PyRosetta module documentation¶

pyrosetta
- io
- logging_support
- method_bindings
  - pose
- mpi
- teaching
- toolbox
- util

Rosetta module documentation¶

rosetta
- ObjexxFCL
  - Fortran
  - bit
  - format
  - internal
    - ObserverMediator
- basic
- core
  - chemical
    - NucleotideTools
    - carbohydrates
    - element
    - gasteiger
    - mainchain_potential
    - mmCIF
    - orbitals
    - rings
    - rna
    - rotamers
    - sdf
  - conformation
    - RotamerSetCacheableDataType
    - carbohydrates
    - membrane
    - orbitals
    - parametric
    - residue_datacache
    - signals
    - symmetry
  - environment
  - enzymes
  - fragment
    - picking_old
      - concepts
      - vall
        
        eval
        
        gen
        
        scores
  - grid
  - id
  - import_pose
    - atom_tree_diffs
    - pose_stream
  - indexed_structure_store
  - init
  - io
    - PositionDdGInfo
    - carbohydrates
    - external
    - mmcif
    - pdb
    - pose_from_sfr
    - pose_to_sfr
    - raw_data
    - rna
    - sequence_comparation
    - serialization
    - silent
  - kinematics
    - tree
  - membrane
  - optimization
    - symmetry
  - pack
    - annealer
    - dunbrack
      - cenrot
    - interaction_graph
    - rotamer_set
      - symmetry
    - rotamers
    - scmin
    - task
  - pose
    - carbohydrates
    - copydofs
    - datacache
    - full_model_info
    - metrics
      - simple_calculators
    - motif
    - ncbb
    - reference_pose
    - rna
    - signals
    - symmetry
  - scoring
    - EnergiesCacheableDataType
    - aa_composition_energy
    - aa_repeat_energy
    - annealing
    - bin_transitions
    - carbohydrates
    - carbon_hbonds
    - constraints
    - cryst
    - custom_pair_distance
    - disulfides
    - dna
    - dssp
    - elec
      - electrie
    - electron_density
    - electron_density_atomwise
    - etable
      - coulomb
      - count_pair
      - etrie
    - fiber_diffraction
    - func
    - geometric_solvation
    - hackaro
    - hbonds
      - hbtrie
    - interface
    - lkball
      - lkbtrie
    - loop_graph
      - evaluator
    - magnesium
    - membrane
    - methods
      - carbohydrates
      - dfire
    - mm
      - mmtrie
    - motif
    - nv
    - orbitals
    - packing
    - packstat
      - old
    - power_diagram
    - rna
      - chemical_shift
      - data
    - sasa
    - saxs
    - sc
    - solid_surface
    - sym_e
    - symmetry
    - trie
    - vdwaals
  - select
    - jump_selector
    - movemap
    - residue_selector
    - util
  - sequence
  - util
- cppdb
- numeric
  - conversions
  - crick_equations
  - expression_parser
  - fourier
  - geometry
    - hashing
  - histograms
  - interpolation
    - spline
  - kdtree
  - kinematic_closure
    - radians
  - linear_algebra
  - model_quality
  - nls
  - random
  - statistics
- protocols
  - RotamerDump
  - aa_composition
  - abinitio
    - abscript
  - analysis
  - anchored_design
  - antibody
    - clusters
    - constraints
    - design
    - grafting
    - residue_selector
    - snugdock
    - task_operations
  - antibody_legacy
  - backbone_moves
    - local_backbone_mover
      - free_peptide_movers
      - gap_solution_pickers
  - backrub
  - branch_angle
  - canonical_sampling
    - mc_convergence_checks
  - carbohydrates
  - cartesian
  - checkpoint
  - cluster
    - calibur
  - comparative_modeling
    - features
  - constraint_generator
  - constraints_additional
  - contact_map
  - coupled_moves
  - cryst
  - cyclic_peptide
    - crosslinker
  - cyclic_peptide_predict
  - ddG
  - ddg
  - denovo_design
    - architects
    - components
    - connection
    - constraints
    - filters
    - movers
    - residue_selectors
    - task_operations
  - design_opt
  - dna
  - docking
    - membrane
    - stateless
  - domain_assembly
  - electron_density
  - environment
    - claims
  - enzdes
    - enzutil
  - enzymatic_movers
  - evaluation
  - evolution
    - AlignmentCleanerTools
  - features
    - RelevantResiduesMode
    - helixAssembly
    - strand_assembly
  - fibril
  - filters
  - fldsgn
    - filters
    - potentials
      - sspot
    - topology
  - flexpack
    - annealer
    - interaction_graph
    - rotamer_set
  - flexpep_docking
  - floppy_tail
  - flxbb
  - fold_from_loops
  - forge
    - build
      - BuildInstructionState
      - SegmentInsertConnectionScheme
    - components
      - VLB_VallMemoryUsage
    - constraints
    - methods
    - remodel
  - frag_picker
    - nonlocal
    - quota
    - scores
  - frags
  - generalized_kinematic_closure
    - filter
    - perturber
    - selector
  - genetic_algorithm
  - geometry
  - grafting
    - simple_movers
  - hbnet
  - helical_bundle
    - parameters
  - helix_capper
  - hotspot_hashing
    - movers
  - hybridization
  - hydrate
  - idealize
  - indel
  - indexed_structure_store
    - filters
  - init
  - interface
  - jd2
    - JobInputterInputSource
    - archive
  - jobdist
  - jumping
  - kinematic_closure
    - perturbers
    - pivot_pickers
    - solution_pickers
  - kinmatch
  - ligand_docking
    - ligand_options
    - rdf
  - loop_build
  - loop_grower
  - loop_modeler
    - perturbers
  - loop_modeling
    - refiners
    - samplers
    - utilities
  - loophash
  - loops
    - filters
    - loop_closure
      - ccd
      - kinematic_closure
    - loop_mover
      - perturb
      - refine
    - loops_definers
  - magnesium
  - make_rot_lib
  - match
    - downstream
    - output
    - upstream
  - matdes
  - md
  - mean_field
  - medal
  - membrane
    - benchmark
    - geometry
    - symmetry
    - visualize
  - metal_interface
  - motif_grafting
    - movers
  - motifs
  - moves
  - mpi_refinement
  - multistate_design
  - ncbb
    - oop
  - neighbor
  - noesy_assign
  - nonlocal
  - normalmode
  - optimize_weights
  - pack_daemon
  - parser
  - pb_potential
  - peptide_deriver
  - pmut_scan
  - pockets
  - pose_length_moves
  - pose_reporters
  - pose_selectors
  - protein_interface_design
    - filters
    - movers
  - qsar
    - scoring_grid
  - rbsegment_relax
  - recces
    - options
    - params
    - sampler
      - rna
    - scratch
  - relax
    - membrane
  - residue_optimization
  - residue_selectors
  - rigid
  - rna
    - denovo
      - base_pairs
      - coarse
      - fragments
      - libraries
      - movers
      - options
      - output
      - secstruct_legacy
      - setup
    - movers
    - setup
  - rosetta_scripts
  - rotamer_recovery
  - rpc
  - sasa_scores
  - scoring
    - methods
      - pcs
      - pcs2
      - pcsTs1
      - pcsTs2
      - pcsTs3
      - pcsTs4
      - saxs
  - seeded_abinitio
  - sewing
    - sampling
      - requirements
    - scoring
  - sic_dock
    - scores
  - simple_filters
  - simple_moves
    - a3b_hbs
    - asym_fold_and_dock
    - bb_sampler
    - bin_transitions
    - chiral
    - hbs
    - oop
    - rational_mc
    - sidechain_moves
    - symmetry
    - triazolamer
  - sparta
  - ss_prediction
  - star
  - stepwise
    - legacy
      - modeler
        
