Scadnano

https://scadnano-python-package.readthedocs.io
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Scadnano is a Python library for describing and designing synthetic DNA nanostructures such as DNA...
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### Inline modification examples

Source: https://scadnano-python-package.readthedocs.io

Examples of creating modification objects for specific sequence extensions.

```python
t6_5p = Modification5Prime(display_text='6T', vendor_code='TTTTTT')
```

```python
t6_3p = Modification3Prime(display_text='6T', vendor_code='TTTTTT') # ERROR
```

--------------------------------

### StrandBuilder Example

Source: https://scadnano-python-package.readthedocs.io

Illustrates building a Strand using chained methods starting from Design.draw_strand(). StrandBuilder is an intermediate object and should not be instantiated directly.

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

--------------------------------

### Example: Creating a Hairpin Strand

Source: https://scadnano-python-package.readthedocs.io

Demonstrates how to create a Strand representing a hairpin using Domain and Loopout objects.

```APIDOC
## Example: Creating a Hairpin Strand

### Description
This example shows how to create a `Strand` that represents a hairpin with a stem length of 10 and a loop length of 5.

### Code
```python
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])
```
```

--------------------------------

### Get DNA Sequence Start Index

Source: https://scadnano-python-package.readthedocs.io

The `dna_index_start_domain()` method returns the starting index of a given domain within the strand's DNA sequence. This is useful for sequence manipulation or analysis.

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

--------------------------------

### Example: Creating a Strand with Chained Methods

Source: https://scadnano-python-package.readthedocs.io

Demonstrates creating a Strand using chained method calls on a Design object.

```APIDOC
## Example: Creating a Strand with Chained Methods

### Description
This example shows how to create a `Strand` using chained method calls, including a loopout, on a `Design` object.

### Code
```python
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)
```
```

--------------------------------

### Example Plate Map Table

Source: https://scadnano-python-package.readthedocs.io

An example of a plate map generated in Markdown table format, showing monomer synthesis layout with associated domains and modifications.

```markdown
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   |      |        |        |      |          |     |     |     |     |      |      |      |

```

--------------------------------

### Example Usage of origami_rectangle.create

Source: https://scadnano-python-package.readthedocs.io

Example call to create a DNA origami rectangle with 8 helices and 10 columns, using the staggered nick pattern. The scaffold strand resulting from this call is visualized.

```python
create(num_helices=8, num_cols=10, nick_pattern=origami_rectangle.staggered)
```

--------------------------------

### Domain Start/End Setting

Source: https://scadnano-python-package.readthedocs.io

Methods to set the start and end positions of a domain.

```APIDOC
## Set Domain End

### Description
Sets the `end` attribute of a `Domain` to the specified value.

### Parameters
* **domain** (Domain) - Required - The domain to modify.
* **end** (int) - Required - The new end position for the domain.

### Returns
None

### Return type
None
```

```APIDOC
## Set Domain Start

### Description
Sets the `start` attribute of a `Domain` to the specified value.

### Parameters
* **domain** (Domain) - Required - The domain to modify.
* **start** (int) - Required - The new start position for the domain.

### Returns
None

### Return type
None
```

--------------------------------

### Strand.dna_index_start_domain

Source: https://scadnano-python-package.readthedocs.io

Finds the starting index of a domain within the strand's DNA sequence.

```APIDOC
## Strand.dna_index_start_domain

### Description
Given a `Domain` or `Loopout` object, this method returns the starting index of that domain within the strand's overall DNA sequence string. For example, if a strand's sequence is 'AAA-C-GG-TTT-ACGT' and it has five domains, the indices returned for these domains would be 0, 3, 4, 6, and 9, respectively.

### Method
`Strand.dna_index_start_domain(domain)`

### Parameters

- **domain** (Domain | Loopout) - The domain or loopout for which to find the starting DNA index.

### Returns

An integer representing the index within the DNA sequence string where the specified domain's sequence begins.

### Example
```python
# Assuming 'my_strand' is a Strand object and 'target_domain' is one of its domains
start_index = my_strand.dna_index_start_domain(target_domain)
```
```

--------------------------------

### Plate Map with well_marker set to '*'

Source: https://scadnano-python-package.readthedocs.io

Example output when well_marker is set to '*' to indicate occupied wells.

