Skip to content

T
three.js

Ablesons / three.js
与 Fork 源项目一致

从无法访问的项目Fork

通知 2
Star 0
Fork 0
T
three.js

体验新版 GitCode，发现更多精彩内容 >>

提交 91b1dbd1 编写于 作者: K kkruups
浏览文件
操作

Revert "Update PDBLoader.js with Comments" 

This reverts commit 6e0892b9.
上级 45c15c79
隐藏空白更改
内联 并排
Showing with 30 addition and 159 deletion
examples/js/loaders/PDBLoader.js
浏览文件 @ 91b1dbd1
......@@ -4,7 +4,7 @@
*/
THREE.PDBLoader = function ( manager ) {
//add your own manager or use default manager
this.manager = ( manager !== undefined ) ? manager : THREE.DefaultLoadingManager;
};
......@@ -49,50 +49,23 @@ THREE.PDBLoader.prototype = {
}
function parseBond( start, length ) {
/*
line1 CONECT 1 2
12345678901234567890123456789001234567890
Siiii)
P1iii)
P2iii)
P3iii)
P4iii)
line2 CONECT 2 1 9 49
satomL1 = 1, satomL2 = 2
P1 = eatomL1 = 2, eatomL2_i = 1,
P2 eatomL2_ii = 9
P3 eatomL2_iii = 49
P4
hL1 = s1e2
hL2 = s1e2 X, s2e9, s2e49
bhash = {s1e2: 0, s2e9: 1, s2e49: 2 ...} //bond connections
bonds = [ [0,1,1], [1, 8, 1], [1, 48, 1 ...]
*/
var eatom = parseInt( lines[ i ].substr( start, length ) );
if ( eatom ) {
//Generate Hash Key from Starting Atom and Connecting End Atom corresponding Connection
var h = hash( satom, eatom );
//if already exists do not create, skip
if ( bhash[ h ] === undefined ) {
//reduce satom and eatom connection by factor of 1 (single bond)
bonds.push( [ satom - 1, eatom - 1, 1 ] );
bhash[ h ] = bonds.length - 1; //identifies bond entry in bonds[bhash[s1e2]] array (key: endpoints Index: bond)
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
//increase last entry by 1, represents multiple bond
// bonds[bhash[h]][2] += 1;
}
......@@ -104,11 +77,6 @@ THREE.PDBLoader.prototype = {
function buildGeometry() {
var build = {
/*
This class is an efficient alternative to Geometry, because it stores all data,
including vertex positions, face indices, normals, colors, UVs, and custom attributes
within buffers; this reduces the cost of passing all this data to the GPU.
*/
geometryAtoms: new THREE.BufferGeometry(),
geometryBonds: new THREE.BufferGeometry(),
json: {
......@@ -130,70 +98,43 @@ THREE.PDBLoader.prototype = {
for ( i = 0, l = atoms.length; i < l; i ++ ) {
/*
//Array of Atoms, Arrays consisting of 4 entries:
[ [X-Coord, Y-Coord, Z-Coord, Color_Array[element_name], Element_Name], ... ]
atoms.push( [ x, y, z, CPK[ e ], capitalize( e ) ] );
*/
var atom = atoms[ i ];
var x = atom[ 0 ];
var x = atom[ 0 ];
var y = atom[ 1 ];
var z = atom[ 2 ];
// Array of Atoms Coord Positions
verticesAtoms.push( x, y, z );
/*
Generate float value representations for each color channels for use
in Float32BufferAttribute for color:
THREE.Float32BufferAttribute( colorsAtoms, 3 ) in
geometryAtoms.addAttribute( 'color', new THREE.Float32BufferAttribute( colorsAtoms, 3 ) );
where geometryAtoms is a BufferGeometry Object
*/
var r = atom[ 3 ][ 0 ] / 255;
var g = atom[ 3 ][ 1 ] / 255;
var b = atom[ 3 ][ 2 ] / 255;
//Generate Array of Color Float32 Arrays Entries for each Atom
colorsAtoms.push( r, g, b );
}
// bonds
/* Graphite
bonds = [ [0,1,1], [1, 8, 1], [1, 48, 1 ...]
*/
for ( i = 0, l = bonds.length; i < l; i ++ ) {
var bond = bonds[ i ];
var start = bond[ 0 ];
var end = bond[ 1 ];
// verticesBonds == verticesAtoms positions multiplied by factor of 3 and incremented
verticesBonds.push( verticesAtoms[ ( start * 3 ) + 0 ] ); //verticesAtoms[0] -- verticesAtoms[3]
verticesBonds.push( verticesAtoms[ ( start * 3 ) + 1 ] ); //verticesAtoms[1] -- verticesAtoms[4]
verticesBonds.push( verticesAtoms[ ( start * 3 ) + 2 ] ); //verticesAtoms[2] -- verticesAtoms[5]
verticesBonds.push( verticesAtoms[ ( end * 3 ) + 0 ] ); //verticesAtoms[3] -- verticesAtoms[24]
verticesBonds.push( verticesAtoms[ ( end * 3 ) + 1 ] ); //verticesAtoms[4] -- verticesAtoms[25]
verticesBonds.push( verticesAtoms[ ( end * 3 ) + 2 ] ); //verticesAtoms[5] -- verticesAtoms[26]
verticesBonds.push( verticesAtoms[ ( start * 3 ) + 0 ] );
verticesBonds.push( verticesAtoms[ ( start * 3 ) + 1 ] );
