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colors.ts
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colors.ts
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import { builtinGradients } from "./Gradient";
import { getAtomProperty } from "./utils/getAtomProperty";
import { CC } from "./WebGL";
export const htmlColors = {
aliceblue: 0xf0f8ff,
antiquewhite: 0xfaebd7,
aqua: 0x00ffff,
aquamarine: 0x7fffd4,
azure: 0xf0ffff,
beige: 0xf5f5dc,
bisque: 0xffe4c4,
black: 0x000000,
blanchedalmond: 0xffebcd,
blue: 0x0000ff,
blueviolet: 0x8a2be2,
brown: 0xa52a2a,
burlywood: 0xdeb887,
cadetblue: 0x5f9ea0,
chartreuse: 0x7fff00,
chocolate: 0xd2691e,
coral: 0xff7f50,
cornflowerblue: 0x6495ed,
cornsilk: 0xfff8dc,
crimson: 0xdc143c,
cyan: 0x00ffff,
darkblue: 0x00008b,
darkcyan: 0x008b8b,
darkgoldenrod: 0xb8860b,
darkgray: 0xa9a9a9,
darkgrey: 0xa9a9a9,
darkgreen: 0x006400,
darkkhaki: 0xbdb76b,
darkmagenta: 0x8b008b,
darkolivegreen: 0x556b2f,
darkorange: 0xff8c00,
darkorchid: 0x9932cc,
darkred: 0x8b0000,
darksalmon: 0xe9967a,
darkseagreen: 0x8fbc8f,
darkslateblue: 0x483d8b,
darkslategray: 0x2f4f4f,
darkslategrey: 0x2f4f4f,
darkturquoise: 0x00ced1,
darkviolet: 0x9400d3,
deeppink: 0xff1493,
deepskyblue: 0x00bfff,
dimgray: 0x696969,
dimgrey: 0x696969,
dodgerblue: 0x1e90ff,
firebrick: 0xb22222,
floralwhite: 0xfffaf0,
forestgreen: 0x228b22,
fuchsia: 0xff00ff,
gainsboro: 0xdcdcdc,
ghostwhite: 0xf8f8ff,
gold: 0xffd700,
goldenrod: 0xdaa520,
gray: 0x808080,
grey: 0x808080,
green: 0x008000,
greenyellow: 0xadff2f,
honeydew: 0xf0fff0,
hotpink: 0xff69b4,
indianred: 0xcd5c5c,
indigo: 0x4b0082,
ivory: 0xfffff0,
khaki: 0xf0e68c,
lavender: 0xe6e6fa,
lavenderblush: 0xfff0f5,
lawngreen: 0x7cfc00,
lemonchiffon: 0xfffacd,
lightblue: 0xadd8e6,
lightcoral: 0xf08080,
lightcyan: 0xe0ffff,
lightgoldenrodyellow: 0xfafad2,
lightgray: 0xd3d3d3,
lightgrey: 0xd3d3d3,
lightgreen: 0x90ee90,
lightpink: 0xffb6c1,
lightsalmon: 0xffa07a,
lightseagreen: 0x20b2aa,
lightskyblue: 0x87cefa,
lightslategray: 0x778899,
lightslategrey: 0x778899,
lightsteelblue: 0xb0c4de,
lightyellow: 0xffffe0,
lime: 0x00ff00,
limegreen: 0x32cd32,
linen: 0xfaf0e6,
magenta: 0xff00ff,
maroon: 0x800000,
mediumaquamarine: 0x66cdaa,
mediumblue: 0x0000cd,
mediumorchid: 0xba55d3,
mediumpurple: 0x9370db,
mediumseagreen: 0x3cb371,
mediumslateblue: 0x7b68ee,
mediumspringgreen: 0x00fa9a,
mediumturquoise: 0x48d1cc,
mediumvioletred: 0xc71585,
midnightblue: 0x191970,
mintcream: 0xf5fffa,
mistyrose: 0xffe4e1,
moccasin: 0xffe4b5,
navajowhite: 0xffdead,
navy: 0x000080,
oldlace: 0xfdf5e6,
olive: 0x808000,
olivedrab: 0x6b8e23,
orange: 0xffa500,
orangered: 0xff4500,
orchid: 0xda70d6,
palegoldenrod: 0xeee8aa,
palegreen: 0x98fb98,
paleturquoise: 0xafeeee,
