scadnano documentation

scadnano

The scadnano Python module is a library for describing synthetic DNA nanostructures (e.g., DNA origami). Installation instructions are at the GitHub repository.

The scadnano project is developed and maintained by the UC Davis Molecular Computing group. Note that cadnano is a separate project, developed and maintained by the Douglas lab at UCSF.

This module is used to write Python scripts creating files readable by scadnano, a web application useful for displaying and manually editing synthetic DNA nanostructures. The purpose of this module is to help automate some of the task of creating DNA designs, as well as making large-scale changes to them that are easier to describe programmatically than to do by hand in scadnano.

If you find scadnano useful in a scientific project, please cite its associated paper:

scadnano: A browser-based, scriptable tool for designing DNA nanostructures.

David Doty, Benjamin L Lee, and Tristan Stérin.

DNA 2020: Proceedings of the 26th International Conference on DNA Computing and Molecular Programming

[ paper | BibTeX ]

This document describes the API for the scadnano Python package, see the repository for additional documentation, such as installation instructions. There is separate documentation for the scadnano web interface.

This library uses typing hints from the Python typing library. (https://docs.python.org/3/library/typing.html) Each function and method indicate intended types of the parameters. However, due to Python’s design, these types are not enforced at runtime. It is suggested to use a static analysis tool such as that provided by an IDE such as PyCharm (https://www.jetbrains.com/pycharm/) to see warnings when the typing rules are violated. Such warnings probably indicate an erroneous usage.

Most of the classes in this module are Python dataclasses (https://docs.python.org/3/library/dataclasses.html) whose fields show up in the documentation. Their types are listed in parentheses after the name of the class; for example Color has int fields Color.r, Color.g, Color.b. In general it is safe to read these fields directly, but not to write to them directly. Setter methods (named set_<fieldname>) are provided for fields where it makes sense to set it to another value than it had originally. However, due to Python naming conventions for dataclass fields and property setters, it is not straightforward to enforce that the fields cannot be written, so the user must take care not to set them.

scadnano.default_scadnano_file_extension = 'sc'

Default filename extension when writing a scadnano file.

class scadnano.Color(r: Union[int, NoneType] = None, g: Union[int, NoneType] = None, b: Union[int, NoneType] = None, hex_string: dataclasses.InitVar = None)

Parameters:

• r (Optional[int]) –

• g (Optional[int]) –

• b (Optional[int]) –

• hex_string (InitVar) –

r: Optional[int] = None

Red component: 0-255.

Optional if Color.hex is given.

g: Optional[int] = None

Green component: 0-255.

Optional if Color.hex is given.

b: Optional[int] = None

Blue component: 0-255.

Optional if Color.hex is given.

hex_string: InitVar = None

Hex color preceded by # sign, e.g., “#ff0000” is red.

Optional if Color.r, Color.g, Color.b are all given.

class scadnano.ColorCycler

Calling next(color_cycler) on a ColorCycler named color_cycler returns a the next Color from a fixed size list, cycling after reaching the end of the list.

To choose new colors, set color_cycler.colors to a new list of Color’s.

property colors: List[Color]

The colors that are cycled through when calling next() on some ColorCycler.

scadnano.default_scaffold_color = Color(r=0, g=102, b=204)

Default color for scaffold strand(s).

scadnano.default_strand_color = Color(r=0, g=0, b=0)

Default color for non-scaffold strand(s).

class scadnano.Grid(value)

Represents default patterns for laying out helices in the side view. Each Grid except Grid.none has an interpretation of a “grid position”, which is a 2D integer coordinate (h, v). (scadnano also allows a 3rd coordinate (h, v, b) specifying a “base offset” at which to position the start of the Helix, which is not relevant for the side view but will eventually be supported to adjust the main view.)

square = 'square'

Square lattice. Increasing h moves right and increasing v moves down. (i.e., “computer screen coordinates” rather than Cartesian coordinates where positive y is up.)

hex = 'hex'

Hexagonal lattice. Uses the “odd-q horizontal layout” coordinate system described here: https://www.redblobgames.com/grids/hexagons/. Incrementing v moves down. Incrementing h moves down and to the right if h is even, and moves up and to the right if h is odd.

honeycomb = 'honeycomb'

Honeycomb lattice. This consists of all the hex lattice positions except where honeycomb lattice disallows grid positions (h, v) with v even and h a multiple of 3 or v odd and h = 1 + a multiple of 3.

However, we use the same convention as cadnano for encoding hex coordinates see misc/cadnano-format-specs/v2.txt. That convention is different from simply excluding coordinates from the hex lattice.

none = 'none'

No fixed grid.

scadnano.DNA_base_wildcard = '?'

Symbol to insert when a DNA sequence has been assigned to a strand through complementarity, but some regions of the strand are not bound to the strand that was just assigned. Also used in case the DNA sequence assigned to a strand is too short; the sequence is padded with DNA_base_wildcard to make its length the same as the length of the strand.

class scadnano.M13Variant(value)

Variants of M13mp18 viral genome. “Standard” variant is p7249. Other variants are longer.

p7249 = 'p7249'

“Standard” variant of M13mp18; 7249 bases long, available from, for example

https://www.tilibit.com/collections/scaffold-dna/products/single-stranded-scaffold-dna-type-p7249

https://www.neb.com/products/n4040-m13mp18-single-stranded-dna

http://www.bayoubiolabs.com/biochemicat/vectors/pUCM13/

p7560 = 'p7560'

Variant of M13mp18 that is 7560 bases long. Available from, for example

https://www.tilibit.com/collections/scaffold-dna/products/single-stranded-scaffold-dna-type-p7560

p8064 = 'p8064'

Variant of M13mp18 that is 8064 bases long. Available from, for example

https://www.tilibit.com/collections/scaffold-dna/products/single-stranded-scaffold-dna-type-p8064

scadnano.m13(rotation=5587, variant=M13Variant.p7249)

The M13mp18 DNA sequence (commonly called simply M13).

By default, starts from cyclic rotation 5587 (with 0-based indexing; commonly this is called rotation 5588, which assumes that indexing begins at 1), as defined in GenBank.

By default, returns the “standard” variant of consisting of 7249 bases, sold by companies such as Tilibit and New England Biolabs.

The actual M13 DNA strand itself is circular, so assigning this sequence to the scaffold Strand in a Design means that the “5’ end” of the scaffold Strand (which is a fiction since the actual circular DNA strand has no endpoint) will have the sequence starting at position 5587 starting at the displayed 5’ in scadnano, assigned until the displayed 3’ end. Assuming the displayed scaffold Strand has length \(n < 7249\), then a loopout of length \(7249 - n\) consisting of the undisplayed bases will be present in the actual DNA structure. For a more detailed discussion of why this particular rotation of M13 is chosen, see Supplementary Note S8 in [Folding DNA to create nanoscale shapes and patterns. Paul W. K. Rothemund, Nature 440:297-302 (2006)].

Parameters:

• rotation (int) – rotation of circular strand. Valid values are 0 through length-1.

• variant (M13Variant) – variant of M13 strand to use

Returns:

M13 strand sequence

Return type:

str

class scadnano.ModificationType(value)

Type of modification (5’, 3’, or internal).

five_prime = "5'"

5’ modification type

three_prime = "5'"

3’ modification type

internal = 'internal'

internal modification type

class scadnano.Modification(display_text, id='WARNING: no id assigned to modification', idt_text=None, connector_length=4)

Abstract case class of modifications (to DNA sequences, e.g., biotin or Cy3). Use concrete subclasses Modification3Prime, Modification5Prime, or ModificationInternal to instantiate.

If Modification.id is not specified, then Modification.idt_text is used as the unique ID. Each Modification.id must be unique. For example if you create a 5’ “modification” to represent 6 T bases: t6_5p = Modification5Prime(display_text='6T', idt_text='TTTTTT') (this is a useful hack for putting single-stranded extensions on strands until loopouts on the end of a strand are supported; see https://github.com/UC-Davis-molecular-computing/scadnano-python-package/issues/2), then this would clash with a similar 3’ modification without specifying unique IDs for them: t6_3p = Modification3Prime(display_text='6T', idt_text='TTTTTT') # ERROR.

In general it is recommended to create a single Modification object for each type of modification in the design. For example, if many strands have a 5’ biotin, then it is recommended to create a single Modification object and re-use it on each strand with a 5’ biotin:

biotin_5p = Modification5Prime(display_text='B', idt_text='/5Biosg/')
design.draw_strand(0, 0).move(8).with_modification_5p(biotin_5p)
design.draw_strand(1, 0).move(8).with_modification_5p(biotin_5p)

Parameters:

• display_text (str) –

• id (str) –

• idt_text (Optional[str]) –

• connector_length (int) –

display_text: str

Short text to display in the web interface as an “icon” visually representing the modification, e.g., 'B' for biotin or 'Cy3' for Cy3.

id: str = 'WARNING: no id assigned to modification'

Representation as a string; used to write in Strand json representation, while the full description of the modification is written under a global key in the Design. If not specified, but Modification.idt_text is specified, then it will be set equal to that.

idt_text: Optional[str] = None

IDT text string specifying this modification (e.g., ‘/5Biosg/’ for 5’ biotin). optional

connector_length: int = 4

Length of “connector” displayed in web interface.

Drawn like a carbon chain to offset the display of the modification vertically from the DNA strand. This field is useful for putting two nearby modifications at different heights so that their text does not overlap.

class scadnano.Modification5Prime(display_text, id='WARNING: no id assigned to modification', idt_text=None, connector_length=4)

5’ modification of DNA sequence, e.g., biotin or Cy3.

In general it is recommended to create a single Modification object for each type of modification in the design. For example, if many strands have a 5’ biotin, then it is recommended to create a single Modification object and re-use it on each strand with a 5’ biotin:

biotin_5p = Modification5Prime(display_text='B', idt_text='/5Biosg/')
design.draw_strand(0, 0).move(8).with_modification_5p(biotin_5p)
design.draw_strand(1, 0).move(8).with_modification_5p(biotin_5p)

Parameters:

• display_text (str) –

• id (str) –

• idt_text (Optional[str]) –

• connector_length (int) –

display_text: str

Short text to display in the web interface as an “icon” visually representing the modification, e.g., 'B' for biotin or 'Cy3' for Cy3.

class scadnano.Modification3Prime(display_text, id='WARNING: no id assigned to modification', idt_text=None, connector_length=4)

3’ modification of DNA sequence, e.g., biotin or Cy3.

In general it is recommended to create a single Modification object for each type of modification in the design. For example, if many strands have a 3’ biotin, then it is recommended to create a single Modification object and re-use it on each strand with a 3’ biotin:

biotin_3p = Modification3Prime(display_text='B', idt_text='/3Bio/')
design.draw_strand(0, 0).move(8).with_modification_3p(biotin_3p)
design.draw_strand(1, 0).move(8).with_modification_3p(biotin_3p)

Parameters:

• display_text (str) –

• id (str) –

• idt_text (Optional[str]) –

• connector_length (int) –

display_text: str

Short text to display in the web interface as an “icon” visually representing the modification, e.g., 'B' for biotin or 'Cy3' for Cy3.

class scadnano.ModificationInternal(display_text, id='WARNING: no id assigned to modification', idt_text=None, connector_length=4, allowed_bases=None)

Internal modification of DNA sequence, e.g., biotin or Cy3.

Parameters:

• display_text (str) –

• id (str) –

• idt_text (Optional[str]) –

• connector_length (int) –

• allowed_bases (Optional[AbstractSet[str]]) –

allowed_bases: Optional[AbstractSet[str]] = None

If None, then this is an internal modification that goes between bases. If instead it is a list of bases, then this is an internal modification that attaches to a base, and this lists the allowed bases for this internal modification to be placed at. For example, internal biotins for IDT must be at a T. If any base is allowed, it should be ['A','C','G','T'].

class scadnano.Position3D(x=0, y=0, z=0)

Position (x,y,z) in 3D space.

Parameters:

• x (float) –

• y (float) –

• z (float) –

x: float = 0

x-coordinate of position. Increasing x moves right in the side view and out of the screen in the main view.

y: float = 0

y-coordinate of position. Increasing y moves down in the side and main views, i.e., “screen coordinates”. (though this can be rotated to Cartesian coordinates, where y goes up, by selecting “invert y/z axes” in the View menu of scadnano.)

z: float = 0

z-coordinate of position. Increasing z moves right in the main view and into the screen in the side view.

clone()

Returns:

copy of this Position3D

Return type:

Position3D

class scadnano.HelixGroup(position=Position3D(x=0, y=0, z=0), pitch=0, roll=0, yaw=0, helices_view_order=None, grid=Grid.none)

Represents a set of properties to apply to a specific group of Helix’s in the Design.

A HelixGroup is useful for grouping together helices that should all be in parallel, as part of a design where different groups are not parallel. In particular, each HelixGroup can be given its own 3D position and pitch/yaw/roll orientation angles. Each HelixGroup does not actually contain its helices; they are associated through the field Helix.group, which is a string representing a key in the dict groups specified in the constructor for Design.

If there are HelixGroup’s explicitly specified, then the field Design.grid is ignored. Each HelixGroup has its own grid, and the fields Helix.position or Helix.grid_position are considered relative to the origin of that HelixGroup (i.e., the value HelixGroup.position). Although an individual Helix can have a non-zero Helix.roll (which is in addition to whatever value there is for HelixGroup.roll), all helices in a group are parallel.

The three angles are interpreted to be applied in the following order: first yaw, then pitch, then roll, using the “intrinsic rotation” convention (see https://en.wikipedia.org/wiki/Euler_angles#Conventions_by_intrinsic_rotations). This convention is not apparent in the scadnano web interface, which only directly shows pitch, but it shows up, for example, in oxDNA export via Design.to_oxdna_format(). See the fields HelixGroup.pitch, HelixGroup.roll, and HelixGroup.yaw for an explanation how to interpret each rotation.

