Python: module rosetta.protocols.antibody.design

rosetta.protocols.antibody.design

index
(built-in)

Bindings for protocols::antibody::design namespace

Classes



builtins.object

AntibodyDesignEnumManager
AntibodyDesignProtocolEnum
AntibodySeqDesignTFCreator
CDRGraftDesignOptions
CDRGraftDesignOptionsParser
CDRSeqDesignOptions
CDRSeqDesignOptionsParser
GeneralAntibodyModeler
MinTypeEnum
MutantPosition
PDBNumbering
SeqDesignStrategyEnum

rosetta.basic.datacache.CacheableData(builtins.object)

NativeAntibodySeq

rosetta.protocols.moves.Mover(builtins.object)

AntibodyDesignMover
AntibodyDesignProtocol
MutateFrameworkForCluster

rosetta.protocols.moves.MoverCreator(builtins.object)

AntibodyDesignMoverCreator
AntibodyDesignProtocolCreator
MutateFrameworkForClusterCreator

class AntibodyDesignEnumManager(builtins.object)

    Methods defined here:

__init__(...) from builtins.PyCapsule
__init__(rosetta.protocols.antibody.design.AntibodyDesignEnumManager) -> NoneType

__new__(*args, **kwargs) from builtins.type
Create and return a new object.  See help(type) for accurate signature.

assign(...) from builtins.PyCapsule
assign(self : rosetta.protocols.antibody.design.AntibodyDesignEnumManager,  : rosetta.protocols.antibody.design.AntibodyDesignEnumManager) -> rosetta.protocols.antibody.design.AntibodyDesignEnumManager

design_protocol_enum_to_string(...) from builtins.PyCapsule
design_protocol_enum_to_string(self : rosetta.protocols.antibody.design.AntibodyDesignEnumManager, design_protocol : rosetta.protocols.antibody.design.AntibodyDesignProtocolEnum) -> str

design_protocol_is_present(...) from builtins.PyCapsule
design_protocol_is_present(self : rosetta.protocols.antibody.design.AntibodyDesignEnumManager, design_protocol : str) -> bool

design_protocol_string_to_enum(...) from builtins.PyCapsule
design_protocol_string_to_enum(self : rosetta.protocols.antibody.design.AntibodyDesignEnumManager, design_protocol : str) -> rosetta.protocols.antibody.design.AntibodyDesignProtocolEnum /////////////// Design Protocol ///////////////////////////////////////////////

min_type_enum_to_string(...) from builtins.PyCapsule
min_type_enum_to_string(self : rosetta.protocols.antibody.design.AntibodyDesignEnumManager, min_type : rosetta.protocols.antibody.design.MinTypeEnum) -> str

min_type_is_present(...) from builtins.PyCapsule
min_type_is_present(self : rosetta.protocols.antibody.design.AntibodyDesignEnumManager, min_type : str) -> bool

min_type_string_to_enum(...) from builtins.PyCapsule
min_type_string_to_enum(self : rosetta.protocols.antibody.design.AntibodyDesignEnumManager, min_type : str) -> rosetta.protocols.antibody.design.MinTypeEnum /////////////// MinType ///////////////////////////////////////////////

seq_design_strategy_enum_to_string(...) from builtins.PyCapsule
seq_design_strategy_enum_to_string(self : rosetta.protocols.antibody.design.AntibodyDesignEnumManager, seq_design_strategy : rosetta.protocols.antibody.design.SeqDesignStrategyEnum) -> str

seq_design_strategy_is_present(...) from builtins.PyCapsule
seq_design_strategy_is_present(self : rosetta.protocols.antibody.design.AntibodyDesignEnumManager, seq_design_strategy : str) -> bool

seq_design_strategy_string_to_enum(...) from builtins.PyCapsule
seq_design_strategy_string_to_enum(self : rosetta.protocols.antibody.design.AntibodyDesignEnumManager, seq_design_strategy : str) -> rosetta.protocols.antibody.design.SeqDesignStrategyEnum /////////////// SeqDesignStrategy ///////////////////////////////////////////////

class AntibodyDesignMover(rosetta.protocols.moves.Mover)

    This class designs antibodies by grafting, using cluster information and constraints to help. It represents the first step in The Rosetta Antibody Designer, but can be used outside of the application. A 2011 Antibody Database is included in the rosetta datase.  Up-to-date versions can be downloaded from To use this class: 1) Use default instruction path, or set one.  Loads CDRs from AntibodyDatabase     *See rosetta_database/sampling/antibodies for file format. 2) Use class interface settings to control sampling.  Loads CDRs from AntibodyDatabase. 3) Use set_cdr_sets to set your own CDRs to graft.

Method resolution order:

AntibodyDesignMover

rosetta.protocols.moves.Mover

builtins.object

Methods defined here:

__init__(...) from builtins.PyCapsule
__init__(*args, **kwargs) Overloaded function. 1. __init__(handle) -> NoneType 2. __init__(self : handle, ab_info : rosetta.protocols.antibody.AntibodyInfo) -> NoneType 3. __init__(handle, rosetta.protocols.antibody.design.AntibodyDesignMover) -> NoneType

__new__(*args, **kwargs) from builtins.type
Create and return a new object.  See help(type) for accurate signature.

apply(...) from builtins.PyCapsule
apply(self : rosetta.protocols.antibody.design.AntibodyDesignMover, pose : rosetta.core.pose.Pose) -> NoneType

assign(...) from builtins.PyCapsule
assign(self : rosetta.protocols.antibody.design.AntibodyDesignMover,  : rosetta.protocols.antibody.design.AntibodyDesignMover) -> rosetta.protocols.antibody.design.AntibodyDesignMover

clone(...) from builtins.PyCapsule
clone(rosetta.protocols.antibody.design.AntibodyDesignMover) -> rosetta.protocols.moves.Mover

fresh_instance(...) from builtins.PyCapsule
fresh_instance(rosetta.protocols.antibody.design.AntibodyDesignMover) -> rosetta.protocols.moves.Mover

get_name(...) from builtins.PyCapsule
get_name(rosetta.protocols.antibody.design.AntibodyDesignMover) -> str

get_top_designs(...) from builtins.PyCapsule
get_top_designs(rosetta.protocols.antibody.design.AntibodyDesignMover) -> rosetta.utility.vector1_std_shared_ptr_core_pose_Pose_t Get the top designs found.  You can then use them in other protocols, dump them, etc. They are in order. - This should be refactored to get_additional_output.

set_cdr_override(...) from builtins.PyCapsule
set_cdr_override(self : rosetta.protocols.antibody.design.AntibodyDesignMover, cdrs_to_design : rosetta.utility.vector1_protocols_antibody_CDRNameEnum) -> NoneType Graft and Sequence design these CDRs.  Overrides all options settings.

set_cdr_set_options(...) from builtins.PyCapsule
set_cdr_set_options(self : rosetta.protocols.antibody.design.AntibodyDesignMover, cdr_set_options : rosetta.utility.vector1_std_shared_ptr_protocols_antibody_CDRSetOptions_t) -> NoneType Set the options which will be used for querying the database

set_defaults(...) from builtins.PyCapsule
set_defaults(rosetta.protocols.antibody.design.AntibodyDesignMover) -> NoneType Reads default CDRGraftInstruction file and creates structs.

set_design_protocol(...) from builtins.PyCapsule
set_design_protocol(self : rosetta.protocols.antibody.design.AntibodyDesignMover, design_protocol : rosetta.protocols.antibody.design.AntibodyDesignProtocolEnum) -> NoneType Set the design protocol.  Default is classic_monte_carlo. Available options are: generalized_monte_carlo, deterministc_graft. . Deterministic Protocol only available if GraftDesigning a single CDR.

set_dock_post_graft(...) from builtins.PyCapsule
set_dock_post_graft(self : rosetta.protocols.antibody.design.AntibodyDesignMover, dock_post_graft : bool) -> NoneType Set the algorithm to run a low-resolution docking step after each graft.  Default false. Uses command-line options for docking.  Lower inner or outer cycles if you are grafting many CDRs.  Still quicker then relax.

set_dock_rounds(...) from builtins.PyCapsule
set_dock_rounds(self : rosetta.protocols.antibody.design.AntibodyDesignMover, dock_rounds : int) -> NoneType

set_epitope_residues(...) from builtins.PyCapsule
set_epitope_residues(self : rosetta.protocols.antibody.design.AntibodyDesignMover, epitope_residues : rosetta.utility.vector1_protocols_antibody_design_PDBNumbering) -> NoneType Set any epitope residues in PDB numbering.  If not set, they will be detected automatically via the interface.

set_graft_design_options(...) from builtins.PyCapsule
set_graft_design_options(self : rosetta.protocols.antibody.design.AntibodyDesignMover, graft_design_options : rosetta.utility.vector1_std_shared_ptr_protocols_antibody_design_CDRGraftDesignOptions_t) -> NoneType Set CDR-specific GraftDesign options

set_inner_cycles(...) from builtins.PyCapsule
set_inner_cycles(self : rosetta.protocols.antibody.design.AntibodyDesignMover, inner_cycles : int) -> NoneType Set the number of inner cycles, which optimizes the structure and sequence of the antibody after any graft. Essentially min cycles.  Recommend 3 cycles if not doing relax as the mintype.

set_instruction_file(...) from builtins.PyCapsule
set_instruction_file(self : rosetta.protocols.antibody.design.AntibodyDesignMover, instruction_file : str) -> NoneType Set the instruction file path to load options from instead of setting these via associated options functions Or loading via cmd-line option.  Gotta love supporting 3 different Rosetta interfaces.

set_interface_dis(...) from builtins.PyCapsule
set_interface_dis(self : rosetta.protocols.antibody.design.AntibodyDesignMover, interface_dis : float) -> NoneType

set_keep_top_designs(...) from builtins.PyCapsule
set_keep_top_designs(self : rosetta.protocols.antibody.design.AntibodyDesignMover, top_designs : int) -> NoneType Sets the protocol to keep a specific number of top designs.  Default is 10

set_neighbor_dis(...) from builtins.PyCapsule
set_neighbor_dis(self : rosetta.protocols.antibody.design.AntibodyDesignMover, neighbor_dis : float) -> NoneType

set_outer_cycles(...) from builtins.PyCapsule
set_outer_cycles(self : rosetta.protocols.antibody.design.AntibodyDesignMover, outer_cycles : int) -> NoneType Set the number of overall rounds.  Each round will choose a CDR and design it and others based on options

set_paratope_cdrs(...) from builtins.PyCapsule
set_paratope_cdrs(self : rosetta.protocols.antibody.design.AntibodyDesignMover, cdrs : rosetta.utility.vector1_bool) -> NoneType Set any paratope CDRs.  If not set, will use all CDRs as the paratope where needed. Used mainly for constraints

set_rb_min_post_graft(...) from builtins.PyCapsule
set_rb_min_post_graft(self : rosetta.protocols.antibody.design.AntibodyDesignMover, rb_min_post_graft : bool) -> NoneType Set the algorithm to run a final rigid-body minimization of antigen/antibody interface post graft.  Useful if not docking - quicker, but less reliable then full dock.

set_scorefunction(...) from builtins.PyCapsule
set_scorefunction(self : rosetta.protocols.antibody.design.AntibodyDesignMover, scorefxn : rosetta.core.scoring.ScoreFunction) -> NoneType /////////////////////////////////////////////////////////////////////////

set_scorefunction_min(...) from builtins.PyCapsule
set_scorefunction_min(self : rosetta.protocols.antibody.design.AntibodyDesignMover, min_scorefxn : rosetta.core.scoring.ScoreFunction) -> NoneType

set_seq_design_options(...) from builtins.PyCapsule
set_seq_design_options(self : rosetta.protocols.antibody.design.AntibodyDesignMover, seq_design_options : rosetta.utility.vector1_std_shared_ptr_protocols_antibody_design_CDRSeqDesignOptions_t) -> NoneType Set CDR-specific SeqDesign options

set_use_epitope_constraints(...) from builtins.PyCapsule
set_use_epitope_constraints(self : rosetta.protocols.antibody.design.AntibodyDesignMover, use_epitope_csts : bool) -> NoneType Setting to use epitope constraints.  Without this false, will not use any set epitope residues.

