List of VARNA parameters and their default value that can be passed as keyword arguments to BasicDraw.update().
The name of keyword argument is listed in the name column in each table.
COLOR_LIST: list
module-attribute
Allowed options for basic color setting
| Name | Object in panel | Default Color |
|---|---|---|
| backbone | Phosphate-sugar backbone (aka skeleton) of the RNA | Cottonwood Gray #595959 |
| background | Background color used within the panel | White #FFFFFF |
| baseInner | Inner base color | White Smoke #F2F2F2 |
| baseName | Nucleotide name | Black #000000 |
| baseNum | Base numbers | Vibrant Black #3F3F3F |
| baseOutline | Outer base color | Cottonwood Gray #595959 |
| bp | Base-pair color | Blue #0000FF |
| nsBasesColor | Non-standard bases (Anything but A, C, G or U) |
White Smoke #F2F2F2 |
BOOLEAN_OPTIONS: list
module-attribute
Boolean option list
| Name | Option | Default |
|---|---|---|
| autoHelices | Annotates each and every helix in the RNA with a unique Hn label |
False |
| autoInteriorLoops | Annotates each and every interior loop of the RNA with a unique In label |
False |
| autoTerminalLoops | Annotates each and every terminal loop of the RNA with a unique Tn label |
False |
| drawBackbone | Backbone drawing | True |
| drawBases | Displays the outline of a nucleotide base | True |
| drawNC | Displays non-canonical base-pairs | True |
| drawTertiary | Display of non-planar base-pairs, i.e. pseudoknots 1 |
True |
| fillBases | Fill bases | True |
| flat | In radiate drawing mode, redraws the whole structure, aligning to a baseline the base featured on the exterior loops (aka "dangling ends") |
True |
-
Since there is no canonical definition of pseudoknotted portions, a maximal planar subset is extracted from the input structure, defined to be the planar portion, and used as a scaffold for the drawing algorithms. ↩
NUMERIC_PARAMS: list
module-attribute
Allowed numeric parameters
| Name | Type | Description | Default |
|---|---|---|---|
| border | (int, int) | Sets the width and height of the panel border, i.e. the gap between the panel boundaries and those of the surface used to draw the RNA. Border setting is ignored if it's smaller than RNA draw. | N/A |
| bpIncrement | float | In linear drawing mode, defines the vertical increment used to separate two successive, nested base-pairs | 0.65 |
| periodNum | int | Sets the interval between two successive base numbers. More specifically, if k is the period, then the first and last bases of the RNA are numbered, along with each base whose number is a multiple of k |
10 |
| resolution | float | Chooses the resolution of a bitmap PNG export, i.e. the multiplier in the number of pixels in each dimension of the exported picture. | 1 |
| rotation | float | Rotates the whole RNA of a certain angular increment | 0 |
| spaceBetweenBases | float | Sets the distance between consecutive bases | 1 |
| zoom | float | Defines the level of zoom and zoom increment used to display the RNA within this panel (min:0.5, max:60) | 1 |
Choices
There are two VARNA parameters, algorithm and bpStyle, takes value from defined options.
BP_STYLES = ['none', 'simple', 'rnaviz', 'lw']
module-attribute
Allowed options for base-pair style (bpStyle), default value is lw
| Label | Description |
|---|---|
| none | Base-pairs are not drawn, but can be implicitly seen from "ladders", i.e helix structures |
| simple | A simple line is used to draw any base-pair, regardless of its type |
| rnaviz | A small square is drawn at equal distance of the two partners |
| lw | Both canonical and non-canonical base-pairs are rendered according to the Leontis/Westhof nomenclature (Default) |
Examples:
>>> BasicDraw.update(bpStyle="simple")
ALGORITHMS = ['line', 'circular', 'radiate', 'naview']
module-attribute
Allowed options for drawing algorithms (algorithm) are line, circular, radiate, and naview. The default value is radiate.
Examples:
>>> BasicDraw.update(algorithm="line")