palevioletred: 0xdb7093,
papayawhip: 0xffefd5,
peachpuff: 0xffdab9,
peru: 0xcd853f,
pink: 0xffc0cb,
plum: 0xdda0dd,
powderblue: 0xb0e0e6,
purple: 0x800080,
rebeccapurple: 0x663399,
red: 0xff0000,
rosybrown: 0xbc8f8f,
royalblue: 0x4169e1,
saddlebrown: 0x8b4513,
salmon: 0xfa8072,
sandybrown: 0xf4a460,
seagreen: 0x2e8b57,
seashell: 0xfff5ee,
sienna: 0xa0522d,
silver: 0xc0c0c0,
skyblue: 0x87ceeb,
slateblue: 0x6a5acd,
slategray: 0x708090,
slategrey: 0x708090,
snow: 0xfffafa,
springgreen: 0x00ff7f,
steelblue: 0x4682b4,
tan: 0xd2b48c,
teal: 0x008080,
thistle: 0xd8bfd8,
tomato: 0xff6347,
turquoise: 0x40e0d0,
violet: 0xee82ee,
wheat: 0xf5deb3,
white: 0xffffff,
whitesmoke: 0xf5f5f5,
yellow: 0xffff00,
yellowgreen: 0x9acd32,
};
export type ColorSpec = keyof typeof htmlColors | number;
(function () {
/**
* Color representation.
* @typedef ColorSpec
* @prop {string} 0xAF10AB - any hex number
* @prop {string} <html color name>
*/
/**
* @typedef ColorschemeSpec
* Built in colorschemes
*
* @example //Using a function in order to define the colors.
download("pdb:4UAA",viewer,{},function(){
viewer.setBackgroundColor(0xffffffff);
var colorAsSnake = function(atom) {
return atom.resi % 2 ? 'white': 'green'
};
viewer.setStyle( {chain:'A'}, { cartoon: {colorfunc: colorAsSnake }});
viewer.setStyle( {chain:'B'}, { stick: {colorscheme: 'yellowCarbon'}});
viewer.render();
});
* @prop {string} <html color>Carbon - use default element colors but with carbon set to specify html color string
* @prop {string} ssPyMOL - PyMol secondary colorscheme
* @prop {string} ssJmol - Jmol secondary colorscheme
* @prop {string} Jmol - Jmol primary colorscheme
* @prop {string} default - default colorscheme
* @prop {string} amino - amino acid colorscheme
* @prop {string} shapely - shapely protien colorscheme
* @prop {string} nucleic - nucleic acid colorscheme
* @prop {string} chain - standard chain colorscheme
* @prop {string} chainHetatm - chain Hetatm colorscheme
* @prop {string} prop - atomSpec property. Example 'b'. See AtomSpec.
* @prop {Gradient} gradient - Allows the user to provide a gradient to the colorscheme. Is either a Gradient object or the name of a built-in gradient (rwb, roygb, sinebow)
* @prop {min} - min value for gradient
* @prop {max} - max value for gradient
* @prop {mid} - mid point value for gradient (for rwb)
* @prop {object} map - map of a certain AtomSpec property to a color of the form `{'prop': 'elem', map:elementColors.greenCarbon}` Allows the user to provide a mapping of elements to colors to the colorscheme. This can be done with any properties, and not just 'elem'.
* @prop {function} colorfunc - Allows the user to provide a function for setting the colorschemes.
