Spaces:
Running
Running
File size: 6,881 Bytes
a28eca3 |
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 |
import {
BufferGeometry,
FileLoader,
Float32BufferAttribute,
Loader,
Color,
SRGBColorSpace
} 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( text ) {
return text.replace( /^\s\s*/, '' ).replace( /\s\s*$/, '' );
}
function capitalize( text ) {
return text.charAt( 0 ).toUpperCase() + text.slice( 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 ].slice( start, start + length ) );
if ( eatom ) {
const h = hash( satom, eatom );
if ( _bhash[ h ] === undefined ) {
_bonds.push( [ satom - 1, eatom - 1, 1 ] );
_bhash[ h ] = _bonds.length - 1;
} else {
// doesn't really work as almost all PDBs
// have just normal bonds appearing multiple
// times instead of being double/triple bonds
// bonds[bhash[h]][2] += 1;
}
}
}
function buildGeometry() {
const build = {
geometryAtoms: new BufferGeometry(),
geometryBonds: new BufferGeometry(),
json: {
atoms: atoms
}
};
const geometryAtoms = build.geometryAtoms;
const geometryBonds = build.geometryBonds;
const verticesAtoms = [];
const colorsAtoms = [];
const verticesBonds = [];
// atoms
const c = new Color();
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;
c.setRGB( r, g, b, SRGBColorSpace );
colorsAtoms.push( c.r, c.g, c.b );
}
// bonds
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 );
}
// build geometry
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 = {};
// parse
const lines = text.split( '\n' );
for ( let i = 0, l = lines.length; i < l; i ++ ) {
if ( lines[ i ].slice( 0, 4 ) === 'ATOM' || lines[ i ].slice( 0, 6 ) === 'HETATM' ) {
const x = parseFloat( lines[ i ].slice( 30, 37 ) );
const y = parseFloat( lines[ i ].slice( 38, 45 ) );
const z = parseFloat( lines[ i ].slice( 46, 53 ) );
const index = parseInt( lines[ i ].slice( 6, 11 ) ) - 1;
let e = trim( lines[ i ].slice( 76, 78 ) ).toLowerCase();
if ( e === '' ) {
e = trim( lines[ i ].slice( 12, 14 ) ).toLowerCase();
}
const atomData = [ x, y, z, CPK[ e ], capitalize( e ) ];
atoms.push( atomData );
_atomMap[ index ] = atomData;
} else if ( lines[ i ].slice( 0, 6 ) === 'CONECT' ) {
const satom = parseInt( lines[ i ].slice( 6, 11 ) );
parseBond( 11, 5, satom, i );
parseBond( 16, 5, satom, i );
parseBond( 21, 5, satom, i );
parseBond( 26, 5, satom, i );
}
}
// build and return geometry
return buildGeometry();
}
}
export { PDBLoader };
|