Parameters:

• position (Position3D) –

• pitch (float) –

• roll (float) –

• yaw (float) –

• helices_view_order (Optional[List[int]]) –

• grid (Grid) –

position: Position3D = Position3D(x=0, y=0, z=0)

The “origin” of this HelixGroup.

pitch: float = 0

Angle in the main view plane; 0 means pointing to the right (min_offset on left, max_offset on right).

Rotation is clockwise in the main view, i.e., clockwise in the Y-Z plane, around the X-axis, when Y-axis points down, Z-axis points right, and X-axis points out of the page. See https://en.wikipedia.org/wiki/Aircraft_principal_axes Units are degrees.

roll: float = 0

Same meaning as Helix.roll, applied to every Helix in the group, i.e., it represents the rotation about the axis of a helix.

Rotation is clockwise in the side view, i.e., in the X-Y plane, around the Z-axis, when X-axis points right, Y-axis points down, and Z-axis points into the page.

yaw: float = 0

Third angle for orientation besides HelixGroup.pitch and HelixGroup.roll. Not visually displayed in scadnano, but here to support more general 3D applications.

Rotation is clockwise while looking down onto the main view, i.e., in the X-Z plane, around the Y-axis, when X-axis points down, Z-axis points right, and Y-axis points into the page. See https://en.wikipedia.org/wiki/Aircraft_principal_axes Units are degrees.

helices_view_order: Optional[List[int]] = None

Order in which to display the Helix’s in the group in the 2D view; if None, then the order is given by the order of the fields Helix.idx for each Helix in this HelixGroup.

grid: Grid = 'none'

Grid of this HelixGroup used to interpret the field Helix.grid_position.

helices_view_order_inverse(idx)

Given a Helix.idx in this HelixGroup, return its view order.

Parameters:

idx (int) – index of Helix in this HelixGroup

Returns:

view order of the Helix

Raises:

ValueError – if idx is not the index of a Helix in this HelixGroup

Return type:

int

class scadnano.Geometry(rise_per_base_pair=0.332, helix_radius=1.0, bases_per_turn=10.5, minor_groove_angle=150.0, inter_helix_gap=1.0)

Parameters controlling some geometric visualization/physical aspects of Design.

Parameters:

• rise_per_base_pair (float) –

• helix_radius (float) –

• bases_per_turn (float) –

• minor_groove_angle (float) –

• inter_helix_gap (float) –

rise_per_base_pair: float = 0.332

Distance in nanometers between two adjacent base pairs along the length of a DNA double helix.

helix_radius: float = 1.0

Radius of a DNA helix in nanometers.

bases_per_turn: float = 10.5

Number of DNA base pairs in a full turn of DNA.

minor_groove_angle: float = 150.0

Minor groove angle in degrees.

inter_helix_gap: float = 1.0

Gap between helices in nanometers (due to electrostatic repulsion; needed to display to scale).

class scadnano.Helix(max_offset=None, min_offset=0, major_tick_start=None, major_tick_distance=None, major_tick_periodic_distances=None, major_ticks=None, grid_position=None, position=None, roll=0, idx=None, group='default_group', _domains=<factory>)

Represents a “helix” where Domain’s could go. Technically a Helix can contain no Domain’s. More commonly, some partial regions of it may have only 1 or 0 Domain’s. So it is best thought of as a “potential” double-helix.

It has a 1-dimensional integer coordinate system given by “offsets”, integers between Helix.min_offset (inclusive) and Helix.max_offset (exclusive). At any valid offset for this Helix, at most two Domain’s may share that offset on this Helix, and if there are exactly two, then one must have Domain.forward = true and the other must have Domain.forward = false.

Once part of a Design, a Helix has an index (accessible via Helix.idx() once the Design is created) representing its order in the list of all Helix’s. This index is how a Domain is associated to the Helix via the integer index Domain.helix.

Parameters:

• max_offset (Optional[int]) –

• min_offset (int) –

• major_tick_start (Optional[int]) –

• major_tick_distance (Optional[int]) –

• major_tick_periodic_distances (Optional[List[int]]) –

• major_ticks (Optional[List[int]]) –

• grid_position (Optional[Tuple[int, int]]) –

• position (Optional[Position3D]) –

• roll (float) –

• idx (Optional[int]) –

• group (str) –

• _domains (List[Domain]) –

max_offset: Optional[int] = None

Maximum offset (exclusive) of Domain that can be drawn on this Helix.

Optional field. If unspecified, it is calculated when the Design is instantiated as the largest Domain.end offset of any Domain in the design.

min_offset: int = 0

Minimum offset (inclusive) of Domain that can be drawn on this Helix.

Optional field. Default value 0.

major_tick_start: Optional[int] = None

Offset of first major tick when not specifying Helix.major_ticks. Used in combination with either Helix.major_tick_distance or Helix.major_tick_periodic_distances.

Optional field. If not specified, is initialized to value Helix.min_offset.

major_tick_distance: Optional[int] = None

Distance between major ticks (bold) delimiting boundaries between bases. Major ticks will appear in the visual interface at positions

Optional field. If 0 then no major ticks are drawn. If not specified then the default value is assumed. If the grid is Grid.square then the default value is 8. If the grid is Grid.hex or Grid.honeycomb then the default value is 7.

major_tick_periodic_distances: Optional[List[int]] = None

Periodic distances between major ticks. For example, setting Helix.major_tick_periodic_distances = [2, 3] and Helix.major_tick_start = 10 means that major ticks will appear at 12, 15, 17, 20, 22, 25, 27, 30, …

Optional field. Helix.major_tick_distance is equivalent to the setting Helix.major_tick_periodic_distances = [Helix.major_tick_distance].

major_ticks: Optional[List[int]] = None

If not None, overrides Helix.major_tick_distance to specify a list of offsets at which to put major ticks.

grid_position: Optional[Tuple[int, int]] = None

(h,v) position of this helix in the side view grid, if Grid.square, Grid.hex , or Grid.honeycomb is used in the Design containing this helix. h and v are in units of “helices”: incrementing h moves right one helix in the grid and incrementing v moves down one helix in the grid. In the case of the hexagonal lattice, The convention is that incrementing v moves down and to the right if h is even, and moves down and to the left if h is odd. This is the “odd-q” coordinate system here: https://www.redblobgames.com/grids/hexagons/) However, the default y position in the main view for helices does not otherwise depend on grid_position. The default is to list the y-coordinates in order by helix idx.

Default is h = 0, v = index of Helix in Design.helices.

In the case of the honeycomb lattice, we use the same convention as cadnano for encoding hex coordinates, see misc/cadnano-format-specs/v2.txt. That convention is different from simply excluding coordinates from the hex lattice.

position: Optional[Position3D] = None

Position (x,y,z) of this Helix in 3D space.

Must be None if Helix.grid_position is specified.

roll: float = 0

Angle around the center of the helix; 0 means pointing straight up in the side view.

Rotation is clockwise in the side view; the same convention as HelixGroup.roll. Units are degrees.

idx: Optional[int] = None

Index of this Helix.

Optional if no other Helix specifies a value for idx. Default is the order of the Helix is listed in constructor for Design.

group: str = 'default_group'

Name of the HelixGroup to which this Helix belongs.

calculate_major_ticks(grid)

Calculates full list of major tick marks, whether using default_major_tick_distance (from Design), Helix.major_tick_distance, or Helix.major_ticks. They are used in reverse order to determine precedence. (e.g., Helix.major_ticks overrides Helix.major_tick_distance, which overrides default_major_tick_distance from Design.

Parameters:

grid (Grid) –

Return type:

List[int]

property domains: List[Domain]

Return Domain’s on this Helix. Assigned when a Design is created using this Helix.

Returns:

Domain’s on this helix

backbone_angle_at_offset(offset, forward, geometry)

Computes the backbone angle at offset for the strand in the direction given by forward.

Parameters:

• offset (int) – offset on this helix

• forward (bool) – whether to compute angle for the forward or reverse strand

• geometry (Geometry) –

Returns:

backbone angle at offset for the strand in the direction given by forward.

Return type:

float

class scadnano.Domain(helix, forward, start, end, deletions=<factory>, insertions=<factory>, name=None, label=None, dna_sequence=None, color=None)

A maximal portion of a Strand that is continguous on a single Helix. A Strand contains a list of Domain’s (and also potentially Loopout’s).

helix: int

index of the Helix on which this Domain resides.

forward: bool

Whether the strand “points” forward (i.e., its 3’ end has a larger offset than its 5’ end). If Domain.forward is True, then Domain.start is the 5’ end of the Domain and Domain.end is the 3’ end of the Domain. If Domain.forward is False, these roles are reversed.

start: int

The smallest offset position of any base on this Domain (3’ end if Domain.forward = False, 5’ end if Domain.forward = True).

end: int

1 plus the largest offset position of any base on this Domain (5’ end if Domain.forward = False, 3’ end if Domain.forward = True). Note that the set of base offsets occupied by this Domain is {start, start+1, …, end-1}, i.e., inclusive for Strand.start but exclusive for Strand.end, the same convention used in Python for slices of lists and strings. (e.g., "abcdef"[1:3] == "bc")

Some methods (such as Domain.dna_sequence_in()) use the convention of being inclusive on both ends and are marked with the word “INCLUSIVE”. (Such a convention is easier to reason about when there are insertions and deletions.)

deletions: List[int]

List of positions of deletions on this Domain.

insertions: List[Tuple[int, int]]

List of (position,num_insertions) pairs on this Domain.

This is the number of extra bases in addition to the base already at this position. The total number of bases at this offset is num_insertions+1.

name: Optional[str] = None

Optional name to give this Domain.

This is used to interoperate with the dsd DNA sequence design package.

label: Optional[DomainLabel] = None

Generic “label” object to associate to this Domain.

Useful for associating extra information with the Domain that will be serialized, for example, for DNA sequence design. It must be an object (e.g., a dict or primitive type such as str or int) that is naturally JSON serializable. (Calling json.dumps on the object should succeed without having to specify a custom encoder.)

dna_sequence: Optional[str] = None

DNA sequence of this Domain, or None if no DNA sequence has been assigned to this Domain’s Strand.

color: Optional[Color] = None

Color to show this domain in the main view. If specified, overrides the field Strand.color.

strand()

Returns:

The Strand that contains this Loopout.

Return type:

Strand

set_name(name)

Sets name of this Domain.

Parameters:

name (str) –

Return type:

None

set_label(label)

Sets label of this Domain.

Parameters:

label (DomainLabel) –

Return type:

None

offset_5p()

5’ offset of this Domain, INCLUSIVE.

Return type:

int

offset_3p()

3’ offset of this Domain, INCLUSIVE.

Return type:

int

contains_offset(offset)

Indicates if offset is the offset of a base on this Domain.

Note that offsets refer to visual portions of the displayed grid for the Helix. If for example, this Domain starts at position 0 and ends at 10, and it has 5 deletions, then it contains the offset 7 even though there is no base 7 positions from the start.

Parameters:

offset (int) –

Return type:

bool

dna_length()

Number of bases in this Domain.

Return type:

int

dna_length_in(left, right)

Number of bases in this Domain between offsets left and right (INCLUSIVE).

Parameters:

• left (int) –

• right (int) –

Return type:

int

visual_length()

Distance between Domain.start offset and Domain.end offset.

This can be more or less than the Domain.dna_length() due to insertions and deletions.

Return type:

int

dna_sequence_in(offset_left, offset_right)

Return DNA sequence of this Domain in the interval of offsets given by [offset_left, offset_right], INCLUSIVE, or None if no DNA sequence has been assigned to this Domain’s Strand.

WARNING: This is inclusive on both ends, unlike other parts of this API where the right endpoint is exclusive. This is to make the notion well-defined when one of the endpoints is on an offset with a deletion or insertion.

Parameters:

• offset_left (int) –

• offset_right (int) –

Return type:

Optional[str]

get_seq_start_idx()

Starting DNA subsequence index for first base of this Domain on its Parent Strand’s DNA sequence.

Return type:

int

domain_offset_to_strand_dna_idx(offset, offset_closer_to_5p)

Convert from offset on this Domain’s Helix to string index on the parent Strand’s DNA sequence.

If offset_closer_to_5p is True, (this only matters if offset contains an insertion) then the only leftmost string index corresponding to this offset is included, otherwise up to the rightmost string index (including all insertions) is included.

Parameters:

• offset (int) –

• offset_closer_to_5p (bool) –

Return type:

int

overlaps(other)

Indicates if this Domain’s set of offsets (the set \(\{x \in \mathbb{N} \mid\) self.start \(\leq x \leq\) self.end \(\}\)) has nonempty intersection with those of other, and they appear on the same helix, and they point in opposite directions.

Parameters:

other (Domain) –

Return type:

bool

overlaps_illegally(other)

Indicates if this Domain’s set of offsets (the set \(\{x \in \mathbb{N} \mid\) self.start \(\leq x \leq\) self.end \(\}\)) has nonempty intersection with those of other, and they appear on the same helix, and they point in the same direction.

Parameters:

other (Domain) –

Return type:

bool

compute_overlap(other)

Return [left,right) offset indicating overlap between this Domain and other.

Return (-1,-1) if they do not overlap (different helices, or non-overlapping regions of the same helix).

Parameters:

other (Domain) –

Return type:

Tuple[int, int]

insertion_offsets()

Return offsets of insertions (but not their lengths).

Return type:

List[int]

is_extreme_domain(five_prime)

Parameters:

five_prime (bool) – whether to ask about 5’ end or 3’ end

Returns:

Whether this Domain is the 5’ or 3’ most Domain on its Strand. (which depends on parameter five_prime

Return type:

bool

is_5p_domain()

Returns:

Whether this Domain is the 5’ most Domain on its Strand.

Return type:

bool

is_3p_domain()

Returns:

Whether this Domain is the 3’ most Domain on its Strand.

Return type:

bool

class scadnano.Loopout(length, name=None, label=None, dna_sequence=None, color=None)

Represents a single-stranded loopout on a Strand.