*/
})();
/** Preset secondary structure color scheme
* @struct
*/
export const ssColors = {
//names are in helix-sheet-coil order
pyMol: { h: 0xff0000, s: 0xffff00, c: 0x00ff00 },
Jmol: { h: 0xff0080, s: 0xffc800, c: 0xffffff },
};
const rasmol = {
H: 0xffffff,
He: 0xffc0cb,
HE: 0xffc0cb,
Li: 0xb22222,
LI: 0xb22222,
B: 0x00ff00,
C: 0xc8c8c8,
N: 0x8f8fff,
O: 0xf00000,
F: 0xdaa520,
Na: 0x0000ff,
NA: 0x0000ff,
Mg: 0x228b22,
MG: 0x228b22,
Al: 0x808090,
AL: 0x808090,
Si: 0xdaa520,
SI: 0xdaa520,
P: 0xffa500,
S: 0xffc832,
Cl: 0x00ff00,
CL: 0x00ff00,
Ca: 0x808090,
CA: 0x808090,
Ti: 0x808090,
TI: 0x808090,
Cr: 0x808090,
CR: 0x808090,
Mn: 0x808090,
MN: 0x808090,
Fe: 0xffa500,
FE: 0xffa500,
Ni: 0xa52a2a,
NI: 0xa52a2a,
Cu: 0xa52a2a,
CU: 0xa52a2a,
Zn: 0xa52a2a,
ZN: 0xa52a2a,
Br: 0xa52a2a,
BR: 0xa52a2a,
Ag: 0x808090,
AG: 0x808090,
I: 0xa020f0,
Ba: 0xffa500,
BA: 0xffa500,
Au: 0xdaa520,
AU: 0xdaa520,
};
/** Preset element coloring - from individual element colors to entire mappings (e.g. 'elementColors.Jmol' colors atoms with Jmol stylings)
* @struct
*/
export const elementColors = {
defaultColor: 0xff1493,
/** Jmol-like element colors*/
Jmol: {
H: 0xffffff,
He: 0xd9ffff,
HE: 0xd9ffff,
Li: 0xcc80ff,
LI: 0xcc80ff,
Be: 0xc2ff00,
BE: 0xc2ff00,
B: 0xffb5b5,
C: 0x909090,
N: 0x3050f8,
O: 0xff0d0d,
F: 0x90e050,
Ne: 0xb3e3f5,
NE: 0xb3e3f5,
Na: 0xab5cf2,
NA: 0xab5cf2,
Mg: 0x8aff00,
MG: 0x8aff00,
Al: 0xbfa6a6,
AL: 0xbfa6a6,
Si: 0xf0c8a0,
SI: 0xf0c8a0,
P: 0xff8000,
S: 0xffff30,
Cl: 0x1ff01f,
CL: 0x1ff01f,
Ar: 0x80d1e3,
AR: 0x80d1e3,
K: 0x8f40d4,
Ca: 0x3dff00,
CA: 0x3dff00,
Sc: 0xe6e6e6,
SC: 0xe6e6e6,
Ti: 0xbfc2c7,
TI: 0xbfc2c7,
V: 0xa6a6ab,
Cr: 0x8a99c7,
CR: 0x8a99c7,
Mn: 0x9c7ac7,
MN: 0x9c7ac7,
Fe: 0xe06633,
FE: 0xe06633,
Co: 0xf090a0,
CO: 0xf090a0,
Ni: 0x50d050,
NI: 0x50d050,
Cu: 0xc88033,
CU: 0xc88033,
Zn: 0x7d80b0,
ZN: 0x7d80b0,
Ga: 0xc28f8f,
GA: 0xc28f8f,
Ge: 0x668f8f,
GE: 0x668f8f,
As: 0xbd80e3,
AS: 0xbd80e3,
Se: 0xffa100,
SE: 0xffa100,
Br: 0xa62929,
BR: 0xa62929,
Kr: 0x5cb8d1,
KR: 0x5cb8d1,
Rb: 0x702eb0,
RB: 0x702eb0,
Sr: 0x00ff00,
SR: 0x00ff00,
Y: 0x94ffff,
Zr: 0x94e0e0,
