three-stdlib 2.25.0 → 2.26.0

package/loaders/PDBLoader.cjs

@@ -1,247 +0,0 @@
-"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;
-        } else {
-        }
-      }
-    }
-    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;

package/loaders/PDBLoader.js

@@ -1,247 +0,0 @@
-import { Loader, FileLoader, BufferGeometry, Float32BufferAttribute } 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(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;
-        } else {
-        }
-      }
-    }
-    function buildGeometry() {
-      const build = {
-        geometryAtoms: new BufferGeometry(),
-        geometryBonds: new 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 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 = {};
-    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();
-  }
-}
-export {
-  PDBLoader
-};