Bindings for protocols::forge::build namespace

Modules
		rosetta.protocols.forge.build.BuildInstructionState rosetta.protocols.forge.build.SegmentInsertConnectionScheme

Classes
		builtins.object BuildInstruction Bridge ConnectRight RelativeConnectRight GrowLeft GrowRight SegmentInsert SegmentRebuild SegmentSwap BuildManager Interval RelativeSequencePosition CountFromLeft   class Bridge(BuildInstruction)     connect two contiguous but disjoint sections of a Pose into one  continuous section     Anchor residues [i,j] to bridge must be adjacent to each other in the  Pose (i+1 = j) and adjacent to a cutpoint.  Both i and j will be idealized  and marked as new moveable positions since the psi @ i and the phi @ j are  undefined.  Depending on the fold tree, this will cause a random swing  either downstream or upstream of the bridge!     Method resolution order: Bridge BuildInstruction builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle) -> NoneType   2. __init__(handle, rosetta.protocols.forge.build.Interval, str) -> NoneType   doc   3. __init__(self : handle, i : rosetta.protocols.forge.build.Interval, ss : str, rts : rosetta.std.weak_ptr_const_core_chemical_ResidueTypeSet_t) -> NoneType   4. __init__(handle, rosetta.protocols.forge.build.Interval, str, str) -> NoneType   doc   5. __init__(self : handle, i : rosetta.protocols.forge.build.Interval, ss : str, aa : str, rts : rosetta.std.weak_ptr_const_core_chemical_ResidueTypeSet_t) -> NoneType   6. __init__(handle, rosetta.protocols.forge.build.Bridge) -> 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.forge.build.Bridge, rval : rosetta.protocols.forge.build.Bridge) -> rosetta.protocols.forge.build.Bridge   copy assignment clone(...) from builtins.PyCapsule clone(rosetta.protocols.forge.build.Bridge) -> rosetta.protocols.forge.build.BuildInstruction   clone this object creates_undefined_backbone(...) from builtins.PyCapsule creates_undefined_backbone(rosetta.protocols.forge.build.Bridge) -> bool   does this object create undefined backbone in the modified region? defined_positions(...) from builtins.PyCapsule defined_positions(rosetta.protocols.forge.build.Bridge) -> rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t   return a copy of the set of positions within the newly modified   region that has a defined conformation.  E.g. existing or copied residues.      A set containing two positions -- interval.left and interval.right.      This set can change wrt length changes in Pose/Conformation being   watched. interval(...) from builtins.PyCapsule interval(rosetta.protocols.forge.build.Bridge) -> rosetta.protocols.forge.build.Interval   a copy of the working range of residues specifying the bridged region   including the anchors      This residue range can change wrt length changes in Pose /Conformation   being watched. movemap(...) from builtins.PyCapsule movemap(rosetta.protocols.forge.build.Bridge) -> rosetta.core.kinematics.MoveMap   return a copy of the MoveMap that defines the moveable/fixed   positions/dofs for this instruction      a MoveMap with [interval.left, interval.right] bb & chi set to true   at the MoveMapTorsionID level      This set can change wrt length changes in Pose/Conformation being   watched. new_positions(...) from builtins.PyCapsule new_positions(rosetta.protocols.forge.build.Bridge) -> rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t   return a copy of the set of positions that are "new" and did   not exist in the original Pose.      A set containing positions spanning [interval.left+1, interval.right-1]. on_residue_append(...) from builtins.PyCapsule on_residue_append(self : rosetta.protocols.forge.build.Bridge, event : rosetta.core.conformation.signals.LengthEvent) -> NoneType   update indexing on residue append on_residue_delete(...) from builtins.PyCapsule on_residue_delete(self : rosetta.protocols.forge.build.Bridge, event : rosetta.core.conformation.signals.LengthEvent) -> NoneType   update indexing on residue delete on_residue_prepend(...) from builtins.PyCapsule on_residue_prepend(self : rosetta.protocols.forge.build.Bridge, event : rosetta.core.conformation.signals.LengthEvent) -> NoneType   update indexing on residue prepend original_deleted_positions(...) from builtins.PyCapsule original_deleted_positions(rosetta.protocols.forge.build.Bridge) -> rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t   return set of positions within the original interval that will   be deleted in this BuildInstruction      A set containing the positions in [original.left+1, original.right-1]. original_fixed_positions(...) from builtins.PyCapsule original_fixed_positions(rosetta.protocols.forge.build.Bridge) -> rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t   return set of any fixed positions necessary with respect to the original   interval and original Pose numbering      Used for ensuring build regions for instructions do not overlap and   so that jumps may be placed correctly.      empty set if no fixed positions necessary original_interval_valid(...) from builtins.PyCapsule original_interval_valid(rosetta.protocols.forge.build.Bridge) -> bool   is the original interval storing valid information, or is empty   or being used for something else?      true, stores valid interval original_kept_positions(...) from builtins.PyCapsule original_kept_positions(rosetta.protocols.forge.build.Bridge) -> rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t   return the set of positions within the original interval that   will be kept in this BuildInstruction      A set containing the endpoints of the original interval. original_mutable_positions(...) from builtins.PyCapsule original_mutable_positions(rosetta.protocols.forge.build.Bridge) -> rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t   return set of any mutable positions necessary with respect to the original   interval and original Pose numbering      Used for ensuring build regions for instructions do not overlap and   so that jumps may be placed correctly. preexisting_positions(...) from builtins.PyCapsule preexisting_positions(rosetta.protocols.forge.build.Bridge) -> rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t   return a copy of the set of positions within the new region   that were pre-existing in the original Pose prior to modify()      A set containing two positions -- interval.left and interval.right. undefined_positions(...) from builtins.PyCapsule undefined_positions(rosetta.protocols.forge.build.Bridge) -> rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t   return a copy of the set of positions within the newly modified   region that has an undefined conformation.  E.g. newly created residues.      A set containing positions spanning [interval.left+1, interval.right-1].      This set can change wrt length changes in Pose/Conformation being   watched. Methods inherited from BuildInstruction: add_dependency_to(...) from builtins.PyCapsule add_dependency_to(self : rosetta.protocols.forge.build.BuildInstruction, i : rosetta.std.weak_ptr_const_protocols_forge_build_BuildInstruction_t) -> NoneType   add an instruction to this BuildInstruction's dependency list      before this instruction's modify() may complete properly, all   instructions in the dependency list must have completed modify() first attach_to(...) from builtins.PyCapsule attach_to(self : rosetta.protocols.forge.build.BuildInstruction, pose : rosetta.core.pose.Pose) -> NoneType   attach to a Pose's conformation clear_dependencies(...) from builtins.PyCapsule clear_dependencies(rosetta.protocols.forge.build.BuildInstruction) -> NoneType   clear the list of dependencies compatible_with(...) from builtins.PyCapsule compatible_with(self : rosetta.protocols.forge.build.BuildInstruction, rval : rosetta.protocols.forge.build.BuildInstruction) -> bool   compares fixed and mutable positions to determine compatibility with   another instruction      override this to obtain custom compatibility check dependencies(...) from builtins.PyCapsule dependencies(rosetta.protocols.forge.build.BuildInstruction) -> rosetta.utility.vector1_std_weak_ptr_const_protocols_forge_build_BuildInstruction_t   the list of instructions whose modify() must complete before   the modify() for this instruction may be called successfully dependent_on(...) from builtins.PyCapsule dependent_on(self : rosetta.protocols.forge.build.BuildInstruction, i : rosetta.std.weak_ptr_const_protocols_forge_build_BuildInstruction_t) -> bool   is this instruction dependent upon the given instruction? detach_after_modify(...) from builtins.PyCapsule detach_after_modify(*args, **kwargs) Overloaded function.   1. detach_after_modify(rosetta.protocols.forge.build.BuildInstruction) -> bool   detach after modify()?      Ordinarily a modify() call consists of attaching as a   length obs of the Pose, actually doing the modify, and then   detaching as a length obs of the Pose.  This flag governs whether   the last detach occurs.   2. detach_after_modify(self : rosetta.protocols.forge.build.BuildInstruction, flag : bool) -> NoneType   set detach after modify()      Ordinarily a modify() call consists of attaching as a   length obs of the Pose, actually doing the modify, and then   detaching as a length obs of the Pose.  This flag governs whether   the last detach occurs. detach_from(...) from builtins.PyCapsule detach_from(rosetta.protocols.forge.build.BuildInstruction) -> NoneType   detach from a Pose's conformation has_dependencies(...) from builtins.PyCapsule has_dependencies(rosetta.protocols.forge.build.BuildInstruction) -> bool   does this BuildInstruction have dependencies? modify(...) from builtins.PyCapsule modify(self : rosetta.protocols.forge.build.BuildInstruction, pose : rosetta.core.pose.Pose) -> rosetta.protocols.forge.build.BuildInstructionState.Enum   modify this pose      the state of the BuildInstruction modify_was_successful(...) from builtins.PyCapsule modify_was_successful(rosetta.protocols.forge.build.BuildInstruction) -> bool   Is the BuildInstruction's state at MODIFY_WAS_SUCCESSFUL?      MODIFY_WAS_SUCCESSFUL indicates the BuildInstruction has   finished modifications to the Pose, and its residue indexing is now   consistent with the newly modified Pose. n_dependencies(...) from builtins.PyCapsule n_dependencies(rosetta.protocols.forge.build.BuildInstruction) -> int   the number of dependencies this BuildInstruction has on_length_change(...) from builtins.PyCapsule on_length_change(self : rosetta.protocols.forge.build.BuildInstruction, event : rosetta.core.conformation.signals.LengthEvent) -> NoneType   update any indexing wrt length change to Pose/Conformation being watched original_interval(...) from builtins.PyCapsule original_interval(rosetta.protocols.forge.build.BuildInstruction) -> rosetta.protocols.forge.build.Interval   return original residue range of this instruction ready(...) from builtins.PyCapsule ready(rosetta.protocols.forge.build.BuildInstruction) -> bool   Is the BuildInstruction's state at READY?      READY indicates the BuildInstruction has been reset   and is ready to modify a Pose. reset_accounting(...) from builtins.PyCapsule reset_accounting(rosetta.protocols.forge.build.BuildInstruction) -> NoneType   reset intervals, positions, etc to initial state and drop   observers.  State set to READY. residue_type_set(...) from builtins.PyCapsule residue_type_set(rosetta.protocols.forge.build.BuildInstruction) -> rosetta.core.chemical.ResidueTypeSet   the residue type set being used state(...) from builtins.PyCapsule state(rosetta.protocols.forge.build.BuildInstruction) -> rosetta.protocols.forge.build.BuildInstructionState.Enum   return the state of this BuildInstruction waiting_on_dependencies(...) from builtins.PyCapsule waiting_on_dependencies(rosetta.protocols.forge.build.BuildInstruction) -> bool   Is the BuildInstruction's state at WAITING_ON_DEPENDENCIES?      WAITING_ON_DEPENDENCIES indicates   the BuildInstruction is waiting for its dependencies to be satisfied   before allowing modifications to proceed.   class BuildInstruction(builtins.object)     tracks modifications to be made and is capable of making residue length changes on a Pose     Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.protocols.forge.build.BuildInstruction) -> NoneType   2. __init__(rosetta.protocols.forge.build.BuildInstruction, rosetta.protocols.forge.build.Interval) -> NoneType   doc   3. __init__(self : rosetta.protocols.forge.build.BuildInstruction, i : rosetta.protocols.forge.build.Interval, rts : rosetta.std.weak_ptr_const_core_chemical_ResidueTypeSet_t) -> NoneType   4. __init__(rosetta.protocols.forge.build.BuildInstruction, rosetta.protocols.forge.build.BuildInstruction) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. add_dependency_to(...) from builtins.PyCapsule add_dependency_to(self : rosetta.protocols.forge.build.BuildInstruction, i : rosetta.std.weak_ptr_const_protocols_forge_build_BuildInstruction_t) -> NoneType   add an instruction to this BuildInstruction's dependency list      before this instruction's modify() may complete properly, all   instructions in the dependency list must have completed modify() first assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.forge.build.BuildInstruction, rval : rosetta.protocols.forge.build.BuildInstruction) -> rosetta.protocols.forge.build.BuildInstruction   copy assignment attach_to(...) from builtins.PyCapsule attach_to(self : rosetta.protocols.forge.build.BuildInstruction, pose : rosetta.core.pose.Pose) -> NoneType   attach to a Pose's conformation clear_dependencies(...) from builtins.PyCapsule clear_dependencies(rosetta.protocols.forge.build.BuildInstruction) -> NoneType   clear the list of dependencies clone(...) from builtins.PyCapsule clone(rosetta.protocols.forge.build.BuildInstruction) -> rosetta.protocols.forge.build.BuildInstruction   clone this object compatible_with(...) from builtins.PyCapsule compatible_with(self : rosetta.protocols.forge.build.BuildInstruction, rval : rosetta.protocols.forge.build.BuildInstruction) -> bool   compares fixed and mutable positions to determine compatibility with   another instruction      override this to obtain custom compatibility check creates_undefined_backbone(...) from builtins.PyCapsule creates_undefined_backbone(rosetta.protocols.forge.build.BuildInstruction) -> bool   does this object create undefined backbone in the modified region? defined_positions(...) from builtins.PyCapsule defined_positions(rosetta.protocols.forge.build.BuildInstruction) -> rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t   return a copy of the set of positions within the newly modified   region that has a defined conformation.  E.g. existing or copied residues.      This set can change wrt length changes in Pose/Conformation being   watched. dependencies(...) from builtins.PyCapsule dependencies(rosetta.protocols.forge.build.BuildInstruction) -> rosetta.utility.vector1_std_weak_ptr_const_protocols_forge_build_BuildInstruction_t   the list of instructions whose modify() must complete before   the modify() for this instruction may be called successfully dependent_on(...) from builtins.PyCapsule dependent_on(self : rosetta.protocols.forge.build.BuildInstruction, i : rosetta.std.weak_ptr_const_protocols_forge_build_BuildInstruction_t) -> bool   is this instruction dependent upon the given instruction? detach_after_modify(...) from builtins.PyCapsule detach_after_modify(*args, **kwargs) Overloaded function.   1. detach_after_modify(rosetta.protocols.forge.build.BuildInstruction) -> bool   detach after modify()?      Ordinarily a modify() call consists of attaching as a   length obs of the Pose, actually doing the modify, and then   detaching as a length obs of the Pose.  This flag governs whether   the last detach occurs.   2. detach_after_modify(self : rosetta.protocols.forge.build.BuildInstruction, flag : bool) -> NoneType   set detach after modify()      Ordinarily a modify() call consists of attaching as a   length obs of the Pose, actually doing the modify, and then   detaching as a length obs of the Pose.  