelix_extent_file() (origami_utils.Origami method) pos_back (base.Nucleotide attribute)

pos_base (base.Nucleotide attribute) pos_stack (base.Nucleotide attribute) prepare_principal_axes_calc() (origami_utils.Origami method) print_arrow_debug_line() (in module origami_utils) print_box_debug_line() (in module origami_utils) print_lorenzo_output() (base.System method)

R

readers (module) rotate() (base.Nucleotide method) (base.Strand method) (base.System method)

S

sequence (base.Strand attribute) set_cm_pos() (base.Strand method) set_sequence() (base.Strand method) set_visibility() (base.System method)

square_contains_exactly_one_nucleotide() (origami_utils.Origami method) Strand (class in base) StrandGenerator (class in generators) System (class in base)

T

translate() (base.Nucleotide method) (base.Strand method) (base.System method)

U

update_system() (origami_utils.Origami method)

V

vb2nuci() (origami_utils.Origami method) vb2vhelix_nucid() (origami_utils.Origami method)

vbase_to_base() (origami_utils.Origami method) vecs2spline() (in module origami_utils)