@anov/3d 0.0.1 → 0.0.2

package/examples/jsm/loaders/PCDLoader.js

@@ -0,0 +1,467 @@
+import {
+	BufferGeometry,
+	Color,
+	FileLoader,
+	Float32BufferAttribute,
+	Int32BufferAttribute,
+	Loader,
+	Points,
+	PointsMaterial
+} from 'three';
+
+class PCDLoader extends Loader {
+
+	constructor( manager ) {
+
+		super( manager );
+
+		this.littleEndian = true;
+
+	}
+
+	load( url, onLoad, onProgress, onError ) {
+
+		const scope = this;
+
+		const loader = new FileLoader( scope.manager );
+		loader.setPath( scope.path );
+		loader.setResponseType( 'arraybuffer' );
+		loader.setRequestHeader( scope.requestHeader );
+		loader.setWithCredentials( scope.withCredentials );
+		loader.load( url, function ( data ) {
+
+			try {
+
+				onLoad( scope.parse( data ) );
+
+			} catch ( e ) {
+
+				if ( onError ) {
+
+					onError( e );
+
+				} else {
+
+					console.error( e );
+
+				}
+
+				scope.manager.itemError( url );
+
+			}
+
+		}, onProgress, onError );
+
+	}
+
+	parse( data ) {
+
+		// from https://gitlab.com/taketwo/three-pcd-loader/blob/master/decompress-lzf.js
+
+		function decompressLZF( inData, outLength ) {
+
+			const inLength = inData.length;
+			const outData = new Uint8Array( outLength );
+			let inPtr = 0;
+			let outPtr = 0;
+			let ctrl;
+			let len;
+			let ref;
+			do {
+
+				ctrl = inData[ inPtr ++ ];
+				if ( ctrl < ( 1 << 5 ) ) {
+
+					ctrl ++;
+					if ( outPtr + ctrl > outLength ) throw new Error( 'Output buffer is not large enough' );
+					if ( inPtr + ctrl > inLength ) throw new Error( 'Invalid compressed data' );
+					do {
+
+						outData[ outPtr ++ ] = inData[ inPtr ++ ];
+
+					} while ( -- ctrl );
+
+				} else {
+
+					len = ctrl >> 5;
+					ref = outPtr - ( ( ctrl & 0x1f ) << 8 ) - 1;
+					if ( inPtr >= inLength ) throw new Error( 'Invalid compressed data' );
+					if ( len === 7 ) {
+
+						len += inData[ inPtr ++ ];
+						if ( inPtr >= inLength ) throw new Error( 'Invalid compressed data' );
+
+					}
+
+					ref -= inData[ inPtr ++ ];
+					if ( outPtr + len + 2 > outLength ) throw new Error( 'Output buffer is not large enough' );
+					if ( ref < 0 ) throw new Error( 'Invalid compressed data' );
+					if ( ref >= outPtr ) throw new Error( 'Invalid compressed data' );
+					do {
+
+						outData[ outPtr ++ ] = outData[ ref ++ ];
+
+					} while ( -- len + 2 );
+
+				}
+
+			} while ( inPtr < inLength );
+
+			return outData;
+
+		}
+
+		function parseHeader( data ) {
+
+			const PCDheader = {};
+			const result1 = data.search( /[\r\n]DATA\s(\S*)\s/i );
+			const result2 = /[\r\n]DATA\s(\S*)\s/i.exec( data.slice( result1 - 1 ) );
+
+			PCDheader.data = result2[ 1 ];
+			PCDheader.headerLen = result2[ 0 ].length + result1;
+			PCDheader.str = data.slice( 0, PCDheader.headerLen );
+
+			// remove comments
+
+			PCDheader.str = PCDheader.str.replace( /#.*/gi, '' );
+
+			// parse
+
+			PCDheader.version = /VERSION (.*)/i.exec( PCDheader.str );
+			PCDheader.fields = /FIELDS (.*)/i.exec( PCDheader.str );
+			PCDheader.size = /SIZE (.*)/i.exec( PCDheader.str );
+			PCDheader.type = /TYPE (.*)/i.exec( PCDheader.str );
+			PCDheader.count = /COUNT (.*)/i.exec( PCDheader.str );
+			PCDheader.width = /WIDTH (.*)/i.exec( PCDheader.str );
+			PCDheader.height = /HEIGHT (.*)/i.exec( PCDheader.str );
