three-stdlib 2.16.0 → 2.16.2

package/loaders/PCDLoader.mjs

@@ -1,248 +0,0 @@
-import { Loader, FileLoader, LoaderUtils, BufferGeometry, Float32BufferAttribute, PointsMaterial, Points } 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, url));
-        } catch (e) {
-          if (onError) {
-            onError(e);
-          } else {
-            console.error(e);
-          }
-          scope.manager.itemError(url);
-        }
-      },
-      onProgress,
-      onError
-    );
-  }
-  parse(data, url) {
-    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 & 31) << 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(data2) {
-      const PCDheader2 = {};
-      const result1 = data2.search(/[\r\n]DATA\s(\S*)\s/i);
-      const result2 = /[\r\n]DATA\s(\S*)\s/i.exec(data2.substr(result1 - 1));
-      PCDheader2.data = result2[1];
-      PCDheader2.headerLen = result2[0].length + result1;
-      PCDheader2.str = data2.substr(0, PCDheader2.headerLen);
-      PCDheader2.str = PCDheader2.str.replace(/\#.*/gi, "");
-      PCDheader2.version = /VERSION (.*)/i.exec(PCDheader2.str);
-      PCDheader2.fields = /FIELDS (.*)/i.exec(PCDheader2.str);
-      PCDheader2.size = /SIZE (.*)/i.exec(PCDheader2.str);
-      PCDheader2.type = /TYPE (.*)/i.exec(PCDheader2.str);
-      PCDheader2.count = /COUNT (.*)/i.exec(PCDheader2.str);
-      PCDheader2.width = /WIDTH (.*)/i.exec(PCDheader2.str);
-      PCDheader2.height = /HEIGHT (.*)/i.exec(PCDheader2.str);
-      PCDheader2.viewpoint = /VIEWPOINT (.*)/i.exec(PCDheader2.str);
-      PCDheader2.points = /POINTS (.*)/i.exec(PCDheader2.str);
-      if (PCDheader2.version !== null)
-        PCDheader2.version = parseFloat(PCDheader2.version[1]);
-      if (PCDheader2.fields !== null)
-        PCDheader2.fields = PCDheader2.fields[1].split(" ");
-      if (PCDheader2.type !== null)
-        PCDheader2.type = PCDheader2.type[1].split(" ");
-      if (PCDheader2.width !== null)
-        PCDheader2.width = parseInt(PCDheader2.width[1]);
-      if (PCDheader2.height !== null)
-        PCDheader2.height = parseInt(PCDheader2.height[1]);
-      if (PCDheader2.viewpoint !== null)
-        PCDheader2.viewpoint = PCDheader2.viewpoint[1];
-      if (PCDheader2.points !== null)
-        PCDheader2.points = parseInt(PCDheader2.points[1], 10);
-      if (PCDheader2.points === null)
-        PCDheader2.points = PCDheader2.width * PCDheader2.height;
-      if (PCDheader2.size !== null) {
-        PCDheader2.size = PCDheader2.size[1].split(" ").map(function(x) {
-          return parseInt(x, 10);
-        });
-      }
-      if (PCDheader2.count !== null) {
-        PCDheader2.count = PCDheader2.count[1].split(" ").map(function(x) {
-          return parseInt(x, 10);
-        });
-      } else {
-        PCDheader2.count = [];
-        for (let i = 0, l = PCDheader2.fields.length; i < l; i++) {
-          PCDheader2.count.push(1);
-        }
-      }
-      PCDheader2.offset = {};
-      let sizeSum = 0;
-      for (let i = 0, l = PCDheader2.fields.length; i < l; i++) {
-        if (PCDheader2.data === "ascii") {
-          PCDheader2.offset[PCDheader2.fields[i]] = i;
-        } else {
-          PCDheader2.offset[PCDheader2.fields[i]] = sizeSum;
-          sizeSum += PCDheader2.size[i] * PCDheader2.count[i];
-        }
-      }
-      PCDheader2.rowSize = sizeSum;
-      return PCDheader2;
-    }
-    const textData = LoaderUtils.decodeText(new Uint8Array(data));
-    const PCDheader = parseHeader(textData);
-    const position = [];
-    const normal = [];
-    const color = [];
-    if (PCDheader.data === "ascii") {
-      const offset = PCDheader.offset;
-      const pcdData = textData.substr(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 !== void 0) {
-          position.push(parseFloat(line[offset.x]));
-          position.push(parseFloat(line[offset.y]));
-          position.push(parseFloat(line[offset.z]));
-        }
-        if (offset.rgb !== void 0) {
-          const rgb = parseFloat(line[offset.rgb]);
-          const r = rgb >> 16 & 255;
-          const g = rgb >> 8 & 255;
-          const b = rgb >> 0 & 255;
-          color.push(r / 255, g / 255, b / 255);
-        }
-        if (offset.normal_x !== void 0) {
-          normal.push(parseFloat(line[offset.normal_x]));
-          normal.push(parseFloat(line[offset.normal_y]));
-          normal.push(parseFloat(line[offset.normal_z]));
-        }
-      }
-    }
-    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 !== void 0) {
-          position.push(dataview.getFloat32(PCDheader.points * offset.x + PCDheader.size[0] * i, this.littleEndian));
-          position.push(dataview.getFloat32(PCDheader.points * offset.y + PCDheader.size[1] * i, this.littleEndian));
-          position.push(dataview.getFloat32(PCDheader.points * offset.z + PCDheader.size[2] * i, this.littleEndian));
-        }
-        if (offset.rgb !== void 0) {
-          color.push(dataview.getUint8(PCDheader.points * offset.rgb + PCDheader.size[3] * i + 2) / 255);
-          color.push(dataview.getUint8(PCDheader.points * offset.rgb + PCDheader.size[3] * i + 1) / 255);
-          color.push(dataview.getUint8(PCDheader.points * offset.rgb + PCDheader.size[3] * i + 0) / 255);
-        }
-        if (offset.normal_x !== void 0) {
-          normal.push(
-            dataview.getFloat32(PCDheader.points * offset.normal_x + PCDheader.size[4] * i, this.littleEndian)
-          );
-          normal.push(
-            dataview.getFloat32(PCDheader.points * offset.normal_y + PCDheader.size[5] * i, this.littleEndian)
-          );
-          normal.push(
-            dataview.getFloat32(PCDheader.points * offset.normal_z + PCDheader.size[6] * i, this.littleEndian)
-          );
-        }
-      }
-    }
-    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 !== void 0) {
-          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 !== void 0) {
-          color.push(dataview.getUint8(row + offset.rgb + 2) / 255);
-          color.push(dataview.getUint8(row + offset.rgb + 1) / 255);
-          color.push(dataview.getUint8(row + offset.rgb + 0) / 255);
-        }
-        if (offset.normal_x !== void 0) {
-          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));
-        }
-      }
-    }
-    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));
-    geometry.computeBoundingSphere();
-    const material = new PointsMaterial({ size: 5e-3 });
-    if (color.length > 0) {
-      material.vertexColors = true;
-    } else {
-      material.color.setHex(Math.random() * 16777215);
-    }
-    const mesh = new Points(geometry, material);
-    let name = url.split("").reverse().join("");
-    name = /([^\/]*)/.exec(name);
-    name = name[1].split("").reverse().join("");
-    mesh.name = name;
-    return mesh;
-  }
-}
-export {
-  PCDLoader
-};

package/loaders/PDBLoader.mjs

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