Methods inherited from rosetta.protocols.moves.Mover:

clear_info(...) from builtins.PyCapsule
clear_info(rosetta.protocols.moves.Mover) -> NoneType Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file. clear_info is called by jd2 before calling apply

create(...) from builtins.PyCapsule
create(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover

get_additional_output(...) from builtins.PyCapsule
get_additional_output(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose fpd Mechanism by which a mover may return multiple output poses from a single input pose.

get_current_job(...) from builtins.PyCapsule
get_current_job(rosetta.protocols.moves.Mover) -> protocols::jobdist::BasicJob

get_current_tag(...) from builtins.PyCapsule
get_current_tag(rosetta.protocols.moves.Mover) -> str A tag is a unique identifier used to identify structures produced by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag.  This functionality is not intended for use with the 2008 job distributor.

get_input_pose(...) from builtins.PyCapsule
get_input_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose

get_last_move_status(...) from builtins.PyCapsule
get_last_move_status(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.MoverStatus returns status after an apply().  The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say "that run was no good, skip it" then use the protected last_move_status(MoverStatus) to change the value that this function will return.

get_native_pose(...) from builtins.PyCapsule
get_native_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose

get_self_ptr(...) from builtins.PyCapsule
get_self_ptr(*args, **kwargs) Overloaded function. 1. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover 2. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover

get_self_weak_ptr(...) from builtins.PyCapsule
get_self_weak_ptr(*args, **kwargs) Overloaded function. 1. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_const_protocols_moves_Mover_t 2. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_protocols_moves_Mover_t

get_type(...) from builtins.PyCapsule
get_type(rosetta.protocols.moves.Mover) -> str

info(...) from builtins.PyCapsule
info(*args, **kwargs) Overloaded function. 1. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t non-const accessor 2. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t const accessor

last_proposal_density_ratio(...) from builtins.PyCapsule
last_proposal_density_ratio(rosetta.protocols.moves.Mover) -> float

name(...) from builtins.PyCapsule
name() -> str

register_options(...) from builtins.PyCapsule
register_options(*args, **kwargs) Overloaded function. 1. register_options() -> NoneType Overload this static method if you access options within the mover. These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method. 2. register_options() -> NoneType 3. register_options() -> NoneType 4. register_options() -> NoneType 5. register_options() -> NoneType 6. register_options() -> NoneType 7. register_options() -> NoneType 8. register_options() -> NoneType 9. register_options() -> NoneType Associates relevant options with the AntibodyModeler class 10. register_options() -> NoneType Associates relevant options with the AntibodyModeler class 11. register_options() -> NoneType Associates relevant options with the SnugDock class 12. register_options() -> NoneType Associates relevant options with the SnugDockProtocol class 13. register_options() -> NoneType Register the options used by this mover with the global options system. 14. register_options() -> NoneType 15. register_options() -> NoneType Associate relevant options with the TemperedDocking class. 16. register_options() -> NoneType 17. register_options() -> NoneType 18. register_options() -> NoneType Associates relevant options with the TemperedDocking class. 19. register_options() -> NoneType 20. register_options() -> NoneType Associates relevant options with the ConstraintSetMover class 21. register_options() -> NoneType 22. register_options() -> NoneType Associates relevant options with the DockingInitialPerturbation class 23. register_options() -> NoneType Associates relevant options with the DockingProtocol class 24. register_options() -> NoneType Associates relevant options with the TemperedDocking class 25. register_options() -> NoneType 26. register_options() -> NoneType 27. register_options() -> NoneType 28. register_options() -> NoneType register options 29. register_options() -> NoneType 30. register_options() -> NoneType Registers applicable options 31. register_options() -> NoneType Register options with the option system. 32. register_options() -> NoneType 33. register_options() -> NoneType 34. register_options() -> NoneType Associates relevant options with the LoopRefineInnerCycle class 35. register_options() -> NoneType Associates relevant options with the LoopRefineInnerCycleContainer class 36. register_options() -> NoneType Associates relevant options with the LoopRefineInnerCycle class 37. register_options() -> NoneType Associates relevant options with the LoopRefineInnerCycle class 38. register_options() -> NoneType 39. register_options() -> NoneType Register options with the option system. 40. register_options() -> NoneType

reinitialize_for_each_job(...) from builtins.PyCapsule
reinitialize_for_each_job(rosetta.protocols.moves.Mover) -> bool Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on each use.

reinitialize_for_new_input(...) from builtins.PyCapsule
reinitialize_for_new_input(rosetta.protocols.moves.Mover) -> bool Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

reset_status(...) from builtins.PyCapsule
reset_status(rosetta.protocols.moves.Mover) -> NoneType resets status to SUCCESS, meant to be used before an apply().  The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

set_current_job(...) from builtins.PyCapsule
set_current_job(self : rosetta.protocols.moves.Mover, job : protocols::jobdist::BasicJob) -> NoneType ////////////////////////////end Job Distributor interface////////////////////////////////////////

set_current_tag(...) from builtins.PyCapsule
set_current_tag(self : rosetta.protocols.moves.Mover, new_tag : str) -> NoneType

set_input_pose(...) from builtins.PyCapsule
set_input_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType setter for poses contained for rms

set_native_pose(...) from builtins.PyCapsule
set_native_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType setter for native poses contained for rms ---- we should get rid of this method? it is widely used, but a bit unsafe

set_type(...) from builtins.PyCapsule
set_type(self : rosetta.protocols.moves.Mover, setting : str) -> NoneType

test_move(...) from builtins.PyCapsule
test_move(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType : Unit test support function.  Apply one move to a given pose.       Allows extra test specific functions to be called before applying

type(...) from builtins.PyCapsule
type(*args, **kwargs) Overloaded function. 1. type(rosetta.protocols.moves.Mover) -> str 2. type(self : rosetta.protocols.moves.Mover, type_in : str) -> NoneType

class AntibodyDesignMoverCreator(rosetta.protocols.moves.MoverCreator)


Method resolution order:

AntibodyDesignMoverCreator

rosetta.protocols.moves.MoverCreator

builtins.object

Methods defined here:

__init__(...) from builtins.PyCapsule
__init__(handle) -> NoneType

__new__(*args, **kwargs) from builtins.type
Create and return a new object.  See help(type) for accurate signature.

assign(...) from builtins.PyCapsule
assign(self : rosetta.protocols.antibody.design.AntibodyDesignMoverCreator,  : rosetta.protocols.antibody.design.AntibodyDesignMoverCreator) -> rosetta.protocols.antibody.design.AntibodyDesignMoverCreator

create_mover(...) from builtins.PyCapsule
create_mover(rosetta.protocols.antibody.design.AntibodyDesignMoverCreator) -> rosetta.protocols.moves.Mover

keyname(...) from builtins.PyCapsule
keyname(rosetta.protocols.antibody.design.AntibodyDesignMoverCreator) -> str

mover_name(...) from builtins.PyCapsule
mover_name() -> str

class AntibodyDesignProtocol(rosetta.protocols.moves.Mover)

    Main AntibodyDesignProtocol, tieing together individual movers and classes.  Main mover for application.

Method resolution order:

AntibodyDesignProtocol

rosetta.protocols.moves.Mover

builtins.object

Methods defined here:

__init__(...) from builtins.PyCapsule
__init__(*args, **kwargs) Overloaded function. 1. __init__(handle) -> NoneType 2. __init__(handle, rosetta.protocols.antibody.design.AntibodyDesignProtocol) -> NoneType

__new__(*args, **kwargs) from builtins.type
Create and return a new object.  See help(type) for accurate signature.

apply(...) from builtins.PyCapsule
apply(self : rosetta.protocols.antibody.design.AntibodyDesignProtocol, pose : rosetta.core.pose.Pose) -> NoneType /////////////////////////////////////////////////////////////////////////

assign(...) from builtins.PyCapsule
assign(self : rosetta.protocols.antibody.design.AntibodyDesignProtocol,  : rosetta.protocols.antibody.design.AntibodyDesignProtocol) -> rosetta.protocols.antibody.design.AntibodyDesignProtocol

clone(...) from builtins.PyCapsule
clone(rosetta.protocols.antibody.design.AntibodyDesignProtocol) -> rosetta.protocols.moves.Mover

fresh_instance(...) from builtins.PyCapsule
fresh_instance(rosetta.protocols.antibody.design.AntibodyDesignProtocol) -> rosetta.protocols.moves.Mover

get_name(...) from builtins.PyCapsule
get_name(rosetta.protocols.antibody.design.AntibodyDesignProtocol) -> str

set_instruction_file_path(...) from builtins.PyCapsule
set_instruction_file_path(self : rosetta.protocols.antibody.design.AntibodyDesignProtocol, instruction_file : str) -> NoneType Set the instruction file path instead of reading it from the cmd-line options.

set_run_relax(...) from builtins.PyCapsule
set_run_relax(self : rosetta.protocols.antibody.design.AntibodyDesignProtocol, setting : bool) -> NoneType Run Dualspace Relax after main design runs

set_run_snugdock(...) from builtins.PyCapsule
set_run_snugdock(self : rosetta.protocols.antibody.design.AntibodyDesignProtocol, setting : bool) -> NoneType Run SnugDock after main design runs

set_scorefxn(...) from builtins.PyCapsule
set_scorefxn(self : rosetta.protocols.antibody.design.AntibodyDesignProtocol, scorefxn : rosetta.core.scoring.ScoreFunction) -> NoneType Set the global scorefunction.  Used for snugdock/relax/total energy/etc. Not Used for Docking within the protocol.

set_scorefxn_min(...) from builtins.PyCapsule
set_scorefxn_min(self : rosetta.protocols.antibody.design.AntibodyDesignProtocol, scorefxn : rosetta.core.scoring.ScoreFunction) -> NoneType Set the min scorefunction used by the AntibodyDesignMover during the Minimization step. Should include dihedral_constraint weights if using default CDR constraints added during the protocol.

Methods inherited from rosetta.protocols.moves.Mover:

clear_info(...) from builtins.PyCapsule
clear_info(rosetta.protocols.moves.Mover) -> NoneType Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file. clear_info is called by jd2 before calling apply

create(...) from builtins.PyCapsule
create(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover

get_additional_output(...) from builtins.PyCapsule
get_additional_output(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose fpd Mechanism by which a mover may return multiple output poses from a single input pose.

get_current_job(...) from builtins.PyCapsule
get_current_job(rosetta.protocols.moves.Mover) -> protocols::jobdist::BasicJob

get_current_tag(...) from builtins.PyCapsule
get_current_tag(rosetta.protocols.moves.Mover) -> str A tag is a unique identifier used to identify structures produced by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag.  This functionality is not intended for use with the 2008 job distributor.

get_input_pose(...) from builtins.PyCapsule
get_input_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose

get_last_move_status(...) from builtins.PyCapsule
get_last_move_status(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.MoverStatus returns status after an apply().  The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say "that run was no good, skip it" then use the protected last_move_status(MoverStatus) to change the value that this function will return.

get_native_pose(...) from builtins.PyCapsule
get_native_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose

get_self_ptr(...) from builtins.PyCapsule
get_self_ptr(*args, **kwargs) Overloaded function. 1. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover 2. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover

get_self_weak_ptr(...) from builtins.PyCapsule
get_self_weak_ptr(*args, **kwargs) Overloaded function. 1. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_const_protocols_moves_Mover_t 2. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_protocols_moves_Mover_t

get_type(...) from builtins.PyCapsule
get_type(rosetta.protocols.moves.Mover) -> str

info(...) from builtins.PyCapsule
info(*args, **kwargs) Overloaded function. 1. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t non-const accessor 2. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t const accessor

last_proposal_density_ratio(...) from builtins.PyCapsule
last_proposal_density_ratio(rosetta.protocols.moves.Mover) -> float

name(...) from builtins.PyCapsule
name() -> str

register_options(...) from builtins.PyCapsule
register_options(*args, **kwargs) Overloaded function. 1. register_options() -> NoneType Overload this static method if you access options within the mover. These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method. 2. register_options() -> NoneType 3. register_options() -> NoneType 4. register_options() -> NoneType 5. register_options() -> NoneType 6. register_options() -> NoneType 7. register_options() -> NoneType 8. register_options() -> NoneType 9. register_options() -> NoneType Associates relevant options with the AntibodyModeler class 10. register_options() -> NoneType Associates relevant options with the AntibodyModeler class 11. register_options() -> NoneType Associates relevant options with the SnugDock class 12. register_options() -> NoneType Associates relevant options with the SnugDockProtocol class 13. register_options() -> NoneType Register the options used by this mover with the global options system. 14. register_options() -> NoneType 15. register_options() -> NoneType Associate relevant options with the TemperedDocking class. 16. register_options() -> NoneType 17. register_options() -> NoneType 18. register_options() -> NoneType Associates relevant options with the TemperedDocking class. 19. register_options() -> NoneType 20. register_options() -> NoneType Associates relevant options with the ConstraintSetMover class 21. register_options() -> NoneType 22. register_options() -> NoneType Associates relevant options with the DockingInitialPerturbation class 23. register_options() -> NoneType Associates relevant options with the DockingProtocol class 24. register_options() -> NoneType Associates relevant options with the TemperedDocking class 25. register_options() -> NoneType 26. register_options() -> NoneType 27. register_options() -> NoneType 28. register_options() -> NoneType register options 29. register_options() -> NoneType 30. register_options() -> NoneType Registers applicable options 31. register_options() -> NoneType Register options with the option system. 32. register_options() -> NoneType 33. register_options() -> NoneType 34. register_options() -> NoneType Associates relevant options with the LoopRefineInnerCycle class 35. register_options() -> NoneType Associates relevant options with the LoopRefineInnerCycleContainer class 36. register_options() -> NoneType Associates relevant options with the LoopRefineInnerCycle class 37. register_options() -> NoneType Associates relevant options with the LoopRefineInnerCycle class 38. register_options() -> NoneType 39. register_options() -> NoneType Register options with the option system. 40. register_options() -> NoneType

reinitialize_for_each_job(...) from builtins.PyCapsule
reinitialize_for_each_job(rosetta.protocols.moves.Mover) -> bool Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on each use.

reinitialize_for_new_input(...) from builtins.PyCapsule
reinitialize_for_new_input(rosetta.protocols.moves.Mover) -> bool Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

reset_status(...) from builtins.PyCapsule
reset_status(rosetta.protocols.moves.Mover) -> NoneType resets status to SUCCESS, meant to be used before an apply().  The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

set_current_job(...) from builtins.PyCapsule
set_current_job(self : rosetta.protocols.moves.Mover, job : protocols::jobdist::BasicJob) -> NoneType ////////////////////////////end Job Distributor interface////////////////////////////////////////

set_current_tag(...) from builtins.PyCapsule
set_current_tag(self : rosetta.protocols.moves.Mover, new_tag : str) -> NoneType

set_input_pose(...) from builtins.PyCapsule
set_input_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType setter for poses contained for rms

set_native_pose(...) from builtins.PyCapsule
set_native_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType setter for native poses contained for rms ---- we should get rid of this method? it is widely used, but a bit unsafe

set_type(...) from builtins.PyCapsule
set_type(self : rosetta.protocols.moves.Mover, setting : str) -> NoneType

test_move(...) from builtins.PyCapsule
test_move(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType : Unit test support function.  Apply one move to a given pose.       Allows extra test specific functions to be called before applying

type(...) from builtins.PyCapsule
type(*args, **kwargs) Overloaded function. 1. type(rosetta.protocols.moves.Mover) -> str 2. type(self : rosetta.protocols.moves.Mover, type_in : str) -> NoneType

class AntibodyDesignProtocolCreator(rosetta.protocols.moves.MoverCreator)


Method resolution order:

AntibodyDesignProtocolCreator

rosetta.protocols.moves.MoverCreator

builtins.object

Methods defined here:

