Bindings for protocols::denovo_design namespace

Modules
		rosetta.protocols.denovo_design.architects rosetta.protocols.denovo_design.components rosetta.protocols.denovo_design.connection rosetta.protocols.denovo_design.constraints rosetta.protocols.denovo_design.filters rosetta.protocols.denovo_design.movers rosetta.protocols.denovo_design.residue_selectors rosetta.protocols.denovo_design.task_operations

Classes
		rosetta.protocols.moves.MoverCreator(builtins.object) DisulfidizeMoverCreator rosetta.protocols.rosetta_scripts.MultiplePoseMover(rosetta.protocols.moves.Mover) DisulfidizeMover   class DisulfidizeMover(rosetta.protocols.rosetta_scripts.MultiplePoseMover)       Method resolution order: DisulfidizeMover rosetta.protocols.rosetta_scripts.MultiplePoseMover 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.denovo_design.DisulfidizeMover) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. build_and_score_disulfide(...) from builtins.PyCapsule build_and_score_disulfide(self : rosetta.protocols.denovo_design.DisulfidizeMover, blank_pose : rosetta.core.pose.Pose, sfxn_disulfonly : rosetta.core.scoring.ScoreFunction, sfxn_full : rosetta.core.scoring.ScoreFunction, relax_bb : bool, res1 : int, res2 : int) -> float   temporarily tries building a disulfide between the given positions, scores, and restores the pose check_disulfide_cb_distance(...) from builtins.PyCapsule check_disulfide_cb_distance(self : rosetta.protocols.denovo_design.DisulfidizeMover, pose : rosetta.core.pose.Pose, res1 : int, res2 : int) -> bool   checks disulfide CB-CB distance check_disulfide_match_rt(...) from builtins.PyCapsule check_disulfide_match_rt(self : rosetta.protocols.denovo_design.DisulfidizeMover, pose : rosetta.core.pose.Pose, res1 : int, res2 : int, disulfPot : rosetta.core.scoring.disulfides.DisulfideMatchingPotential, mirror : bool) -> bool   checks disulfide match rt check_disulfide_score(...) from builtins.PyCapsule check_disulfide_score(self : rosetta.protocols.denovo_design.DisulfidizeMover, pose : rosetta.core.pose.Pose, res1 : int, res2 : int, sfxn_disulfonly : rosetta.core.scoring.ScoreFunction, sfxn_full : rosetta.core.scoring.ScoreFunction) -> bool   checks disulfide rosetta score check_disulfide_seqpos(...) from builtins.PyCapsule check_disulfide_seqpos(self : rosetta.protocols.denovo_design.DisulfidizeMover, res1 : int, res2 : int) -> bool   checks seqpos to ensure that min_loop is satisfied check_residue_type(...) from builtins.PyCapsule check_residue_type(self : rosetta.protocols.denovo_design.DisulfidizeMover, pose : rosetta.core.pose.Pose, res : int) -> bool   checks seqpos to ensure that min_loop is satisfied clone(...) from builtins.PyCapsule clone(rosetta.protocols.denovo_design.DisulfidizeMover) -> rosetta.protocols.moves.Mover   return a fresh instance of this class in an owning pointer find_current_disulfides(...) from builtins.PyCapsule find_current_disulfides(self : rosetta.protocols.denovo_design.DisulfidizeMover, pose : rosetta.core.pose.Pose, subset1 : rosetta.utility.vector1_bool, subset2 : rosetta.utility.vector1_bool) -> rosetta.utility.vector1_std_pair_unsigned_long_unsigned_long_t   finds disulfides within a pose subset find_possible_disulfides(...) from builtins.PyCapsule find_possible_disulfides(*args, **kwargs) Overloaded function.   