three-stdlib
Version:
stand-alone library of threejs examples
248 lines (247 loc) • 7.11 kB
JavaScript
import { Loader, FileLoader, BufferGeometry, Float32BufferAttribute } from "three";
class PDBLoader extends Loader {
constructor(manager) {
super(manager);
}
load(url, onLoad, onProgress, onError) {
const scope = this;
const loader = new FileLoader(scope.manager);
loader.setPath(scope.path);
loader.setRequestHeader(scope.requestHeader);
loader.setWithCredentials(scope.withCredentials);
loader.load(
url,
function(text) {
try {
onLoad(scope.parse(text));
} catch (e) {
if (onError) {
onError(e);
} else {
console.error(e);
}
scope.manager.itemError(url);
}
},
onProgress,
onError
);
}
// Based on CanvasMol PDB parser
parse(text) {
function trim(text2) {
return text2.replace(/^\s\s*/, "").replace(/\s\s*$/, "");
}
function capitalize(text2) {
return text2.charAt(0).toUpperCase() + text2.substr(1).toLowerCase();
}
function hash(s, e) {
return "s" + Math.min(s, e) + "e" + Math.max(s, e);
}
function parseBond(start, length, satom, i) {
const eatom = parseInt(lines[i].substr(start, length));
if (eatom) {
const h = hash(satom, eatom);
if (_bhash[h] === void 0) {
_bonds.push([satom - 1, eatom - 1, 1]);
_bhash[h] = _bonds.length - 1;
}
}
}
function buildGeometry() {
const build = {
geometryAtoms: new BufferGeometry(),
geometryBonds: new BufferGeometry(),
json: {
atoms
}
};
const geometryAtoms = build.geometryAtoms;
const geometryBonds = build.geometryBonds;
const verticesAtoms = [];
const colorsAtoms = [];
const verticesBonds = [];
for (let i = 0, l = atoms.length; i < l; i++) {
const atom = atoms[i];
const x = atom[0];
const y = atom[1];
const z = atom[2];
verticesAtoms.push(x, y, z);
const r = atom[3][0] / 255;
const g = atom[3][1] / 255;
const b = atom[3][2] / 255;
colorsAtoms.push(r, g, b);
}
for (let i = 0, l = _bonds.length; i < l; i++) {
const bond = _bonds[i];
const start = bond[0];
const end = bond[1];
const startAtom = _atomMap[start];
const endAtom = _atomMap[end];
let x = startAtom[0];
let y = startAtom[1];
let z = startAtom[2];
verticesBonds.push(x, y, z);
x = endAtom[0];
y = endAtom[1];
z = endAtom[2];
verticesBonds.push(x, y, z);
}
geometryAtoms.setAttribute("position", new Float32BufferAttribute(verticesAtoms, 3));
geometryAtoms.setAttribute("color", new Float32BufferAttribute(colorsAtoms, 3));
geometryBonds.setAttribute("position", new Float32BufferAttribute(verticesBonds, 3));
return build;
}
const CPK = {
h: [255, 255, 255],
he: [217, 255, 255],
li: [204, 128, 255],
be: [194, 255, 0],
b: [255, 181, 181],
c: [144, 144, 144],
n: [48, 80, 248],
o: [255, 13, 13],
f: [144, 224, 80],
ne: [179, 227, 245],
na: [171, 92, 242],
mg: [138, 255, 0],
al: [191, 166, 166],
si: [240, 200, 160],
p: [255, 128, 0],
s: [255, 255, 48],
cl: [31, 240, 31],
ar: [128, 209, 227],
k: [143, 64, 212],
ca: [61, 255, 0],
