Bindings for core::id namespace

Classes
		builtins.object AtomID AtomID_Map_bool_t AtomID_Map_bool AtomID_Map_core_id_AtomID_t AtomID_Map_AtomID AtomID_Map_core_id_TorsionID_t AtomID_Map_double_t AtomID_Map_Real AtomID_Map_numeric_xyzVector_double_t AtomID_Map_std_shared_ptr_core_kinematics_tree_Atom_t BondID DOF_ID DOF_ID_Map_bool_t DOF_ID_Map_core_id_TorsionID_t DOF_ID_Range DOF_Type JumpID MainchainTorsionType NamedAtomID NamedAtomID_Map_core_id_NamedAtomID_t NamedAtomID_Map_NamedAtomID NamedStubID SequenceMapping StubID TorsionID TorsionID_Range TorsionType rosetta.basic.datacache.CacheableData(builtins.object) CacheableAtomID_MapVector rosetta.utility.excn.EXCN_Msg_Exception(rosetta.utility.excn.EXCN_Exception) EXCN_AtomNotFound   class AtomID(builtins.object)     Atom identifier class.  Defined by the atom number and the residue number.     Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.core.id.AtomID) -> NoneType   2. __init__(self : rosetta.core.id.AtomID, src : rosetta.core.id.AtomID) -> NoneType   3. __init__(self : rosetta.core.id.AtomID, atomno_in : int, rsd_in : int) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. __str__(...) from builtins.PyCapsule __str__(rosetta.core.id.AtomID) -> str assign(...) from builtins.PyCapsule assign(self : rosetta.core.id.AtomID,  : rosetta.core.id.AtomID) -> rosetta.core.id.AtomID atomno(...) from builtins.PyCapsule atomno(*args, **kwargs) Overloaded function.   1. atomno(rosetta.core.id.AtomID) -> int   Returns the AtomID atom number   2. atomno(rosetta.core.id.AtomID) -> int rsd(...) from builtins.PyCapsule rsd(*args, **kwargs) Overloaded function.   1. rsd(rosetta.core.id.AtomID) -> int   Returns the AtomID residue number   2. rsd(rosetta.core.id.AtomID) -> int valid(...) from builtins.PyCapsule valid(rosetta.core.id.AtomID) -> bool   Returns true if the AtomID is valid      must return false for BOGUS_ATOM_ID   class AtomID_Map_AtomID(AtomID_Map_core_id_AtomID_t)       Method resolution order: AtomID_Map_AtomID AtomID_Map_core_id_AtomID_t builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(rosetta.core.id.AtomID_Map_AtomID) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. Methods inherited from AtomID_Map_core_id_AtomID_t: __call__(...) from builtins.PyCapsule __call__(*args, **kwargs) Overloaded function.   1. __call__(self : rosetta.core.id.AtomID_Map_core_id_AtomID_t, id : core::id::AtomID) -> core::id::AtomID   2. __call__(self : rosetta.core.id.AtomID_Map_core_id_AtomID_t, id : core::id::AtomID) -> core::id::AtomID   3. __call__(self : rosetta.core.id.AtomID_Map_core_id_AtomID_t, i_res : int, i_atom : int) -> core::id::AtomID   4. __call__(self : rosetta.core.id.AtomID_Map_core_id_AtomID_t, i_res : int, i_atom : int) -> core::id::AtomID   5. __call__(self : rosetta.core.id.AtomID_Map_core_id_AtomID_t, i_res : int) -> rosetta.utility.vector1_core_id_AtomID   6. __call__(self : rosetta.core.id.AtomID_Map_core_id_AtomID_t, i_res : int) -> rosetta.utility.vector1_core_id_AtomID __getitem__(...) from builtins.PyCapsule __getitem__(*args, **kwargs) Overloaded function.   1. __getitem__(self : rosetta.core.id.AtomID_Map_core_id_AtomID_t, id : core::id::AtomID) -> core::id::AtomID   2. __getitem__(self : rosetta.core.id.AtomID_Map_core_id_AtomID_t, id : core::id::AtomID) -> core::id::AtomID   3. __getitem__(self : rosetta.core.id.AtomID_Map_core_id_AtomID_t, i_res : int) -> rosetta.utility.vector1_core_id_AtomID   4. __getitem__(self : rosetta.core.id.AtomID_Map_core_id_AtomID_t, i_res : int) -> rosetta.utility.vector1_core_id_AtomID all_default(...) from builtins.PyCapsule all_default(rosetta.core.id.AtomID_Map_core_id_AtomID_t) -> bool assign(...) from builtins.PyCapsule assign(self : rosetta.core.id.AtomID_Map_core_id_AtomID_t,  : rosetta.core.id.AtomID_Map_core_id_AtomID_t) -> rosetta.core.id.AtomID_Map_core_id_AtomID_t clear(...) from builtins.PyCapsule clear(*args, **kwargs) Overloaded function.   1. clear(rosetta.core.id.AtomID_Map_core_id_AtomID_t) -> NoneType   2. clear(self : rosetta.core.id.AtomID_Map_core_id_AtomID_t, default_value_a : core::id::AtomID) -> NoneType default_value(...) from builtins.PyCapsule default_value(*args, **kwargs) Overloaded function.   1. default_value(rosetta.core.id.AtomID_Map_core_id_AtomID_t) -> core::id::AtomID   2. default_value(self : rosetta.core.id.AtomID_Map_core_id_AtomID_t, default_value_a : core::id::AtomID) -> NoneType empty(...) from builtins.PyCapsule empty(rosetta.core.id.AtomID_Map_core_id_AtomID_t) -> bool fill(...) from builtins.PyCapsule fill(rosetta.core.id.AtomID_Map_core_id_AtomID_t) -> NoneType fill_with(...) from builtins.PyCapsule fill_with(*args, **kwargs) Overloaded function.   1. fill_with(self : rosetta.core.id.AtomID_Map_core_id_AtomID_t, value : core::id::AtomID) -> NoneType   2. fill_with(self : rosetta.core.id.AtomID_Map_core_id_AtomID_t, seqpos : int, value : core::id::AtomID) -> NoneType finalize(...) from builtins.PyCapsule finalize(rosetta.core.id.AtomID_Map_core_id_AtomID_t) -> NoneType get(...) from builtins.PyCapsule get(self : rosetta.core.id.AtomID_Map_core_id_AtomID_t, id : core::id::AtomID) -> core::id::AtomID has(...) from builtins.PyCapsule has(self : rosetta.core.id.AtomID_Map_core_id_AtomID_t, id : core::id::AtomID) -> bool n_atom(...) from builtins.PyCapsule n_atom(self : rosetta.core.id.AtomID_Map_core_id_AtomID_t, i_res : int) -> int n_residue(...) from builtins.PyCapsule n_residue(rosetta.core.id.AtomID_Map_core_id_AtomID_t) -> int resize(...) from builtins.PyCapsule resize(*args, **kwargs) Overloaded function.   1. resize(self : rosetta.core.id.AtomID_Map_core_id_AtomID_t, n_res : int) -> NoneType   2. resize(self : rosetta.core.id.AtomID_Map_core_id_AtomID_t, i_res : int, n_atom : int) -> NoneType   3. resize(self : rosetta.core.id.AtomID_Map_core_id_AtomID_t, i_res : int, n_atom : int, value : core::id::AtomID) -> NoneType set(...) from builtins.PyCapsule set(self : rosetta.core.id.AtomID_Map_core_id_AtomID_t, id : core::id::AtomID, value : core::id::AtomID) -> NoneType shrink(...) from builtins.PyCapsule shrink(rosetta.core.id.AtomID_Map_core_id_AtomID_t) -> NoneType size(...) from builtins.PyCapsule size(rosetta.core.id.AtomID_Map_core_id_AtomID_t) -> int swap(...) from builtins.PyCapsule swap(self : rosetta.core.id.AtomID_Map_core_id_AtomID_t, s : rosetta.core.id.AtomID_Map_core_id_AtomID_t) -> NoneType update_sequence_numbering(...) from builtins.PyCapsule update_sequence_numbering(self : rosetta.core.id.AtomID_Map_core_id_AtomID_t, new_size : int, old2new : rosetta.utility.vector1_unsigned_long) -> NoneType   class AtomID_Map_Real(AtomID_Map_double_t)       Method resolution order: AtomID_Map_Real AtomID_Map_double_t builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(rosetta.core.id.AtomID_Map_Real) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. Methods inherited from AtomID_Map_double_t: __call__(...) from builtins.PyCapsule __call__(*args, **kwargs) Overloaded function.   1. __call__(self : rosetta.core.id.AtomID_Map_double_t, id : core::id::AtomID) -> float   2. __call__(self : rosetta.core.id.AtomID_Map_double_t, id : core::id::AtomID) -> float   3. __call__(self : rosetta.core.id.AtomID_Map_double_t, i_res : int, i_atom : int) -> float   4. __call__(self : rosetta.core.id.AtomID_Map_double_t, i_res : int, i_atom : int) -> float   5. __call__(self : rosetta.core.id.AtomID_Map_double_t, i_res : int) -> rosetta.utility.vector1_double   6. __call__(self : rosetta.core.id.AtomID_Map_double_t, i_res : int) -> rosetta.utility.vector1_double __getitem__(...) from builtins.PyCapsule __getitem__(*args, **kwargs) Overloaded function.   1. __getitem__(self : rosetta.core.id.AtomID_Map_double_t, id : core::id::AtomID) -> float   2. __getitem__(self : rosetta.core.id.AtomID_Map_double_t, id : core::id::AtomID) -> float   3. __getitem__(self : rosetta.core.id.AtomID_Map_double_t, i_res : int) -> rosetta.utility.vector1_double   4. __getitem__(self : rosetta.core.id.AtomID_Map_double_t, i_res : int) -> rosetta.utility.vector1_double all_default(...) from builtins.PyCapsule all_default(rosetta.core.id.AtomID_Map_double_t) -> bool assign(...) from builtins.PyCapsule assign(self : rosetta.core.id.AtomID_Map_double_t,  : rosetta.core.id.AtomID_Map_double_t) -> rosetta.core.id.AtomID_Map_double_t clear(...) from builtins.PyCapsule clear(*args, **kwargs) Overloaded function.   