color theme and list tweaks, added turbo

src/mol-theme/color/polymer-index.ts

@@ -6,7 +6,7 @@
 
 import { Color } from '../../mol-util/color';
 import { Location } from '../../mol-model/location';
-import { StructureElement, Link } from '../../mol-model/structure';
+import { StructureElement, Link, Structure } from '../../mol-model/structure';
 import { ColorTheme, LocationColor } from '../color';
 import { ParamDefinition as PD } from '../../mol-util/param-definition'
 import { ThemeDataContext } from '../../mol-theme/theme';
@@ -18,28 +18,39 @@ const DefaultColor = Color(0xCCCCCC)
 const Description = 'Gives every polymer a unique color based on the position (index) of the polymer in the list of polymers in the structure.'
 
 export const PolymerIndexColorThemeParams = {
-    ...getPaletteParams({ scaleList: 'red-yellow-blue' }),
+    ...getPaletteParams({ type: 'set', setList: 'set-3' }),
 }
 export type PolymerIndexColorThemeParams = typeof PolymerIndexColorThemeParams
 export function getPolymerIndexColorThemeParams(ctx: ThemeDataContext) {
-    return PolymerIndexColorThemeParams // TODO return copy
+    const params = PD.clone(PolymerIndexColorThemeParams)
+    if (ctx.structure) {
+        if (getPolymerChainCount(ctx.structure.root) > 12) {
+            params.palette.defaultValue.name = 'scale'
+            params.palette.defaultValue.params = { list: 'red-yellow-blue' }
+        }
+    }
+    return params
 }
 export type PolymerIndexColorThemeProps = PD.Values<typeof PolymerIndexColorThemeParams>
 
+function getPolymerChainCount(structure: Structure) {
+    let polymerChainCount = 0
+    const { units } = structure
+    for (let i = 0, il = units.length; i <il; ++i) {
+        if (units[i].polymerElements.length > 0) ++polymerChainCount
+    }
+    return polymerChainCount
+}
+
 export function PolymerIndexColorTheme(ctx: ThemeDataContext, props: PD.Values<PolymerIndexColorThemeParams>): ColorTheme<PolymerIndexColorThemeParams> {
     let color: LocationColor
     let legend: ScaleLegend | TableLegend | undefined
 
     if (ctx.structure) {
-        const { units } = ctx.structure.root
-        let polymerCount = 0
-        for (let i = 0, il = units.length; i <il; ++i) {
-            if (units[i].polymerElements.length > 0) ++polymerCount
-        }
-
-        const palette = getPalette(polymerCount, props)
+        const palette = getPalette(getPolymerChainCount(ctx.structure.root), props)
         legend = palette.legend
 
+        const { units } = ctx.structure.root
         const unitIdColor = new Map<number, Color>()
         for (let i = 0, j = 0, il = units.length; i <il; ++i) {
             if (units[i].polymerElements.length > 0) {

src/mol-theme/color/sequence-id.ts

@@ -17,7 +17,7 @@ const DefaultColor = Color(0xCCCCCC)
 const Description = 'Gives every polymer residue a color based on its `seq_id` value.'
 
 export const SequenceIdColorThemeParams = {
-    list: PD.ColorList<ColorListName>('rainbow', ColorListOptionsScale),
+    list: PD.ColorList<ColorListName>('turbo', ColorListOptionsScale),
 }
 export type SequenceIdColorThemeParams = typeof SequenceIdColorThemeParams
 export function getSequenceIdColorThemeParams(ctx: ThemeDataContext) {

src/mol-theme/color/unit-index.ts

@@ -18,11 +18,18 @@ const DefaultColor = Color(0xCCCCCC)
 const Description = 'Gives every unit (single chain or collection of single elements) a unique color based on the position (index) of the unit in the list of units in the structure.'
 
