Before you turn this problem in, make sure everything runs as expected. First, restart the kernel (in the menubar, select Kernel$\rightarrow$Restart) and then run all cells (in the menubar, select Cell$\rightarrow$Run All).
Make sure you fill in any place that says YOUR CODE HERE
or "YOUR ANSWER HERE", as well as your name and collaborators below:
NAME = ""
COLLABORATORS = ""
- [Install third-party external packages](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/01.01-PyRosetta-Google-Drive-Setup.ipynb#Install-third-party-external-packages)
- [Pip:](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/01.01-PyRosetta-Google-Drive-Setup.ipynb#Pip:)
- [Conda:](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/01.01-PyRosetta-Google-Drive-Setup.ipynb#Conda:)
PyMOLMover
¶pyrosetta.distributed.viewer
¶- [Available `viewer` objects:](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/02.08-Visualization-and-pyrosetta.distributed.viewer.ipynb#Available-`viewer`-objects:)
- [Available `viewer.presets` objects:](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/02.08-Visualization-and-pyrosetta.distributed.viewer.ipynb#Available-`viewer.presets`-objects:)
- [`viewer` objects contain docstrings as user documentation:](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/02.08-Visualization-and-pyrosetta.distributed.viewer.ipynb#`viewer`-objects-contain-docstrings-as-user-documentation:)
- [`viewer.presets` objects contain docstrings as brief descriptions of each preset visualization](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/02.08-Visualization-and-pyrosetta.distributed.viewer.ipynb#`viewer.presets`-objects-contain-docstrings-as-brief-descriptions-of-each-preset-visualization)
ligand.wts
Scorefunction¶XMLObjects
Using the ref2015.wts
Scorefunction¶GALigandDock
Protocol with pyrosetta.distributed
Using the beta_cart.wts
Scorefunction¶- [Inspect the scores for the `GALigandDock` trajectories:](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/08.02-Ligand-Docking-pyrosetta.distributed.ipynb#Inspect-the-scores-for-the-`GALigandDock`-trajectories:)
- [Now that we have performed `GALigandDock`, we can plot the ligand binding energy landscape:](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/08.02-Ligand-Docking-pyrosetta.distributed.ipynb#Now-that-we-have-performed-`GALigandDock`,-we-can-plot-the-ligand-binding-energy-landscape:)
.pdb
File LINK
Records - [A1.2 Design using the `N[^P][T]` motif](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/13.02-Glycan-Modeling-and-Design.ipynb#A1.2-Design-using-the-`N[^P][T]`-motif)
- [A2. Adding a man5 glycan:](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/13.02-Glycan-Modeling-and-Design.ipynb#A2.-Adding-a-man5-glycan:)
- [A3. Modeling glycans](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/13.02-Glycan-Modeling-and-Design.ipynb#A3.-Modeling-glycans)
multiprocessing
dask
- [1. Parallelize script in an interactive session:](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/16.03-GNU-Parallel-Via-Slurm.ipynb#1.-Parallelize-script-in-an-interactive-session:)
- [2. Parallelize script on a high-performance computing cluster with Slurm scheduling (non-interactive submission):](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/16.03-GNU-Parallel-Via-Slurm.ipynb#2.-Parallelize-script-on-a-high-performance-computing-cluster-with-Slurm-scheduling-(non-interactive-submission):)
- [3. Submit jobs individually to the SLURM scheduler:](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/16.03-GNU-Parallel-Via-Slurm.ipynb#3.-Submit-jobs-individually-to-the-SLURM-scheduler:)
dask
Module¶- [We can make use of the `dask` library to parallelize code](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/16.04-dask.delayed-Via-Slurm.ipynb#We-can-make-use-of-the-`dask`-library-to-parallelize-code)
- [Consider the following example that runs within this Jupyter notebook kernel just fine but could be parallelized:](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/16.04-dask.delayed-Via-Slurm.ipynb#Consider-the-following-example-that-runs-within-this-Jupyter-notebook-kernel-just-fine-but-could-be-parallelized:)
pyrosetta.distributed
¶