index.md

PyRosetta

Keyword Index

• AddMembraneMover
  • Setting up a membrane protein in the bilayer
• aldose
  • RosettaCarbohydrates
• AndResidueSelector
  • Protein Design 2
• angle_max()
  • High-Resolution Movers
• annotated_sequence()
  • Pose Basics
• Antibody
  • Working With Antibodies
• assign()
  • Basic Folding Algorithm
• asymmetric
  • Working With Symmetry
• Atom objects
  • Score Function Basics
• atom_index()
  • Getting spatial features from a Pose
• AtomID
  • Getting spatial features from a Pose
• bilayer
  • Setting up a membrane protein in the bilayer
• boltzmann()
  • High-Resolution Movers
• bond_angle()
  • Protein Geometry
• bond_length()
  • Getting spatial features from a Pose
• Bundle
  • De Novo Parametric Backbone Design
• BundleGridSampler
  • De Novo Parametric Backbone Design
• CA_rmsd()
  • Protein Design with a Resfile and FastRelax
• carbohydrate
  • RosettaCarbohydrates
  • RosettaCarbohydrates: Trees, Selectors and Movers
  • RosettaCarbohydrates: Modeling and Design
• cartesian
  • Packing and Relax
• CDR
  • Working With Antibodies
• CDRResidueSelector
  • Packing and Relax
  • RosettaAntibody Framework
• centroid
  • Low-Res Scoring and Fragments
• chain()
  • Working with Pose residues
• ChainSelector
  • Protein Design 2
  • HBNet Before Design
• ClassicFragmentMover()
  • Low-Res Scoring and Fragments
• classify_base_pairs
  • RNA in PyRosetta
• cleanATOM
  • Pose Basics
• clone()
  • Packing and Relax
• conf2pdb_chain()
  • Protein Design with a Resfile and FastRelax
• conformation()
  • Getting spatial features from a Pose
• create_score_function()
  • Low-Res Scoring and Fragments
  • Protein Design with a Resfile and FastRelax
• crystal
  • Working With Density
• density
  • Working With Density
• design
  • RosettaCarbohydrates: Modeling and Design
• DockingLowRes()
  • Docking Moves in Rosetta
• DockingSlideIntoContact()
  • Docking Moves in Rosetta
• DockMCMProtocol()
  • Docking Moves in Rosetta
• EDGE
  • Docking Moves in Rosetta
• EM
  • Working With Density
• EMapVector()
  • Practice: Analyzing energy between residues
• energies()
  • Side Chain Conformations and Dunbrack Energies
• etable_atom_pair_energies()
  • Score Function Basics
• fa_standard
  • Low-Res Scoring and Fragments
• FaDockingSlideIntoContact()
  • Docking Moves in Rosetta
• FARFAR protocol
  • RNA in PyRosetta
• FastDesign
  • Protein Design with a Resfile and FastRelax
  • Protein Design 2
• FastRelax
  • Packing and Relax
  • Protein Design with a Resfile and FastRelax
  • Protein Design 2
  • Point Mutation Scan
• FFT
  • Fast Fourier Transform Based Docking via ZDOCK
• fold_tree()
  • Docking Moves in Rosetta
• furanose
  • RosettaCarbohydrates
• get_hbonds()
  • Score Function Basics
• get_residues_from_subset
  • Protein Design 2
• get_score_function()
  • Score Function Basics
• getPoseExtraScore
  • HBNet Before Design
• ggplot2
  • Point Mutation Scan
• glucose
  • RosettaCarbohydrates
  • RosettaCarbohydrates: Trees, Selectors and Movers
  • RosettaCarbohydrates: Modeling and Design
• glycan
  • RosettaCarbohydrates
  • RosettaCarbohydrates: Trees, Selectors and Movers
  • RosettaCarbohydrates: Modeling and Design
• GlycanTreeSet
  • RosettaCarbohydrates
• HBNet
  • HBNet Before Design
• help()
  • Accessing PyRosetta Documentation
• IncludeCurrent
  • Protein Design with a Resfile and FastRelax
• InitializeFromCommandline
  • Packing and Relax
• InterGroupInterfaceByVectorSelector
  • HBNet Before Design
• Jump
  • Docking Moves in Rosetta
• keep_history()
  • High-Resolution Movers
• ketose
  • RosettaCarbohydrates
• label_energy()
  • Energies and the PyMOL Mover
• LoadDensityMapMover
  • Working With Density
• MakeBundle
  • De Novo Parametric Backbone Design
• mannose
  • RosettaCarbohydrates
  • RosettaCarbohydrates: Trees, Selectors and Movers
  • RosettaCarbohydrates: Modeling and Design
• map
  • Working With Density
• membrane
  • Setting up a membrane protein in the bilayer
• Metropolis
  • Basic Folding Algorithm
• MinMover()
  • High-Resolution Movers
• MonteCarlo()
  • High-Resolution Movers
• MoveMap
  • High-Resolution Movers
• MoveMapFactory
  • Packing and Relax
  • Protein Design with a Resfile and FastRelax
• Mover
  • RosettaCarbohydrates: Trees, Selectors and Movers
• mutate_position
  • RNA in PyRosetta
• NeighborhoodResidueSelector
  • Packing and Relax
  • Point Mutation Scan
• nhbonds()
  • Score Function Basics
• NoRepackDisulfides
  • Protein Design with a Resfile and FastRelax
  • Protein Design 2
  • Point Mutation Scan
• NotResidueSelector
  • Protein Design 2
• number()
  • Working with Pose residues
• OCTOPUS