1. find_possible_disulfides(self : rosetta.protocols.denovo_design.DisulfidizeMover, pose : rosetta.core.pose.Pose, residueset1 : rosetta.utility.vector1_bool, residueset2 : rosetta.utility.vector1_bool, sfxn : rosetta.core.scoring.ScoreFunction) -> rosetta.utility.vector1_std_pair_unsigned_long_unsigned_long_t   find disulfides in the given neighborhood   2. find_possible_disulfides(self : rosetta.protocols.denovo_design.DisulfidizeMover, pose : rosetta.core.pose.Pose, set1 : rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t, set2 : rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t, sfxn : rosetta.core.scoring.ScoreFunction) -> rosetta.utility.vector1_std_pair_unsigned_long_unsigned_long_t   find disulfides in the given neighborhood between residues in set 1 and residues in set 2 get_name(...) from builtins.PyCapsule get_name(rosetta.protocols.denovo_design.DisulfidizeMover) -> str   Return the name of this mover. make_disulfide(...) from builtins.PyCapsule make_disulfide(self : rosetta.protocols.denovo_design.DisulfidizeMover, pose : rosetta.core.pose.Pose, res1 : int, res2 : int, relax_bb : bool, sfxn : rosetta.core.scoring.ScoreFunction) -> NoneType   forms a disulfide between res1 and res2, optionally allowing backbone movement make_disulfides(...) from builtins.PyCapsule make_disulfides(self : rosetta.protocols.denovo_design.DisulfidizeMover, pose : rosetta.core.pose.Pose, disulf : rosetta.utility.vector1_std_pair_unsigned_long_unsigned_long_t, relax_bb : bool, sfxn : rosetta.core.scoring.ScoreFunction) -> NoneType   creates disulfides given the list of pairs given mixed_disulfide(...) from builtins.PyCapsule mixed_disulfide(self : rosetta.protocols.denovo_design.DisulfidizeMover, pose : rosetta.core.pose.Pose, res1 : int, res2 : int) -> bool   Returns true if this is a mixed D/L disulfide, false otherwise. mutate_disulfides_to_ala(...) from builtins.PyCapsule mutate_disulfides_to_ala(self : rosetta.protocols.denovo_design.DisulfidizeMover, pose : rosetta.core.pose.Pose, current_ds : rosetta.utility.vector1_std_pair_unsigned_long_unsigned_long_t) -> NoneType   mutates the given disulfides to ALA recursive_multiple_disulfide_former(...) from builtins.PyCapsule recursive_multiple_disulfide_former(self : rosetta.protocols.denovo_design.DisulfidizeMover, disulfides_formed : rosetta.utility.vector1_std_pair_unsigned_long_unsigned_long_t, disulfides_possible : rosetta.utility.vector1_std_pair_unsigned_long_unsigned_long_t) -> rosetta.utility.vector1_utility_vector1_std_pair_unsigned_long_unsigned_long_std_allocator_std_pair_unsigned_long_unsigned_long_t   Function for recursively creating multiple disulfides set_cys_types(...) from builtins.PyCapsule set_cys_types(self : rosetta.protocols.denovo_design.DisulfidizeMover, lcys : bool, dcys : bool) -> NoneType   Set the types of cysteines that we design with:      By default, we use only L-cysteine (not D-cysteine). set_match_rt_limit(...) from builtins.PyCapsule set_match_rt_limit(self : rosetta.protocols.denovo_design.DisulfidizeMover, matchrtval : float) -> NoneType   sets the maximum allowed "match-rt-limit" (default=1.0)      Changed from default=2.0 by VKM on 19 Aug 2015 after fixing major bug in  DisulfideMatchPotential. set_max_disulf_score(...) from builtins.PyCapsule set_max_disulf_score(self : rosetta.protocols.denovo_design.DisulfidizeMover, maxscoreval : float) -> NoneType   sets the maximum allowed per-disulfide dslf_fa13 score (default=0.0) set_min_loop(...) from builtins.PyCapsule set_min_loop(self : rosetta.protocols.denovo_design.DisulfidizeMover, minloopval : int) -> NoneType   sets the min_loop value (number of residues between disulfide-joined residues) (default=8) set_mutate_gly(...) from builtins.PyCapsule set_mutate_gly(self : rosetta.protocols.denovo_design.DisulfidizeMover, mutate_gly : bool) -> NoneType   If true, GLY --> CYS mutations will be allowed. Default=false set_mutate_pro(...) from builtins.PyCapsule set_mutate_pro(self : rosetta.protocols.denovo_design.DisulfidizeMover, mutate_pro : bool) -> NoneType   If true, PRO --> CYS mutations will be allowed. Default=false set_scorefxn(...) from builtins.PyCapsule set_scorefxn(self : rosetta.protocols.denovo_design.DisulfidizeMover, sfxn_in : rosetta.core.scoring.ScoreFunction) -> NoneType   Set the scorefunction to use for scoring disulfides, minimizing, and repacking.      