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提交 f92b7df7 编写于 作者: M Mr.doob
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Simplified PDBLoader.

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examples/js/loaders/PDBLoader.js
浏览文件 @ f92b7df7
......@@ -2,235 +2,225 @@
* @author alteredq / http://alteredqualia.com/
*/
THREE.PDBLoader = function ( showStatus ) {
THREE.PDBLoader = function () {};
THREE.Loader.call( this, showStatus );
THREE.PDBLoader.prototype = {
};
constructor: THREE.OBJLoader,
THREE.PDBLoader.prototype = new THREE.Loader();
THREE.PDBLoader.prototype.constructor = THREE.PDBLoader;
THREE.PDBLoader.prototype.supr = THREE.Loader.prototype;
load: function ( url, callback ) {
THREE.PDBLoader.prototype.load = function ( url, callback ) {
var worker, scope = this;
var worker, scope = this;
this.loadAjaxPDB( this, url, callback );
this.onLoadStart();
this.loadAjaxPDB( this, url, callback );
},
};
loadAjaxPDB: function ( context, url, callback, callbackProgress ) {
THREE.PDBLoader.prototype.loadAjaxPDB = function ( context, url, callback, callbackProgress ) {
var xhr = new XMLHttpRequest();
var xhr = new XMLHttpRequest();
var length = 0;
var length = 0;
xhr.onreadystatechange = function () {
xhr.onreadystatechange = function () {
if ( xhr.readyState === xhr.DONE ) {
if ( xhr.readyState === xhr.DONE ) {
if ( xhr.status === 200 || xhr.status === 0 ) {
if ( xhr.status === 200 || xhr.status === 0 ) {
if ( xhr.responseText ) {
if ( xhr.responseText ) {
var json = context.parsePDB( xhr.responseText );
context.createModel( json, callback );
var json = context.parsePDB( xhr.responseText );
context.createModel( json, callback );
} else {
} else {
console.warn( "THREE.PDBLoader: [" + url + "] seems to be unreachable or file there is empty" );
console.warn( "THREE.PDBLoader: [" + url + "] seems to be unreachable or file there is empty" );
}
}
// in context of more complex asset initialization
// do not block on single failed file
// maybe should go even one more level up
} else {
context.onLoadComplete();
console.error( "THREE.PDBLoader: Couldn't load [" + url + "] [" + xhr.status + "]" );
} else {
}
console.error( "THREE.PDBLoader: Couldn't load [" + url + "] [" + xhr.status + "]" );
} else if ( xhr.readyState === xhr.LOADING ) {
}
if ( callbackProgress ) {
} else if ( xhr.readyState === xhr.LOADING ) {
if ( length === 0 ) {
if ( callbackProgress ) {
length = xhr.getResponseHeader( "Content-Length" );
if ( length === 0 ) {
}
length = xhr.getResponseHeader( "Content-Length" );
callbackProgress( { total: length, loaded: xhr.responseText.length } );
}
callbackProgress( { total: length, loaded: xhr.responseText.length } );
} else if ( xhr.readyState === xhr.HEADERS_RECEIVED ) {
}
length = xhr.getResponseHeader( "Content-Length" );
} else if ( xhr.readyState === xhr.HEADERS_RECEIVED ) {
}
length = xhr.getResponseHeader( "Content-Length" );
};
}
xhr.open( "GET", url, true );
if ( xhr.overrideMimeType ) xhr.overrideMimeType( "text/plain; charset=x-user-defined" );
xhr.setRequestHeader( "Content-Type", "text/plain" );
xhr.send( null );
};
},
xhr.open( "GET", url, true );
if ( xhr.overrideMimeType ) xhr.overrideMimeType( "text/plain; charset=x-user-defined" );
xhr.setRequestHeader( "Content-Type", "text/plain" );
xhr.send( null );
// Based on CanvasMol PDB parser
};
parsePDB: function ( text ) {
// Based on CanvasMol PDB parser
function trim( text ) {
THREE.PDBLoader.prototype.parsePDB = function ( text ) {
return text.replace(/^\s\s*/, '').replace(/\s\s*$/, '');
function trim( text ) {
}
return text.replace(/^\s\s*/, '').replace(/\s\s*$/, '');
function capitalize( text ) {
}
return text.charAt(0).toUpperCase() + text.substr(1).toLowerCase();
function capitalize( text ) {
}
return text.charAt(0).toUpperCase() + text.substr(1).toLowerCase();
function hash( s, e ) {
}
return "s" + Math.min( s, e ) + "e" + Math.max( s, e );
function hash( s, e ) {
}
return "s" + Math.min( s, e ) + "e" + Math.max( s, e );
function parseBond( start, length ) {
}
var eatom = parseInt( lines[ i ].substr( start, length ) );
function parseBond( start, length ) {
if( eatom ) {
var eatom = parseInt( lines[ i ].substr( start, length ) );