sc: [230, 230, 230],
ti: [191, 194, 199],
v: [166, 166, 171],
cr: [138, 153, 199],
mn: [156, 122, 199],
fe: [224, 102, 51],
co: [240, 144, 160],
ni: [80, 208, 80],
cu: [200, 128, 51],
zn: [125, 128, 176],
ga: [194, 143, 143],
ge: [102, 143, 143],
as: [189, 128, 227],
se: [255, 161, 0],
br: [166, 41, 41],
kr: [92, 184, 209],
rb: [112, 46, 176],
sr: [0, 255, 0],
y: [148, 255, 255],
zr: [148, 224, 224],
nb: [115, 194, 201],
mo: [84, 181, 181],
tc: [59, 158, 158],
ru: [36, 143, 143],
rh: [10, 125, 140],
pd: [0, 105, 133],
ag: [192, 192, 192],
cd: [255, 217, 143],
in: [166, 117, 115],
sn: [102, 128, 128],
sb: [158, 99, 181],
te: [212, 122, 0],
i: [148, 0, 148],
xe: [66, 158, 176],
cs: [87, 23, 143],
ba: [0, 201, 0],
la: [112, 212, 255],
ce: [255, 255, 199],
pr: [217, 255, 199],
nd: [199, 255, 199],
pm: [163, 255, 199],
sm: [143, 255, 199],
eu: [97, 255, 199],
gd: [69, 255, 199],
tb: [48, 255, 199],
dy: [31, 255, 199],
ho: [0, 255, 156],
er: [0, 230, 117],
tm: [0, 212, 82],
yb: [0, 191, 56],
lu: [0, 171, 36],
hf: [77, 194, 255],
ta: [77, 166, 255],
w: [33, 148, 214],
re: [38, 125, 171],
os: [38, 102, 150],
ir: [23, 84, 135],
pt: [208, 208, 224],
au: [255, 209, 35],
hg: [184, 184, 208],
tl: [166, 84, 77],
pb: [87, 89, 97],
bi: [158, 79, 181],
po: [171, 92, 0],
at: [117, 79, 69],
rn: [66, 130, 150],
fr: [66, 0, 102],
ra: [0, 125, 0],
ac: [112, 171, 250],
th: [0, 186, 255],
pa: [0, 161, 255],
u: [0, 143, 255],
np: [0, 128, 255],
pu: [0, 107, 255],
am: [84, 92, 242],
cm: [120, 92, 227],
bk: [138, 79, 227],
cf: [161, 54, 212],
es: [179, 31, 212],
fm: [179, 31, 186],
md: [179, 13, 166],
no: [189, 13, 135],
lr: [199, 0, 102],
rf: [204, 0, 89],
db: [209, 0, 79],
sg: [217, 0, 69],
bh: [224, 0, 56],
hs: [230, 0, 46],
mt: [235, 0, 38],
ds: [235, 0, 38],
rg: [235, 0, 38],
cn: [235, 0, 38],
uut: [235, 0, 38],
uuq: [235, 0, 38],
uup: [235, 0, 38],
uuh: [235, 0, 38],
uus: [235, 0, 38],
uuo: [235, 0, 38]
};
const atoms = [];
const _bonds = [];
const _bhash = {};
const _atomMap = {};
const lines = text.split("\n");
for (let i = 0, l = lines.length; i < l; i++) {
if (lines[i].substr(0, 4) === "ATOM" || lines[i].substr(0, 6) === "HETATM") {
const x = parseFloat(lines[i].substr(30, 7));
const y = parseFloat(lines[i].substr(38, 7));
const z = parseFloat(lines[i].substr(46, 7));
const index = parseInt(lines[i].substr(6, 5)) - 1;
let e = trim(lines[i].substr(76, 2)).toLowerCase();
if (e === "") {
e = trim(lines[i].substr(12, 2)).toLowerCase();
}
const atomData = [x, y, z, CPK[e], capitalize(e)];
atoms.push(atomData);
_atomMap[index] = atomData;
} else if (lines[i].substr(0, 6) === "CONECT") {
const satom = parseInt(lines[i].substr(6, 5));
parseBond(11, 5, satom, i);
parseBond(16, 5, satom, i);
parseBond(21, 5, satom, i);
parseBond(26, 5, satom, i);
}
}
return buildGeometry();
}
}
export {
PDBLoader
};
//# sourceMappingURL=PDBLoader.js.map