ZR: 0x94e0e0,
Nb: 0x73c2c9,
NB: 0x73c2c9,
Mo: 0x54b5b5,
MO: 0x54b5b5,
Tc: 0x3b9e9e,
TC: 0x3b9e9e,
Ru: 0x248f8f,
RU: 0x248f8f,
Rh: 0x0a7d8c,
RH: 0x0a7d8c,
Pd: 0x006985,
PD: 0x006985,
Ag: 0xc0c0c0,
AG: 0xc0c0c0,
Cd: 0xffd98f,
CD: 0xffd98f,
In: 0xa67573,
IN: 0xa67573,
Sn: 0x668080,
SN: 0x668080,
Sb: 0x9e63b5,
SB: 0x9e63b5,
Te: 0xd47a00,
TE: 0xd47a00,
I: 0x940094,
Xe: 0x429eb0,
XE: 0x429eb0,
Cs: 0x57178f,
CS: 0x57178f,
Ba: 0x00c900,
BA: 0x00c900,
La: 0x70d4ff,
LA: 0x70d4ff,
Ce: 0xffffc7,
CE: 0xffffc7,
Pr: 0xd9ffc7,
PR: 0xd9ffc7,
Nd: 0xc7ffc7,
ND: 0xc7ffc7,
Pm: 0xa3ffc7,
PM: 0xa3ffc7,
Sm: 0x8fffc7,
SM: 0x8fffc7,
Eu: 0x61ffc7,
EU: 0x61ffc7,
Gd: 0x45ffc7,
GD: 0x45ffc7,
Tb: 0x30ffc7,
TB: 0x30ffc7,
Dy: 0x1fffc7,
DY: 0x1fffc7,
Ho: 0x00ff9c,
HO: 0x00ff9c,
Er: 0x00e675,
ER: 0x00e675,
Tm: 0x00d452,
TM: 0x00d452,
Yb: 0x00bf38,
YB: 0x00bf38,
Lu: 0x00ab24,
LU: 0x00ab24,
Hf: 0x4dc2ff,
HF: 0x4dc2ff,
Ta: 0x4da6ff,
TA: 0x4da6ff,
W: 0x2194d6,
Re: 0x267dab,
RE: 0x267dab,
Os: 0x266696,
OS: 0x266696,
Ir: 0x175487,
IR: 0x175487,
Pt: 0xd0d0e0,
PT: 0xd0d0e0,
Au: 0xffd123,
AU: 0xffd123,
Hg: 0xb8b8d0,
HG: 0xb8b8d0,
Tl: 0xa6544d,
TL: 0xa6544d,
Pb: 0x575961,
PB: 0x575961,
Bi: 0x9e4fb5,
BI: 0x9e4fb5,
Po: 0xab5c00,
PO: 0xab5c00,
At: 0x754f45,
AT: 0x754f45,
Rn: 0x428296,
RN: 0x428296,
Fr: 0x420066,
FR: 0x420066,
Ra: 0x007d00,
RA: 0x007d00,
Ac: 0x70abfa,
AC: 0x70abfa,
Th: 0x00baff,
TH: 0x00baff,
Pa: 0x00a1ff,
PA: 0x00a1ff,
U: 0x008fff,
Np: 0x0080ff,
NP: 0x0080ff,
Pu: 0x006bff,
PU: 0x006bff,
Am: 0x545cf2,
AM: 0x545cf2,
Cm: 0x785ce3,
CM: 0x785ce3,
Bk: 0x8a4fe3,
BK: 0x8a4fe3,
Cf: 0xa136d4,
CF: 0xa136d4,
Es: 0xb31fd4,
ES: 0xb31fd4,
Fm: 0xb31fba,
FM: 0xb31fba,
Md: 0xb30da6,
MD: 0xb30da6,
No: 0xbd0d87,
NO: 0xbd0d87,
Lr: 0xc70066,
LR: 0xc70066,
Rf: 0xcc0059,
RF: 0xcc0059,
Db: 0xd1004f,
DB: 0xd1004f,
Sg: 0xd90045,
SG: 0xd90045,
Bh: 0xe00038,
BH: 0xe00038,
Hs: 0xe6002e,
HS: 0xe6002e,
Mt: 0xeb0026,
MT: 0xeb0026,
},
/** rasmol-like element colors */
rasmol,
defaultColors: {
...rasmol,
},
greenCarbon: {
...rasmol,
C: 0x00ff00,
},
cyanCarbon: {
...rasmol,
C: 0x00ffff,
},
magentaCarbon: {
...rasmol,