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

--------------------------------

### GET /domain_at

Source: https://scadnano-python-package.readthedocs.io

Returns the domain that overlaps a specific offset on a helix.

```APIDOC
## GET /domain_at

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

### Parameters
#### Query Parameters
- **helix** (int) - Required
- **offset** (int) - Required
- **forward** (bool) - Required
```

--------------------------------

### Get 5' Offset

Source: https://scadnano-python-package.readthedocs.io

Returns the inclusive 5' offset of the entire strand.

```python
strand.offset_5p()
```

--------------------------------

### Markdown Plate Map Output

Source: https://scadnano-python-package.readthedocs.io

Example of the default Markdown table output generated by to_table().

```markdown
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   |      |        |        |      |          |     |     |     |     |      |      |      |
```

--------------------------------

### Create Strand with Multiple Domains

Source: https://scadnano-python-package.readthedocs.io

Assign StrandBuilder to a variable for complex strand creation, especially when using loops. This example demonstrates creating a scaffold strand with several domains and a 5' modification.

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

--------------------------------

### Create a Hairpin Strand

Source: https://scadnano-python-package.readthedocs.io

Demonstrates creating a hairpin structure using Domain and Loopout objects. Ensure scadnano is imported as sc.

```python
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])
```

--------------------------------

### Create Strand with Extensions

Source: https://scadnano-python-package.readthedocs.io

Use this to create a `Strand` with `Extension`s on both the 5' and 3' ends, flanking a central `Domain`. Ensure `scadnano` is imported.

```python
import scadnano as sc

domain = sc.Domain(helix=0, forward=True, start=0, end=10)
left_toehold = sc.Extension(num_bases=3)
right_toehold = sc.Extension(num_bases=2)
strand = sc.Strand([left_toehold, domain, right_toehold])
```

--------------------------------

### Create Strand with Chained Methods

Source: https://scadnano-python-package.readthedocs.io

Illustrates creating a strand using chained method calls on a Design object. Requires scadnano imported as sc.

```python
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)
```

--------------------------------

### Draw a strand using chained methods

Source: https://scadnano-python-package.readthedocs.io

Demonstrates building a strand domain by domain from 5' to 3' using chained method calls.

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

--------------------------------

### Strands by Helix

Source: https://scadnano-python-package.readthedocs.io

Retrieves lists of strands that start or end on a specific helix.

```APIDOC
## Strands Ending on Helix

### Description
Returns a list of `Strand` objects whose 3' end is located on the specified helix.

### Parameters
* **helix** (int) - Required - The index of the helix.

### Returns
A list of `Strand` objects ending on the specified helix.

### Return type
List[Strand]
```

```APIDOC
## Strands Starting on Helix

### Description
Returns a list of `Strand` objects whose 5' end is located on the specified helix.

### Parameters
* **helix** (int) - Required - The index of the helix.

### Returns
A list of `Strand` objects starting on the specified helix.

### Return type
List[Strand]
```