__init__(...) from builtins.PyCapsule
__init__(handle) -> NoneType

__new__(*args, **kwargs) from builtins.type
Create and return a new object.  See help(type) for accurate signature.

assign(...) from builtins.PyCapsule
assign(self : rosetta.protocols.antibody.design.AntibodyDesignProtocolCreator,  : rosetta.protocols.antibody.design.AntibodyDesignProtocolCreator) -> rosetta.protocols.antibody.design.AntibodyDesignProtocolCreator

create_mover(...) from builtins.PyCapsule
create_mover(rosetta.protocols.antibody.design.AntibodyDesignProtocolCreator) -> rosetta.protocols.moves.Mover

keyname(...) from builtins.PyCapsule
keyname(rosetta.protocols.antibody.design.AntibodyDesignProtocolCreator) -> str

mover_name(...) from builtins.PyCapsule
mover_name() -> str

class AntibodyDesignProtocolEnum(builtins.object)

    Methods defined here:

__eq__(...) from builtins.PyCapsule
__eq__(rosetta.protocols.antibody.design.AntibodyDesignProtocolEnum, rosetta.protocols.antibody.design.AntibodyDesignProtocolEnum) -> bool

__hash__(...) from builtins.PyCapsule
__hash__(rosetta.protocols.antibody.design.AntibodyDesignProtocolEnum) -> int

__init__(...) from builtins.PyCapsule
__init__(*args, **kwargs) Overloaded function. 1. __init__(rosetta.protocols.antibody.design.AntibodyDesignProtocolEnum, int) -> NoneType 2. __init__(rosetta.protocols.antibody.design.AntibodyDesignProtocolEnum, int) -> NoneType

__int__(...) from builtins.PyCapsule
__int__(rosetta.protocols.antibody.design.AntibodyDesignProtocolEnum) -> int

__ne__(...) from builtins.PyCapsule
__ne__(rosetta.protocols.antibody.design.AntibodyDesignProtocolEnum, rosetta.protocols.antibody.design.AntibodyDesignProtocolEnum) -> bool

__new__(*args, **kwargs) from builtins.type
Create and return a new object.  See help(type) for accurate signature.

__repr__(...) from builtins.PyCapsule
__repr__(rosetta.protocols.antibody.design.AntibodyDesignProtocolEnum) -> str

Data and other attributes defined here:

DesignProtocolEnum_total = AntibodyDesignProtocolEnum.DesignProtocolEnum_total

deterministic_graft = AntibodyDesignProtocolEnum.DesignProtocolEnum_total

even_cluster_monte_carlo = AntibodyDesignProtocolEnum.even_cluster_monte_carlo

even_length_cluster_monte_carlo = AntibodyDesignProtocolEnum.even_length_cluster_monte_carlo

generalized_monte_carlo = AntibodyDesignProtocolEnum.generalized_monte_carlo

class AntibodySeqDesignTFCreator(builtins.object)

    Create a TaskFactory or individual TaskOperations based on a set of options These options are mainly for per-CDR and per-framework control of sequence design

Methods defined here:

__init__(...) from builtins.PyCapsule
__init__(*args, **kwargs) Overloaded function. 1. __init__(rosetta.protocols.antibody.design.AntibodySeqDesignTFCreator, rosetta.protocols.antibody.AntibodyInfo) -> NoneType doc 2. __init__(self : rosetta.protocols.antibody.design.AntibodySeqDesignTFCreator, ab_info : rosetta.protocols.antibody.AntibodyInfo, force_north_paper_db : bool) -> NoneType 3. __init__(rosetta.protocols.antibody.design.AntibodySeqDesignTFCreator, rosetta.protocols.antibody.AntibodyInfo, rosetta.utility.vector1_std_shared_ptr_protocols_antibody_design_CDRSeqDesignOptions_t) -> NoneType doc 4. __init__(rosetta.protocols.antibody.design.AntibodySeqDesignTFCreator, rosetta.protocols.antibody.AntibodyInfo, rosetta.utility.vector1_std_shared_ptr_protocols_antibody_design_CDRSeqDesignOptions_t, bool) -> NoneType doc 5. __init__(self : rosetta.protocols.antibody.design.AntibodySeqDesignTFCreator, ab_info : rosetta.protocols.antibody.AntibodyInfo, design_options : rosetta.utility.vector1_std_shared_ptr_protocols_antibody_design_CDRSeqDesignOptions_t, force_north_paper_db : bool, stem_size : int) -> NoneType

__new__(*args, **kwargs) from builtins.type
Create and return a new object.  See help(type) for accurate signature.

assign(...) from builtins.PyCapsule
assign(self : rosetta.protocols.antibody.design.AntibodySeqDesignTFCreator,  : rosetta.protocols.antibody.design.AntibodySeqDesignTFCreator) -> rosetta.protocols.antibody.design.AntibodySeqDesignTFCreator

design_antigen(...) from builtins.PyCapsule
design_antigen(self : rosetta.protocols.antibody.design.AntibodySeqDesignTFCreator, antigen_design : bool) -> NoneType Normally, we do not want to design the antigen residues - but perhaps someday we will. If False, turn design off for the antigen for any TF creation.

design_framework(...) from builtins.PyCapsule
design_framework(self : rosetta.protocols.antibody.design.AntibodySeqDesignTFCreator, framework_design : bool) -> NoneType Design any framework residues included in the task. Default True. If False, turn design off for the framework for any TF creation.

design_proline(...) from builtins.PyCapsule
design_proline(self : rosetta.protocols.antibody.design.AntibodySeqDesignTFCreator, setting : bool) -> NoneType Keep proline fixed for design. If using profile design, this should not really come into play.

disable_design_for_non_designing_cdrs(...) from builtins.PyCapsule
disable_design_for_non_designing_cdrs(self : rosetta.protocols.antibody.design.AntibodySeqDesignTFCreator, tf : rosetta.core.pack.task.TaskFactory, pose : rosetta.core.pose.Pose) -> NoneType Turns off CDRs for design that are set to off.

disable_proline_design(...) from builtins.PyCapsule
disable_proline_design(self : rosetta.protocols.antibody.design.AntibodySeqDesignTFCreator, tf : rosetta.core.pack.task.TaskFactory, pose : rosetta.core.pose.Pose) -> NoneType

generate_task_op_all_cdr_design(...) from builtins.PyCapsule
generate_task_op_all_cdr_design(*args, **kwargs) Overloaded function. 1. generate_task_op_all_cdr_design(self : rosetta.protocols.antibody.design.AntibodySeqDesignTFCreator, pose : rosetta.core.pose.Pose) -> rosetta.protocols.toolbox.task_operations.RestrictToLoopsAndNeighbors Create a TaskOp to limit Packing and Design to CDR loops and neighbors. 2. generate_task_op_all_cdr_design(self : rosetta.protocols.antibody.design.AntibodySeqDesignTFCreator, pose : rosetta.core.pose.Pose, design_neighbors : bool) -> rosetta.protocols.toolbox.task_operations.RestrictToLoopsAndNeighbors Create a TaskOp to limit Packing and Design to CDR loops and neighbors.

generate_task_op_cdr_design(...) from builtins.PyCapsule
generate_task_op_cdr_design(*args, **kwargs) Overloaded function. 1. generate_task_op_cdr_design(self : rosetta.protocols.antibody.design.AntibodySeqDesignTFCreator, pose : rosetta.core.pose.Pose) -> rosetta.protocols.toolbox.task_operations.RestrictToLoopsAndNeighbors Create a TaskOp to limit Packing and Design to only CDR loops with design on.  Use neighbor distance. 2. generate_task_op_cdr_design(self : rosetta.protocols.antibody.design.AntibodySeqDesignTFCreator, pose : rosetta.core.pose.Pose, design_neighbors : bool) -> rosetta.protocols.toolbox.task_operations.RestrictToLoopsAndNeighbors Create a TaskOp to limit Packing and Design to only CDR loops with design on.  Use neighbor distance. 3. generate_task_op_cdr_design(self : rosetta.protocols.antibody.design.AntibodySeqDesignTFCreator, pose : rosetta.core.pose.Pose, cdrs : rosetta.utility.vector1_bool) -> rosetta.protocols.toolbox.task_operations.RestrictToLoopsAndNeighbors Create a TaskOp for only CDR loops set to True in the boolean vector. 4. generate_task_op_cdr_design(self : rosetta.protocols.antibody.design.AntibodySeqDesignTFCreator, pose : rosetta.core.pose.Pose, cdrs : rosetta.utility.vector1_bool, design_neighbors : bool) -> rosetta.protocols.toolbox.task_operations.RestrictToLoopsAndNeighbors Create a TaskOp for only CDR loops set to True in the boolean vector.

generate_task_op_cdr_profiles(...) from builtins.PyCapsule
generate_task_op_cdr_profiles(self : rosetta.protocols.antibody.design.AntibodySeqDesignTFCreator, pose : rosetta.core.pose.Pose) -> protocols::antibody::task_operations::AddCDRProfilesOperation Setup the CDRProfilesOperation and conservative/basic design   according to primary and fallback strategies and which CDRs are set to design.   Pre-load the data

generate_tf_seq_design(...) from builtins.PyCapsule
generate_tf_seq_design(*args, **kwargs) Overloaded function. 1. generate_tf_seq_design(self : rosetta.protocols.antibody.design.AntibodySeqDesignTFCreator, pose : rosetta.core.pose.Pose) -> rosetta.core.pack.task.TaskFactory Create the FULL TaskFactory for antibody sequence design. There are no limits to repacking or design - AKA NO RestrictToLoops. Optionally disable framework residues for design Optionally disable antigen residues for design. Optionally disable framework conservative residues -> Combine with other Tasks for general design requirements. 2. generate_tf_seq_design(self : rosetta.protocols.antibody.design.AntibodySeqDesignTFCreator, pose : rosetta.core.pose.Pose, disable_non_designing_cdrs : bool) -> rosetta.core.pack.task.TaskFactory Create the FULL TaskFactory for antibody sequence design. There are no limits to repacking or design - AKA NO RestrictToLoops. Optionally disable framework residues for design Optionally disable antigen residues for design. Optionally disable framework conservative residues -> Combine with other Tasks for general design requirements.

generate_tf_seq_design_graft_design(...) from builtins.PyCapsule
generate_tf_seq_design_graft_design(self : rosetta.protocols.antibody.design.AntibodySeqDesignTFCreator, pose : rosetta.core.pose.Pose, cdr : rosetta.protocols.antibody.CDRNameEnum, neighbor_cdr_min : rosetta.utility.vector1_bool) -> rosetta.core.pack.task.TaskFactory Create the TaskFactory used for sequence design during the GraftDesign stage. This limits design to the passed CDR, optionally designing neighbor CDRs specified in options and included in min.   Basically will create a TF including CDRs you are minimizing and any neighbors.   It will then use settings in your Options classes and class settings such as framework or antigen design to create the TF,   disabling CDRs that are not allowed to design as well as framework or antigen regions. Optionally design any neighbor framework residues Optionally design any neighbor antigen residues Optionally disable framework conservative residues

get_cdr_design_options(...) from builtins.PyCapsule
get_cdr_design_options(*args, **kwargs) Overloaded function. 1. get_cdr_design_options(rosetta.protocols.antibody.design.AntibodySeqDesignTFCreator) -> rosetta.utility.vector1_std_shared_ptr_protocols_antibody_design_CDRSeqDesignOptions_t Get modifiable options 2. get_cdr_design_options(self : rosetta.protocols.antibody.design.AntibodySeqDesignTFCreator, cdr : rosetta.protocols.antibody.CDRNameEnum) -> rosetta.protocols.antibody.design.CDRSeqDesignOptions Get modifiable options

neighbor_detection_dis(...) from builtins.PyCapsule
neighbor_detection_dis(self : rosetta.protocols.antibody.design.AntibodySeqDesignTFCreator, neighbor_distance : float) -> NoneType Repack neighbors of CDR's being designed within this distance.

set_cdr_design_options(...) from builtins.PyCapsule
set_cdr_design_options(*args, **kwargs) Overloaded function. 1. set_cdr_design_options(self : rosetta.protocols.antibody.design.AntibodySeqDesignTFCreator, cdr : rosetta.protocols.antibody.CDRNameEnum, design_options : rosetta.protocols.antibody.design.CDRSeqDesignOptions) -> NoneType Set design options for single CDR 2. set_cdr_design_options(self : rosetta.protocols.antibody.design.AntibodySeqDesignTFCreator, design_options : rosetta.utility.vector1_std_shared_ptr_protocols_antibody_design_CDRSeqDesignOptions_t) -> NoneType Set design options for All CDRs

set_design_H3_stem(...) from builtins.PyCapsule
set_design_H3_stem(self : rosetta.protocols.antibody.design.AntibodySeqDesignTFCreator, design_H3_stem : bool) -> NoneType Enable design of the first 2 and last 3 residues of the H3 loop.  These are off by default as to help hinder the transition from extended to kinked and vice versa during sequence design.

set_design_framework_conservative(...) from builtins.PyCapsule
set_design_framework_conservative(self : rosetta.protocols.antibody.design.AntibodySeqDesignTFCreator, design_framework_conservative : bool) -> NoneType Use the Conservative Design TaskOP if designing Framework residues. Default true. Recommended.

set_design_framework_conserved_res(...) from builtins.PyCapsule
set_design_framework_conserved_res(self : rosetta.protocols.antibody.design.AntibodySeqDesignTFCreator, design_framework_conserved_res : bool) -> NoneType Enable design of 100% conserved framework positions during TF generation. Default false.  Will be expanded.

set_probability_data_cutoff(...) from builtins.PyCapsule
set_probability_data_cutoff(self : rosetta.protocols.antibody.design.AntibodySeqDesignTFCreator, cutoff : int) -> NoneType Use conservative mutations (or alternative method) instead of using cluster sequence probabilities for design if the number of sequences in the particular CDR's cluster probability data is lower than this cutoff. Default is 10.  This is why we try and stay in type 1 lengths during graft.

set_zero_prob_weight_at(...) from builtins.PyCapsule
set_zero_prob_weight_at(self : rosetta.protocols.antibody.design.AntibodySeqDesignTFCreator, weight : float) -> NoneType Use these weights during probabilistic design for data that is normally zero.

class CDRGraftDesignOptions(builtins.object)

    Class that holds CDRGraftDesign Options.  Now that GraftDesign is not a separate 'thing', this should be split into CDRGraftOptions and CDRMinOptions eventually.

