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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
CCD
Loop Modeling
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
cut-point variant
Loop Modeling
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
fold_tree_from_loops
Loop Modeling
FoldTree
Loop Modeling
furanose
RosettaCarbohydrates
GeneralizedKIC
Using Rosetta Gen KIC
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
KIC
Loop Modeling
label_energy()
Energies and the PyMOL Mover
LoadDensityMapMover
Working With Density
loop modeling
Using Rosetta Gen KIC
loops
Loop Modeling
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
Loop Modeling
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
Visualization with the
PyMOLMover
, PyRosetta ColabPyMOL integration
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
Visualization with the
PyMOLMover
, PyRosetta ColabPyMOL integration
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