One could think of a Loopout as a type of Domain, but none of the fields of Domain make sense for Loopout, so they are not related to each other in the type hierarchy. It is interpreted that a Loopout is a single-stranded region bridging two Domain’s that are connected to Helix’s. It is illegal for two consecutive Domain’s to both be Loopout’s, or for a Loopout to occur on either end of the Strand (i.e., each Strand must begin and end with a Domain or Extension).

For example, one use of a loopout is to describe a hairpin (a.k.a., stem-loop). The following creates a Strand that represents a hairpin with a stem length of 10 and a loop length of 5.

import scadnano as sc

domain_f = sc.Domain(helix=0, forward=True, start=0, end=10)
loop = sc.Loopout(length=5)
domain_r = sc.Domain(helix=0, forward=False, start=0, end=10)
hairpin = sc.Strand([domain_f, loop, domain_r])

It can also be created with chained method calls

import scadnano as sc

design = sc.Design(helices=[sc.Helix(max_offset=10)])
design.draw_strand(0,0).move(10).loopout(0,5).move(-10)

length: int

Length (in DNA bases) of this Loopout.

name: Optional[str] = None

Optional name to give this Loopout.

This is used to interoperate with the dsd DNA sequence design package.

label: Optional[DomainLabel] = None

Generic “label” object to associate to this Loopout.

Useful for associating extra information with the Loopout that will be serialized, for example, for DNA sequence design. It must be an object (e.g., a dict or primitive type such as str or int) that is naturally JSON serializable. (Calling json.dumps on the object should succeed without having to specify a custom encoder.)

dna_sequence: Optional[str] = None

DNA sequence of this Loopout, or None if no DNA sequence has been assigned.

color: Optional[Color] = None

Color to show this loopout in the main view. If specified, overrides the field Strand.color.

strand()

Returns:

The Strand that contains this Loopout.

Return type:

Strand

set_name(name)

Sets name of this Loopout.

Parameters:

name (str) –

Return type:

None

set_label(label)

Sets label of this Loopout.

Parameters:

label (Optional[DomainLabel]) –

Return type:

None

dna_length()

Length of this Loopout; same as field Loopout.length.

Return type:

int

get_seq_start_idx()

Starting DNA subsequence index for first base of this Loopout on its Strand’s DNA sequence.

Return type:

int

class scadnano.Extension(num_bases, display_length=1.0, display_angle=35.0, label=None, name=None, dna_sequence=None, color=None)

Represents a single-stranded extension on either the 3’ or 5’ end of Strand.

One could think of an Extension as a type of Domain, but none of the fields of Domain make sense for Extension, so they are not related to each other in the type hierarchy. It is interpreted that an Extension is a single-stranded region that resides on either the 3’ or 5’ end of the Strand. It is illegal for an Extension to be placed in the middle of the Strand or for an Extension to be adjacent to a Loopout.

import scadnano as sc

domain = sc.Domain(helix=0, forward=True, start=0, end=10)
left_toehold = sc.Extension(num_bases=6)
right_toehold = sc.Extension(num_bases=5)
strand = sc.Strand([left_toehold, domain, right_toehold])

It can also be created with chained method calls

import scadnano as sc

design = sc.Design(helices=[sc.Helix(max_offset=10)])
design.draw_strand(0,0).extension_5p(3).move(10).extension_3p(2)

which makes this strand with an Extension on the side of the length-10 Domain:

[
 \              >
  \            /
   \          /
    ----------

num_bases: int

Length (in DNA bases) of this Extension.

display_length: float = 1.0

Length (in nm) to display the line representing the Extension in the scadnano web app.

display_angle: float = 35.0

Angle (in degrees) to display in the scadnano web app.

This angle is relative to the “rotation frame” of the adjacent domain. 0 degrees means parallel to the adjacent domain. 90 degrees means pointing away from the helix. 180 degrees means means antiparallel to the adjacent domain (overlapping). If a forward strand, will go above the strand; if a reverse strand, will go below, for degrees strictly between 0 and 180.

label: Optional[DomainLabel] = None

Generic “label” object to associate to this Extension.

Useful for associating extra information with the Extension that will be serialized, for example, for DNA sequence design. It must be an object (e.g., a dict or primitive type such as str or int) that is naturally JSON serializable. (Calling json.dumps on the object should succeed without having to specify a custom encoder.)

name: Optional[str] = None

Optional name to give this Extension.

dna_sequence: Optional[str] = None

DNA sequence of this Extension, or None if no DNA sequence has been assigned.

color: Optional[Color] = None

Color to show this extension in the main view. If specified, overrides the field Strand.color.

dna_length()

Length of this Extension; same as field Extension.num_bases.

Return type:

int

set_label(label)

Sets label of this Extension.

Parameters:

label (Optional[DomainLabel]) –

Return type:

None

set_name(name)

Sets name of this Extension.

Parameters:

name (str) –

Return type:

None

scadnano.wc(seq)

Return reverse Watson-Crick complement of seq.

Parameters:

seq (str) –

Return type:

str

class scadnano.IDTFields(scale='25nm', purification='STD', plate=None, well=None)

Data required when ordering DNA strands from the synthesis company IDT (Integrated DNA Technologies). This data is used when automatically generating files used to order DNA from IDT.

When exporting to IDT files via Design.write_idt_plate_excel_file() or Design.write_idt_bulk_input_file(), the field Strand.name is used for the name if it exists, otherwise a reasonable default is chosen.

Parameters:

• scale (str) –

• purification (str) –

• plate (Optional[str]) –

• well (Optional[str]) –

scale: str = '25nm'

Synthesis scale at which to synthesize the strand (third field in IDT bulk input: https://www.idtdna.com/site/order/oligoentry). Choices supplied by IDT at the time this was written: "25nm", "100nm", "250nm", "1um", "5um", "10um", "4nmU", "20nmU", "PU", "25nmS".

Optional field.

purification: str = 'STD'

Purification options (fourth field in IDT bulk input: https://www.idtdna.com/site/order/oligoentry). Choices supplied by IDT at the time this was written: "STD", "PAGE", "HPLC", "IEHPLC", "RNASE", "DUALHPLC", "PAGEHPLC".

Optional field.

plate: Optional[str] = None

Name of plate in case this strand will be ordered on a 96-well or 384-well plate.

Optional field, but non-optional if IDTFields.well is not None.

well: Optional[str] = None

Well position on plate in case this strand will be ordered on a 96-well or 384-well plate.

Optional field, but non-optional if IDTFields.plate is not None.

class scadnano.StrandBuilder(design, helix, offset)

Represents a Strand that is being built in an existing Design.

This is an intermediate object created when using chained method building by calling Design.draw_strand(), for example

design.draw_strand(0, 0).to(10).cross(1).to(5).with_modification_5p(mod.biotin_5p).as_scaffold()

StrandBuilder should generally not be created directly. Although it is convenient to use chained method calls, it is also sometimes useful to assign the StrandBuilder object into a variable and then call the methods on that variable. For example, this code is equivalent to the above line:

strand_builder = design.draw_strand(0, 0)
strand_builder.to(10)
strand_builder.cross(1)
strand_builder.to(5)
strand_builder.with_modification_5p(mod.biotin_5p)
strand_builder.as_scaffold()

cross(helix, offset=None, move=None)

Add crossover. To have any effect, must be followed by call to StrandBuilder.to() or StrandBuilder.move().

Parameters:

• helix (int) – Helix to crossover to

• offset (Optional[int]) – new offset on helix. If not specified, defaults to current offset. (i.e., a “vertical” crossover) Mutually excusive with move.

• move (Optional[int]) – Relative distance to new offset on helix from current offset. If not specified, defaults to using parameter offset. Mutually excusive with offset.

Returns:

self

Return type:

StrandBuilder[StrandLabel, DomainLabel]

loopout(helix, length, offset=None, move=None)

Like StrandBuilder.cross(), but creates a Loopout instead of a crossover.

Parameters:

• helix (int) – Helix to crossover to

• length (int) – length of Loopout to add

• offset (Optional[int]) – new offset on helix. If not specified, defaults to current offset. (i.e., a “vertical” loopout) Mutually excusive with move.

• move (Optional[int]) – Relative distance to new offset on helix from current offset. If not specified, defaults to using parameter offset. Mutually excusive with offset.

Returns:

self

Return type:

StrandBuilder[StrandLabel, DomainLabel]

extension_3p(num_bases, display_length=1.0, display_angle=35.0)

Creates an Extension after verifying that it is valid to add an Extension to the Strand as a 3’ Extension.

Parameters:

• num_bases (int) – number of bases of Extension to add

• display_length (float) – display length of Extension to add

• display_angle (float) – display angle of Extension to add

Returns:

self

Return type:

StrandBuilder[StrandLabel, DomainLabel]

extension_5p(num_bases, display_length=1.0, display_angle=35.0)

Creates an Extension after verifying that it is valid to add an Extension to the Strand as a 5’ Extension.

Parameters:

• num_bases (int) – number of bases of Extension to add

• display_length (float) – display length of Extension to add

• display_angle (float) – display angle of Extension to add

Returns:

self

Return type:

StrandBuilder[StrandLabel, DomainLabel]

move(delta)

Extends this StrandBuilder on the current helix to offset given by the current offset plus delta, which adds a new Domain to the Strand being built. This is a “relative move”, whereas StrandBuilder.to() and StrandBuilder.update_to() are “absolute moves”.

This updates the underlying Design with a new Domain, and if StrandBuilder.loopout() was last called on this StrandBuilder, also a new Loopout.

If two instances of StrandBuilder.move() are chained together, this creates two domains on the same helix. The two offsets must move in the same direction. In other words, if we call .move(o1).move(o2), then o1 and o2 must be either both negative or both positive.

Parameters:

delta (int) – Distance to new offset to extend to, compared to current offset. If less than current offset, the new Domain is reverse, otherwise it is forward.

Returns:

self

Return type:

StrandBuilder[StrandLabel, DomainLabel]

to(offset)

Extends this StrandBuilder on the current helix to offset offset, which adds a new Domain to the Strand being built. This is an “absolute move”, whereas StrandBuilder.move() is a “relative move”.

This updates the underlying Design with a new Domain, and if StrandBuilder.loopout() was last called on this StrandBuilder, also a new Loopout.

If two instances of StrandBuilder.to() are chained together, this creates two domains on the same helix. The two offsets must move in the same direction. In other words, if the starting offset is s, and we call .to(o1).to(o2), then either s < o1 < o2 or o2 < o1 < s must be true.

To simply change the current offset after calling StrandBuilder.to(), without creating a new Domain, call StrandBuilder.update_to() instead.

Parameters:

offset (int) – new offset to extend to. If less than current offset, the new Domain is reverse, otherwise it is forward.

Returns:

self

Return type:

StrandBuilder[StrandLabel, DomainLabel]

update_to(offset)

Like StrandBuilder.to(), but changes the current offset without creating a new Domain. So unlike StrandBuilder.to(), several consecutive calls to StrandBuilder.update_to() are equivalent to only making the final call.

Generally there’s no point in calling StrandBuilder.update_to() in one line of code. It is intended to help when a large, complex strand is being constructed in a loop.

If StrandBuilder.cross() or StrandBuilder.loopout() was just called, then StrandBuilder.to() and StrandBuilder.update_to() have the same effect.

Parameters:

offset (int) – new offset to extend to. If less than offset of the last call to StrandBuilder.cross() or StrandBuilder.loopout(), the new Domain is reverse, otherwise it is forward.

Returns:

self

Return type:

StrandBuilder[StrandLabel, DomainLabel]

as_circular()

Makes Strand being built circular.

Returns:

self

Return type:

StrandBuilder[StrandLabel, DomainLabel]

as_scaffold()

Makes Strand being built a scaffold.

Returns:

self

Return type:

StrandBuilder[StrandLabel, DomainLabel]

with_idt(scale='25nm', purification='STD', plate=None, well=None)

Gives IDTFields value to Strand being built. Only a name is required; other fields are given reasonable default values.

Parameters:

• scale (str) – see IDTFields.scale

• purification (str) – see IDTFields.purification

• plate (Optional[str]) – see IDTFields.plate

• well (Optional[str]) – see IDTFields.well

Returns:

self

Return type:

StrandBuilder[StrandLabel, DomainLabel]

with_modification_5p(mod)

Sets Strand being built to have given 5’ modification.

Parameters:

mod (Modification5Prime) – 5’ modification

Returns:

self

Return type:

StrandBuilder[StrandLabel, DomainLabel]

with_modification_3p(mod)

Sets Strand being built to have given 3’ modification.

Parameters:

mod (Modification3Prime) – 3’ modification

Returns:

self

Return type:

StrandBuilder[StrandLabel, DomainLabel]

with_modification_internal(idx, mod, warn_on_no_dna)

Sets Strand being built to have given internal modification.

Parameters:

• idx (int) – idx along DNA sequence of internal modification

• mod (ModificationInternal) – internal modification

• warn_on_no_dna (bool) – whether to print warning to screen if DNA has not been assigned

Returns:

self

Return type:

StrandBuilder[StrandLabel, DomainLabel]

with_color(color)

Sets Strand being built to have given color.

Parameters:

color (Color) – color to set for Strand

Returns:

self

Return type:

StrandBuilder[StrandLabel, DomainLabel]

with_sequence(sequence, assign_complement=False)

Assigns sequence as DNA sequence of the Strand being built. This should be done after the Strand’s structure is done being built, e.g.,

design.draw_strand(0, 0).to(10).cross(1).to(5).with_sequence('AAAAAAAAAACGCGC')

Parameters:

• sequence (str) – the DNA sequence to assign to the Strand

• assign_complement (bool) – whether to automatically assign the complement to existing Strand’s bound to this Strand. This has the same meaning as the parameter assign_complement in Design.assign_dna().