1. clear(rosetta.core.id.AtomID_Map_double_t) -> NoneType   2. clear(self : rosetta.core.id.AtomID_Map_double_t, default_value_a : float) -> NoneType default_value(...) from builtins.PyCapsule default_value(*args, **kwargs) Overloaded function.   1. default_value(rosetta.core.id.AtomID_Map_double_t) -> float   2. default_value(self : rosetta.core.id.AtomID_Map_double_t, default_value_a : float) -> NoneType empty(...) from builtins.PyCapsule empty(rosetta.core.id.AtomID_Map_double_t) -> bool fill(...) from builtins.PyCapsule fill(rosetta.core.id.AtomID_Map_double_t) -> NoneType fill_with(...) from builtins.PyCapsule fill_with(*args, **kwargs) Overloaded function.   1. fill_with(self : rosetta.core.id.AtomID_Map_double_t, value : float) -> NoneType   2. fill_with(self : rosetta.core.id.AtomID_Map_double_t, seqpos : int, value : float) -> NoneType finalize(...) from builtins.PyCapsule finalize(rosetta.core.id.AtomID_Map_double_t) -> NoneType get(...) from builtins.PyCapsule get(self : rosetta.core.id.AtomID_Map_double_t, id : core::id::AtomID) -> float has(...) from builtins.PyCapsule has(self : rosetta.core.id.AtomID_Map_double_t, id : core::id::AtomID) -> bool n_atom(...) from builtins.PyCapsule n_atom(self : rosetta.core.id.AtomID_Map_double_t, i_res : int) -> int n_residue(...) from builtins.PyCapsule n_residue(rosetta.core.id.AtomID_Map_double_t) -> int resize(...) from builtins.PyCapsule resize(*args, **kwargs) Overloaded function.   1. resize(self : rosetta.core.id.AtomID_Map_double_t, n_res : int) -> NoneType   2. resize(self : rosetta.core.id.AtomID_Map_double_t, i_res : int, n_atom : int) -> NoneType   3. resize(self : rosetta.core.id.AtomID_Map_double_t, i_res : int, n_atom : int, value : float) -> NoneType set(...) from builtins.PyCapsule set(self : rosetta.core.id.AtomID_Map_double_t, id : core::id::AtomID, value : float) -> NoneType shrink(...) from builtins.PyCapsule shrink(rosetta.core.id.AtomID_Map_double_t) -> NoneType size(...) from builtins.PyCapsule size(rosetta.core.id.AtomID_Map_double_t) -> int swap(...) from builtins.PyCapsule swap(self : rosetta.core.id.AtomID_Map_double_t, s : rosetta.core.id.AtomID_Map_double_t) -> NoneType update_sequence_numbering(...) from builtins.PyCapsule update_sequence_numbering(self : rosetta.core.id.AtomID_Map_double_t, new_size : int, old2new : rosetta.utility.vector1_unsigned_long) -> NoneType   class AtomID_Map_bool(AtomID_Map_bool_t)       Method resolution order: AtomID_Map_bool AtomID_Map_bool_t builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(rosetta.core.id.AtomID_Map_bool) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. Methods inherited from AtomID_Map_bool_t: __call__(...) from builtins.PyCapsule __call__(*args, **kwargs) Overloaded function.   1. __call__(self : rosetta.core.id.AtomID_Map_bool_t, id : core::id::AtomID) -> bool   2. __call__(self : rosetta.core.id.AtomID_Map_bool_t, id : core::id::AtomID) -> rosetta.std._Bit_reference   3. __call__(self : rosetta.core.id.AtomID_Map_bool_t, i_res : int, i_atom : int) -> bool   4. __call__(self : rosetta.core.id.AtomID_Map_bool_t, i_res : int, i_atom : int) -> rosetta.std._Bit_reference   5. __call__(self : rosetta.core.id.AtomID_Map_bool_t, i_res : int) -> rosetta.utility.vector1_bool   6. __call__(self : rosetta.core.id.AtomID_Map_bool_t, i_res : int) -> rosetta.utility.vector1_bool __getitem__(...) from builtins.PyCapsule __getitem__(*args, **kwargs) Overloaded function.   1. __getitem__(self : rosetta.core.id.AtomID_Map_bool_t, id : core::id::AtomID) -> bool   2. __getitem__(self : rosetta.core.id.AtomID_Map_bool_t, id : core::id::AtomID) -> rosetta.std._Bit_reference   3. __getitem__(self : rosetta.core.id.AtomID_Map_bool_t, i_res : int) -> rosetta.utility.vector1_bool   4. __getitem__(self : rosetta.core.id.AtomID_Map_bool_t, i_res : int) -> rosetta.utility.vector1_bool all_default(...) from builtins.PyCapsule all_default(rosetta.core.id.AtomID_Map_bool_t) -> bool assign(...) from builtins.PyCapsule assign(self : rosetta.core.id.AtomID_Map_bool_t,  : rosetta.core.id.AtomID_Map_bool_t) -> rosetta.core.id.AtomID_Map_bool_t clear(...) from builtins.PyCapsule clear(*args, **kwargs) Overloaded function.   1. clear(rosetta.core.id.AtomID_Map_bool_t) -> NoneType   2. clear(self : rosetta.core.id.AtomID_Map_bool_t, default_value_a : bool) -> NoneType default_value(...) from builtins.PyCapsule default_value(*args, **kwargs) Overloaded function.   1. default_value(rosetta.core.id.AtomID_Map_bool_t) -> bool   2. default_value(self : rosetta.core.id.AtomID_Map_bool_t, default_value_a : bool) -> NoneType empty(...) from builtins.PyCapsule empty(rosetta.core.id.AtomID_Map_bool_t) -> bool fill(...) from builtins.PyCapsule fill(rosetta.core.id.AtomID_Map_bool_t) -> NoneType fill_with(...) from builtins.PyCapsule fill_with(*args, **kwargs) Overloaded function.   1. fill_with(self : rosetta.core.id.AtomID_Map_bool_t, value : bool) -> NoneType   2. fill_with(self : rosetta.core.id.AtomID_Map_bool_t, seqpos : int, value : bool) -> NoneType finalize(...) from builtins.PyCapsule finalize(rosetta.core.id.AtomID_Map_bool_t) -> NoneType get(...) from builtins.PyCapsule get(self : rosetta.core.id.AtomID_Map_bool_t, id : core::id::AtomID) -> bool has(...) from builtins.PyCapsule has(self : rosetta.core.id.AtomID_Map_bool_t, id : core::id::AtomID) -> bool n_atom(...) from builtins.PyCapsule n_atom(self : rosetta.core.id.AtomID_Map_bool_t, i_res : int) -> int n_residue(...) from builtins.PyCapsule n_residue(rosetta.core.id.AtomID_Map_bool_t) -> int resize(...) from builtins.PyCapsule resize(*args, **kwargs) Overloaded function.   1. resize(self : rosetta.core.id.AtomID_Map_bool_t, n_res : int) -> NoneType   2. resize(self : rosetta.core.id.AtomID_Map_bool_t, i_res : int, n_atom : int) -> NoneType   3. resize(self : rosetta.core.id.AtomID_Map_bool_t, i_res : int, n_atom : int, value : bool) -> NoneType set(...) from builtins.PyCapsule set(self : rosetta.core.id.AtomID_Map_bool_t, id : core::id::AtomID, value : bool) -> NoneType shrink(...) from builtins.PyCapsule shrink(rosetta.core.id.AtomID_Map_bool_t) -> NoneType size(...) from builtins.PyCapsule size(rosetta.core.id.AtomID_Map_bool_t) -> int swap(...) from builtins.PyCapsule swap(self : rosetta.core.id.AtomID_Map_bool_t, s : rosetta.core.id.AtomID_Map_bool_t) -> NoneType update_sequence_numbering(...) from builtins.PyCapsule update_sequence_numbering(self : rosetta.core.id.AtomID_Map_bool_t, new_size : int, old2new : rosetta.utility.vector1_unsigned_long) -> NoneType   class AtomID_Map_bool_t(builtins.object)       Methods defined here: __call__(...) from builtins.PyCapsule __call__(*args, **kwargs) Overloaded function.   1. __call__(self : rosetta.core.id.AtomID_Map_bool_t, id : core::id::AtomID) -> bool   2. __call__(self : rosetta.core.id.AtomID_Map_bool_t, id : core::id::AtomID) -> rosetta.std._Bit_reference   3. __call__(self : rosetta.core.id.AtomID_Map_bool_t, i_res : int, i_atom : int) -> bool   4. __call__(self : rosetta.core.id.AtomID_Map_bool_t, i_res : int, i_atom : int) -> rosetta.std._Bit_reference   5. __call__(self : rosetta.core.id.AtomID_Map_bool_t, i_res : int) -> rosetta.utility.vector1_bool   6. __call__(self : rosetta.core.id.AtomID_Map_bool_t, i_res : int) -> rosetta.utility.vector1_bool __getitem__(...) from builtins.PyCapsule __getitem__(*args, **kwargs) Overloaded function.   