Style File Format
FlatProt uses TOML files for defining custom styles for protein visualizations. This document explains the format and options available for styling different elements of the visualization.
Overview
Style files allow you to customize the appearance of various elements in the FlatProt visualization, including:
- Secondary structure elements (helices, sheets, coils)
- Annotations (points, lines, areas)
File Format
Style files use the TOML format, with each section defining styles for a specific element type.
Example Style File
# Secondary structure styles
[helix]
fill_color = "#FF5733"
stroke_color = "#000000"
stroke_width = 1.5
amplitude = 0.5
[sheet]
fill_color = "#33FF57"
stroke_color = "#000000"
stroke_width = 1.0
min_sheet_length = 3
[coil]
stroke_color = "#888888"
stroke_width = 1.0
# Annotation styles
[point_annotation]
fill_color = "#3357FF"
stroke_color = "#000000"
radius = 5.0
[line_annotation]
stroke_color = "#FF33A8"
stroke_width = 2.0
[area_annotation]
fill_color = "#FFFF33"
fill_opacity = 0.5
stroke_color = "#000000"
stroke_width = 1.0
padding = 2.0
smoothing_window = 3
interpolation_points = 10
Style Sections
Secondary Structure Styles
These sections define the appearance of secondary structure elements rendered in the visualization. Common properties like color, stroke_color, stroke_width, and opacity are inherited but can be overridden.
Helix Style ([helix])
Defines the appearance of alpha helices, typically rendered as zigzag ribbons.
| Property | Type | Default | Description |
|---|---|---|---|
color |
Color | "#ff0000" |
Fill color for the helix ribbon (default red). |
stroke_color |
Color | "#000000" |
Color for the outline/stroke (default black). |
stroke_width |
Float | 1.0 |
Reference width; used as a base for other dimensions. |
opacity |
Float | 1.0 |
Opacity of the helix element (0.0 to 1.0). |
ribbon_thickness |
Float | 8.0 |
Thickness of the zigzag ribbon. |
wavelength |
Float | 10.0 |
Length of one full zigzag cycle along the helix axis. |
amplitude |
Float | 3.0 |
Height of the zigzag peaks/valleys from the center line. |
min_helix_length |
Integer | 4 |
Minimum number of residues required to draw a zigzag shape instead of a simple line. |
simplified_width |
Float | 2.0 |
Line width used when the helix is rendered as a simple line (below min_helix_length). |
Sheet Style ([sheet])
Defines the appearance of beta sheets, typically rendered as arrows.
| Property | Type | Default | Description |
|---|---|---|---|
color |
Color | "#0000ff" |
Fill color for the sheet arrow (default blue). |
stroke_color |
Color | "#000000" |
Color for the outline/stroke (default black). |
stroke_width |
Float | 1.0 |
Reference width; primarily defines the base width of the arrow body. |
opacity |
Float | 1.0 |
Opacity of the sheet element (0.0 to 1.0). |
arrow_width |
Float | 8.0 |
Width of the arrowhead base relative to the start point. |
min_sheet_length |
Integer | 3 |
Minimum number of residues required to draw an arrow shape instead of a line. |
simplified_width |
Float | 2.0 |
Line width used when the sheet is rendered as a simple line (below min_sheet_length). |
Coil Style ([coil])
Defines the appearance of coil regions, typically rendered as smoothed lines.
| Property | Type | Default | Description |
|---|---|---|---|
color |
Color | "#5b5859" |
Color used for the coil line (default light grey). This often isn't visible as coils usually only have a stroke. |
stroke_color |
Color | "#000000" |
Color for the coil line (default black). |
stroke_width |
Float | 1.0 |
Width of the coil line. |
opacity |
Float | 1.0 |
Opacity of the coil line (0.0 to 1.0). |
smoothing_factor |
Float | 0.1 |
Fraction of points to keep during smoothing (0.0=max smoothing, 1.0=no smoothing). |
Annotation Styles
Point Annotation Style
The [point_annotation] section defines the appearance of point annotations.
| Property | Type | Description |
|---|---|---|
fill_color |
Color | Fill color for point markers |
stroke_color |
Color | Outline color for point markers |
radius |
Float | Radius of point markers |
Line Annotation Style
The [line_annotation] section defines the appearance of line annotations.
| Property | Type | Description |
|---|---|---|
stroke_color |
Color | Color for line annotations |
stroke_width |
Float | Width of line annotations |
Area Annotation Style
The [area_annotation] section defines the appearance of area annotations.
| Property | Type | Description |
|---|---|---|
fill_color |
Color | Fill color for area annotations |
fill_opacity |
Float | Opacity for area fills (0.0-1.0) |
stroke_color |
Color | Outline color for areas |
stroke_width |
Float | Width of the area outline |
padding |
Float | Padding around the area |
smoothing_window |
Integer | Window size for smoothing the area outline |
interpolation_points |
Integer | Number of points to use for interpolation |
Color Formats
Colors can be specified in any of the following formats:
- Hex codes:
"#FF5733"(with or without the#prefix) - RGB format:
"rgb(255, 87, 51)" - RGBA format:
"rgba(255, 87, 51, 0.5)" - Named colors:
"red","blue","green", etc.
Default Styles
If a style file is not provided, or if certain properties are omitted, FlatProt will use default styles. You only need to specify the properties you want to customize.
Validation
FlatProt validates style files to ensure they have the correct format and property types. If a style file is invalid, an error message will be displayed explaining the issue.