{
 "cells": [
  {
   "cell_type": "markdown",
   "id": "eee7146f",
   "metadata": {},
   "source": [
    "# [PyRosetta](https://RosettaCommons.github.io/PyRosetta.notebooks)\n",
    "\n",
    "## Keyword Index\n",
    "\n",
    "* AddMembraneMover\n",
    "    - [Setting up a membrane protein in the bilayer](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/15.01-Accounting-for-the-lipid-bilayer.ipynb#Setting-up-a-membrane-protein-in-the-bilayer)\n",
    "* aldose\n",
    "    - [RosettaCarbohydrates](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/13.00-RosettaCarbohydrates-Working-with-Glycans.ipynb#RosettaCarbohydrates)\n",
    "* AndResidueSelector\n",
    "    - [Protein Design 2](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/06.04-Protein-Design-2.ipynb#Protein-Design-2)\n",
    "* angle_max()\n",
    "    - [High-Resolution Movers](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/05.01-High-Res-Movers.ipynb#High-Resolution-Movers)\n",
    "* annotated_sequence()\n",
    "    - [Pose Basics](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/02.01-Pose-Basics.ipynb#Pose-Basics)\n",
    "* Antibody\n",
    "    - [Working With Antibodies](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/12.00-Working-With-Antibodies.ipynb#Working-With-Antibodies)\n",
    "* assign()\n",
    "    - [Basic Folding Algorithm](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/04.01-Basic-Folding-Algorithm.ipynb#Basic-Folding-Algorithm)\n",
    "* asymmetric\n",
    "    - [Working With Symmetry](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/10.00-Working-With-Symmetry.ipynb#Working-With-Symmetry)\n",
    "* Atom objects\n",
    "    - [Score Function Basics](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/03.01-Score-Function-Basics.ipynb#Score-Function-Basics)\n",
    "* atom_index()\n",
    "    - [Getting spatial features from a Pose](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/02.04-Getting-Spatial-Features-from-Pose.ipynb#Getting-spatial-features-from-a-Pose)\n",
    "* AtomID\n",
    "    - [Getting spatial features from a Pose](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/02.04-Getting-Spatial-Features-from-Pose.ipynb#Getting-spatial-features-from-a-Pose)\n",
    "* bilayer\n",
    "    - [Setting up a membrane protein in the bilayer](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/15.01-Accounting-for-the-lipid-bilayer.ipynb#Setting-up-a-membrane-protein-in-the-bilayer)\n",
    "* boltzmann()\n",
    "    - [High-Resolution Movers](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/05.01-High-Res-Movers.ipynb#High-Resolution-Movers)\n",
    "* bond_angle()\n",
    "    - [Protein Geometry](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/02.05-Protein-Geometry.ipynb#Protein-Geometry)\n",
    "* bond_length()\n",
    "    - [Getting spatial features from a Pose](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/02.04-Getting-Spatial-Features-from-Pose.ipynb#Getting-spatial-features-from-a-Pose)\n",
    "* Bundle\n",
    "    - [*De Novo* Parametric Backbone Design](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/06.06-Introduction-to-Parametric-backbone-design.ipynb#*De-Novo*-Parametric-Backbone-Design)\n",
    "* BundleGridSampler\n",
    "    - [*De Novo* Parametric Backbone Design](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/06.06-Introduction-to-Parametric-backbone-design.ipynb#*De-Novo*-Parametric-Backbone-Design)\n",
    "* CA_rmsd()\n",
    "    - [Protein Design with a Resfile and FastRelax](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/06.03-Design-with-a-resfile-and-relax.ipynb#Protein-Design-with-a-Resfile-and-FastRelax)\n",
    "* carbohydrate\n",
    "    - [RosettaCarbohydrates](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/13.00-RosettaCarbohydrates-Working-with-Glycans.ipynb#RosettaCarbohydrates)\n",
    "    - [RosettaCarbohydrates: Trees, Selectors and Movers](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/13.01-Glycan-Trees-Selectors-and-Movers.ipynb#RosettaCarbohydrates:-Trees,-Selectors-and-Movers)\n",
    "    - [RosettaCarbohydrates: Modeling and Design](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/13.02-Glycan-Modeling-and-Design.ipynb#RosettaCarbohydrates:-Modeling-and-Design)\n",
    "* cartesian\n",
    "    - [Packing and Relax](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/06.02-Packing-design-and-regional-relax.ipynb#Packing-and-Relax)\n",
    "* CCD\n",
    "    - [Loop Modeling](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/09.00-Loop-Modeling.ipynb#Loop-Modeling)\n",
    "* CDR\n",
    "    - [Working With Antibodies](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/12.00-Working-With-Antibodies.ipynb#Working-With-Antibodies)\n",
    "* CDRResidueSelector\n",
    "    - [Packing and Relax](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/06.02-Packing-design-and-regional-relax.ipynb#Packing-and-Relax)\n",
    "    - [RosettaAntibody Framework](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/12.01-RosettaAntibody-Framework-and-SimpleMetrics.ipynb#RosettaAntibody-Framework)\n",
    "* centroid\n",
