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198e1f4
Add SDFLoader for parsing MDL SDF files
jakekinchen d096166
Merge pull request #1 from jakekinchen/codex/implement-sdfloader-for-…
jakekinchen 58aaaca
Refactor SDFLoader with enhanced error handling and documentation
jakekinchen d247821
feat: introduce SDFParser and refactor SDFLoader to use it; add tests…
jakekinchen a6054bd
refactor: remove SDFParser and associated tests; no longer needed for…
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,80 @@ | ||
| <!DOCTYPE html> | ||
| <html lang="en"> | ||
| <head> | ||
| <meta charset="utf-8" /> | ||
| <base href="../../../" /> | ||
| <script src="page.js"></script> | ||
| <link type="text/css" rel="stylesheet" href="page.css" /> | ||
| </head> | ||
| <body> | ||
| [page:Loader] → | ||
|
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| <h1>[name]</h1> | ||
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| <p class="desc"> | ||
| A loader for visualising molecules contained in <a href="https://en.wikipedia.org/wiki/Chemical_table_file#Molfile">MDL Molfile / SDF</a> files. | ||
| The loader creates two <a href="/docs/#api/en/objects/InstancedMesh">InstancedMesh</a> objects – spheres for atoms and cylinders for bonds – and returns them in a single [page:Group]. | ||
| </p> | ||
|
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| <h2>Import</h2> | ||
| <p> | ||
| [name] is an add-on, and must therefore be imported explicitly. See | ||
| [link:#manual/introduction/Installation Installation / Addons]. | ||
| </p> | ||
|
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| <code> | ||
| import { SDFLoader } from 'three/addons/loaders/SDFLoader.js'; | ||
| </code> | ||
|
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| <h2>Code Example</h2> | ||
|
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| <code> | ||
| const loader = new SDFLoader(); | ||
| loader.load( 'models/sdf/benzene.sdf', function ( group ) { | ||
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| // `group` is a THREE.Group containing two InstancedMesh children: | ||
| // * atoms – spheres | ||
| // * bonds – cylinders | ||
| scene.add( group ); | ||
|
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| } ); | ||
| </code> | ||
|
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| <h2>Examples</h2> | ||
| <p> | ||
| [example:webgl_loader_sdf] | ||
| </p> | ||
|
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| <h2>Constructor</h2> | ||
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| <h3>[name]( [param:LoadingManager manager] )</h3> | ||
| <p> | ||
| [page:LoadingManager manager] — The [page:LoadingManager loadingManager] for the loader to use. Default is [page:LoadingManager THREE.DefaultLoadingManager]. | ||
| </p> | ||
| <p>Creates a new [name].</p> | ||
|
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| <h2>Properties</h2> | ||
| <p>See the base [page:Loader] class for common properties.</p> | ||
| <p> | ||
| [property:Object elementColors] — Map of element symbol → atom colour (hex). Can be customised via [page:setElementData].<br /> | ||
| [property:Object elementRadii] — Map of element symbol → van-der-Waals radius (Å). Can be customised via [page:setElementData]. | ||
| </p> | ||
|
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| <h2>Methods</h2> | ||
| <p>See the base [page:Loader] class for common methods.</p> | ||
|
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| <h3>[method:undefined load]( [param:String url], [param:Function onLoad], [param:Function onProgress], [param:Function onError] )</h3> | ||
| <p> | ||
| Begin loading the file from <code>url</code>. The <code>onLoad</code> callback is passed the returned [page:Group]. | ||
| </p> | ||
|
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| <h3>[method:Group parse]( [param:String text] )</h3> | ||
| <p>Parse a Molfile / SDF molecule string and return a [page:Group] as described above.</p> | ||
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| <h3>[method:this setElementData]( [param:Object colors], [param:Object radii] )</h3> | ||