1. __getitem__(self : rosetta.core.id.AtomID_Map_bool_t, id : core::id::AtomID) -> bool   2. __getitem__(self : rosetta.core.id.AtomID_Map_bool_t, id : core::id::AtomID) -> rosetta.std._Bit_reference   3. __getitem__(self : rosetta.core.id.AtomID_Map_bool_t, i_res : int) -> rosetta.utility.vector1_bool   4. __getitem__(self : rosetta.core.id.AtomID_Map_bool_t, i_res : int) -> rosetta.utility.vector1_bool __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.core.id.AtomID_Map_bool_t) -> NoneType   2. __init__(self : rosetta.core.id.AtomID_Map_bool_t, default_value_a : bool) -> NoneType   3. __init__(self : rosetta.core.id.AtomID_Map_bool_t, n_res : int) -> NoneType   4. __init__(self : rosetta.core.id.AtomID_Map_bool_t, n_res : int, default_value_a : bool) -> NoneType   5. __init__(self : rosetta.core.id.AtomID_Map_bool_t,  : rosetta.core.id.AtomID_Map_bool_t) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. all_default(...) from builtins.PyCapsule all_default(rosetta.core.id.AtomID_Map_bool_t) -> bool assign(...) from builtins.PyCapsule assign(self : rosetta.core.id.AtomID_Map_bool_t,  : rosetta.core.id.AtomID_Map_bool_t) -> rosetta.core.id.AtomID_Map_bool_t clear(...) from builtins.PyCapsule clear(*args, **kwargs) Overloaded function.   1. clear(rosetta.core.id.AtomID_Map_bool_t) -> NoneType   2. clear(self : rosetta.core.id.AtomID_Map_bool_t, default_value_a : bool) -> NoneType default_value(...) from builtins.PyCapsule default_value(*args, **kwargs) Overloaded function.   1. default_value(rosetta.core.id.AtomID_Map_bool_t) -> bool   2. default_value(self : rosetta.core.id.AtomID_Map_bool_t, default_value_a : bool) -> NoneType empty(...) from builtins.PyCapsule empty(rosetta.core.id.AtomID_Map_bool_t) -> bool fill(...) from builtins.PyCapsule fill(rosetta.core.id.AtomID_Map_bool_t) -> NoneType fill_with(...) from builtins.PyCapsule fill_with(*args, **kwargs) Overloaded function.   1. fill_with(self : rosetta.core.id.AtomID_Map_bool_t, value : bool) -> NoneType   2. fill_with(self : rosetta.core.id.AtomID_Map_bool_t, seqpos : int, value : bool) -> NoneType finalize(...) from builtins.PyCapsule finalize(rosetta.core.id.AtomID_Map_bool_t) -> NoneType get(...) from builtins.PyCapsule get(self : rosetta.core.id.AtomID_Map_bool_t, id : core::id::AtomID) -> bool has(...) from builtins.PyCapsule has(self : rosetta.core.id.AtomID_Map_bool_t, id : core::id::AtomID) -> bool n_atom(...) from builtins.PyCapsule n_atom(self : rosetta.core.id.AtomID_Map_bool_t, i_res : int) -> int n_residue(...) from builtins.PyCapsule n_residue(rosetta.core.id.AtomID_Map_bool_t) -> int resize(...) from builtins.PyCapsule resize(*args, **kwargs) Overloaded function.   1. resize(self : rosetta.core.id.AtomID_Map_bool_t, n_res : int) -> NoneType   2. resize(self : rosetta.core.id.AtomID_Map_bool_t, i_res : int, n_atom : int) -> NoneType   3. resize(self : rosetta.core.id.AtomID_Map_bool_t, i_res : int, n_atom : int, value : bool) -> NoneType set(...) from builtins.PyCapsule set(self : rosetta.core.id.AtomID_Map_bool_t, id : core::id::AtomID, value : bool) -> NoneType shrink(...) from builtins.PyCapsule shrink(rosetta.core.id.AtomID_Map_bool_t) -> NoneType size(...) from builtins.PyCapsule size(rosetta.core.id.AtomID_Map_bool_t) -> int swap(...) from builtins.PyCapsule swap(self : rosetta.core.id.AtomID_Map_bool_t, s : rosetta.core.id.AtomID_Map_bool_t) -> NoneType update_sequence_numbering(...) from builtins.PyCapsule update_sequence_numbering(self : rosetta.core.id.AtomID_Map_bool_t, new_size : int, old2new : rosetta.utility.vector1_unsigned_long) -> NoneType   class AtomID_Map_core_id_AtomID_t(builtins.object)       Methods defined here: __call__(...) from builtins.PyCapsule __call__(*args, **kwargs) Overloaded function.   1. __call__(self : rosetta.core.id.AtomID_Map_core_id_AtomID_t, id : core::id::AtomID) -> core::id::AtomID   2. __call__(self : rosetta.core.id.AtomID_Map_core_id_AtomID_t, id : core::id::AtomID) -> core::id::AtomID   3. __call__(self : rosetta.core.id.AtomID_Map_core_id_AtomID_t, i_res : int, i_atom : int) -> core::id::AtomID   4. __call__(self : rosetta.core.id.AtomID_Map_core_id_AtomID_t, i_res : int, i_atom : int) -> core::id::AtomID   5. __call__(self : rosetta.core.id.AtomID_Map_core_id_AtomID_t, i_res : int) -> rosetta.utility.vector1_core_id_AtomID   6. __call__(self : rosetta.core.id.AtomID_Map_core_id_AtomID_t, i_res : int) -> rosetta.utility.vector1_core_id_AtomID __getitem__(...) from builtins.PyCapsule __getitem__(*args, **kwargs) Overloaded function.   1. __getitem__(self : rosetta.core.id.AtomID_Map_core_id_AtomID_t, id : core::id::AtomID) -> core::id::AtomID   2. __getitem__(self : rosetta.core.id.AtomID_Map_core_id_AtomID_t, id : core::id::AtomID) -> core::id::AtomID   3. __getitem__(self : rosetta.core.id.AtomID_Map_core_id_AtomID_t, i_res : int) -> rosetta.utility.vector1_core_id_AtomID   4. __getitem__(self : rosetta.core.id.AtomID_Map_core_id_AtomID_t, i_res : int) -> rosetta.utility.vector1_core_id_AtomID __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.core.id.AtomID_Map_core_id_AtomID_t) -> NoneType   2. __init__(self : rosetta.core.id.AtomID_Map_core_id_AtomID_t, default_value_a : core::id::AtomID) -> NoneType   3. __init__(self : rosetta.core.id.AtomID_Map_core_id_AtomID_t, n_res : int) -> NoneType   4. __init__(self : rosetta.core.id.AtomID_Map_core_id_AtomID_t, n_res : int, default_value_a : core::id::AtomID) -> NoneType   5. __init__(self : rosetta.core.id.AtomID_Map_core_id_AtomID_t,  : rosetta.core.id.AtomID_Map_core_id_AtomID_t) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. all_default(...) from builtins.PyCapsule all_default(rosetta.core.id.AtomID_Map_core_id_AtomID_t) -> bool assign(...) from builtins.PyCapsule assign(self : rosetta.core.id.AtomID_Map_core_id_AtomID_t,  : rosetta.core.id.AtomID_Map_core_id_AtomID_t) -> rosetta.core.id.AtomID_Map_core_id_AtomID_t clear(...) from builtins.PyCapsule clear(*args, **kwargs) Overloaded function.   1. clear(rosetta.core.id.AtomID_Map_core_id_AtomID_t) -> NoneType   2. clear(self : rosetta.core.id.AtomID_Map_core_id_AtomID_t, default_value_a : core::id::AtomID) -> NoneType default_value(...) from builtins.PyCapsule default_value(*args, **kwargs) Overloaded function.   1. default_value(rosetta.core.id.AtomID_Map_core_id_AtomID_t) -> core::id::AtomID   2. default_value(self : rosetta.core.id.AtomID_Map_core_id_AtomID_t, default_value_a : core::id::AtomID) -> NoneType empty(...) from builtins.PyCapsule empty(rosetta.core.id.AtomID_Map_core_id_AtomID_t) -> bool fill(...) from builtins.PyCapsule fill(rosetta.core.id.AtomID_Map_core_id_AtomID_t) -> NoneType fill_with(...) from builtins.PyCapsule fill_with(*args, **kwargs) Overloaded function.   1. fill_with(self : rosetta.core.id.AtomID_Map_core_id_AtomID_t, value : core::id::AtomID) -> NoneType   2. fill_with(self : rosetta.core.id.AtomID_Map_core_id_AtomID_t, seqpos : int, value : core::id::AtomID) -> NoneType finalize(...) from builtins.PyCapsule finalize(rosetta.core.id.AtomID_Map_core_id_AtomID_t) -> NoneType get(...) from builtins.PyCapsule get(self : rosetta.core.id.AtomID_Map_core_id_AtomID_t, id : core::id::AtomID) -> core::id::AtomID has(...) from builtins.PyCapsule has(self : rosetta.core.id.AtomID_Map_core_id_AtomID_t, id : core::id::AtomID) -> bool n_atom(...) from builtins.PyCapsule n_atom(self : rosetta.core.id.AtomID_Map_core_id_AtomID_t, i_res : int) -> int n_residue(...) from builtins.PyCapsule n_residue(rosetta.core.id.AtomID_Map_core_id_AtomID_t) -> int resize(...) from builtins.PyCapsule resize(*args, **kwargs) Overloaded function.   1. resize(self : rosetta.core.id.AtomID_Map_core_id_AtomID_t, n_res : int) -> NoneType   2. resize(self : rosetta.core.id.AtomID_Map_core_id_AtomID_t, i_res : int, n_atom : int) -> NoneType   3. resize(self : rosetta.core.id.AtomID_Map_core_id_AtomID_t, i_res : int, n_atom : int, value : core::id::AtomID) -> NoneType set(...) from builtins.PyCapsule set(self : rosetta.core.id.AtomID_Map_core_id_AtomID_t, id : core::id::AtomID, value : core::id::AtomID) -> NoneType shrink(...) from builtins.PyCapsule shrink(rosetta.core.id.AtomID_Map_core_id_AtomID_t) -> NoneType size(...) from builtins.PyCapsule size(rosetta.core.id.AtomID_Map_core_id_AtomID_t) -> int swap(...) from builtins.PyCapsule swap(self : rosetta.core.id.AtomID_Map_core_id_AtomID_t, s : rosetta.core.id.AtomID_Map_core_id_AtomID_t) -> NoneType update_sequence_numbering(...) from builtins.PyCapsule update_sequence_numbering(self : rosetta.core.id.AtomID_Map_core_id_AtomID_t, new_size : int, old2new : rosetta.utility.vector1_unsigned_long) -> NoneType   class AtomID_Map_core_id_TorsionID_t(builtins.object)       Methods defined here: __call__(...) from builtins.PyCapsule __call__(*args, **kwargs) Overloaded function.   