    "    - [Low-Res Scoring and Fragments](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/04.02-Low-Res-Scoring-and-Fragments.ipynb#Low-Res-Scoring-and-Fragments)\n",
    "* chain()\n",
    "    - [Working with Pose residues](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/02.02-Working-with-Pose-Residues.ipynb#Working-with-Pose-residues)\n",
    "* ChainSelector\n",
    "    - [Protein Design 2](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/06.04-Protein-Design-2.ipynb#Protein-Design-2)\n",
    "    - [HBNet Before Design](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/06.05-HBNet-Before-Design.ipynb#HBNet-Before-Design)\n",
    "* ClassicFragmentMover()\n",
    "    - [Low-Res Scoring and Fragments](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/04.02-Low-Res-Scoring-and-Fragments.ipynb#Low-Res-Scoring-and-Fragments)\n",
    "* classify_base_pairs\n",
    "    - [RNA in PyRosetta](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/14.00-RNA-Basics.ipynb#RNA-in-PyRosetta)\n",
    "* cleanATOM\n",
    "    - [Pose Basics](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/02.01-Pose-Basics.ipynb#Pose-Basics)\n",
    "* clone()\n",
    "    - [Packing and Relax](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/06.02-Packing-design-and-regional-relax.ipynb#Packing-and-Relax)\n",
    "* conf2pdb_chain()\n",
    "    - [Protein Design with a Resfile and FastRelax](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/06.03-Design-with-a-resfile-and-relax.ipynb#Protein-Design-with-a-Resfile-and-FastRelax)\n",
    "* conformation()\n",
    "    - [Getting spatial features from a Pose](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/02.04-Getting-Spatial-Features-from-Pose.ipynb#Getting-spatial-features-from-a-Pose)\n",
    "* create_score_function()\n",
    "    - [Low-Res Scoring and Fragments](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/04.02-Low-Res-Scoring-and-Fragments.ipynb#Low-Res-Scoring-and-Fragments)\n",
    "    - [Protein Design with a Resfile and FastRelax](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/06.03-Design-with-a-resfile-and-relax.ipynb#Protein-Design-with-a-Resfile-and-FastRelax)\n",
    "* crystal\n",
    "    - [Working With Density](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/11.00-Working-With-Density.ipynb#Working-With-Density)\n",
    "* cut-point variant\n",
    "    - [Loop Modeling](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/09.00-Loop-Modeling.ipynb#Loop-Modeling)\n",
    "* density\n",
    "    - [Working With Density](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/11.00-Working-With-Density.ipynb#Working-With-Density)\n",
    "* design\n",
    "    - [RosettaCarbohydrates: Modeling and Design](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/13.02-Glycan-Modeling-and-Design.ipynb#RosettaCarbohydrates:-Modeling-and-Design)\n",
    "* DockingLowRes()\n",
    "    - [Docking Moves in Rosetta](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/07.02-Docking-Moves-in-Rosetta.ipynb#Docking-Moves-in-Rosetta)\n",
    "* DockingSlideIntoContact()\n",
    "    - [Docking Moves in Rosetta](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/07.02-Docking-Moves-in-Rosetta.ipynb#Docking-Moves-in-Rosetta)\n",
    "* DockMCMProtocol()\n",
    "    - [Docking Moves in Rosetta](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/07.02-Docking-Moves-in-Rosetta.ipynb#Docking-Moves-in-Rosetta)\n",
    "* EDGE\n",
    "    - [Docking Moves in Rosetta](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/07.02-Docking-Moves-in-Rosetta.ipynb#Docking-Moves-in-Rosetta)\n",
    "* EM\n",
    "    - [Working With Density](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/11.00-Working-With-Density.ipynb#Working-With-Density)\n",
    "* EMapVector()\n",
    "    - [Practice: Analyzing energy between residues](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/03.02-Analyzing-energy-between-residues.ipynb#Practice:-Analyzing-energy-between-residues)\n",
    "* energies()\n",
    "    - [Side Chain Conformations and Dunbrack Energies](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/06.01-Side-Chain-Conformations-and-Dunbrack-Energies.ipynb#Side-Chain-Conformations-and-Dunbrack-Energies)\n",
    "* etable_atom_pair_energies()\n",
    "    - [Score Function Basics](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/03.01-Score-Function-Basics.ipynb#Score-Function-Basics)\n",
    "* fa_standard\n",
    "    - [Low-Res Scoring and Fragments](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/04.02-Low-Res-Scoring-and-Fragments.ipynb#Low-Res-Scoring-and-Fragments)\n",
    "* FaDockingSlideIntoContact()\n",
    "    - [Docking Moves in Rosetta](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/07.02-Docking-Moves-in-Rosetta.ipynb#Docking-Moves-in-Rosetta)\n",
    "* FARFAR protocol\n",
    "    - [RNA in PyRosetta](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/14.00-RNA-Basics.ipynb#RNA-in-PyRosetta)\n",
    "* FastDesign\n",
    "    - [Protein Design with a Resfile and FastRelax](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/06.03-Design-with-a-resfile-and-relax.ipynb#Protein-Design-with-a-Resfile-and-FastRelax)\n",