+			PCDheader.viewpoint = /VIEWPOINT (.*)/i.exec( PCDheader.str );
+			PCDheader.points = /POINTS (.*)/i.exec( PCDheader.str );
+
+			// evaluate
+
+			if ( PCDheader.version !== null )
+				PCDheader.version = parseFloat( PCDheader.version[ 1 ] );
+
+			PCDheader.fields = ( PCDheader.fields !== null ) ? PCDheader.fields[ 1 ].split( ' ' ) : [];
+
+			if ( PCDheader.type !== null )
+				PCDheader.type = PCDheader.type[ 1 ].split( ' ' );
+
+			if ( PCDheader.width !== null )
+				PCDheader.width = parseInt( PCDheader.width[ 1 ] );
+
+			if ( PCDheader.height !== null )
+				PCDheader.height = parseInt( PCDheader.height[ 1 ] );
+
+			if ( PCDheader.viewpoint !== null )
+				PCDheader.viewpoint = PCDheader.viewpoint[ 1 ];
+
+			if ( PCDheader.points !== null )
+				PCDheader.points = parseInt( PCDheader.points[ 1 ], 10 );
+
+			if ( PCDheader.points === null )
+				PCDheader.points = PCDheader.width * PCDheader.height;
+
+			if ( PCDheader.size !== null ) {
+
+				PCDheader.size = PCDheader.size[ 1 ].split( ' ' ).map( function ( x ) {
+
+					return parseInt( x, 10 );
+
+				} );
+
+			}
+
+			if ( PCDheader.count !== null ) {
+
+				PCDheader.count = PCDheader.count[ 1 ].split( ' ' ).map( function ( x ) {
+
+					return parseInt( x, 10 );
+
+				} );
+
+			} else {
+
+				PCDheader.count = [];
+
+				for ( let i = 0, l = PCDheader.fields.length; i < l; i ++ ) {
+
+					PCDheader.count.push( 1 );
+
+				}
+
+			}
+
+			PCDheader.offset = {};
+
+			let sizeSum = 0;
+
+			for ( let i = 0, l = PCDheader.fields.length; i < l; i ++ ) {
+
+				if ( PCDheader.data === 'ascii' ) {
+
+					PCDheader.offset[ PCDheader.fields[ i ] ] = i;
+
+				} else {
+
+					PCDheader.offset[ PCDheader.fields[ i ] ] = sizeSum;
+					sizeSum += PCDheader.size[ i ] * PCDheader.count[ i ];
+
+				}
+
+			}
+
+			// for binary only
+
+			PCDheader.rowSize = sizeSum;
+
+			return PCDheader;
+
+		}
+
+		const textData = new TextDecoder().decode( data );
+
+		// parse header (always ascii format)
+
+		const PCDheader = parseHeader( textData );
+
+		// parse data
+
+		const position = [];
+		const normal = [];
+		const color = [];
+		const intensity = [];
+		const label = [];
+
+		const c = new Color();
+
+		// ascii
+
+		if ( PCDheader.data === 'ascii' ) {
+
+			const offset = PCDheader.offset;
+			const pcdData = textData.slice( PCDheader.headerLen );
+			const lines = pcdData.split( '\n' );
+
+			for ( let i = 0, l = lines.length; i < l; i ++ ) {
+
+				if ( lines[ i ] === '' ) continue;
+
+				const line = lines[ i ].split( ' ' );
+
+				if ( offset.x !== undefined ) {
+
+					position.push( parseFloat( line[ offset.x ] ) );
+					position.push( parseFloat( line[ offset.y ] ) );
+					position.push( parseFloat( line[ offset.z ] ) );
+
+				}
+
+				if ( offset.rgb !== undefined ) {
+
+					const rgb_field_index = PCDheader.fields.findIndex( ( field ) => field === 'rgb' );
+					const rgb_type = PCDheader.type[ rgb_field_index ];
+
+					const float = parseFloat( line[ offset.rgb ] );
+					let rgb = float;
+
+					if ( rgb_type === 'F' ) {
+
+						// treat float values as int
+						// https://github.com/daavoo/pyntcloud/pull/204/commits/7b4205e64d5ed09abe708b2e91b615690c24d518
+						const farr = new Float32Array( 1 );
+						farr[ 0 ] = float;
+						rgb = new Int32Array( farr.buffer )[ 0 ];