--------------------------------

### Loading Designs from Files

Source: https://scadnano-python-package.readthedocs.io

Details on how to load `Design` objects from cadnano v2 files, scadnano JSON files, and JSON strings.

```APIDOC
## Loading Designs from Files

### Description
This section covers the static methods available on the `Design` class for loading DNA designs from various sources, including cadnano v2 JSON files or dictionaries, and scadnano-specific JSON files or strings.

### Methods

#### `static Design.from_cadnano_v2(directory='', filename=None, json_dict=None)`
Creates a `Design` from a cadnano v2 JSON file or a Python dictionary representing the JSON content. Requires exactly one of `filename` or `json_dict` to be specified.

**Parameters:**
*   `directory` (str): Directory containing the `filename`. Ignored if `json_dict` is provided.
*   `filename` (str | None): Name of the cadnano v2 JSON file.
*   `json_dict` (dict | None): A Python dictionary representing the cadnano v2 JSON content.

**Returns:**
*   `Design`: An equivalent `Design` object.

#### `static Design.from_scadnano_file(filename)`
Loads a `Design` from a specified scadnano JSON file (ending in `.sc`).

**Parameters:**
*   `filename` (str): The path to the scadnano JSON file.

**Returns:**
*   `Design`: The `Design` object described in the file.

#### `static Design.from_scadnano_json_map(json_map)`
Loads a `Design` from a Python dictionary (JSON object).

**Parameters:**
*   `json_map` (dict): A dictionary representing the `Design` structure.

**Returns:**
*   `Design`: The `Design` object described by the dictionary.

#### `static Design.from_scadnano_json_str(json_str)`
Loads a `Design` from a JSON string.

**Parameters:**
*   `json_str` (str): A string containing the JSON description of the `Design`.

**Returns:**
*   `Design`: The `Design` object described in the JSON string.

### Request Example
```python
# Load from cadnano v2 file
design1 = Design.from_cadnano_v2(filename='my_design.json')

# Load from scadnano file
design2 = Design.from_scadnano_file('my_scadnano_design.sc')

# Load from JSON string
json_data = '{"helices": [], "strands": []}'
design3 = Design.from_scadnano_json_str(json_data)
```
```

--------------------------------

### Set Strand as Scaffold Using Method

Source: https://scadnano-python-package.readthedocs.io

Alternatively, create a `sc.Strand` object and then call the `.set_scaffold()` method to designate it as a scaffold. Ensure `scadnano` is imported as `sc`.

```python
import scadnano as sc

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

--------------------------------

### Get 3' Offset

Source: https://scadnano-python-package.readthedocs.io

Returns the inclusive 3' offset of the entire strand.

```python
strand.offset_3p()
```

--------------------------------

### StrandBuilder.move()

Source: https://scadnano-python-package.readthedocs.io

Extends the StrandBuilder with a new Domain relative to the current offset. If two instances of move() are chained, the offsets must move in the same direction.

```APIDOC
## POST /strandbuilder/move

### Description
Extends the StrandBuilder with a new Domain relative to the current offset. If two instances of move() are chained, the offsets must move in the same direction.

### Method
POST

### Endpoint
/strandbuilder/move

### Parameters
#### Query Parameters
- **delta** (int) - Required - 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.

### Request Example
```json
{
  "delta": 5
}
```

### Response
#### Success Response (200)
- **self** (StrandBuilder) - Returns the StrandBuilder instance.

#### Response Example
```json
{
  "self": "<StrandBuilder object>"
}
```
```

--------------------------------

### Get Helix Pitch

Source: https://scadnano-python-package.readthedocs.io

Retrieves the pitch of a given helix, which is the same as the pitch of its associated HelixGroup.

```python
pitch_of_helix(_helix_)
```

--------------------------------

### POST /strand/as_scaffold

Source: https://scadnano-python-package.readthedocs.io

Marks the strand currently being built as a scaffold.

```APIDOC
## POST /strand/as_scaffold

### Description
Makes the Strand being built a scaffold.

### Method
POST

### Response
#### Success Response (200)
- **self** (StrandBuilder) - The current StrandBuilder instance.
```

--------------------------------

### GET /base_pairs

Source: https://scadnano-python-package.readthedocs.io

Retrieves a mapping of helix indices to offsets where base pairs exist.