| <p>Merge <code>colors</code> and/or <code>radii</code> into the default element data.</p> | ||
|
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| <h2>Source</h2> | ||
| <p>[link:https://github.com/mrdoob/three.js/blob/master/examples/jsm/loaders/SDFLoader.js examples/jsm/loaders/SDFLoader.js]</p> | ||
| </body> | ||
| </html> |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,195 @@ | ||
| import { | ||
| Loader, | ||
| FileLoader, | ||
| Group, | ||
| Vector3, | ||
| Color, | ||
| SphereGeometry, | ||
| CylinderGeometry, | ||
| MeshLambertMaterial, | ||
| InstancedMesh, | ||
| Matrix4, | ||
| Quaternion | ||
| } from 'three'; | ||
|
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| const DEFAULT_VDW_RADIUS = { | ||
| H: 0.31, C: 0.76, N: 0.71, O: 0.66, F: 0.57, | ||
| P: 1.07, S: 1.05, Cl: 1.02, Br: 1.2, I: 1.39 | ||
| }; | ||
|
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| const DEFAULT_ELEMENT_COLOR = { | ||
| H: 0xffffff, C: 0x909090, N: 0x3050f8, O: 0xff0d0d, F: 0x90e050, | ||
| P: 0xff8000, S: 0xffff30, Cl: 0x1ff01f, Br: 0xa62929, I: 0x940094 | ||
| }; | ||
|
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| /** | ||
| * SDFLoader — A loader for MDL Molfile / SDF chemical structure files. | ||
| * | ||
| * The loader parses the textual SDF data and returns a `THREE.Group` containing two | ||
| * `THREE.InstancedMesh` children: one for the atoms (spheres) and one for the bonds (cylinders). | ||
| * | ||
| * In addition to efficient rendering via instancing, the loader allows customisation of element | ||
| * colours and van-der-Waals radii via the `setElementData` method. | ||
| * | ||
| * Example usage: | ||
| * ```js | ||
| * import { SDFLoader } from 'three/addons/loaders/SDFLoader.js'; | ||
| * | ||
| * const loader = new SDFLoader(); | ||
| * loader.load( 'models/sdf/benzene.sdf', group => { | ||
| * scene.add( group ); | ||
| * } ); | ||
| * ``` | ||
| * | ||
| * @see examples/webgl_loader_sdf | ||
| */ | ||
| class SDFLoader extends Loader { | ||
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| constructor( manager ) { | ||
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| super( manager ); | ||
| this.elementRadii = { ...DEFAULT_VDW_RADIUS }; | ||
| this.elementColors = { ...DEFAULT_ELEMENT_COLOR }; | ||
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| } | ||
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| setElementData( colors, radii ) { | ||
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| if ( colors ) Object.assign( this.elementColors, colors ); | ||
| if ( radii ) Object.assign( this.elementRadii, radii ); | ||
| return this; | ||
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| } | ||
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| load( url, onLoad, onProgress, onError ) { | ||
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| const loader = new FileLoader( this.manager ); | ||
| loader.setPath( this.path ); | ||
| loader.setRequestHeader( this.requestHeader ); | ||
| loader.setWithCredentials( this.withCredentials ); | ||
| loader.setResponseType( 'text' ); | ||
| loader.load( url, text => { | ||
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| try { | ||
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| onLoad( this.parse( text ) ); | ||
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| } catch ( e ) { | ||
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| if ( onError ) { | ||
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| onError( e ); | ||
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| } else { | ||
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| console.error( e ); | ||
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| } | ||
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| this.manager.itemError( url ); | ||
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| } | ||
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| }, onProgress, onError ); | ||
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| } | ||
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| parse( text ) { | ||
|