Clones the input scorefunction; does not copy it. set_set1_selector(...) from builtins.PyCapsule set_set1_selector(self : rosetta.protocols.denovo_design.DisulfidizeMover, selector : rosetta.core.select.residue_selector.ResidueSelector) -> NoneType   sets the selector for set 1 -- disulfides will connect residues in set 1 to residues in set 2 set_set2_selector(...) from builtins.PyCapsule set_set2_selector(self : rosetta.protocols.denovo_design.DisulfidizeMover, selector : rosetta.core.select.residue_selector.ResidueSelector) -> NoneType   sets the selector for set 2 -- disulfides will connect residues in set 1 to residues in set 2 tag_disulfide(...) from builtins.PyCapsule tag_disulfide(self : rosetta.protocols.denovo_design.DisulfidizeMover, pose : rosetta.core.pose.Pose, res1 : int, res2 : int) -> NoneType   creates a residue tags on disulfides to inform users that this disulfide was created by disulfidize tag_disulfides(...) from builtins.PyCapsule tag_disulfides(self : rosetta.protocols.denovo_design.DisulfidizeMover, pose : rosetta.core.pose.Pose, disulf : rosetta.utility.vector1_std_pair_unsigned_long_unsigned_long_t) -> NoneType   creates a residue tags on disulfides to inform users that this disulfide was created by disulfidize Methods inherited from rosetta.protocols.rosetta_scripts.MultiplePoseMover: apply(...) from builtins.PyCapsule apply(self : rosetta.protocols.rosetta_scripts.MultiplePoseMover, pose : rosetta.core.pose.Pose) -> NoneType fresh_instance(...) from builtins.PyCapsule fresh_instance(rosetta.protocols.rosetta_scripts.MultiplePoseMover) -> rosetta.protocols.moves.Mover get_additional_output(...) from builtins.PyCapsule get_additional_output(rosetta.protocols.rosetta_scripts.MultiplePoseMover) -> rosetta.core.pose.Pose set_previous_mover(...) from builtins.PyCapsule set_previous_mover(self : rosetta.protocols.rosetta_scripts.MultiplePoseMover, m : rosetta.protocols.moves.Mover) -> NoneType   Used by RosettaScripts to set the previous mover to pull poses from set_rosetta_scripts_tag(...) from builtins.PyCapsule set_rosetta_scripts_tag(self : rosetta.protocols.rosetta_scripts.MultiplePoseMover, tag : rosetta.utility.tag.Tag) -> NoneType   sets rosettascripts tag Methods inherited from rosetta.protocols.moves.Mover: assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.moves.Mover, other : rosetta.protocols.moves.Mover) -> 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_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 DisulfidizeMoverCreator(rosetta.protocols.moves.MoverCreator)       Method resolution order: DisulfidizeMoverCreator 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.denovo_design.DisulfidizeMoverCreator,  : rosetta.protocols.denovo_design.DisulfidizeMoverCreator) -> rosetta.protocols.denovo_design.DisulfidizeMoverCreator create_mover(...) from builtins.PyCapsule create_mover(rosetta.protocols.denovo_design.DisulfidizeMoverCreator) -> rosetta.protocols.moves.Mover keyname(...) from builtins.PyCapsule keyname(rosetta.protocols.denovo_design.DisulfidizeMoverCreator) -> str mover_name(...) from builtins.PyCapsule mover_name() -> str