Returns:

self

Return type:

StrandBuilder[StrandLabel, DomainLabel]

with_domain_sequence(sequence, assign_complement=False)

Assigns sequence as DNA sequence of the most recently created Domain in the Strand being built. This should be called immediately after a Domain is created via a call to StrandBuilder.to(), StrandBuilder.update_to(), StrandBuilder.move(), StrandBuilder.extension_5p(), StrandBuilder.extension_3p(), or StrandBuilder.loopout(), e.g.,

design.draw_strand(0, 5)\
    .extension_5p(2).with_domain_sequence('TT')\
    .to(8).with_domain_sequence('AAA')\
    .cross(1).move(-3).with_domain_sequence('TTT')\
    .loopout(2, 4).with_domain_sequence('CCCC')\
    .to(10).with_domain_sequence('GGGGG')\
    .extension_3p(4).with_domain_sequence('AAAA')

Parameters:

• sequence (str) – the DNA sequence to assign to the Domain

• assign_complement (bool) – whether to automatically assign the complement to existing Strand’s bound to this Strand. This has the same meaning as the parameter assign_complement in Design.assign_dna().

Returns:

self

Return type:

StrandBuilder[StrandLabel, DomainLabel]

with_domain_color(color)

Sets most recent Domain/Loopout/Extension to have given color.

Parameters:

color (Color) – color to set for Domain/Loopout/Extension

Returns:

self

Return type:

StrandBuilder[StrandLabel, DomainLabel]

with_name(name)

Assigns name as name of the Strand being built.

design.draw_strand(0, 0).to(10).cross(1).to(5).with_name('scaffold')

Parameters:

name (str) – name to assign to the Strand

Returns:

self

Return type:

StrandBuilder[StrandLabel, DomainLabel]

with_label(label)

Assigns label as label of the Strand being built.

design.draw_strand(0, 0).to(10).cross(1).to(5).with_label('scaffold')

Parameters:

label (StrandLabel) – label to assign to the Strand

Returns:

self

Return type:

StrandBuilder[StrandLabel, DomainLabel]

with_domain_name(name)

Assigns name as of the most recently created Domain or Loopout in the Strand being built. This should be called immediately after a Domain is created via a call to StrandBuilder.to(), StrandBuilder.move(), StrandBuilder.update_to(), or StrandBuilder.loopout(), e.g.,

design.draw_strand(0, 0).to(10).with_domain_name('dom1*').cross(1).to(5).with_domain_name('dom1')

Parameters:

name (str) – name to assign to the most recently created Domain or Loopout

Returns:

self

Return type:

StrandBuilder[StrandLabel, DomainLabel]

with_domain_label(label)

Assigns label as label of the most recently created Domain or Loopout in the Strand being built. This should be called immediately after a Domain or Loopout is created via a call to StrandBuilder.to(), StrandBuilder.move(), StrandBuilder.update_to(), or StrandBuilder.loopout(), e.g.,

design.draw_strand(0, 5)\
    .to(8).with_domain_label('domain 1')\
    .cross(1)\
    .to(5).with_domain_label('domain 2')\
    .loopout(2, 4).with_domain_label('domain 3')\
    .to(10).with_domain_label('domain 4')

Parameters:

label (DomainLabel) – label to assign to the Domain or Loopout

Returns:

self

Return type:

StrandBuilder[StrandLabel, DomainLabel]

with_deletions(deletions)

Assigns deletions as the deletion(s) of the most recently created Domain the Strand being built. This should be called immediately after a Domain is created via a call to StrandBuilder.to(), StrandBuilder.move(), StrandBuilder.update_to(), e.g.,

design.draw_strand(0, 0)\
    .move(8).with_deletions(4)\
    .cross(1)\
    .move(-8).with_deletions([2, 3])

Parameters:

deletions (Union[int, Iterable[int]]) – a single int, or an Iterable of ints, indicating the offset at which to put the deletion(s)

Returns:

self

Return type:

StrandBuilder[StrandLabel, DomainLabel]

with_insertions(insertions)

Assigns insertions as the insertion(s) of the most recently created Domain the Strand being built. This should be called immediately after a Domain is created via a call to StrandBuilder.to(), StrandBuilder.move(), StrandBuilder.update_to(), e.g.,

design.draw_strand(0, 0)\
    .move(8).with_insertions((4, 2))\
    .cross(1)\
    .move(-8).with_insertions([(2, 3), (3, 3)])

Parameters:

insertions (Union[Tuple[int, int], Iterable[Tuple[int, int]]]) – a single pair of ints (tuple), or an Iterable of pairs of ints (tuples) indicating the offset at which to put the insertion(s)

Returns:

self

Return type:

StrandBuilder[StrandLabel, DomainLabel]

class scadnano.Strand(domains, circular=False, color=None, idt=None, is_scaffold=False, modification_5p=None, modification_3p=None, modifications_int=None, name=None, label=None, _helix_idx_domain_map=None, dna_sequence=None)

Represents a single strand of DNA.

Each maximal portion that is continguous on a single Helix is a Domain. Crossovers from one Helix to another are implicitly from the 3’ end of one of this Strand’s Domain’s to the 5’ end of the next Domain.

A portion of the Strand not associated to any Helix is represented by a Loopout. Two Loopout’s cannot occur consecutively on a Strand, nor can a Strand contain only a Loopout but no Domain.

One can set the strand to be a scaffold in the constructor:

import scadnano as sc

scaffold_domains = [ ... ]
scaffold_strand = sc.Strand(domains=scaffold_domains, is_scaffold=True)

or by calling Strand.set_scaffold() on the Strand object:

import scadnano as sc

scaffold_domains = [ ... ]
scaffold_strand = sc.Strand(domains=scaffold_domains)
scaffold_strand.set_scaffold()

Both will give the strand the same color that cadnano uses for the scaffold.

property dna_sequence: Optional[str]

Do not assign directly to this field. Always use Design.assign_dna (for complementarity checking) or Strand.set_dna_sequence (without complementarity checking, to allow mismatches).

Note that this does not include any IDT codes for Modification’s. To include those call Strand.idt_dna_sequence().

domains: List[Union[Domain[DomainLabel], Loopout[DomainLabel], Extension[DomainLabel]]]

Domain’s (or Loopout’s) composing this Strand. Each Domain is contiguous on a single Helix and could be either single-stranded or double-stranded, whereas each Loopout is single-stranded and has no associated Helix.

circular: bool = False

If True, this Strand is circular and has no 5’ or 3’ end. Although there is still a first and last Domain, we interpret there to be a crossover from the 3’ end of the last domain to the 5’ end of the first domain, and any circular permutation of Strand.domains should result in a functionally equivalent Strand. It is illegal to have a Modification5Prime or Modification3Prime on a circular Strand.

color: Optional[Color] = None

Color to show this strand in the main view. If not specified in the constructor, a color is assigned by cycling through a list of defaults given by ColorCycler.colors()

idt: Optional[IDTFields] = None

Fields used when ordering strands from the synthesis company IDT (Integrated DNA Technologies, Coralville, IA). If present (i.e., not equal to None) then the method Design.write_idt_bulk_input_file() can be called to automatically generate an text file for ordering strands in test tubes: https://www.idtdna.com/site/order/oligoentry, as can the method Design.write_idt_plate_excel_file() for writing a Microsoft Excel file that can be uploaded to IDT’s website for describing DNA sequences to be ordered in 96-well or 384-well plates: https://www.idtdna.com/site/order/plate/index/dna/1800

is_scaffold: bool = False

Indicates whether this Strand is a scaffold for a DNA origami. If any Strand in a Design is a scaffold, then the design is considered a DNA origami design.

modification_5p: Optional[Modification5Prime] = None

5’ modification; None if there is no 5’ modification. Illegal to have if Strand.circular is True.

modification_3p: Optional[Modification3Prime] = None

3’ modification; None if there is no 3’ modification. Illegal to have if Strand.circular is True.

modifications_int: Dict[int, ModificationInternal]

Modification’s to the DNA sequence (e.g., biotin, Cy3/Cy5 fluorphores).

Maps index within DNA sequence to modification. If the internal modification is attached to a base (e.g., internal biotin, /iBiodT/ from IDT), then the index is that of the base. If it goes between two bases (e.g., internal Cy3, /iCy3/ from IDT), then the index is that of the previous base, e.g., to put a Cy3 between bases at indices 3 and 4, the index should be 3. So for an internal modified base on a sequence of length n, the allowed indices are 0,…,n-1, and for an internal modification that goes between bases, the allowed indices are 0,…,n-2.

name: Optional[str] = None

Optional name to give the strand. If specified it is shown on mouseover in the scadnano web interface.

This is used to interoperate with the dsd DNA sequence design package.

label: Optional[StrandLabel] = None

Generic “label” object to associate to this Strand.

Useful for associating extra information with the Strand that will be serialized, for example, for DNA sequence design. It must be an object (e.g., a dict or primitive type such as str or int) that is naturally JSON serializable. (Calling json.dumps on the object should succeed without having to specify a custom encoder.)

rotate_domains(rotation, forward=True)

“Rotates” the strand by replacing domains with a circular rotation, e.g., if the domains are

A, B, C, D, E, F

then strand.rotate_domains(2) makes the Strand have the same domains, but in this order:

E, F, A, B, C, D

and strand.rotate_domains(2, forward=False) makes

C, D, E, F, A, B

Parameters:

• rotation (int) – Amount to rotate domains.

• forward (bool) – Whether to move domains forward (wrapping off 3’ end back to 5’ end) or backward (wrapping off 5’ end back to 3’ end).

Return type:

None

set_scaffold(is_scaf=True)

Sets this Strand as a scaffold. Alters color to default scaffold color.

If is_scaf == False, sets this strand as not a scaffold, and leaves the color alone.

Parameters:

is_scaf (bool) –

Return type:

None

set_name(name)

Sets name of this Strand.

Parameters:

name (str) –

Return type:

None

set_label(label)

Sets label of this Strand.

Parameters:

label (Any) –

Return type:

None

set_color(color)

Sets color of this Strand.

Parameters:

color (Color) –

Return type:

None

set_circular(circular=True)

Sets this to be a circular Strand (or non-circular if optional parameter is False).

Parameters:

circular (bool) – whether to make this Strand circular (True) or linear (False)

Raises:

StrandError – if this Strand has a 5’ or 3’ modification

Return type:

None

set_linear()

Makes this a linear (non-circular) Strand. Equivalent to calling self.set_circular(False).

Return type:

None

set_domains(domains)

Sets the Domain’s/Loopout’s of this Strand to be domains, which can contain a mix of Domain’s and Loopout’s, just like the field Strand.domains.

Parameters:

domains (Iterable[Union[Domain[DomainLabel], Loopout[DomainLabel]]]) – The new sequence of Domain’s/Loopout’s to use for this Strand.

Raises:

StrandError – if domains has two consecutive Loopout’s, consists of just a single Loopout’s, or starts or ends with a Loopout

Return type:

None

idt_export_name(unique_names=False)

Parameters:

unique_names (bool) – If True and default name is used, enforces that strand names must be unique by encoding the forward/reverse Boolean into the name. If False (the default), uses cadnano’s exact naming convention, which allows two strands to have the same default name, if they begin and end at the same (helix,offset) pair (but point in opposite directions at each). Has no effect if Strand.idt or Strand.name are defined; if those are used, they must be explicitly set to be unique.

Returns:

If Strand.name is not None, return Strand.name, otherwise return the result of Strand.default_export_name() with parameter unique_names.

Return type:

str

default_export_name(unique_names=False)

Returns a default name to use when exporting the DNA sequence. Uses cadnano’s naming convention of, for example ‘ST2[5]4[10]’ to indicate a strand that starts at helix 2, offset 5, and ends at helix 4, offset 10. Note that this naming convention is not unique: two strands in the system could share this name. To ensure it is unique, set the parameter unique_names to True, which will modify the name with forward/reverse information from the first domain that uniquely identifies the strand, e.g., ‘ST2[5]F4[10]’ or ‘ST2[5]R4[10]’.

If the strand is a scaffold (i.e., if Strand.is_scaffold is True), then the name will begin with ‘SCAF’ instead of ‘ST’.

Parameters:

unique_names (bool) – If True, enforces that strand names must be unique by encoding the forward/reverse Boolean into the name. If False (the default), uses cadnano’s exact naming convention, which allows two strands to have the same default name, if they begin and end at the same (helix,offset) pair (but point in opposite directions at each).

Returns:

default name to export (used, for example, by idt DNA export methods Design.write_idt_plate_excel_file() and Design.write_idt_bulk_input_file() if Strand.name and Strand.idt.name are both not set)

Return type:

str

set_modification_5p(mod=None)

Sets 5’ modification to be mod. mod cannot be non-None if Strand.circular is True.

Parameters:

mod (Optional[Modification5Prime]) –

Return type:

None

set_modification_3p(mod=None)

Sets 3’ modification to be mod. mod cannot be non-None if Strand.circular is True.

Parameters:

mod (Optional[Modification3Prime]) –

Return type:

None

remove_modification_5p()

Removes 5’ modification.

Return type:

None

remove_modification_3p()

Removes 3’ modification.

Return type:

None

set_modification_internal(idx, mod, warn_on_no_dna=True)

Adds internal modification mod at given DNA index idx.

Parameters:

• idx (int) –

• mod (ModificationInternal) –

• warn_on_no_dna (bool) –

Return type:

None

remove_modification_internal(idx)

Removes internal modification at given DNA index idx.

Parameters:

idx (int) –

Return type:

None

first_domain()

First domain on this Strand.

Return type:

Domain

last_domain()

Last domain on this Strand.

Return type:

Domain

dna_sequence_delimited(delimiter)

Parameters:

delimiter (str) – string to put in between DNA sequences of each domain

Returns:

DNA sequence of this Strand, with delimiter in between DNA sequences of each Domain or Loopout.

Return type:

str

set_dna_sequence(sequence)

Set this Strand’s DNA sequence to seq WITHOUT checking for complementarity with overlapping Strand’s or automatically assigning their sequences. To assign a sequence to a Strand and have the overlapping Strand’s automatically have the appropriate Watson-Crick complements assigned, use Design.assign_dna.

All whitespace in sequence is removed, and lowercase bases ‘a’, ‘c’, ‘g’, ‘t’ are converted to uppercase.

sequence, after all whitespace is removed, must be exactly the same length as Strand.dna_length(). Wildcard symbols (DNA_case_wildcard) are allowed to leave part of the DNA unassigned.