    "    - [Protein Design 2](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/06.04-Protein-Design-2.ipynb#Protein-Design-2)\n",
    "* FastRelax\n",
    "    - [Packing and Relax](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/06.02-Packing-design-and-regional-relax.ipynb#Packing-and-Relax)\n",
    "    - [Protein Design with a Resfile and FastRelax](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/06.03-Design-with-a-resfile-and-relax.ipynb#Protein-Design-with-a-Resfile-and-FastRelax)\n",
    "    - [Protein Design 2](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/06.04-Protein-Design-2.ipynb#Protein-Design-2)\n",
    "    - [**Point Mutation Scan**](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/06.08-Point-Mutation-Scan.ipynb#**Point-Mutation-Scan**)\n",
    "* FFT\n",
    "    - [Fast Fourier Transform Based Docking via ZDOCK](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/07.01-Fast-Fourier-Transform-Based-Docking-via-ZDOCK.ipynb#Fast-Fourier-Transform-Based-Docking-via-ZDOCK)\n",
    "* fold_tree()\n",
    "    - [Docking Moves in Rosetta](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/07.02-Docking-Moves-in-Rosetta.ipynb#Docking-Moves-in-Rosetta)\n",
    "* fold_tree_from_loops\n",
    "    - [Loop Modeling](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/09.00-Loop-Modeling.ipynb#Loop-Modeling)\n",
    "* FoldTree\n",
    "    - [Loop Modeling](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/09.00-Loop-Modeling.ipynb#Loop-Modeling)\n",
    "* furanose\n",
    "    - [RosettaCarbohydrates](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/13.00-RosettaCarbohydrates-Working-with-Glycans.ipynb#RosettaCarbohydrates)\n",
    "* GeneralizedKIC\n",
    "    - [Using Rosetta Gen KIC](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/09.01-Using-Gen-KIC.ipynb#Using-Rosetta-Gen-KIC)\n",
    "* get_hbonds()\n",
    "    - [Score Function Basics](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/03.01-Score-Function-Basics.ipynb#Score-Function-Basics)\n",
    "* get_residues_from_subset\n",
    "    - [Protein Design 2](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/06.04-Protein-Design-2.ipynb#Protein-Design-2)\n",
    "* get_score_function()\n",
    "    - [Score Function Basics](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/03.01-Score-Function-Basics.ipynb#Score-Function-Basics)\n",
    "* getPoseExtraScore\n",
    "    - [HBNet Before Design](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/06.05-HBNet-Before-Design.ipynb#HBNet-Before-Design)\n",
    "* ggplot2\n",
    "    - [**Point Mutation Scan**](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/06.08-Point-Mutation-Scan.ipynb#**Point-Mutation-Scan**)\n",
    "* glucose\n",
    "    - [RosettaCarbohydrates](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/13.00-RosettaCarbohydrates-Working-with-Glycans.ipynb#RosettaCarbohydrates)\n",
    "    - [RosettaCarbohydrates: Trees, Selectors and Movers](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/13.01-Glycan-Trees-Selectors-and-Movers.ipynb#RosettaCarbohydrates:-Trees,-Selectors-and-Movers)\n",
    "    - [RosettaCarbohydrates: Modeling and Design](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/13.02-Glycan-Modeling-and-Design.ipynb#RosettaCarbohydrates:-Modeling-and-Design)\n",
    "* glycan\n",
    "    - [RosettaCarbohydrates](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/13.00-RosettaCarbohydrates-Working-with-Glycans.ipynb#RosettaCarbohydrates)\n",
    "    - [RosettaCarbohydrates: Trees, Selectors and Movers](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/13.01-Glycan-Trees-Selectors-and-Movers.ipynb#RosettaCarbohydrates:-Trees,-Selectors-and-Movers)\n",
    "    - [RosettaCarbohydrates: Modeling and Design](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/13.02-Glycan-Modeling-and-Design.ipynb#RosettaCarbohydrates:-Modeling-and-Design)\n",
    "* GlycanTreeSet\n",
    "    - [RosettaCarbohydrates](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/13.00-RosettaCarbohydrates-Working-with-Glycans.ipynb#RosettaCarbohydrates)\n",
    "* HBNet\n",
    "    - [HBNet Before Design](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/06.05-HBNet-Before-Design.ipynb#HBNet-Before-Design)\n",
    "* help()\n",
    "    - [Accessing PyRosetta Documentation](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/02.03-Accessing-PyRosetta-Documentation.ipynb#Accessing-PyRosetta-Documentation)\n",
    "* IncludeCurrent\n",
    "    - [Protein Design with a Resfile and FastRelax](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/06.03-Design-with-a-resfile-and-relax.ipynb#Protein-Design-with-a-Resfile-and-FastRelax)\n",
    "* InitializeFromCommandline\n",
    "    - [Packing and Relax](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/06.02-Packing-design-and-regional-relax.ipynb#Packing-and-Relax)\n",
    "* InterGroupInterfaceByVectorSelector\n",
    "    - [HBNet Before Design](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/06.05-HBNet-Before-Design.ipynb#HBNet-Before-Design)\n",
    "* Jump\n",
    "    - [Docking Moves in Rosetta](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/07.02-Docking-Moves-in-Rosetta.ipynb#Docking-Moves-in-Rosetta)\n",