var h = hash( satom, eatom );
if( eatom ) {
if ( bhash[ h ] == undefined ) {
var h = hash( satom, eatom );
bonds.push( [ satom - 1, eatom - 1, 1 ] );
bhash[ h ] = bonds.length - 1;
if ( bhash[ h ] == undefined ) {
} else {
bonds.push( [ satom - 1, eatom - 1, 1 ] );
bhash[ h ] = bonds.length - 1;
// 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;
} 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;
}
}
}
}
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 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 atoms = [];
var bonds = [];
var histogram = {};
var lines = text.split( "\n" );
var bhash = {};
var x, y, z, e;
var lines = text.split( "\n" );
for( var i = 0, il = lines.length; i < il; ++ i ) {
var x, y, z, e;
if( lines[i].substr(0,4)=="ATOM" || lines[i].substr(0,6)=="HETATM" ) {
for( var i = 0, il = lines.length; i < il; ++ i ) {
x = parseFloat( lines[i].substr(30,7) );
y = parseFloat( lines[i].substr(38,7) );
z = parseFloat( lines[i].substr(46,7) );
if( lines[i].substr(0,4)=="ATOM" || lines[i].substr(0,6)=="HETATM" ) {
e = trim( lines[i].substr(76,2) ).toLowerCase();
x = parseFloat( lines[i].substr(30,7) );
y = parseFloat( lines[i].substr(38,7) );
z = parseFloat( lines[i].substr(46,7) );
if ( e=="" ) e = trim(lines[i].substr(12,2)).toLowerCase();
atoms.push( [ x,y,z, CPK[e], capitalize(e) ] );
e = trim( lines[i].substr(76,2) ).toLowerCase();
if (histogram[e]==undefined) histogram[e] = 1;
else histogram[e] += 1;
if ( e=="" ) e = trim(lines[i].substr(12,2)).toLowerCase();
atoms.push( [ x,y,z, CPK[e], capitalize(e) ] );
} else if(lines[i].substr(0,6)=="CONECT") {
if (histogram[e]==undefined) histogram[e] = 1;
else histogram[e] += 1;
var satom = parseInt( lines[i].substr(6,5) );
} else if(lines[i].substr(0,6)=="CONECT") {
parseBond(11,5);
parseBond(16,5);
parseBond(21,5);
parseBond(26,5);
var satom = parseInt( lines[i].substr(6,5) );
}
parseBond(11,5);
parseBond(16,5);
parseBond(21,5);
parseBond(26,5);
}
}
return { "ok": true, "atoms": atoms, "bonds": bonds, "histogram": histogram };
}
},
return { "ok": true, "atoms": atoms, "bonds": bonds, "histogram": histogram };
createModel: function ( json, callback ) {
};
var scope = this,
geometryAtoms = new THREE.Geometry(),
geometryBonds = new THREE.Geometry();
THREE.PDBLoader.prototype.createModel = function ( json, callback ) {
geometryAtoms.elements = [];
var scope = this,
geometryAtoms = new THREE.Geometry(),
geometryBonds = new THREE.Geometry();
var atoms = json.atoms;
var bonds = json.bonds;
geometryAtoms.elements = [];
for ( var i = 0; i < atoms.length; i ++ ) {
var atoms = json.atoms;
var bonds = json.bonds;
var atom = atoms[ i ];
for ( var i = 0; i < atoms.length; i ++ ) {
var x = atom[ 0 ];
var y = atom[ 1 ];
var z = atom[ 2 ];
var atom = atoms[ i ];
var position = new THREE.Vector3( x, y, z );
geometryAtoms.vertices.push( position );
var x = atom[ 0 ];
var y = atom[ 1 ];
var z = atom[ 2 ];
var r = atom[ 3 ][ 0 ] / 255;
var g = atom[ 3 ][ 1 ] / 255;
var b = atom[ 3 ][ 2 ] / 255;
var color = new THREE.Color();
color.setRGB( r, g, b );
var position = new THREE.Vector3( x, y, z );
geometryAtoms.vertices.push( position );
geometryAtoms.colors.push( color );
var r = atom[ 3 ][ 0 ] / 255;
var g = atom[ 3 ][ 1 ] / 255;
var b = atom[ 3 ][ 2 ] / 255;
var color = new THREE.Color();
color.setRGB( r, g, b );
geometryAtoms.elements.push( atom[ 4 ] );
geometryAtoms.colors.push( color );
}
geometryAtoms.elements.push( atom[ 4 ] );
for ( var i = 0; i < bonds.length; i ++ ) {
}
var bond = bonds[ i ];
for ( var i = 0; i < bonds.length; i ++ ) {
var start = bond[ 0 ];
var end = bond[ 1 ];
var bond = bonds[ i ];
var vertex1 = geometryAtoms.vertices[ start ];
var vertex2 = geometryAtoms.vertices[ end ];
var start = bond[ 0 ];
var end = bond[ 1 ];
geometryBonds.vertices.push( vertex1.clone() );
geometryBonds.vertices.push( vertex2.clone() );
var vertex1 = geometryAtoms.vertices[ start ];
var vertex2 = geometryAtoms.vertices[ end ];
}
geometryBonds.vertices.push( vertex1.clone() );
geometryBonds.vertices.push( vertex2.clone() );
callback( geometryAtoms, geometryBonds );
}
callback( geometryAtoms, geometryBonds );
};
}
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