1. __call__(self : rosetta.core.id.AtomID_Map_core_id_TorsionID_t, id : core::id::AtomID) -> core::id::TorsionID   2. __call__(self : rosetta.core.id.AtomID_Map_core_id_TorsionID_t, id : core::id::AtomID) -> core::id::TorsionID   3. __call__(self : rosetta.core.id.AtomID_Map_core_id_TorsionID_t, i_res : int, i_atom : int) -> core::id::TorsionID   4. __call__(self : rosetta.core.id.AtomID_Map_core_id_TorsionID_t, i_res : int, i_atom : int) -> core::id::TorsionID   5. __call__(self : rosetta.core.id.AtomID_Map_core_id_TorsionID_t, i_res : int) -> rosetta.utility.vector1_core_id_TorsionID   6. __call__(self : rosetta.core.id.AtomID_Map_core_id_TorsionID_t, i_res : int) -> rosetta.utility.vector1_core_id_TorsionID __getitem__(...) from builtins.PyCapsule __getitem__(*args, **kwargs) Overloaded function.   1. __getitem__(self : rosetta.core.id.AtomID_Map_core_id_TorsionID_t, id : core::id::AtomID) -> core::id::TorsionID   2. __getitem__(self : rosetta.core.id.AtomID_Map_core_id_TorsionID_t, id : core::id::AtomID) -> core::id::TorsionID   3. __getitem__(self : rosetta.core.id.AtomID_Map_core_id_TorsionID_t, i_res : int) -> rosetta.utility.vector1_core_id_TorsionID   4. __getitem__(self : rosetta.core.id.AtomID_Map_core_id_TorsionID_t, i_res : int) -> rosetta.utility.vector1_core_id_TorsionID __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.core.id.AtomID_Map_core_id_TorsionID_t) -> NoneType   2. __init__(self : rosetta.core.id.AtomID_Map_core_id_TorsionID_t, default_value_a : core::id::TorsionID) -> NoneType   3. __init__(self : rosetta.core.id.AtomID_Map_core_id_TorsionID_t, n_res : int) -> NoneType   4. __init__(self : rosetta.core.id.AtomID_Map_core_id_TorsionID_t, n_res : int, default_value_a : core::id::TorsionID) -> NoneType   5. __init__(self : rosetta.core.id.AtomID_Map_core_id_TorsionID_t,  : rosetta.core.id.AtomID_Map_core_id_TorsionID_t) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. all_default(...) from builtins.PyCapsule all_default(rosetta.core.id.AtomID_Map_core_id_TorsionID_t) -> bool assign(...) from builtins.PyCapsule assign(self : rosetta.core.id.AtomID_Map_core_id_TorsionID_t,  : rosetta.core.id.AtomID_Map_core_id_TorsionID_t) -> rosetta.core.id.AtomID_Map_core_id_TorsionID_t clear(...) from builtins.PyCapsule clear(*args, **kwargs) Overloaded function.   1. clear(rosetta.core.id.AtomID_Map_core_id_TorsionID_t) -> NoneType   2. clear(self : rosetta.core.id.AtomID_Map_core_id_TorsionID_t, default_value_a : core::id::TorsionID) -> NoneType default_value(...) from builtins.PyCapsule default_value(*args, **kwargs) Overloaded function.   1. default_value(rosetta.core.id.AtomID_Map_core_id_TorsionID_t) -> core::id::TorsionID   2. default_value(self : rosetta.core.id.AtomID_Map_core_id_TorsionID_t, default_value_a : core::id::TorsionID) -> NoneType empty(...) from builtins.PyCapsule empty(rosetta.core.id.AtomID_Map_core_id_TorsionID_t) -> bool fill(...) from builtins.PyCapsule fill(rosetta.core.id.AtomID_Map_core_id_TorsionID_t) -> NoneType fill_with(...) from builtins.PyCapsule fill_with(*args, **kwargs) Overloaded function.   1. fill_with(self : rosetta.core.id.AtomID_Map_core_id_TorsionID_t, value : core::id::TorsionID) -> NoneType   2. fill_with(self : rosetta.core.id.AtomID_Map_core_id_TorsionID_t, seqpos : int, value : core::id::TorsionID) -> NoneType finalize(...) from builtins.PyCapsule finalize(rosetta.core.id.AtomID_Map_core_id_TorsionID_t) -> NoneType get(...) from builtins.PyCapsule get(self : rosetta.core.id.AtomID_Map_core_id_TorsionID_t, id : core::id::AtomID) -> core::id::TorsionID has(...) from builtins.PyCapsule has(self : rosetta.core.id.AtomID_Map_core_id_TorsionID_t, id : core::id::AtomID) -> bool n_atom(...) from builtins.PyCapsule n_atom(self : rosetta.core.id.AtomID_Map_core_id_TorsionID_t, i_res : int) -> int n_residue(...) from builtins.PyCapsule n_residue(rosetta.core.id.AtomID_Map_core_id_TorsionID_t) -> int resize(...) from builtins.PyCapsule resize(*args, **kwargs) Overloaded function.   1. resize(self : rosetta.core.id.AtomID_Map_core_id_TorsionID_t, n_res : int) -> NoneType   2. resize(self : rosetta.core.id.AtomID_Map_core_id_TorsionID_t, i_res : int, n_atom : int) -> NoneType   3. resize(self : rosetta.core.id.AtomID_Map_core_id_TorsionID_t, i_res : int, n_atom : int, value : core::id::TorsionID) -> NoneType set(...) from builtins.PyCapsule set(self : rosetta.core.id.AtomID_Map_core_id_TorsionID_t, id : core::id::AtomID, value : core::id::TorsionID) -> NoneType shrink(...) from builtins.PyCapsule shrink(rosetta.core.id.AtomID_Map_core_id_TorsionID_t) -> NoneType size(...) from builtins.PyCapsule size(rosetta.core.id.AtomID_Map_core_id_TorsionID_t) -> int swap(...) from builtins.PyCapsule swap(self : rosetta.core.id.AtomID_Map_core_id_TorsionID_t, s : rosetta.core.id.AtomID_Map_core_id_TorsionID_t) -> NoneType update_sequence_numbering(...) from builtins.PyCapsule update_sequence_numbering(self : rosetta.core.id.AtomID_Map_core_id_TorsionID_t, new_size : int, old2new : rosetta.utility.vector1_unsigned_long) -> NoneType   class AtomID_Map_double_t(builtins.object)       Methods defined here: __call__(...) from builtins.PyCapsule __call__(*args, **kwargs) Overloaded function.   1. __call__(self : rosetta.core.id.AtomID_Map_double_t, id : core::id::AtomID) -> float   2. __call__(self : rosetta.core.id.AtomID_Map_double_t, id : core::id::AtomID) -> float   3. __call__(self : rosetta.core.id.AtomID_Map_double_t, i_res : int, i_atom : int) -> float   4. __call__(self : rosetta.core.id.AtomID_Map_double_t, i_res : int, i_atom : int) -> float   5. __call__(self : rosetta.core.id.AtomID_Map_double_t, i_res : int) -> rosetta.utility.vector1_double   6. __call__(self : rosetta.core.id.AtomID_Map_double_t, i_res : int) -> rosetta.utility.vector1_double __getitem__(...) from builtins.PyCapsule __getitem__(*args, **kwargs) Overloaded function.   1. __getitem__(self : rosetta.core.id.AtomID_Map_double_t, id : core::id::AtomID) -> float   2. __getitem__(self : rosetta.core.id.AtomID_Map_double_t, id : core::id::AtomID) -> float   3. __getitem__(self : rosetta.core.id.AtomID_Map_double_t, i_res : int) -> rosetta.utility.vector1_double   4. __getitem__(self : rosetta.core.id.AtomID_Map_double_t, i_res : int) -> rosetta.utility.vector1_double __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.core.id.AtomID_Map_double_t) -> NoneType   2. __init__(self : rosetta.core.id.AtomID_Map_double_t, default_value_a : float) -> NoneType   3. __init__(self : rosetta.core.id.AtomID_Map_double_t, n_res : int) -> NoneType   4. __init__(self : rosetta.core.id.AtomID_Map_double_t, n_res : int, default_value_a : float) -> NoneType   5. __init__(self : rosetta.core.id.AtomID_Map_double_t,  : rosetta.core.id.AtomID_Map_double_t) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. all_default(...) from builtins.PyCapsule all_default(rosetta.core.id.AtomID_Map_double_t) -> bool assign(...) from builtins.PyCapsule assign(self : rosetta.core.id.AtomID_Map_double_t,  : rosetta.core.id.AtomID_Map_double_t) -> rosetta.core.id.AtomID_Map_double_t clear(...) from builtins.PyCapsule clear(*args, **kwargs) Overloaded function.   1. clear(rosetta.core.id.AtomID_Map_double_t) -> NoneType   2. clear(self : rosetta.core.id.AtomID_Map_double_t, default_value_a : float) -> NoneType default_value(...) from builtins.PyCapsule default_value(*args, **kwargs) Overloaded function.   1. default_value(rosetta.core.id.AtomID_Map_double_t) -> float   2. default_value(self : rosetta.core.id.AtomID_Map_double_t, default_value_a : float) -> NoneType empty(...) from builtins.PyCapsule empty(rosetta.core.id.AtomID_Map_double_t) -> bool fill(...) from builtins.PyCapsule fill(rosetta.core.id.AtomID_Map_double_t) -> NoneType fill_with(...) from builtins.PyCapsule fill_with(*args, **kwargs) Overloaded function.   