Parameters:

sequence (str) –

Return type:

None

dna_length()

Return sum of DNA length of Domain’s and Loopout’s of this Strand.

Return type:

int

bound_domains()

Domain’s of this Strand that are not Loopout’s.

Return type:

List[Domain]

offset_5p()

5’ offset of this entire Strand, INCLUSIVE.

Return type:

int

offset_3p()

3’ offset of this entire Strand, INCLUSIVE.

Return type:

int

overlaps(other)

Indicates whether self overlaps other_strand, meaning that the set of offsets occupied by self has nonempty intersection with those occupied by other_strand.

Parameters:

other (Strand) –

Return type:

bool

assign_dna_complement_from(other)

Assuming a DNA sequence has been assigned to other, assign its Watson-Crick complement to the portions of this Strand that are bound to other.

Generally this is not called directly; use Design.assign_dna() to assign a DNA sequence to a Strand. The method Design.assign_dna() will calculate which other Strand’s need to be assigned via Strand.assign_dna_complement_from().

However, it is permitted to assign the field Strand.dna_sequence directly via the method Strand.set_dna_sequence(). This is used, for instance, to assign a DNA sequence to a Strand bound to another Strand with an assigned DNA sequence where they overlap. In this case no error checking about sequence complementarity is done. This can be used to intentionally assign mismatching DNA sequences to Strand’s that are bound on a Helix.

Parameters:

other (Strand) –

Return type:

None

dna_index_start_domain(domain)

Returns index in DNA sequence of domain, e.g., if there are five domains

012 3 45 678 9 AAA-C-GG-TTT-ACGT

Then their indices, respectively in order, are 0, 3, 4, 6, 9.

Parameters:

domain (Union[Domain, Loopout]) –

any:

to find the start DNA index of

Returns:

index (within DNA sequence string) of substring of DNA starting with given Domain

Return type:

int

first_bound_domain()

First Domain (i.e., not a Loopout) on this Strand.

Currently the first and last strand must not be Loopout’s, so this should return the same domain as Strand.first_domain(), but in case an initial or final Loopout is supported in the future, this method is provided.

Return type:

Domain

last_bound_domain()

Last Domain (i.e., not a Loopout) on this Strand.

Currently the first and last strand must not be Loopout’s, so this should return the same domain as Strand.first_domain(), but in case an initial or final Loopout is supported in the future, this method is provided.

Return type:

Domain

reverse()

Reverses “polarity” of this Strand.

Does NOT check whether this keeps the Design legal, so be cautious in calling this method directly. To reverse every Strand, called Design.reverse_all(). If the design was legal before, it will be legal after calling that method.

Return type:

None

idt_dna_sequence()

Returns:

DNA sequence as it needs to be typed to order from IDT, with Modification5Prime’s, Modification3Prime’s, and ModificationInternal’s represented with text codes, e.g., “/5Biosg/ACGT” for sequence ACGT with a 5’ biotin modification.

Return type:

str

no_modifications_version()

Returns:

version of this Strand with no DNA modifications.

Return type:

Strand

class scadnano.StrandOrder(value)

Which part of a Strand to use for sorting in the key function returned by strand_order_key_function().

five_prime = 0

5’ end of the strand

three_prime = 1

3’ end of the strand

five_or_three_prime = 2

Either 5’ end or 3’ end is used, whichever is first according to the sort order.

top_left_domain = 3

The start offset of the “top-left” Domain of the Strand: the Domain whose Domain.helix is minimal, and, among all such Domain’s, the one with minimal Domain.start.

scadnano.strand_order_key_function(*, column_major=True, strand_order)

Returns a key function indicating a sorted order for Strand’s. Useful as a parameter for Design.().

Parameters:

• column_major (bool) – If true, column major order is used: ordered by base offset first, then by helix. Otherwise row-major order is used: ordered by helix first, then by base offset.

• strand_order (StrandOrder) – Which part of the strand to use as a key for the sorted order. See StrandOrder for definitions.

Returns:

A key function that can be passed to Design.() to specify a sorted order for the Strand’s.

Return type:

Callable[[Strand], Any]

exception scadnano.IllegalDesignError(the_cause)

Indicates that some aspect of the Design object is illegal.

Parameters:

the_cause (str) –

Return type:

None

exception scadnano.StrandError(strand, the_cause)

Indicates that the Design is illegal due to some specific Strand. Information about the Strand is embedded in the error message when this exception is raised that helps to identify which Strand caused the problem.

Parameters:

• strand (Strand) –

• the_cause (str) –

Return type:

None

class scadnano.PlateType(value)

Represents two different types of plates in which DNA sequences can be ordered.

wells96 = 96

96-well plate.

wells384 = 384

384-well plate.

num_wells_per_plate()

Returns:

number of wells in this plate type

Return type:

int

min_wells_per_plate()

Returns:

minimum number of wells in this plate type to avoid extra charge by IDT

Return type:

int

class scadnano.PlateMap(plate_name, plate_type, well_to_strand)

Represents a “plate map”, i.e., a drawing of a 96-well or 384-well plate, indicating which subset of wells in the plate have strands. It is an intermediate representation of structured data about the plate map that is converted to a visual form, such as Markdown, via the export_* methods.

Parameters:

• plate_name (str) –

• plate_type (PlateType) –

• well_to_strand (Dict[str, Strand]) –

plate_name: str

Name of this plate.

plate_type: PlateType

Type of this plate (96-well or 384-well).

well_to_strand: Dict[str, Strand]

dictionary mapping the name of each well (e.g., “C4”) to the strand in that well.

Wells with no strand in the PlateMap are not keys in the dictionary.

to_table(well_marker=None, title_level=3, warn_unsupported_title_format=True, vertical_borders=False, tablefmt='pipe', stralign='default', missingval='', showindex='default', disable_numparse=False, colalign=None)

Exports this plate map to string format, with a header indicating information such as the plate’s name and volume to pipette. By default the text format is Markdown, which can be rendered in a jupyter notebook using display and Markdown from the package IPython.display:

plate_maps = design.plate_maps()
maps_strs = '\n\n'.join(plate_map.to_table() for plate_map in plate_maps)
from IPython.display import display, Markdown
display(Markdown(maps_strs))

Markdown format is used by default, generating a string such as this:

plate "5 monomer synthesis"

|     | 1    | 2      | 3      | 4    | 5        | 6   | 7   | 8   | 9   | 10   | 11   | 12   |
|-----|------|--------|--------|------|----------|-----|-----|-----|-----|------|------|------|
| A   | mon0 | mon0_F |        | adp0 |          |     |     |     |     |      |      |      |
| B   | mon1 | mon1_Q | mon1_F | adp1 | adp_sst1 |     |     |     |     |      |      |      |
| C   | mon2 | mon2_F | mon2_Q | adp2 | adp_sst2 |     |     |     |     |      |      |      |
| D   | mon3 | mon3_Q | mon3_F | adp3 | adp_sst3 |     |     |     |     |      |      |      |
| E   | mon4 |        | mon4_Q | adp4 | adp_sst4 |     |     |     |     |      |      |      |
| F   |      |        |        | adp5 |          |     |     |     |     |      |      |      |
| G   |      |        |        |      |          |     |     |     |     |      |      |      |
| H   |      |        |        |      |          |     |     |     |     |      |      |      |

or, with the PlateMap.to_table() parameter well_marker set to '*' (in case you don’t need to see the strand names and just want to see which wells are marked):

|     | 1   | 2   | 3   | 4   | 5   | 6   | 7   | 8   | 9   | 10   | 11   | 12   |
|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|------|------|------|
| A   | *   | *   |     | *   |     |     |     |     |     |      |      |      |
| B   | *   | *   | *   | *   | *   |     |     |     |     |      |      |      |
| C   | *   | *   | *   | *   | *   |     |     |     |     |      |      |      |
| D   | *   | *   | *   | *   | *   |     |     |     |     |      |      |      |
| E   | *   |     | *   | *   | *   |     |     |     |     |      |      |      |
| F   |     |     |     | *   |     |     |     |     |     |      |      |      |
| G   |     |     |     |     |     |     |     |     |     |      |      |      |
| H   |     |     |     |     |     |     |     |     |     |      |      |      |

If well_marker is not specified, then each strand must have a name. well_marker can also be a function of the well; for instance, if it is the identity function lambda x:x, then each well has its own address as the entry:

|     | 1   | 2   | 3   | 4   | 5   | 6   | 7   | 8   | 9   | 10   | 11   | 12   |
|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|------|------|------|
| A   | A1  | A2  |     | A4  |     |     |     |     |     |      |      |      |
| B   | B1  | B2  | B3  | B4  | B5  |     |     |     |     |      |      |      |
| C   | C1  | C2  | C3  | C4  | C5  |     |     |     |     |      |      |      |
| D   | D1  | D2  | D3  | D4  | D5  |     |     |     |     |      |      |      |
| E   | E1  |     | E3  | E4  | E5  |     |     |     |     |      |      |      |
| F   |     |     |     | F4  |     |     |     |     |     |      |      |      |
| G   |     |     |     |     |     |     |     |     |     |      |      |      |
| H   |     |     |     |     |     |     |     |     |     |      |      |      |

This method uses the Python tabulate package (https://pypi.org/project/tabulate/). The parameters are identical to that of the tabulate function and are passed along to it, except for tabular_data and headers, which are computed from this plate map. In particular, the parameter tablefmt has default value ‘pipe’, which creates a Markdown format. To create other formats such as HTML, change the value of tablefmt; see https://github.com/astanin/python-tabulate#readme for other possible formats.

Parameters:

• well_marker (Optional[Union[str, Callable[[str], str]]]) – By default the strand’s name is put in the relevant plate entry. If well_marker is specified and is a string, then that string is put into every well with a strand in the plate map instead. This is useful for printing plate maps that just put, for instance, an ‘X’ in the well to pipette (e.g., specify well_marker='X'), e.g., for experimental mixes that use only some strands in the plate. To enable the string to depend on the well position (instead of being the same string in every well), well_marker can also be a function that takes as input a string representing the well (such as "B3" or "E11"), and outputs a string. For example, giving the identity function mix.to_table(well_marker=lambda x: x) puts the well address itself in the well.

• title_level (int) – The “title” is the first line of the returned string, which contains the plate’s name and volume to pipette. The title_level controls the size, with 1 being the largest size, (header level 1, e.g., # title in Markdown or <h1>title</h1> in HTML) and 6 being the smallest size.

• warn_unsupported_title_format (bool) – If True, prints a warning if tablefmt is a currently unsupported option for the title. The currently supported formats for the title are ‘github’, ‘html’, ‘unsafehtml’, ‘rst’, ‘latex’, ‘latex_raw’, ‘latex_booktabs’, “latex_longtable”. If tablefmt is another valid option, then the title will be the Markdown format, i.e., same as for tablefmt = ‘github’.

• vertical_borders (bool) – If true, then tablefmt must be set to html or unsafehtml, and the returned HTML will use inline styles to ensure there are vertical borders between columns of the table. The vertical borders make it easier to see which column a well is in. This is useful when rendering in a Jupyter notebook, since the inline styles will be preserved when saving the Jupyter notebook using the nbconvert tool: https://nbconvert.readthedocs.io/en/latest/

• tablefmt (str) – By default set to ‘pipe’ to create a Markdown table. For other options see https://github.com/astanin/python-tabulate#readme

• stralign (str) – See https://github.com/astanin/python-tabulate#readme

• missingval (str) – See https://github.com/astanin/python-tabulate#readme

• showindex (str) – See https://github.com/astanin/python-tabulate#readme

• disable_numparse (bool) – See https://github.com/astanin/python-tabulate#readme

• colalign (Optional[bool]) – See https://github.com/astanin/python-tabulate#readme

Returns:

a string representation of this plate map

Return type:

str

scadnano.bases_complementary(base1, base2, allow_wildcard=False, allow_none=False)

Indicates if base1 and base2 are complementary DNA bases.

Parameters:

• base1 (str) – first DNA base

• base2 (str) – second DNA base

• allow_wildcard (bool) – if true a “wildcard” (the symbol ‘?’) is considered to be complementary to anything

• allow_none (bool) – if true the object None is considered to be complementary to anything

Returns:

whether base1 and base2 are complementary DNA bases

Return type:

bool

scadnano.reverse_complementary(seq1, seq2, allow_wildcard=False, allow_none=False)

Indicates if seq1 and seq2 are reverse complementary DNA sequences.

Parameters:

• seq1 (str) – first DNA sequence

• seq1 – second DNA sequence

• allow_wildcard (bool) – if true a “wildcard” (the symbol ‘?’) is considered to be complementary to anything

• allow_none (bool) – if true the object None is considered to be complementary to anything

• seq2 (str) –

Returns:

whether seq1 and seq2 are reverse complementary DNA sequences

Return type:

bool

class scadnano.Design(*, helices=None, groups=None, strands=None, grid=Grid.none, helices_view_order=None, geometry=None)

Object representing the entire design of the DNA structure.

automatically_assign_color: bool = True

If automatically_assign_color = False, then for any Strand such that Strand.color = None, do not automatically assign a Color to it. In this case color will be set to its default of None and will not be written to the JSON with Design.write_scadnano_file() or Design.to_json().

strands: List[Strand[StrandLabel, DomainLabel]]

All of the Strand’s in this Design.

Required field.

geometry: Geometry

Controls some geometric/physical aspects of this Design.

groups: Dict[str, HelixGroup] = None

HelixGroup’s in this Design.

helices: Dict[int, Helix] = None

All of the Helix’s in this Design. This is a dictionary mapping index to the Helix with that index; if helices have indices 0, 1, …, num_helices-1, then this can be used as a list of Helices.

Optional field. If not specified, then the number of helices will be just large enough to store the largest index Domain.helix stored in any Domain in Design.strands.

property helices_view_order: List[int]

Return helices_view_order of this Design if no HelixGroup’s are being used, otherwise raise a ValueError.

Returns:

helices_view_order of this Design

property grid: Grid

Return grid of this Design if no HelixGroup’s are being used, otherwise raise a ValueError.