This flag governs whether   the last detach occurs. detach_from(...) from builtins.PyCapsule detach_from(rosetta.protocols.forge.build.BuildInstruction) -> NoneType   detach from a Pose's conformation has_dependencies(...) from builtins.PyCapsule has_dependencies(rosetta.protocols.forge.build.BuildInstruction) -> bool   does this BuildInstruction have dependencies? interval(...) from builtins.PyCapsule interval(rosetta.protocols.forge.build.BuildInstruction) -> rosetta.protocols.forge.build.Interval   a copy of the working range of residues specifying the modified region      This residue range can change wrt length changes in Pose /Conformation   being watched. modify(...) from builtins.PyCapsule modify(self : rosetta.protocols.forge.build.BuildInstruction, pose : rosetta.core.pose.Pose) -> rosetta.protocols.forge.build.BuildInstructionState.Enum   modify this pose      the state of the BuildInstruction modify_was_successful(...) from builtins.PyCapsule modify_was_successful(rosetta.protocols.forge.build.BuildInstruction) -> bool   Is the BuildInstruction's state at MODIFY_WAS_SUCCESSFUL?      MODIFY_WAS_SUCCESSFUL indicates the BuildInstruction has   finished modifications to the Pose, and its residue indexing is now   consistent with the newly modified Pose. movemap(...) from builtins.PyCapsule movemap(rosetta.protocols.forge.build.BuildInstruction) -> rosetta.core.kinematics.MoveMap   return a copy of the MoveMap that defines the moveable/fixed   positions/dofs for this instruction      This set can change wrt length changes in Pose/Conformation being   watched. n_dependencies(...) from builtins.PyCapsule n_dependencies(rosetta.protocols.forge.build.BuildInstruction) -> int   the number of dependencies this BuildInstruction has new_positions(...) from builtins.PyCapsule new_positions(rosetta.protocols.forge.build.BuildInstruction) -> rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t   return a copy of the set of positions that are "new" and did   not exist in the original Pose. on_length_change(...) from builtins.PyCapsule on_length_change(self : rosetta.protocols.forge.build.BuildInstruction, event : rosetta.core.conformation.signals.LengthEvent) -> NoneType   update any indexing wrt length change to Pose/Conformation being watched on_residue_append(...) from builtins.PyCapsule on_residue_append(self : rosetta.protocols.forge.build.BuildInstruction, event : rosetta.core.conformation.signals.LengthEvent) -> NoneType   update indexing on residue append on_residue_delete(...) from builtins.PyCapsule on_residue_delete(self : rosetta.protocols.forge.build.BuildInstruction, event : rosetta.core.conformation.signals.LengthEvent) -> NoneType   update indexing on residue delete on_residue_prepend(...) from builtins.PyCapsule on_residue_prepend(self : rosetta.protocols.forge.build.BuildInstruction, event : rosetta.core.conformation.signals.LengthEvent) -> NoneType   update indexing on residue prepend original_deleted_positions(...) from builtins.PyCapsule original_deleted_positions(rosetta.protocols.forge.build.BuildInstruction) -> rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t   return set of positions within the original interval that will   be deleted in this BuildInstruction original_fixed_positions(...) from builtins.PyCapsule original_fixed_positions(rosetta.protocols.forge.build.BuildInstruction) -> rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t   return set of any fixed positions necessary with respect to the original   interval and original Pose numbering      Used for ensuring build regions for instructions do not overlap and   so that jumps may be placed correctly.      empty set if no fixed positions necessary original_interval(...) from builtins.PyCapsule original_interval(rosetta.protocols.forge.build.BuildInstruction) -> rosetta.protocols.forge.build.Interval   return original residue range of this instruction original_interval_valid(...) from builtins.PyCapsule original_interval_valid(rosetta.protocols.forge.build.BuildInstruction) -> bool   is the original interval storing valid information, or is empty   or being used for something else? original_kept_positions(...) from builtins.PyCapsule original_kept_positions(rosetta.protocols.forge.build.BuildInstruction) -> rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t   return the set of positions within the original interval that   will be kept in this BuildInstruction original_mutable_positions(...) from builtins.PyCapsule original_mutable_positions(rosetta.protocols.forge.build.BuildInstruction) -> rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t   return set of any mutable positions necessary with respect to the original   interval and original Pose numbering      Used for ensuring build regions for instructions do not overlap and   so that jumps may be placed correctly. preexisting_positions(...) from builtins.PyCapsule preexisting_positions(rosetta.protocols.forge.build.BuildInstruction) -> rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t   return a copy of the set of positions within the new region   that were pre-existing in the original Pose prior to modify() ready(...) from builtins.PyCapsule ready(rosetta.protocols.forge.build.BuildInstruction) -> bool   Is the BuildInstruction's state at READY?      READY indicates the BuildInstruction has been reset   and is ready to modify a Pose. reset_accounting(...) from builtins.PyCapsule reset_accounting(rosetta.protocols.forge.build.BuildInstruction) -> NoneType   reset intervals, positions, etc to initial state and drop   observers.  State set to READY. residue_type_set(...) from builtins.PyCapsule residue_type_set(rosetta.protocols.forge.build.BuildInstruction) -> rosetta.core.chemical.ResidueTypeSet   the residue type set being used state(...) from builtins.PyCapsule state(rosetta.protocols.forge.build.BuildInstruction) -> rosetta.protocols.forge.build.BuildInstructionState.Enum   return the state of this BuildInstruction undefined_positions(...) from builtins.PyCapsule undefined_positions(rosetta.protocols.forge.build.BuildInstruction) -> rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t   return a copy of the set of positions within the newly modified   region that has an undefined conformation.  E.g. newly created residues.      This set can change wrt length changes in Pose/Conformation being   watched. waiting_on_dependencies(...) from builtins.PyCapsule waiting_on_dependencies(rosetta.protocols.forge.build.BuildInstruction) -> bool   Is the BuildInstruction's state at WAITING_ON_DEPENDENCIES?      WAITING_ON_DEPENDENCIES indicates   the BuildInstruction is waiting for its dependencies to be satisfied   before allowing modifications to proceed.   class BuildManager(builtins.object)     a container for managing BuildInstructions     Compatibility checks wrt dependencies currently do not exist.  It remains to be seen how to handle this.     Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle) -> NoneType   2. __init__(handle, rosetta.protocols.forge.build.BuildManager) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. add(...) from builtins.PyCapsule add(self : rosetta.protocols.forge.build.BuildManager, bi : protocols::forge::build::BuildInstruction) -> NoneType   add an instruction directly (no copy) assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.forge.build.BuildManager, rval : rosetta.protocols.forge.build.BuildManager) -> rosetta.protocols.forge.build.BuildManager   copy assignment begin(...) from builtins.PyCapsule begin(rosetta.protocols.forge.build.BuildManager) -> __gnu_cxx::__normal_iterator<std::shared_ptr<protocols::forge::build::BuildInstruction> const*, std::vector<std::shared_ptr<protocols::forge::build::BuildInstruction>, std::allocator<std::shared_ptr<protocols::forge::build::BuildInstruction> > > >   const iterator pointing to the first instruction clear(...) from builtins.PyCapsule clear(rosetta.protocols.forge.build.BuildManager) -> NoneType   clear all instructions clear_dependencies(...) from builtins.PyCapsule clear_dependencies(rosetta.protocols.forge.build.BuildManager) -> int   clear all dependencies      number of dependencies dropped clone(...) from builtins.PyCapsule clone(rosetta.protocols.forge.build.BuildManager) -> rosetta.protocols.forge.build.BuildManager   clone this object compatibility_check(...) from builtins.PyCapsule compatibility_check(rosetta.protocols.forge.build.BuildManager) -> bool   check if instruction regions are compatible with each other      true if regions compatible, false if regions incompatible create(...) from builtins.PyCapsule create(rosetta.protocols.forge.build.BuildManager) -> rosetta.protocols.forge.build.BuildManager   create a new instance of this type of object create_directed_dependency(...) from builtins.PyCapsule create_directed_dependency(self : rosetta.protocols.forge.build.BuildManager, u : protocols::forge::build::BuildInstruction, v : protocols::forge::build::BuildInstruction) -> NoneType   create a directed dependency: instruction 'u' must complete   before instruction 'v' can complete, i.e. 'v' depends on 'u' defined_positions(...) from builtins.PyCapsule defined_positions(rosetta.protocols.forge.build.BuildManager) -> rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t   return a copy of the set of positions within the newly modified   regions that have a defined conformation.  E.g. existing or copied residues.      If modify() has not been called will return an empty set. dependencies_exist(...) from builtins.PyCapsule dependencies_exist(rosetta.protocols.forge.build.BuildManager) -> bool   have dependencies been defined? dummy_modify(...) from builtins.PyCapsule dummy_modify(self : rosetta.protocols.forge.build.BuildManager, nres : int) -> int   a dry run of modify() with an all-ala helical Pose of the given  length      The length of the dummy structure to use.      The final length of the modified Pose.      Use this to do a fake run of modify() if you need any   position or mapping information prior to actually calling modify(). empty(...) from builtins.PyCapsule empty(rosetta.protocols.forge.build.BuildManager) -> bool   no instructions? end(...) from builtins.PyCapsule end(rosetta.protocols.forge.build.BuildManager) -> __gnu_cxx::__normal_iterator<std::shared_ptr<protocols::forge::build::BuildInstruction> const*, std::vector<std::shared_ptr<protocols::forge::build::BuildInstruction>, std::allocator<std::shared_ptr<protocols::forge::build::BuildInstruction> > > >   const iterator pointing just beyond the last instruction modified2original_interval_endpoints(...) from builtins.PyCapsule modified2original_interval_endpoints(rosetta.protocols.forge.build.BuildManager) -> rosetta.std.map_unsigned_long_unsigned_long   return a map translating modified interval endpoints to original   interval endpoints      modified intervals with no equivalent original interval (e.g. cases   such as insertions) will not appear in this map      map; empty if modify() has not yet been called modify(...) from builtins.PyCapsule modify(self : rosetta.protocols.forge.build.BuildManager, pose : rosetta.core.pose.Pose) -> rosetta.std.map_unsigned_long_unsigned_long   modify the pose using the instructions in this container      the Pose to modify      a map translating original residue -> modified residue for   positions that existed within both the original Pose and modified Pose movemap(...) from builtins.PyCapsule movemap(rosetta.protocols.forge.build.BuildManager) -> rosetta.core.kinematics.MoveMap   return the combined movemap from all instructions in this manager      If modify() has not been called will return an empty MoveMap. movemap_as_OP(...) from builtins.PyCapsule movemap_as_OP(rosetta.protocols.forge.build.BuildManager) -> rosetta.core.kinematics.MoveMap n_dependencies(...) from builtins.PyCapsule n_dependencies(rosetta.protocols.forge.build.BuildManager) -> int   the number of dependencies currently defined (i.e. # of edges in   the dependency graph) new_positions(...) from builtins.PyCapsule new_positions(rosetta.protocols.forge.build.BuildManager) -> rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t   return a copy of the set of positions that are "new" and did   not exist in the original Pose.      If modify() has not been called will return an empty set. original2modified(...) from builtins.PyCapsule original2modified(rosetta.protocols.forge.build.BuildManager) -> rosetta.std.map_unsigned_long_unsigned_long   return a map translating original residue -> modified residue for   positions that existed within both the original Pose and modified Pose      map; empty if modify() has not yet been called original2modified_interval_endpoints(...) from builtins.PyCapsule original2modified_interval_endpoints(rosetta.protocols.forge.build.BuildManager) -> rosetta.std.map_unsigned_long_unsigned_long   return a map translating original interval endpoints to modified   interval endpoints      modified intervals with no equivalent original interval (e.g. cases   such as insertions) will not appear in this map      map; empty if modify() has not yet been called original_deleted_positions(...) from builtins.PyCapsule original_deleted_positions(rosetta.protocols.forge.build.BuildManager) -> rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t   return set of positions within the original intervals that will   be deleted by the BuildInstructions      returns valid data even without calling modify() original_kept_positions(...) from builtins.PyCapsule original_kept_positions(rosetta.protocols.forge.build.BuildManager) -> rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t   return the set of positions within the original intervals that   will be kept by the BuildInstructions      returns valid data even without calling modify() positions(...) from builtins.PyCapsule positions(rosetta.protocols.forge.build.BuildManager) -> rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t   return all positions within the modified intervals      Since this encompasses everything this is typically not useful   except for overall tracking purposes.      If modify() has not been called will return an empty set. preexisting_positions(...) from builtins.PyCapsule preexisting_positions(rosetta.protocols.forge.build.BuildManager) -> rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t   return the set of positions within the new regions that were   pre-existing in the original Pose prior to calling modify()      If modify() has not been called will return an empty set. reset_accounting(...) from builtins.PyCapsule reset_accounting(rosetta.protocols.forge.build.BuildManager) -> NoneType   reset all accounting info (intervals, positions, etc) to initial   state sequence_mapping(...) from builtins.PyCapsule sequence_mapping(rosetta.protocols.forge.build.BuildManager) -> rosetta.core.id.SequenceMapping   SequenceMapping consistent with the original -> modified mapping from the   most recent modify() call      valid Sequence mapping if modify() was called; otherwise returns   NULL      This mapping contains the same information as original2modified()   combined with original2modified_interval_endpoints(). size(...) from builtins.PyCapsule size(rosetta.protocols.forge.build.BuildManager) -> int   current number of instructions undefined_positions(...) from builtins.PyCapsule undefined_positions(rosetta.protocols.forge.build.BuildManager) -> rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t   return a copy of the set of positions within the newly modified   regions that have an undefined conformation.  E.g. newly created residues.      If modify() has not been called will return an empty set. union_of_intervals_containing_undefined_positions(...) from builtins.PyCapsule union_of_intervals_containing_undefined_positions(rosetta.protocols.forge.build.BuildManager) -> rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t   the positions representing the union of all intervals containing   positions with undefined conformation      Useful as a reference for defining neighborhoods around   loop modeled regions.      If modify() has not been called will return an empty set.   class ConnectRight(BuildInstruction)     instruction to connect one Pose onto the right side of another     Denote pose_left = [a,b] and pose_right = [c,d] and the newly  connected pose_left + pose_right = pose_total = [a,d].  