From 56550162a8f2c4092cde943b8c1ee0144f4e990c Mon Sep 17 00:00:00 2001
From: Sebastian Raschka <mail@sebastianraschka.com>
Date: Fri, 19 May 2017 00:07:51 -0400
Subject: [PATCH] add file links to tutorials for easy view and access (#28)

---
 ...g_with_MOL2_Structures_in_DataFrames.ipynb | 54 ++++++++++-
 ...ng_with_PDB_Structures_in_DataFrames.ipynb | 94 +++++++++++++++++--
 2 files changed, 137 insertions(+), 11 deletions(-)

diff --git a/docs/sources/tutorials/Working_with_MOL2_Structures_in_DataFrames.ipynb b/docs/sources/tutorials/Working_with_MOL2_Structures_in_DataFrames.ipynb
index bdd2258..021a622 100644
--- a/docs/sources/tutorials/Working_with_MOL2_Structures_in_DataFrames.ipynb
+++ b/docs/sources/tutorials/Working_with_MOL2_Structures_in_DataFrames.ipynb
@@ -88,6 +88,13 @@
     "pmol = PandasMol2().read_mol2('./data/1b5e_1.mol2')"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "[File link: [1b5e_1.mol2](https://raw.githubusercontent.com/rasbt/biopandas/master/docs/sources/tutorials/data/1b5e_1.mol2)]"
+   ]
+  },
   {
    "cell_type": "markdown",
    "metadata": {},
@@ -106,6 +113,13 @@
     "pmol = PandasMol2().read_mol2('./data/40_mol2_files.mol2.gz')"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "[File link: [40_mol2_files.mol2.gz](https://github.com/rasbt/biopandas/blob/master/docs/sources/tutorials/data/40_mol2_files.mol2.gz?raw=true)]"
+   ]
+  },
   {
    "cell_type": "markdown",
    "metadata": {},
@@ -504,6 +518,13 @@
     "pmol.df.tail(10)"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "[File link: [1b5e_1.mol2](https://raw.githubusercontent.com/rasbt/biopandas/master/docs/sources/tutorials/data/1b5e_1.mol2)]"
+   ]
+  },
   {
    "cell_type": "markdown",
    "metadata": {},
@@ -861,7 +882,9 @@
   {
    "cell_type": "code",
    "execution_count": 5,
-   "metadata": {},
+   "metadata": {
+    "collapsed": true
+   },
    "outputs": [],
    "source": [
     "from biopandas.mol2 import PandasMol2\n",
@@ -869,6 +892,13 @@
     "pmol = PandasMol2().read_mol2('./data/1b5e_1.mol2')"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "[File link: [1b5e_1.mol2](https://raw.githubusercontent.com/rasbt/biopandas/master/docs/sources/tutorials/data/1b5e_1.mol2)]"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": 6,
@@ -1032,6 +1062,13 @@
     "print('All-atom RMSD: %.4f Angstrom' % r_all)"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "[File links: [1b5e_1.mol2](https://raw.githubusercontent.com/rasbt/biopandas/master/docs/sources/tutorials/data/1b5e_1.mol2), [1b5e_2.mol2](https://raw.githubusercontent.com/rasbt/biopandas/master/docs/sources/tutorials/data/1b5e_2.mol2)]"
+   ]
+  },
   {
    "cell_type": "markdown",
    "metadata": {},
@@ -1528,6 +1565,13 @@
     "print('First 10 lines:\\n', mol2_cont[:10])"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "[File link: [40_mol2_files.mol2](https://raw.githubusercontent.com/rasbt/biopandas/master/docs/sources/tutorials/data/40_mol2_files.mol2)]"
+   ]
+  },
   {
    "cell_type": "markdown",
    "metadata": {},
@@ -1538,7 +1582,9 @@
   {
    "cell_type": "code",
    "execution_count": 55,
-   "metadata": {},
+   "metadata": {
+    "collapsed": true
+   },
    "outputs": [],
    "source": [
     "pdmol = PandasMol2()\n",
@@ -1560,7 +1606,7 @@
  "metadata": {
   "anaconda-cloud": {},
   "kernelspec": {
-   "display_name": "Python [default]",
+   "display_name": "Python 3",
    "language": "python",
    "name": "python3"
   },
@@ -1574,7 +1620,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.5.2"
+   "version": "3.6.0"
   }
  },
  "nbformat": 4,
diff --git a/docs/sources/tutorials/Working_with_PDB_Structures_in_DataFrames.ipynb b/docs/sources/tutorials/Working_with_PDB_Structures_in_DataFrames.ipynb
index 318913c..77cbae4 100644
--- a/docs/sources/tutorials/Working_with_PDB_Structures_in_DataFrames.ipynb
+++ b/docs/sources/tutorials/Working_with_PDB_Structures_in_DataFrames.ipynb
@@ -79,7 +79,9 @@
   {
    "cell_type": "code",
    "execution_count": 3,
-   "metadata": {},
+   "metadata": {
+    "collapsed": true
+   },
    "outputs": [],
    "source": [
     "from biopandas.pdb import PandasPdb\n",
@@ -118,6 +120,13 @@
     "ppdb.read_pdb('./data/3eiy.pdb')"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "[File link: [3eiy.pdb](https://raw.githubusercontent.com/rasbt/biopandas/master/docs/sources/tutorials/data/3eiy.pdb)]"