```APIDOC
## GET /base_pairs

### Description
Returns a dictionary mapping each helix index to a list of offsets where base pairs are located.

### Parameters
#### Query Parameters
- **allow_mismatches** (bool) - Optional - If True, includes all offsets where there is both a forward and reverse domain.
```

--------------------------------

### scadnano.write_file_same_name_as_running_python_script

Source: https://scadnano-python-package.readthedocs.io

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.

```APIDOC
## scadnano.write_file_same_name_as_running_python_script

### Description
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.

### Method
N/A (Function)

### Endpoint
N/A (Function)

### Parameters
#### Path Parameters
None

#### Query Parameters
None

#### Request Body
None

### 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. (Optional, defaults to '.')
* **add_extension** (bool) - whether to replace .py with extension (Optional)
* **filename** (str or None) - filename to use instead of the currently running script (Optional)

### Request Example
```python
scadnano.write_file_same_name_as_running_python_script("Hello, world!", ".txt", directory="/tmp")
```

### Response
#### Success Response (200)
* **None**: This function does not return any value.

#### Response Example
```json
{
  "example": null
}
```
```

--------------------------------

### Create Scaffold Strand with StrandBuilder

Source: https://scadnano-python-package.readthedocs.io

Use the `StrandBuilder.as_scaffold()` method after defining a strand with `design.strand()` to set it as a scaffold. This method is chained after strand definition and movement operations.

```python
import scadnano as sc

design = sc.Design(helices=[sc.Helix(max_offset=100) for _ in range(2)])
scaffold_strand = design.strand(0, 0).move(100).cross(1).move(-100).as_scaffold()
```

--------------------------------

### Strand Creation and Scaffold Assignment

Source: https://scadnano-python-package.readthedocs.io

Demonstrates different ways to create a Strand object and designate it as a scaffold.

```APIDOC
## Strand Creation and Scaffold Assignment

### Description
This section illustrates how to create a `sc.Strand` object and set it as a scaffold using various methods.

### Methods

1.  **Constructor**: Initialize a `Strand` with `is_scaffold=True`.
2.  **`set_scaffold()` method**: Call this method on an existing `Strand` object.
3.  **`StrandBuilder.as_scaffold()`**: Use the builder pattern when creating a strand via `Design.strand()`.

### Parameters for `sc.Strand` constructor:

- **domains** (List[Domain | Loopout | Extension]) - Required - The domains that make up the strand.
- **circular** (bool) - Optional - If True, the strand is circular.
- **color** (Color | None) - Optional - The color to display the strand.
- **vendor_fields** (VendorFields | None) - Optional - Vendor-specific fields.
- **is_scaffold** (bool) - Optional - If True, this strand is a scaffold.
- **modification_5p** (Modification5Prime | None) - Optional - 5' modification.
- **modification_3p** (Modification3Prime | None) - Optional - 3' modification.
- **modifications_int** (Dict[int, ModificationInternal]) - Optional - Internal modifications.
- **name** (str | None) - Optional - The name of the strand.
- **label** (str | None) - Optional - A label for the strand.
- **_helix_idx_domain_map** (Dict[int, List[Domain]]) - Internal mapping.
- **dna_sequence** (Optional[str]) - Optional - The DNA sequence of the strand.

### Request Example (Constructor)
```python
import scadnano as sc

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

### Request Example (`set_scaffold()`)
```python
import scadnano as sc

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

### Request Example (`StrandBuilder.as_scaffold()`)
```python
import scadnano as sc

design = sc.Design(helices=[sc.Helix(max_offset=100) for _ in range(2)])
scaffold_strand = design.strand(0, 0).move(100).cross(1).move(-100).as_scaffold()
```

### Notes
By default, scaffold strands are assigned a color that cadnano uses for scaffolds.
```

--------------------------------

### Get Domain Deletions

Source: https://scadnano-python-package.readthedocs.io

Returns a list of integer positions representing deletions within this Domain.