        protein
        
        rna
      - screener
    - modeler
      - align
      - movemap
      - options
      - packer
      - polar_hydrogens
      - precomputed
      - protein
        
        checker
        
        loop_close
      - rna
        
        bulge
        
        checker
        
        o2prime
        
        phosphate
        
        rigid_body
        
        sugar
      - working_parameters
    - monte_carlo
      - mover
        
        options
      - options
      - rna
      - submotif
    - options
    - sampler
      - copy_dofs
      - input_streams
      - jump
      - protein
      - rigid_body
      - rna
      - screener
    - screener
    - setup
  - struct_fragment
  - surface_docking
  - symmetric_docking
    - membrane
  - toolbox
    - match_enzdes_util
    - pose_manipulation
    - pose_metric_calculators
    - rigid_body
    - rotamer_set_operations
    - sample_around
    - task_operations
  - topology_broker
    - claims
    - weights
  - trajectory
  - ub_e2c
  - unfolded_state_energy_calculator
  - viewer
    - graphics_states_param
  - vip
  - wum
- std
- utility
  - excn
  - factory
  - file
  - graph
  - has_insertion_operator_implementation
  - io
    - mpi_stream
  - json_spirit
  - keys
  - libsvm
  - options
  - py
  - signals
  - sql_database
  - tag
  - tools
  - xsd_util