    "* keep_history()\n",
    "    - [High-Resolution Movers](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/05.01-High-Res-Movers.ipynb#High-Resolution-Movers)\n",
    "* ketose\n",
    "    - [RosettaCarbohydrates](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/13.00-RosettaCarbohydrates-Working-with-Glycans.ipynb#RosettaCarbohydrates)\n",
    "* KIC\n",
    "    - [Loop Modeling](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/09.00-Loop-Modeling.ipynb#Loop-Modeling)\n",
    "* label_energy()\n",
    "    - [Energies and the PyMOL Mover](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/03.03-Energies-and-the-PyMOLMover.ipynb#Energies-and-the-PyMOL-Mover)\n",
    "* LoadDensityMapMover\n",
    "    - [Working With Density](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/11.00-Working-With-Density.ipynb#Working-With-Density)\n",
    "* loop modeling\n",
    "    - [Using Rosetta Gen KIC](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/09.01-Using-Gen-KIC.ipynb#Using-Rosetta-Gen-KIC)\n",
    "* loops\n",
    "    - [Loop Modeling](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/09.00-Loop-Modeling.ipynb#Loop-Modeling)\n",
    "* MakeBundle\n",
    "    - [*De Novo* Parametric Backbone Design](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/06.06-Introduction-to-Parametric-backbone-design.ipynb#*De-Novo*-Parametric-Backbone-Design)\n",
    "* mannose\n",
    "    - [RosettaCarbohydrates](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/13.00-RosettaCarbohydrates-Working-with-Glycans.ipynb#RosettaCarbohydrates)\n",
    "    - [RosettaCarbohydrates: Trees, Selectors and Movers](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/13.01-Glycan-Trees-Selectors-and-Movers.ipynb#RosettaCarbohydrates:-Trees,-Selectors-and-Movers)\n",
    "    - [RosettaCarbohydrates: Modeling and Design](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/13.02-Glycan-Modeling-and-Design.ipynb#RosettaCarbohydrates:-Modeling-and-Design)\n",
    "* map\n",
    "    - [Working With Density](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/11.00-Working-With-Density.ipynb#Working-With-Density)\n",
    "* membrane\n",
    "    - [Setting up a membrane protein in the bilayer](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/15.01-Accounting-for-the-lipid-bilayer.ipynb#Setting-up-a-membrane-protein-in-the-bilayer)\n",
    "* Metropolis\n",
    "    - [Basic Folding Algorithm](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/04.01-Basic-Folding-Algorithm.ipynb#Basic-Folding-Algorithm)\n",
    "* MinMover()\n",
    "    - [High-Resolution Movers](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/05.01-High-Res-Movers.ipynb#High-Resolution-Movers)\n",
    "* MonteCarlo()\n",
    "    - [High-Resolution Movers](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/05.01-High-Res-Movers.ipynb#High-Resolution-Movers)\n",
    "* MoveMap\n",
    "    - [High-Resolution Movers](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/05.01-High-Res-Movers.ipynb#High-Resolution-Movers)\n",
    "    - [Loop Modeling](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/09.00-Loop-Modeling.ipynb#Loop-Modeling)\n",
    "* MoveMapFactory\n",
    "    - [Packing and Relax](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/06.02-Packing-design-and-regional-relax.ipynb#Packing-and-Relax)\n",
    "    - [Protein Design with a Resfile and FastRelax](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/06.03-Design-with-a-resfile-and-relax.ipynb#Protein-Design-with-a-Resfile-and-FastRelax)\n",
    "* Mover\n",
    "    - [RosettaCarbohydrates: Trees, Selectors and Movers](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/13.01-Glycan-Trees-Selectors-and-Movers.ipynb#RosettaCarbohydrates:-Trees,-Selectors-and-Movers)\n",
    "* mutate_position\n",
    "    - [RNA in PyRosetta](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/14.00-RNA-Basics.ipynb#RNA-in-PyRosetta)\n",
    "* NeighborhoodResidueSelector\n",
    "    - [Packing and Relax](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/06.02-Packing-design-and-regional-relax.ipynb#Packing-and-Relax)\n",
    "    - [**Point Mutation Scan**](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/06.08-Point-Mutation-Scan.ipynb#**Point-Mutation-Scan**)\n",
    "* nhbonds()\n",
    "    - [Score Function Basics](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/03.01-Score-Function-Basics.ipynb#Score-Function-Basics)\n",
    "* NoRepackDisulfides\n",
    "    - [Protein Design with a Resfile and FastRelax](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/06.03-Design-with-a-resfile-and-relax.ipynb#Protein-Design-with-a-Resfile-and-FastRelax)\n",
    "    - [Protein Design 2](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/06.04-Protein-Design-2.ipynb#Protein-Design-2)\n",
    "    - [**Point Mutation Scan**](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/06.08-Point-Mutation-Scan.ipynb#**Point-Mutation-Scan**)\n",
    "* NotResidueSelector\n",
    "    - [Protein Design 2](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/06.04-Protein-Design-2.ipynb#Protein-Design-2)\n",
    "* number()\n",