Methods defined here:

__init__(...) from builtins.PyCapsule
__init__(*args, **kwargs) Overloaded function. 1. __init__(rosetta.protocols.antibody.design.CDRGraftDesignOptions) -> NoneType 2. __init__(self : rosetta.protocols.antibody.design.CDRGraftDesignOptions, cdr : rosetta.protocols.antibody.CDRNameEnum) -> NoneType 3. __init__(self : rosetta.protocols.antibody.design.CDRGraftDesignOptions, src : rosetta.protocols.antibody.design.CDRGraftDesignOptions) -> NoneType

__new__(*args, **kwargs) from builtins.type
Create and return a new object.  See help(type) for accurate signature.

assign(...) from builtins.PyCapsule
assign(self : rosetta.protocols.antibody.design.CDRGraftDesignOptions,  : rosetta.protocols.antibody.design.CDRGraftDesignOptions) -> rosetta.protocols.antibody.design.CDRGraftDesignOptions

clone(...) from builtins.PyCapsule
clone(rosetta.protocols.antibody.design.CDRGraftDesignOptions) -> rosetta.protocols.antibody.design.CDRGraftDesignOptions

design(...) from builtins.PyCapsule
design(*args, **kwargs) Overloaded function. 1. design(self : rosetta.protocols.antibody.design.CDRGraftDesignOptions, design : bool) -> NoneType Should this CDR be designed? 2. design(rosetta.protocols.antibody.design.CDRGraftDesignOptions) -> bool Should this CDR be designed?

min_neighbor_sc(...) from builtins.PyCapsule
min_neighbor_sc(*args, **kwargs) Overloaded function. 1. min_neighbor_sc(self : rosetta.protocols.antibody.design.CDRGraftDesignOptions, min_neighbor_sc : bool) -> NoneType Minimize neighbor sidechains? 2. min_neighbor_sc(rosetta.protocols.antibody.design.CDRGraftDesignOptions) -> bool

min_rb(...) from builtins.PyCapsule
min_rb(*args, **kwargs) Overloaded function. 1. min_rb(self : rosetta.protocols.antibody.design.CDRGraftDesignOptions, min_rb : bool) -> NoneType Use rigid body optimization during minimization of the CDR (Minimize jump bt antigen and antibody)? Does nothing if repacking the cdr.  Default False. 2. min_rb(rosetta.protocols.antibody.design.CDRGraftDesignOptions) -> bool

min_sc(...) from builtins.PyCapsule
min_sc(*args, **kwargs) Overloaded function. 1. min_sc(self : rosetta.protocols.antibody.design.CDRGraftDesignOptions, min_sc : bool) -> NoneType Minimize sidechains during minimization (relax/min/etc) (default True? 2. min_sc(rosetta.protocols.antibody.design.CDRGraftDesignOptions) -> bool

mintype(...) from builtins.PyCapsule
mintype(*args, **kwargs) Overloaded function. 1. mintype(self : rosetta.protocols.antibody.design.CDRGraftDesignOptions, mintype : rosetta.protocols.antibody.design.MinTypeEnum) -> NoneType Options are: relax, minimize, repack, dualspace. Default is repack for time, but relax is the best 2. mintype(rosetta.protocols.antibody.design.CDRGraftDesignOptions) -> rosetta.protocols.antibody.design.MinTypeEnum

neighbor_min(...) from builtins.PyCapsule
neighbor_min(*args, **kwargs) Overloaded function. 1. neighbor_min(self : rosetta.protocols.antibody.design.CDRGraftDesignOptions, neighbor_min : rosetta.utility.vector1_protocols_antibody_CDRNameEnum) -> NoneType Set other CDRs to minimize when this CDR is minimized 2. neighbor_min(rosetta.protocols.antibody.design.CDRGraftDesignOptions) -> rosetta.utility.vector1_protocols_antibody_CDRNameEnum

neighbor_min_add(...) from builtins.PyCapsule
neighbor_min_add(self : rosetta.protocols.antibody.design.CDRGraftDesignOptions, cdr : rosetta.protocols.antibody.CDRNameEnum) -> NoneType

neighbor_min_clear(...) from builtins.PyCapsule
neighbor_min_clear(rosetta.protocols.antibody.design.CDRGraftDesignOptions) -> NoneType

set_cdr(...) from builtins.PyCapsule
set_cdr(self : rosetta.protocols.antibody.design.CDRGraftDesignOptions, cdr : rosetta.protocols.antibody.CDRNameEnum) -> NoneType Set the CDR type for this instance of options.

set_defaults(...) from builtins.PyCapsule
set_defaults(rosetta.protocols.antibody.design.CDRGraftDesignOptions) -> NoneType Set defaults - !!! these are not the defaults from the database default instruction file. Use the parser to parse those instructions if you wish.

weight(...) from builtins.PyCapsule
weight(*args, **kwargs) Overloaded function. 1. weight(self : rosetta.protocols.antibody.design.CDRGraftDesignOptions, weight : float) -> NoneType Set the weight we will use for choosing this particular CDR for design. 2. weight(rosetta.protocols.antibody.design.CDRGraftDesignOptions) -> float Return the weight we will use for choosing this particular CDR for design.

class CDRGraftDesignOptionsParser(builtins.object)

    Methods defined here:

__init__(...) from builtins.PyCapsule
__init__(*args, **kwargs) Overloaded function. 1. __init__(rosetta.protocols.antibody.design.CDRGraftDesignOptionsParser) -> NoneType 2. __init__(self : rosetta.protocols.antibody.design.CDRGraftDesignOptionsParser,  : rosetta.protocols.antibody.design.CDRGraftDesignOptionsParser) -> NoneType

__new__(*args, **kwargs) from builtins.type
Create and return a new object.  See help(type) for accurate signature.

assign(...) from builtins.PyCapsule
assign(self : rosetta.protocols.antibody.design.CDRGraftDesignOptionsParser,  : rosetta.protocols.antibody.design.CDRGraftDesignOptionsParser) -> rosetta.protocols.antibody.design.CDRGraftDesignOptionsParser

parse_default_and_user_options(...) from builtins.PyCapsule
parse_default_and_user_options(*args, **kwargs) Overloaded function. 1. parse_default_and_user_options(self : rosetta.protocols.antibody.design.CDRGraftDesignOptionsParser, cdr : rosetta.protocols.antibody.CDRNameEnum, filename : str) -> rosetta.protocols.antibody.design.CDRGraftDesignOptions Parse default_instructions (mainly used for AbDesign) then parse user file 2. parse_default_and_user_options(self : rosetta.protocols.antibody.design.CDRGraftDesignOptionsParser, filename : str) -> rosetta.utility.vector1_std_shared_ptr_protocols_antibody_design_CDRGraftDesignOptions_t

parse_options(...) from builtins.PyCapsule
parse_options(*args, **kwargs) Overloaded function. 1. parse_options(self : rosetta.protocols.antibody.design.CDRGraftDesignOptionsParser, cdr : rosetta.protocols.antibody.CDRNameEnum, filename : str) -> rosetta.protocols.antibody.design.CDRGraftDesignOptions 2. parse_options(self : rosetta.protocols.antibody.design.CDRGraftDesignOptionsParser, filename : str) -> rosetta.utility.vector1_std_shared_ptr_protocols_antibody_design_CDRGraftDesignOptions_t

class CDRSeqDesignOptions(builtins.object)

    Methods defined here:

__init__(...) from builtins.PyCapsule
__init__(*args, **kwargs) Overloaded function. 1. __init__(rosetta.protocols.antibody.design.CDRSeqDesignOptions) -> NoneType 2. __init__(self : rosetta.protocols.antibody.design.CDRSeqDesignOptions, cdr : rosetta.protocols.antibody.CDRNameEnum) -> NoneType 3. __init__(self : rosetta.protocols.antibody.design.CDRSeqDesignOptions, src : rosetta.protocols.antibody.design.CDRSeqDesignOptions) -> NoneType

__new__(*args, **kwargs) from builtins.type
Create and return a new object.  See help(type) for accurate signature.

assign(...) from builtins.PyCapsule
assign(self : rosetta.protocols.antibody.design.CDRSeqDesignOptions,  : rosetta.protocols.antibody.design.CDRSeqDesignOptions) -> rosetta.protocols.antibody.design.CDRSeqDesignOptions

cdr(...) from builtins.PyCapsule
cdr(rosetta.protocols.antibody.design.CDRSeqDesignOptions) -> rosetta.protocols.antibody.CDRNameEnum

clone(...) from builtins.PyCapsule
clone(rosetta.protocols.antibody.design.CDRSeqDesignOptions) -> rosetta.protocols.antibody.design.CDRSeqDesignOptions

design(...) from builtins.PyCapsule
design(*args, **kwargs) Overloaded function. 1. design(self : rosetta.protocols.antibody.design.CDRSeqDesignOptions, design : bool) -> NoneType 2. design(rosetta.protocols.antibody.design.CDRSeqDesignOptions) -> bool

design_strategy(...) from builtins.PyCapsule
design_strategy(*args, **kwargs) Overloaded function. 1. design_strategy(self : rosetta.protocols.antibody.design.CDRSeqDesignOptions, strategy : rosetta.protocols.antibody.design.SeqDesignStrategyEnum) -> NoneType 2. design_strategy(rosetta.protocols.antibody.design.CDRSeqDesignOptions) -> rosetta.protocols.antibody.design.SeqDesignStrategyEnum

fallback(...) from builtins.PyCapsule
fallback(rosetta.protocols.antibody.design.CDRSeqDesignOptions) -> bool

fallback_strategy(...) from builtins.PyCapsule
fallback_strategy(*args, **kwargs) Overloaded function. 1. fallback_strategy(self : rosetta.protocols.antibody.design.CDRSeqDesignOptions, strategy : rosetta.protocols.antibody.design.SeqDesignStrategyEnum) -> NoneType Set the fallback strategy - which will be used if using a profile-based primary strategy, and there is not enough data 2. fallback_strategy(rosetta.protocols.antibody.design.CDRSeqDesignOptions) -> rosetta.protocols.antibody.design.SeqDesignStrategyEnum

set_cdr(...) from builtins.PyCapsule
set_cdr(self : rosetta.protocols.antibody.design.CDRSeqDesignOptions, cdr : rosetta.protocols.antibody.CDRNameEnum) -> NoneType

set_defaults(...) from builtins.PyCapsule
set_defaults(rosetta.protocols.antibody.design.CDRSeqDesignOptions) -> NoneType

class CDRSeqDesignOptionsParser(builtins.object)

    Methods defined here:

__init__(...) from builtins.PyCapsule
__init__(*args, **kwargs) Overloaded function. 1. __init__(rosetta.protocols.antibody.design.CDRSeqDesignOptionsParser) -> NoneType 2. __init__(self : rosetta.protocols.antibody.design.CDRSeqDesignOptionsParser,  : rosetta.protocols.antibody.design.CDRSeqDesignOptionsParser) -> NoneType

__new__(*args, **kwargs) from builtins.type
Create and return a new object.  See help(type) for accurate signature.

assign(...) from builtins.PyCapsule
assign(self : rosetta.protocols.antibody.design.CDRSeqDesignOptionsParser,  : rosetta.protocols.antibody.design.CDRSeqDesignOptionsParser) -> rosetta.protocols.antibody.design.CDRSeqDesignOptionsParser

parse_default_and_user_options(...) from builtins.PyCapsule
parse_default_and_user_options(*args, **kwargs) Overloaded function. 1. parse_default_and_user_options(self : rosetta.protocols.antibody.design.CDRSeqDesignOptionsParser, cdr : rosetta.protocols.antibody.CDRNameEnum, filename : str) -> rosetta.protocols.antibody.design.CDRSeqDesignOptions Parse default_instructions (mainly used for AbDesign) then parse user file 2. parse_default_and_user_options(self : rosetta.protocols.antibody.design.CDRSeqDesignOptionsParser, filename : str) -> rosetta.utility.vector1_std_shared_ptr_protocols_antibody_design_CDRSeqDesignOptions_t

parse_options(...) from builtins.PyCapsule
parse_options(*args, **kwargs) Overloaded function. 1. parse_options(self : rosetta.protocols.antibody.design.CDRSeqDesignOptionsParser, cdr : rosetta.protocols.antibody.CDRNameEnum, filename : str) -> rosetta.protocols.antibody.design.CDRSeqDesignOptions 2. parse_options(self : rosetta.protocols.antibody.design.CDRSeqDesignOptionsParser, filename : str) -> rosetta.utility.vector1_std_shared_ptr_protocols_antibody_design_CDRSeqDesignOptions_t ALL CDRs

class GeneralAntibodyModeler(builtins.object)

    Basic Class that can run modeling for various protocols. Does not do any design.  Setup design TF via AntibodySeqDesignTFCreator.