 export const UnitIndexColorThemeParams = {
-    ...getPaletteParams({ type: 'scale', scaleList: 'red-yellow-blue' }),
+    ...getPaletteParams({ type: 'set', setList: 'set-3' }),
 }
 export type UnitIndexColorThemeParams = typeof UnitIndexColorThemeParams
 export function getUnitIndexColorThemeParams(ctx: ThemeDataContext) {
-    return UnitIndexColorThemeParams // TODO return copy
+    const params = PD.clone(UnitIndexColorThemeParams)
+    if (ctx.structure) {
+        if (ctx.structure.root.units.length > 12) {
+            params.palette.defaultValue.name = 'scale'
+            params.palette.defaultValue.params = { list: 'red-yellow-blue' }
+        }
+    }
+    return params
 }
 
 export function UnitIndexColorTheme(ctx: ThemeDataContext, props: PD.Values<UnitIndexColorThemeParams>): ColorTheme<UnitIndexColorThemeParams> {

src/mol-util/color/lists.ts

@@ -165,33 +165,43 @@ export const ColorLists = {
     /**
      * Matplotlib colormaps, including various perceptually uniform shades, see https://bids.github.io/colormap/
      */
-    'magma': ColorList('Magma', 'diverging',
+    'magma': ColorList('Magma', 'sequential',
         'Perceptually uniform shades of black-red-white',
         [0x420f74, 0x4a1079, 0x52127c, 0x5a157e, 0x61187f, 0x691c80, 0x711f81, 0x792281, 0x812581, 0x892881, 0x912a80, 0x992d7f, 0xa12f7e, 0xa9327c, 0xb1357a, 0xb93778, 0xc23a75, 0xca3e72, 0xd1426e, 0xd9466a, 0xe04b66, 0xe65162, 0xec585f, 0xf0605d, 0xf4685b, 0xf7715b, 0xf97b5d, 0xfb8460, 0xfc8e63, 0xfd9768, 0xfda16e, 0xfeaa74, 0xfeb37b, 0xfebc82, 0xfec689, 0xfdcf92, 0xfdd89a, 0xfde1a3, 0xfceaac, 0xfcf3b5, 0xfbfcbf]
     ),
-    'inferno': ColorList('Inferno', 'diverging',
+    'inferno': ColorList('Inferno', 'sequential',
         'Perceptually uniform shades of black-red-yellow',
         [0x480b6a, 0x500d6c, 0x58106d, 0x60136e, 0x68166e, 0x70196e, 0x781c6d, 0x801f6b, 0x88216a, 0x902468, 0x982765, 0xa02a62, 0xa72d5f, 0xaf315b, 0xb73456, 0xbe3852, 0xc53d4d, 0xcc4148, 0xd24742, 0xd94d3d, 0xde5337, 0xe45a31, 0xe8612b, 0xed6825, 0xf0701e, 0xf37918, 0xf68111, 0xf88a0b, 0xfa9306, 0xfb9d06, 0xfba60b, 0xfbb014, 0xfbb91e, 0xf9c32a, 0xf8cd37, 0xf5d745, 0xf3e056, 0xf1e968, 0xf1f27d, 0xf5f891, 0xfcfea4],
     ),
-    'plasma': ColorList('Plasma', 'diverging',
+    'plasma': ColorList('Plasma', 'sequential',
         'Perceptually uniform shades of blue-red-yellow',
         [0x1b068c, 0x250591, 0x2f0495, 0x380499, 0x40039c, 0x49029f, 0x5101a2, 0x5901a4, 0x6100a6, 0x6800a7, 0x7000a8, 0x7801a8, 0x7f03a7, 0x8607a6, 0x8e0ca4, 0x9511a1, 0x9b179e, 0xa21c9a, 0xa82296, 0xae2791, 0xb42d8d, 0xb93388, 0xbe3883, 0xc33e7f, 0xc8447a, 0xcd4975, 0xd14f71, 0xd6556d, 0xda5a68, 0xde6064, 0xe26660, 0xe56c5b, 0xe97257, 0xec7853, 0xef7e4e, 0xf2854a, 0xf58b46, 0xf79241, 0xf9993d, 0xfaa039, 0xfca735, 0xfdaf31, 0xfdb62d, 0xfdbe29, 0xfdc626, 0xfcce25, 0xfad624, 0xf8df24, 0xf5e726, 0xf2f026, 0xeff821]
     ),