    "    - [Working with Pose residues](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/02.02-Working-with-Pose-Residues.ipynb#Working-with-Pose-residues)\n",
    "* OCTOPUS\n",
    "    - [Setting up a membrane protein in the bilayer](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/15.01-Accounting-for-the-lipid-bilayer.ipynb#Setting-up-a-membrane-protein-in-the-bilayer)\n",
    "* OperateOnResidueSubset\n",
    "    - [Protein Design 2](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/06.04-Protein-Design-2.ipynb#Protein-Design-2)\n",
    "    - [HBNet Before Design](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/06.05-HBNet-Before-Design.ipynb#HBNet-Before-Design)\n",
    "    - [HBNet Before Design](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/06.05-HBNet-Before-Design.ipynb#HBNet-Before-Design)\n",
    "    - [**Point Mutation Scan**](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/06.08-Point-Mutation-Scan.ipynb#**Point-Mutation-Scan**)\n",
    "* OperateOnResidueSubsetOperation\n",
    "    - [Packing and Relax](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/06.02-Packing-design-and-regional-relax.ipynb#Packing-and-Relax)\n",
    "* output_decoy()\n",
    "    - [Docking Moves in Rosetta](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/07.02-Docking-Moves-in-Rosetta.ipynb#Docking-Moves-in-Rosetta)\n",
    "* PackRotamersMover\n",
    "    - [Packing and Relax](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/06.02-Packing-design-and-regional-relax.ipynb#Packing-and-Relax)\n",
    "    - [HBNet Before Design](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/06.05-HBNet-Before-Design.ipynb#HBNet-Before-Design)\n",
    "* Parametric\n",
    "    - [*De Novo* Parametric Backbone Design](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/06.06-Introduction-to-Parametric-backbone-design.ipynb#*De-Novo*-Parametric-Backbone-Design)\n",
    "* pdb2pose()\n",
    "    - [Working with Pose residues](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/02.02-Working-with-Pose-Residues.ipynb#Working-with-Pose-residues)\n",
    "    - [Practice: Analyzing energy between residues](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/03.02-Analyzing-energy-between-residues.ipynb#Practice:-Analyzing-energy-between-residues)\n",
    "* phi()\n",
    "    - [Side Chain Conformations and Dunbrack Energies](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/06.01-Side-Chain-Conformations-and-Dunbrack-Energies.ipynb#Side-Chain-Conformations-and-Dunbrack-Energies)\n",
    "* Pose()\n",
    "    - [Basic Folding Algorithm](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/04.01-Basic-Folding-Algorithm.ipynb#Basic-Folding-Algorithm)\n",
    "* pose2pdb()\n",
    "    - [Working with Pose residues](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/02.02-Working-with-Pose-Residues.ipynb#Working-with-Pose-residues)\n",
    "* pose_from_pdb()\n",
    "    - [Pose Basics](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/02.01-Pose-Basics.ipynb#Pose-Basics)\n",
    "* pose_from_rcsb\n",
    "    - [Protein Design 2](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/06.04-Protein-Design-2.ipynb#Protein-Design-2)\n",
    "* pose_from_rcsb()\n",
    "    - [Practice: Analyzing energy between residues](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/03.02-Analyzing-energy-between-residues.ipynb#Practice:-Analyzing-energy-between-residues)\n",
    "    - [Protein Design with a Resfile and FastRelax](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/06.03-Design-with-a-resfile-and-relax.ipynb#Protein-Design-with-a-Resfile-and-FastRelax)\n",
    "* pose_from_sequence()\n",
    "    - [Protein Geometry](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/02.05-Protein-Geometry.ipynb#Protein-Geometry)\n",
    "    - [Basic Folding Algorithm](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/04.01-Basic-Folding-Algorithm.ipynb#Basic-Folding-Algorithm)\n",
    "* prediction\n",
    "    - [RosettaCarbohydrates: Modeling and Design](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/13.02-Glycan-Modeling-and-Design.ipynb#RosettaCarbohydrates:-Modeling-and-Design)\n",
    "* PreventRepackingRLT\n",
    "    - [Packing and Relax](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/06.02-Packing-design-and-regional-relax.ipynb#Packing-and-Relax)\n",
    "    - [HBNet Before Design](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/06.05-HBNet-Before-Design.ipynb#HBNet-Before-Design)\n",
    "* psi()\n",
    "    - [Side Chain Conformations and Dunbrack Energies](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/06.01-Side-Chain-Conformations-and-Dunbrack-Energies.ipynb#Side-Chain-Conformations-and-Dunbrack-Energies)\n",
    "* PyJobDistributor()\n",
    "    - [Docking Moves in Rosetta](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/07.02-Docking-Moves-in-Rosetta.ipynb#Docking-Moves-in-Rosetta)\n",
    "* PyMOLMover\n",
    "    - [Visualization with the `PyMOLMover`](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/02.06-Visualization-and-PyMOL-Mover.ipynb#Visualization-with-the-`PyMOLMover`)\n",