Methods defined here:

__init__(...) from builtins.PyCapsule
__init__(*args, **kwargs) Overloaded function. 1. __init__(self : rosetta.protocols.antibody.design.GeneralAntibodyModeler, ab_info : rosetta.protocols.antibody.AntibodyInfo) -> NoneType 2. __init__(self : rosetta.protocols.antibody.design.GeneralAntibodyModeler,  : rosetta.protocols.antibody.design.GeneralAntibodyModeler) -> NoneType

__new__(*args, **kwargs) from builtins.type
Create and return a new object.  See help(type) for accurate signature.

ab_dock_chains(...) from builtins.PyCapsule
ab_dock_chains(self : rosetta.protocols.antibody.design.GeneralAntibodyModeler, ab_dock_chains : str) -> NoneType Set the ab_dock chains, which will be used for any docking or minimization on the jump.  (LH_A, L_H, etc. - A for antigen)

apply_A_LH_foldtree(...) from builtins.PyCapsule
apply_A_LH_foldtree(self : rosetta.protocols.antibody.design.GeneralAntibodyModeler, pose : rosetta.core.pose.Pose) -> NoneType Applies a docking foldtree..  Forked from AbInfo - Its version uses hardcoded order of the PDB.  However, this calls docking FT, which is hard coded as well for now. Fix Me.

assign(...) from builtins.PyCapsule
assign(self : rosetta.protocols.antibody.design.GeneralAntibodyModeler,  : rosetta.protocols.antibody.design.GeneralAntibodyModeler) -> rosetta.protocols.antibody.design.GeneralAntibodyModeler

backrub_cdrs(...) from builtins.PyCapsule
backrub_cdrs(*args, **kwargs) Overloaded function. 1. backrub_cdrs(self : rosetta.protocols.antibody.design.GeneralAntibodyModeler, pose : rosetta.core.pose.Pose) -> NoneType Run the BackrubProtocol on the CDRs.  Control backrub through cmd-line. 2. backrub_cdrs(self : rosetta.protocols.antibody.design.GeneralAntibodyModeler, pose : rosetta.core.pose.Pose, min_sc : bool) -> NoneType Run the BackrubProtocol on the CDRs.  Control backrub through cmd-line. 3. backrub_cdrs(self : rosetta.protocols.antibody.design.GeneralAntibodyModeler, pose : rosetta.core.pose.Pose, min_sc : bool, include_neighbor_sc : bool) -> NoneType Run the BackrubProtocol on the CDRs.  Control backrub through cmd-line.

cdr_overhang(...) from builtins.PyCapsule
cdr_overhang(self : rosetta.protocols.antibody.design.GeneralAntibodyModeler, cdr : rosetta.protocols.antibody.CDRNameEnum, overhang : int) -> NoneType How many residues on either side of the CDR to include in CDR - modeling? (Default is 2)

dock_high_res(...) from builtins.PyCapsule
dock_high_res(*args, **kwargs) Overloaded function. 1. dock_high_res(self : rosetta.protocols.antibody.design.GeneralAntibodyModeler, pose : rosetta.core.pose.Pose) -> NoneType 2. dock_high_res(self : rosetta.protocols.antibody.design.GeneralAntibodyModeler, pose : rosetta.core.pose.Pose, first_cycle : int) -> NoneType 3. dock_high_res(self : rosetta.protocols.antibody.design.GeneralAntibodyModeler, pose : rosetta.core.pose.Pose, first_cycle : int, second_cycle : int) -> NoneType

dock_low_res(...) from builtins.PyCapsule
dock_low_res(*args, **kwargs) Overloaded function. 1. dock_low_res(self : rosetta.protocols.antibody.design.GeneralAntibodyModeler, pose : rosetta.core.pose.Pose) -> NoneType Dock the antibody. Using A for designation of Antigen chains. Not full antigen chains. (L_A, LH_A, L_H, etc.) 2. dock_low_res(self : rosetta.protocols.antibody.design.GeneralAntibodyModeler, pose : rosetta.core.pose.Pose, pack_interface : bool) -> NoneType Dock the antibody. Using A for designation of Antigen chains. Not full antigen chains. (L_A, LH_A, L_H, etc.)

extend_CDR(...) from builtins.PyCapsule
extend_CDR(self : rosetta.protocols.antibody.design.GeneralAntibodyModeler, pose : rosetta.core.pose.Pose, cdr : rosetta.protocols.antibody.CDRNameEnum) -> NoneType Randomizes the dihedrals of the CDR.

get_cdr_loop_with_overhang(...) from builtins.PyCapsule
get_cdr_loop_with_overhang(self : rosetta.protocols.antibody.design.GeneralAntibodyModeler, pose : rosetta.core.pose.Pose, cdr : rosetta.protocols.antibody.CDRNameEnum) -> rosetta.protocols.loops.Loop

get_cdr_loops(...) from builtins.PyCapsule
get_cdr_loops(self : rosetta.protocols.antibody.design.GeneralAntibodyModeler, pose : rosetta.core.pose.Pose) -> rosetta.protocols.loops.Loops Get CDR loops with cutpoint in the middle.

get_cdr_loops_with_overhang(...) from builtins.PyCapsule
get_cdr_loops_with_overhang(self : rosetta.protocols.antibody.design.GeneralAntibodyModeler, pose : rosetta.core.pose.Pose) -> rosetta.protocols.loops.Loops Get CDR loops with set overhang with cutpoint at the stop position +1.

get_cdrs_movemap_with_overhang(...) from builtins.PyCapsule
get_cdrs_movemap_with_overhang(*args, **kwargs) Overloaded function. 1. get_cdrs_movemap_with_overhang(self : rosetta.protocols.antibody.design.GeneralAntibodyModeler, pose : rosetta.core.pose.Pose) -> rosetta.core.kinematics.MoveMap 2. get_cdrs_movemap_with_overhang(self : rosetta.protocols.antibody.design.GeneralAntibodyModeler, pose : rosetta.core.pose.Pose, min_bb : bool) -> rosetta.core.kinematics.MoveMap 3. get_cdrs_movemap_with_overhang(self : rosetta.protocols.antibody.design.GeneralAntibodyModeler, pose : rosetta.core.pose.Pose, min_bb : bool, min_sc : bool) -> rosetta.core.kinematics.MoveMap 4. get_cdrs_movemap_with_overhang(self : rosetta.protocols.antibody.design.GeneralAntibodyModeler, pose : rosetta.core.pose.Pose, min_bb : bool, min_sc : bool, include_neighbor_sc : bool) -> rosetta.core.kinematics.MoveMap 5. get_cdrs_movemap_with_overhang(self : rosetta.protocols.antibody.design.GeneralAntibodyModeler, pose : rosetta.core.pose.Pose, min_bb : bool, min_sc : bool, include_neighbor_sc : bool, include_neighbor_bb : bool) -> rosetta.core.kinematics.MoveMap

get_movemap_from_task(...) from builtins.PyCapsule
get_movemap_from_task(self : rosetta.protocols.antibody.design.GeneralAntibodyModeler, pose : rosetta.core.pose.Pose, task : rosetta.core.pack.task.PackerTask) -> rosetta.core.kinematics.MoveMap

interface_detection_dis(...) from builtins.PyCapsule
interface_detection_dis(*args, **kwargs) Overloaded function. 1. interface_detection_dis(self : rosetta.protocols.antibody.design.GeneralAntibodyModeler, interface_distance : float) -> NoneType Set a value for interface detection across the class. 2. interface_detection_dis(rosetta.protocols.antibody.design.GeneralAntibodyModeler) -> float

minimize_cdrs(...) from builtins.PyCapsule
minimize_cdrs(*args, **kwargs) Overloaded function. 1. minimize_cdrs(self : rosetta.protocols.antibody.design.GeneralAntibodyModeler, pose : rosetta.core.pose.Pose) -> NoneType Vanilla minimizer using dfpmin_armijo_nonmonotone at .001 tolerance (or lfbgs for cartmin). 2. minimize_cdrs(self : rosetta.protocols.antibody.design.GeneralAntibodyModeler, pose : rosetta.core.pose.Pose, min_sc : bool) -> NoneType Vanilla minimizer using dfpmin_armijo_nonmonotone at .001 tolerance (or lfbgs for cartmin). 3. minimize_cdrs(self : rosetta.protocols.antibody.design.GeneralAntibodyModeler, pose : rosetta.core.pose.Pose, min_sc : bool, include_neighbor_sc : bool) -> NoneType Vanilla minimizer using dfpmin_armijo_nonmonotone at .001 tolerance (or lfbgs for cartmin). 4. minimize_cdrs(self : rosetta.protocols.antibody.design.GeneralAntibodyModeler, pose : rosetta.core.pose.Pose, min_sc : bool, include_neighbor_sc : bool, min_interface : bool) -> NoneType Vanilla minimizer using dfpmin_armijo_nonmonotone at .001 tolerance (or lfbgs for cartmin). 5. minimize_cdrs(self : rosetta.protocols.antibody.design.GeneralAntibodyModeler, pose : rosetta.core.pose.Pose, min_sc : bool, include_neighbor_sc : bool, min_interface : bool, cartmin : bool) -> NoneType Vanilla minimizer using dfpmin_armijo_nonmonotone at .001 tolerance (or lfbgs for cartmin). 6. minimize_cdrs(self : rosetta.protocols.antibody.design.GeneralAntibodyModeler, pose : rosetta.core.pose.Pose, min_sc : bool, include_neighbor_sc : bool, min_interface : bool, cartmin : bool, use_talaris_cartmin : bool) -> NoneType Vanilla minimizer using dfpmin_armijo_nonmonotone at .001 tolerance (or lfbgs for cartmin).

minimize_interface(...) from builtins.PyCapsule
minimize_interface(*args, **kwargs) Overloaded function. 1. minimize_interface(self : rosetta.protocols.antibody.design.GeneralAntibodyModeler, pose : rosetta.core.pose.Pose) -> NoneType 2. minimize_interface(self : rosetta.protocols.antibody.design.GeneralAntibodyModeler, pose : rosetta.core.pose.Pose, min_interface_sc : bool) -> NoneType

neighbor_detection_dis(...) from builtins.PyCapsule
neighbor_detection_dis(*args, **kwargs) Overloaded function. 1. neighbor_detection_dis(self : rosetta.protocols.antibody.design.GeneralAntibodyModeler, neighbor_distance : float) -> NoneType 2. neighbor_detection_dis(rosetta.protocols.antibody.design.GeneralAntibodyModeler) -> float

relax_cdrs(...) from builtins.PyCapsule
relax_cdrs(*args, **kwargs) Overloaded function. 1. relax_cdrs(self : rosetta.protocols.antibody.design.GeneralAntibodyModeler, pose : rosetta.core.pose.Pose) -> NoneType Relax CDRs using FastRelax.  CentroidRelax unfortunately does not work well.  Perhaps with centroid rotamers.. Cluster Constraints should already be set. Optionally use start_coordinate constraints. All coordinate constraints on the pose will then be removed. 2. relax_cdrs(self : rosetta.protocols.antibody.design.GeneralAntibodyModeler, pose : rosetta.core.pose.Pose, include_neighbor_sc : bool) -> NoneType Relax CDRs using FastRelax.  CentroidRelax unfortunately does not work well.  Perhaps with centroid rotamers.. Cluster Constraints should already be set. Optionally use start_coordinate constraints. All coordinate constraints on the pose will then be removed. 3. relax_cdrs(self : rosetta.protocols.antibody.design.GeneralAntibodyModeler, pose : rosetta.core.pose.Pose, include_neighbor_sc : bool, starting_coordinate_constraints : bool) -> NoneType Relax CDRs using FastRelax.  CentroidRelax unfortunately does not work well.  Perhaps with centroid rotamers.. Cluster Constraints should already be set. Optionally use start_coordinate constraints. All coordinate constraints on the pose will then be removed. 4. relax_cdrs(self : rosetta.protocols.antibody.design.GeneralAntibodyModeler, pose : rosetta.core.pose.Pose, include_neighbor_sc : bool, starting_coordinate_constraints : bool, min_interface : bool) -> NoneType Relax CDRs using FastRelax.  CentroidRelax unfortunately does not work well.  Perhaps with centroid rotamers.. Cluster Constraints should already be set. Optionally use start_coordinate constraints. All coordinate constraints on the pose will then be removed. 5. relax_cdrs(self : rosetta.protocols.antibody.design.GeneralAntibodyModeler, pose : rosetta.core.pose.Pose, include_neighbor_sc : bool, starting_coordinate_constraints : bool, min_interface : bool, dualspace : bool) -> NoneType Relax CDRs using FastRelax.  CentroidRelax unfortunately does not work well.  Perhaps with centroid rotamers.. Cluster Constraints should already be set. Optionally use start_coordinate constraints. All coordinate constraints on the pose will then be removed.

relax_interface(...) from builtins.PyCapsule
relax_interface(*args, **kwargs) Overloaded function. 1. relax_interface(self : rosetta.protocols.antibody.design.GeneralAntibodyModeler, pose : rosetta.core.pose.Pose) -> NoneType 2. relax_interface(self : rosetta.protocols.antibody.design.GeneralAntibodyModeler, pose : rosetta.core.pose.Pose, min_interface_sc : bool) -> NoneType

repack_antibody_interface(...) from builtins.PyCapsule
repack_antibody_interface(self : rosetta.protocols.antibody.design.GeneralAntibodyModeler, pose : rosetta.core.pose.Pose) -> NoneType Repack the interface between antibody and antigen, but only pack antibody.

repack_antigen_ab_interface(...) from builtins.PyCapsule
repack_antigen_ab_interface(self : rosetta.protocols.antibody.design.GeneralAntibodyModeler, pose : rosetta.core.pose.Pose) -> NoneType Repack the interface between Antibody and Antigen.

repack_antigen_interface(...) from builtins.PyCapsule
repack_antigen_interface(self : rosetta.protocols.antibody.design.GeneralAntibodyModeler, pose : rosetta.core.pose.Pose) -> NoneType Repack the interface between antibody and antigen, but only pack antigen.

repack_cdrs(...) from builtins.PyCapsule
repack_cdrs(*args, **kwargs) Overloaded function. 1. repack_cdrs(self : rosetta.protocols.antibody.design.GeneralAntibodyModeler, pose : rosetta.core.pose.Pose) -> NoneType Repack the CDRs given.  Nothing special. 2. repack_cdrs(self : rosetta.protocols.antibody.design.GeneralAntibodyModeler, pose : rosetta.core.pose.Pose, include_neighbor_sc : bool) -> NoneType Repack the CDRs given.  Nothing special.

reset_task_factory(...) from builtins.PyCapsule
reset_task_factory(rosetta.protocols.antibody.design.GeneralAntibodyModeler) -> NoneType

set_cdr(...) from builtins.PyCapsule
set_cdr(self : rosetta.protocols.antibody.design.GeneralAntibodyModeler, cdr : rosetta.protocols.antibody.CDRNameEnum, setting : bool) -> NoneType Set to model CDRs.  Default is all of them false.

set_cdr_only(...) from builtins.PyCapsule
set_cdr_only(self : rosetta.protocols.antibody.design.GeneralAntibodyModeler, cdr : rosetta.protocols.antibody.CDRNameEnum, setting : bool) -> NoneType Set to model only one cdr, or all others but one.

set_cdr_range(...) from builtins.PyCapsule
set_cdr_range(self : rosetta.protocols.antibody.design.GeneralAntibodyModeler, cdr_start : rosetta.protocols.antibody.CDRNameEnum, cdr_end : rosetta.protocols.antibody.CDRNameEnum, setting : bool) -> NoneType Set a range of CDRs.

