Fixed small camera issues

gabrielelanaro · Jan 14, 2015 · 5ecf853 · 5ecf853
1 parent ebdd71d
commit 5ecf853
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Showing 3 changed files with 17 additions and 33 deletions.
diff --git a/chemview/static/chemview.js b/chemview/static/chemview.js
@@ -24,7 +24,7 @@ var MolecularViewer = function ($el) {
 	};
 
 	this.camera_z = -150;
-	this.perspectiveCamera = new THREE.PerspectiveCamera(20, this.container.whratio, 1, 800);
+	this.perspectiveCamera = new THREE.PerspectiveCamera(20, this.container.whratio, 0.1, 800);
 	this.perspectiveCamera.position.set(0, 0, this.camera_z);
 	this.perspectiveCamera.lookAt(new THREE.Vector3(0, 0, 0));
 	this.orthographicCamera = new THREE.OrthographicCamera();

diff --git a/chemview/viewer.py b/chemview/viewer.py
@@ -209,8 +209,8 @@ def add_isosurface(self, function, isolevel=0.3, resolution=32, style="wireframe
 
         # We want to make a container that contains the whole molecule
         # and surface
-        area_min = self.coordinates.min(axis=0) - 0.5
-        area_max = self.coordinates.max(axis=0) + 0.5
+        area_min = self.coordinates.min(axis=0) - 0.2
+        area_max = self.coordinates.max(axis=0) + 0.2
 
         x = np.linspace(area_min[0], area_max[0], resolution)
         y = np.linspace(area_min[1], area_max[1], resolution)

diff --git a/examples/Molecular Orbitals.ipynb b/examples/Molecular Orbitals.ipynb
@@ -1,7 +1,7 @@
 {
  "metadata": {
   "name": "",
-  "signature": "sha256:8483459a9ad54c353d4cb9e80ce1d7e6a42e047f8a9dd50e3d8d016faeac74c6"
+  "signature": "sha256:5df287995a349ef3d453e1c65f19922c3b08ea8990cfa09a31fac543006d6739"
  },
  "nbformat": 3,
  "nbformat_minor": 0,
@@ -25,15 +25,6 @@
      "language": "python",
      "metadata": {},
      "outputs": [
-      {
-       "output_type": "stream",
-       "stream": "stderr",
-       "text": [
-        "/home/gabriele/miniconda/envs/test_install/lib/python3.4/site-packages/numba/tests/__init__.py:393: UserWarning: Failed to enable faulthandler due to:\n",
-        "IOStream has no fileno.\n",
-        "  warnings.warn(msg.format(err=e))\n"
-       ]
-      },
       {
        "javascript": [
         "$(\"head\").append($(\"<link/>\").attr({\n",
@@ -83,7 +74,7 @@
        "metadata": {},
        "output_type": "display_data",
        "text": [
-        "<IPython.core.display.Javascript at 0x7f7affc65080>"
+        "<IPython.core.display.Javascript at 0x7f196158f1d0>"
        ]
       },
       {
@@ -373,7 +364,7 @@
        "metadata": {},
        "output_type": "display_data",
        "text": [
-        "<IPython.core.display.Javascript at 0x7f7ae04414e0>"
+        "<IPython.core.display.Javascript at 0x7f1945ce1510>"
        ]
       },
       {
@@ -520,7 +511,7 @@
        "metadata": {},
        "output_type": "display_data",
        "text": [
-        "<IPython.core.display.Javascript at 0x7f7ae043feb8>"
+        "<IPython.core.display.Javascript at 0x7f1945d18510>"
        ]
       }
      ],
@@ -536,21 +527,13 @@
       "\n",
       "mo_coefficients = df.read('mocoeffs')\n",
       "gbasis = df.read('gbasis')\n",
-      "molecule = df.read('molecule')"
+      "molecule = df.read('molecule')\n",
+      "molecule.guess_bonds()"
      ],
      "language": "python",
      "metadata": {},
-     "outputs": [
-      {
-       "ename": "SyntaxError",
-       "evalue": "invalid syntax (__init__.py, line 15)",
-       "output_type": "pyerr",
-       "traceback": [
-        "\u001b[1;36m  File \u001b[1;32m\"/home/gabriele/miniconda/envs/test_install/lib/python3.4/site-packages/chemlab/__init__.py\"\u001b[1;36m, line \u001b[1;32m15\u001b[0m\n\u001b[1;33m    except ValueError, e:\u001b[0m\n\u001b[1;37m                     ^\u001b[0m\n\u001b[1;31mSyntaxError\u001b[0m\u001b[1;31m:\u001b[0m invalid syntax\n"
-       ]
-      }
-     ],
-     "prompt_number": 2
+     "outputs": [],
+     "prompt_number": 7
     },
     {
      "cell_type": "code",
@@ -560,17 +543,18 @@
       "\n",
       "f = molecular_orbital(molecule.r_array, mo_coefficients[0][-1], gbasis)\n",
       "\n",
-      "mv = MolecularViewer(molecule.r_array, {'atom_types': molecule.type_array})\n",
-      "mv.ball_and_sticks()\n",
-      "mv.add_isosurface(f, isolevel=0.3, style='wireframe', color=0xff0000)\n",
-      "mv.add_isosurface(f, isolevel=-0.3, style='wireframe', color=0x0000ff)\n",
+      "mv = MolecularViewer(molecule.r_array, {'atom_types': molecule.type_array,\n",
+      "                                        'bonds': molecule.bonds})\n",
+      "mv.wireframe()\n",
+      "mv.add_isosurface(f, isolevel=0.3, color=0xff0000)\n",
+      "mv.add_isosurface(f, isolevel=-0.3, color=0x0000ff)\n",
       "\n",
       "mv"
      ],
      "language": "python",
      "metadata": {},
      "outputs": [],
-     "prompt_number": 4
+     "prompt_number": 14
     },
     {
      "cell_type": "code",