If 'b' of  pose_left is an upper terminus or 'c' of pose_right is a lower terminus,  then ConnectRight will start a new chain in the Conformation at 'c' when  constructing pose_total, otherwise it will continue the chain at 'b'.     Method resolution order: ConnectRight BuildInstruction builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle) -> NoneType   2. __init__(self : handle, left_position : int, right_position : int, pose_right : rosetta.core.pose.Pose) -> NoneType   3. __init__(handle, rosetta.protocols.forge.build.ConnectRight) -> 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.forge.build.ConnectRight, rval : rosetta.protocols.forge.build.ConnectRight) -> rosetta.protocols.forge.build.ConnectRight   copy assignment clone(...) from builtins.PyCapsule clone(rosetta.protocols.forge.build.ConnectRight) -> rosetta.protocols.forge.build.BuildInstruction   clone this object creates_undefined_backbone(...) from builtins.PyCapsule creates_undefined_backbone(rosetta.protocols.forge.build.ConnectRight) -> bool   does this object create undefined backbone in the modified region?      false defined_positions(...) from builtins.PyCapsule defined_positions(rosetta.protocols.forge.build.ConnectRight) -> rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t   return a copy of the set of positions within the newly modified   region that has a defined conformation.  E.g. existing or copied residues.      A set spanning the entire interval -- all positions are defined.      This set can change wrt length changes in Pose/Conformation being   watched. extract_rt(...) from builtins.PyCapsule extract_rt(self : rosetta.protocols.forge.build.ConnectRight, pose : rosetta.core.pose.Pose, jump_start_residue : int, jump_stop_residue : int) -> NoneType   extract appropriately computed transform between two stubs that   represent a jump in the given Pose between the two residues and set it   as the rt for this ConnectRight      The Pose to use.      The starting residue of the jump.   This residue should be the equivalent of the jump position on pose_left.      The stopping residue of the jump.   This residue should be the equivalent of the jump position on pose_right.      Uses left_stub_atoms() and right_stub_atoms() as the stub atoms   to compute the transform.  Remember to set use_rt() to True after   calling this function if you want to actually use the transform   during modify(). interval(...) from builtins.PyCapsule interval(rosetta.protocols.forge.build.ConnectRight) -> rosetta.protocols.forge.build.Interval   a copy of the working range of residues specifying the modified region      before modify() holds [1, pose_right.n_residue()]; after   modify() holds [1 + pose_left.n_residue(), pose_right.n_residue + pose_left.n_residue()]      This can change if listening to Conformation LengthEvents left_stub_atoms(...) from builtins.PyCapsule left_stub_atoms(*args, **kwargs) Overloaded function.   1. left_stub_atoms(rosetta.protocols.forge.build.ConnectRight) -> rosetta.utility.vector1_std_string   Use these atoms to compute the stub on pose_left.   Default ["CA", "N", "CA", "C"].      This is an array with 4 elements in the same order as Stub   initialization: 'center atom', 'point1', 'point2', 'point3'.  See   Stub docs for more details.   2. left_stub_atoms(self : rosetta.protocols.forge.build.ConnectRight, atoms : rosetta.utility.vector1_std_string) -> NoneType   Use these atoms to compute the stub on pose_left.   Default ["CA", "N", "CA", "C"].      This is an array with 4 elements in the same order as Stub   initialization: 'center atom', 'point1', 'point2', 'point3'.  See   Stub docs for more details. movemap(...) from builtins.PyCapsule movemap(rosetta.protocols.forge.build.ConnectRight) -> rosetta.core.kinematics.MoveMap   return a copy of the MoveMap that defines the moveable/fixed   positions/dofs for this instruction      a MoveMap with [interval.left, interval.right] bb set to false   at the MoveMapTorsionID level      This set can change wrt length changes in Pose/Conformation being   watched. new_positions(...) from builtins.PyCapsule new_positions(rosetta.protocols.forge.build.ConnectRight) -> rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t   return a copy of the set of positions that are "new" and did   not exist in the original Pose.      A set spanning the entire interval -- all positions are new. on_residue_append(...) from builtins.PyCapsule on_residue_append(self : rosetta.protocols.forge.build.ConnectRight, event : rosetta.core.conformation.signals.LengthEvent) -> NoneType   update indexing on residue append on_residue_delete(...) from builtins.PyCapsule on_residue_delete(self : rosetta.protocols.forge.build.ConnectRight, event : rosetta.core.conformation.signals.LengthEvent) -> NoneType   update indexing on residue delete on_residue_prepend(...) from builtins.PyCapsule on_residue_prepend(self : rosetta.protocols.forge.build.ConnectRight, event : rosetta.core.conformation.signals.LengthEvent) -> NoneType   update indexing on residue prepend original_deleted_positions(...) from builtins.PyCapsule original_deleted_positions(rosetta.protocols.forge.build.ConnectRight) -> rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t   return set of positions within the original interval that will   be deleted in this BuildInstruction      An empty set -- no positions are deleted. original_fixed_positions(...) from builtins.PyCapsule original_fixed_positions(rosetta.protocols.forge.build.ConnectRight) -> rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t   return set of any fixed positions necessary with respect to the original   interval and original Pose numbering      Used for ensuring build regions for instructions do not overlap and   so that jumps may be placed correctly.      empty set if no fixed positions original_interval_valid(...) from builtins.PyCapsule original_interval_valid(rosetta.protocols.forge.build.ConnectRight) -> bool   is the original interval storing valid information, or is empty   or being used for something else?      false, stores invalid interval original_kept_positions(...) from builtins.PyCapsule original_kept_positions(rosetta.protocols.forge.build.ConnectRight) -> rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t   return the set of positions within the original interval that   will be kept in this BuildInstruction      An empty set -- no positions are kept. original_mutable_positions(...) from builtins.PyCapsule original_mutable_positions(rosetta.protocols.forge.build.ConnectRight) -> rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t   return set of any mutable positions necessary with respect to the original   interval and original Pose numbering      Used for ensuring build regions for instructions do not overlap and   so that jumps may be placed correctly.      empty set if no mutable positions pose_right(...) from builtins.PyCapsule pose_right(rosetta.protocols.forge.build.ConnectRight) -> rosetta.core.pose.Pose   connect this pose to the right of pose_left when modify( pose_left )   is called preexisting_positions(...) from builtins.PyCapsule preexisting_positions(rosetta.protocols.forge.build.ConnectRight) -> rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t   return a copy of the set of positions within the new region   that were pre-existing in the original Pose prior to modify()      An empty set -- no positions are pre-existing. right_stub_atoms(...) from builtins.PyCapsule right_stub_atoms(*args, **kwargs) Overloaded function.   1. right_stub_atoms(rosetta.protocols.forge.build.ConnectRight) -> rosetta.utility.vector1_std_string   Use these atoms to compute the stub on pose_right.   Default ["CA", "N", "CA", "C"].      This is an array with 4 elements in the same order as Stub   initialization: 'center atom', 'point1', 'point2', 'point3'.  See   Stub docs for more details.   2. right_stub_atoms(self : rosetta.protocols.forge.build.ConnectRight, atoms : rosetta.utility.vector1_std_string) -> NoneType   Use these atoms to compute the stub on pose_right.   Default ["CA", "N", "CA", "C"].      This is an array with 4 elements in the same order as Stub   initialization: 'center atom', 'point1', 'point2', 'point3'.  See   Stub docs for more details. rt(...) from builtins.PyCapsule rt(*args, **kwargs) Overloaded function.   1. rt(rosetta.protocols.forge.build.ConnectRight) -> rosetta.core.kinematics.RT   the rotation-translation representing an explicit transform from   the stub on pose_left to the stub on pose_right, i.e. the representation   of the "jump"   2. rt(self : rosetta.protocols.forge.build.ConnectRight, transform : rosetta.core.kinematics.RT) -> NoneType   the rotation-translation representing an explicit transform from   the stub on pose_left to the stub on pose_right, i.e. the representation   of the "jump" undefined_positions(...) from builtins.PyCapsule undefined_positions(rosetta.protocols.forge.build.ConnectRight) -> rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t   return a copy of the set of positions within the newly modified   region that has an undefined conformation.  E.g. newly created residues.      An empty set -- no undefined positions.      This set can change wrt length changes in Pose/Conformation being   watched. use_rt(...) from builtins.PyCapsule use_rt(*args, **kwargs) Overloaded function.   1. use_rt(rosetta.protocols.forge.build.ConnectRight) -> bool   apply the transform over the jump connection between pose_left and   pose_right?  default False   2. use_rt(self : rosetta.protocols.forge.build.ConnectRight, flag : bool) -> NoneType   apply the transform over the jump connection between pose_left and   pose_right?  default False Methods inherited from BuildInstruction: add_dependency_to(...) from builtins.PyCapsule add_dependency_to(self : rosetta.protocols.forge.build.BuildInstruction, i : rosetta.std.weak_ptr_const_protocols_forge_build_BuildInstruction_t) -> NoneType   add an instruction to this BuildInstruction's dependency list      before this instruction's modify() may complete properly, all   instructions in the dependency list must have completed modify() first attach_to(...) from builtins.PyCapsule attach_to(self : rosetta.protocols.forge.build.BuildInstruction, pose : rosetta.core.pose.Pose) -> NoneType   attach to a Pose's conformation clear_dependencies(...) from builtins.PyCapsule clear_dependencies(rosetta.protocols.forge.build.BuildInstruction) -> NoneType   clear the list of dependencies compatible_with(...) from builtins.PyCapsule compatible_with(self : rosetta.protocols.forge.build.BuildInstruction, rval : rosetta.protocols.forge.build.BuildInstruction) -> bool   compares fixed and mutable positions to determine compatibility with   another instruction      override this to obtain custom compatibility check dependencies(...) from builtins.PyCapsule dependencies(rosetta.protocols.forge.build.BuildInstruction) -> rosetta.utility.vector1_std_weak_ptr_const_protocols_forge_build_BuildInstruction_t   the list of instructions whose modify() must complete before   the modify() for this instruction may be called successfully dependent_on(...) from builtins.PyCapsule dependent_on(self : rosetta.protocols.forge.build.BuildInstruction, i : rosetta.std.weak_ptr_const_protocols_forge_build_BuildInstruction_t) -> bool   is this instruction dependent upon the given instruction? detach_after_modify(...) from builtins.PyCapsule detach_after_modify(*args, **kwargs) Overloaded function.   1. detach_after_modify(rosetta.protocols.forge.build.BuildInstruction) -> bool   detach after modify()?      Ordinarily a modify() call consists of attaching as a   length obs of the Pose, actually doing the modify, and then   detaching as a length obs of the Pose.  This flag governs whether   the last detach occurs.   2. detach_after_modify(self : rosetta.protocols.forge.build.BuildInstruction, flag : bool) -> NoneType   set detach after modify()      Ordinarily a modify() call consists of attaching as a   length obs of the Pose, actually doing the modify, and then   detaching as a length obs of the Pose.  This flag governs whether   the last detach occurs. detach_from(...) from builtins.PyCapsule detach_from(rosetta.protocols.forge.build.BuildInstruction) -> NoneType   detach from a Pose's conformation has_dependencies(...) from builtins.PyCapsule has_dependencies(rosetta.protocols.forge.build.BuildInstruction) -> bool   does this BuildInstruction have dependencies? modify(...) from builtins.PyCapsule modify(self : rosetta.protocols.forge.build.BuildInstruction, pose : rosetta.core.pose.Pose) -> rosetta.protocols.forge.build.BuildInstructionState.Enum   modify this pose      the state of the BuildInstruction modify_was_successful(...) from builtins.PyCapsule modify_was_successful(rosetta.protocols.forge.build.BuildInstruction) -> bool   Is the BuildInstruction's state at MODIFY_WAS_SUCCESSFUL?      MODIFY_WAS_SUCCESSFUL indicates the BuildInstruction has   finished modifications to the Pose, and its residue indexing is now   consistent with the newly modified Pose. n_dependencies(...) from builtins.PyCapsule n_dependencies(rosetta.protocols.forge.build.BuildInstruction) -> int   the number of dependencies this BuildInstruction has on_length_change(...) from builtins.PyCapsule on_length_change(self : rosetta.protocols.forge.build.BuildInstruction, event : rosetta.core.conformation.signals.LengthEvent) -> NoneType   update any indexing wrt length change to Pose/Conformation being watched original_interval(...) from builtins.PyCapsule original_interval(rosetta.protocols.forge.build.BuildInstruction) -> rosetta.protocols.forge.build.Interval   return original residue range of this instruction ready(...) from builtins.PyCapsule ready(rosetta.protocols.forge.build.BuildInstruction) -> bool   Is the BuildInstruction's state at READY?      READY indicates the BuildInstruction has been reset   and is ready to modify a Pose. reset_accounting(...) from builtins.PyCapsule reset_accounting(rosetta.protocols.forge.build.BuildInstruction) -> NoneType   reset intervals, positions, etc to initial state and drop   observers.  State set to READY. residue_type_set(...) from builtins.PyCapsule residue_type_set(rosetta.protocols.forge.build.BuildInstruction) -> rosetta.core.chemical.ResidueTypeSet   the residue type set being used state(...) from builtins.PyCapsule state(rosetta.protocols.forge.build.BuildInstruction) -> rosetta.protocols.forge.build.BuildInstructionState.Enum   return the state of this BuildInstruction waiting_on_dependencies(...) from builtins.PyCapsule waiting_on_dependencies(rosetta.protocols.forge.build.BuildInstruction) -> bool   Is the BuildInstruction's state at WAITING_ON_DEPENDENCIES?      WAITING_ON_DEPENDENCIES indicates   the BuildInstruction is waiting for its dependencies to be satisfied   before allowing modifications to proceed.   class CountFromLeft(RelativeSequencePosition)     count starting from interval().left in a BuildInstruction     Method resolution order: CountFromLeft RelativeSequencePosition builtins.object Methods defined here: __call__(...) from builtins.PyCapsule __call__(self : rosetta.protocols.forge.build.CountFromLeft, i : rosetta.std.weak_ptr_const_protocols_forge_build_BuildInstruction_t) -> int __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle) -> NoneType   2. __init__(handle, rosetta.protocols.forge.build.CountFromLeft) -> 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.forge.build.CountFromLeft,  : rosetta.protocols.forge.build.CountFromLeft) -> rosetta.protocols.forge.build.CountFromLeft clone(...) from builtins.PyCapsule clone(rosetta.protocols.forge.build.CountFromLeft) -> rosetta.protocols.forge.build.RelativeSequencePosition Data descriptors defined here: left_skip p   class GrowLeft(BuildInstruction)     instruction to create an n-side extension     Use this for n-side insertions, but typically not n-terminal  extensions unless necessary.  It does not automatically cover the  additional residue on the right endpoint that needs to move during  n-terminal extensions due to invalid phi torsion.  For that case,  use the SegmentRebuild class replacing the n-terminal residue with  desired length+1.     