three-stdlib 2.15.0 → 2.15.2

package/loaders/PDBLoader.js

@@ -1,73 +1,68 @@
-import { Loader, FileLoader, BufferGeometry, Float32BufferAttribute } from 'three';
-
-class PDBLoader extends Loader {
+"use strict";
+Object.defineProperties(exports, { __esModule: { value: true }, [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 FileLoader(scope.manager);
+    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);
+    loader.load(
+      url,
+      function(text) {
+        try {
+          onLoad(scope.parse(text));
+        } catch (e) {
+          if (onError) {
+            onError(e);
+          } else {
+            console.error(e);
+          }
+          scope.manager.itemError(url);
         }
-
-        scope.manager.itemError(url);
-      }
-    }, onProgress, onError);
-  } // Based on CanvasMol PDB parser
-
-
+      },
+      onProgress,
+      onError
+    );
+  }
   parse(text) {
-    function trim(text) {
-      return text.replace(/^\s\s*/, '').replace(/\s\s*$/, '');
+    function trim(text2) {
+      return text2.replace(/^\s\s*/, "").replace(/\s\s*$/, "");
     }
-
-    function capitalize(text) {
-      return text.charAt(0).toUpperCase() + text.substr(1).toLowerCase();
+    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);
+      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] === undefined) {
+        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(),
+        geometryAtoms: new THREE.BufferGeometry(),
+        geometryBonds: new THREE.BufferGeometry(),
         json: {
-          atoms: atoms
+          atoms
         }
       };
       const geometryAtoms = build.geometryAtoms;
       const geometryBonds = build.geometryBonds;
       const verticesAtoms = [];
       const colorsAtoms = [];
-      const verticesBonds = []; // atoms
-
+      const verticesBonds = [];
       for (let i = 0, l = atoms.length; i < l; i++) {
         const atom = atoms[i];
         const x = atom[0];
@@ -78,9 +73,7 @@ class PDBLoader extends Loader {
         const g = atom[3][1] / 255;
         const b = atom[3][2] / 255;
         colorsAtoms.push(r, g, b);
-      } // bonds
-
-
+      }
       for (let i = 0, l = _bonds.length; i < l; i++) {
         const bond = _bonds[i];
         const start = bond[0];
@@ -95,15 +88,12 @@ class PDBLoader extends Loader {
         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));
+      }
+      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],
@@ -227,38 +217,30 @@ class PDBLoader extends Loader {
     const atoms = [];
     const _bonds = [];
     const _bhash = {};
-    const _atomMap = {}; // parse
-
-    const lines = text.split('\n');
-
+    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') {
+      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 === '') {
+        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') {
+      } 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);
       }
-    } // build and return geometry
-
-
+    }
     return buildGeometry();
   }
-
 }
-
-export { PDBLoader };
+exports.PDBLoader = PDBLoader;

package/loaders/PDBLoader.mjs

@@ -0,0 +1,246 @@
+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
+    );
+  }
+  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
+};