Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

add file links to tutorials for easy view and access #28

Merged
merged 1 commit into from
May 19, 2017
Merged
Show file tree
Hide file tree
Changes from all commits
Commits
File filter

Filter by extension

Filter by extension

Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
Original file line number Diff line number Diff line change
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,
Expand Down
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