    "    - [Visualization with the `PyMOLMover`, PyRosetta ColabPyMOL integration](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/02.07-Visualization-and-PyMOL-Mover.PyRosetta-ColabPyMOL-integration.ipynb#Visualization-with-the-`PyMOLMover`,-PyRosetta-ColabPyMOL-integration)\n",
    "* pyranose\n",
    "    - [RosettaCarbohydrates](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/13.00-RosettaCarbohydrates-Working-with-Glycans.ipynb#RosettaCarbohydrates)\n",
    "* RAbD\n",
    "    - [Working With Antibodies](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/12.00-Working-With-Antibodies.ipynb#Working-With-Antibodies)\n",
    "* random move\n",
    "    - [Basic Folding Algorithm](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/04.01-Basic-Folding-Algorithm.ipynb#Basic-Folding-Algorithm)\n",
    "* read_fragment_file()\n",
    "    - [Low-Res Scoring and Fragments](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/04.02-Low-Res-Scoring-and-Fragments.ipynb#Low-Res-Scoring-and-Fragments)\n",
    "* ReadResfile\n",
    "    - [Protein Design with a Resfile and FastRelax](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/06.03-Design-with-a-resfile-and-relax.ipynb#Protein-Design-with-a-Resfile-and-FastRelax)\n",
    "* refinement\n",
    "    - [Working With Density](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/11.00-Working-With-Density.ipynb#Working-With-Density)\n",
    "* RepeatMover()\n",
    "    - [High-Resolution Movers](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/05.01-High-Res-Movers.ipynb#High-Resolution-Movers)\n",
    "* Resfile\n",
    "    - [Protein Design with a Resfile and FastRelax](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/06.03-Design-with-a-resfile-and-relax.ipynb#Protein-Design-with-a-Resfile-and-FastRelax)\n",
    "* ResfileCommandOperation\n",
    "    - [Protein Design with a Resfile and FastRelax](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/06.03-Design-with-a-resfile-and-relax.ipynb#Protein-Design-with-a-Resfile-and-FastRelax)\n",
    "* residue_hbonds()\n",
    "    - [Score Function Basics](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/03.01-Score-Function-Basics.ipynb#Score-Function-Basics)\n",
    "* residue_total_energies()\n",
    "    - [Side Chain Conformations and Dunbrack Energies](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/06.01-Side-Chain-Conformations-and-Dunbrack-Energies.ipynb#Side-Chain-Conformations-and-Dunbrack-Energies)\n",
    "* ResidueNameSelector\n",
    "    - [Protein Design 2](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/06.04-Protein-Design-2.ipynb#Protein-Design-2)\n",
    "* ResiduePDBInfoHasLabelSelector\n",
    "    - [HBNet Before Design](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/06.05-HBNet-Before-Design.ipynb#HBNet-Before-Design)\n",
    "* ResiduePropertySelector\n",
    "    - [Protein Design 2](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/06.04-Protein-Design-2.ipynb#Protein-Design-2)\n",
    "* ResidueSelector\n",
    "    - [Packing and Relax](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/06.02-Packing-design-and-regional-relax.ipynb#Packing-and-Relax)\n",
    "    - [Protein Design with a Resfile and FastRelax](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/06.03-Design-with-a-resfile-and-relax.ipynb#Protein-Design-with-a-Resfile-and-FastRelax)\n",
    "    - [Protein Design 2](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/06.04-Protein-Design-2.ipynb#Protein-Design-2)\n",
    "    - [**Point Mutation Scan**](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/06.08-Point-Mutation-Scan.ipynb#**Point-Mutation-Scan**)\n",
    "    - [RosettaCarbohydrates: Trees, Selectors and Movers](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/13.01-Glycan-Trees-Selectors-and-Movers.ipynb#RosettaCarbohydrates:-Trees,-Selectors-and-Movers)\n",
    "* RestrictAbsentCanonicalAASRLT\n",
    "    - [Protein Design 2](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/06.04-Protein-Design-2.ipynb#Protein-Design-2)\n",
    "    - [**Point Mutation Scan**](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/06.08-Point-Mutation-Scan.ipynb#**Point-Mutation-Scan**)\n",
    "* RestrictToRepacking\n",
    "    - [Packing and Relax](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/06.02-Packing-design-and-regional-relax.ipynb#Packing-and-Relax)\n",
    "* RestrictToRepackingRLT\n",
    "    - [Protein Design 2](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/06.04-Protein-Design-2.ipynb#Protein-Design-2)\n",
    "    - [HBNet Before Design](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/06.05-HBNet-Before-Design.ipynb#HBNet-Before-Design)\n",
    "    - [**Point Mutation Scan**](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/06.08-Point-Mutation-Scan.ipynb#**Point-Mutation-Scan**)\n",
    "* ReturnSidechainMover()\n",
    "    - [Docking Moves in Rosetta](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/07.02-Docking-Moves-in-Rosetta.ipynb#Docking-Moves-in-Rosetta)\n",
    "* RigidBodyPerturbMover()\n",
    "    - [Docking Moves in Rosetta](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/07.02-Docking-Moves-in-Rosetta.ipynb#Docking-Moves-in-Rosetta)\n",
    "* RigidBodyTransMover\n",