+
+					}
+
+					const r = ( ( rgb >> 16 ) & 0x0000ff ) / 255;
+					const g = ( ( rgb >> 8 ) & 0x0000ff ) / 255;
+					const b = ( ( rgb >> 0 ) & 0x0000ff ) / 255;
+
+					c.set( r, g, b ).convertSRGBToLinear();
+
+					color.push( c.r, c.g, c.b );
+
+				}
+
+				if ( offset.normal_x !== undefined ) {
+
+					normal.push( parseFloat( line[ offset.normal_x ] ) );
+					normal.push( parseFloat( line[ offset.normal_y ] ) );
+					normal.push( parseFloat( line[ offset.normal_z ] ) );
+
+				}
+
+				if ( offset.intensity !== undefined ) {
+
+					intensity.push( parseFloat( line[ offset.intensity ] ) );
+
+				}
+
+				if ( offset.label !== undefined ) {
+
+					label.push( parseInt( line[ offset.label ] ) );
+
+				}
+
+			}
+
+		}
+
+		// binary-compressed
+
+		// normally data in PCD files are organized as array of structures: XYZRGBXYZRGB
+		// binary compressed PCD files organize their data as structure of arrays: XXYYZZRGBRGB
+		// that requires a totally different parsing approach compared to non-compressed data
+
+		if ( PCDheader.data === 'binary_compressed' ) {
+
+			const sizes = new Uint32Array( data.slice( PCDheader.headerLen, PCDheader.headerLen + 8 ) );
+			const compressedSize = sizes[ 0 ];
+			const decompressedSize = sizes[ 1 ];
+			const decompressed = decompressLZF( new Uint8Array( data, PCDheader.headerLen + 8, compressedSize ), decompressedSize );
+			const dataview = new DataView( decompressed.buffer );
+
+			const offset = PCDheader.offset;
+
+			for ( let i = 0; i < PCDheader.points; i ++ ) {
+
+				if ( offset.x !== undefined ) {
+
+					const xIndex = PCDheader.fields.indexOf( 'x' );
+					const yIndex = PCDheader.fields.indexOf( 'y' );
+					const zIndex = PCDheader.fields.indexOf( 'z' );
+					position.push( dataview.getFloat32( ( PCDheader.points * offset.x ) + PCDheader.size[ xIndex ] * i, this.littleEndian ) );
+					position.push( dataview.getFloat32( ( PCDheader.points * offset.y ) + PCDheader.size[ yIndex ] * i, this.littleEndian ) );
+					position.push( dataview.getFloat32( ( PCDheader.points * offset.z ) + PCDheader.size[ zIndex ] * i, this.littleEndian ) );
+
+				}
+
+				if ( offset.rgb !== undefined ) {
+
+					const rgbIndex = PCDheader.fields.indexOf( 'rgb' );
+
+					const r = dataview.getUint8( ( PCDheader.points * offset.rgb ) + PCDheader.size[ rgbIndex ] * i + 2 ) / 255.0;
+					const g = dataview.getUint8( ( PCDheader.points * offset.rgb ) + PCDheader.size[ rgbIndex ] * i + 1 ) / 255.0;
+					const b = dataview.getUint8( ( PCDheader.points * offset.rgb ) + PCDheader.size[ rgbIndex ] * i + 0 ) / 255.0;
+
+					c.set( r, g, b ).convertSRGBToLinear();
+
+					color.push( c.r, c.g, c.b );
+
+				}
+
+				if ( offset.normal_x !== undefined ) {
+
+					const xIndex = PCDheader.fields.indexOf( 'normal_x' );
+					const yIndex = PCDheader.fields.indexOf( 'normal_y' );
+					const zIndex = PCDheader.fields.indexOf( 'normal_z' );
+					normal.push( dataview.getFloat32( ( PCDheader.points * offset.normal_x ) + PCDheader.size[ xIndex ] * i, this.littleEndian ) );
+					normal.push( dataview.getFloat32( ( PCDheader.points * offset.normal_y ) + PCDheader.size[ yIndex ] * i, this.littleEndian ) );
+					normal.push( dataview.getFloat32( ( PCDheader.points * offset.normal_z ) + PCDheader.size[ zIndex ] * i, this.littleEndian ) );
