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add file links to tutorials for easy view and access (#28)
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@rasbt
rasbt committed May 19, 2017
1 parent 7a7279d commit 5655016
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Showing 2 changed files with 137 additions and 11 deletions.
54 changes: 50 additions & 4 deletions docs/sources/tutorials/Working_with_MOL2_Structures_in_DataFrames.ipynb
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Expand Up @@ -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": {},
Expand All @@ -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": {},
Expand Down Expand Up @@ -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": {},
Expand Down Expand Up @@ -861,14 +882,23 @@
{
"cell_type": "code",
"execution_count": 5,
"metadata": {},
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"from biopandas.mol2 import PandasMol2\n",
"\n",
"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,
Expand Down Expand Up @@ -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": {},
Expand Down Expand Up @@ -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": {},
Expand All @@ -1538,7 +1582,9 @@
{
"cell_type": "code",
"execution_count": 55,
"metadata": {},
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"pdmol = PandasMol2()\n",
Expand All @@ -1560,7 +1606,7 @@
"metadata": {
"anaconda-cloud": {},
"kernelspec": {
"display_name": "Python [default]",
"display_name": "Python 3",
"language": "python",
"name": "python3"
},
Expand All @@ -1574,7 +1620,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.5.2"
"version": "3.6.0"
}
},
"nbformat": 4,
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94 changes: 87 additions & 7 deletions docs/sources/tutorials/Working_with_PDB_Structures_in_DataFrames.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -79,7 +79,9 @@
{
"cell_type": "code",
"execution_count": 3,
"metadata": {},
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"from biopandas.pdb import PandasPdb\n",
Expand Down Expand Up @@ -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": {},
Expand Down Expand Up @@ -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": {},
Expand Down Expand Up @@ -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": {},
Expand Down Expand Up @@ -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": {},
Expand Down Expand Up @@ -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,
Expand Down Expand Up @@ -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,
Expand Down Expand Up @@ -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",
Expand All @@ -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": {},
Expand Down Expand Up @@ -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": {},
Expand All @@ -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",
Expand All @@ -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": {},
Expand All @@ -2009,20 +2080,29 @@
{
"cell_type": "code",
"execution_count": 41,
"metadata": {},
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"ppdb.to_pdb(path='./data/3eiy_stripped.pdb.gz', \n",
" records=['ATOM', 'HETATM', 'OTHERS'], \n",
" 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"
},
Expand All @@ -2036,7 +2116,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.5.2"
"version": "3.6.0"
}
},
"nbformat": 4,
Expand Down

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