set_cdrs(...) from builtins.PyCapsule
set_cdrs(self : rosetta.protocols.antibody.design.GeneralAntibodyModeler, cdrs : rosetta.utility.vector1_bool) -> NoneType

set_dock_high_res_scorefunction(...) from builtins.PyCapsule
set_dock_high_res_scorefunction(self : rosetta.protocols.antibody.design.GeneralAntibodyModeler, scorefxn : rosetta.core.scoring.ScoreFunction) -> NoneType

set_dock_low_res_scorefunction(...) from builtins.PyCapsule
set_dock_low_res_scorefunction(self : rosetta.protocols.antibody.design.GeneralAntibodyModeler, scorefxn : rosetta.core.scoring.ScoreFunction) -> NoneType

set_scorefunction(...) from builtins.PyCapsule
set_scorefunction(self : rosetta.protocols.antibody.design.GeneralAntibodyModeler, scorefxn : rosetta.core.scoring.ScoreFunction) -> NoneType

set_scorefunction_min(...) from builtins.PyCapsule
set_scorefunction_min(self : rosetta.protocols.antibody.design.GeneralAntibodyModeler, scorefxn : rosetta.core.scoring.ScoreFunction) -> NoneType Set scorefunction used for bb minimization.

set_task_factory(...) from builtins.PyCapsule
set_task_factory(self : rosetta.protocols.antibody.design.GeneralAntibodyModeler, tf : rosetta.core.pack.task.TaskFactory) -> NoneType

class MinTypeEnum(builtins.object)

    Methods defined here:

__eq__(...) from builtins.PyCapsule
__eq__(rosetta.protocols.antibody.design.MinTypeEnum, rosetta.protocols.antibody.design.MinTypeEnum) -> bool

__hash__(...) from builtins.PyCapsule
__hash__(rosetta.protocols.antibody.design.MinTypeEnum) -> int

__init__(...) from builtins.PyCapsule
__init__(*args, **kwargs) Overloaded function. 1. __init__(rosetta.protocols.antibody.design.MinTypeEnum, int) -> NoneType 2. __init__(rosetta.protocols.antibody.design.MinTypeEnum, int) -> NoneType

__int__(...) from builtins.PyCapsule
__int__(rosetta.protocols.antibody.design.MinTypeEnum) -> int

__ne__(...) from builtins.PyCapsule
__ne__(rosetta.protocols.antibody.design.MinTypeEnum, rosetta.protocols.antibody.design.MinTypeEnum) -> bool

__new__(*args, **kwargs) from builtins.type
Create and return a new object.  See help(type) for accurate signature.

__repr__(...) from builtins.PyCapsule
__repr__(rosetta.protocols.antibody.design.MinTypeEnum) -> str

Data and other attributes defined here:

MinTypeEnum_total = MinTypeEnum.MinTypeEnum_total

backrub_protocol = MinTypeEnum.backrub_protocol

centroid_relax = MinTypeEnum.centroid_relax

dualspace = MinTypeEnum.dualspace

minimize = MinTypeEnum.minimize

minimize_cartesian = MinTypeEnum.minimize_cartesian

no_min = MinTypeEnum.MinTypeEnum_total

relax = MinTypeEnum.relax

repack = MinTypeEnum.repack

class MutantPosition(builtins.object)

    Methods defined here:

__init__(...) from builtins.PyCapsule
__init__(*args, **kwargs) Overloaded function. 1. __init__(rosetta.protocols.antibody.design.MutantPosition) -> NoneType 2. __init__(self : rosetta.protocols.antibody.design.MutantPosition,  : rosetta.protocols.antibody.design.MutantPosition) -> NoneType

__new__(*args, **kwargs) from builtins.type
Create and return a new object.  See help(type) for accurate signature.

assign(...) from builtins.PyCapsule
assign(self : rosetta.protocols.antibody.design.MutantPosition,  : rosetta.protocols.antibody.design.MutantPosition) -> rosetta.protocols.antibody.design.MutantPosition

Data descriptors defined here:

mutants_allowed_

numbering_scheme_

pdb_position_

class MutateFrameworkForCluster(rosetta.protocols.moves.Mover)

    Mutates framework positions to what is needed for a particular cluster if that cluster has needed mutations. Will use clusters from pose data cache if there, otherwise, will use clusters set from AntibodyInfo. Use set_cdr or set_cdrs to limit to a particular CDR or set of CDRs.

Method resolution order:

MutateFrameworkForCluster

rosetta.protocols.moves.Mover

builtins.object

Methods defined here:

__init__(...) from builtins.PyCapsule
__init__(*args, **kwargs) Overloaded function. 1. __init__(handle) -> NoneType 2. __init__(self : handle, ab_info : rosetta.protocols.antibody.AntibodyInfo) -> NoneType 3. __init__(handle, rosetta.protocols.antibody.design.MutateFrameworkForCluster) -> NoneType

__new__(*args, **kwargs) from builtins.type
Create and return a new object.  See help(type) for accurate signature.

apply(...) from builtins.PyCapsule
apply(self : rosetta.protocols.antibody.design.MutateFrameworkForCluster, pose : rosetta.core.pose.Pose) -> NoneType

assign(...) from builtins.PyCapsule
assign(self : rosetta.protocols.antibody.design.MutateFrameworkForCluster,  : rosetta.protocols.antibody.design.MutateFrameworkForCluster) -> rosetta.protocols.antibody.design.MutateFrameworkForCluster

framework_dependant_clusters(...) from builtins.PyCapsule
framework_dependant_clusters(rosetta.protocols.antibody.design.MutateFrameworkForCluster) -> rosetta.utility.vector1_protocols_antibody_clusters_CDRClusterEnum Get all framework dependant clusters in list

framework_dependant_mutations(...) from builtins.PyCapsule
framework_dependant_mutations(self : rosetta.protocols.antibody.design.MutateFrameworkForCluster, pose : rosetta.core.pose.Pose, cluster : rosetta.protocols.antibody.clusters.CDRClusterEnum, resnum : int) -> rosetta.utility.vector1_bool Get all framework mutations for a particular framework dependent position, regardless of whether that cluster is in the pose.

framework_dependant_positions(...) from builtins.PyCapsule
framework_dependant_positions(*args, **kwargs) Overloaded function. 1. framework_dependant_positions(self : rosetta.protocols.antibody.design.MutateFrameworkForCluster, pose : rosetta.core.pose.Pose) -> rosetta.utility.vector1_bool Get all framework positions that would be required by clusters regardless of whether that cluster is in the pose. 2. framework_dependant_positions(self : rosetta.protocols.antibody.design.MutateFrameworkForCluster, pose : rosetta.core.pose.Pose, cluster : rosetta.protocols.antibody.clusters.CDRClusterEnum) -> rosetta.utility.vector1_bool Get all framework positions that would be required by a cluster regardless of whether that cluster is in the pose.

fresh_instance(...) from builtins.PyCapsule
fresh_instance(rosetta.protocols.antibody.design.MutateFrameworkForCluster) -> rosetta.protocols.moves.Mover

get_name(...) from builtins.PyCapsule
get_name(rosetta.protocols.antibody.design.MutateFrameworkForCluster) -> str

has_framework_dependant_cluster(...) from builtins.PyCapsule
has_framework_dependant_cluster(self : rosetta.protocols.antibody.design.MutateFrameworkForCluster, pose : rosetta.core.pose.Pose, cdr : rosetta.protocols.antibody.CDRNameEnum) -> bool

has_framework_dependant_clusters(...) from builtins.PyCapsule
has_framework_dependant_clusters(self : rosetta.protocols.antibody.design.MutateFrameworkForCluster, pose : rosetta.core.pose.Pose) -> bool //////// Helper functions //////////////

keep_current(...) from builtins.PyCapsule
keep_current(self : rosetta.protocols.antibody.design.MutateFrameworkForCluster, keep_current : bool) -> NoneType Set to keep the current amino acid(s) for the position in the mutation set. Each position is not 100 percent a particular mutant for a cluster, so we allow this by default and hope Rosetta can choose properly.

set_cdr_only(...) from builtins.PyCapsule
set_cdr_only(self : rosetta.protocols.antibody.design.MutateFrameworkForCluster, cdr : rosetta.protocols.antibody.CDRNameEnum) -> NoneType

set_cdrs(...) from builtins.PyCapsule
set_cdrs(self : rosetta.protocols.antibody.design.MutateFrameworkForCluster, cdrs : rosetta.utility.vector1_bool) -> NoneType

set_pack_shell(...) from builtins.PyCapsule
set_pack_shell(self : rosetta.protocols.antibody.design.MutateFrameworkForCluster, pack_shell : float) -> NoneType Set the distance for the packing shell.

set_scorefxn(...) from builtins.PyCapsule
set_scorefxn(self : rosetta.protocols.antibody.design.MutateFrameworkForCluster, scorefxn : rosetta.core.scoring.ScoreFunction) -> NoneType

Methods inherited from rosetta.protocols.moves.Mover:

clear_info(...) from builtins.PyCapsule
clear_info(rosetta.protocols.moves.Mover) -> NoneType Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file. clear_info is called by jd2 before calling apply

clone(...) from builtins.PyCapsule
clone(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover Return a clone of the Mover object.

create(...) from builtins.PyCapsule
create(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover

get_additional_output(...) from builtins.PyCapsule
get_additional_output(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose fpd Mechanism by which a mover may return multiple output poses from a single input pose.

get_current_job(...) from builtins.PyCapsule
get_current_job(rosetta.protocols.moves.Mover) -> protocols::jobdist::BasicJob

get_current_tag(...) from builtins.PyCapsule
get_current_tag(rosetta.protocols.moves.Mover) -> str A tag is a unique identifier used to identify structures produced by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag.  This functionality is not intended for use with the 2008 job distributor.

get_input_pose(...) from builtins.PyCapsule
get_input_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose

get_last_move_status(...) from builtins.PyCapsule
get_last_move_status(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.MoverStatus returns status after an apply().  The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say "that run was no good, skip it" then use the protected last_move_status(MoverStatus) to change the value that this function will return.

get_native_pose(...) from builtins.PyCapsule
get_native_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose

get_self_ptr(...) from builtins.PyCapsule
get_self_ptr(*args, **kwargs) Overloaded function. 1. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover 2. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover

get_self_weak_ptr(...) from builtins.PyCapsule
get_self_weak_ptr(*args, **kwargs) Overloaded function. 1. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_const_protocols_moves_Mover_t 2. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_protocols_moves_Mover_t

get_type(...) from builtins.PyCapsule
get_type(rosetta.protocols.moves.Mover) -> str

info(...) from builtins.PyCapsule
info(*args, **kwargs) Overloaded function. 1. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t non-const accessor 2. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t const accessor

last_proposal_density_ratio(...) from builtins.PyCapsule
last_proposal_density_ratio(rosetta.protocols.moves.Mover) -> float

name(...) from builtins.PyCapsule
name() -> str

register_options(...) from builtins.PyCapsule
register_options(*args, **kwargs) Overloaded function. 1. register_options() -> NoneType Overload this static method if you access options within the mover. These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method. 2. register_options() -> NoneType 3. register_options() -> NoneType 4. register_options() -> NoneType 5. register_options() -> NoneType 6. register_options() -> NoneType 7. register_options() -> NoneType 8. register_options() -> NoneType 9. register_options() -> NoneType Associates relevant options with the AntibodyModeler class 10. register_options() -> NoneType Associates relevant options with the AntibodyModeler class 11. register_options() -> NoneType Associates relevant options with the SnugDock class 12. register_options() -> NoneType Associates relevant options with the SnugDockProtocol class 13. register_options() -> NoneType Register the options used by this mover with the global options system. 14. register_options() -> NoneType 15. register_options() -> NoneType Associate relevant options with the TemperedDocking class. 16. register_options() -> NoneType 17. register_options() -> NoneType 18. register_options() -> NoneType Associates relevant options with the TemperedDocking class. 19. register_options() -> NoneType 20. register_options() -> NoneType Associates relevant options with the ConstraintSetMover class 21. register_options() -> NoneType 22. register_options() -> NoneType Associates relevant options with the DockingInitialPerturbation class 23. register_options() -> NoneType Associates relevant options with the DockingProtocol class 24. register_options() -> NoneType Associates relevant options with the TemperedDocking class 25. register_options() -> NoneType 26. register_options() -> NoneType 27. register_options() -> NoneType 28. register_options() -> NoneType register options 29. register_options() -> NoneType 30. register_options() -> NoneType Registers applicable options 31. register_options() -> NoneType Register options with the option system. 32. register_options() -> NoneType 33. register_options() -> NoneType 34. register_options() -> NoneType Associates relevant options with the LoopRefineInnerCycle class 35. register_options() -> NoneType Associates relevant options with the LoopRefineInnerCycleContainer class 36. register_options() -> NoneType Associates relevant options with the LoopRefineInnerCycle class 37. register_options() -> NoneType Associates relevant options with the LoopRefineInnerCycle class 38. register_options() -> NoneType 39. register_options() -> NoneType Register options with the option system. 40. register_options() -> NoneType

reinitialize_for_each_job(...) from builtins.PyCapsule
reinitialize_for_each_job(rosetta.protocols.moves.Mover) -> bool Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on each use.

reinitialize_for_new_input(...) from builtins.PyCapsule
reinitialize_for_new_input(rosetta.protocols.moves.Mover) -> bool Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

reset_status(...) from builtins.PyCapsule
reset_status(rosetta.protocols.moves.Mover) -> NoneType resets status to SUCCESS, meant to be used before an apply().  The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

set_current_job(...) from builtins.PyCapsule
set_current_job(self : rosetta.protocols.moves.Mover, job : protocols::jobdist::BasicJob) -> NoneType ////////////////////////////end Job Distributor interface////////////////////////////////////////

set_current_tag(...) from builtins.PyCapsule
set_current_tag(self : rosetta.protocols.moves.Mover, new_tag : str) -> NoneType

set_input_pose(...) from builtins.PyCapsule
set_input_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType setter for poses contained for rms

set_native_pose(...) from builtins.PyCapsule
set_native_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType setter for native poses contained for rms ---- we should get rid of this method? it is widely used, but a bit unsafe

set_type(...) from builtins.PyCapsule
set_type(self : rosetta.protocols.moves.Mover, setting : str) -> NoneType

test_move(...) from builtins.PyCapsule
test_move(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType : Unit test support function.  Apply one move to a given pose.       Allows extra test specific functions to be called before applying

type(...) from builtins.PyCapsule
type(*args, **kwargs) Overloaded function. 1. type(rosetta.protocols.moves.Mover) -> str 2. type(self : rosetta.protocols.moves.Mover, type_in : str) -> NoneType

class MutateFrameworkForClusterCreator(rosetta.protocols.moves.MoverCreator)


Method resolution order:

MutateFrameworkForClusterCreator

rosetta.protocols.moves.MoverCreator

builtins.object

Methods defined here:

__init__(...) from builtins.PyCapsule
__init__(handle) -> NoneType

__new__(*args, **kwargs) from builtins.type
Create and return a new object.  See help(type) for accurate signature.

assign(...) from builtins.PyCapsule
assign(self : rosetta.protocols.antibody.design.MutateFrameworkForClusterCreator,  : rosetta.protocols.antibody.design.MutateFrameworkForClusterCreator) -> rosetta.protocols.antibody.design.MutateFrameworkForClusterCreator

create_mover(...) from builtins.PyCapsule
create_mover(rosetta.protocols.antibody.design.MutateFrameworkForClusterCreator) -> rosetta.protocols.moves.Mover

keyname(...) from builtins.PyCapsule
keyname(rosetta.protocols.antibody.design.MutateFrameworkForClusterCreator) -> str

mover_name(...) from builtins.PyCapsule
mover_name() -> str

class NativeAntibodySeq(rosetta.basic.datacache.CacheableData)

    Class that keeps track of the 'native' sequence during design.  Native means that no design has occured. Used for conservative base design to keep it from hopping around residue types.