+   ]
+  },
   {
    "cell_type": "markdown",
    "metadata": {},
@@ -147,6 +156,13 @@
     "ppdb.read_pdb('./data/3eiy.pdb.gz')"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "[File link: [3eiy.pdb.gz](https://github.com/rasbt/biopandas/blob/master/docs/sources/tutorials/data/3eiy.pdb.gz?raw=true)]"
+   ]
+  },
   {
    "cell_type": "markdown",
    "metadata": {},
@@ -387,6 +403,13 @@
     "ppdb.df.keys()"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "[File link: [3eiy.pdb](https://raw.githubusercontent.com/rasbt/biopandas/master/docs/sources/tutorials/data/3eiy.pdb)]"
+   ]
+  },
   {
    "cell_type": "markdown",
    "metadata": {},
@@ -926,6 +949,13 @@
     "ppdb.df['ATOM'].head()"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "[File link: [3eiy.pdb.gz](https://github.com/rasbt/biopandas/blob/master/docs/sources/tutorials/data/3eiy.pdb.gz?raw=true)]"
+   ]
+  },
   {
    "cell_type": "markdown",
    "metadata": {},
@@ -1332,13 +1362,22 @@
   {
    "cell_type": "code",
    "execution_count": 22,
-   "metadata": {},
+   "metadata": {
+    "collapsed": true
+   },
    "outputs": [],
    "source": [
     "from biopandas.pdb import PandasPdb\n",
     "ppdb = PandasPdb().read_pdb('./data/3eiy.pdb.gz')"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "[File link: [3eiy.pdb.gz](https://github.com/rasbt/biopandas/blob/master/docs/sources/tutorials/data/3eiy.pdb.gz?raw=true)]"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": 23,
@@ -1485,6 +1524,13 @@
     "print('RMSD: %.4f Angstrom' % r)"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "[File links: [lig_conf_1.pdb](https://raw.githubusercontent.com/rasbt/biopandas/master/docs/sources/tutorials/data/lig_conf_1.pdb), [lig_conf_2.pdb](https://raw.githubusercontent.com/rasbt/biopandas/master/docs/sources/tutorials/data/lig_conf_2.pdb)]"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": 28,
@@ -1610,7 +1656,9 @@
   {
    "cell_type": "code",
    "execution_count": 32,
-   "metadata": {},
+   "metadata": {
+    "collapsed": true
+   },
    "outputs": [],
    "source": [
     "p_1 = PandasPdb().read_pdb('./data/3eiy.pdb')\n",
@@ -1619,6 +1667,13 @@
     "distances = p_1.distance(xyz=reference_point, record='ATOM')"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "[File link: [3eiy.pdb](https://raw.githubusercontent.com/rasbt/biopandas/master/docs/sources/tutorials/data/3eiy.pdb)]"
+   ]
+  },
   {
    "cell_type": "markdown",
    "metadata": {},
@@ -1980,6 +2035,13 @@
     "ppdb.df['ATOM'] = ppdb.df['ATOM'][ppdb.df['ATOM']['element_symbol'] != 'H']"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "[File link: [3eiy.pdb.gz](https://github.com/rasbt/biopandas/blob/master/docs/sources/tutorials/data/3eiy.pdb.gz?raw=true)]"
+   ]
+  },
   {
    "cell_type": "markdown",
    "metadata": {},
@@ -1990,7 +2052,9 @@
   {
    "cell_type": "code",
    "execution_count": 40,
-   "metadata": {},
+   "metadata": {
+    "collapsed": true
+   },
    "outputs": [],
    "source": [
     "ppdb.to_pdb(path='./data/3eiy_stripped.pdb', \n",
@@ -1999,6 +2063,13 @@
     "            append_newline=True)"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "[File link: [3eiy_stripped.pdb](https://raw.githubusercontent.com/rasbt/biopandas/master/docs/sources/tutorials/data/3eiy_stripped.pdb)]"
+   ]
+  },
   {
    "cell_type": "markdown",
    "metadata": {},
@@ -2009,7 +2080,9 @@
   {
    "cell_type": "code",
    "execution_count": 41,
-   "metadata": {},
+   "metadata": {
+    "collapsed": true
+   },
    "outputs": [],
    "source": [
     "ppdb.to_pdb(path='./data/3eiy_stripped.pdb.gz', \n",
@@ -2017,12 +2090,19 @@
     "            gz=True, \n",
     "            append_newline=True)"
    ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "[File link: [3eiy_stripped.pdb.gz](https://github.com/rasbt/biopandas/blob/master/docs/sources/tutorials/data/3eiy_stripped.pdb.gz?raw=true)]"
+   ]
   }
  ],
  "metadata": {
   "anaconda-cloud": {},
   "kernelspec": {
-   "display_name": "Python [default]",
+   "display_name": "Python 3",
    "language": "python",
    "name": "python3"
   },
@@ -2036,7 +2116,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.5.2"
+   "version": "3.6.0"
   }
  },
  "nbformat": 4,