```python
deletions _: List[int]_¶
```

--------------------------------

### Design Creation and Strand Manipulation

Source: https://scadnano-python-package.readthedocs.io

Demonstrates how to add strands with domains and loopouts to a Design object, and how StrandBuilder methods modify the Design.

```APIDOC
## Design Creation and Strand Manipulation

### Description
This section illustrates the creation of `Strand` objects with multiple `Domain`s and the inclusion of `Loopout`s. It also explains how methods on the `StrandBuilder` object, such as `to()`, `cross()`, and `loopout()`, modify the `Design` by updating `Strand` objects.

### Methods

#### `design.add_strand(strand)`
Adds a `Strand` to the `Design`.

#### `design.draw_strand(helix, offset)`
Initiates the drawing of a new `Strand` on a specified `Helix` at a given `offset`. Returns a `StrandBuilder` object.

#### `StrandBuilder.to(offset)`
Extends the current `Strand` to a new `offset` on the same helix. Modifies the `Design`.

#### `StrandBuilder.cross(helix)`
Initiates a crossover to a different `Helix` at the current offset. Modifies the `Design`.

#### `StrandBuilder.loopout(length)`
Adds a `Loopout` of a specified `length`. Modifies the `Design`.

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

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

### Response Example
```python
# The design object is modified in place.
# The second example results in:
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),
]))
```
```

--------------------------------

### Get Yaw of Helix

Source: https://scadnano-python-package.readthedocs.io

Retrieves the yaw value of a given helix, which is equivalent to the yaw of its HelixGroup.

```python
yaw_of_helix(_helix_)[source]¶
```

--------------------------------

### Create Scaffold Strand in Constructor

Source: https://scadnano-python-package.readthedocs.io

Use the `is_scaffold=True` argument in the `sc.Strand` constructor to designate a strand as a scaffold. Ensure `scadnano` is imported as `sc`.

```python
import scadnano as sc

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

--------------------------------

### Get Last Domain of a Strand

Source: https://scadnano-python-package.readthedocs.io

Retrieves the last domain on the strand. This is useful for accessing the 3' end of the strand.

```python
strand.last_domain()
```

--------------------------------

### Plate Map with identity function well_marker

Source: https://scadnano-python-package.readthedocs.io

Example output using a lambda function as a well_marker to display well addresses.

```markdown
|     | 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   |     |     |     |     |     |     |     |     |     |      |      |      |
```

--------------------------------

### Get Strand Version Without Modifications

Source: https://scadnano-python-package.readthedocs.io

Returns a new Strand object that is identical to the current one but without any DNA modifications.

```python
strand.no_modifications_version()
```

--------------------------------

### StrandBuilder.with_domain_name()

Source: https://scadnano-python-package.readthedocs.io

Assigns a name to the most recently created Domain or Loopout. Should be called immediately after creating a Domain or Loopout.

```APIDOC
## POST /strandbuilder/with_domain_name

### Description
Assigns a name to the most recently created Domain or Loopout. Should be called immediately after creating a Domain or Loopout.

### Method
POST

### Endpoint
/strandbuilder/with_domain_name

### Parameters
#### Query Parameters
- **name** (str) - Required - The name to assign to the Domain or Loopout.

### Request Example
```json
{
  "name": "my_domain"
}
```

### Response
#### Success Response (200)
- **self** (StrandBuilder) - Returns the StrandBuilder instance.

#### Response Example
```json
{
  "self": "<StrandBuilder object>"
}
```
```

--------------------------------

### Get Domain DNA Sequence

Source: https://scadnano-python-package.readthedocs.io

Retrieves the DNA sequence string for this Domain. Returns None if no sequence is assigned to the parent Strand.

```python
dna_sequence _: str | None_ _ = None_¶
```

--------------------------------

### Set Domain Color

Source: https://scadnano-python-package.readthedocs.io

Use `with_domain_color()` to set the color of the most recently created `Domain`, `Loopout`, or `Extension`. This method is chainable.