  • Setting up a membrane protein in the bilayer
• OperateOnResidueSubset
  • Protein Design 2
  • HBNet Before Design
  • HBNet Before Design
  • Point Mutation Scan
• OperateOnResidueSubsetOperation
  • Packing and Relax
• output_decoy()
  • Docking Moves in Rosetta
• PackRotamersMover
  • Packing and Relax
  • HBNet Before Design
• Parametric
  • De Novo Parametric Backbone Design
• pdb2pose()
  • Working with Pose residues
  • Practice: Analyzing energy between residues
• phi()
  • Side Chain Conformations and Dunbrack Energies
• Pose()
  • Basic Folding Algorithm
• pose2pdb()
  • Working with Pose residues
• pose_from_pdb()
  • Pose Basics
• pose_from_rcsb
  • Protein Design 2
• pose_from_rcsb()
  • Practice: Analyzing energy between residues
  • Protein Design with a Resfile and FastRelax
• pose_from_sequence()
  • Protein Geometry
  • Basic Folding Algorithm
• prediction
  • RosettaCarbohydrates: Modeling and Design
• PreventRepackingRLT
  • Packing and Relax
  • HBNet Before Design
• psi()
  • Side Chain Conformations and Dunbrack Energies
• PyJobDistributor()
  • Docking Moves in Rosetta
• PyMOLMover
  • Visualization with the PyMOLMover
• pyranose
  • RosettaCarbohydrates
• RAbD
  • Working With Antibodies
• random move
  • Basic Folding Algorithm
• read_fragment_file()
  • Low-Res Scoring and Fragments
• ReadResfile
  • Protein Design with a Resfile and FastRelax
• refinement
  • Working With Density
• RepeatMover()
  • High-Resolution Movers
• Resfile
  • Protein Design with a Resfile and FastRelax
• ResfileCommandOperation
  • Protein Design with a Resfile and FastRelax
• residue_hbonds()
  • Score Function Basics
• residue_total_energies()
  • Side Chain Conformations and Dunbrack Energies
• ResidueNameSelector
  • Protein Design 2
• ResiduePDBInfoHasLabelSelector
  • HBNet Before Design
• ResiduePropertySelector
  • Protein Design 2
• ResidueSelector
  • Packing and Relax
  • Protein Design with a Resfile and FastRelax
  • Protein Design 2
  • Point Mutation Scan
  • RosettaCarbohydrates: Trees, Selectors and Movers
• RestrictAbsentCanonicalAASRLT
  • Protein Design 2
  • Point Mutation Scan
• RestrictToRepacking
  • Packing and Relax
• RestrictToRepackingRLT
  • Protein Design 2
  • HBNet Before Design
  • Point Mutation Scan
• ReturnSidechainMover()
  • Docking Moves in Rosetta
• RigidBodyPerturbMover()
  • Docking Moves in Rosetta
• RigidBodyTransMover
  • Point Mutation Scan
• RNA fragment assembly
  • RNA in PyRosetta
• RNA minimize
  • RNA in PyRosetta
• RNA motifs
  • RNA in PyRosetta
• RNA score terms
  • RNA in PyRosetta
• RNA thread
  • RNA in PyRosetta
• RNA torsions
  • RNA in PyRosetta
• rna_denovo
  • RNA in PyRosetta
• RNA_HelixAssembler
  • RNA in PyRosetta
• RosettaAntibody
  • Working With Antibodies
• RosettaAntibodyDesign
  • Working With Antibodies
• RosettaScripts
  • RosettaScripts in PyRosetta
• saccharide
  • RosettaCarbohydrates
• score function
  • Score Function Basics
• score3
  • Low-Res Scoring and Fragments
• ScoreFunction()
  • Score Function Basics
  • Low-Res Scoring and Fragments
• scoring move
  • Basic Folding Algorithm
• script
  • RosettaScripts in PyRosetta
• send_energy()
  • Energies and the PyMOL Mover
• send_hbonds()
  • Visualization with the PyMOLMover
  • Energies and the PyMOL Mover
• sequence()
  • Pose Basics
• SequenceMetric
  • Packing and Relax
• SequenceMover()
  • High-Resolution Movers
• set_bb()
  • High-Resolution Movers
• set_phi()
  • Protein Geometry
• set_psi()
  • Protein Geometry
• set_weight()
  • Score Function Basics
  • Low-Res Scoring and Fragments
• SetupForSymmetryMover
  • Working With Symmetry
• ShearMover()
  • High-Resolution Movers
• show()
  • Score Function Basics
• SimpleMetric
  • Packing and Relax
• SmallMover()
  • High-Resolution Movers
• sugar
  • RosettaCarbohydrates
  • RosettaCarbohydrates
  • RosettaCarbohydrates: Trees, Selectors and Movers
  • RosettaCarbohydrates: Modeling and Design
• SwitchResidueTypeMover()
  • Docking Moves in Rosetta
• SwitchResidueTypeSetMover()
  • Low-Res Scoring and Fragments
• symmetry
  • Working With Symmetry
• TaskFactory
  • Packing and Relax
  • Protein Design with a Resfile and FastRelax
  • Protein Design 2
  • Point Mutation Scan
• TaskOperation
  • Packing and Relax
  • Protein Design with a Resfile and FastRelax
  • Protein Design 2
  • Point Mutation Scan
• total_residue()
  • Working with Pose residues
• TrialMover()
  • High-Resolution Movers
• virtual
  • Working With Symmetry
• X-ray
  • Working With Density
• xml
  • RosettaScripts in PyRosetta
• XMLObjects
  • RosettaScripts in PyRosetta
• xyz()
  • Protein Geometry
• ZDOCK
  • Fast Fourier Transform Based Docking via ZDOCK