+
+				}
+
+				if ( offset.intensity !== undefined ) {
+
+					const intensityIndex = PCDheader.fields.indexOf( 'intensity' );
+					intensity.push( dataview.getFloat32( ( PCDheader.points * offset.intensity ) + PCDheader.size[ intensityIndex ] * i, this.littleEndian ) );
+
+				}
+
+				if ( offset.label !== undefined ) {
+
+					const labelIndex = PCDheader.fields.indexOf( 'label' );
+					label.push( dataview.getInt32( ( PCDheader.points * offset.label ) + PCDheader.size[ labelIndex ] * i, this.littleEndian ) );
+
+				}
+
+			}
+
+		}
+
+		// binary
+
+		if ( PCDheader.data === 'binary' ) {
+
+			const dataview = new DataView( data, PCDheader.headerLen );
+			const offset = PCDheader.offset;
+
+			for ( let i = 0, row = 0; i < PCDheader.points; i ++, row += PCDheader.rowSize ) {
+
+				if ( offset.x !== undefined ) {
+
+					position.push( dataview.getFloat32( row + offset.x, this.littleEndian ) );
+					position.push( dataview.getFloat32( row + offset.y, this.littleEndian ) );
+					position.push( dataview.getFloat32( row + offset.z, this.littleEndian ) );
+
+				}
+
+				if ( offset.rgb !== undefined ) {
+
+					const r = dataview.getUint8( row + offset.rgb + 2 ) / 255.0;
+					const g = dataview.getUint8( row + offset.rgb + 1 ) / 255.0;
+					const b = dataview.getUint8( row + offset.rgb + 0 ) / 255.0;
+
+					c.set( r, g, b ).convertSRGBToLinear();
+
+					color.push( c.r, c.g, c.b );
+
+				}
+
+				if ( offset.normal_x !== undefined ) {
+
+					normal.push( dataview.getFloat32( row + offset.normal_x, this.littleEndian ) );
+					normal.push( dataview.getFloat32( row + offset.normal_y, this.littleEndian ) );
+					normal.push( dataview.getFloat32( row + offset.normal_z, this.littleEndian ) );
+
+				}
+
+				if ( offset.intensity !== undefined ) {
+
+					intensity.push( dataview.getFloat32( row + offset.intensity, this.littleEndian ) );
+
+				}
+
+				if ( offset.label !== undefined ) {
+
+					label.push( dataview.getInt32( row + offset.label, this.littleEndian ) );
+
+				}
+
+			}
+
+		}
+
+		// build geometry
+
+		const geometry = new BufferGeometry();
+
+		if ( position.length > 0 ) geometry.setAttribute( 'position', new Float32BufferAttribute( position, 3 ) );
+		if ( normal.length > 0 ) geometry.setAttribute( 'normal', new Float32BufferAttribute( normal, 3 ) );
+		if ( color.length > 0 ) geometry.setAttribute( 'color', new Float32BufferAttribute( color, 3 ) );
+		if ( intensity.length > 0 ) geometry.setAttribute( 'intensity', new Float32BufferAttribute( intensity, 1 ) );
+		if ( label.length > 0 ) geometry.setAttribute( 'label', new Int32BufferAttribute( label, 1 ) );
+
+		geometry.computeBoundingSphere();
+
+		// build material
+
+		const material = new PointsMaterial( { size: 0.005 } );
+
+		if ( color.length > 0 ) {
+
+			material.vertexColors = true;
+
+		}
+
+		// build point cloud
+
+		return new Points( geometry, material );
+
+	}
+
+}
+
+export { PCDLoader };

package/examples/jsm/loaders/PDBLoader.js

@@ -0,0 +1,232 @@
+import {
+	BufferGeometry,
+	FileLoader,
+	Float32BufferAttribute,
+	Loader,
+	Color
+} 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.set( r, g, b ).convertSRGBToLinear();
+
+				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 };