--------------------------------

### StrandBuilder.with_domain_label()

Source: https://scadnano-python-package.readthedocs.io

Assigns a label to the most recently created Domain or Loopout. Should be called immediately after creating a Domain or Loopout.

```APIDOC
## POST /strandbuilder/with_domain_label

### Description
Assigns a label to the most recently created Domain or Loopout. Should be called immediately after creating a Domain or Loopout.

### Method
POST

### Endpoint
/strandbuilder/with_domain_label

### Parameters
#### Query Parameters
- **label** (str) - Required - The label to assign to the Domain or Loopout.

### Request Example
```json
{
  "label": "domain 1"
}
```

### Response
#### Success Response (200)
- **self** (StrandBuilder) - Returns the StrandBuilder instance.

#### Response Example
```json
{
  "self": "<StrandBuilder object>"
}
```
```

--------------------------------

### Get Modifications of a Specific Type

Source: https://scadnano-python-package.readthedocs.io

Retrieves a set of modifications from a design, optionally filtered by type (5', 3', or internal). If no type is specified, all modifications are returned.

```python
modifications(mod_type=None)
```

--------------------------------

### StrandBuilder.with_domain_color()

Source: https://scadnano-python-package.readthedocs.io

Sets the color for the most recent Domain, Loopout, or Extension.

```APIDOC
## POST /strandbuilder/with_domain_color

### Description
Sets the color for the most recent Domain, Loopout, or Extension.

### Method
POST

### Endpoint
/strandbuilder/with_domain_color

### Parameters
#### Query Parameters
- **color** (Color) - Required - The color to set for the Domain/Loopout/Extension.

### Request Example
```json
{
  "color": "blue"
}
```

### Response
#### Success Response (200)
- **self** (StrandBuilder) - Returns the StrandBuilder instance.

#### Response Example
```json
{
  "self": "<StrandBuilder object>"
}
```
```

--------------------------------

### Create Domain Object

Source: https://scadnano-python-package.readthedocs.io

Represents a contiguous portion of a Strand on a single Helix. Domains can store sequence, color, deletions, and insertions. Initialize with helix, direction, start, and end positions.

```python
_class _scadnano.Domain(_helix_ , _forward_ , _start_ , _end_ , _deletions= <factory>_, _insertions= <factory>_, _name=None_ , _label=None_ , _dna_sequence=None_ , _color=None_)[source]¶
```

--------------------------------

### Get Last Bound Domain of a Strand

Source: https://scadnano-python-package.readthedocs.io

Retrieves the last non-Loopout domain on the strand. This is typically the same as the last domain but accounts for potential future support of initial or final Loopout domains.

```python
strand.last_bound_domain()
```

--------------------------------

### StrandBuilder.to()

Source: https://scadnano-python-package.readthedocs.io

Extends the StrandBuilder on the current helix to a specified offset, adding a new Domain. This is an absolute move. Chained calls require offsets to move in the same direction.

```APIDOC
## POST /strandbuilder/to

### Description
Extends the StrandBuilder on the current helix to a specified offset, adding a new Domain. This is an absolute move. Chained calls require offsets to move in the same direction.

### Method
POST

### Endpoint
/strandbuilder/to

### Parameters
#### Query Parameters
- **offset** (int) - Required - New offset to extend to. If less than current offset, the new Domain is reverse, otherwise it is forward.

### Request Example
```json
{
  "offset": 10
}
```

### Response
#### Success Response (200)
- **self** (StrandBuilder) - Returns the StrandBuilder instance.

#### Response Example
```json
{
  "self": "<StrandBuilder object>"
}
```
```