Method resolution order: GrowLeft BuildInstruction builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle) -> NoneType   2. __init__(handle, int, str) -> NoneType   doc   3. __init__(handle, int, str, str) -> NoneType   doc   4. __init__(self : handle, pos : int, ss : str, aa : str, rts : rosetta.std.weak_ptr_const_core_chemical_ResidueTypeSet_t) -> NoneType   5. __init__(handle, rosetta.protocols.forge.build.GrowLeft) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. aa(...) from builtins.PyCapsule aa(rosetta.protocols.forge.build.GrowLeft) -> str   get annotated amino acid string assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.forge.build.GrowLeft, rval : rosetta.protocols.forge.build.GrowLeft) -> rosetta.protocols.forge.build.GrowLeft   copy assignment clone(...) from builtins.PyCapsule clone(rosetta.protocols.forge.build.GrowLeft) -> rosetta.protocols.forge.build.BuildInstruction   clone this object creates_undefined_backbone(...) from builtins.PyCapsule creates_undefined_backbone(rosetta.protocols.forge.build.GrowLeft) -> bool   does this object create undefined backbone in the modified region?      true defined_positions(...) from builtins.PyCapsule defined_positions(rosetta.protocols.forge.build.GrowLeft) -> rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t   return a copy of the set of positions within the newly modified   region that has a defined conformation.  E.g. existing or copied residues.      An empty set -- no positions are defined.      This set can change wrt length changes in Pose/Conformation being   watched. interval(...) from builtins.PyCapsule interval(rosetta.protocols.forge.build.GrowLeft) -> rosetta.protocols.forge.build.Interval   a copy of the working range of residues specifying the modified region      This can change if listening to Conformation LengthEvents movemap(...) from builtins.PyCapsule movemap(rosetta.protocols.forge.build.GrowLeft) -> rosetta.core.kinematics.MoveMap   return a copy of the MoveMap that defines the moveable/fixed   positions/dofs for this instruction      a MoveMap with [interval.left, interval.right] bb & chi set to true   at the MoveMapTorsionID level      This set can change wrt length changes in Pose/Conformation being   watched. new_positions(...) from builtins.PyCapsule new_positions(rosetta.protocols.forge.build.GrowLeft) -> rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t   return a copy of the set of positions that are "new" and did   not exist in the original Pose.      A set of positions spanning the entire region -- all positions   are new. on_residue_append(...) from builtins.PyCapsule on_residue_append(self : rosetta.protocols.forge.build.GrowLeft, event : rosetta.core.conformation.signals.LengthEvent) -> NoneType   update indexing on residue append on_residue_delete(...) from builtins.PyCapsule on_residue_delete(self : rosetta.protocols.forge.build.GrowLeft, event : rosetta.core.conformation.signals.LengthEvent) -> NoneType   update indexing on residue delete on_residue_prepend(...) from builtins.PyCapsule on_residue_prepend(self : rosetta.protocols.forge.build.GrowLeft, event : rosetta.core.conformation.signals.LengthEvent) -> NoneType   update indexing on residue prepend original_deleted_positions(...) from builtins.PyCapsule original_deleted_positions(rosetta.protocols.forge.build.GrowLeft) -> rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t   return set of positions within the original interval that will   be deleted in this BuildInstruction      An empty set -- no positions are deleted. original_fixed_positions(...) from builtins.PyCapsule original_fixed_positions(rosetta.protocols.forge.build.GrowLeft) -> rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t   return set of any fixed positions necessary with respect to the original   interval and original Pose numbering      Used for ensuring build regions for instructions do not overlap and   so that jumps may be placed correctly.      empty set if no fixed positions original_interval_valid(...) from builtins.PyCapsule original_interval_valid(rosetta.protocols.forge.build.GrowLeft) -> bool   is the original interval storing valid information, or is empty   or being used for something else?      false, stores invalid interval original_kept_positions(...) from builtins.PyCapsule original_kept_positions(rosetta.protocols.forge.build.GrowLeft) -> rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t   return the set of positions within the original interval that   will be kept in this BuildInstruction      An empty set -- no positions are kept. original_mutable_positions(...) from builtins.PyCapsule original_mutable_positions(rosetta.protocols.forge.build.GrowLeft) -> rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t   return set of any mutable positions necessary with respect to the original   interval and original Pose numbering      Used for ensuring build regions for instructions do not overlap and   so that jumps may be placed correctly.      empty set if no mutable positions pos(...) from builtins.PyCapsule pos(rosetta.protocols.forge.build.GrowLeft) -> int   grow left from this anchor position      this can change if listening to Conformation LengthEvents   Use original_interval() to get the original anchor position. preexisting_positions(...) from builtins.PyCapsule preexisting_positions(rosetta.protocols.forge.build.GrowLeft) -> rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t   return a copy of the set of positions within the new region   that were pre-existing in the original Pose prior to modify()      An empty set -- no positions are pre-existing. ss(...) from builtins.PyCapsule ss(rosetta.protocols.forge.build.GrowLeft) -> str   get secondary structure string undefined_positions(...) from builtins.PyCapsule undefined_positions(rosetta.protocols.forge.build.GrowLeft) -> rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t   return a copy of the set of positions within the newly modified   region that has an undefined conformation.  E.g. newly created residues.      A set of positions spanning the entire region -- all positions   are undefined.      This set can change wrt length changes in Pose/Conformation being   watched. Methods inherited from BuildInstruction: add_dependency_to(...) from builtins.PyCapsule add_dependency_to(self : rosetta.protocols.forge.build.BuildInstruction, i : rosetta.std.weak_ptr_const_protocols_forge_build_BuildInstruction_t) -> NoneType   add an instruction to this BuildInstruction's dependency list      before this instruction's modify() may complete properly, all   instructions in the dependency list must have completed modify() first attach_to(...) from builtins.PyCapsule attach_to(self : rosetta.protocols.forge.build.BuildInstruction, pose : rosetta.core.pose.Pose) -> NoneType   attach to a Pose's conformation clear_dependencies(...) from builtins.PyCapsule clear_dependencies(rosetta.protocols.forge.build.BuildInstruction) -> NoneType   clear the list of dependencies compatible_with(...) from builtins.PyCapsule compatible_with(self : rosetta.protocols.forge.build.BuildInstruction, rval : rosetta.protocols.forge.build.BuildInstruction) -> bool   compares fixed and mutable positions to determine compatibility with   another instruction      override this to obtain custom compatibility check dependencies(...) from builtins.PyCapsule dependencies(rosetta.protocols.forge.build.BuildInstruction) -> rosetta.utility.vector1_std_weak_ptr_const_protocols_forge_build_BuildInstruction_t   the list of instructions whose modify() must complete before   the modify() for this instruction may be called successfully dependent_on(...) from builtins.PyCapsule dependent_on(self : rosetta.protocols.forge.build.BuildInstruction, i : rosetta.std.weak_ptr_const_protocols_forge_build_BuildInstruction_t) -> bool   is this instruction dependent upon the given instruction? detach_after_modify(...) from builtins.PyCapsule detach_after_modify(*args, **kwargs) Overloaded function.   1. detach_after_modify(rosetta.protocols.forge.build.BuildInstruction) -> bool   detach after modify()?      Ordinarily a modify() call consists of attaching as a   length obs of the Pose, actually doing the modify, and then   detaching as a length obs of the Pose.  This flag governs whether   the last detach occurs.   2. detach_after_modify(self : rosetta.protocols.forge.build.BuildInstruction, flag : bool) -> NoneType   set detach after modify()      Ordinarily a modify() call consists of attaching as a   length obs of the Pose, actually doing the modify, and then   detaching as a length obs of the Pose.  This flag governs whether   the last detach occurs. detach_from(...) from builtins.PyCapsule detach_from(rosetta.protocols.forge.build.BuildInstruction) -> NoneType   detach from a Pose's conformation has_dependencies(...) from builtins.PyCapsule has_dependencies(rosetta.protocols.forge.build.BuildInstruction) -> bool   does this BuildInstruction have dependencies? modify(...) from builtins.PyCapsule modify(self : rosetta.protocols.forge.build.BuildInstruction, pose : rosetta.core.pose.Pose) -> rosetta.protocols.forge.build.BuildInstructionState.Enum   modify this pose      the state of the BuildInstruction modify_was_successful(...) from builtins.PyCapsule modify_was_successful(rosetta.protocols.forge.build.BuildInstruction) -> bool   Is the BuildInstruction's state at MODIFY_WAS_SUCCESSFUL?      MODIFY_WAS_SUCCESSFUL indicates the BuildInstruction has   finished modifications to the Pose, and its residue indexing is now   consistent with the newly modified Pose. n_dependencies(...) from builtins.PyCapsule n_dependencies(rosetta.protocols.forge.build.BuildInstruction) -> int   the number of dependencies this BuildInstruction has on_length_change(...) from builtins.PyCapsule on_length_change(self : rosetta.protocols.forge.build.BuildInstruction, event : rosetta.core.conformation.signals.LengthEvent) -> NoneType   update any indexing wrt length change to Pose/Conformation being watched original_interval(...) from builtins.PyCapsule original_interval(rosetta.protocols.forge.build.BuildInstruction) -> rosetta.protocols.forge.build.Interval   return original residue range of this instruction ready(...) from builtins.PyCapsule ready(rosetta.protocols.forge.build.BuildInstruction) -> bool   Is the BuildInstruction's state at READY?      READY indicates the BuildInstruction has been reset   and is ready to modify a Pose. reset_accounting(...) from builtins.PyCapsule reset_accounting(rosetta.protocols.forge.build.BuildInstruction) -> NoneType   reset intervals, positions, etc to initial state and drop   observers.  State set to READY. residue_type_set(...) from builtins.PyCapsule residue_type_set(rosetta.protocols.forge.build.BuildInstruction) -> rosetta.core.chemical.ResidueTypeSet   the residue type set being used state(...) from builtins.PyCapsule state(rosetta.protocols.forge.build.BuildInstruction) -> rosetta.protocols.forge.build.BuildInstructionState.Enum   return the state of this BuildInstruction waiting_on_dependencies(...) from builtins.PyCapsule waiting_on_dependencies(rosetta.protocols.forge.build.BuildInstruction) -> bool   Is the BuildInstruction's state at WAITING_ON_DEPENDENCIES?      WAITING_ON_DEPENDENCIES indicates   the BuildInstruction is waiting for its dependencies to be satisfied   before allowing modifications to proceed.   class GrowRight(BuildInstruction)     instruction to create a c-side extension     Use this for c-side insertions but typically not c-terminal  extensions unless necessary.  It does not automatically cover the  additional residue on the left endpoint that needs to move during  c-terminal extensions due to invalid psi torsion. For that case,  use the SegmentRebuild class replacing the c-terminal residue with  desired length+1.     Method resolution order: GrowRight BuildInstruction builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle) -> NoneType   2. __init__(handle, int, str) -> NoneType   doc   3. __init__(handle, int, str, str) -> NoneType   doc   4. __init__(self : handle, pos : int, ss : str, aa : str, rts : rosetta.std.weak_ptr_const_core_chemical_ResidueTypeSet_t) -> NoneType   5. __init__(handle, rosetta.protocols.forge.build.GrowRight) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. aa(...) from builtins.PyCapsule aa(rosetta.protocols.forge.build.GrowRight) -> str   get annotated amino acid string assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.forge.build.GrowRight, rval : rosetta.protocols.forge.build.GrowRight) -> rosetta.protocols.forge.build.GrowRight   copy assignment clone(...) from builtins.PyCapsule clone(rosetta.protocols.forge.build.GrowRight) -> rosetta.protocols.forge.build.BuildInstruction   clone this object creates_undefined_backbone(...) from builtins.PyCapsule creates_undefined_backbone(rosetta.protocols.forge.build.GrowRight) -> bool   does this object create undefined backbone in the modified region?      true defined_positions(...) from builtins.PyCapsule defined_positions(rosetta.protocols.forge.build.GrowRight) -> rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t   return a copy of the set of positions within the newly modified   region that has a defined conformation.  E.g. existing or copied residues.      An empty set -- no positions are defined.      This set can change wrt length changes in Pose/Conformation being   watched. interval(...) from builtins.PyCapsule interval(rosetta.protocols.forge.build.GrowRight) -> rosetta.protocols.forge.build.Interval   a copy of the working range of residues specifying the modified region      This can change if listening to Conformation LengthEvents movemap(...) from builtins.PyCapsule movemap(rosetta.protocols.forge.build.GrowRight) -> rosetta.core.kinematics.MoveMap   return a copy of the MoveMap that defines the moveable/fixed   positions/dofs for this instruction      a MoveMap with [interval.left, interval.right] bb & chi set to true   at the MoveMapTorsionID level      This set can change wrt length changes in Pose/Conformation being   watched. new_positions(...) from builtins.PyCapsule new_positions(rosetta.protocols.forge.build.GrowRight) -> rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t   return a copy of the set of positions that are "new" and did   not exist in the original Pose.      A set of positions spanning the entire region -- all positions   are new. on_residue_append(...) from builtins.PyCapsule on_residue_append(self : rosetta.protocols.forge.build.GrowRight, event : rosetta.core.conformation.signals.LengthEvent) -> NoneType   update indexing on residue append on_residue_delete(...) from builtins.PyCapsule on_residue_delete(self : rosetta.protocols.forge.build.GrowRight, event : rosetta.core.conformation.signals.LengthEvent) -> NoneType   update indexing on residue delete on_residue_prepend(...) from builtins.PyCapsule on_residue_prepend(self : rosetta.protocols.forge.build.GrowRight, event : rosetta.core.conformation.signals.LengthEvent) -> NoneType   update indexing on residue prepend original_deleted_positions(...) from builtins.PyCapsule original_deleted_positions(rosetta.protocols.forge.build.GrowRight) -> rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t   return set of positions within the original interval that will   be deleted in this BuildInstruction      An empty set -- no positions are deleted. original_fixed_positions(...) from builtins.PyCapsule original_fixed_positions(rosetta.protocols.forge.build.GrowRight) -> rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t   return set of any fixed positions necessary with respect to the original   interval and original Pose numbering      Used for ensuring build regions for instructions do not overlap and   so that jumps may be placed correctly.      empty set if no fixed positions original_interval_valid(...) from builtins.PyCapsule original_interval_valid(rosetta.protocols.forge.build.GrowRight) -> bool   is the original interval storing valid information, or is empty   or being used for something else?      false, stores invalid interval original_kept_positions(...) from builtins.PyCapsule original_kept_positions(rosetta.protocols.forge.build.GrowRight) -> rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t   return the set of positions within the original interval that   will be kept in this BuildInstruction      An empty set -- no positions are kept. original_mutable_positions(...) from builtins.PyCapsule original_mutable_positions(rosetta.protocols.forge.build.GrowRight) -> rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t   return set of any mutable positions necessary with respect to the original   interval and original Pose numbering      Used for ensuring build regions for instructions do not overlap and   so that jumps may be placed correctly.      