Returns:

grid of this Design

set_grid(grid)

Sets the grid of the default HelixGroup, if the default is being used, otherwise raises an exception.

Parameters:

grid (Grid) – new grid to set for the (only) HelixGroup in this Design

Raises:

IllegalDesignError – if there is more than one HelixGroup in this Design

Return type:

None

helices_idxs_in_group(group_name)

Indexes of Helix’s in this group. Must be associated with a Design for this to work.

Parameters:

group_name (str) – name of group

Returns:

list of indices of Helix’s in this HelixGroup

Return type:

List[int]

pitch_of_helix(helix)

Same as the pitch of helix’s HelixGroup

Parameters:

helix (Helix) –

Return type:

float

yaw_of_helix(helix)

Same as the yaw of helix’s HelixGroup

Parameters:

helix (Helix) –

Return type:

float

roll_of_helix(helix)

Roll of helix’s HelixGroup plus Helix.roll

Parameters:

helix (Helix) –

Return type:

float

static from_scadnano_file(filename)

Loads a Design from the file with the given name.

Parameters:

filename (str) – name of the file with the design. Should be a JSON file ending in .sc

Returns:

Design described in the file

Return type:

Design

static from_scadnano_json_str(json_str)

Loads a Design from the given JSON string.

Parameters:

json_str (str) – JSON description of the Design

Returns:

Design described in the JSON string

Return type:

Design

static from_scadnano_json_map(json_map)

Loads a Design from the given JSON object (i.e., Python object obtained by calling json.loads(json_str) from a string representing contents of a JSON file.

Parameters:

json_map (dict) – map describing the Design; should be JSON serializable via encode(json_map)

Returns:

Design described in the object

Return type:

Design

property scaffold: Optional[Strand]

Returns the first scaffold in this Design, if there is one, or None otherwise.

base_pairs(allow_mismatches=False)

Base pairs in this design, represented as a dict mapping a Helix.idx to a list of offsets on that helix where two strands are.

If a Helix has no base pairs, then its Helix.idx is not a key in the returned dict.

Parameters:

allow_mismatches (bool) – if True, then all offsets on a Helix where there is both a forward and reverse Domain will be included. Otherwise, only offsets where the Domain’s have complementary bases will be included.

Returns:

all base pairs (helix_idx, offset) in this Design

Return type:

Dict[int, List[int]]

static from_cadnano_v2(directory='', filename=None, json_dict=None)

Creates a Design from a cadnano v2 design. The design can either be specified as a filename (assumed to be the a JSON file containing the cadnano design) or as a Python dictionary, assumed to be the result of importing the JSON from the cadnano file.

Exactly one of filename or json_dict should be specified.

Parameters:

• directory (str) – directory in which to look for filename; current directory by default. Ignored if json_dict is specified.

• filename (Optional[str]) – name of file containing cadnano design. Mutually exclusive with json_dict.

• json_dict (Optional[dict]) – cadnano design represented as a Python dict. (assumed to be the result of json.load on a cadnano file)

Returns:

An scadnano design equivalent to the specified cadnano design.

Return type:

Design

plate_maps(warn_duplicate_strand_names=True, plate_type=PlateType.wells96, strands=None)

Returns a list of PlateMap’s from this Design. Each PlateMap can be exported to a string, in Markdown format by default, by calling PlateMap.to_table(), generating a string such as this:

plate "5 monomer synthesis"

|     | 1    | 2      | 3      | 4    | 5        | 6   | 7   | 8   | 9   | 10   | 11   | 12   |
|-----|------|--------|--------|------|----------|-----|-----|-----|-----|------|------|------|
| A   | mon0 | mon0_F |        | adp0 |          |     |     |     |     |      |      |      |
| B   | mon1 | mon1_Q | mon1_F | adp1 | adp_sst1 |     |     |     |     |      |      |      |
| C   | mon2 | mon2_F | mon2_Q | adp2 | adp_sst2 |     |     |     |     |      |      |      |
| D   | mon3 | mon3_Q | mon3_F | adp3 | adp_sst3 |     |     |     |     |      |      |      |
| E   | mon4 |        | mon4_Q | adp4 | adp_sst4 |     |     |     |     |      |      |      |
| F   |      |        |        | adp5 |          |     |     |     |     |      |      |      |
| G   |      |        |        |      |          |     |     |     |     |      |      |      |
| H   |      |        |        |      |          |     |     |     |     |      |      |      |

See the documentation for PlateMap.to_table() for more information on configuring the returned string format.

All Strand’s in the design that have a field Strand.idt with Strand.idt.plate specified are included in some returned PlateMap. The number of PlateMap’s in the returned list is equal to the number of different plate names specified across all Strand’s in the design.

If parameter strands is given, then a subset of strands is included. This is useful for specifying a mix of strands for a particular experiment, which come from a plate but does not include every strand in the plate.

Parameters:

• warn_duplicate_strand_names (bool) – If True, prints a warning to the screen if multiple Strand’s exist with the same value for Strand.name.

• plate_type (PlateType) – Type of plate: 96 or 384 well.

• strands (Optional[Iterable[Strand]]) – If specified, only the Strand’s in strands are put in the PlateMap.

Returns:

list of PlateMap’s for Strand’s in this design with IDT plates specified; length of list is equal to number of unique plate names among all Strand’s in this design

Return type:

List[PlateMap]

modifications(mod_type=None)

Returns either set of all modifications in this Design, or set of all modifications of a given type (5’, 3’, or internal).

Parameters:

mod_type (Optional[ModificationType]) – type of modifications (5’, 3’, or internal); if not specified, all three types are returned

Returns:

Set of all modifications in this Design (possibly of a given type).

Return type:

Set[Modification]

draw_strand(helix, offset)

Used for chained method building the Strand domain by domain, in order from 5’ to 3’. For example

design.draw_strand(0, 7).to(10).cross(1).to(5).cross(2).to(15)

This creates a Strand in this Design equivalent to

design.add_strand(Strand([
    sc.Domain(0, True, 7, 10),
    sc.Domain(1, False, 5, 10),
    sc.Domain(2, True, 5, 15),
]))

Loopouts can also be included:

design.draw_strand(0, 7).to(10).cross(1).to(5).loopout(2, 3).to(15)

This creates a Strand in this Design equivalent to

design.add_strand(Strand([
    sc.Domain(0, True, 7, 10),
    sc.Domain(1, False, 5, 10),
    sc.Loopout(3),
    sc.Domain(2, True, 5, 15),
]))

Each call to Design.draw_strand(), StrandBuilder.cross(), StrandBuilder.loopout(), StrandBuilder.to() StrandBuilder.move() StrandBuilder.update_to(), returns a StrandBuilder object.

Each call to StrandBuilder.to(), StrandBuilder.move(), StrandBuilder.update_to(), or StrandBuilder.loopout() modifies the Design by replacing the Strand with an updated version.

See the documentation for StrandBuilder for the methods available to call in this way.

Parameters:

• helix (int) – starting Helix

• offset (int) – starting offset on helix

Returns:

StrandBuilder object representing the partially completed Strand

Return type:

StrandBuilder

strand(helix, offset)

Same functionality as Design.draw_strand().

Deprecated since version 0.17.2: Use Design.draw_strand() instead, which is a better name. This method will be removed in a future version.

Parameters:

• helix (int) –

• offset (int) –

Return type:

StrandBuilder

assign_m13_to_scaffold(rotation=5587, variant=M13Variant.p7249)

Assigns the scaffold to be the sequence of M13: m13() with the given rotation and M13Variant.

Raises IllegalDesignError if the number of scaffolds is not exactly 1.

Parameters:

• rotation (int) – rotation of M13 to use. See m13() for explanation.

• variant (M13Variant) – which variant of M13 to use. See M13Variant.

Return type:

None

to_cadnano_v2_serializable(name='')

Converts the design to a JSON-serializable Python object (a dict) representing the cadnano v2 format. Calling json.dumps on this object will result in a string representing the cadnano c2 format; this is essentially what is done in Design.to_cadnano_v2_json().

Please see the spec https://github.com/UC-Davis-molecular-computing/scadnano-python-package/blob/main/misc/cadnano-format-specs/v2.txt for more info on that format.

Parameters:

name (str) – Name of the design.

Returns:

a Python dict representing the cadnano v2 format for this Design

Return type:

Dict[str, Any]

to_cadnano_v2_json(name='', whitespace=True)

Converts the design to the cadnano v2 format.

Please see the spec https://github.com/UC-Davis-molecular-computing/scadnano-python-package/blob/main/misc/cadnano-format-specs/v2.txt for more info on that format.

If the cadnano file is intended to be used with CanDo (https://cando-dna-origami.org/), the optional parameter whitespace must be set to False.

Parameters:

• name (str) – Name of the design.

• whitespace (bool) – Whether to include whitespace in the exported file. Set to False to use this with CanDo (https://cando-dna-origami.org/), since that tool generates an error if the cadnano file contains whitespace.

Returns:

a string in the cadnano v2 format representing this Design

Return type:

str

set_helices_view_order(helices_view_order)

Sets helices_view_order.

Parameters:

helices_view_order (List[int]) – new view order of helices

Return type:

None

strands_starting_on_helix(helix)

Return list of Strand’s that begin (have their 5’ end) on the Helix with index helix.

Parameters:

helix (int) –

Return type:

List[Strand]

strands_ending_on_helix(helix)

Return list of Strand’s that finish (have their 3’ end) on the Helix with index helix.

Parameters:

helix (int) –

Return type:

List[Strand]

domain_at(helix, offset, forward)

Return Domain that overlaps offset on helix with idx helix and has Domain.forward = True, or None if there is no such Domain.

Parameters:

• helix (int) – TODO

• offset (int) – TODO

• forward (bool) – TODO

Returns:

TODO

Return type:

Optional[Domain]

domains_at(helix, offset)

Return list of Domain’s that overlap offset on helix with idx helix.

If constructed properly, this list should have 0, 1, or 2 elements.

Parameters:

• helix (int) –

• offset (int) –

Return type:

List[Domain]

add_strand(strand)

Add strand to this design.

Parameters:

strand (Strand) –

Return type:

None

remove_strand(strand)

Remove strand from this design.

Parameters:

strand (Strand) –

Return type:

None

append_domain(strand, domain)

Same as Design.insert_domain, but inserts at end.

Parameters:

• strand (Strand) – strand to append domain to

• domain (Union[Domain, Loopout, Extension]) – Domain or Loopout to append to Strand

Return type:

None

insert_domain(strand, order, domain)

Insert Domain into strand at index given by order. Uses same indexing as Python lists, e.g., design.insert_domain(strand, domain, 0) inserts domain as the new first Domain.

Parameters:

• strand (Strand) –

• order (int) –

• domain (Union[Domain, Loopout, Extension]) –

Return type:

None

remove_domain(strand, domain)

Remove Domain from strand.

Parameters:

• strand (Strand) –

• domain (Union[Domain, Loopout]) –

Return type:

None

to_json(suppress_indent=True)

Return string representing this Design, suitable for reading by scadnano if written to a JSON file ending in extension default_scadnano_file_extension.

Parameters:

suppress_indent (bool) –

whether to suppress indenting JSON for “small” objects such as short lists, e.g., grid coordinates. If True, something like this will be written:

{
  "grid_position": [1, 2]
}

instead of this:

{
  "grid_position": [
    1,
    2
  ]
}

Return type:

str

add_deletion(helix, offset)

Adds a deletion to every scadnano.Strand at the given helix and base offset.

Parameters:

• helix (int) –

• offset (int) –

Return type:

None

add_insertion(helix, offset, length)

Adds an insertion with the given length to every scadnano.Strand at the given helix and base offset, with the given length.

Parameters:

• helix (int) –

• offset (int) –

• length (int) –

Return type:

None

set_start(domain, start)

Sets Domain.start to start.

Parameters:

• domain (Domain) –

• start (int) –

Return type:

None

set_end(domain, end)

Sets Domain.end to end.

Parameters:

• domain (Domain) –

• end (int) –

Return type:

None

move_strand_offsets(delta)

Moves all strands backward (if delta < 0) or forward (if delta > 0) by delta.

Parameters:

delta (int) –

Return type:

None

move_strands_on_helices(delta)

Moves all strands up (if delta < 0) or down (if delta > 0) by the number of helices given by delta.

Parameters:

delta (int) –

Return type:

None

assign_dna(strand, sequence, assign_complement=True, domain=None, check_length=False)

Assigns sequence as DNA sequence of strand.

If any scadnano.Strand is bound to strand, it is assigned the reverse Watson-Crick complement of the relevant portion, and any remaining portions of the other strand that have not already been assigned a DNA sequence are assigned to be the symbol DNA_base_wildcard.

Before assigning, sequence is first forced to be the same length as strand as follows: If sequence is longer, it is truncated. If sequence is shorter, it is padded with DNA_base_wildcard’s. This can be disabled by setting check_length to True, in which case the method raises an IllegalDesignError if the lengths do not match.

All whitespace in sequence is removed, and lowercase bases ‘a’, ‘c’, ‘g’, ‘t’ are converted to uppercase.

Parameters:

• strand (Strand) – Strand to assign DNA sequence to

• sequence (str) – string of DNA bases to assign

• assign_complement (bool) – Whether to assign the complement DNA sequence to any Strand that is bound to this one (default True)

• domain (Optional[Union[Domain, Loopout, Extension]]) – Domain on strand to assign. If None, then the whole Strand is given a DNA sequence. Otherwise, only domain is assigned, and the rest of the Domain’s on strand are left alone (either keeping their DNA sequence, or being assigned DNA_base_wildcard if no DNA sequence was previously assigned.) If domain is specified, then len(sequence) must be least than or equal to the number of bases on domain. (i.e., domain.dna_length())

• check_length (bool) – If True, raises IllegalDesignError if length of Strand or Domain being assigned to does not match the length of the DNA sequence.

Raises:

IllegalDesignError – If check_length is True and the length of Strand or Domain being assigned to does not match the length of the DNA sequence.