    "    - [**Point Mutation Scan**](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/06.08-Point-Mutation-Scan.ipynb#**Point-Mutation-Scan**)\n",
    "* RNA fragment assembly\n",
    "    - [RNA in PyRosetta](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/14.00-RNA-Basics.ipynb#RNA-in-PyRosetta)\n",
    "* RNA minimize\n",
    "    - [RNA in PyRosetta](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/14.00-RNA-Basics.ipynb#RNA-in-PyRosetta)\n",
    "* RNA motifs\n",
    "    - [RNA in PyRosetta](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/14.00-RNA-Basics.ipynb#RNA-in-PyRosetta)\n",
    "* RNA score terms\n",
    "    - [RNA in PyRosetta](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/14.00-RNA-Basics.ipynb#RNA-in-PyRosetta)\n",
    "* RNA thread\n",
    "    - [RNA in PyRosetta](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/14.00-RNA-Basics.ipynb#RNA-in-PyRosetta)\n",
    "* RNA torsions\n",
    "    - [RNA in PyRosetta](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/14.00-RNA-Basics.ipynb#RNA-in-PyRosetta)\n",
    "* rna_denovo\n",
    "    - [RNA in PyRosetta](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/14.00-RNA-Basics.ipynb#RNA-in-PyRosetta)\n",
    "* RNA_HelixAssembler\n",
    "    - [RNA in PyRosetta](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/14.00-RNA-Basics.ipynb#RNA-in-PyRosetta)\n",
    "* RosettaAntibody\n",
    "    - [Working With Antibodies](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/12.00-Working-With-Antibodies.ipynb#Working-With-Antibodies)\n",
    "* RosettaAntibodyDesign\n",
    "    - [Working With Antibodies](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/12.00-Working-With-Antibodies.ipynb#Working-With-Antibodies)\n",
    "* RosettaScripts\n",
    "    - [RosettaScripts in PyRosetta](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/02.08-RosettaScripts-in-PyRosetta.ipynb#RosettaScripts-in-PyRosetta)\n",
    "* saccharide\n",
    "    - [RosettaCarbohydrates](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/13.00-RosettaCarbohydrates-Working-with-Glycans.ipynb#RosettaCarbohydrates)\n",
    "* score function\n",
    "    - [Score Function Basics](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/03.01-Score-Function-Basics.ipynb#Score-Function-Basics)\n",
    "* score3\n",
    "    - [Low-Res Scoring and Fragments](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/04.02-Low-Res-Scoring-and-Fragments.ipynb#Low-Res-Scoring-and-Fragments)\n",
    "* ScoreFunction()\n",
    "    - [Score Function Basics](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/03.01-Score-Function-Basics.ipynb#Score-Function-Basics)\n",
    "    - [Low-Res Scoring and Fragments](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/04.02-Low-Res-Scoring-and-Fragments.ipynb#Low-Res-Scoring-and-Fragments)\n",
    "* scoring move\n",
    "    - [Basic Folding Algorithm](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/04.01-Basic-Folding-Algorithm.ipynb#Basic-Folding-Algorithm)\n",
    "* script\n",
    "    - [RosettaScripts in PyRosetta](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/02.08-RosettaScripts-in-PyRosetta.ipynb#RosettaScripts-in-PyRosetta)\n",
    "* send_energy()\n",
    "    - [Energies and the PyMOL Mover](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/03.03-Energies-and-the-PyMOLMover.ipynb#Energies-and-the-PyMOL-Mover)\n",
    "* send_hbonds()\n",
    "    - [Visualization with the `PyMOLMover`](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/02.06-Visualization-and-PyMOL-Mover.ipynb#Visualization-with-the-`PyMOLMover`)\n",
    "    - [Visualization with the `PyMOLMover`, PyRosetta ColabPyMOL integration](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/02.07-Visualization-and-PyMOL-Mover.PyRosetta-ColabPyMOL-integration.ipynb#Visualization-with-the-`PyMOLMover`,-PyRosetta-ColabPyMOL-integration)\n",
    "    - [Energies and the PyMOL Mover](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/03.03-Energies-and-the-PyMOLMover.ipynb#Energies-and-the-PyMOL-Mover)\n",
    "* sequence()\n",
    "    - [Pose Basics](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/02.01-Pose-Basics.ipynb#Pose-Basics)\n",
    "* SequenceMetric\n",
    "    - [Packing and Relax](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/06.02-Packing-design-and-regional-relax.ipynb#Packing-and-Relax)\n",
    "* SequenceMover()\n",
    "    - [High-Resolution Movers](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/05.01-High-Res-Movers.ipynb#High-Resolution-Movers)\n",
    "* set_bb()\n",
    "    - [High-Resolution Movers](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/05.01-High-Res-Movers.ipynb#High-Resolution-Movers)\n",
    "* set_phi()\n",
    "    - [Protein Geometry](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/02.05-Protein-Geometry.ipynb#Protein-Geometry)\n",
    "* set_psi()\n",
    "    - [Protein Geometry](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/02.05-Protein-Geometry.ipynb#Protein-Geometry)\n",
    "* set_weight()\n",
    "    - [Score Function Basics](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/03.01-Score-Function-Basics.ipynb#Score-Function-Basics)\n",