empty set if no mutable positions pos(...) from builtins.PyCapsule pos(rosetta.protocols.forge.build.GrowRight) -> int   grow right from this anchor position      This can change if listening to Conformation LengthEvents.   Use original_interval() to get the original anchor position. preexisting_positions(...) from builtins.PyCapsule preexisting_positions(rosetta.protocols.forge.build.GrowRight) -> rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t   return a copy of the set of positions within the new region   that were pre-existing in the original Pose prior to modify()      An empty set -- no positions are pre-existing. ss(...) from builtins.PyCapsule ss(rosetta.protocols.forge.build.GrowRight) -> str   get secondary structure string undefined_positions(...) from builtins.PyCapsule undefined_positions(rosetta.protocols.forge.build.GrowRight) -> rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t   return a copy of the set of positions within the newly modified   region that has an undefined conformation.  E.g. newly created residues.      A set of positions spanning the entire region -- all positions   are undefined.      This set can change wrt length changes in Pose/Conformation being   watched. Methods inherited from BuildInstruction: add_dependency_to(...) from builtins.PyCapsule add_dependency_to(self : rosetta.protocols.forge.build.BuildInstruction, i : rosetta.std.weak_ptr_const_protocols_forge_build_BuildInstruction_t) -> NoneType   add an instruction to this BuildInstruction's dependency list      before this instruction's modify() may complete properly, all   instructions in the dependency list must have completed modify() first attach_to(...) from builtins.PyCapsule attach_to(self : rosetta.protocols.forge.build.BuildInstruction, pose : rosetta.core.pose.Pose) -> NoneType   attach to a Pose's conformation clear_dependencies(...) from builtins.PyCapsule clear_dependencies(rosetta.protocols.forge.build.BuildInstruction) -> NoneType   clear the list of dependencies compatible_with(...) from builtins.PyCapsule compatible_with(self : rosetta.protocols.forge.build.BuildInstruction, rval : rosetta.protocols.forge.build.BuildInstruction) -> bool   compares fixed and mutable positions to determine compatibility with   another instruction      override this to obtain custom compatibility check dependencies(...) from builtins.PyCapsule dependencies(rosetta.protocols.forge.build.BuildInstruction) -> rosetta.utility.vector1_std_weak_ptr_const_protocols_forge_build_BuildInstruction_t   the list of instructions whose modify() must complete before   the modify() for this instruction may be called successfully dependent_on(...) from builtins.PyCapsule dependent_on(self : rosetta.protocols.forge.build.BuildInstruction, i : rosetta.std.weak_ptr_const_protocols_forge_build_BuildInstruction_t) -> bool   is this instruction dependent upon the given instruction? detach_after_modify(...) from builtins.PyCapsule detach_after_modify(*args, **kwargs) Overloaded function.   1. detach_after_modify(rosetta.protocols.forge.build.BuildInstruction) -> bool   detach after modify()?      Ordinarily a modify() call consists of attaching as a   length obs of the Pose, actually doing the modify, and then   detaching as a length obs of the Pose.  This flag governs whether   the last detach occurs.   2. detach_after_modify(self : rosetta.protocols.forge.build.BuildInstruction, flag : bool) -> NoneType   set detach after modify()      Ordinarily a modify() call consists of attaching as a   length obs of the Pose, actually doing the modify, and then   detaching as a length obs of the Pose.  This flag governs whether   the last detach occurs. detach_from(...) from builtins.PyCapsule detach_from(rosetta.protocols.forge.build.BuildInstruction) -> NoneType   detach from a Pose's conformation has_dependencies(...) from builtins.PyCapsule has_dependencies(rosetta.protocols.forge.build.BuildInstruction) -> bool   does this BuildInstruction have dependencies? modify(...) from builtins.PyCapsule modify(self : rosetta.protocols.forge.build.BuildInstruction, pose : rosetta.core.pose.Pose) -> rosetta.protocols.forge.build.BuildInstructionState.Enum   modify this pose      the state of the BuildInstruction modify_was_successful(...) from builtins.PyCapsule modify_was_successful(rosetta.protocols.forge.build.BuildInstruction) -> bool   Is the BuildInstruction's state at MODIFY_WAS_SUCCESSFUL?      MODIFY_WAS_SUCCESSFUL indicates the BuildInstruction has   finished modifications to the Pose, and its residue indexing is now   consistent with the newly modified Pose. n_dependencies(...) from builtins.PyCapsule n_dependencies(rosetta.protocols.forge.build.BuildInstruction) -> int   the number of dependencies this BuildInstruction has on_length_change(...) from builtins.PyCapsule on_length_change(self : rosetta.protocols.forge.build.BuildInstruction, event : rosetta.core.conformation.signals.LengthEvent) -> NoneType   update any indexing wrt length change to Pose/Conformation being watched original_interval(...) from builtins.PyCapsule original_interval(rosetta.protocols.forge.build.BuildInstruction) -> rosetta.protocols.forge.build.Interval   return original residue range of this instruction ready(...) from builtins.PyCapsule ready(rosetta.protocols.forge.build.BuildInstruction) -> bool   Is the BuildInstruction's state at READY?      READY indicates the BuildInstruction has been reset   and is ready to modify a Pose. reset_accounting(...) from builtins.PyCapsule reset_accounting(rosetta.protocols.forge.build.BuildInstruction) -> NoneType   reset intervals, positions, etc to initial state and drop   observers.  State set to READY. residue_type_set(...) from builtins.PyCapsule residue_type_set(rosetta.protocols.forge.build.BuildInstruction) -> rosetta.core.chemical.ResidueTypeSet   the residue type set being used state(...) from builtins.PyCapsule state(rosetta.protocols.forge.build.BuildInstruction) -> rosetta.protocols.forge.build.BuildInstructionState.Enum   return the state of this BuildInstruction waiting_on_dependencies(...) from builtins.PyCapsule waiting_on_dependencies(rosetta.protocols.forge.build.BuildInstruction) -> bool   Is the BuildInstruction's state at WAITING_ON_DEPENDENCIES?      WAITING_ON_DEPENDENCIES indicates   the BuildInstruction is waiting for its dependencies to be satisfied   before allowing modifications to proceed.   class Interval(builtins.object)     simple struct defining a closed interval of residues [left, right] where left <= right     Methods defined here: __eq__(...) from builtins.PyCapsule __eq__(self : rosetta.protocols.forge.build.Interval, rval : rosetta.protocols.forge.build.Interval) -> bool   operator == __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.protocols.forge.build.Interval) -> NoneType   2. __init__(self : rosetta.protocols.forge.build.Interval, l : int, r : int) -> NoneType   3. __init__(self : rosetta.protocols.forge.build.Interval, rval : rosetta.protocols.forge.build.Interval) -> 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.forge.build.Interval, rval : rosetta.protocols.forge.build.Interval) -> rosetta.protocols.forge.build.Interval   copy assignment contains(...) from builtins.PyCapsule contains(self : rosetta.protocols.forge.build.Interval, point : int) -> bool   is a point contained in this interval? intersects(...) from builtins.PyCapsule intersects(self : rosetta.protocols.forge.build.Interval, rval : rosetta.protocols.forge.build.Interval) -> bool   do the two intervals intersect? length(...) from builtins.PyCapsule length(rosetta.protocols.forge.build.Interval) -> int   length of the interval Data descriptors defined here: left right   class RelativeConnectRight(ConnectRight)     version of ConnectRight instruction that depends upon results from another BuildInstruction     Method resolution order: RelativeConnectRight ConnectRight BuildInstruction builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle) -> NoneType   2. __init__(self : handle, rp : protocols::forge::build::RelativeSequencePosition, right_position : int, pose_right : rosetta.core.pose.Pose) -> NoneType   3. __init__(handle, rosetta.protocols.forge.build.RelativeConnectRight) -> 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.forge.build.RelativeConnectRight, rval : rosetta.protocols.forge.build.RelativeConnectRight) -> rosetta.protocols.forge.build.RelativeConnectRight   copy assignment clone(...) from builtins.PyCapsule clone(rosetta.protocols.forge.build.RelativeConnectRight) -> rosetta.protocols.forge.build.BuildInstruction   clone this object modify_impl(...) from builtins.PyCapsule modify_impl(self : rosetta.protocols.forge.build.RelativeConnectRight, pose_left : rosetta.core.pose.Pose) -> NoneType   do the actual work of modifying the Pose original_fixed_positions(...) from builtins.PyCapsule original_fixed_positions(rosetta.protocols.forge.build.RelativeConnectRight) -> rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t   return set of any fixed positions necessary with respect to the original   interval and original Pose numbering      always empty set, no fixed positions      Used for ensuring build regions for instructions do not overlap and   so that jumps may be placed correctly.  There is currently no way to   represent the dependent fixed position, so we're forced to return an empty   set. Methods inherited from ConnectRight: creates_undefined_backbone(...) from builtins.PyCapsule creates_undefined_backbone(rosetta.protocols.forge.build.ConnectRight) -> bool   does this object create undefined backbone in the modified region?      false defined_positions(...) from builtins.PyCapsule defined_positions(rosetta.protocols.forge.build.ConnectRight) -> rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t   return a copy of the set of positions within the newly modified   region that has a defined conformation.  E.g. existing or copied residues.      A set spanning the entire interval -- all positions are defined.      This set can change wrt length changes in Pose/Conformation being   watched. extract_rt(...) from builtins.PyCapsule extract_rt(self : rosetta.protocols.forge.build.ConnectRight, pose : rosetta.core.pose.Pose, jump_start_residue : int, jump_stop_residue : int) -> NoneType   extract appropriately computed transform between two stubs that   represent a jump in the given Pose between the two residues and set it   as the rt for this ConnectRight      The Pose to use.      The starting residue of the jump.   This residue should be the equivalent of the jump position on pose_left.      The stopping residue of the jump.   This residue should be the equivalent of the jump position on pose_right.      Uses left_stub_atoms() and right_stub_atoms() as the stub atoms   to compute the transform.  Remember to set use_rt() to True after   calling this function if you want to actually use the transform   during modify(). interval(...) from builtins.PyCapsule interval(rosetta.protocols.forge.build.ConnectRight) -> rosetta.protocols.forge.build.Interval   a copy of the working range of residues specifying the modified region      before modify() holds [1, pose_right.n_residue()]; after   modify() holds [1 + pose_left.n_residue(), pose_right.n_residue + pose_left.n_residue()]      This can change if listening to Conformation LengthEvents left_stub_atoms(...) from builtins.PyCapsule left_stub_atoms(*args, **kwargs) Overloaded function.   1. left_stub_atoms(rosetta.protocols.forge.build.ConnectRight) -> rosetta.utility.vector1_std_string   Use these atoms to compute the stub on pose_left.   Default ["CA", "N", "CA", "C"].      This is an array with 4 elements in the same order as Stub   initialization: 'center atom', 'point1', 'point2', 'point3'.  See   Stub docs for more details.   2. left_stub_atoms(self : rosetta.protocols.forge.build.ConnectRight, atoms : rosetta.utility.vector1_std_string) -> NoneType   Use these atoms to compute the stub on pose_left.   Default ["CA", "N", "CA", "C"].      This is an array with 4 elements in the same order as Stub   initialization: 'center atom', 'point1', 'point2', 'point3'.  See   Stub docs for more details. movemap(...) from builtins.PyCapsule movemap(rosetta.protocols.forge.build.ConnectRight) -> rosetta.core.kinematics.MoveMap   return a copy of the MoveMap that defines the moveable/fixed   positions/dofs for this instruction      a MoveMap with [interval.left, interval.right] bb set to false   at the MoveMapTorsionID level      This set can change wrt length changes in Pose/Conformation being   watched. new_positions(...) from builtins.PyCapsule new_positions(rosetta.protocols.forge.build.ConnectRight) -> rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t   return a copy of the set of positions that are "new" and did   not exist in the original Pose.      A set spanning the entire interval -- all positions are new. on_residue_append(...) from builtins.PyCapsule on_residue_append(self : rosetta.protocols.forge.build.ConnectRight, event : rosetta.core.conformation.signals.LengthEvent) -> NoneType   update indexing on residue append on_residue_delete(...) from builtins.PyCapsule on_residue_delete(self : rosetta.protocols.forge.build.ConnectRight, event : rosetta.core.conformation.signals.LengthEvent) -> NoneType   update indexing on residue delete on_residue_prepend(...) from builtins.PyCapsule on_residue_prepend(self : rosetta.protocols.forge.build.ConnectRight, event : rosetta.core.conformation.signals.LengthEvent) -> NoneType   update indexing on residue prepend original_deleted_positions(...) from builtins.PyCapsule original_deleted_positions(rosetta.protocols.forge.build.ConnectRight) -> rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t   return set of positions within the original interval that will   be deleted in this BuildInstruction      An empty set -- no positions are deleted. original_interval_valid(...) from builtins.PyCapsule original_interval_valid(rosetta.protocols.forge.build.ConnectRight) -> bool   is the original interval storing valid information, or is empty   or being used for something else?      false, stores invalid interval original_kept_positions(...) from builtins.PyCapsule original_kept_positions(rosetta.protocols.forge.build.ConnectRight) -> rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t   return the set of positions within the original interval that   will be kept in this BuildInstruction      An empty set -- no positions are kept. original_mutable_positions(...) from builtins.PyCapsule original_mutable_positions(rosetta.protocols.forge.build.ConnectRight) -> rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t   return set of any mutable positions necessary with respect to the original   interval and original Pose numbering      Used for ensuring build regions for instructions do not overlap and   so that jumps may be placed correctly.      empty set if no mutable positions pose_right(...) from builtins.PyCapsule pose_right(rosetta.protocols.forge.build.ConnectRight) -> rosetta.core.pose.Pose   connect this pose to the right of pose_left when modify( pose_left )   is called preexisting_positions(...) from builtins.PyCapsule preexisting_positions(rosetta.protocols.forge.build.ConnectRight) -> rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t   return a copy of the set of positions within the new region   that were pre-existing in the original Pose prior to modify()      An empty set -- no positions are pre-existing. right_stub_atoms(...) from builtins.PyCapsule right_stub_atoms(*args, **kwargs) Overloaded function.   1. right_stub_atoms(rosetta.protocols.forge.build.ConnectRight) -> rosetta.utility.vector1_std_string   Use these atoms to compute the stub on pose_right.   Default ["CA", "N", "CA", "C"].      This is an array with 4 elements in the same order as Stub   initialization: 'center atom', 'point1', 'point2', 'point3'.  