C: 0xff00ff,
},
yellowCarbon: {
...rasmol,
C: 0xffff00,
},
whiteCarbon: {
...rasmol,
C: 0xffffff,
},
orangeCarbon: {
...rasmol,
C: 0xffa500,
},
purpleCarbon: {
...rasmol,
C: 0x800080,
},
blueCarbon: {
...rasmol,
C: 0x0000ff,
},
};
export const residues = {
/** @property standard amino acid color scheme*/
amino: {
ALA: 0xc8c8c8,
ARG: 0x145aff,
ASN: 0x00dcdc,
ASP: 0xe60a0a,
CYS: 0xe6e600,
GLN: 0x00dcdc,
GLU: 0xe60a0a,
GLY: 0xebebeb,
HIS: 0x8282d2,
ILE: 0x0f820f,
LEU: 0x0f820f,
LYS: 0x145aff,
MET: 0xe6e600,
PHE: 0x3232aa,
PRO: 0xdc9682,
SER: 0xfa9600,
THR: 0xfa9600,
TRP: 0xb45ab4,
TYR: 0x3232aa,
VAL: 0x0f820f,
ASX: 0xff69b4,
GLX: 0xff69b4,
},
/** @property shapely amino acid color scheme*/
shapely: {
ALA: 0x8cff8c,
ARG: 0x00007c,
ASN: 0xff7c70,
ASP: 0xa00042,
CYS: 0xffff70,
GLN: 0xff4c4c,
GLU: 0x660000,
GLY: 0xffffff,
HIS: 0x7070ff,
ILE: 0x004c00,
LEU: 0x455e45,
LYS: 0x4747b8,
MET: 0xb8a042,
PHE: 0x534c52,
PRO: 0x525252,
SER: 0xff7042,
THR: 0xb84c00,
TRP: 0x4f4600,
TYR: 0x8c704c,
VAL: 0xff8cff,
ASX: 0xff00ff,
GLX: 0xff00ff,
},
/** @property nucleic acid color scheme*/
nucleic: {
A: 0xa0a0ff,
G: 0xff7070,
I: 0x80ffff,
C: 0xff8c4b,
T: 0xa0ffa0,
U: 0xff8080,
},
};
export const chains = {
/** @property chain based standard color scheme */
atom: {
A: 0xc0d0ff,
B: 0xb0ffb0,
C: 0xffc0c8,
D: 0xffff80,
E: 0xffc0ff,
F: 0xb0f0f0,
G: 0xffd070,
H: 0xf08080,
I: 0xf5deb3,
J: 0x00bfff,
K: 0xcd5c5c,
L: 0x66cdaa,
M: 0x9acd32,
N: 0xee82ee,
O: 0x00ced1,
P: 0x00ff7f,
Q: 0x3cb371,
R: 0x00008b,
S: 0xbdb76b,
T: 0x006400,
U: 0x800000,
V: 0x808000,
W: 0x800080,
X: 0x008080,
Y: 0xb8860b,
Z: 0xb22222,
},
/** @property hetatm color scheme */
hetatm: {
A: 0x90a0cf,
B: 0x80cf98,
C: 0xcf90b0,
D: 0xcfcf70,
E: 0xcf90cf,
F: 0x80c0c0,
G: 0xcfa060,
H: 0xc05070,
I: 0xc5ae83,
J: 0x00a7cf,
K: 0xb54c4c,
L: 0x56b592,
M: 0x8ab52a,
N: 0xbe72be,
O: 0x00b6a1,
P: 0x00cf6f,
Q: 0x349b61,
R: 0x0000bb,
S: 0xa59f5b,
T: 0x009400,
U: 0xb00000,
V: 0xb0b000,
W: 0xb000b0,
X: 0x00b0b0,
Y: 0xe8b613,
Z: 0xc23232,
},
};
/**
* built in color schemes
* @example //Using a function in order to define the colors.