Method resolution order:

NativeAntibodySeq

rosetta.basic.datacache.CacheableData

builtins.object

Methods defined here:

__init__(...) from builtins.PyCapsule
__init__(*args, **kwargs) Overloaded function. 1. __init__(self : handle, pose : rosetta.core.pose.Pose, ab_info : rosetta.protocols.antibody.AntibodyInfo) -> NoneType 2. __init__(handle, rosetta.protocols.antibody.design.NativeAntibodySeq) -> NoneType

__new__(*args, **kwargs) from builtins.type
Create and return a new object.  See help(type) for accurate signature.

assign(...) from builtins.PyCapsule
assign(self : rosetta.protocols.antibody.design.NativeAntibodySeq,  : rosetta.protocols.antibody.design.NativeAntibodySeq) -> rosetta.protocols.antibody.design.NativeAntibodySeq

clone(...) from builtins.PyCapsule
clone(rosetta.protocols.antibody.design.NativeAntibodySeq) -> rosetta.basic.datacache.CacheableData

get_sequence(...) from builtins.PyCapsule
get_sequence(self : rosetta.protocols.antibody.design.NativeAntibodySeq, pose : rosetta.core.pose.Pose) -> str Get the full pose sequence.

set_from_cdr(...) from builtins.PyCapsule
set_from_cdr(self : rosetta.protocols.antibody.design.NativeAntibodySeq, pose : rosetta.core.pose.Pose, cdr : rosetta.protocols.antibody.CDRNameEnum) -> NoneType Sets the sequence from the CDR of the PDB into this class and into the pose.

set_sequence(...) from builtins.PyCapsule
set_sequence(self : rosetta.protocols.antibody.design.NativeAntibodySeq, pose : rosetta.core.pose.Pose) -> NoneType Sets the sequence from the PDB into this class and into the pose.

set_to_pose(...) from builtins.PyCapsule
set_to_pose(self : rosetta.protocols.antibody.design.NativeAntibodySeq, pose : rosetta.core.pose.Pose) -> NoneType Set this class to the pose datacache.

Methods inherited from rosetta.basic.datacache.CacheableData:

get_self_ptr(...) from builtins.PyCapsule
get_self_ptr(*args, **kwargs) Overloaded function. 1. get_self_ptr(rosetta.basic.datacache.CacheableData) -> rosetta.basic.datacache.CacheableData self pointers 2. get_self_ptr(rosetta.basic.datacache.CacheableData) -> rosetta.basic.datacache.CacheableData

get_self_weak_ptr(...) from builtins.PyCapsule
get_self_weak_ptr(*args, **kwargs) Overloaded function. 1. get_self_weak_ptr(rosetta.basic.datacache.CacheableData) -> rosetta.std.weak_ptr_const_basic_datacache_CacheableData_t 2. get_self_weak_ptr(rosetta.basic.datacache.CacheableData) -> rosetta.std.weak_ptr_basic_datacache_CacheableData_t

class PDBNumbering(builtins.object)

    Move this somewhere in pose or pose_selection.  PDBInfo's ResidueKey should be public and passed around in the first place. Super-basic numbering struct.

Methods defined here:

__init__(...) from builtins.PyCapsule
__init__(rosetta.protocols.antibody.design.PDBNumbering) -> NoneType

__new__(*args, **kwargs) from builtins.type
Create and return a new object.  See help(type) for accurate signature.

Data descriptors defined here:

chain

icode

resnum

class SeqDesignStrategyEnum(builtins.object)

    Methods defined here:

__eq__(...) from builtins.PyCapsule
__eq__(rosetta.protocols.antibody.design.SeqDesignStrategyEnum, rosetta.protocols.antibody.design.SeqDesignStrategyEnum) -> bool

__hash__(...) from builtins.PyCapsule
__hash__(rosetta.protocols.antibody.design.SeqDesignStrategyEnum) -> int

__init__(...) from builtins.PyCapsule
__init__(*args, **kwargs) Overloaded function. 1. __init__(rosetta.protocols.antibody.design.SeqDesignStrategyEnum, int) -> NoneType 2. __init__(rosetta.protocols.antibody.design.SeqDesignStrategyEnum, int) -> NoneType

__int__(...) from builtins.PyCapsule
__int__(rosetta.protocols.antibody.design.SeqDesignStrategyEnum) -> int

__ne__(...) from builtins.PyCapsule
__ne__(rosetta.protocols.antibody.design.SeqDesignStrategyEnum, rosetta.protocols.antibody.design.SeqDesignStrategyEnum) -> bool

__new__(*args, **kwargs) from builtins.type
Create and return a new object.  See help(type) for accurate signature.

__repr__(...) from builtins.PyCapsule
__repr__(rosetta.protocols.antibody.design.SeqDesignStrategyEnum) -> str

Data and other attributes defined here:

SeqDesignStrategyEnum_total = SeqDesignStrategyEnum.SeqDesignStrategyEnum_total

seq_design_basic = SeqDesignStrategyEnum.seq_design_basic

seq_design_conservative = SeqDesignStrategyEnum.seq_design_conservative

seq_design_none = SeqDesignStrategyEnum.SeqDesignStrategyEnum_total

seq_design_profile_sets = SeqDesignStrategyEnum.seq_design_profile_sets

seq_design_profile_sets_combined = SeqDesignStrategyEnum.seq_design_profile_sets_combined

seq_design_profiles = SeqDesignStrategyEnum.seq_design_profiles

Functions


add_loops_from_bool_vector(...) method of builtins.PyCapsule instance
add_loops_from_bool_vector(*args, **kwargs) Overloaded function. 1. add_loops_from_bool_vector(loops : rosetta.protocols.loops.Loops, residues : rosetta.utility.vector1_bool) -> NoneType 2. add_loops_from_bool_vector(loops : rosetta.protocols.loops.Loops, residues : rosetta.utility.vector1_bool, add_cutpoints : bool) -> NoneType

check_cb(...) method of builtins.PyCapsule instance
check_cb(*args, **kwargs) Overloaded function. 1. check_cb(pose : rosetta.core.pose.Pose, residues : rosetta.utility.vector1_bool) -> (bool, int) 2. check_cb(pose : rosetta.core.pose.Pose, loops : rosetta.protocols.loops.Loops) -> (bool, int)

design_protocol_to_enum(...) method of builtins.PyCapsule instance
design_protocol_to_enum(design_type : str) -> rosetta.protocols.antibody.design.AntibodyDesignProtocolEnum

design_protocol_to_string(...) method of builtins.PyCapsule instance
design_protocol_to_string(design_type : rosetta.protocols.antibody.design.AntibodyDesignProtocolEnum) -> str

disable_conserved_framework_positions(...) method of builtins.PyCapsule instance
disable_conserved_framework_positions(ab_info : rosetta.protocols.antibody.AntibodyInfo, pose : rosetta.core.pose.Pose) -> rosetta.core.pack.task.operation.RestrictResidueToRepacking Disable design for conserved framework positions. TODO: Needs to be expanded to read positions from database.

disable_design_antigen(...) method of builtins.PyCapsule instance
disable_design_antigen(ab_info : rosetta.protocols.antibody.AntibodyInfo, pose : rosetta.core.pose.Pose) -> rosetta.core.pack.task.operation.RestrictResidueToRepacking Disable design of the antigen residues

disable_design_cdr(...) method of builtins.PyCapsule instance
disable_design_cdr(ab_info : rosetta.protocols.antibody.AntibodyInfo, cdr : rosetta.protocols.antibody.CDRNameEnum, pose : rosetta.core.pose.Pose) -> rosetta.core.pack.task.operation.RestrictResidueToRepacking Get a Restrict operation to turn OFF design for particular CDRs.

disable_design_cdrs(...) method of builtins.PyCapsule instance
disable_design_cdrs(ab_info : rosetta.protocols.antibody.AntibodyInfo, pose : rosetta.core.pose.Pose) -> rosetta.core.pack.task.operation.RestrictResidueToRepacking Get a Restrict operation to turn OFF design for all CDRs.

disable_design_framework(...) method of builtins.PyCapsule instance
disable_design_framework(*args, **kwargs) Overloaded function. 1. disable_design_framework(ab_info : rosetta.protocols.antibody.AntibodyInfo, pose : rosetta.core.pose.Pose) -> rosetta.core.pack.task.operation.RestrictResidueToRepacking Disable design of the framework residues 2. disable_design_framework(ab_info : rosetta.protocols.antibody.AntibodyInfo, pose : rosetta.core.pose.Pose, cdr4_as_framework : bool) -> rosetta.core.pack.task.operation.RestrictResidueToRepacking Disable design of the framework residues

disable_design_region(...) method of builtins.PyCapsule instance
disable_design_region(*args, **kwargs) Overloaded function. 1. disable_design_region(ab_info : rosetta.protocols.antibody.AntibodyInfo, pose : rosetta.core.pose.Pose, region : rosetta.protocols.antibody.AntibodyRegionEnum) -> rosetta.core.pack.task.operation.RestrictResidueToRepacking Disable design of any particular region of the antibody complex. 2. disable_design_region(ab_info : rosetta.protocols.antibody.AntibodyInfo, pose : rosetta.core.pose.Pose, region : rosetta.protocols.antibody.AntibodyRegionEnum, cdr4_as_framework : bool) -> rosetta.core.pack.task.operation.RestrictResidueToRepacking Disable design of any particular region of the antibody complex.

disable_h3_stem_positions(...) method of builtins.PyCapsule instance
disable_h3_stem_positions(*args, **kwargs) Overloaded function. 1. disable_h3_stem_positions(ab_info : rosetta.protocols.antibody.AntibodyInfo, pose : rosetta.core.pose.Pose) -> rosetta.core.pack.task.operation.RestrictResidueToRepacking Disable design of the first 2 and last 3 residues of the H3 CDR (North CDR definitions - kink determinants) 2. disable_h3_stem_positions(ab_info : rosetta.protocols.antibody.AntibodyInfo, pose : rosetta.core.pose.Pose, nter_stem : int) -> rosetta.core.pack.task.operation.RestrictResidueToRepacking Disable design of the first 2 and last 3 residues of the H3 CDR (North CDR definitions - kink determinants) 3. disable_h3_stem_positions(ab_info : rosetta.protocols.antibody.AntibodyInfo, pose : rosetta.core.pose.Pose, nter_stem : int, cter_stem : int) -> rosetta.core.pack.task.operation.RestrictResidueToRepacking Disable design of the first 2 and last 3 residues of the H3 CDR (North CDR definitions - kink determinants)

get_ab_design_dock_high_scorefxn(...) method of builtins.PyCapsule instance
get_ab_design_dock_high_scorefxn() -> rosetta.core.scoring.ScoreFunction

get_ab_design_dock_low_scorefxn(...) method of builtins.PyCapsule instance
get_ab_design_dock_low_scorefxn() -> rosetta.core.scoring.ScoreFunction

get_ab_design_global_scorefxn(...) method of builtins.PyCapsule instance
get_ab_design_global_scorefxn(*args, **kwargs) Overloaded function. 1. get_ab_design_global_scorefxn() -> rosetta.core.scoring.ScoreFunction 2. get_ab_design_global_scorefxn(tag : rosetta.utility.tag.Tag, data : rosetta.basic.datacache.DataMap) -> rosetta.core.scoring.ScoreFunction Get Global Scorefxn from RS

get_ab_design_min_scorefxn(...) method of builtins.PyCapsule instance
get_ab_design_min_scorefxn(*args, **kwargs) Overloaded function. 1. get_ab_design_min_scorefxn() -> rosetta.core.scoring.ScoreFunction 2. get_ab_design_min_scorefxn(tag : rosetta.utility.tag.Tag, data : rosetta.basic.datacache.DataMap) -> rosetta.core.scoring.ScoreFunction

get_all_graft_permutations(...) method of builtins.PyCapsule instance
get_all_graft_permutations(permutations : rosetta.utility.vector1_utility_vector1_unsigned_long_std_allocator_unsigned_long_t, totals : rosetta.utility.vector1_unsigned_long, n : int) -> rosetta.utility.vector1_utility_vector1_unsigned_long_std_allocator_unsigned_long_t Gets all possible graft permutations. all_permutations is a list of vectors corresponding to cdrs_to_design vector.  Essentially, each inner index describes a position in the cdr_set. Indexes correspond to CDRNameEnum, and whose values correspond to the cdr_set index.  If the value is 0, it means no cdr in set. Example: <1, 0, 1, 1, 1, 1>.  This is a possible combination to try graft, the second CDR, H2 is not part of the combination.