Functions
		abego_str(...) method of builtins.PyCapsule instance abego_str(abego : rosetta.utility.vector1_std_string) -> str abego_vector(...) method of builtins.PyCapsule instance abego_vector(ab : str) -> rosetta.utility.vector1_std_string add_chain_from_pose(...) method of builtins.PyCapsule instance add_chain_from_pose(to_add : rosetta.core.pose.Pose, combined : rosetta.core.pose.Pose) -> NoneType   dumps a pose into another pose as a new chain add_remark(...) method of builtins.PyCapsule instance add_remark(remarks : rosetta.core.io.Remarks, num : int, str_val : str) -> NoneType   adds a remark to a Remarks object, splitting it into multiple remarks if it is too long add_residues_to_pose(...) method of builtins.PyCapsule instance add_residues_to_pose(pose : rosetta.core.pose.Pose, template_pose : rosetta.core.pose.Pose, new_chain : bool) -> NoneType   adds residues from template_pose to pose.  If new_chain == true, creates covalent bond construct_dummy_pose(...) method of builtins.PyCapsule instance construct_dummy_pose(*args, **kwargs) Overloaded function.   1. construct_dummy_pose(restype_name : str) -> rosetta.core.pose.Pose   builds an extended-conformation poly-XXX pose   2. construct_dummy_pose(restype_name : str, length : int) -> rosetta.core.pose.Pose   3. construct_dummy_pose(restype : rosetta.core.chemical.ResidueType) -> rosetta.core.pose.Pose   4. construct_dummy_pose(restype : rosetta.core.chemical.ResidueType, length : int) -> rosetta.core.pose.Pose construct_poly_ala_pose(...) method of builtins.PyCapsule instance construct_poly_ala_pose(*args, **kwargs) Overloaded function.   1. construct_poly_ala_pose(pose : rosetta.core.pose.Pose, keep_disulf : bool, set1 : rosetta.utility.vector1_bool, set2 : rosetta.utility.vector1_bool) -> NoneType   creates a poly-ala pose where every non-gly, non-cyd, protein residue except those in the given set are converted to alanine      If keep_chirality is true, the D-amino acids are mutated to D-alanine.   2. construct_poly_ala_pose(pose : rosetta.core.pose.Pose, keep_disulf : bool, set1 : rosetta.utility.vector1_bool, set2 : rosetta.utility.vector1_bool, keep_chirality : bool) -> NoneType   creates a poly-ala pose where every non-gly, non-cyd, protein residue except those in the given set are converted to alanine      If keep_chirality is true, the D-amino acids are mutated to D-alanine.   3. construct_poly_ala_pose(pose : rosetta.core.pose.Pose, keep_disulf : bool, res_set : rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t) -> NoneType   creates a poly-ala pose where every non-gly, non-cyd, protein residue except those in the given set are converted to alanine      If keep_chirality is true, the D-amino acids are mutated to D-alanine.   4. construct_poly_ala_pose(pose : rosetta.core.pose.Pose, keep_disulf : bool, res_set : rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t, keep_chirality : bool) -> NoneType   creates a poly-ala pose where every non-gly, non-cyd, protein residue except those in the given set are converted to alanine      If keep_chirality is true, the D-amino acids are mutated to D-alanine. count_bulges(...) method of builtins.PyCapsule instance count_bulges(perm : rosetta.protocols.denovo_design.components.StructureData, segment : str) -> int   counts the beta-bulges in the given segment. This simply counts all abego A's in the segment extract_int(...) method of builtins.PyCapsule instance extract_int(num : float, m : int, n : int) -> int   given a number 0 <= x < 1, calculate an integer