three-stdlib/loaders/PDBLoader.cjs.map

stand-alone library of threejs examples

{"version":3,"file":"PDBLoader.cjs","sources":["../../src/loaders/PDBLoader.js"],"sourcesContent":["import { BufferGeometry, FileLoader, Float32BufferAttribute, Loader } from 'three'\n\nclass PDBLoader extends Loader {\n  constructor(manager) {\n    super(manager)\n  }\n\n  load(url, onLoad, onProgress, onError) {\n    const scope = this\n\n    const loader = new FileLoader(scope.manager)\n    loader.setPath(scope.path)\n    loader.setRequestHeader(scope.requestHeader)\n    loader.setWithCredentials(scope.withCredentials)\n    loader.load(\n      url,\n      function (text) {\n        try {\n          onLoad(scope.parse(text))\n        } catch (e) {\n          if (onError) {\n            onError(e)\n          } else {\n            console.error(e)\n          }\n\n          scope.manager.itemError(url)\n        }\n      },\n      onProgress,\n      onError,\n    )\n  }\n\n  // Based on CanvasMol PDB parser\n\n  parse(text) {\n    function trim(text) {\n      return text.replace(/^\\s\\s*/, '').replace(/\\s\\s*$/, '')\n    }\n\n    function capitalize(text) {\n      return text.charAt(0).toUpperCase() + text.substr(1).toLowerCase()\n    }\n\n    function hash(s, e) {\n      return 's' + Math.min(s, e) + 'e' + Math.max(s, e)\n    }\n\n    function parseBond(start, length, satom, i) {\n      const eatom = parseInt(lines[i].substr(start, length))\n\n      if (eatom) {\n        const h = hash(satom, eatom)\n\n        if (_bhash[h] === undefined) {\n          _bonds.push([satom - 1, eatom - 1, 1])\n          _bhash[h] = _bonds.length - 1\n        } else {\n          // doesn't really work as almost all PDBs\n          // have just normal bonds appearing multiple\n          // times instead of being double/triple bonds\n          // bonds[bhash[h]][2] += 1;\n        }\n      }\n    }\n\n    function buildGeometry() {\n      const build = {\n        geometryAtoms: new BufferGeometry(),\n        geometryBonds: new BufferGeometry(),\n        json: {\n          atoms: atoms,\n        },\n      }\n\n      const geometryAtoms = build.geometryAtoms\n      const geometryBonds = build.geometryBonds\n\n      const verticesAtoms = []\n      const colorsAtoms = []\n      const verticesBonds = []\n\n      // atoms\n\n      for (let i = 0, l = atoms.length; i < l; i++) {\n        const atom = atoms[i]\n\n        const x = atom[0]\n        const y = atom[1]\n        const z = atom[2]\n\n        verticesAtoms.push(x, y, z)\n\n        const r = atom[3][0] / 255\n        const g = atom[3][1] / 255\n        const b = atom[3][2] / 255\n\n        colorsAtoms.push(r, g, b)\n      }\n\n      // bonds\n\n      for (let i = 0, l = _bonds.length; i < l; i++) {\n        const bond = _bonds[i]\n\n        const start = bond[0]\n        const end = bond[1]\n\n        const startAtom = _atomMap[start]\n        const endAtom = _atomMap[end]\n\n        let x = startAtom[0]\n        let y = startAtom[1]\n        let z = startAtom[2]\n\n        verticesBonds.push(x, y, z)\n\n        x = endAtom[0]\n        y = endAtom[1]\n        z = endAtom[2]\n\n        verticesBonds.push(x, y, z)\n      }\n\n      // build geometry\n\n      geometryAtoms.setAttribute('position', new Float32BufferAttribute(verticesAtoms, 3))\n      geometryAtoms.setAttribute('color', new Float32BufferAttribute(colorsAtoms, 3))\n\n      geometryBonds.setAttribute('position', new Float32BufferAttribute(verticesBonds, 3))\n\n      return build\n    }\n\n    const CPK = {\n      h: [255, 255, 255],\n      he: [217, 255, 255],\n      li: [204, 128, 255],\n      be: [194, 255, 0],\n      b: [255, 181, 181],\n      c: [144, 144, 144],\n      n: [48, 80, 248],\n      o: [255, 13, 13],\n      f: [144, 224, 80],\n      ne: [179, 227, 245],\n      na: [171, 92, 242],\n      mg: [138, 255, 0],\n      al: [191, 166, 166],\n      si: [240, 200, 160],\n      p: [255, 128, 0],\n      s: [255, 255, 48],\n      cl: [31, 240, 31],\n      ar: [128, 209, 227],\n      k: [143, 64, 212],\n      ca: [61, 255, 0],\n      sc: [230, 230, 230],\n      ti: [191, 194, 199],\n      v: [166, 166, 171],\n      cr: [138, 153, 199],\n      mn: [156, 122, 199],\n      fe: [224, 102, 51],\n      co: [240, 144, 160],\n      ni: [80, 208, 80],\n      cu: [200, 128, 51],\n      zn: [125, 128, 176],\n      ga: [194, 143, 143],\n      ge: [102, 143, 143],\n      as: [189, 128, 227],\n      se: [255, 161, 0],\n      br: [166, 41, 41],\n      kr: [92, 184, 209],\n      rb: [112, 46, 176],\n      sr: [0, 255, 0],\n      y: [148, 255, 255],\n      zr: [148, 224, 224],\n      nb: [115, 194, 201],\n      mo: [84, 181, 181],\n      tc: [59, 158, 158],\n      ru: [36, 143, 143],\n      rh: [10, 125, 140],\n      pd: [0, 105, 133],\n      ag: [192, 192, 192],\n      cd: [255, 217, 143],\n      in: [166, 117, 115],\n      sn: [102, 128, 128],\n      sb: [158, 99, 181],\n      te: [212, 122, 0],\n      i: [148, 0, 148],\n      xe: [66, 158, 176],\n      cs: [87, 23, 143],\n      ba: [0, 201, 0],\n      la: [112, 212, 255],\n      ce: [255, 255, 199],\n      pr: [217, 255, 199],\n      nd: [199, 255, 199],\n      pm: [163, 255, 199],\n      sm: [143, 255, 199],\n      eu: [97, 255, 199],\n      gd: [69, 255, 199],\n      tb: [48, 255, 199],\n      dy: [31, 255, 199],\n      ho: [0, 255, 156],\n      er: [0, 230, 117],\n      tm: [0, 212, 82],\n      yb: [0, 191, 56],\n      lu: [0, 171, 36],\n      hf: [77, 194, 255],\n      ta: [77, 166, 255],\n      w: [33, 148, 214],\n      re: [38, 125, 171],\n      os: [38, 102, 150],\n      ir: [23, 84, 135],\n      pt: [208, 208, 224],\n      au: [255, 209, 35],\n      hg: [184, 184, 208],\n      tl: [166, 84, 77],\n      pb: [87, 89, 97],\n      bi: [158, 79, 181],\n      po: [171, 92, 0],\n      at: [117, 79, 69],\n      rn: [66, 130, 150],\n      fr: [66, 0, 102],\n      ra: [0, 125, 0],\n      ac: [112, 171, 250],\n      th: [0, 186, 255],\n      pa: [0, 161, 255],\n      u: [0, 143, 255],\n      np: [0, 128, 255],\n      pu: [0, 107, 255],\n      am: [84, 92, 242],\n      cm: [120, 92, 227],\n      bk: [138, 79, 227],\n      cf: [161, 54, 212],\n      es: [179, 31, 212],\n      fm: [179, 31, 186],\n      md: [179, 13, 166],\n      no: [189, 13, 135],\n      lr: [199, 0, 102],\n      rf: [204, 0, 89],\n      db: [209, 0, 79],\n      sg: [217, 0, 69],\n      bh: [224, 0, 56],\n      hs: [230, 0, 46],\n      mt: [235, 0, 38],\n      ds: [235, 0, 38],\n      rg: [235, 0, 38],\n      cn: [235, 0, 38],\n      uut: [235, 0, 38],\n      uuq: [235, 0, 38],\n      uup: [235, 0, 38],\n      uuh: [235, 0, 38],\n      uus: [235, 0, 38],\n      uuo: [235, 0, 38],\n    }\n\n    const atoms = []\n\n    const _bonds = []\n    const _bhash = {}\n    const _atomMap = {}\n\n    // parse\n\n    const lines = text.split('\\n')\n\n    for (let i = 0, l = lines.length; i < l; i++) {\n      if (lines[i].substr(0, 4) === 'ATOM' || lines[i].substr(0, 6) === 'HETATM') {\n        const x = parseFloat(lines[i].substr(30, 7))\n        const y = parseFloat(lines[i].substr(38, 7))\n        const z = parseFloat(lines[i].substr(46, 7))\n        const index = parseInt(lines[i].substr(6, 5)) - 1\n\n        let e = trim(lines[i].substr(76, 2)).toLowerCase()\n\n        if (e === '') {\n          e = trim(lines[i].substr(12, 2)).toLowerCase()\n        }\n\n        const atomData = [x, y, z, CPK[e], capitalize(e)]\n\n        atoms.push(atomData)\n        _atomMap[index] = atomData\n      } else if (lines[i].substr(0, 6) === 'CONECT') {\n        const satom = parseInt(lines[i].substr(6, 5))\n\n        parseBond(11, 5, satom, i)\n        parseBond(16, 5, satom, i)\n        parseBond(21, 5, satom, i)\n        parseBond(26, 5, satom, i)\n      }\n    }\n\n    // build and return geometry\n\n    return buildGeometry()\n  }\n}\n\nexport { PDBLoader 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