{ "cells": [ { "cell_type": "markdown", "metadata": {}, "source": [ "\n", "*This notebook contains material from [PyRosetta](https://RosettaCommons.github.io/PyRosetta);\n", "content is available [on Github](https://github.com/RosettaCommons/PyRosetta.notebooks.git).*" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "\n", "< [PyData Integration](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/11.00-PyData-integration.ipynb) | [Contents](toc.ipynb) | [Index](index.ipynb) |
"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# Distributed analysis example: exhaustive ddG PSSM\n",
"\n",
"## Notes\n",
"This tutorial will walk you through how to generate an exhaustive ddG PSSM in PyRosetta using the PyData stack for analysis and distributed computing.\n",
"\n",
"## Citation\n",
"[Integration of the Rosetta Suite with the Python Software Stack via reproducible packaging and core programming interfaces for distributed simulation](https://doi.org/10.1002/pro.3721)\n",
"\n",
"Alexander S. Ford, Brian D. Weitzner, Christopher D. Bahl\n",
"\n",
"## Manual\n",
"Documentation for the `pyrosetta.distributed` namespace can be found here: https://nbviewer.jupyter.org/github/proteininnovation/Rosetta-PyData_Integration/blob/master/distributed_overview.ipynb"
]
},
{
"cell_type": "code",
"execution_count": 1,
"metadata": {},
"outputs": [],
"source": [
"import logging\n",
"logging.basicConfig(level=logging.INFO)"
]
},
{
"cell_type": "code",
"execution_count": 2,
"metadata": {},
"outputs": [],
"source": [
"import pandas\n",
"import seaborn\n",
"import matplotlib"
]
},
{
"cell_type": "code",
"execution_count": 3,
"metadata": {},
"outputs": [],
"source": [
"import Bio.SeqUtils\n",
"import Bio.Data.IUPACData as IUPACData"
]
},
{
"cell_type": "code",
"execution_count": 4,
"metadata": {},
"outputs": [],
"source": [
"import pyrosetta\n",
"import pyrosetta.distributed.io as io\n",
"import pyrosetta.distributed.packed_pose as packed_pose\n",
"import pyrosetta.distributed.tasks.rosetta_scripts as rosetta_scripts\n",
"import pyrosetta.distributed.tasks.score as score"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Create test pose, initialize rosetta and pack"
]
},
{
"cell_type": "code",
"execution_count": 5,
"metadata": {},
"outputs": [],
"source": [
"input_protocol = \"\"\"\n",
"