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| // Use internal lightweight parser so loader is self-contained | ||
| /* eslint-disable padded-blocks */ | ||
| const { atoms, bonds } = ( () => { | ||
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| const lines = text.split( /\r?\n/ ); | ||
| let i = 3; | ||
| const counts = lines[ i ++ ].trim().split( /\s+/ ); | ||
| const natoms = parseInt( counts[ 0 ] ); | ||
| const nbonds = parseInt( counts[ 1 ] ); | ||
| if ( isNaN( natoms ) || isNaN( nbonds ) ) throw new Error( 'SDFLoader: invalid counts line' ); | ||
| const atoms = []; | ||
|
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| for ( let k = 0; k < natoms; k ++, i ++ ) { | ||
| const l = lines[ i ]; | ||
| if ( ! l || l.length < 31 ) throw new Error( `SDFLoader: invalid atom line ${ i + 1 }` ); | ||
| const x = parseFloat( l.substr( 0, 10 ) ); | ||
| const y = parseFloat( l.substr( 10, 10 ) ); | ||
| const z = parseFloat( l.substr( 20, 10 ) ); | ||
| const element = l.substr( 31, 3 ).trim() || 'C'; | ||
| atoms.push( { position: new Vector3( x, y, z ), element } ); | ||
| } | ||
|
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| const bonds = []; | ||
| while ( bonds.length < nbonds && i < lines.length ) { | ||
| const l = lines[ i ++ ]; | ||
| if ( ! l ) continue; | ||
| if ( l.startsWith( 'M' ) ) break; | ||
| if ( l.length < 9 ) continue; | ||
| const a1 = parseInt( l.slice( 0, 3 ) ) - 1; | ||
| const a2 = parseInt( l.slice( 3, 6 ) ) - 1; | ||
| const type = parseInt( l.slice( 6, 9 ) ) || 1; | ||
| if ( isNaN( a1 ) || isNaN( a2 ) || a1 < 0 || a2 < 0 || a1 >= natoms || a2 >= natoms ) continue; | ||
| bonds.push( [ a1, a2, type ] ); | ||
| } | ||
|
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| return { atoms, bonds }; | ||
|
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| } )(); | ||
| /* eslint-enable padded-blocks */ | ||
|
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| return this._buildSceneGraph( atoms, bonds ); | ||
|
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| } | ||
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| _buildSceneGraph( atoms, bonds ) { | ||
|
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| const group = new Group(); | ||
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| const sphereGeo = new SphereGeometry( 1, 16, 16 ); | ||
| const atomMat = new MeshLambertMaterial(); | ||
| const atomMesh = new InstancedMesh( sphereGeo, atomMat, atoms.length ); | ||
| const m = new Matrix4(); | ||
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| atoms.forEach( ( atom, idx ) => { | ||
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| const r = ( this.elementRadii[ atom.element ] || 0.75 ) * 0.2; | ||
| m.makeScale( r, r, r ); | ||
| m.setPosition( atom.position ); | ||
| atomMesh.setMatrixAt( idx, m ); | ||
| const color = this.elementColors[ atom.element ] || 0xcccccc; | ||
| atomMesh.setColorAt( idx, new Color( color ) ); | ||
|
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| } ); | ||
| atomMesh.instanceMatrix.needsUpdate = true; | ||
| atomMesh.instanceColor.needsUpdate = true; | ||
| group.add( atomMesh ); | ||
|
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| const cylGeo = new CylinderGeometry( 0.05, 0.05, 1, 8 ); | ||
| const bondMat = new MeshLambertMaterial( { color: 0xaaaaaa } ); | ||
| const bondMesh = new InstancedMesh( cylGeo, bondMat, bonds.length ); | ||
| const up = new Vector3( 0, 1, 0 ); | ||
| const q = new Quaternion(); | ||
|
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| bonds.forEach( ( [ a, b, bondType ], idx ) => { | ||
|
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| const v1 = atoms[ a ].position; | ||
| const v2 = atoms[ b ].position; | ||
| const mid = v1.clone().add( v2 ).multiplyScalar( 0.5 ); | ||
| const dir = v2.clone().sub( v1 ); | ||
| const len = dir.length(); | ||
| q.setFromUnitVectors( up, dir.clone().normalize() ); | ||
| m.makeRotationFromQuaternion( q ); | ||
| m.setPosition( mid ); | ||
| m.scale( new Vector3( 1, len, 1 ) ); | ||
| bondMesh.setMatrixAt( idx, m ); | ||
|
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| } ); | ||
