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Merge pull request #24 from Autodesk/dev
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Dev
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@avirshup
avirshup authored Jul 26, 2016
2 parents 6768e79 + 0018314 commit 7d632d6
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9 changes: 9 additions & 0 deletions moldesign/_notebooks/Example 1. Build and simulate DNA.ipynb
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Expand Up @@ -335,6 +335,15 @@
"interact_manual(plot_rmsd)\n",
"rs"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": []
}
],
"metadata": {
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102 changes: 63 additions & 39 deletions moldesign/_notebooks/Tutorial 1. Making a molecule.ipynb
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Expand Up @@ -4,7 +4,11 @@
"cell_type": "markdown",
"metadata": {},
"source": [
"<a href=\"http://moldesign.bionano.autodesk.com\" target=\"_blank\"><img src=\"img/Top.png\"></a>\n",
"\n",
"<span style=\"float:right\"><a href=\"http://moldesign.bionano.autodesk.com/\" target=\"_blank\" title=\"About\">About</a>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href=\"https://forum.bionano.autodesk.com/c/Molecular-Design-Toolkit\" target=\"_blank\" title=\"Forum\">Forum</a>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href=\"https://github.com/autodesk/molecular-design-toolkit/issues\" target=\"_blank\" title=\"Issues\">Issues</a>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href=\"http://bionano.autodesk.com/MolecularDesignToolkit/explore.html\" target=\"_blank\" title=\"Tutorials\">Tutorials</a>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href=\"http://autodesk.github.io/molecular-design-toolkit/\" target=\"_blank\" title=\"Documentation\">Documentation</a></span>\n",
"</span>\n",
"![Molecular Design Toolkit](img/top.png)\n",
"<br>\n",
"\n",
"<center><h1>Tutorial 1: Making a molecule</h1></center>\n",
"\n",
Expand All @@ -19,11 +23,13 @@
"=======\n",
"---\n",
" - [1. Import the toolkit](#1.-Import-the-toolkit)\n",
" - [A. Optional: Set up your computing backend](#A.-Optional:-Set-up-your-computing-backend)\n",
" - [2. Read in the molecule](#2.-Read-in-the-molecule)\n",
" - [3. Draw it](#3.-Draw-it)\n",
" - [4. Inspect it](#4.-Inspect-it)\n",
" - [5. Move it](#5.-Move-it)\n",
" - [6. Write it](#6.-Write-it)\n"
" - [4. Simulate it](#4.-Simulate-it)\n",
" - [5. Minimize it](#5.-Minimize-it)\n",
" - [6. Write it](#6.-Write-it)\n",
" - [7. Examine it](#7.-Examine-it)"
]
},
{
Expand All @@ -46,6 +52,26 @@
"import moldesign.units as u"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"### A. Optional: Set up your computing backend\n",
"\n",
"By default, MDT is configured to use Autodesk's free demo cluster on the cloud. However, if you'd like to run jobs elsewhere (e.g., on your local computer, on your private cloud cluster, etc.), you can set that up by running `mdt.configure()`."
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": false
},
"outputs": [],
"source": [
"mdt.configure()"
]
},
{
"cell_type": "markdown",
"metadata": {},
Expand All @@ -61,11 +87,11 @@
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": true
"collapsed": false
},
"outputs": [],
"source": [
"molecule = mdt.read('data/bipyridine.sdf')"
"molecule = mdt.read('data/butane.xyz')"
]
},
{
Expand Down Expand Up @@ -131,7 +157,8 @@
},
"outputs": [],
"source": [
"molecule.set_energy_model(mdt.models.RHF, basis='sto-3g')"
"molecule.set_energy_model(mdt.models.RHF, basis='sto-3g')\n",
"properties = molecule.calculate()"
]
},
{
Expand All @@ -142,20 +169,9 @@
},
"outputs": [],
"source": [
"properties = molecule.calculate()\n",
"print properties.keys()\n",
"print 'Energy: ', properties['potential_energy']"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": false
},
"outputs": [],
"source": [
"atom.bonds"
"print 'Energy: ', properties['potential_energy']\n",
"molecule.draw_orbitals()"
]
},
{
Expand All @@ -173,7 +189,7 @@
},
"outputs": [],
"source": [
"mdt.widgets.GeometryBuilder(molecule)"
"mintraj = molecule.minimize()"
]
},
{
Expand All @@ -184,36 +200,46 @@
},
"outputs": [],
"source": [
"atom.distance(molecule.atoms[0])"
"mintraj.draw_orbitals()"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## 6. Write it"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": false
"collapsed": true
},
"outputs": [],
"source": [
"atom.calc_distances(molecule.atoms)"
"molecule.write('my_first_molecule.xyz')"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": false
"collapsed": true
},
"outputs": [],
"source": [
"mdt.angle(molecule.atoms[0], molecule.atoms[1], molecule.atoms[2])"
"mintraj.write('my_first_minimization.P.gz')"
]
},
{
"cell_type": "markdown",
"metadata": {},
"metadata": {
"collapsed": false
},
"source": [
"## 6. Write it"
"## 7. Examine it\n",
"There are any number of directions to go from here. For this tutorial, try click on some bonds to check the molecule's geometry."
]
},
{
Expand All @@ -224,28 +250,26 @@
},
"outputs": [],
"source": [
"molecule.write('my_first_molecule.xyz')"
"mdt.widgets.GeometryBuilder(molecule)"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": false
},
"outputs": [],
"cell_type": "markdown",
"metadata": {},
"source": [
"!cat my_first_molecule.xyz"
"You can also use the corresponding python functions to measure these parameters:"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": true
"collapsed": false
},
"outputs": [],
"source": []
"source": [
"mdt.dihedral(*molecule.atoms[:4]).to(u.degrees)"
]
}
],
"metadata": {
Expand All @@ -264,7 +288,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython2",
"version": "2.7.11"
"version": "2.7.12"
}
},
"nbformat": 4,
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