See   Stub docs for more details.   2. right_stub_atoms(self : rosetta.protocols.forge.build.ConnectRight, atoms : rosetta.utility.vector1_std_string) -> NoneType   Use these atoms to compute the stub on pose_right.   Default ["CA", "N", "CA", "C"].      This is an array with 4 elements in the same order as Stub   initialization: 'center atom', 'point1', 'point2', 'point3'.  See   Stub docs for more details. rt(...) from builtins.PyCapsule rt(*args, **kwargs) Overloaded function.   1. rt(rosetta.protocols.forge.build.ConnectRight) -> rosetta.core.kinematics.RT   the rotation-translation representing an explicit transform from   the stub on pose_left to the stub on pose_right, i.e. the representation   of the "jump"   2. rt(self : rosetta.protocols.forge.build.ConnectRight, transform : rosetta.core.kinematics.RT) -> NoneType   the rotation-translation representing an explicit transform from   the stub on pose_left to the stub on pose_right, i.e. the representation   of the "jump" undefined_positions(...) from builtins.PyCapsule undefined_positions(rosetta.protocols.forge.build.ConnectRight) -> rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t   return a copy of the set of positions within the newly modified   region that has an undefined conformation.  E.g. newly created residues.      An empty set -- no undefined positions.      This set can change wrt length changes in Pose/Conformation being   watched. use_rt(...) from builtins.PyCapsule use_rt(*args, **kwargs) Overloaded function.   1. use_rt(rosetta.protocols.forge.build.ConnectRight) -> bool   apply the transform over the jump connection between pose_left and   pose_right?  default False   2. use_rt(self : rosetta.protocols.forge.build.ConnectRight, flag : bool) -> NoneType   apply the transform over the jump connection between pose_left and   pose_right?  default False Methods inherited from BuildInstruction: add_dependency_to(...) from builtins.PyCapsule add_dependency_to(self : rosetta.protocols.forge.build.BuildInstruction, i : rosetta.std.weak_ptr_const_protocols_forge_build_BuildInstruction_t) -> NoneType   add an instruction to this BuildInstruction's dependency list      before this instruction's modify() may complete properly, all   instructions in the dependency list must have completed modify() first attach_to(...) from builtins.PyCapsule attach_to(self : rosetta.protocols.forge.build.BuildInstruction, pose : rosetta.core.pose.Pose) -> NoneType   attach to a Pose's conformation clear_dependencies(...) from builtins.PyCapsule clear_dependencies(rosetta.protocols.forge.build.BuildInstruction) -> NoneType   clear the list of dependencies compatible_with(...) from builtins.PyCapsule compatible_with(self : rosetta.protocols.forge.build.BuildInstruction, rval : rosetta.protocols.forge.build.BuildInstruction) -> bool   compares fixed and mutable positions to determine compatibility with   another instruction      override this to obtain custom compatibility check dependencies(...) from builtins.PyCapsule dependencies(rosetta.protocols.forge.build.BuildInstruction) -> rosetta.utility.vector1_std_weak_ptr_const_protocols_forge_build_BuildInstruction_t   the list of instructions whose modify() must complete before   the modify() for this instruction may be called successfully dependent_on(...) from builtins.PyCapsule dependent_on(self : rosetta.protocols.forge.build.BuildInstruction, i : rosetta.std.weak_ptr_const_protocols_forge_build_BuildInstruction_t) -> bool   is this instruction dependent upon the given instruction? detach_after_modify(...) from builtins.PyCapsule detach_after_modify(*args, **kwargs) Overloaded function.   1. detach_after_modify(rosetta.protocols.forge.build.BuildInstruction) -> bool   detach after modify()?      Ordinarily a modify() call consists of attaching as a   length obs of the Pose, actually doing the modify, and then   detaching as a length obs of the Pose.  This flag governs whether   the last detach occurs.   2. detach_after_modify(self : rosetta.protocols.forge.build.BuildInstruction, flag : bool) -> NoneType   set detach after modify()      Ordinarily a modify() call consists of attaching as a   length obs of the Pose, actually doing the modify, and then   detaching as a length obs of the Pose.  This flag governs whether   the last detach occurs. detach_from(...) from builtins.PyCapsule detach_from(rosetta.protocols.forge.build.BuildInstruction) -> NoneType   detach from a Pose's conformation has_dependencies(...) from builtins.PyCapsule has_dependencies(rosetta.protocols.forge.build.BuildInstruction) -> bool   does this BuildInstruction have dependencies? modify(...) from builtins.PyCapsule modify(self : rosetta.protocols.forge.build.BuildInstruction, pose : rosetta.core.pose.Pose) -> rosetta.protocols.forge.build.BuildInstructionState.Enum   modify this pose      the state of the BuildInstruction modify_was_successful(...) from builtins.PyCapsule modify_was_successful(rosetta.protocols.forge.build.BuildInstruction) -> bool   Is the BuildInstruction's state at MODIFY_WAS_SUCCESSFUL?      MODIFY_WAS_SUCCESSFUL indicates the BuildInstruction has   finished modifications to the Pose, and its residue indexing is now   consistent with the newly modified Pose. n_dependencies(...) from builtins.PyCapsule n_dependencies(rosetta.protocols.forge.build.BuildInstruction) -> int   the number of dependencies this BuildInstruction has on_length_change(...) from builtins.PyCapsule on_length_change(self : rosetta.protocols.forge.build.BuildInstruction, event : rosetta.core.conformation.signals.LengthEvent) -> NoneType   update any indexing wrt length change to Pose/Conformation being watched original_interval(...) from builtins.PyCapsule original_interval(rosetta.protocols.forge.build.BuildInstruction) -> rosetta.protocols.forge.build.Interval   return original residue range of this instruction ready(...) from builtins.PyCapsule ready(rosetta.protocols.forge.build.BuildInstruction) -> bool   Is the BuildInstruction's state at READY?      READY indicates the BuildInstruction has been reset   and is ready to modify a Pose. reset_accounting(...) from builtins.PyCapsule reset_accounting(rosetta.protocols.forge.build.BuildInstruction) -> NoneType   reset intervals, positions, etc to initial state and drop   observers.  State set to READY. residue_type_set(...) from builtins.PyCapsule residue_type_set(rosetta.protocols.forge.build.BuildInstruction) -> rosetta.core.chemical.ResidueTypeSet   the residue type set being used state(...) from builtins.PyCapsule state(rosetta.protocols.forge.build.BuildInstruction) -> rosetta.protocols.forge.build.BuildInstructionState.Enum   return the state of this BuildInstruction waiting_on_dependencies(...) from builtins.PyCapsule waiting_on_dependencies(rosetta.protocols.forge.build.BuildInstruction) -> bool   Is the BuildInstruction's state at WAITING_ON_DEPENDENCIES?      WAITING_ON_DEPENDENCIES indicates   the BuildInstruction is waiting for its dependencies to be satisfied   before allowing modifications to proceed.   class RelativeSequencePosition(builtins.object)     computes a position wrt values in given BuildInstruction     Methods defined here: __call__(...) from builtins.PyCapsule __call__(self : rosetta.protocols.forge.build.RelativeSequencePosition, i : rosetta.std.weak_ptr_const_protocols_forge_build_BuildInstruction_t) -> int __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.protocols.forge.build.RelativeSequencePosition, rosetta.protocols.forge.build.RelativeSequencePosition) -> NoneType   2. __init__(rosetta.protocols.forge.build.RelativeSequencePosition) -> 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.forge.build.RelativeSequencePosition,  : rosetta.protocols.forge.build.RelativeSequencePosition) -> rosetta.protocols.forge.build.RelativeSequencePosition clone(...) from builtins.PyCapsule clone(rosetta.protocols.forge.build.RelativeSequencePosition) -> rosetta.protocols.forge.build.RelativeSequencePosition   class SegmentInsert(BuildInstruction)     insert an external segment flanked by new regions     Similar to SegmentRebuild, but with the addition of a defined  segment located in the modified region.     Method resolution order: SegmentInsert BuildInstruction builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle) -> NoneType   2. __init__(handle, rosetta.protocols.forge.build.Interval, str, rosetta.core.pose.Pose) -> NoneType   doc   3. __init__(handle, rosetta.protocols.forge.build.Interval, str, rosetta.core.pose.Pose, bool) -> NoneType   doc   4. __init__(self : handle, i : rosetta.protocols.forge.build.Interval, ss : str, insert : rosetta.core.pose.Pose, keep_known_bb_torsions_at_junctions : bool, connection_scheme : rosetta.protocols.forge.build.SegmentInsertConnectionScheme.Enum) -> NoneType   5. __init__(handle, rosetta.protocols.forge.build.Interval, str, str, rosetta.core.pose.Pose) -> NoneType   doc   6. __init__(handle, rosetta.protocols.forge.build.Interval, str, str, rosetta.core.pose.Pose, bool) -> NoneType   doc   7. __init__(self : handle, i : rosetta.protocols.forge.build.Interval, ss : str, aa : str, insert : rosetta.core.pose.Pose, keep_known_bb_torsions_at_junctions : bool, connection_scheme : rosetta.protocols.forge.build.SegmentInsertConnectionScheme.Enum) -> NoneType   8. __init__(handle, rosetta.protocols.forge.build.SegmentInsert) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. aa(...) from builtins.PyCapsule aa(rosetta.protocols.forge.build.SegmentInsert) -> str   get annotated amino acid string (includes insertion point as '^') assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.forge.build.SegmentInsert, rval : rosetta.protocols.forge.build.SegmentInsert) -> rosetta.protocols.forge.build.SegmentInsert   copy assignment clone(...) from builtins.PyCapsule clone(rosetta.protocols.forge.build.SegmentInsert) -> rosetta.protocols.forge.build.BuildInstruction   clone this object creates_undefined_backbone(...) from builtins.PyCapsule creates_undefined_backbone(rosetta.protocols.forge.build.SegmentInsert) -> bool   does this object create undefined backbone in the modified region? defined_positions(...) from builtins.PyCapsule defined_positions(rosetta.protocols.forge.build.SegmentInsert) -> rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t   return a copy of the set of positions within the newly modified   region that has a defined conformation.  E.g. existing or copied residues.      This set can change wrt length changes in Pose/Conformation being   watched. flanking_left_aa(...) from builtins.PyCapsule flanking_left_aa(rosetta.protocols.forge.build.SegmentInsert) -> str   get the annotated aa string of the flanking residues to the left   of the insertion point flanking_left_nres(...) from builtins.PyCapsule flanking_left_nres(rosetta.protocols.forge.build.SegmentInsert) -> int   get the number of flanking residues to the left of the insertion   point flanking_left_ss(...) from builtins.PyCapsule flanking_left_ss(rosetta.protocols.forge.build.SegmentInsert) -> str   get the ss string of the flanking residues to the left of the   insertion point flanking_right_aa(...) from builtins.PyCapsule flanking_right_aa(rosetta.protocols.forge.build.SegmentInsert) -> str   get the annotated aa string of the flanking residues to the right   of the insertion point flanking_right_nres(...) from builtins.PyCapsule flanking_right_nres(rosetta.protocols.forge.build.SegmentInsert) -> int   get the number of flanking residues to the right of the insertion   point flanking_right_ss(...) from builtins.PyCapsule flanking_right_ss(rosetta.protocols.forge.build.SegmentInsert) -> str   get the ss string of the flanking residues to the right of the   insertion point insert_connection_scheme(...) from builtins.PyCapsule insert_connection_scheme(rosetta.protocols.forge.build.SegmentInsert) -> rosetta.protocols.forge.build.SegmentInsertConnectionScheme.Enum   get the insert connection scheme -- whether the insertion will   be glued on the N-side, C-side, or if SegmentInsert will pick randomly   between the two insert_pose(...) from builtins.PyCapsule insert_pose(rosetta.protocols.forge.build.SegmentInsert) -> rosetta.core.pose.Pose   the pose to insert insert_pose_torsion_override_movemap(...) from builtins.PyCapsule insert_pose_torsion_override_movemap(*args, **kwargs) Overloaded function.   1. insert_pose_torsion_override_movemap(rosetta.protocols.forge.build.SegmentInsert) -> rosetta.core.kinematics.MoveMap   a torsion (bb/chi) specific override movemap indexed wrt the insert Pose   (residue indices may only be within the range [1, insert_pose.n_residue()]      When generating the movemap(), this torsion movemap will be enforced.   Only *explicit* settings of TorsionType, MoveMapTorsionID, and TorsionID will   be honored.  Implicit false settings are ignored.   2. insert_pose_torsion_override_movemap(self : rosetta.protocols.forge.build.SegmentInsert, mm : rosetta.core.kinematics.MoveMap) -> NoneType   set a torsion (bb/chi) specific override movemap indexed wrt the insert   Pose (residue indices may only be within the range [1, insert_pose.n_residue()]      When generating the movemap(), this torsion movemap will be enforced.   Only *explicit* settings of TorsionType, MoveMapTorsionID, and TorsionID will   be honored.  Implicit false settings are ignored. insertion_char(...) from builtins.PyCapsule insertion_char() -> str   the character representing the insertion point      '^' insertion_end_residue(...) from builtins.PyCapsule insertion_end_residue(rosetta.protocols.forge.build.SegmentInsert) -> int   get the residue at the end of the insertion relative to the   modified interval (flanking positions are not part of the insertion!) insertion_point_absolute_index(...) from builtins.PyCapsule insertion_point_absolute_index(rosetta.protocols.forge.build.SegmentInsert) -> int   get the absolute index of the insertion point with respect to the   flanking regions (i.e. the index inside the ss string) insertion_start_residue(...) from builtins.PyCapsule insertion_start_residue(rosetta.protocols.forge.build.SegmentInsert) -> int   get the residue at the start of the insertion relative to the   modified interval (flanking positions are not part of the insertion!) interval(...) from builtins.PyCapsule interval(rosetta.protocols.forge.build.SegmentInsert) -> rosetta.protocols.forge.build.Interval   a copy of the working range of residues specifying the modified region      This residue range can change wrt length changes in Pose /Conformation   being watched. keep_known_bb_torsions_at_junctions(...) from builtins.PyCapsule keep_known_bb_torsions_at_junctions(rosetta.protocols.forge.build.SegmentInsert) -> bool   Attempt to keep the phi at original_interval().left and the psi+omega   at original_interval().right present from the original Pose in the modified   Pose?  Not applicable for pure insertions.  Default False. movemap(...) from builtins.PyCapsule movemap(rosetta.protocols.forge.build.SegmentInsert) -> rosetta.core.kinematics.MoveMap   return a copy of the MoveMap that defines the moveable/fixed   positions/dofs for this instruction      TO BE FILLED IN      This set can change wrt length changes in Pose/Conformation being   watched. new_positions(...) from builtins.PyCapsule new_positions(rosetta.protocols.forge.build.SegmentInsert) -> rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t   return a copy of the set of positions that are "new" and did   not exist in the original Pose. on_residue_append(...) from builtins.PyCapsule on_residue_append(self : rosetta.protocols.forge.build.SegmentInsert, event : rosetta.core.conformation.signals.LengthEvent) -> NoneType   update indexing on residue append on_residue_delete(...) from builtins.PyCapsule on_residue_delete(self : rosetta.protocols.forge.build.SegmentInsert, event : rosetta.core.conformation.signals.LengthEvent) -> NoneType   update indexing on residue delete on_residue_prepend(...) from builtins.PyCapsule on_residue_prepend(self : rosetta.protocols.forge.build.SegmentInsert, event : rosetta.core.conformation.signals.LengthEvent) -> NoneType   update indexing on residue prepend original_deleted_positions(...) from builtins.PyCapsule original_deleted_positions(rosetta.protocols.forge.build.SegmentInsert) -> rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t   return set of positions within the original interval that will   be deleted in this BuildInstruction original_fixed_positions(...) from builtins.PyCapsule original_fixed_positions(rosetta.protocols.forge.build.SegmentInsert) -> rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t   return set of any fixed positions necessary with respect to the original   interval and original Pose numbering      Used for ensuring build regions for instructions do not overlap and   so that jumps may be placed correctly.      