| bondMesh.instanceMatrix.needsUpdate = true; | ||
| group.add( bondMesh ); | ||
|
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| return group; | ||
|
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| } | ||
|
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| } | ||
|
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| export { SDFLoader }; | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,17 @@ | ||
| benzene | ||
| threejs 2025 | ||
|
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| 6 6 0 0 0 0 0 0 0 0999 V2000 | ||
| 0.0000 1.3960 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 | ||
| -1.2094 0.6980 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 | ||
| -1.2094 -0.6980 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 | ||
| 0.0000 -1.3960 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 | ||
| 1.2094 -0.6980 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 | ||
| 1.2094 0.6980 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 | ||
| 1 2 1 0 0 0 0 | ||
| 2 3 2 0 0 0 0 | ||
| 3 4 1 0 0 0 0 | ||
| 4 5 2 0 0 0 0 | ||
| 5 6 1 0 0 0 0 | ||
| 6 1 2 0 0 0 0 | ||
| M END |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,54 @@ | ||
| Caffeine | ||
| ChemDraw03112406102D | ||
|
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| 24 25 0 0 0 0 0 0 0 0999 V2000 | ||
| 0.7145 -0.4125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 | ||
| 0.7145 0.4125 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 | ||
| 0.0000 0.8250 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 | ||
| -0.7145 0.4125 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 | ||
| -0.7145 -0.4125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 | ||
| 0.0000 -0.8250 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 | ||
| 1.4289 -0.8250 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 | ||
| -1.4289 -0.8250 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 | ||
| 1.4289 0.8250 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 | ||
| -1.4289 0.8250 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 | ||
| 0.0000 1.6500 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 | ||
| 0.0000 2.4750 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 | ||
| 0.7145 2.8875 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 | ||
| 0.7145 3.7125 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 | ||
| 1.4289 2.4750 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 | ||
| 0.7145 2.0625 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 | ||
| 2.1434 0.4125 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 | ||
| 1.4289 1.6500 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 | ||
| 2.1434 0.8250 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 | ||
| -2.1434 0.4125 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 | ||
| -1.4289 1.6500 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 | ||
| -2.1434 0.8250 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 | ||
| 0.0000 -1.6500 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 | ||
| -0.7145 2.8875 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 | ||
| 1 2 1 0 0 0 0 | ||
| 2 3 1 0 0 0 0 | ||
| 3 4 1 0 0 0 0 | ||
| 4 5 1 0 0 0 0 | ||
| 5 6 1 0 0 0 0 | ||
| 6 1 1 0 0 0 0 | ||
| 1 7 2 0 0 0 0 | ||
| 5 8 2 0 0 0 0 | ||
| 2 9 1 0 0 0 0 | ||
| 4 10 1 0 0 0 0 | ||
| 3 11 1 0 0 0 0 | ||
| 11 12 1 0 0 0 0 | ||
| 12 13 1 0 0 0 0 | ||
| 13 14 1 0 0 0 0 | ||
| 13 15 1 0 0 0 0 | ||
| 13 16 1 0 0 0 0 | ||
| 9 17 1 0 0 0 0 | ||
| 9 18 1 0 0 0 0 | ||
| 9 19 1 0 0 0 0 | ||
| 10 20 1 0 0 0 0 | ||
| 10 21 1 0 0 0 0 | ||
| 10 22 1 0 0 0 0 | ||
| 6 23 1 0 0 0 0 | ||
| 12 24 1 0 0 0 0 | ||
| M END | ||
| $$$$ |
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I vote to remove
SDFLoaderand implement the JSON parsing right in the example. The loader contains too much application specific code.There was a problem hiding this comment.
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The SDF parsing library could be imported like in other examples:
three.js/examples/webgl_loader_ifc.html
Lines 26 to 28 in c6e73de