scadnano
dev
scadnano
Index
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Index
A
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B
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C
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D
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E
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F
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G
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H
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I
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L
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M
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N
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O
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P
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R
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S
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T
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U
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V
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W
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X
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Y
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Z
A
add_deletion() (scadnano.Design method)
add_full_crossover() (scadnano.Design method)
add_half_crossover() (scadnano.Design method)
add_helix() (scadnano.Design method)
add_insertion() (scadnano.Design method)
add_nick() (scadnano.Design method)
add_strand() (scadnano.Design method)
allowed_bases (scadnano.ModificationInternal attribute)
angle_distance() (in module scadnano)
angle_from_helix_to_helix() (in module scadnano)
append_domain() (scadnano.Design method)
as_circular() (scadnano.StrandBuilder method)
as_scaffold() (scadnano.StrandBuilder method)
assign_dna() (scadnano.Design method)
assign_dna_complement_from() (scadnano.Strand method)
assign_m13_to_scaffold() (scadnano.Design method)
automatically_assign_color (scadnano.Design attribute)
average_angle() (in module scadnano)
B
b (scadnano.Color attribute)
backbone_angle_at_offset() (scadnano.Helix method)
base_pairs() (scadnano.Design method)
bases_complementary() (in module scadnano)
bases_per_turn (scadnano.Geometry attribute)
bound_domains() (scadnano.Strand method)
C
calculate_major_ticks() (scadnano.Helix method)
calculate_position() (scadnano.Helix method)
circular (scadnano.Strand attribute)
Color (class in scadnano)
color (scadnano.Domain attribute)
(scadnano.Extension attribute)
(scadnano.Loopout attribute)
(scadnano.Strand attribute)
ColorCycler (class in scadnano)
colors (scadnano.ColorCycler property)
compute_overlap() (scadnano.Domain method)
compute_relaxed_roll_delta() (scadnano.Helix method)
connector_length (scadnano.Modification attribute)
contains_offset() (scadnano.Domain method)
create() (in module origami_rectangle)
cross() (scadnano.StrandBuilder method)
crossover_addresses() (scadnano.Helix method)
D
default_export_name() (scadnano.Strand method)
default_scadnano_file_extension (in module scadnano)
default_scaffold_color (in module scadnano)
default_strand_color (in module scadnano)
deletions (scadnano.Domain attribute)
Design (class in scadnano)
display_angle (scadnano.Extension attribute)
display_length (scadnano.Extension attribute)
display_text (scadnano.Modification attribute)
(scadnano.Modification3Prime attribute)
(scadnano.Modification5Prime attribute)
DNA_base_wildcard (in module scadnano)
dna_index_start_domain() (scadnano.Strand method)
dna_length() (scadnano.Domain method)
(scadnano.Extension method)
(scadnano.Loopout method)
(scadnano.Strand method)
dna_length_in() (scadnano.Domain method)
dna_sequence (scadnano.Domain attribute)
(scadnano.Extension attribute)
(scadnano.Loopout attribute)
(scadnano.Strand property)
dna_sequence_delimited() (scadnano.Strand method)
dna_sequence_in() (scadnano.Domain method)
Domain (class in scadnano)
domain_at() (scadnano.Design method)
domain_offset_to_strand_dna_idx() (scadnano.Domain method)
domains (scadnano.Helix property)
(scadnano.Strand attribute)
domains_at() (scadnano.Design method)
draw_strand() (scadnano.Design method)
E
end (scadnano.Domain attribute)
even (in module origami_rectangle)
(origami_rectangle.NickPattern attribute)
Extension (class in scadnano)
extension_3p() (scadnano.StrandBuilder method)
extension_5p() (scadnano.StrandBuilder method)
F
first_bound_domain() (scadnano.Strand method)
first_domain() (scadnano.Strand method)