verticesBonds.push( verticesAtoms[ ( start * 3 ) + 2 ] );
verticesBonds.push( verticesAtoms[ ( end * 3 ) + 0 ] );
verticesBonds.push( verticesAtoms[ ( end * 3 ) + 1 ] );
verticesBonds.push( verticesAtoms[ ( end * 3 ) + 2 ] );
}
// build geometry
/* BufferAttribute class stores data for an attribute (such as vertex positions, face indices, normals, colors, UVs, and any custom attributes )
associated with a BufferGeometry, which allows for more efficient passing of data to the GPU.
*/
geometryAtoms.addAttribute( 'position', new THREE.Float32BufferAttribute( verticesAtoms, 3 ) );
geometryAtoms.addAttribute( 'color', new THREE.Float32BufferAttribute( colorsAtoms, 3 ) );
......@@ -202,23 +143,7 @@ THREE.PDBLoader.prototype = {
return build;
}
/* https://en.wikipedia.org/wiki/CPK_coloring?oldformat=true
CPK coloring is a popular color convention for distinguishing atoms of different chemical elements in molecular models.
(CPK <== Corey, Pauling, Koltun)
CPK molecular models designed by chemists Robert Corey and Linus Pauling, and improved by Walter Koltun
Koltun Colors Scheme for Periodic Table:
White for hydrogen
Black for carbon
Blue for nitrogen
Red for oxygen
Deep yellow for sulfur
Purple for phosphorus
Light, medium, medium dark, and dark green for the halogens (F, Cl, Br, I)
Silver for metals (Co, Fe, Ni, Cu)
*/
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 ] };
......@@ -231,63 +156,27 @@ THREE.PDBLoader.prototype = {
var x, y, z, e;
// parse
//Decompose text into Array: (an array entry for each line)
var lines = text.split( '\n' );
for ( var i = 0, l = lines.length; i < l; i ++ ) {
// extract atom coords from pdb
//Also SDF file Format similar to PDB file format: http://link.fyicenter.com/out.php?ID=571
/*
https://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#ATOM
e x y z
ATOM 2 C 1 -8.580 0.025 -4.537 1.00 0.00
12345678901234567890123456789012345678901234567890123456789012345678901234567890
0**4 Ei) Xiiiiii)Yiiiiii)Ziiiiii)
or
https://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#HETATM
x y z
HETATM 1 C01 UNK A 1 -10.447 3.465 0.000 0.00 0.00 0
12345678901234567890123456789012345678901234567890123456789012345678901234567890
0****6 Xiiiiii)Yiiiiii)Ziiiiii)
*/
if ( lines[ i ].substr( 0, 4 ) === 'ATOM' || lines[ i ].substr( 0, 6 ) === 'HETATM' ) {
//extract x,y,z coord for each atom from pdb file extracted lines
//extract values from locations for each coord
if ( lines[ i ].substr( 0, 4 ) === 'ATOM' || lines[ i ].substr( 0, 6 ) === 'HETATM' ) {
x = parseFloat( lines[ i ].substr( 30, 7 ) );
y = parseFloat( lines[ i ].substr( 38, 7 ) );
z = parseFloat( lines[ i ].substr( 46, 7 ) );
//If long line extract Chemistry Element from near the end of line
e = trim( lines[ i ].substr( 76, 2 ) ).toLowerCase();
//If not a long line extract the Chemistry from near the beginning of line
if ( e === '' ) {
//extract first 2 characters of Chemical Element Name
/*
e
ATOM 2 C 1 -8.580 0.025 -4.537 1.00 0.00
1234567890123567890123567890123567890123567890123567890123567890123567890
0**4 E i)
*/
e = trim( lines[ i ].substr( 12, 2 ) ).toLowerCase();
}
//add atoms to atoms array
atoms.push( [ x, y, z, CPK[ e ], capitalize( e ) ] );
//create histogram
if ( histogram[ e ] === undefined ) {
histogram[ e ] = 1;
......@@ -299,25 +188,7 @@ THREE.PDBLoader.prototype = {
}
} else if ( lines[ i ].substr( 0, 6 ) === 'CONECT' ) {
/*
https://www.wwpdb.org/documentation/file-format-content/format33/sect10.html#CONECT
The CONECT records specify connectivity between atoms for which coordinates are supplied.
CONECT 1 2
12345678901234567890123456789001234567890
Siiii)
Piiii)
Piiii)
Piiii)
Piiii)
CONECT 2 1 9 49
CONECT 3 4
*/
//Extract Bonds per line
//Get the 1st atom_serial_num per line & convert String Representation to Int
var satom = parseInt( lines[ i ].substr( 6, 5 ) );
parseBond( 11, 5 );
......
Markdown is supported
0% 或 .
You are about to add 0 people to the discussion. Proceed with caution.
先完成此消息的编辑！
想要评论请 注册 或