$3Dmol.download("pdb:4UAA",viewer,{},function(){
viewer.setBackgroundColor(0xffffffff);
var colorAsSnake = function(atom) {
return atom.resi % 2 ? 'white': 'green'
};
viewer.setStyle( {chain:'A'}, { cartoon: {colorfunc: colorAsSnake }});
viewer.setStyle( {chain:'B'}, { stick: {colorscheme: 'yellowCarbon'}});
viewer.render();
});
* The user can pass all of these values directly as the colorscheme and they will use the respective colorscheme */
export const builtinColorSchemes = {
ssPyMol: { prop: "ss", map: ssColors.pyMol },
ssJmol: { prop: "ss", map: ssColors.Jmol },
Jmol: { prop: "elem", map: elementColors.Jmol },
amino: { prop: "resn", map: residues.amino },
shapely: { prop: "resn", map: residues.shapely },
nucleic: { prop: "resn", map: residues.nucleic },
chain: { prop: "chain", map: chains.atom },
rasmol: { prop: "elem", map: elementColors.rasmol },
default: { prop: "elem", map: elementColors.defaultColors },
greenCarbon: { prop: "elem", map: elementColors.greenCarbon },
chainHetatm: { prop: "chain", map: chains.hetatm },
cyanCarbon: { prop: "elem", map: elementColors.cyanCarbon },
magentaCarbon: { prop: "elem", map: elementColors.magentaCarbon },
purpleCarbon: { prop: "elem", map: elementColors.purpleCarbon },
whiteCarbon: { prop: "elem", map: elementColors.whiteCarbon },
orangeCarbon: { prop: "elem", map: elementColors.orangeCarbon },
yellowCarbon: { prop: "elem", map: elementColors.yellowCarbon },
blueCarbon: { prop: "elem", map: elementColors.blueCarbon },
};
/** Return proper color for atom given style
* @param {AtomSpec} atom
* @param {AtomStyle} style
* @return {Color}
*/
export function getColorFromStyle(atom, style) {
var scheme = style.colorscheme;
if (typeof builtinColorSchemes[scheme] != "undefined") {
scheme = builtinColorSchemes[scheme];
} else if (typeof scheme == "string" && scheme.endsWith("Carbon")) {
//any color you want of carbon
var ccolor = scheme
.substring(0, scheme.lastIndexOf("Carbon"))
.toLowerCase();
if (typeof htmlColors[ccolor] != "undefined") {
var newscheme = {...elementColors.defaultColors};
newscheme.C = htmlColors[ccolor];
builtinColorSchemes[scheme] = { prop: "elem", map: newscheme };
scheme = builtinColorSchemes[scheme];
}
}
var color = atom.color;
if (typeof style.color != "undefined" && style.color != "spectrum")
color = style.color;
if (typeof scheme != "undefined") {
var prop, val;
if (typeof elementColors[scheme] != "undefined") {
//name of builtin colorscheme
scheme = elementColors[scheme];
if (typeof scheme[atom[scheme.prop]] != "undefined") {
color = scheme.map[atom[scheme.prop]];
}
} else if (typeof scheme[atom[scheme.prop]] != "undefined") {
//actual color scheme provided
color = scheme.map[atom[scheme.prop]];
} else if (
typeof scheme.prop != "undefined" &&
typeof scheme.gradient != "undefined"
) {
//apply a property mapping
prop = scheme.prop;
var grad = scheme.gradient; //redefining scheme
if (typeof builtinGradients[grad] != "undefined") {
grad = new builtinGradients[grad](
scheme.min,
scheme.max,
scheme.mid
);
}
var range = grad.range() || [-1, 1]; //sensible default
val = getAtomProperty(atom, prop);
if (val != null) {
color = grad.valueToHex(val, range);
}
} else if (
typeof scheme.prop != "undefined" &&
typeof scheme.map != "undefined"
) {
//apply a discrete property mapping
prop = scheme.prop;
val = getAtomProperty(atom, prop);
if (typeof scheme.map[val] != "undefined") {
color = scheme.map[val];
}
} else if (typeof style.colorscheme[atom.elem] != "undefined") {
//actual color scheme provided
color = style.colorscheme[atom.elem];
} else {
console.log("Could not interpret colorscheme " + scheme);
}
} else if (typeof style.colorfunc != "undefined") {
//this is a user provided function for turning an atom into a color
color = style.colorfunc(atom);
}
var C = CC.color(color);
return C;
};