--------------------------------

### StrandBuilder.with_color()

Source: https://scadnano-python-package.readthedocs.io

Sets the color for the Strand being built.

```APIDOC
## POST /strandbuilder/with_color

### Description
Sets the color for the Strand being built.

### Method
POST

### Endpoint
/strandbuilder/with_color

### Parameters
#### Query Parameters
- **color** (Color) - Required - The color to set for the Strand.

### Request Example
```json
{
  "color": "red"
}
```

### Response
#### Success Response (200)
- **self** (StrandBuilder) - Returns the StrandBuilder instance.

#### Response Example
```json
{
  "self": "<StrandBuilder object>"
}
```
```

--------------------------------

### Conditionally Add Modifications in a Loop

Source: https://scadnano-python-package.readthedocs.io

Use StrandBuilder within loops to create multiple strands with conditional modifications. This example adds a 5' biotin modification only to the first strand created in the loop.

```python
for i in range(n):
    sb = design.draw_strand(0, 10).move(10).with_name(f'strand {i}')
    if i == 0:
        sb.with_modification_5p(mod.biotin_5p)
```

--------------------------------

### Create Strand with Chained Extension Methods

Source: https://scadnano-python-package.readthedocs.io

This method allows for creating a `Strand` with `Extension`s using chained method calls on a `Design` object. It's a concise way to define strands with specific end modifications.

```python
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)
```

--------------------------------

### Export Design to JSON string

Source: https://scadnano-python-package.readthedocs.io

Returns a string representation of the Design, suitable for saving as a JSON file that scadnano can read. Control JSON indentation for readability.

```python
to_json(_suppress_indent =True_)
```

--------------------------------

### Get DNA Sequence within Range

Source: https://scadnano-python-package.readthedocs.io

Returns the DNA sequence of this Domain within a specified range of offsets (inclusive). Returns None if no sequence is assigned to the parent Strand. Note: This method is inclusive on both ends.

```python
dna_sequence_in(_offset_left_ , _offset_right_)[source]¶
```

--------------------------------

### Rotate Strand Domains Backward

Source: https://scadnano-python-package.readthedocs.io

Rotates the domains of the strand backward, moving domains from the 5' end to the 3' end. For example, A, B, C, D, E, F rotated by 2 with forward=False becomes C, D, E, F, A, B.

```python
strand.rotate_domains(_rotation_ , _forward =False)
```

--------------------------------

### StrandBuilder.with_deletions()

Source: https://scadnano-python-package.readthedocs.io

Assigns deletions to the most recently created Domain. Should be called immediately after creating a Domain.

```APIDOC
## POST /strandbuilder/with_deletions

### Description
Assigns deletions to the most recently created Domain. Should be called immediately after creating a Domain.

### Method
POST

### Endpoint
/strandbuilder/with_deletions

### Parameters
#### Query Parameters
- **deletions** (int | Iterable[int]) - Required - A single int or an Iterable of ints indicating the offset for the deletion(s).

### Request Example
```json
{
  "deletions": [2, 3]
}
```

### Response
#### Success Response (200)
- **self** (StrandBuilder) - Returns the StrandBuilder instance.

#### Response Example
```json
{
  "self": "<StrandBuilder object>"
}
```
```

--------------------------------

### Define and apply 5' modifications

Source: https://scadnano-python-package.readthedocs.io

Create a single Modification5Prime object and reuse it across multiple strands to ensure consistent vendor codes.

```python
biotin_5p = Modification5Prime(display_text='B', vendor_code='/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)
```

--------------------------------

### Rotate Strand Domains Forward

Source: https://scadnano-python-package.readthedocs.io

Rotates the domains of the strand forward, moving domains from the 3' end to the 5' end. For example, A, B, C, D, E, F rotated by 2 becomes E, F, A, B, C, D.

```python
strand.rotate_domains(_rotation_ , _forward =True_)
```

--------------------------------

### Define and apply 3' modifications

Source: https://scadnano-python-package.readthedocs.io

Create a single Modification3Prime object and reuse it across multiple strands to ensure consistent vendor codes.

```python
biotin_3p = Modification3Prime(display_text='B', vendor_code='/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)
```