Return type:

None

to_idt_bulk_input_format(delimiter=',', key=None, warn_duplicate_name=False, only_strands_with_idt=False, export_scaffold=False, export_non_modified_strand_version=False)

Called by Design.write_idt_bulk_input_file() to determine what string to write to the file. This function can be used to get the string directly without creating a file.

Parameters have the same meaning as in Design.write_idt_bulk_input_file().

Returns:

string that is written to the file in the method Design.write_idt_bulk_input_file().

Parameters:

• delimiter (str) –

• key (Optional[Callable[[Strand], Any]]) –

• warn_duplicate_name (bool) –

• only_strands_with_idt (bool) –

• export_scaffold (bool) –

• export_non_modified_strand_version (bool) –

Return type:

str

write_idt_bulk_input_file(*, directory='.', filename=None, key=None, extension=None, delimiter=',', warn_duplicate_name=True, only_strands_with_idt=False, export_scaffold=False, export_non_modified_strand_version=False)

Write .idt text file encoding the strands of this Design with the field Strand.idt, suitable for pasting into the “Bulk Input” field of IDT (Integrated DNA Technologies, Coralville, IA, https://www.idtdna.com/), with the output file having the same name as the running script but with .py changed to .idt, unless filename is explicitly specified. For instance, if the script is named my_origami.py, then the sequences will be written to my_origami.idt. If filename is not specified but extension is, then that extension is used instead of idt. At least one of filename or extension must be None.

The string written is that returned by Design.to_idt_bulk_input_format().

Parameters:

• directory (str) – specifies a directory in which to place the file, either absolute or relative to the current working directory. Default is the current working directory.

• filename (Optional[str]) – optional custom filename to use (instead of currently running script)

• key (Optional[Callable[[Strand], Any]]) –

  key function used to determine order in which to output strand sequences. Some useful defaults are provided by strand_order_key_function()

• extension (Optional[str]) – alternate filename extension to use (instead of idt)

• delimiter (str) – is the symbol to delimit the four IDT fields name,sequence,scale,purification.

• warn_duplicate_name (bool) – if True prints a warning when two different Strand’s have the same IDTFields.name and the same Strand.dna_sequence. An IllegalDesignError is raised (regardless of the value of this parameter) if two different Strand’s have the same name but different sequences, IDT scales, or IDT purifications.

• only_strands_with_idt (bool) – If False (the default), all non-scaffold sequences are output, with reasonable default values chosen if the field Strand.idt is missing. (though scaffold is included if export_scaffold is True). If True, then strands lacking the field Strand.idt will not be exported.

• export_scaffold (bool) – If False (the default), scaffold sequences are not exported. If True, scaffold sequences on strands output according to only_strands_with_idt (i.e., scaffolds will be exported, unless they lack the field Strand.idt and only_strands_with_idt is True).

• export_non_modified_strand_version (bool) – For any Strand with a Modification, also export a version of the Strand without any modifications. The name for this Strand is the original name with ‘_nomods’ appended to it.

Return type:

None

write_idt_plate_excel_file(*, directory='.', filename=None, key=None, warn_duplicate_name=False, only_strands_with_idt=False, export_scaffold=False, use_default_plates=True, warn_using_default_plates=True, plate_type=PlateType.wells96, export_non_modified_strand_version=False)

Write .xls (Microsoft Excel) file encoding the strands of this Design with the field Strand.idt, suitable for uploading to IDT (Integrated DNA Technologies, Coralville, IA, https://www.idtdna.com/) to describe a 96-well or 384-well plate (https://www.idtdna.com/site/order/plate/index/dna/), with the output file having the same name as the running script but with .py changed to .xls, unless filename is explicitly specified. For instance, if the script is named my_origami.py, then the sequences will be written to my_origami.xls.

If the last plate as fewer than 24 strands for a 96-well plate, or fewer than 96 strands for a 384-well plate, then the last two plates are rebalanced to ensure that each plate has at least that number of strands, because IDT charges extra for a plate with too few strands: https://www.idtdna.com/pages/products/custom-dna-rna/dna-oligos/custom-dna-oligos

Parameters:

• directory (str) – specifies a directory in which to place the file, either absolute or relative to the current working directory. Default is the current working directory.

• filename (Optional[str]) – custom filename if default (explained above) is not desired

• key (Optional[Callable[[Strand], Any]]) –

  key function used to determine order in which to output strand sequences. Some useful defaults are provided by strand_order_key_function()

• warn_duplicate_name (bool) – if True prints a warning when two different Strand’s have the same IDTFields.name and the same Strand.dna_sequence. An IllegalDesignError is raised (regardless of the value of this parameter) if two different Strand’s have the same name but different sequences, IDT scales, or IDT purifications.

• only_strands_with_idt (bool) – If False (the default), all non-scaffold sequences are output, with reasonable default values chosen if the field Strand.idt is missing. (though scaffold is included if export_scaffold is True). If True, then strands lacking the field Strand.idt will not be exported. If False, then use_default_plates must be True.

• export_scaffold (bool) – If False (the default), scaffold sequences are not exported. If True, scaffold sequences on strands output according to only_strands_with_idt (i.e., scaffolds will be exported, unless they lack the field Strand.idt and only_strands_with_idt is True).

• use_default_plates (bool) – Use default values for plate and well (ignoring those in idt fields, which may be None). If False, each Strand to export must have the field Strand.idt, so in particular the parameter only_strands_with_idt must be True.

• warn_using_default_plates (bool) – specifies whether, if use_default_plates is True, to print a warning for strands whose Strand.idt has the fields IDTFields.plate and IDTFields.well, since use_default_plates directs these fields to be ignored.

• plate_type (PlateType) – a PlateType specifying whether to use a 96-well plate or a 384-well plate if the use_default_plates parameter is True. Ignored if use_default_plates is False, because in that case the wells are explicitly set by the user, who is free to use coordinates for either plate type.

• export_non_modified_strand_version (bool) – For any Strand with a Modification, also export a version of the Strand without any modifications. The name for this Strand is the original name with ‘_nomods’ appended to it.

Return type:

None

to_oxview_format(warn_duplicate_strand_names=True, use_strand_colors=True)

Exports to oxView format.

Parameters:

• warn_duplicate_strand_names (bool) – if True, prints a warning to the screen indicating when strands are found to have duplicate names. (default: True)

• use_strand_color – if True (default), sets the color of each nucleotide in a strand in oxView to the color of the strand.

• use_strand_colors (bool) –

Return type:

dict

write_oxview_file(directory='.', filename=None, warn_duplicate_strand_names=True, use_strand_colors=True)

Writes an oxView file rerpesenting this design.

Parameters:

• directory (str) – directy in which to write the file (default: current working directory)

• filename (Optional[str]) – name of the file to write (default: name of the running script with .oxview extension)

• warn_duplicate_strand_names (bool) – if True, prints a warning to the screen indicating when strands are found to have duplicate names. (default: True)

• use_strand_color – if True (default), sets the color of each nucleotide in a strand in oxView to the color of the strand.

• use_strand_colors (bool) –

Return type:

None

to_oxdna_format(warn_duplicate_strand_names=True)

Exports to oxdna format.

The three angles of each HelixGroup are interpreted to be applied in the following order: first HelixGroup.yaw, then HelixGroup.pitch, then HelixGroup.roll, using the “intrinsic rotation” convention (see https://en.wikipedia.org/wiki/Euler_angles#Conventions_by_intrinsic_rotations). The value Helix.roll is added to the value HelixGroup.roll.

Parameters:

warn_duplicate_strand_names (bool) – If True, prints a warning to the screen indicating when strands are found to have duplicate names.

Returns:

two strings that are the contents of the .dat and .top file suitable for reading by oxdna (https://sulcgroup.github.io/oxdna-viewer/)

Return type:

Tuple[str, str]

write_oxdna_files(directory='.', filename_no_extension=None, warn_duplicate_strand_names=True)

Write text file representing this Design, suitable for reading by oxdna (https://sulcgroup.github.io/oxdna-viewer/), with the output files having the same name as the running script but with .py changed to .dat and .top, unless filename_no_extension is explicitly specified. For instance, if the script is named my_origami.py, then the design will be written to my_origami.dat and my_origami.top.

The strings written are those returned by Design.to_oxdna_format().

The three angles of each HelixGroup are interpreted to be applied in the following order: first HelixGroup.yaw, then HelixGroup.pitch, then HelixGroup.roll, using the “intrinsic rotation” convention (see https://en.wikipedia.org/wiki/Euler_angles#Conventions_by_intrinsic_rotations). The value Helix.roll is added to the value HelixGroup.roll.

Parameters:

• directory (str) – directory in which to put file (default: current working directory)

• filename_no_extension (Optional[str]) – filename without extension (default: name of running script without .py).

• warn_duplicate_strand_names (bool) – If True, prints a warning to the screen indicating when strands are found to have duplicate names.

Return type:

None

write_scadnano_file(filename=None, directory='.', extension=None, suppress_indent=True, warn_duplicate_strand_names=True)

Write text file representing this Design, suitable for reading by the scadnano web interface, with the output file having the same name as the running script but with .py changed to default_scadnano_file_extension, unless filename is explicitly specified. For instance, if the script is named my_origami.py, then the design will be written to my_origami.sc. If extension is specified (but filename is not), then the design will be written to my_origami.<extension>

The string written is that returned by Design.to_json().

Parameters:

• filename (Optional[str]) – filename (default: name of script with .py replaced by .sc). Mutually exclusive with extension

• directory (str) – directory in which to put file (default: current working directory)

• extension (Optional[str]) – extension for filename (default: .sc) Mutually exclusive with filename

• warn_duplicate_strand_names (bool) – If True, prints a warning to the screen indicating when strands are found to have duplicate names.

• suppress_indent (bool) –

  whether to suppress indenting JSON for “small” objects such as short lists, e.g., grid coordinates. If True, something like this will be written:

  {
    "grid_position": [1, 2]
  }
  

  instead of this:

  {
    "grid_position": [
      1,
      2
    ]
  }
  

Return type:

None

write_cadnano_v2_file(directory='.', filename=None, whitespace=True)

Write .json file representing this Design, suitable for reading by cadnano v2.

The string written is that returned by Design.to_cadnano_v2().

If the cadnano file is intended to be used with CanDo (https://cando-dna-origami.org/), the optional parameter whitespace must be set to False.

Parameters:

• directory (str) – directory in which to place the file, either absolute or relative to the current working directory. Default is the current working directory.

• whitespace (bool) – Whether to include whitespace in the exported file. Set to False to use this with CanDo (https://cando-dna-origami.org/), since that tool generates an error if the cadnano file contains whitespace.

• filename (Optional[str]) – The output file has the same name as the running script but with .py changed to .json, unless filename is explicitly specified. For instance, if the script is named my_origami.py, then if filename is not specified, the design will be written to my_origami.json.

Return type:

None

add_nick(helix, offset, forward, new_color=True)

Add nick to Domain on Helix with index helix, in direction given by forward, at offset offset. The two Domain’s created by this nick will have 5’/3’ ends at offsets offset and offset-1.

For example, if there is a Domain with Domain.helix = 0, Domain.forward = True, Domain.start = 0, Domain.end = 10, then calling add_nick(helix=0, offset=5, forward=True) will split it into two Domain’s, with one domains having the fields Domain.helix = 0, Domain.forward = True, Domain.start = 0, Domain.end = 5, (recall that Domain.end is exclusive, meaning that the largest offset on this Domain is 4 = offset-1) and the other domain having the fields Domain.helix = 0, Domain.forward = True, Domain.start = 5, Domain.end = 10.

If the Strand is circular, then it will be made linear with the 5’ and 3’ ends at the nick position, modified in place. Otherwise, this Strand will be deleted from the design, and two new Strand’s will be added.

Parameters:

• helix (int) – index of helix where nick will occur

• offset (int) – offset to nick (nick will be between offset and offset-1)

• forward (bool) – forward or reverse Domain on helix at offset?

• new_color (bool) – whether to assign a new color to one of the Strand’s resulting from the nick. If False, both Strand’s created have the same color as the original. If True, one Strand keeps the same color as the original and the other is assigned a new color.

Return type:

None

ligate(helix, offset, forward)

Reverse operation of Design.add_nick(). “Ligates” a nick between two adjacent Domain’s in the same direction on a Helix with index helix, in direction given by forward, at offset offset.

For example, if there are a Domain’s with Domain.helix = 0, Domain.forward = True, Domain.start = 0, Domain.end = 5, (recall that Domain.end is exclusive, meaning that the largest offset on this Domain is 4 = offset-1) and the other domain having the fields Domain.helix = 0, Domain.forward = True, Domain.start = 5, Domain.end = 10. then calling ligate(helix=0, offset=5, forward=True) will combine them into one Domain, having the fields Domain.helix = 0, Domain.forward = True, Domain.start = 0, Domain.end = 10.

If the Domain’s are on the same Strand (i.e., they are the 5’ and 3’ ends of that Strand, which is necessarily linear), then the Strand is made is circular in place, Otherwise, the two Strand’s of each Domain will be joined into one, replacing the previous strand on the 5’-most side of the nick (i.e., the one whose 3’ end terminated at the nick), and deleting the other strand.

Parameters:

• helix (int) – index of helix where nick will be ligated

• offset (int) – offset to ligate (nick to ligate must be between offset and offset-1)

• forward (bool) – forward or reverse Domain on helix at offset?

Return type:

None

add_half_crossover(helix, helix2, offset, forward, offset2=None, forward2=None)

Add a half crossover from helix helix at offset offset to helix2, on the strand with Strand.forward = forward.

Unlike Design.add_full_crossover(), which automatically adds a nick between the two half-crossovers, to call this method, there must already be nicks adjacent to the given offsets on the given helices. (either on the left or right side)

If the crossover is within a Strand, i.e., between its 5’ and ‘ ends, the Strand will simply be made circular, modifying it in place. Otherwise, the old two Strand’s will be deleted, and a new Strand added.