1. fill_with(self : rosetta.core.id.AtomID_Map_double_t, value : float) -> NoneType   2. fill_with(self : rosetta.core.id.AtomID_Map_double_t, seqpos : int, value : float) -> NoneType finalize(...) from builtins.PyCapsule finalize(rosetta.core.id.AtomID_Map_double_t) -> NoneType get(...) from builtins.PyCapsule get(self : rosetta.core.id.AtomID_Map_double_t, id : core::id::AtomID) -> float has(...) from builtins.PyCapsule has(self : rosetta.core.id.AtomID_Map_double_t, id : core::id::AtomID) -> bool n_atom(...) from builtins.PyCapsule n_atom(self : rosetta.core.id.AtomID_Map_double_t, i_res : int) -> int n_residue(...) from builtins.PyCapsule n_residue(rosetta.core.id.AtomID_Map_double_t) -> int resize(...) from builtins.PyCapsule resize(*args, **kwargs) Overloaded function.   1. resize(self : rosetta.core.id.AtomID_Map_double_t, n_res : int) -> NoneType   2. resize(self : rosetta.core.id.AtomID_Map_double_t, i_res : int, n_atom : int) -> NoneType   3. resize(self : rosetta.core.id.AtomID_Map_double_t, i_res : int, n_atom : int, value : float) -> NoneType set(...) from builtins.PyCapsule set(self : rosetta.core.id.AtomID_Map_double_t, id : core::id::AtomID, value : float) -> NoneType shrink(...) from builtins.PyCapsule shrink(rosetta.core.id.AtomID_Map_double_t) -> NoneType size(...) from builtins.PyCapsule size(rosetta.core.id.AtomID_Map_double_t) -> int swap(...) from builtins.PyCapsule swap(self : rosetta.core.id.AtomID_Map_double_t, s : rosetta.core.id.AtomID_Map_double_t) -> NoneType update_sequence_numbering(...) from builtins.PyCapsule update_sequence_numbering(self : rosetta.core.id.AtomID_Map_double_t, new_size : int, old2new : rosetta.utility.vector1_unsigned_long) -> NoneType   class AtomID_Map_numeric_xyzVector_double_t(builtins.object)       Methods defined here: __call__(...) from builtins.PyCapsule __call__(*args, **kwargs) Overloaded function.   1. __call__(self : rosetta.core.id.AtomID_Map_numeric_xyzVector_double_t, id : core::id::AtomID) -> rosetta.numeric.xyzVector_double_t   2. __call__(self : rosetta.core.id.AtomID_Map_numeric_xyzVector_double_t, id : core::id::AtomID) -> rosetta.numeric.xyzVector_double_t   3. __call__(self : rosetta.core.id.AtomID_Map_numeric_xyzVector_double_t, i_res : int, i_atom : int) -> rosetta.numeric.xyzVector_double_t   4. __call__(self : rosetta.core.id.AtomID_Map_numeric_xyzVector_double_t, i_res : int, i_atom : int) -> rosetta.numeric.xyzVector_double_t   5. __call__(self : rosetta.core.id.AtomID_Map_numeric_xyzVector_double_t, i_res : int) -> rosetta.utility.vector1_numeric_xyzVector_double_t   6. __call__(self : rosetta.core.id.AtomID_Map_numeric_xyzVector_double_t, i_res : int) -> rosetta.utility.vector1_numeric_xyzVector_double_t __getitem__(...) from builtins.PyCapsule __getitem__(*args, **kwargs) Overloaded function.   1. __getitem__(self : rosetta.core.id.AtomID_Map_numeric_xyzVector_double_t, id : core::id::AtomID) -> rosetta.numeric.xyzVector_double_t   2. __getitem__(self : rosetta.core.id.AtomID_Map_numeric_xyzVector_double_t, id : core::id::AtomID) -> rosetta.numeric.xyzVector_double_t   3. __getitem__(self : rosetta.core.id.AtomID_Map_numeric_xyzVector_double_t, i_res : int) -> rosetta.utility.vector1_numeric_xyzVector_double_t   4. __getitem__(self : rosetta.core.id.AtomID_Map_numeric_xyzVector_double_t, i_res : int) -> rosetta.utility.vector1_numeric_xyzVector_double_t __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.core.id.AtomID_Map_numeric_xyzVector_double_t) -> NoneType   2. __init__(self : rosetta.core.id.AtomID_Map_numeric_xyzVector_double_t, default_value_a : rosetta.numeric.xyzVector_double_t) -> NoneType   3. __init__(self : rosetta.core.id.AtomID_Map_numeric_xyzVector_double_t, n_res : int) -> NoneType   4. __init__(self : rosetta.core.id.AtomID_Map_numeric_xyzVector_double_t, n_res : int, default_value_a : rosetta.numeric.xyzVector_double_t) -> NoneType   5. __init__(self : rosetta.core.id.AtomID_Map_numeric_xyzVector_double_t,  : rosetta.core.id.AtomID_Map_numeric_xyzVector_double_t) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. all_default(...) from builtins.PyCapsule all_default(rosetta.core.id.AtomID_Map_numeric_xyzVector_double_t) -> bool assign(...) from builtins.PyCapsule assign(self : rosetta.core.id.AtomID_Map_numeric_xyzVector_double_t,  : rosetta.core.id.AtomID_Map_numeric_xyzVector_double_t) -> rosetta.core.id.AtomID_Map_numeric_xyzVector_double_t clear(...) from builtins.PyCapsule clear(*args, **kwargs) Overloaded function.   1. clear(rosetta.core.id.AtomID_Map_numeric_xyzVector_double_t) -> NoneType   2. clear(self : rosetta.core.id.AtomID_Map_numeric_xyzVector_double_t, default_value_a : rosetta.numeric.xyzVector_double_t) -> NoneType default_value(...) from builtins.PyCapsule default_value(*args, **kwargs) Overloaded function.   1. default_value(rosetta.core.id.AtomID_Map_numeric_xyzVector_double_t) -> rosetta.numeric.xyzVector_double_t   2. default_value(self : rosetta.core.id.AtomID_Map_numeric_xyzVector_double_t, default_value_a : rosetta.numeric.xyzVector_double_t) -> NoneType empty(...) from builtins.PyCapsule empty(rosetta.core.id.AtomID_Map_numeric_xyzVector_double_t) -> bool fill(...) from builtins.PyCapsule fill(rosetta.core.id.AtomID_Map_numeric_xyzVector_double_t) -> NoneType fill_with(...) from builtins.PyCapsule fill_with(*args, **kwargs) Overloaded function.   1. fill_with(self : rosetta.core.id.AtomID_Map_numeric_xyzVector_double_t, value : rosetta.numeric.xyzVector_double_t) -> NoneType   2. fill_with(self : rosetta.core.id.AtomID_Map_numeric_xyzVector_double_t, seqpos : int, value : rosetta.numeric.xyzVector_double_t) -> NoneType finalize(...) from builtins.PyCapsule finalize(rosetta.core.id.AtomID_Map_numeric_xyzVector_double_t) -> NoneType get(...) from builtins.PyCapsule get(self : rosetta.core.id.AtomID_Map_numeric_xyzVector_double_t, id : core::id::AtomID) -> rosetta.numeric.xyzVector_double_t has(...) from builtins.PyCapsule has(self : rosetta.core.id.AtomID_Map_numeric_xyzVector_double_t, id : core::id::AtomID) -> bool n_atom(...) from builtins.PyCapsule n_atom(self : rosetta.core.id.AtomID_Map_numeric_xyzVector_double_t, i_res : int) -> int n_residue(...) from builtins.PyCapsule n_residue(rosetta.core.id.AtomID_Map_numeric_xyzVector_double_t) -> int resize(...) from builtins.PyCapsule resize(*args, **kwargs) Overloaded function.   1. resize(self : rosetta.core.id.AtomID_Map_numeric_xyzVector_double_t, n_res : int) -> NoneType   2. resize(self : rosetta.core.id.AtomID_Map_numeric_xyzVector_double_t, i_res : int, n_atom : int) -> NoneType   3. resize(self : rosetta.core.id.AtomID_Map_numeric_xyzVector_double_t, i_res : int, n_atom : int, value : rosetta.numeric.xyzVector_double_t) -> NoneType set(...) from builtins.PyCapsule set(self : rosetta.core.id.AtomID_Map_numeric_xyzVector_double_t, id : core::id::AtomID, value : rosetta.numeric.xyzVector_double_t) -> NoneType shrink(...) from builtins.PyCapsule shrink(rosetta.core.id.AtomID_Map_numeric_xyzVector_double_t) -> NoneType size(...) from builtins.PyCapsule size(rosetta.core.id.AtomID_Map_numeric_xyzVector_double_t) -> int swap(...) from builtins.PyCapsule swap(self : rosetta.core.id.AtomID_Map_numeric_xyzVector_double_t, s : rosetta.core.id.AtomID_Map_numeric_xyzVector_double_t) -> NoneType update_sequence_numbering(...) from builtins.PyCapsule update_sequence_numbering(self : rosetta.core.id.AtomID_Map_numeric_xyzVector_double_t, new_size : int, old2new : rosetta.utility.vector1_unsigned_long) -> NoneType   class AtomID_Map_std_shared_ptr_core_kinematics_tree_Atom_t(builtins.object)       Methods defined here: __call__(...) from builtins.PyCapsule __call__(*args, **kwargs) Overloaded function.   