--------------------------------

### Loopout Class

Source: https://scadnano-python-package.readthedocs.io

Details about the Loopout class, its parameters, and methods.

```APIDOC
## Loopout Class

### Description
A `Loopout` represents 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`.

### Parameters
- **length** (int) - Required - Length (in DNA bases) of this `Loopout`.
- **name** (str | None) - Optional - Optional name to give this `Loopout`.
- **label** (str | None) - Optional - Label to associate with this `Loopout`.
- **dna_sequence** (str | None) - Optional - DNA sequence of this `Loopout`.
- **color** (Color | None) - Optional - Color to show this loopout in the main view.

### Methods
- **dna_length()** - Returns the length of this `Loopout`.
- **get_seq_start_idx()** - Returns the starting DNA subsequence index for the first base of this `Loopout`.
- **set_label(label)** - Sets the label of this `Loopout`.
- **set_name(name)** - Sets the name of this `Loopout`.
- **strand()** - Returns the `Strand` that contains this `Loopout`.
- **vendor_dna_sequence()** - Returns the vendor DNA sequence of this `Loopout`.
```

--------------------------------

### Geometry Class Initialization

Source: https://scadnano-python-package.readthedocs.io

Initialize the `Geometry` class to control visualization parameters for a `Design`. Adjust parameters like `rise_per_base_pair` and `helix_radius` to customize the 2D representation of DNA structures.

```python
sc.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_)
```

--------------------------------

### Add Label to a Domain

Source: https://scadnano-python-package.readthedocs.io

Use `with_domain_label()` immediately after creating a domain or loopout with `to()`, `move()`, `update_to()`, or `loopout()` to assign a label. This method is chainable.

```python
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')
```

--------------------------------

### Export to cadnano v2

Source: https://scadnano-python-package.readthedocs.io

Methods for exporting the design to cadnano v2 format as a string or a serializable dictionary.

```APIDOC
## POST /design/to_cadnano_v2

### Description
Converts the design to a string in the cadnano v2 format.

### Parameters
#### Request Body
- **name** (str) - Optional - Name of the design.
- **whitespace** (bool) - Optional - Whether to include whitespace. Set to False for CanDo compatibility.

### Response
#### Success Response (200)
- **body** (str) - The cadnano v2 formatted string.

## POST /design/to_cadnano_v2_serializable

### Description
Converts the design to a JSON-serializable Python dictionary representing the cadnano v2 format.

### Parameters
#### Request Body
- **name** (str) - Optional - Name of the design.

### Response
#### Success Response (200)
- **body** (dict) - A dictionary representing the cadnano v2 format.
```

--------------------------------

### Strand Metadata and Export Methods

Source: https://scadnano-python-package.readthedocs.io

Methods for managing strand labels, names, scaffold status, and vendor export formatting.

```APIDOC
## set_label(label)

### Description
Sets the label of the strand.

### Parameters
- **label** (Any) - Required - The label to set.

## set_name(name)

### Description
Sets the name of the strand.

### Parameters
- **name** (str) - Required - The name to set.

## set_scaffold(is_scaf=True)

### Description
Sets the strand as a scaffold and updates its color.

### Parameters
- **is_scaf** (bool) - Optional - Whether the strand is a scaffold.

## vendor_dna_sequence(domain_delimiter='')

### Description
Returns the DNA sequence formatted for ordering from a synthesis vendor.

### Parameters
- **domain_delimiter** (str) - Optional - String to insert between DNA sequences.

### Response
- **str** - The formatted DNA sequence.
```

--------------------------------

### Insert Domain into Strand

Source: https://scadnano-python-package.readthedocs.io

Inserts a domain into a strand at a specified order. Uses Python list-like indexing for insertion position. Requires strand, order, and domain as arguments.

```python
design.insert_domain(strand, domain, 0)
```
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