empty set if no fixed positions necessary original_interval_valid(...) from builtins.PyCapsule original_interval_valid(rosetta.protocols.forge.build.SegmentInsert) -> bool   is the original interval storing valid information, or is empty   or being used for something else?      always false, original interval invalid original_kept_positions(...) from builtins.PyCapsule original_kept_positions(rosetta.protocols.forge.build.SegmentInsert) -> rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t   return the set of positions within the original interval that   will be kept in this BuildInstruction      An empty set -- no positions are kept. original_mutable_positions(...) from builtins.PyCapsule original_mutable_positions(rosetta.protocols.forge.build.SegmentInsert) -> rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t   return set of any mutable positions necessary with respect to the original   interval and original Pose numbering      Used for ensuring build regions for instructions do not overlap and   so that jumps may be placed correctly. performing_pure_insertion(...) from builtins.PyCapsule performing_pure_insertion(rosetta.protocols.forge.build.SegmentInsert) -> bool   performing a pure insertion/extension?      True if SegmentInsert was initialized with an interval whose   left endpoint == 0, False otherwise. preexisting_positions(...) from builtins.PyCapsule preexisting_positions(rosetta.protocols.forge.build.SegmentInsert) -> rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t   return a copy of the set of positions within the new region   that were pre-existing in the original Pose prior to modify()      An empty set, there are no pre-existing positions. ss(...) from builtins.PyCapsule ss(rosetta.protocols.forge.build.SegmentInsert) -> str   get secondary structure string (includes insertion point as '^') undefined_positions(...) from builtins.PyCapsule undefined_positions(rosetta.protocols.forge.build.SegmentInsert) -> rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t   return a copy of the set of positions within the newly modified   region that has an undefined conformation.  E.g. newly created residues.      This set can change wrt length changes in Pose/Conformation being   watched. Methods inherited from BuildInstruction: add_dependency_to(...) from builtins.PyCapsule add_dependency_to(self : rosetta.protocols.forge.build.BuildInstruction, i : rosetta.std.weak_ptr_const_protocols_forge_build_BuildInstruction_t) -> NoneType   add an instruction to this BuildInstruction's dependency list      before this instruction's modify() may complete properly, all   instructions in the dependency list must have completed modify() first attach_to(...) from builtins.PyCapsule attach_to(self : rosetta.protocols.forge.build.BuildInstruction, pose : rosetta.core.pose.Pose) -> NoneType   attach to a Pose's conformation clear_dependencies(...) from builtins.PyCapsule clear_dependencies(rosetta.protocols.forge.build.BuildInstruction) -> NoneType   clear the list of dependencies compatible_with(...) from builtins.PyCapsule compatible_with(self : rosetta.protocols.forge.build.BuildInstruction, rval : rosetta.protocols.forge.build.BuildInstruction) -> bool   compares fixed and mutable positions to determine compatibility with   another instruction      override this to obtain custom compatibility check dependencies(...) from builtins.PyCapsule dependencies(rosetta.protocols.forge.build.BuildInstruction) -> rosetta.utility.vector1_std_weak_ptr_const_protocols_forge_build_BuildInstruction_t   the list of instructions whose modify() must complete before   the modify() for this instruction may be called successfully dependent_on(...) from builtins.PyCapsule dependent_on(self : rosetta.protocols.forge.build.BuildInstruction, i : rosetta.std.weak_ptr_const_protocols_forge_build_BuildInstruction_t) -> bool   is this instruction dependent upon the given instruction? detach_after_modify(...) from builtins.PyCapsule detach_after_modify(*args, **kwargs) Overloaded function.   1. detach_after_modify(rosetta.protocols.forge.build.BuildInstruction) -> bool   detach after modify()?      Ordinarily a modify() call consists of attaching as a   length obs of the Pose, actually doing the modify, and then   detaching as a length obs of the Pose.  This flag governs whether   the last detach occurs.   2. detach_after_modify(self : rosetta.protocols.forge.build.BuildInstruction, flag : bool) -> NoneType   set detach after modify()      Ordinarily a modify() call consists of attaching as a   length obs of the Pose, actually doing the modify, and then   detaching as a length obs of the Pose.  This flag governs whether   the last detach occurs. detach_from(...) from builtins.PyCapsule detach_from(rosetta.protocols.forge.build.BuildInstruction) -> NoneType   detach from a Pose's conformation has_dependencies(...) from builtins.PyCapsule has_dependencies(rosetta.protocols.forge.build.BuildInstruction) -> bool   does this BuildInstruction have dependencies? modify(...) from builtins.PyCapsule modify(self : rosetta.protocols.forge.build.BuildInstruction, pose : rosetta.core.pose.Pose) -> rosetta.protocols.forge.build.BuildInstructionState.Enum   modify this pose      the state of the BuildInstruction modify_was_successful(...) from builtins.PyCapsule modify_was_successful(rosetta.protocols.forge.build.BuildInstruction) -> bool   Is the BuildInstruction's state at MODIFY_WAS_SUCCESSFUL?      MODIFY_WAS_SUCCESSFUL indicates the BuildInstruction has   finished modifications to the Pose, and its residue indexing is now   consistent with the newly modified Pose. n_dependencies(...) from builtins.PyCapsule n_dependencies(rosetta.protocols.forge.build.BuildInstruction) -> int   the number of dependencies this BuildInstruction has on_length_change(...) from builtins.PyCapsule on_length_change(self : rosetta.protocols.forge.build.BuildInstruction, event : rosetta.core.conformation.signals.LengthEvent) -> NoneType   update any indexing wrt length change to Pose/Conformation being watched original_interval(...) from builtins.PyCapsule original_interval(rosetta.protocols.forge.build.BuildInstruction) -> rosetta.protocols.forge.build.Interval   return original residue range of this instruction ready(...) from builtins.PyCapsule ready(rosetta.protocols.forge.build.BuildInstruction) -> bool   Is the BuildInstruction's state at READY?      READY indicates the BuildInstruction has been reset   and is ready to modify a Pose. reset_accounting(...) from builtins.PyCapsule reset_accounting(rosetta.protocols.forge.build.BuildInstruction) -> NoneType   reset intervals, positions, etc to initial state and drop   observers.  State set to READY. residue_type_set(...) from builtins.PyCapsule residue_type_set(rosetta.protocols.forge.build.BuildInstruction) -> rosetta.core.chemical.ResidueTypeSet   the residue type set being used state(...) from builtins.PyCapsule state(rosetta.protocols.forge.build.BuildInstruction) -> rosetta.protocols.forge.build.BuildInstructionState.Enum   return the state of this BuildInstruction waiting_on_dependencies(...) from builtins.PyCapsule waiting_on_dependencies(rosetta.protocols.forge.build.BuildInstruction) -> bool   Is the BuildInstruction's state at WAITING_ON_DEPENDENCIES?      WAITING_ON_DEPENDENCIES indicates   the BuildInstruction is waiting for its dependencies to be satisfied   before allowing modifications to proceed.   class SegmentRebuild(BuildInstruction)     instruction to rebuild a segment     Handles both cut based rebuilding (i.e. loops) and continuous  rebuilding adjacent to the boundary of a chain, such as n-term/c-term  extensions.     Method resolution order: SegmentRebuild BuildInstruction builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle) -> NoneType   2. __init__(handle, rosetta.protocols.forge.build.Interval, str) -> NoneType   doc   3. __init__(handle, rosetta.protocols.forge.build.Interval, str, rosetta.std.weak_ptr_const_core_chemical_ResidueTypeSet_t) -> NoneType   doc   4. __init__(self : handle, i : rosetta.protocols.forge.build.Interval, ss : str, rts : rosetta.std.weak_ptr_const_core_chemical_ResidueTypeSet_t, keep_known_bb_torsions_at_junctions : bool) -> NoneType   5. __init__(handle, rosetta.protocols.forge.build.Interval, str, str) -> NoneType   doc   6. __init__(handle, rosetta.protocols.forge.build.Interval, str, str, rosetta.std.weak_ptr_const_core_chemical_ResidueTypeSet_t) -> NoneType   doc   7. __init__(self : handle, i : rosetta.protocols.forge.build.Interval, ss : str, aa : str, rts : rosetta.std.weak_ptr_const_core_chemical_ResidueTypeSet_t, keep_known_bb_torsions_at_junctions : bool) -> NoneType   8. __init__(handle, rosetta.protocols.forge.build.SegmentRebuild) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. aa(...) from builtins.PyCapsule aa(rosetta.protocols.forge.build.SegmentRebuild) -> str   get annotated amino acid string assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.forge.build.SegmentRebuild, rval : rosetta.protocols.forge.build.SegmentRebuild) -> rosetta.protocols.forge.build.SegmentRebuild   copy assignment clone(...) from builtins.PyCapsule clone(rosetta.protocols.forge.build.SegmentRebuild) -> rosetta.protocols.forge.build.BuildInstruction   clone this object creates_undefined_backbone(...) from builtins.PyCapsule creates_undefined_backbone(rosetta.protocols.forge.build.SegmentRebuild) -> bool   does this object create undefined backbone in the modified region?      true defined_positions(...) from builtins.PyCapsule defined_positions(rosetta.protocols.forge.build.SegmentRebuild) -> rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t   return a copy of the set of positions within the newly modified   region that has a defined conformation.  E.g. existing or copied residues.      An empty set -- no positions are defined.      This set can change wrt length changes in Pose/Conformation being   watched. interval(...) from builtins.PyCapsule interval(rosetta.protocols.forge.build.SegmentRebuild) -> rosetta.protocols.forge.build.Interval   a copy of the working range of residues specifying the modified region      this can change if listening to Conformation LengthEvents keep_known_bb_torsions_at_junctions(...) from builtins.PyCapsule keep_known_bb_torsions_at_junctions(rosetta.protocols.forge.build.SegmentRebuild) -> bool   Attempt to keep the omega at original_interval().left-1, the phi   at original_interval().left and the psi+omega at original_interval().right   present from the original Pose in the modified Pose?  Default False movemap(...) from builtins.PyCapsule movemap(rosetta.protocols.forge.build.SegmentRebuild) -> rosetta.core.kinematics.MoveMap   return a copy of the MoveMap that defines the moveable/fixed   positions/dofs for this instruction      a MoveMap with [interval.left, interval.right] bb & chi set to true   at the MoveMapTorsionID level      This set can change wrt length changes in Pose/Conformation being   watched. new_positions(...) from builtins.PyCapsule new_positions(rosetta.protocols.forge.build.SegmentRebuild) -> rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t   return a copy of the set of positions that are "new" and did   not exist in the original Pose.      A set of positions spanning the entire modified interval -- all   positions are undefined. on_residue_append(...) from builtins.PyCapsule on_residue_append(self : rosetta.protocols.forge.build.SegmentRebuild, event : rosetta.core.conformation.signals.LengthEvent) -> NoneType   update indexing on residue append on_residue_delete(...) from builtins.PyCapsule on_residue_delete(self : rosetta.protocols.forge.build.SegmentRebuild, event : rosetta.core.conformation.signals.LengthEvent) -> NoneType   update indexing on residue delete on_residue_prepend(...) from builtins.PyCapsule on_residue_prepend(self : rosetta.protocols.forge.build.SegmentRebuild, event : rosetta.core.conformation.signals.LengthEvent) -> NoneType   update indexing on residue prepend original_deleted_positions(...) from builtins.PyCapsule original_deleted_positions(rosetta.protocols.forge.build.SegmentRebuild) -> rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t   return set of positions within the original interval that will   be deleted in this BuildInstruction      A set containing all positions in the original interval. original_fixed_positions(...) from builtins.PyCapsule original_fixed_positions(rosetta.protocols.forge.build.SegmentRebuild) -> rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t   return set of any fixed positions necessary with respect to the original   interval and original Pose numbering      Used for ensuring build regions for instructions do not overlap and   so that jumps may be placed correctly.  If SegmentRebuild has dependencies,   the set of positions shrinks from the endpoints of [original_left - 1, original_right + 1]   down to an empty set in the assumption that the user is requesting an   advanced feature and knows what they're doing around the endpoints,   e.g. rebuilding directly adjacent to a swapped out section.      empty set if no fixed positions original_interval_valid(...) from builtins.PyCapsule original_interval_valid(rosetta.protocols.forge.build.SegmentRebuild) -> bool   is the original interval storing valid information, or is empty   or being used for something else?      true, stores valid interval original_kept_positions(...) from builtins.PyCapsule original_kept_positions(rosetta.protocols.forge.build.SegmentRebuild) -> rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t   return the set of positions within the original interval that   will be kept in this BuildInstruction      An empty set -- no positions are kept. original_mutable_positions(...) from builtins.PyCapsule original_mutable_positions(rosetta.protocols.forge.build.SegmentRebuild) -> rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t   return set of any mutable positions necessary with respect to the original   interval and original Pose numbering      Used for ensuring build regions for instructions do not overlap and   so that jumps may be placed correctly.      empty set if no mutable positions preexisting_positions(...) from builtins.PyCapsule preexisting_positions(rosetta.protocols.forge.build.SegmentRebuild) -> rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t   return a copy of the set of positions within the new region   that were pre-existing in the original Pose prior to modify()      An empty set -- no positions are pre-existing. ss(...) from builtins.PyCapsule ss(rosetta.protocols.forge.build.SegmentRebuild) -> str   get secondary structure string undefined_positions(...) from builtins.PyCapsule undefined_positions(rosetta.protocols.forge.build.SegmentRebuild) -> rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t   return a copy of the set of positions within the newly modified   region that has an undefined conformation.  E.g. newly created residues.      A set of positions spanning the entire modified interval -- all   positions are undefined.      