1. __call__(self : rosetta.core.id.AtomID_Map_std_shared_ptr_core_kinematics_tree_Atom_t, id : core::id::AtomID) -> core::kinematics::tree::Atom   2. __call__(self : rosetta.core.id.AtomID_Map_std_shared_ptr_core_kinematics_tree_Atom_t, id : core::id::AtomID) -> core::kinematics::tree::Atom   3. __call__(self : rosetta.core.id.AtomID_Map_std_shared_ptr_core_kinematics_tree_Atom_t, i_res : int, i_atom : int) -> core::kinematics::tree::Atom   4. __call__(self : rosetta.core.id.AtomID_Map_std_shared_ptr_core_kinematics_tree_Atom_t, i_res : int, i_atom : int) -> core::kinematics::tree::Atom   5. __call__(self : rosetta.core.id.AtomID_Map_std_shared_ptr_core_kinematics_tree_Atom_t, i_res : int) -> rosetta.utility.vector1_std_shared_ptr_core_kinematics_tree_Atom_t   6. __call__(self : rosetta.core.id.AtomID_Map_std_shared_ptr_core_kinematics_tree_Atom_t, i_res : int) -> rosetta.utility.vector1_std_shared_ptr_core_kinematics_tree_Atom_t __getitem__(...) from builtins.PyCapsule __getitem__(*args, **kwargs) Overloaded function.   1. __getitem__(self : rosetta.core.id.AtomID_Map_std_shared_ptr_core_kinematics_tree_Atom_t, id : core::id::AtomID) -> core::kinematics::tree::Atom   2. __getitem__(self : rosetta.core.id.AtomID_Map_std_shared_ptr_core_kinematics_tree_Atom_t, id : core::id::AtomID) -> core::kinematics::tree::Atom   3. __getitem__(self : rosetta.core.id.AtomID_Map_std_shared_ptr_core_kinematics_tree_Atom_t, i_res : int) -> rosetta.utility.vector1_std_shared_ptr_core_kinematics_tree_Atom_t   4. __getitem__(self : rosetta.core.id.AtomID_Map_std_shared_ptr_core_kinematics_tree_Atom_t, i_res : int) -> rosetta.utility.vector1_std_shared_ptr_core_kinematics_tree_Atom_t __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.core.id.AtomID_Map_std_shared_ptr_core_kinematics_tree_Atom_t) -> NoneType   2. __init__(self : rosetta.core.id.AtomID_Map_std_shared_ptr_core_kinematics_tree_Atom_t, default_value_a : core::kinematics::tree::Atom) -> NoneType   3. __init__(self : rosetta.core.id.AtomID_Map_std_shared_ptr_core_kinematics_tree_Atom_t, n_res : int) -> NoneType   4. __init__(self : rosetta.core.id.AtomID_Map_std_shared_ptr_core_kinematics_tree_Atom_t, n_res : int, default_value_a : core::kinematics::tree::Atom) -> NoneType   5. __init__(self : rosetta.core.id.AtomID_Map_std_shared_ptr_core_kinematics_tree_Atom_t,  : rosetta.core.id.AtomID_Map_std_shared_ptr_core_kinematics_tree_Atom_t) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. all_default(...) from builtins.PyCapsule all_default(rosetta.core.id.AtomID_Map_std_shared_ptr_core_kinematics_tree_Atom_t) -> bool assign(...) from builtins.PyCapsule assign(self : rosetta.core.id.AtomID_Map_std_shared_ptr_core_kinematics_tree_Atom_t,  : rosetta.core.id.AtomID_Map_std_shared_ptr_core_kinematics_tree_Atom_t) -> rosetta.core.id.AtomID_Map_std_shared_ptr_core_kinematics_tree_Atom_t clear(...) from builtins.PyCapsule clear(*args, **kwargs) Overloaded function.   1. clear(rosetta.core.id.AtomID_Map_std_shared_ptr_core_kinematics_tree_Atom_t) -> NoneType   2. clear(self : rosetta.core.id.AtomID_Map_std_shared_ptr_core_kinematics_tree_Atom_t, default_value_a : core::kinematics::tree::Atom) -> NoneType default_value(...) from builtins.PyCapsule default_value(*args, **kwargs) Overloaded function.   1. default_value(rosetta.core.id.AtomID_Map_std_shared_ptr_core_kinematics_tree_Atom_t) -> core::kinematics::tree::Atom   2. default_value(self : rosetta.core.id.AtomID_Map_std_shared_ptr_core_kinematics_tree_Atom_t, default_value_a : core::kinematics::tree::Atom) -> NoneType empty(...) from builtins.PyCapsule empty(rosetta.core.id.AtomID_Map_std_shared_ptr_core_kinematics_tree_Atom_t) -> bool fill(...) from builtins.PyCapsule fill(rosetta.core.id.AtomID_Map_std_shared_ptr_core_kinematics_tree_Atom_t) -> NoneType fill_with(...) from builtins.PyCapsule fill_with(*args, **kwargs) Overloaded function.   1. fill_with(self : rosetta.core.id.AtomID_Map_std_shared_ptr_core_kinematics_tree_Atom_t, value : core::kinematics::tree::Atom) -> NoneType   2. fill_with(self : rosetta.core.id.AtomID_Map_std_shared_ptr_core_kinematics_tree_Atom_t, seqpos : int, value : core::kinematics::tree::Atom) -> NoneType finalize(...) from builtins.PyCapsule finalize(rosetta.core.id.AtomID_Map_std_shared_ptr_core_kinematics_tree_Atom_t) -> NoneType get(...) from builtins.PyCapsule get(self : rosetta.core.id.AtomID_Map_std_shared_ptr_core_kinematics_tree_Atom_t, id : core::id::AtomID) -> core::kinematics::tree::Atom has(...) from builtins.PyCapsule has(self : rosetta.core.id.AtomID_Map_std_shared_ptr_core_kinematics_tree_Atom_t, id : core::id::AtomID) -> bool n_atom(...) from builtins.PyCapsule n_atom(self : rosetta.core.id.AtomID_Map_std_shared_ptr_core_kinematics_tree_Atom_t, i_res : int) -> int n_residue(...) from builtins.PyCapsule n_residue(rosetta.core.id.AtomID_Map_std_shared_ptr_core_kinematics_tree_Atom_t) -> int resize(...) from builtins.PyCapsule resize(*args, **kwargs) Overloaded function.   1. resize(self : rosetta.core.id.AtomID_Map_std_shared_ptr_core_kinematics_tree_Atom_t, n_res : int) -> NoneType   2. resize(self : rosetta.core.id.AtomID_Map_std_shared_ptr_core_kinematics_tree_Atom_t, i_res : int, n_atom : int) -> NoneType   3. resize(self : rosetta.core.id.AtomID_Map_std_shared_ptr_core_kinematics_tree_Atom_t, i_res : int, n_atom : int, value : core::kinematics::tree::Atom) -> NoneType set(...) from builtins.PyCapsule set(self : rosetta.core.id.AtomID_Map_std_shared_ptr_core_kinematics_tree_Atom_t, id : core::id::AtomID, value : core::kinematics::tree::Atom) -> NoneType shrink(...) from builtins.PyCapsule shrink(rosetta.core.id.AtomID_Map_std_shared_ptr_core_kinematics_tree_Atom_t) -> NoneType size(...) from builtins.PyCapsule size(rosetta.core.id.AtomID_Map_std_shared_ptr_core_kinematics_tree_Atom_t) -> int swap(...) from builtins.PyCapsule swap(self : rosetta.core.id.AtomID_Map_std_shared_ptr_core_kinematics_tree_Atom_t, s : rosetta.core.id.AtomID_Map_std_shared_ptr_core_kinematics_tree_Atom_t) -> NoneType update_sequence_numbering(...) from builtins.PyCapsule update_sequence_numbering(self : rosetta.core.id.AtomID_Map_std_shared_ptr_core_kinematics_tree_Atom_t, new_size : int, old2new : rosetta.utility.vector1_unsigned_long) -> NoneType   class BondID(builtins.object)     ////////////////////////////////////////////////////////////////////////////  two more classes, temporary for testing purposes ////////////////////////////////////////////////////////////////////////////     Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.core.id.BondID) -> NoneType   2. __init__(self : rosetta.core.id.BondID, a1 : rosetta.core.id.AtomID, a2 : rosetta.core.id.AtomID) -> NoneType   3. __init__(self : rosetta.core.id.BondID,  : rosetta.core.id.BondID) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. has(...) from builtins.PyCapsule has(self : rosetta.core.id.BondID, id : rosetta.core.id.AtomID) -> bool other_atom(...) from builtins.PyCapsule other_atom(self : rosetta.core.id.BondID, id : rosetta.core.id.AtomID) -> rosetta.core.id.AtomID reverse(...) from builtins.PyCapsule reverse(rosetta.core.id.BondID) -> NoneType reversed(...) from builtins.PyCapsule reversed(rosetta.core.id.BondID) -> rosetta.core.id.BondID Data descriptors defined here: atom1 atom2   class CacheableAtomID_MapVector(rosetta.basic.datacache.CacheableData)     AtomID_Map< xyzVector< Real > >     Method resolution order: CacheableAtomID_MapVector rosetta.basic.datacache.CacheableData builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle) -> NoneType   2. __init__(handle, rosetta.core.id.CacheableAtomID_MapVector) -> 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.core.id.CacheableAtomID_MapVector,  : rosetta.core.id.CacheableAtomID_MapVector) -> rosetta.core.id.CacheableAtomID_MapVector clone(...) from builtins.PyCapsule clone(rosetta.core.id.CacheableAtomID_MapVector) -> rosetta.basic.datacache.CacheableData map(...) from builtins.PyCapsule map(*args, **kwargs) Overloaded function.   1. map(rosetta.core.id.CacheableAtomID_MapVector) -> rosetta.core.id.AtomID_Map_numeric_xyzVector_double_t   2. map(rosetta.core.id.CacheableAtomID_MapVector) -> rosetta.core.id.AtomID_Map_numeric_xyzVector_double_t Methods inherited from rosetta.basic.datacache.CacheableData: get_self_ptr(...) from builtins.PyCapsule get_self_ptr(*args, **kwargs) Overloaded function.   