    "    - [Low-Res Scoring and Fragments](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/04.02-Low-Res-Scoring-and-Fragments.ipynb#Low-Res-Scoring-and-Fragments)\n",
    "* SetupForSymmetryMover\n",
    "    - [Working With Symmetry](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/10.00-Working-With-Symmetry.ipynb#Working-With-Symmetry)\n",
    "* ShearMover()\n",
    "    - [High-Resolution Movers](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/05.01-High-Res-Movers.ipynb#High-Resolution-Movers)\n",
    "* show()\n",
    "    - [Score Function Basics](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/03.01-Score-Function-Basics.ipynb#Score-Function-Basics)\n",
    "* SimpleMetric\n",
    "    - [Packing and Relax](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/06.02-Packing-design-and-regional-relax.ipynb#Packing-and-Relax)\n",
    "* SmallMover()\n",
    "    - [High-Resolution Movers](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/05.01-High-Res-Movers.ipynb#High-Resolution-Movers)\n",
    "* sugar\n",
    "    - [RosettaCarbohydrates](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/13.00-RosettaCarbohydrates-Working-with-Glycans.ipynb#RosettaCarbohydrates)\n",
    "    - [RosettaCarbohydrates](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/13.00-RosettaCarbohydrates-Working-with-Glycans.ipynb#RosettaCarbohydrates)\n",
    "    - [RosettaCarbohydrates: Trees, Selectors and Movers](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/13.01-Glycan-Trees-Selectors-and-Movers.ipynb#RosettaCarbohydrates:-Trees,-Selectors-and-Movers)\n",
    "    - [RosettaCarbohydrates: Modeling and Design](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/13.02-Glycan-Modeling-and-Design.ipynb#RosettaCarbohydrates:-Modeling-and-Design)\n",
    "* SwitchResidueTypeMover()\n",
    "    - [Docking Moves in Rosetta](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/07.02-Docking-Moves-in-Rosetta.ipynb#Docking-Moves-in-Rosetta)\n",
    "* SwitchResidueTypeSetMover()\n",
    "    - [Low-Res Scoring and Fragments](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/04.02-Low-Res-Scoring-and-Fragments.ipynb#Low-Res-Scoring-and-Fragments)\n",
    "* symmetry\n",
    "    - [Working With Symmetry](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/10.00-Working-With-Symmetry.ipynb#Working-With-Symmetry)\n",
    "* TaskFactory\n",
    "    - [Packing and Relax](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/06.02-Packing-design-and-regional-relax.ipynb#Packing-and-Relax)\n",
    "    - [Protein Design with a Resfile and FastRelax](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/06.03-Design-with-a-resfile-and-relax.ipynb#Protein-Design-with-a-Resfile-and-FastRelax)\n",
    "    - [Protein Design 2](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/06.04-Protein-Design-2.ipynb#Protein-Design-2)\n",
    "    - [**Point Mutation Scan**](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/06.08-Point-Mutation-Scan.ipynb#**Point-Mutation-Scan**)\n",
    "* TaskOperation\n",
    "    - [Packing and Relax](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/06.02-Packing-design-and-regional-relax.ipynb#Packing-and-Relax)\n",
    "    - [Protein Design with a Resfile and FastRelax](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/06.03-Design-with-a-resfile-and-relax.ipynb#Protein-Design-with-a-Resfile-and-FastRelax)\n",
    "    - [Protein Design 2](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/06.04-Protein-Design-2.ipynb#Protein-Design-2)\n",
    "    - [**Point Mutation Scan**](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/06.08-Point-Mutation-Scan.ipynb#**Point-Mutation-Scan**)\n",
    "* total_residue()\n",
    "    - [Working with Pose residues](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/02.02-Working-with-Pose-Residues.ipynb#Working-with-Pose-residues)\n",
    "* TrialMover()\n",
    "    - [High-Resolution Movers](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/05.01-High-Res-Movers.ipynb#High-Resolution-Movers)\n",
    "* virtual\n",
    "    - [Working With Symmetry](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/10.00-Working-With-Symmetry.ipynb#Working-With-Symmetry)\n",
    "* X-ray\n",
    "    - [Working With Density](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/11.00-Working-With-Density.ipynb#Working-With-Density)\n",
    "* xml\n",
    "    - [RosettaScripts in PyRosetta](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/02.08-RosettaScripts-in-PyRosetta.ipynb#RosettaScripts-in-PyRosetta)\n",
    "* XMLObjects\n",
    "    - [RosettaScripts in PyRosetta](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/02.08-RosettaScripts-in-PyRosetta.ipynb#RosettaScripts-in-PyRosetta)\n",
    "* xyz()\n",
    "    - [Protein Geometry](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/02.05-Protein-Geometry.ipynb#Protein-Geometry)\n",
    "* ZDOCK\n",
    "    - [Fast Fourier Transform Based Docking via ZDOCK](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/07.01-Fast-Fourier-Transform-Based-Docking-via-ZDOCK.ipynb#Fast-Fourier-Transform-Based-Docking-via-ZDOCK)"
   ]
  }
 ],
 "metadata": {},
 "nbformat": 4,
 "nbformat_minor": 5
}