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未验证 提交 c1c1c983 编写于 作者: M Mr.doob 提交者： GitHub
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Merge pull request #19242 from Mugen87/dev41 

PDBLoader: Remove assumption of continuously defined atoms.
上级 21ab863e fa20ab77
隐藏空白更改
内联 并排
Showing with 59 addition and 60 deletion
examples/js/loaders/PDBLoader.js
浏览文件 @ c1c1c983
......@@ -57,10 +57,10 @@ THREE.PDBLoader.prototype = Object.assign( Object.create( THREE.Loader.prototype
var h = hash( satom, eatom );
if ( bhash[ h ] === undefined ) {
if ( _bhash[ h ] === undefined ) {
bonds.push( [ satom - 1, eatom - 1, 1 ] );
bhash[ h ] = bonds.length - 1;
_bonds.push( [ satom - 1, eatom - 1, 1 ] );
_bhash[ h ] = _bonds.length - 1;
} else {
......@@ -81,8 +81,7 @@ THREE.PDBLoader.prototype = Object.assign( Object.create( THREE.Loader.prototype
geometryAtoms: new THREE.BufferGeometry(),
geometryBonds: new THREE.BufferGeometry(),
json: {
atoms: atoms,
bonds: bonds
atoms: atoms
}
};
......@@ -90,6 +89,7 @@ THREE.PDBLoader.prototype = Object.assign( Object.create( THREE.Loader.prototype
var geometryBonds = build.geometryBonds;
var i, l;
var x, y, z;
var verticesAtoms = [];
var colorsAtoms = [];
......@@ -101,9 +101,9 @@ THREE.PDBLoader.prototype = Object.assign( Object.create( THREE.Loader.prototype
var atom = atoms[ i ];
var x = atom[ 0 ];
var y = atom[ 1 ];
var z = atom[ 2 ];
x = atom[ 0 ];
y = atom[ 1 ];
z = atom[ 2 ];
verticesAtoms.push( x, y, z );
......@@ -117,20 +117,27 @@ THREE.PDBLoader.prototype = Object.assign( Object.create( THREE.Loader.prototype
// bonds
for ( i = 0, l = bonds.length; i < l; i ++ ) {
for ( i = 0, l = _bonds.length; i < l; i ++ ) {
var bond = bonds[ i ];
var bond = _bonds[ i ];
var start = bond[ 0 ];
var end = bond[ 1 ];
verticesBonds.push( verticesAtoms[ ( start * 3 ) + 0 ] );
verticesBonds.push( verticesAtoms[ ( start * 3 ) + 1 ] );
verticesBonds.push( verticesAtoms[ ( start * 3 ) + 2 ] );
var startAtom = _atomMap[ start ];
var endAtom = _atomMap[ end ];
verticesBonds.push( verticesAtoms[ ( end * 3 ) + 0 ] );
verticesBonds.push( verticesAtoms[ ( end * 3 ) + 1 ] );
verticesBonds.push( verticesAtoms[ ( end * 3 ) + 2 ] );
x = startAtom[ 0 ];
y = startAtom[ 1 ];
z = startAtom[ 2 ];
verticesBonds.push( x, y, z );
x = endAtom[ 0 ];
y = endAtom[ 1 ];
z = endAtom[ 2 ];
verticesBonds.push( x, y, z );
}
......@@ -148,10 +155,10 @@ THREE.PDBLoader.prototype = Object.assign( Object.create( THREE.Loader.prototype
var 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 ] };
var atoms = [];
var bonds = [];
var histogram = {};
var bhash = {};
var _bonds = [];
var _bhash = {};
var _atomMap = {};
var x, y, z, index, e;
......@@ -176,17 +183,10 @@ THREE.PDBLoader.prototype = Object.assign( Object.create( THREE.Loader.prototype
}
atoms[ index ] = [ x, y, z, CPK[ e ], capitalize( e ) ];
if ( histogram[ e ] === undefined ) {
histogram[ e ] = 1;
var atomData = [ x, y, z, CPK[ e ], capitalize( e ) ];
} else {
histogram[ e ] += 1;
}
atoms.push( atomData );
_atomMap[ index ] = atomData;
} else if ( lines[ i ].substr( 0, 6 ) === 'CONECT' ) {
......
