updated example and version

Author: chrisjsewell

pandas3js/__init__.py

@@ -5,7 +5,7 @@
 
 """
 
-__version__ = '0.1.5.2'
+__version__ = '0.1.6'
 
 from pandas3js import models
 from pandas3js import views

pandas3js_example.ipynb

@@ -2,11 +2,19 @@
  "cells": [
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 1,
    "metadata": {
     "init_cell": true
    },
-   "outputs": [],
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "0.1.6\n"
+     ]
+    }
+   ],
    "source": [
     "import numpy as np \n",
     "import pandas as pd\n",
@@ -93,6 +101,15 @@
     "# Object Types"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "collapsed": true
+   },
+   "outputs": [],
+   "source": []
+  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -108,6 +125,8 @@
     "        'otype':['pandas3js.models.'+options['Object']],\n",
     "         'position':[(options['x'],0,0)],\n",
     "         'visible':[options['Visible']]})\n",
+    "    if 'Icosahedron' in options['Object']:\n",
+    "        df['detail'] = 1\n",
     "    if 'Triclinic' in options['Object']:\n",
     "        pjs.utils.tuple_to_df(df,'b',(0.5,1,0))\n",
     "        pjs.utils.tuple_to_df(df,'c',(0,.5,1))\n",
@@ -166,7 +185,7 @@
     "                        for q in cdata['charge']]\n",
     "    geometry.change_by_df(df,otype_column='otype')\n",
     "\n",
-    "gui, gcollect, opts = pjs.views.create_gui(geometry,callback,\n",
+    "gui, gcollect, opts = pjs.views.create_gui(callback=callback,\n",
     "            height=200,width=200,camera_position=[.5,0,-4],\n",
     "            show_object_info=True,otype_column='otype',\n",
     "            opts_choice={'Color':['c1','c2']},\n",
@@ -220,16 +239,28 @@
    "outputs": [],
    "source": [
     "# pip install jsonextended\n",
-    "import jsonextended as ejson\n",
-    "import urllib #urllib2 for python3\n",
-    "f = urllib.urlopen(\n",
-    "    'https://raw.githubusercontent.com/chrisjsewell'\n",
-    "    '/jsonextended/master/jsonextended/parsers/crystal_test.data')\n",
-    "parser = ejson.parsers.CrystalDFTParser()\n",
-    "parser.read_file(f)\n",
-    "f.close()\n",
-    "\n",
-    "data = ejson.dict_combine_lists(parser.data,['id','x/a','y/b','z/c','atomic_number'],'ixyzn')\n",
+    "from jsonextended import edict, utils, _example_data_folder\n",
+    "from jsonextended.complex_parsers import crystal_dft"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "datapath = utils.get_data_path('data.crystal.out',_example_data_folder)\n",
+    "parser = crystal_dft.CrystalDFTParser()\n",
+    "data = parser.read_file(datapath)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "data = edict.combine_lists(data,['id','x/a','y/b','z/c','atomic_number'],'ixyzn')\n",
     "geometry = pjs.models.GeometricCollection()\n",
     "\n",
     "# create bounding box\n",
@@ -242,7 +273,8 @@
     "# create atoms\n",
     "for d in data['initial']['primitive']['geometry']['ixyzn'].values():\n",
     "    x,y,z = d['x/a']*a_vec+d['y/b']*b_vec+d['z/c']*c_vec\n",
-    "    atom = pjs.models.Sphere(id=d['id'],position=(x,y,z))\n",
+    "    #atom = pjs.models.Sphere(id=d['id'],position=(x,y,z))\n",
+    "    atom = pjs.models.Icosahedron(id=d['id'],position=(x,y,z),detail=1)\n",
     "    atom.color = atom.label_color = pjs.atom.map_atoms(d['atomic_number'],'color')\n",
     "    atom.radius = pjs.atom.map_atoms(d['atomic_number'],'RCov')\n",
     "    atom.label = pjs.atom.map_atoms(d['atomic_number'],'Symbol')\n",
@@ -278,31 +310,46 @@
  "metadata": {
   "hide_input": false,
   "kernelspec": {
-   "display_name": "Python 2",
+   "display_name": "Python 3",
    "language": "python",
-   "name": "python2"
+   "name": "python3"
   },
   "language_info": {
    "codemirror_mode": {
     "name": "ipython",
-    "version": 2
+    "version": 3
    },
    "file_extension": ".py",
    "mimetype": "text/x-python",
    "name": "python",
    "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython2",
-   "version": "2.7.13"
+   "pygments_lexer": "ipython3",
+   "version": "3.6.1"
   },
   "nav_menu": {},
   "toc": {
+   "colors": {
+    "hover_highlight": "#DAA520",
+    "navigate_num": "#000000",
+    "navigate_text": "#333333",
+    "running_highlight": "#FF0000",
+    "selected_highlight": "#FFD700",
+    "sidebar_border": "#EEEEEE",
+    "wrapper_background": "#FFFFFF"
+   },
+   "moveMenuLeft": true,
+   "nav_menu": {
+    "height": "105px",
+    "width": "252px"
+   },
    "navigate_menu": true,
    "number_sections": true,
    "sideBar": true,
    "threshold": 4,
    "toc_cell": false,
    "toc_section_display": "block",
-   "toc_window_display": false
+   "toc_window_display": false,
+   "widenNotebook": false
   }
  },
  "nbformat": 4,