five_or_three_prime (scadnano.StrandOrder attribute)
five_prime (scadnano.ModificationType attribute)
(scadnano.StrandOrder attribute)
forward (scadnano.Domain attribute)
from_cadnano_v2() (scadnano.Design static method)
from_scadnano_file() (scadnano.Design static method)
from_scadnano_json_map() (scadnano.Design static method)
from_scadnano_json_str() (scadnano.Design static method)
G
g (scadnano.Color attribute)
Geometry (class in scadnano)
geometry (scadnano.Design attribute)
get_seq_start_idx() (scadnano.Domain method)
(scadnano.Loopout method)
Grid (class in scadnano)
grid (scadnano.Design property)
(scadnano.HelixGroup attribute)
grid_position (scadnano.Helix attribute)
grid_position_to_position() (in module scadnano)
group (scadnano.Helix attribute)
groups (scadnano.Design attribute)
H
helices (scadnano.Design attribute)
helices_idxs_in_group() (scadnano.Design method)
helices_view_order (scadnano.Design property)
(scadnano.HelixGroup attribute)
helices_view_order_inverse() (scadnano.HelixGroup method)
Helix (class in scadnano)
helix (scadnano.Domain attribute)
helix_radius (scadnano.Geometry attribute)
HelixGroup (class in scadnano)
hex (scadnano.Grid attribute)
hex_string (scadnano.Color attribute)
honeycomb (scadnano.Grid attribute)
I
idx (scadnano.Helix attribute)
IllegalDesignError
inline_deletions_insertions() (scadnano.Design method)
insert_domain() (scadnano.Design method)
insertion_offsets() (scadnano.Domain method)
insertions (scadnano.Domain attribute)
inter_helix_gap (scadnano.Geometry attribute)
internal (scadnano.ModificationType attribute)
is_3p_domain() (scadnano.Domain method)
is_5p_domain() (scadnano.Domain method)
is_extreme_domain() (scadnano.Domain method)
is_scaffold (scadnano.Strand attribute)
L
label (scadnano.Domain attribute)
(scadnano.Extension attribute)
(scadnano.Loopout attribute)
(scadnano.Strand attribute)
last_bound_domain() (scadnano.Strand method)
last_domain() (scadnano.Strand method)
length (scadnano.Loopout attribute)
ligate() (scadnano.Design method)
Loopout (class in scadnano)
loopout() (scadnano.StrandBuilder method)
M
m13() (in module scadnano)
M13Variant (class in scadnano)
major_tick_distance (scadnano.Helix attribute)
major_tick_periodic_distances (scadnano.Helix attribute)
major_tick_start (scadnano.Helix attribute)
major_ticks (scadnano.Helix attribute)
max_offset (scadnano.Helix attribute)
min_offset (scadnano.Helix attribute)
min_wells_per_plate() (scadnano.PlateType method)
minimum_strain_angle() (in module scadnano)
minor_groove_angle (scadnano.Geometry attribute)
Modification (class in scadnano)
Modification3Prime (class in scadnano)
Modification5Prime (class in scadnano)
modification_3p (scadnano.Strand attribute)
modification_5p (scadnano.Strand attribute)
ModificationInternal (class in scadnano)
modifications() (scadnano.Design method)
modifications_int (scadnano.Strand attribute)
ModificationType (class in scadnano)
module
origami_rectangle
scadnano
move() (scadnano.StrandBuilder method)
move_strand_offsets() (scadnano.Design method)
move_strands_on_helices() (scadnano.Design method)
N
name (scadnano.Domain attribute)
(scadnano.Extension attribute)
(scadnano.Loopout attribute)
(scadnano.Strand attribute)
NickPattern (class in origami_rectangle)
no_modifications_version() (scadnano.Strand method)
none (scadnano.Grid attribute)
num_bases (scadnano.Extension attribute)
num_wells_per_plate() (scadnano.PlateType method)
O
odd (in module origami_rectangle)
(origami_rectangle.NickPattern attribute)
offset_3p() (scadnano.Domain method)
(scadnano.Strand method)
offset_5p() (scadnano.Domain method)
(scadnano.Strand method)
origami_rectangle
module
overlaps() (scadnano.Domain method)
(scadnano.Strand method)
overlaps_illegally() (scadnano.Domain method)
P
p7249 (scadnano.M13Variant attribute)
p7560 (scadnano.M13Variant attribute)
p8064 (scadnano.M13Variant attribute)
p8634 (scadnano.M13Variant attribute)
pitch (scadnano.HelixGroup attribute)
pitch_of_helix() (scadnano.Design method)
plate (scadnano.VendorFields attribute)
plate_maps() (scadnano.Design method)
plate_name (scadnano.PlateMap attribute)
plate_type (scadnano.PlateMap attribute)
PlateMap (class in scadnano)
PlateType (class in scadnano)
position (scadnano.Helix attribute)
(scadnano.HelixGroup attribute)
Position3D (class in scadnano)
purification (scadnano.VendorFields attribute)
R
r (scadnano.Color attribute)
relax_helix_rolls() (scadnano.Design method)
relax_roll() (scadnano.Helix method)
remove_domain() (scadnano.Design method)
remove_modification_3p() (scadnano.Strand method)