get_cdr_set_options(...) method of builtins.PyCapsule instance
get_cdr_set_options(*args, **kwargs) Overloaded function. 1. get_cdr_set_options() -> rosetta.utility.vector1_std_shared_ptr_protocols_antibody_CDRSetOptions_t Get default options 2. get_cdr_set_options(instruction_file : str) -> rosetta.utility.vector1_std_shared_ptr_protocols_antibody_CDRSetOptions_t Get options from an instruction file

get_cluster_profile_probability_data(...) method of builtins.PyCapsule instance
get_cluster_profile_probability_data(*args, **kwargs) Overloaded function. 1. get_cluster_profile_probability_data(ab_info : rosetta.protocols.antibody.AntibodyInfo, pose : rosetta.core.pose.Pose, cdrs : rosetta.utility.vector1_bool, no_data_cdrs : rosetta.utility.vector1_bool) -> rosetta.std.map_unsigned_long_std_map_core_chemical_AA_double_std_less_core_chemical_AA_std_allocator_std_pair_const_core_chemical_AA_double_t Get probability data for a given set of CDRs.  Will fill in the no_data_cdrs; 2. get_cluster_profile_probability_data(ab_info : rosetta.protocols.antibody.AntibodyInfo, pose : rosetta.core.pose.Pose, cdrs : rosetta.utility.vector1_bool, no_data_cdrs : rosetta.utility.vector1_bool, prob_cutoff : int) -> rosetta.std.map_unsigned_long_std_map_core_chemical_AA_double_std_less_core_chemical_AA_std_allocator_std_pair_const_core_chemical_AA_double_t Get probability data for a given set of CDRs.  Will fill in the no_data_cdrs; 3. get_cluster_profile_probability_data(ab_info : rosetta.protocols.antibody.AntibodyInfo, pose : rosetta.core.pose.Pose, cdrs : rosetta.utility.vector1_bool, no_data_cdrs : rosetta.utility.vector1_bool, prob_cutoff : int, use_outliers : bool) -> rosetta.std.map_unsigned_long_std_map_core_chemical_AA_double_std_less_core_chemical_AA_std_allocator_std_pair_const_core_chemical_AA_double_t Get probability data for a given set of CDRs.  Will fill in the no_data_cdrs; 4. get_cluster_profile_probability_data(ab_info : rosetta.protocols.antibody.AntibodyInfo, pose : rosetta.core.pose.Pose, cdrs : rosetta.utility.vector1_bool, no_data_cdrs : rosetta.utility.vector1_bool, prob_cutoff : int, use_outliers : bool, force_north_db : bool) -> rosetta.std.map_unsigned_long_std_map_core_chemical_AA_double_std_less_core_chemical_AA_std_allocator_std_pair_const_core_chemical_AA_double_t Get probability data for a given set of CDRs.  Will fill in the no_data_cdrs; 5. get_cluster_profile_probability_data(ab_info : rosetta.protocols.antibody.AntibodyInfo, pose : rosetta.core.pose.Pose, seq_design_options : rosetta.utility.vector1_std_shared_ptr_protocols_antibody_design_CDRSeqDesignOptions_t, no_data_cdrs : rosetta.utility.vector1_bool) -> rosetta.std.map_unsigned_long_std_map_core_chemical_AA_double_std_less_core_chemical_AA_std_allocator_std_pair_const_core_chemical_AA_double_t 6. get_cluster_profile_probability_data(ab_info : rosetta.protocols.antibody.AntibodyInfo, pose : rosetta.core.pose.Pose, seq_design_options : rosetta.utility.vector1_std_shared_ptr_protocols_antibody_design_CDRSeqDesignOptions_t, no_data_cdrs : rosetta.utility.vector1_bool, prob_cutoff : int) -> rosetta.std.map_unsigned_long_std_map_core_chemical_AA_double_std_less_core_chemical_AA_std_allocator_std_pair_const_core_chemical_AA_double_t 7. get_cluster_profile_probability_data(ab_info : rosetta.protocols.antibody.AntibodyInfo, pose : rosetta.core.pose.Pose, seq_design_options : rosetta.utility.vector1_std_shared_ptr_protocols_antibody_design_CDRSeqDesignOptions_t, no_data_cdrs : rosetta.utility.vector1_bool, prob_cutoff : int, use_outliers : bool) -> rosetta.std.map_unsigned_long_std_map_core_chemical_AA_double_std_less_core_chemical_AA_std_allocator_std_pair_const_core_chemical_AA_double_t 8. get_cluster_profile_probability_data(ab_info : rosetta.protocols.antibody.AntibodyInfo, pose : rosetta.core.pose.Pose, seq_design_options : rosetta.utility.vector1_std_shared_ptr_protocols_antibody_design_CDRSeqDesignOptions_t, no_data_cdrs : rosetta.utility.vector1_bool, prob_cutoff : int, use_outliers : bool, force_north_db : bool) -> rosetta.std.map_unsigned_long_std_map_core_chemical_AA_double_std_less_core_chemical_AA_std_allocator_std_pair_const_core_chemical_AA_double_t

get_dock_chains_from_ab_dock_chains(...) method of builtins.PyCapsule instance
get_dock_chains_from_ab_dock_chains(ab_info : rosetta.protocols.antibody.AntibodyInfo, ab_dock_chains : str) -> str Convert an ab_dock_chain (L_H/ LH_A, etc. to the full dock chain string)

get_graft_design_options(...) method of builtins.PyCapsule instance
get_graft_design_options(*args, **kwargs) Overloaded function. 1. get_graft_design_options() -> rosetta.utility.vector1_std_shared_ptr_protocols_antibody_design_CDRGraftDesignOptions_t Get default options 2. get_graft_design_options(instruction_file : str) -> rosetta.utility.vector1_std_shared_ptr_protocols_antibody_design_CDRGraftDesignOptions_t Get options from an instruction file

get_native_sequence(...) method of builtins.PyCapsule instance
get_native_sequence(pose : rosetta.core.pose.Pose) -> str

get_pdb_numbering_from_single_string(...) method of builtins.PyCapsule instance
get_pdb_numbering_from_single_string(pdb_residue : str) -> rosetta.protocols.antibody.design.PDBNumbering Get the PDBNumbering from strings such as: 1A, 1A:I, 1:A:~, 1:A:I with A being chain A and I being an insertion code.

get_pdb_numbering_from_strings(...) method of builtins.PyCapsule instance
get_pdb_numbering_from_strings(pdb_residues : rosetta.utility.vector1_std_string) -> rosetta.utility.vector1_protocols_antibody_design_PDBNumbering Get PDBNumbering from a vector of strings:   Example: 1A, 1A:I, 1:A:~, 1:A:I with A being chain A and I being an insertion code.

get_resnum_from_pdb_numbering(...) method of builtins.PyCapsule instance
get_resnum_from_pdb_numbering(pose : rosetta.core.pose.Pose, pdb_residues : rosetta.utility.vector1_protocols_antibody_design_PDBNumbering) -> rosetta.utility.vector1_bool Get a boolean vector from a string of PDBNumbering.  No error checking.  Use with caution.

get_resnum_from_single_string(...) method of builtins.PyCapsule instance
get_resnum_from_single_string(pose : rosetta.core.pose.Pose, pdb_residue : str) -> int Get a resnum from strings such as: 1A, 1A:I, 1:A:~, 1:A:I with A being chain A and I being an insertion code.

get_resnum_from_single_string_w_landmark(...) method of builtins.PyCapsule instance
get_resnum_from_single_string_w_landmark(ab_info : rosetta.protocols.antibody.AntibodyInfo, pose : rosetta.core.pose.Pose, pdb_residue : str, scheme : rosetta.protocols.antibody.AntibodyNumberingSchemeEnum) -> int Get a resnum using the PDBLandmark from strings such as: 1A, 1A:I, 1:A:~, 1:A:I with A being chain A and I being an insertion code.

get_resnum_from_strings(...) method of builtins.PyCapsule instance
get_resnum_from_strings(pose : rosetta.core.pose.Pose, pdb_residues : rosetta.utility.vector1_std_string) -> rosetta.utility.vector1_bool get a boolean vector from a vector of strings:   Example: 1A, 1A:I, 1:A:~, 1:A:I with A being chain A and I being an insertion code.

get_resnums_from_strings_with_ranges(...) method of builtins.PyCapsule instance
get_resnums_from_strings_with_ranges(pose : rosetta.core.pose.Pose, pdb_residues : rosetta.utility.vector1_std_string) -> rosetta.utility.vector1_bool Get a boolean vector of resnums with ranges, where a - indicates range. Parses strings for PDB resnums such as 1A, 1A:I, 1:A:~, 1:A:I with A being chain A and I being an insertion code. Example: 1A-10A or 1A-10A:I

get_seq_design_options(...) method of builtins.PyCapsule instance
get_seq_design_options(*args, **kwargs) Overloaded function. 1. get_seq_design_options() -> rosetta.utility.vector1_std_shared_ptr_protocols_antibody_design_CDRSeqDesignOptions_t Get default options 2. get_seq_design_options(instruction_file : str) -> rosetta.utility.vector1_std_shared_ptr_protocols_antibody_design_CDRSeqDesignOptions_t Get options from an instruction file

has_native_sequence(...) method of builtins.PyCapsule instance
has_native_sequence(pose : rosetta.core.pose.Pose) -> bool

insert_cdr_into_antibody(...) method of builtins.PyCapsule instance
insert_cdr_into_antibody(*args, **kwargs) Overloaded function. 1. insert_cdr_into_antibody(ab_info : rosetta.protocols.antibody.AntibodyInfo, cdr : rosetta.protocols.antibody.CDRNameEnum, pose : rosetta.core.pose.Pose, cdr_piece : rosetta.core.pose.Pose) -> NoneType Use insert_pose_into_pose to replace the cdr_piece with the current antibody's CDR.  No modeling or superposition.  For that, use protocols/grafting 2. insert_cdr_into_antibody(ab_info : rosetta.protocols.antibody.AntibodyInfo, cdr : rosetta.protocols.antibody.CDRNameEnum, pose : rosetta.core.pose.Pose, cdr_piece : rosetta.core.pose.Pose, overhang : int) -> NoneType Use insert_pose_into_pose to replace the cdr_piece with the current antibody's CDR.  No modeling or superposition.  For that, use protocols/grafting

seq_design_strategy_to_enum(...) method of builtins.PyCapsule instance
seq_design_strategy_to_enum(strategy : str) -> rosetta.protocols.antibody.design.SeqDesignStrategyEnum

seq_design_strategy_to_string(...) method of builtins.PyCapsule instance
seq_design_strategy_to_string(strategy : rosetta.protocols.antibody.design.SeqDesignStrategyEnum) -> str

set_native_cdr_sequence(...) method of builtins.PyCapsule instance
set_native_cdr_sequence(ab_info : rosetta.protocols.antibody.AntibodyInfo, cdr : rosetta.protocols.antibody.CDRNameEnum, pose : rosetta.core.pose.Pose) -> NoneType Set the native CDR sequence into the pose datacache If none is set in the pose, will add it.

Data

DesignProtocolEnum_total = AntibodyDesignProtocolEnum.DesignProtocolEnum_total
MinTypeEnum_total = MinTypeEnum.MinTypeEnum_total
SeqDesignStrategyEnum_total = SeqDesignStrategyEnum.SeqDesignStrategyEnum_total
backrub_protocol = MinTypeEnum.backrub_protocol
centroid_relax = MinTypeEnum.centroid_relax
deterministic_graft = AntibodyDesignProtocolEnum.DesignProtocolEnum_total
dualspace = MinTypeEnum.dualspace
even_cluster_monte_carlo = AntibodyDesignProtocolEnum.even_cluster_monte_carlo
even_length_cluster_monte_carlo = AntibodyDesignProtocolEnum.even_length_cluster_monte_carlo
generalized_monte_carlo = AntibodyDesignProtocolEnum.generalized_monte_carlo
minimize = MinTypeEnum.minimize
minimize_cartesian = MinTypeEnum.minimize_cartesian
no_min = MinTypeEnum.MinTypeEnum_total
relax = MinTypeEnum.relax
repack = MinTypeEnum.repack
seq_design_basic = SeqDesignStrategyEnum.seq_design_basic
seq_design_conservative = SeqDesignStrategyEnum.seq_design_conservative
seq_design_none = SeqDesignStrategyEnum.SeqDesignStrategyEnum_total
seq_design_profile_sets = SeqDesignStrategyEnum.seq_design_profile_sets
seq_design_profile_sets_combined = SeqDesignStrategyEnum.seq_design_profile_sets_combined
seq_design_profiles = SeqDesignStrategyEnum.seq_design_profiles

Data
		DesignProtocolEnum_total = AntibodyDesignProtocolEnum.DesignProtocolEnum_total MinTypeEnum_total = MinTypeEnum.MinTypeEnum_total SeqDesignStrategyEnum_total = SeqDesignStrategyEnum.SeqDesignStrategyEnum_total backrub_protocol = MinTypeEnum.backrub_protocol centroid_relax = MinTypeEnum.centroid_relax deterministic_graft = AntibodyDesignProtocolEnum.DesignProtocolEnum_total dualspace = MinTypeEnum.dualspace even_cluster_monte_carlo = AntibodyDesignProtocolEnum.even_cluster_monte_carlo even_length_cluster_monte_carlo = AntibodyDesignProtocolEnum.even_length_cluster_monte_carlo generalized_monte_carlo = AntibodyDesignProtocolEnum.generalized_monte_carlo minimize = MinTypeEnum.minimize minimize_cartesian = MinTypeEnum.minimize_cartesian no_min = MinTypeEnum.MinTypeEnum_total relax = MinTypeEnum.relax repack = MinTypeEnum.repack seq_design_basic = SeqDesignStrategyEnum.seq_design_basic seq_design_conservative = SeqDesignStrategyEnum.seq_design_conservative seq_design_none = SeqDesignStrategyEnum.SeqDesignStrategyEnum_total seq_design_profile_sets = SeqDesignStrategyEnum.seq_design_profile_sets seq_design_profile_sets_combined = SeqDesignStrategyEnum.seq_design_profile_sets_combined seq_design_profiles = SeqDesignStrategyEnum.seq_design_profiles