This set can change wrt length changes in Pose/Conformation being   watched. Methods inherited from BuildInstruction: add_dependency_to(...) from builtins.PyCapsule add_dependency_to(self : rosetta.protocols.forge.build.BuildInstruction, i : rosetta.std.weak_ptr_const_protocols_forge_build_BuildInstruction_t) -> NoneType   add an instruction to this BuildInstruction's dependency list      before this instruction's modify() may complete properly, all   instructions in the dependency list must have completed modify() first attach_to(...) from builtins.PyCapsule attach_to(self : rosetta.protocols.forge.build.BuildInstruction, pose : rosetta.core.pose.Pose) -> NoneType   attach to a Pose's conformation clear_dependencies(...) from builtins.PyCapsule clear_dependencies(rosetta.protocols.forge.build.BuildInstruction) -> NoneType   clear the list of dependencies compatible_with(...) from builtins.PyCapsule compatible_with(self : rosetta.protocols.forge.build.BuildInstruction, rval : rosetta.protocols.forge.build.BuildInstruction) -> bool   compares fixed and mutable positions to determine compatibility with   another instruction      override this to obtain custom compatibility check dependencies(...) from builtins.PyCapsule dependencies(rosetta.protocols.forge.build.BuildInstruction) -> rosetta.utility.vector1_std_weak_ptr_const_protocols_forge_build_BuildInstruction_t   the list of instructions whose modify() must complete before   the modify() for this instruction may be called successfully dependent_on(...) from builtins.PyCapsule dependent_on(self : rosetta.protocols.forge.build.BuildInstruction, i : rosetta.std.weak_ptr_const_protocols_forge_build_BuildInstruction_t) -> bool   is this instruction dependent upon the given instruction? detach_after_modify(...) from builtins.PyCapsule detach_after_modify(*args, **kwargs) Overloaded function.   1. detach_after_modify(rosetta.protocols.forge.build.BuildInstruction) -> bool   detach after modify()?      Ordinarily a modify() call consists of attaching as a   length obs of the Pose, actually doing the modify, and then   detaching as a length obs of the Pose.  This flag governs whether   the last detach occurs.   2. detach_after_modify(self : rosetta.protocols.forge.build.BuildInstruction, flag : bool) -> NoneType   set detach after modify()      Ordinarily a modify() call consists of attaching as a   length obs of the Pose, actually doing the modify, and then   detaching as a length obs of the Pose.  This flag governs whether   the last detach occurs. detach_from(...) from builtins.PyCapsule detach_from(rosetta.protocols.forge.build.BuildInstruction) -> NoneType   detach from a Pose's conformation has_dependencies(...) from builtins.PyCapsule has_dependencies(rosetta.protocols.forge.build.BuildInstruction) -> bool   does this BuildInstruction have dependencies? modify(...) from builtins.PyCapsule modify(self : rosetta.protocols.forge.build.BuildInstruction, pose : rosetta.core.pose.Pose) -> rosetta.protocols.forge.build.BuildInstructionState.Enum   modify this pose      the state of the BuildInstruction modify_was_successful(...) from builtins.PyCapsule modify_was_successful(rosetta.protocols.forge.build.BuildInstruction) -> bool   Is the BuildInstruction's state at MODIFY_WAS_SUCCESSFUL?      MODIFY_WAS_SUCCESSFUL indicates the BuildInstruction has   finished modifications to the Pose, and its residue indexing is now   consistent with the newly modified Pose. n_dependencies(...) from builtins.PyCapsule n_dependencies(rosetta.protocols.forge.build.BuildInstruction) -> int   the number of dependencies this BuildInstruction has on_length_change(...) from builtins.PyCapsule on_length_change(self : rosetta.protocols.forge.build.BuildInstruction, event : rosetta.core.conformation.signals.LengthEvent) -> NoneType   update any indexing wrt length change to Pose/Conformation being watched original_interval(...) from builtins.PyCapsule original_interval(rosetta.protocols.forge.build.BuildInstruction) -> rosetta.protocols.forge.build.Interval   return original residue range of this instruction ready(...) from builtins.PyCapsule ready(rosetta.protocols.forge.build.BuildInstruction) -> bool   Is the BuildInstruction's state at READY?      READY indicates the BuildInstruction has been reset   and is ready to modify a Pose. reset_accounting(...) from builtins.PyCapsule reset_accounting(rosetta.protocols.forge.build.BuildInstruction) -> NoneType   reset intervals, positions, etc to initial state and drop   observers.  State set to READY. residue_type_set(...) from builtins.PyCapsule residue_type_set(rosetta.protocols.forge.build.BuildInstruction) -> rosetta.core.chemical.ResidueTypeSet   the residue type set being used state(...) from builtins.PyCapsule state(rosetta.protocols.forge.build.BuildInstruction) -> rosetta.protocols.forge.build.BuildInstructionState.Enum   return the state of this BuildInstruction waiting_on_dependencies(...) from builtins.PyCapsule waiting_on_dependencies(rosetta.protocols.forge.build.BuildInstruction) -> bool   Is the BuildInstruction's state at WAITING_ON_DEPENDENCIES?      WAITING_ON_DEPENDENCIES indicates   the BuildInstruction is waiting for its dependencies to be satisfied   before allowing modifications to proceed.   class SegmentSwap(BuildInstruction)     instruction to swap a segment with an external segment     Method resolution order: SegmentSwap BuildInstruction builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle) -> NoneType   2. __init__(self : handle, i : rosetta.protocols.forge.build.Interval, swap_in_movemap : rosetta.core.kinematics.MoveMap, swap_in : rosetta.core.pose.Pose) -> NoneType   3. __init__(handle, rosetta.protocols.forge.build.SegmentSwap) -> 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.forge.build.SegmentSwap, rval : rosetta.protocols.forge.build.SegmentSwap) -> rosetta.protocols.forge.build.SegmentSwap   copy assignment clone(...) from builtins.PyCapsule clone(rosetta.protocols.forge.build.SegmentSwap) -> rosetta.protocols.forge.build.BuildInstruction   clone this object creates_undefined_backbone(...) from builtins.PyCapsule creates_undefined_backbone(rosetta.protocols.forge.build.SegmentSwap) -> bool   does this object create undefined backbone in the modified region? defined_positions(...) from builtins.PyCapsule defined_positions(rosetta.protocols.forge.build.SegmentSwap) -> rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t   return a copy of the set of positions within the newly modified   region that has a defined conformation.  E.g. existing or copied residues.      A set of positions spanning the interval -- all positions are   are defined.      This set can change wrt length changes in Pose/Conformation being   watched. interval(...) from builtins.PyCapsule interval(rosetta.protocols.forge.build.SegmentSwap) -> rosetta.protocols.forge.build.Interval   a copy of the working range of residues specifying the swapped region      This residue range can change wrt length changes in Pose /Conformation   being watched. movemap(...) from builtins.PyCapsule movemap(rosetta.protocols.forge.build.SegmentSwap) -> rosetta.core.kinematics.MoveMap   return a copy of the MoveMap that defines the moveable/fixed   positions/dofs for this instruction      a MoveMap with [interval.left, interval.right] bb set to false   at the MoveMapTorsionID level      This set can change wrt length changes in Pose/Conformation being   watched. new_positions(...) from builtins.PyCapsule new_positions(rosetta.protocols.forge.build.SegmentSwap) -> rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t   return a copy of the set of positions that are "new" and did   not exist in the original Pose.      A set of positions spanning the interval -- all positions are   are defined. on_residue_append(...) from builtins.PyCapsule on_residue_append(self : rosetta.protocols.forge.build.SegmentSwap, event : rosetta.core.conformation.signals.LengthEvent) -> NoneType   update indexing on residue append on_residue_delete(...) from builtins.PyCapsule on_residue_delete(self : rosetta.protocols.forge.build.SegmentSwap, event : rosetta.core.conformation.signals.LengthEvent) -> NoneType   update indexing on residue delete on_residue_prepend(...) from builtins.PyCapsule on_residue_prepend(self : rosetta.protocols.forge.build.SegmentSwap, event : rosetta.core.conformation.signals.LengthEvent) -> NoneType   update indexing on residue prepend original_deleted_positions(...) from builtins.PyCapsule original_deleted_positions(rosetta.protocols.forge.build.SegmentSwap) -> rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t   return set of positions within the original interval that will   be deleted in this BuildInstruction      An empty set -- no positions are deleted. original_fixed_positions(...) from builtins.PyCapsule original_fixed_positions(rosetta.protocols.forge.build.SegmentSwap) -> rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t   return set of any fixed positions necessary with respect to the original   interval and original Pose numbering      Used for ensuring build regions for instructions do not overlap and   so that jumps may be placed correctly.      empty set if no fixed positions necessary original_interval_valid(...) from builtins.PyCapsule original_interval_valid(rosetta.protocols.forge.build.SegmentSwap) -> bool   is the original interval storing valid information, or is empty   or being used for something else?      true, stores valid interval original_kept_positions(...) from builtins.PyCapsule original_kept_positions(rosetta.protocols.forge.build.SegmentSwap) -> rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t   return the set of positions within the original interval that   will be kept in this BuildInstruction      An empty set -- no positions are kept. original_mutable_positions(...) from builtins.PyCapsule original_mutable_positions(rosetta.protocols.forge.build.SegmentSwap) -> rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t   return set of any mutable positions necessary with respect to the original   interval and original Pose numbering      Used for ensuring build regions for instructions do not overlap and   so that jumps may be placed correctly. preexisting_positions(...) from builtins.PyCapsule preexisting_positions(rosetta.protocols.forge.build.SegmentSwap) -> rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t   return a copy of the set of positions within the new region   that were pre-existing in the original Pose prior to modify()      An empty set -- no positions are pre-existing. swap_in(...) from builtins.PyCapsule swap_in(rosetta.protocols.forge.build.SegmentSwap) -> rosetta.core.pose.Pose   the pose to swap in swap_in_movemap(...) from builtins.PyCapsule swap_in_movemap(rosetta.protocols.forge.build.SegmentSwap) -> rosetta.core.kinematics.MoveMap   fixed backbone residues in this movemap will be used for new jumps      Procedure will attempt to honor this movemap as much as it can.   The caveat is that sequences of calls to some FoldTree routines may shift   the jumps internally in a way that is not easily predictable.  If the   procedure cannot  find an allowed residue for a jump, it will make a jump   to the (lower) median residue in the disconnected fold tree interval. undefined_positions(...) from builtins.PyCapsule undefined_positions(rosetta.protocols.forge.build.SegmentSwap) -> rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t   return a copy of the set of positions within the newly modified   region that has an undefined conformation.  E.g. newly created residues.      An empty set -- no undefined positions.      This set can change wrt length changes in Pose/Conformation being   watched. Methods inherited from BuildInstruction: add_dependency_to(...) from builtins.PyCapsule add_dependency_to(self : rosetta.protocols.forge.build.BuildInstruction, i : rosetta.std.weak_ptr_const_protocols_forge_build_BuildInstruction_t) -> NoneType   add an instruction to this BuildInstruction's dependency list      before this instruction's modify() may complete properly, all   instructions in the dependency list must have completed modify() first attach_to(...) from builtins.PyCapsule attach_to(self : rosetta.protocols.forge.build.BuildInstruction, pose : rosetta.core.pose.Pose) -> NoneType   attach to a Pose's conformation clear_dependencies(...) from builtins.PyCapsule clear_dependencies(rosetta.protocols.forge.build.BuildInstruction) -> NoneType   clear the list of dependencies compatible_with(...) from builtins.PyCapsule compatible_with(self : rosetta.protocols.forge.build.BuildInstruction, rval : rosetta.protocols.forge.build.BuildInstruction) -> bool   compares fixed and mutable positions to determine compatibility with   another instruction      override this to obtain custom compatibility check dependencies(...) from builtins.PyCapsule dependencies(rosetta.protocols.forge.build.BuildInstruction) -> rosetta.utility.vector1_std_weak_ptr_const_protocols_forge_build_BuildInstruction_t   the list of instructions whose modify() must complete before   the modify() for this instruction may be called successfully dependent_on(...) from builtins.PyCapsule dependent_on(self : rosetta.protocols.forge.build.BuildInstruction, i : rosetta.std.weak_ptr_const_protocols_forge_build_BuildInstruction_t) -> bool   is this instruction dependent upon the given instruction? detach_after_modify(...) from builtins.PyCapsule detach_after_modify(*args, **kwargs) Overloaded function.   1. detach_after_modify(rosetta.protocols.forge.build.BuildInstruction) -> bool   detach after modify()?      Ordinarily a modify() call consists of attaching as a   length obs of the Pose, actually doing the modify, and then   detaching as a length obs of the Pose.  This flag governs whether   the last detach occurs.   2. detach_after_modify(self : rosetta.protocols.forge.build.BuildInstruction, flag : bool) -> NoneType   set detach after modify()      Ordinarily a modify() call consists of attaching as a   length obs of the Pose, actually doing the modify, and then   detaching as a length obs of the Pose.  This flag governs whether   the last detach occurs. detach_from(...) from builtins.PyCapsule detach_from(rosetta.protocols.forge.build.BuildInstruction) -> NoneType   detach from a Pose's conformation has_dependencies(...) from builtins.PyCapsule has_dependencies(rosetta.protocols.forge.build.BuildInstruction) -> bool   does this BuildInstruction have dependencies? modify(...) from builtins.PyCapsule modify(self : rosetta.protocols.forge.build.BuildInstruction, pose : rosetta.core.pose.Pose) -> rosetta.protocols.forge.build.BuildInstructionState.Enum   modify this pose      the state of the BuildInstruction modify_was_successful(...) from builtins.PyCapsule modify_was_successful(rosetta.protocols.forge.build.BuildInstruction) -> bool   Is the BuildInstruction's state at MODIFY_WAS_SUCCESSFUL?      MODIFY_WAS_SUCCESSFUL indicates the BuildInstruction has   finished modifications to the Pose, and its residue indexing is now   consistent with the newly modified Pose. n_dependencies(...) from builtins.PyCapsule n_dependencies(rosetta.protocols.forge.build.BuildInstruction) -> int   the number of dependencies this BuildInstruction has on_length_change(...) from builtins.PyCapsule on_length_change(self : rosetta.protocols.forge.build.BuildInstruction, event : rosetta.core.conformation.signals.LengthEvent) -> NoneType   update any indexing wrt length change to Pose/Conformation being watched original_interval(...) from builtins.PyCapsule original_interval(rosetta.protocols.forge.build.BuildInstruction) -> rosetta.protocols.forge.build.Interval   return original residue range of this instruction ready(...) from builtins.PyCapsule ready(rosetta.protocols.forge.build.BuildInstruction) -> bool   Is the BuildInstruction's state at READY?      READY indicates the BuildInstruction has been reset   and is ready to modify a Pose. reset_accounting(...) from builtins.PyCapsule reset_accounting(rosetta.protocols.forge.build.BuildInstruction) -> NoneType   reset intervals, positions, etc to initial state and drop   observers.  State set to READY. residue_type_set(...) from builtins.PyCapsule residue_type_set(rosetta.protocols.forge.build.BuildInstruction) -> rosetta.core.chemical.ResidueTypeSet   the residue type set being used state(...) from builtins.PyCapsule state(rosetta.protocols.forge.build.BuildInstruction) -> rosetta.protocols.forge.build.BuildInstructionState.Enum   return the state of this BuildInstruction waiting_on_dependencies(...) from builtins.PyCapsule waiting_on_dependencies(rosetta.protocols.forge.build.BuildInstruction) -> bool   Is the BuildInstruction's state at WAITING_ON_DEPENDENCIES?      WAITING_ON_DEPENDENCIES indicates   the BuildInstruction is waiting for its dependencies to be satisfied   before allowing modifications to proceed.