remove_modification_5p() (scadnano.Strand method)
remove_modification_internal() (scadnano.Strand method)
remove_strand() (scadnano.Design method)
reverse() (scadnano.Strand method)
reverse_all() (scadnano.Design method)
reverse_complementary() (in module scadnano)
rise_per_base_pair (scadnano.Geometry attribute)
roll (scadnano.Helix attribute)
(scadnano.HelixGroup attribute)
roll_of_helix() (scadnano.Design method)
rotate_domains() (scadnano.Strand method)
S
scadnano
module
scaffold (scadnano.Design property)
scale (scadnano.VendorFields attribute)
set_circular() (scadnano.Strand method)
set_color() (scadnano.Strand method)
set_dna_sequence() (scadnano.Strand method)
set_domains() (scadnano.Strand method)
set_end() (scadnano.Design method)
set_grid() (scadnano.Design method)
set_helices_view_order() (scadnano.Design method)
set_label() (scadnano.Domain method)
(scadnano.Extension method)
(scadnano.Loopout method)
(scadnano.Strand method)
set_linear() (scadnano.Strand method)
set_modification_3p() (scadnano.Strand method)
set_modification_5p() (scadnano.Strand method)
set_modification_internal() (scadnano.Strand method)
set_name() (scadnano.Domain method)
(scadnano.Extension method)
(scadnano.Loopout method)
(scadnano.Strand method)
set_scaffold() (scadnano.Strand method)
set_start() (scadnano.Design method)
square (scadnano.Grid attribute)
staggered (in module origami_rectangle)
(origami_rectangle.NickPattern attribute)
staggered_opposite (in module origami_rectangle)
(origami_rectangle.NickPattern attribute)
start (scadnano.Domain attribute)
Strand (class in scadnano)
strand() (scadnano.Design method)
(scadnano.Domain method)
(scadnano.Extension method)
(scadnano.Loopout method)
strand_order_key_function() (in module scadnano)
strand_with_name() (scadnano.Design method)
StrandBuilder (class in scadnano)
StrandError
StrandOrder (class in scadnano)
strands (scadnano.Design attribute)
strands_ending_on_helix() (scadnano.Design method)
strands_starting_on_helix() (scadnano.Design method)
sum_squared_angle_distances() (in module scadnano)
T
three_prime (scadnano.ModificationType attribute)
(scadnano.StrandOrder attribute)
to() (scadnano.StrandBuilder method)
to_cadnano_v2_json() (scadnano.Design method)
to_cadnano_v2_serializable() (scadnano.Design method)
to_idt_bulk_input_format() (scadnano.Design method)
to_json() (scadnano.Design method)
to_oxdna_format() (scadnano.Design method)
to_oxview_format() (scadnano.Design method)
to_oxview_json() (scadnano.Design method)
to_table() (scadnano.PlateMap method)
top_left_domain (scadnano.StrandOrder attribute)
U
update_to() (scadnano.StrandBuilder method)
V
vendor_code (scadnano.Modification attribute)
(scadnano.Modification3Prime attribute)
(scadnano.Modification5Prime attribute)
vendor_dna_sequence() (scadnano.Domain method)
(scadnano.Extension method)
(scadnano.Loopout method)
(scadnano.Strand method)
vendor_export_name() (scadnano.Strand method)
vendor_fields (scadnano.Strand attribute)
VendorFields (class in scadnano)
visual_length() (scadnano.Domain method)
W
wc() (in module scadnano)
well (scadnano.VendorFields attribute)
well_to_strand (scadnano.PlateMap attribute)
wells384 (scadnano.PlateType attribute)
wells96 (scadnano.PlateType attribute)
with_color() (scadnano.StrandBuilder method)
with_deletions() (scadnano.StrandBuilder method)
with_domain_color() (scadnano.StrandBuilder method)
with_domain_label() (scadnano.StrandBuilder method)
with_domain_name() (scadnano.StrandBuilder method)
with_domain_sequence() (scadnano.StrandBuilder method)
with_insertions() (scadnano.StrandBuilder method)
with_label() (scadnano.StrandBuilder method)
with_modification_3p() (scadnano.StrandBuilder method)
with_modification_5p() (scadnano.StrandBuilder method)
with_modification_internal() (scadnano.StrandBuilder method)
with_name() (scadnano.StrandBuilder method)
with_sequence() (scadnano.StrandBuilder method)
with_vendor_fields() (scadnano.StrandBuilder method)
write_cadnano_v2_file() (scadnano.Design method)
write_file_same_name_as_running_python_script() (in module scadnano)
write_idt_bulk_input_file() (scadnano.Design method)
write_idt_plate_excel_file() (scadnano.Design method)
write_oxdna_files() (scadnano.Design method)
write_oxview_file() (scadnano.Design method)
write_scadnano_file() (scadnano.Design method)
X
x (scadnano.Position3D attribute)
Y
y (scadnano.Position3D attribute)
yaw (scadnano.HelixGroup attribute)
yaw_of_helix() (scadnano.Design method)
Z
z (scadnano.Position3D attribute)
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