Parameters:

• helix (int) – index of one helix of half crossover

• helix2 (int) – index of other helix of half crossover

• offset (int) – offset on helix at which to add half crossover

• forward (bool) – direction of Strand on helix to which to add half crossover

• offset2 (Optional[int]) – offset on helix2 at which to add half crossover. If not specified, defaults to offset

• forward2 (Optional[bool]) – direction of Strand on helix2 to which to add half crossover. If not specified, defaults to the negation of forward

Return type:

None

add_full_crossover(helix, helix2, offset, forward, offset2=None, forward2=None)

Adds two half-crossovers, one at offset and another at offset-1. Other arguments have the same meaning as in Design.add_half_crossover(). A nick is automatically added on helix helix between offset and offset-1 if one is not already present, and similarly for offset2 on helix helix2.

Parameters:

• helix (int) – index of one helix of half crossover

• helix2 (int) – index of other helix of half crossover

• offset (int) – offset on helix at which to add half crossover

• forward (bool) – direction of Strand on helix to which to add half crossover

• offset2 (Optional[int]) – offset on helix2 at which to add half crossover. If not specified, defaults to offset

• forward2 (Optional[bool]) – direction of Strand on helix2 to which to add half crossover. If not specified, defaults to the negation of forward

Return type:

None

inline_deletions_insertions()

Converts deletions and insertions by “inlining” them. Insertions and deletions are removed, and their domains have their lengths altered. Also, major tick marks on the helices will be shifted to preserve their adjacency to bases already present. For example, if there are major tick marks at 0, 8, 18, 24, and a deletion between 0 and 8:

0      8         18    24    30
|--X---|---------|-----|------

then the domain is shortened by 1, the tick marks become 0, 7, 15, 23, and the helix’s maximum offset is shrunk by 1:

0     7         17    23    29
|-----|---------|-----|------

Similarly, if there are insertions (in the example below, the “2” represents an insertion of length 2, which represents 3 total bases), they are expanded

0      8         18    24    30
|--2---|---------|-----|------

then the domain is lengthened by 3:

0        10        20    26    32
|--------|---------|-----|------

And it works if there are both insertions and deletions:

0      8         18    24    30
|--2---|---------|--X--|------

then the domain is lengthened by 3:

0        10        20   25    31
|--------|---------|----|------

We assume that a major tick mark appears just to the LEFT of the offset it encodes, so the minimum and maximum offsets for tick marks are respectively the helix’s minimum offset and 1 plus its maximum offset, the latter being just to the right of the last offset on the helix.

Return type:

None

reverse_all()

Reverses “polarity” of every Strand in this Design.

No attempt is made to make any assigned DNA sequences match by reversing or rearranging them. Every Strand keeps the same DNA sequence it had before (unreversed), if one was assigned. It is recommended to assign/reassign DNA sequences after doing this operation.

Return type:

None

strand_with_name(name)

Parameters:

name (str) – name of a Strand.

Returns:

the Strand with name name, or None if no Strand in the Design has that name.

Return type:

Optional[Strand]

add_helix(idx, helix)

Adds helix as a new Helix with index idx to this Design.

Parameters:

• idx (int) – index of new Helix

• helix (Helix) – the new Helix

Return type:

None

scadnano.write_file_same_name_as_running_python_script(contents, extension, directory='.', filename=None, add_extension=False)

Writes a text file with contents whose name is (by default) the same as the name of the currently running script, but with extension .py changed to extension.

Parameters:

• contents (str) – contents of file to write

• extension (str) – extension to use

• directory (str) – directory in which to write file. If not specified, the current working directory is used.

• filename (Optional[str]) – filename to use instead of the currently running script

• add_extension (bool) –

Return type:

None

scadnano.grid_position_to_position(grid_position, grid, geometry)

Converts a grid position to a 3D position (a Position3D).

Parameters:

• grid_position (Tuple[int, int]) – pair of ints representing a grid position

• grid (Grid) – the Grid; cannot be Grid.none

• geometry (Geometry) – the Geometry object defining spacing parameters between grid positions

Returns:

the Position3D represented by grid_position in the grid grid; Note that the Position3D.z coordinate is always 0.

Return type:

Position3D

origami_rectangle

The origami_rectangle module defines the function origami_rectangle.create() for creating a DNA origami rectangle using the scadnano module.

class origami_rectangle.NickPattern(value)

Represents options for where to place nicks between staples.

staggered = 1

A nick appears in a given helix and column if the parity of the helix and column match (both even or both odd).

staggered_opposite = 2

A nick appears in a given helix and column if the parity of the helix and column don’t match (one is even and the other is odd).

CURRENTLY UNSUPPORTED.

even = 3

A nick appears in every column and only even-index helices.

CURRENTLY UNSUPPORTED.

odd = 4

A nick appears in every column and only odd-index helices.

CURRENTLY UNSUPPORTED.

origami_rectangle.staggered = NickPattern.staggered

Convenience reference defined so one can type origami_rectangle.staggered instead of origami_rectangle.NickPattern.staggered.

origami_rectangle.staggered_opposite = NickPattern.staggered_opposite

Convenience reference defined so one can type origami_rectangle.staggered_opposite instead of origami_rectangle.NickPattern.staggered_opposite.

CURRENTLY UNSUPPORTED.

origami_rectangle.even = NickPattern.even

Convenience reference defined so one can type origami_rectangle.even instead of origami_rectangle.NickPattern.even.

CURRENTLY UNSUPPORTED.

origami_rectangle.odd = NickPattern.odd

Convenience reference defined so one can type origami_rectangle.odd instead of origami_rectangle.NickPattern.odd.

CURRENTLY UNSUPPORTED.

origami_rectangle.create(*, num_helices, num_cols, assign_seq=True, seam_left_column=- 1, nick_pattern=NickPattern.staggered, twist_correction_deletion_spacing=0, twist_correction_start_col=1, twist_correction_deletion_offset=- 1, num_flanking_columns=1, num_flanking_helices=0, custom_scaffold=None, edge_staples=True, scaffold_nick_offset=- 1)

Creates a DNA origami rectangle with a given number of helices and “columns” (16-base-wide region in each helix). The columns include the 16-base regions on the end where potential “edge staples” go, as well as the two-column-wide “seam” region in the middle.

Below is an example diagram of the staples created by this function.

Consider for example the function call create(num_helices=8, num_cols=10, nick_pattern=origami_rectangle.staggered). The scaffold strand resulting from this call is shown below:

  #       C0       #       C1       #       C2       #       C3       #       C4       #       C5       #       C6       #       C7       #       C8       #       C9       #
H0 +--------------- ---------------- ---------------- ---------------- ---------------- ---------------- ---------------- ---------------- ---------------- ---------------+
   |                                                                                                                                                                       |
H1 +--------------- ---------------- ---------------- ---------------- ---------------+ +--------------- ---------------- ---------------- ---------------- ---------------+
                                                                                      | |
H2 +--------------- ---------------- ---------------- ---------------- ---------------+ +--------------- ---------------- ---------------- ---------------- ---------------+
   |                                                                                                                                                                       |
H3 +--------------- ---------------- ---------------- ---------------- ---------------+ +--------------- ---------------- ---------------- ---------------- ---------------+
                                                                                      | |
H4 +--------------- ---------------- ---------------- ---------------- ---------------+ +--------------- ---------------- ---------------- ---------------- ---------------+
   |                                                                                                                                                                       |
H5 +--------------- ---------------- ---------------- ---------------- ---------------+ +--------------- ---------------- ---------------- ---------------- ---------------+
                                                                                      | |
H6 +--------------- ---------------- ---------------- ---------------- ---------------+ +--------------- ---------------- ---------------- ---------------- ---------------+
   |                                                                                                                                                                       |
H7 +--------------- ---------------- ---------------- ---------------- ---------------] <--------------- ---------------- ---------------- ---------------- ---------------+

Helix indices are labelled H0, H1, … and column indices are labeled C0, C1, … Each single symbol -, +, <, >, [, ], + represents one DNA base, so each column is 16 bases wide. The # is a visual delimiter between columns and does not represent any bases, nor do spaces between the base-representing symbols. The 5’ end of a strand is indicated with [ or ] and the 3’ end is indicated with > or <. A crossover is indicated with

+
|
+

Below are the staples resulting from this same call.

  #       C0       #       C1       #       C2       #       C3       #       C4       #       C5       #       C6       #       C7       #       C8       #       C9       #
H0 <--------------+ +--------------- -------]<------+ +--------------- -------]<------+ +--------------- -------]<------+ +--------------- -------]<------+ +--------------]
                  | |                               | |                                                                 | |                               | |                               
H1 [--------------+ +------>[------+ +--------------+ +------>[------+ +--------------+ +------>[------+ +--------------+ +------>[------+ +--------------+ +-------------->
                                   | |                               | |                               | |                               | |                               
H2 <--------------+ +--------------+ +------]<------+ +--------------+ +------]<------+ +--------------+ +------]<------+ +--------------+ +------]<------+ +--------------]
                  | |                               | |                                                                 | |                               | |                               
H3 [--------------+ +------>[------+ +--------------+ +------>[------+ +--------------+ +------>[------+ +--------------+ +------>[------+ +--------------+ +-------------->
                                   | |                               | |                               | |                               | |                               
H4 <--------------+ +--------------+ +------]<------+ +--------------+ +------]<------+ +--------------+ +------]<------+ +--------------+ +------]<------+ +--------------]
                  | |                               | |                                                                 | |                               | |                               
H5 [--------------+ +------>[------+ +--------------+ +------>[------+ +--------------+ +------>[------+ +--------------+ +------>[------+ +--------------+ +-------------->
                                   | |                               | |                               | |                               | |                               
H6 <--------------+ +--------------+ +------]<------+ +--------------+ +------]<------+ +--------------+ +------]<------+ +--------------+ +------]<------+ +--------------]
                  | |                               | |                                                                 | |                               | |                               
H7 [--------------+ +------>[------- ---------------+ +------>[------- ---------------+ +------>[------- ---------------+ +------>[------- ---------------+ +-------------->

The seam crosses columns C4 and C5. The left and right edge staples respectively are in columns C0 and C9.

Prints warning if number of bases exceeds 7249 (length of standard M13 scaffold strand), but does not otherwise cause an error.

Here’s an example of using origami_rectangle.create to create a design for a 16-helix rectangle and write it to a file readable by scadnano. (By default the output file name is the same as the script calling scadnano.Design.write_scadnano_file() but with the extension .py changed to .dna.)

import origami_rectangle as rect

# XXX: ensure num_cols is even since we divide it by 2
design = rect.create(num_helices=16, num_cols=24, nick_pattern=rect.staggered)
design.write_scadnano_file()

However, we caution that create() is not intended to be very extensible for creating many different types of DNA origami. It is more intended as an example whose source code can be an efficient reference to learn the scadnano API.

Parameters:

• num_helices (int) – number of helices. must be even.

• num_cols (int) – number of “columns” as defined above. must be even and at least 4.

• assign_seq (bool) – whether to assign a DNA sequence to the scaffold. If True, uses custom_scaffold if it is not None, or M13 otherwise.

• seam_left_column (int) – specifies the location of the seam. (i.e., scaffold crossovers in the middle of the origami.) If positive, the seam occupies two columns, and seam_left_column specifies the column on the left. To make the crossover geometry work out, a nonnegative seam_left_column must be even, greater than 0, and less than num_helices - 2. If negative, it is calculated automatically to be roughly in the middle.

• nick_pattern (NickPattern) – describes whether nicks between staples should be “staggered” or not. See origami_rectangle.NickPattern for details.

• twist_correction_deletion_spacing (int) – If twist_correction_deletion_spacing > 0, adds deletions between crossovers in one out of every twist_correction_deletion_spacing columns. See this paper for an explanation of twist correction in DNA origami: Programmable molecular recognition based on the geometry of DNA nanostructures, Sungwook Woo and Paul W. K. Rothemund, Nature Chemistry, volume 3, pages 620–627 (2011) https://doi.org/10.1038/nchem.1070

• twist_correction_start_col (int) – ignored if twist_correction_deletion_spacing <= 0, otherwise it indicates the column at which to put the first deletions. Default = 1.

• twist_correction_deletion_offset (int) – the relative offset of the deletion, relative to the left side of the column.

• num_flanking_columns (int) – the number of empty columns on the helix on each side of the origami.

• num_flanking_helices (int) – the number of empty helices above and below the origami.

• custom_scaffold (Optional[str]) – the scaffold sequence to use. If set to None, the standard 7249-base M13 is used: scadnano.m13().

• edge_staples (bool) – indicates whether to include the edge staples. (Leaving them out prevents multiple origami rectangles from polymerizing in solution due to base stacking interactions on the left and right edges of the origami rectangle.)

• scaffold_nick_offset (int) – the position of the “nick” on the scaffold (the M13 scaffold is circular, so for such a scaffold this really represents where any unused and undepicted bases of the scaffold will form a loop-out). If negative (default value) then it will be chosen to be along the origami seam.

Returns:

a Design representing a DNA origami rectangle

Return type:

Design

Interoperability - cadnano v2

Scadnano provides function to convert design to and from cadnano v2:

• scadnano.DNADesign.from_cadnano_v2() will create a scadnano DNADesign from a cadnanov2 json file.

• scadnano.DNADesign.export_cadnano_v2() will produce a cadnanov2 json file from a scadnano design.

Important

All cadnanov2 designs can be imported to scadnano. However not all scadnano designs can be imported to cadnanov2, to be importable to cadnanov2 a scadnano design need to comply with the following points:

• The design cannot feature any Loopout as it is not a concept that exists in cadnanov2.

• Following cadnanov2 conventions, helices with even number must have their scaffold going forward and helices with odd number backward.

Also note that maximum helices offsets can be altered in a scadnano to cadnanov2 conversion as cadnanov2 needs max offsets to be a multiple of 21 in the hex grid and 32 in the rectangular grid. The conversion algorithm will choose the lowest multiple of 21 or 32 which fits the entire design.

The cadnanov2 json format does not embed sequences hence they will be lost after conversion.

Indices and tables

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