1. get_self_ptr(rosetta.basic.datacache.CacheableData) -> rosetta.basic.datacache.CacheableData   self pointers   2. get_self_ptr(rosetta.basic.datacache.CacheableData) -> rosetta.basic.datacache.CacheableData get_self_weak_ptr(...) from builtins.PyCapsule get_self_weak_ptr(*args, **kwargs) Overloaded function.   1. get_self_weak_ptr(rosetta.basic.datacache.CacheableData) -> rosetta.std.weak_ptr_const_basic_datacache_CacheableData_t   2. get_self_weak_ptr(rosetta.basic.datacache.CacheableData) -> rosetta.std.weak_ptr_basic_datacache_CacheableData_t   class DOF_ID(builtins.object)     Kinematics DOF identifier class     Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.core.id.DOF_ID) -> NoneType   2. __init__(self : rosetta.core.id.DOF_ID, atom_id_in : rosetta.core.id.AtomID, type_in : rosetta.core.id.DOF_Type) -> NoneType   3. __init__(self : rosetta.core.id.DOF_ID,  : rosetta.core.id.DOF_ID) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. __str__(...) from builtins.PyCapsule __str__(rosetta.core.id.DOF_ID) -> str assign(...) from builtins.PyCapsule assign(self : rosetta.core.id.DOF_ID,  : rosetta.core.id.DOF_ID) -> rosetta.core.id.DOF_ID atom_id(...) from builtins.PyCapsule atom_id(rosetta.core.id.DOF_ID) -> rosetta.core.id.AtomID atomno(...) from builtins.PyCapsule atomno(rosetta.core.id.DOF_ID) -> int rsd(...) from builtins.PyCapsule rsd(rosetta.core.id.DOF_ID) -> int type(...) from builtins.PyCapsule type(rosetta.core.id.DOF_ID) -> rosetta.core.id.DOF_Type valid(...) from builtins.PyCapsule valid(rosetta.core.id.DOF_ID) -> bool   Is this DOF_ID valid?      Must return false for BOGUS_TORSION_ID.   class DOF_ID_Map_bool_t(builtins.object)       Methods defined here: __call__(...) from builtins.PyCapsule __call__(*args, **kwargs) Overloaded function.   1. __call__(self : rosetta.core.id.DOF_ID_Map_bool_t, id : rosetta.core.id.DOF_ID) -> bool   2. __call__(self : rosetta.core.id.DOF_ID_Map_bool_t, id : rosetta.core.id.DOF_ID) -> rosetta.std._Bit_reference   3. __call__(self : rosetta.core.id.DOF_ID_Map_bool_t, i_res : int, i_atom : int, dof : rosetta.core.id.DOF_Type) -> bool   4. __call__(self : rosetta.core.id.DOF_ID_Map_bool_t, i_res : int, i_atom : int, dof : rosetta.core.id.DOF_Type) -> rosetta.std._Bit_reference   5. __call__(self : rosetta.core.id.DOF_ID_Map_bool_t, dof : rosetta.core.id.DOF_Type) -> rosetta.core.id.AtomID_Map_bool_t   6. __call__(self : rosetta.core.id.DOF_ID_Map_bool_t, dof : rosetta.core.id.DOF_Type) -> rosetta.core.id.AtomID_Map_bool_t __getitem__(...) from builtins.PyCapsule __getitem__(*args, **kwargs) Overloaded function.   1. __getitem__(self : rosetta.core.id.DOF_ID_Map_bool_t, id : rosetta.core.id.DOF_ID) -> bool   2. __getitem__(self : rosetta.core.id.DOF_ID_Map_bool_t, id : rosetta.core.id.DOF_ID) -> rosetta.std._Bit_reference   3. __getitem__(self : rosetta.core.id.DOF_ID_Map_bool_t, dof : rosetta.core.id.DOF_Type) -> rosetta.core.id.AtomID_Map_bool_t   4. __getitem__(self : rosetta.core.id.DOF_ID_Map_bool_t, dof : rosetta.core.id.DOF_Type) -> rosetta.core.id.AtomID_Map_bool_t __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.core.id.DOF_ID_Map_bool_t) -> NoneType   doc   2. __init__(self : rosetta.core.id.DOF_ID_Map_bool_t, default_value_a : bool) -> NoneType   3. __init__(rosetta.core.id.DOF_ID_Map_bool_t, int) -> NoneType   doc   4. __init__(self : rosetta.core.id.DOF_ID_Map_bool_t, n_res : int, default_value_a : bool) -> NoneType   5. __init__(self : rosetta.core.id.DOF_ID_Map_bool_t,  : rosetta.core.id.DOF_ID_Map_bool_t) -> 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.core.id.DOF_ID_Map_bool_t,  : rosetta.core.id.DOF_ID_Map_bool_t) -> rosetta.core.id.DOF_ID_Map_bool_t clear(...) from builtins.PyCapsule clear(rosetta.core.id.DOF_ID_Map_bool_t) -> NoneType default_value(...) from builtins.PyCapsule default_value(*args, **kwargs) Overloaded function.   1. default_value(self : rosetta.core.id.DOF_ID_Map_bool_t, dof : rosetta.core.id.DOF_Type) -> bool   2. default_value(self : rosetta.core.id.DOF_ID_Map_bool_t, dof : rosetta.core.id.DOF_Type, default_value_a : bool) -> NoneType   3. default_value(self : rosetta.core.id.DOF_ID_Map_bool_t, default_value_a : bool) -> NoneType empty(...) from builtins.PyCapsule empty(rosetta.core.id.DOF_ID_Map_bool_t) -> bool finalize(...) from builtins.PyCapsule finalize(rosetta.core.id.DOF_ID_Map_bool_t) -> NoneType n_atom(...) from builtins.PyCapsule n_atom(self : rosetta.core.id.DOF_ID_Map_bool_t, i_res : int) -> int n_residue(...) from builtins.PyCapsule n_residue(rosetta.core.id.DOF_ID_Map_bool_t) -> int resize(...) from builtins.PyCapsule resize(*args, **kwargs) Overloaded function.   1. resize(self : rosetta.core.id.DOF_ID_Map_bool_t, n_res : int) -> NoneType   2. resize(self : rosetta.core.id.DOF_ID_Map_bool_t, i_res : int, n_atom : int) -> NoneType   3. resize(self : rosetta.core.id.DOF_ID_Map_bool_t, i_res : int, n_atom : int, value : bool) -> NoneType set(...) from builtins.PyCapsule set(*args, **kwargs) Overloaded function.   1. set(self : rosetta.core.id.DOF_ID_Map_bool_t, dof : rosetta.core.id.DOF_Type) -> NoneType   2. set(self : rosetta.core.id.DOF_ID_Map_bool_t, dof : rosetta.core.id.DOF_Type, value : bool) -> NoneType shrink(...) from builtins.PyCapsule shrink(rosetta.core.id.DOF_ID_Map_bool_t) -> NoneType size(...) from builtins.PyCapsule size(rosetta.core.id.DOF_ID_Map_bool_t) -> int swap(...) from builtins.PyCapsule swap(self : rosetta.core.id.DOF_ID_Map_bool_t, s : rosetta.core.id.DOF_ID_Map_bool_t) -> NoneType   class DOF_ID_Map_core_id_TorsionID_t(builtins.object)       Methods defined here: __call__(...) from builtins.PyCapsule __call__(*args, **kwargs) Overloaded function.   1. __call__(self : rosetta.core.id.DOF_ID_Map_core_id_TorsionID_t, id : rosetta.core.id.DOF_ID) -> core::id::TorsionID   2. __call__(self : rosetta.core.id.DOF_ID_Map_core_id_TorsionID_t, id : rosetta.core.id.DOF_ID) -> core::id::TorsionID   3. __call__(self : rosetta.core.id.DOF_ID_Map_core_id_TorsionID_t, i_res : int, i_atom : int, dof : rosetta.core.id.DOF_Type) -> core::id::TorsionID   4. __call__(self : rosetta.core.id.DOF_ID_Map_core_id_TorsionID_t, i_res : int, i_atom : int, dof : rosetta.core.id.DOF_Type) -> core::id::TorsionID   5. __call__(self : rosetta.core.id.DOF_ID_Map_core_id_TorsionID_t, dof : rosetta.core.id.DOF_Type) -> rosetta.core.id.AtomID_Map_core_id_TorsionID_t   6. __call__(self : rosetta.core.id.DOF_ID_Map_core_id_TorsionID_t, dof : rosetta.core.id.DOF_Type) -> rosetta.core.id.AtomID_Map_core_id_TorsionID_t __getitem__(...) from builtins.PyCapsule __getitem__(*args, **kwargs) Overloaded function.   1. __getitem__(self : rosetta.core.id.DOF_ID_Map_core_id_TorsionID_t, id : rosetta.core.id.DOF_ID) -> core::id::TorsionID   2. __getitem__(self : rosetta.core.id.DOF_ID_Map_core_id_TorsionID_t, id : rosetta.core.id.DOF_ID) -> core::id::TorsionID   3. __getitem__(self : rosetta.core.id.DOF_ID_Map_core_id_TorsionID_t, dof : rosetta.core.id.DOF_Type) -> rosetta.core.id.AtomID_Map_core_id_TorsionID_t   4. __getitem__(self : rosetta.core.id.DOF_ID_Map_core_id_TorsionID_t, dof : rosetta.core.id.DOF_Type) -> rosetta.core.id.AtomID_Map_core_id_TorsionID_t __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.core.id.DOF_ID_Map_core_id_TorsionID_t) -> NoneType   doc   2. __init__(self : rosetta.core.id.DOF_ID_Map_core_id_TorsionID_t, default_value_a : core::id::TorsionID) -> NoneType   3. __init__(rosetta.core.id.DOF_ID_Map_core_id_TorsionID_t, int) -> NoneType   doc   4. __init__(self : rosetta.core.id.DOF_ID_Map_core_id_TorsionID_t, n_res : int, default_value_a : core::id::TorsionID) -> NoneType   5. __init__(self : rosetta.core.id.DOF_ID_Map_core_id_TorsionID_t,  : rosetta.core.id.DOF_ID_Map_core_id_TorsionID_t) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. clear(...) from builtins.PyCapsule clear(rosetta.core.id.DOF_ID_Map_core_id_TorsionID_t) -> NoneType default_value(...) from builtins.PyCapsule default_value(*args, **kwargs) Overloaded function.   