simsite/frontend/node_modules/three-stdlib/loaders/PDBLoader.cjs

"use strict";
Object.defineProperty(exports, Symbol.toStringTag, { value: "Module" });
const THREE = require("three");
class PDBLoader extends THREE.Loader {
  constructor(manager) {
    super(manager);
  }
  load(url, onLoad, onProgress, onError) {
    const scope = this;
    const loader = new THREE.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(text2) {
      return text2.replace(/^\s\s*/, "").replace(/\s\s*$/, "");
    }
    function capitalize(text2) {
      return text2.charAt(0).toUpperCase() + text2.substr(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].substr(start, length));
      if (eatom) {
        const h = hash(satom, eatom);
        if (_bhash[h] === void 0) {
          _bonds.push([satom - 1, eatom - 1, 1]);
          _bhash[h] = _bonds.length - 1;
        }
      }
    }
    function buildGeometry() {
      const build = {
        geometryAtoms: new THREE.BufferGeometry(),
        geometryBonds: new THREE.BufferGeometry(),
        json: {
          atoms
        }
      };
      const geometryAtoms = build.geometryAtoms;
      const geometryBonds = build.geometryBonds;
      const verticesAtoms = [];
      const colorsAtoms = [];
      const verticesBonds = [];
      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;
        colorsAtoms.push(r, g, b);
      }
      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);
      }
      geometryAtoms.setAttribute("position", new THREE.Float32BufferAttribute(verticesAtoms, 3));
      geometryAtoms.setAttribute("color", new THREE.Float32BufferAttribute(colorsAtoms, 3));
      geometryBonds.setAttribute("position", new THREE.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 = {};
    const lines = text.split("\n");
    for (let i = 0, l = lines.length; i < l; i++) {
      if (lines[i].substr(0, 4) === "ATOM" || lines[i].substr(0, 6) === "HETATM") {
        const x = parseFloat(lines[i].substr(30, 7));
        const y = parseFloat(lines[i].substr(38, 7));
        const z = parseFloat(lines[i].substr(46, 7));
        const index = parseInt(lines[i].substr(6, 5)) - 1;
        let e = trim(lines[i].substr(76, 2)).toLowerCase();
        if (e === "") {
          e = trim(lines[i].substr(12, 2)).toLowerCase();
        }
        const atomData = [x, y, z, CPK[e], capitalize(e)];
        atoms.push(atomData);
        _atomMap[index] = atomData;
      } else if (lines[i].substr(0, 6) === "CONECT") {
        const satom = parseInt(lines[i].substr(6, 5));
        parseBond(11, 5, satom, i);
        parseBond(16, 5, satom, i);
        parseBond(21, 5, satom, i);
        parseBond(26, 5, satom, i);
      }
    }
    return buildGeometry();
  }
}
exports.PDBLoader = PDBLoader;
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