M <= x <= N  NOTE THAT THIS FUNCTION MODIFIES THE PARAMETER find_jump_rec(...) method of builtins.PyCapsule instance find_jump_rec(ft : rosetta.core.kinematics.FoldTree, residue : int) -> int   helper function that looks for the given residue in a fold tree and returns the jump that controls its 6D-DoFs get_remark_line(...) method of builtins.PyCapsule instance get_remark_line(it_rem : __gnu_cxx::__normal_iterator<core::io::RemarkInfo const*, std::vector<core::io::RemarkInfo, std::allocator<core::io::RemarkInfo> > >, end : __gnu_cxx::__normal_iterator<core::io::RemarkInfo const*, std::vector<core::io::RemarkInfo, std::allocator<core::io::RemarkInfo> > >) -> str get_resid(...) method of builtins.PyCapsule instance get_resid(sd : rosetta.protocols.denovo_design.components.StructureData, resid_str : str) -> int get_residue_selector(...) method of builtins.PyCapsule instance get_residue_selector(data : rosetta.basic.datacache.DataMap, name : str) -> rosetta.core.select.residue_selector.ResidueSelector get_strandpairings(...) method of builtins.PyCapsule instance get_strandpairings(perm : rosetta.protocols.denovo_design.components.StructureData, use_register_shift : bool) -> str   gets all strand pairings from a perm      if use_register_shift=0, the returned register shift is 99 insert_peptide_edges(...) method of builtins.PyCapsule instance insert_peptide_edges(ft : rosetta.core.kinematics.FoldTree, jedge : rosetta.core.kinematics.Edge) -> NoneType   inserts the peptide edges to accomodate the new jump edge given linear_chainbreak(...) method of builtins.PyCapsule instance linear_chainbreak(pose : rosetta.core.pose.Pose, pos : int) -> float   evaluate linear chainbreak at a position      If necessary, will evaluate using a copy of the Pose with a cut   fold tree.  If cutpoint variants are present at chainbreak, will use   existing variants and not modify them.  If cutpoint variants are not   found will add them and then remove them once calculation is finished.   Eventually this should be merged into protocols/forge/methods/linear_chainbreak.cc   However, the changes I needed to make to that file break certain parts   of remodel loop_start_without_overlap(...) method of builtins.PyCapsule instance loop_start_without_overlap(pose : rosetta.core.pose.Pose, startres : int, overlap : int) -> int loop_stop_without_overlap(...) method of builtins.PyCapsule instance loop_stop_without_overlap(pose : rosetta.core.pose.Pose, stopres : int, overlap : int) -> int parse_length_string(...) method of builtins.PyCapsule instance parse_length_string(len_str : str) -> rosetta.utility.vector1_unsigned_long rebuild_missing_atoms(...) method of builtins.PyCapsule instance rebuild_missing_atoms(pose : rosetta.core.pose.Pose, resi : int) -> NoneType   given a residue, rebuilds all missing atoms remove_all_jump_atoms(...) method of builtins.PyCapsule instance remove_all_jump_atoms(orig : rosetta.core.kinematics.FoldTree) -> rosetta.core.kinematics.FoldTree remove_missing_jump_atoms(...) method of builtins.PyCapsule instance remove_missing_jump_atoms(pose : rosetta.core.pose.Pose, orig : rosetta.core.kinematics.FoldTree) -> rosetta.core.kinematics.FoldTree same_pose(...) method of builtins.PyCapsule instance same_pose(pose1 : rosetta.core.pose.Pose, pose2 : rosetta.core.pose.Pose) -> bool   Tells whether the two given poses are identical based on # resides and dihedrals slide_jump(...) method of builtins.PyCapsule instance slide_jump(ft_orig : rosetta.core.kinematics.FoldTree, jump_idx : int, new_start : int, new_stop : int) -> rosetta.core.kinematics.FoldTree