examples/jsm/loaders/PDBLoader.d.ts
浏览文件 @ c1c1c983
......@@ -8,8 +8,7 @@ export interface PDB {
geometryAtoms: BufferGeometry;
geometryBonds: BufferGeometry;
json: {
atoms: any[][],
bonds: number[][]
atoms: any[][]
}
}
......
examples/jsm/loaders/PDBLoader.js
浏览文件 @ c1c1c983
......@@ -64,10 +64,10 @@ PDBLoader.prototype = Object.assign( Object.create( Loader.prototype ), {
var h = hash( satom, eatom );
if ( bhash[ h ] === undefined ) {
if ( _bhash[ h ] === undefined ) {
bonds.push( [ satom - 1, eatom - 1, 1 ] );
bhash[ h ] = bonds.length - 1;
_bonds.push( [ satom - 1, eatom - 1, 1 ] );
_bhash[ h ] = _bonds.length - 1;
} else {
......@@ -88,8 +88,7 @@ PDBLoader.prototype = Object.assign( Object.create( Loader.prototype ), {
geometryAtoms: new BufferGeometry(),
geometryBonds: new BufferGeometry(),
json: {
atoms: atoms,
bonds: bonds
atoms: atoms
}
};
......@@ -97,6 +96,7 @@ PDBLoader.prototype = Object.assign( Object.create( Loader.prototype ), {
var geometryBonds = build.geometryBonds;
var i, l;
var x, y, z;
var verticesAtoms = [];
var colorsAtoms = [];
......@@ -108,9 +108,9 @@ PDBLoader.prototype = Object.assign( Object.create( Loader.prototype ), {
var atom = atoms[ i ];
var x = atom[ 0 ];
var y = atom[ 1 ];
var z = atom[ 2 ];
x = atom[ 0 ];
y = atom[ 1 ];
z = atom[ 2 ];
verticesAtoms.push( x, y, z );
......@@ -124,20 +124,27 @@ PDBLoader.prototype = Object.assign( Object.create( Loader.prototype ), {
// bonds
for ( i = 0, l = bonds.length; i < l; i ++ ) {
for ( i = 0, l = _bonds.length; i < l; i ++ ) {
var bond = bonds[ i ];
var bond = _bonds[ i ];
var start = bond[ 0 ];
var end = bond[ 1 ];
verticesBonds.push( verticesAtoms[ ( start * 3 ) + 0 ] );
verticesBonds.push( verticesAtoms[ ( start * 3 ) + 1 ] );
verticesBonds.push( verticesAtoms[ ( start * 3 ) + 2 ] );
var startAtom = _atomMap[ start ];
var endAtom = _atomMap[ end ];
verticesBonds.push( verticesAtoms[ ( end * 3 ) + 0 ] );
verticesBonds.push( verticesAtoms[ ( end * 3 ) + 1 ] );
verticesBonds.push( verticesAtoms[ ( end * 3 ) + 2 ] );
x = startAtom[ 0 ];
y = startAtom[ 1 ];
z = startAtom[ 2 ];
verticesBonds.push( x, y, z );
x = endAtom[ 0 ];
y = endAtom[ 1 ];
z = endAtom[ 2 ];
verticesBonds.push( x, y, z );
}
......@@ -155,10 +162,10 @@ PDBLoader.prototype = Object.assign( Object.create( Loader.prototype ), {
var 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 ] };
var atoms = [];
var bonds = [];
var histogram = {};
var bhash = {};
var _bonds = [];
var _bhash = {};
var _atomMap = {};
var x, y, z, index, e;
......@@ -183,17 +190,10 @@ PDBLoader.prototype = Object.assign( Object.create( Loader.prototype ), {
}
atoms[ index ] = [ x, y, z, CPK[ e ], capitalize( e ) ];
if ( histogram[ e ] === undefined ) {
histogram[ e ] = 1;
var atomData = [ x, y, z, CPK[ e ], capitalize( e ) ];
} else {
histogram[ e ] += 1;
}
atoms.push( atomData );
_atomMap[ index ] = atomData;
} else if ( lines[ i ].substr( 0, 6 ) === 'CONECT' ) {
......
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