-    'viridis': ColorList('Viridis', 'diverging',
+    'viridis': ColorList('Viridis', 'sequential',
         'Perceptually uniform shades of blue-green-yellow',
         [0x45085b, 0x470f62, 0x471669, 0x481d6f, 0x482374, 0x472a79, 0x46307d, 0x453681, 0x433c84, 0x414286, 0x3e4888, 0x3c4d8a, 0x3a538b, 0x37588c, 0x355d8c, 0x32628d, 0x30678d, 0x2e6c8e, 0x2c718e, 0x2a768e, 0x287a8e, 0x267f8e, 0x24848d, 0x23898d, 0x218d8c, 0x1f928c, 0x1e978a, 0x1e9b89, 0x1ea087, 0x20a585, 0x23a982, 0x28ae7f, 0x2eb27c, 0x35b778, 0x3dbb74, 0x45bf6f, 0x4fc369, 0x59c764, 0x64cb5d, 0x70ce56, 0x7cd24f, 0x88d547, 0x95d73f, 0xa2da37, 0xafdc2e, 0xbdde26, 0xcae01e, 0xd7e219, 0xe4e318, 0xf1e51c, 0xfde724]
     ),
-    'cividis': ColorList('Cividis', 'diverging',
+    'cividis': ColorList('Cividis', 'sequential',
         'Perceptually uniform shades of blue-green-yellow, should look effectively identical to colorblind and non-colorblind users',
         [0x002c67, 0x003070, 0x083370, 0x16366f, 0x1f3a6e, 0x273d6d, 0x2e416c, 0x34446c, 0x39486c, 0x3f4b6b, 0x444f6b, 0x49526b, 0x4e566c, 0x52596c, 0x575d6d, 0x5b606e, 0x60646e, 0x64676f, 0x686b71, 0x6d6e72, 0x717273, 0x757575, 0x797977, 0x7e7d78, 0x838078, 0x878478, 0x8c8878, 0x918c77, 0x968f77, 0x9b9376, 0xa09775, 0xa59b73, 0xaa9f72, 0xafa370, 0xb4a76f, 0xb9ab6d, 0xbeb06a, 0xc4b468, 0xc9b865, 0xcebc62, 0xd4c15e, 0xd9c55a, 0xdfca56, 0xe4ce51, 0xead34c, 0xefd846, 0xf5dc3f, 0xfbe136, 0xfde737]
     ),
-    'twilight': ColorList('Twilight', 'diverging',
+    'twilight': ColorList('Twilight', 'sequential',
         'Perceptually uniform shades of white-blue-black-red-white, cyclic',
         [0xdfd9e1, 0xd8d7dd, 0xced3d8, 0xc2cdd3, 0xb4c7ce, 0xa7c0ca, 0x9ab8c7, 0x8eb0c5, 0x83a8c3, 0x7a9fc2, 0x7297c0, 0x6b8ebf, 0x6684bd, 0x637bbb, 0x6171b9, 0x5f67b6, 0x5e5cb2, 0x5e51ad, 0x5d46a7, 0x5c3c9f, 0x5b3196, 0x58278b, 0x531e7d, 0x4d176e, 0x46135f, 0x3e1151, 0x381045, 0x32113b, 0x301336, 0x361138, 0x3e113c, 0x471240, 0x521445, 0x5e1749, 0x6a1a4d, 0x761e4f, 0x812350, 0x8b2a50, 0x95324f, 0x9d3a4f, 0xa5434f, 0xac4d50, 0xb25752, 0xb86155, 0xbc6c59, 0xc0775f, 0xc48267, 0xc78d70, 0xc9987b, 0xcca389, 0xceae97, 0xd2b8a6, 0xd6c1b5, 0xdacac4, 0xddd1d1, 0xe0d6db, 0xe1d8e1]
     ),
 
-    /** Other */
-    'rainbow': ColorList('Rainbow', 'diverging',
+    /**
+     * https://ai.googleblog.com/2019/08/turbo-improved-rainbow-colormap-for.html
+     */
+    'turbo': ColorList('Turbo', 'sequential',
+        'Improved (smooth) rainbow colormap for visualization',
+        [0x4a41b5, 0x4a58dd, 0x426ff2, 0x3987f9, 0x2f9df5, 0x28b2e9, 0x25c6d8, 0x27d7c4, 0x2ee5ae, 0x3bf098, 0x4df884, 0x62fd70, 0x7bfe5f, 0x95fb51, 0xaff444, 0xc8ea3a, 0xdedd32, 0xf0cc2c, 0xfeb927, 0xffa423, 0xff8e1f, 0xff761c, 0xf65f18, 0xe54813, 0xd0330e, 0xba2208, 0xa51403, 0x960d00]
+    ),
+
+    /**
+     * Other
+     */
+    'rainbow': ColorList('Rainbow', 'sequential',
         '',
         [ 0x3361E1, 0x35A845, 0xF9FF00, 0xEC8711, 0xBF2222 ]
     ),