1. default_value(self : rosetta.core.id.DOF_ID_Map_core_id_TorsionID_t, dof : rosetta.core.id.DOF_Type) -> core::id::TorsionID   2. default_value(self : rosetta.core.id.DOF_ID_Map_core_id_TorsionID_t, dof : rosetta.core.id.DOF_Type, default_value_a : core::id::TorsionID) -> NoneType   3. default_value(self : rosetta.core.id.DOF_ID_Map_core_id_TorsionID_t, default_value_a : core::id::TorsionID) -> NoneType empty(...) from builtins.PyCapsule empty(rosetta.core.id.DOF_ID_Map_core_id_TorsionID_t) -> bool finalize(...) from builtins.PyCapsule finalize(rosetta.core.id.DOF_ID_Map_core_id_TorsionID_t) -> NoneType n_atom(...) from builtins.PyCapsule n_atom(self : rosetta.core.id.DOF_ID_Map_core_id_TorsionID_t, i_res : int) -> int n_residue(...) from builtins.PyCapsule n_residue(rosetta.core.id.DOF_ID_Map_core_id_TorsionID_t) -> int resize(...) from builtins.PyCapsule resize(*args, **kwargs) Overloaded function.   1. resize(self : rosetta.core.id.DOF_ID_Map_core_id_TorsionID_t, n_res : int) -> NoneType   2. resize(self : rosetta.core.id.DOF_ID_Map_core_id_TorsionID_t, i_res : int, n_atom : int) -> NoneType   3. resize(self : rosetta.core.id.DOF_ID_Map_core_id_TorsionID_t, i_res : int, n_atom : int, value : core::id::TorsionID) -> NoneType set(...) from builtins.PyCapsule set(*args, **kwargs) Overloaded function.   1. set(self : rosetta.core.id.DOF_ID_Map_core_id_TorsionID_t, dof : rosetta.core.id.DOF_Type) -> NoneType   2. set(self : rosetta.core.id.DOF_ID_Map_core_id_TorsionID_t, dof : rosetta.core.id.DOF_Type, value : core::id::TorsionID) -> NoneType shrink(...) from builtins.PyCapsule shrink(rosetta.core.id.DOF_ID_Map_core_id_TorsionID_t) -> NoneType size(...) from builtins.PyCapsule size(rosetta.core.id.DOF_ID_Map_core_id_TorsionID_t) -> int swap(...) from builtins.PyCapsule swap(self : rosetta.core.id.DOF_ID_Map_core_id_TorsionID_t, s : rosetta.core.id.DOF_ID_Map_core_id_TorsionID_t) -> NoneType   class DOF_ID_Range(builtins.object)     Kinematics DOF identifier (with range) class     Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.core.id.DOF_ID_Range) -> NoneType   2. __init__(self : rosetta.core.id.DOF_ID_Range, dof_id : rosetta.core.id.DOF_ID, min : float, max : float) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. __str__(...) from builtins.PyCapsule __str__(rosetta.core.id.DOF_ID_Range) -> str dof_id(...) from builtins.PyCapsule dof_id(rosetta.core.id.DOF_ID_Range) -> rosetta.core.id.DOF_ID max(...) from builtins.PyCapsule max(rosetta.core.id.DOF_ID_Range) -> float min(...) from builtins.PyCapsule min(rosetta.core.id.DOF_ID_Range) -> float   class DOF_Type(builtins.object)     DOF (degrees of freedom) type       - PHI     : torsion or improper angle - THETA   : bond angle - D       : distance - RB1-RB6 : rigid-body jump translation and rotation     Methods defined here: __eq__(...) from builtins.PyCapsule __eq__(rosetta.core.id.DOF_Type, rosetta.core.id.DOF_Type) -> bool __hash__(...) from builtins.PyCapsule __hash__(rosetta.core.id.DOF_Type) -> int __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.core.id.DOF_Type, int) -> NoneType   2. __init__(rosetta.core.id.DOF_Type, int) -> NoneType __int__(...) from builtins.PyCapsule __int__(rosetta.core.id.DOF_Type) -> int __ne__(...) from builtins.PyCapsule __ne__(rosetta.core.id.DOF_Type, rosetta.core.id.DOF_Type) -> bool __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. __repr__(...) from builtins.PyCapsule __repr__(rosetta.core.id.DOF_Type) -> str Data and other attributes defined here: D = DOF_Type.D PHI = DOF_Type.PHI RB1 = DOF_Type.RB1 RB2 = DOF_Type.RB2 RB3 = DOF_Type.RB3 RB4 = DOF_Type.RB4 RB5 = DOF_Type.RB5 RB6 = DOF_Type.RB6 THETA = DOF_Type.THETA   class EXCN_AtomNotFound(rosetta.utility.excn.EXCN_Msg_Exception)       Method resolution order: EXCN_AtomNotFound rosetta.utility.excn.EXCN_Msg_Exception rosetta.utility.excn.EXCN_Exception rosetta.utility.excn.EXCN_Base builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(self : handle,  : rosetta.core.id.NamedAtomID) -> NoneType   2. __init__(handle, rosetta.core.id.EXCN_AtomNotFound) -> 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.core.id.EXCN_AtomNotFound,  : rosetta.core.id.EXCN_AtomNotFound) -> rosetta.core.id.EXCN_AtomNotFound atom(...) from builtins.PyCapsule atom(rosetta.core.id.EXCN_AtomNotFound) -> rosetta.core.id.NamedAtomID Methods inherited from rosetta.utility.excn.EXCN_Msg_Exception: add_msg(...) from builtins.PyCapsule add_msg(self : rosetta.utility.excn.EXCN_Msg_Exception, str : str) -> NoneType msg(...) from builtins.PyCapsule msg(rosetta.utility.excn.EXCN_Msg_Exception) -> str Methods inherited from rosetta.utility.excn.EXCN_Base: __str__(...) from builtins.PyCapsule __str__(rosetta.utility.excn.EXCN_Base) -> str   class JumpID(builtins.object)     /brief  Torsion identifier class   Note the order of the elements in construction calls:          ( residue, type, torsion )          sort of from least to most specific     Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.core.id.JumpID) -> NoneType   2. __init__(self : rosetta.core.id.JumpID, rsd1_in : int, rsd2_in : int) -> NoneType   3. __init__(self : rosetta.core.id.JumpID,  : rosetta.core.id.JumpID) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. __str__(...) from builtins.PyCapsule __str__(rosetta.core.id.JumpID) -> str rsd1(...) from builtins.PyCapsule rsd1(rosetta.core.id.JumpID) -> int rsd2(...) from builtins.PyCapsule rsd2(*args, **kwargs) Overloaded function.   1. rsd2(rosetta.core.id.JumpID) -> int   2. rsd2(rosetta.core.id.JumpID) -> int valid(...) from builtins.PyCapsule valid(rosetta.core.id.JumpID) -> bool   Is this id valid?      Must return false for BOGUS_TORSION_ID   class MainchainTorsionType(builtins.object)       Methods defined here: __eq__(...) from builtins.PyCapsule __eq__(rosetta.core.id.MainchainTorsionType, rosetta.core.id.MainchainTorsionType) -> bool __hash__(...) from builtins.PyCapsule __hash__(rosetta.core.id.MainchainTorsionType) -> int __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.core.id.MainchainTorsionType, int) -> NoneType   2. __init__(rosetta.core.id.MainchainTorsionType, int) -> NoneType __int__(...) from builtins.PyCapsule __int__(rosetta.core.id.MainchainTorsionType) -> int __ne__(...) from builtins.PyCapsule __ne__(rosetta.core.id.MainchainTorsionType, rosetta.core.id.MainchainTorsionType) -> bool __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. __repr__(...) from builtins.PyCapsule __repr__(rosetta.core.id.MainchainTorsionType) -> str Data and other attributes defined here: omega2_dihedral = MainchainTorsionType.omega2_dihedral omega3_dihedral = MainchainTorsionType.omega3_dihedral omega_dihedral = MainchainTorsionType.omega_dihedral phi_dihedral = MainchainTorsionType.phi_dihedral psi_dihedral = MainchainTorsionType.psi_dihedral   class NamedAtomID(builtins.object)     Atom identifier class     Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.core.id.NamedAtomID) -> NoneType   2. __init__(self : rosetta.core.id.NamedAtomID, src : rosetta.core.id.NamedAtomID) -> NoneType   3. __init__(self : rosetta.core.id.NamedAtomID, atom_in : str, rsd_in : int) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. __str__(...) from builtins.PyCapsule __str__(rosetta.core.id.NamedAtomID) -> str assign(...) from builtins.PyCapsule assign(self : rosetta.core.id.NamedAtomID,  : rosetta.core.id.NamedAtomID) -> rosetta.core.id.NamedAtomID atom(...) from builtins.PyCapsule atom(*args, **kwargs) Overloaded function.   1. atom(rosetta.core.id.NamedAtomID) -> str   2. atom(rosetta.core.id.NamedAtomID) -> str rsd(...) from builtins.PyCapsule rsd(*args, **kwargs) Overloaded function.   1. rsd(rosetta.core.id.NamedAtomID) -> int   2. rsd(rosetta.core.id.NamedAtomID) -> int to_string(...) from builtins.PyCapsule to_string(rosetta.core.id.NamedAtomID) -> str valid(...) from builtins.PyCapsule valid(rosetta.core.id.NamedAtomID) -> bool   Is this id valid?      Must return false for BOGUS_ATOM_ID   class NamedAtomID_Map_NamedAtomID(NamedAtomID_Map_core_id_NamedAtomID_t)       Method resolution order: NamedAtomID_Map_NamedAtomID NamedAtomID_Map_core_id_NamedAtomID_t builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.core.id.NamedAtomID_Map_NamedAtomID) -> NoneType   2. __init__(self : rosetta.core.id.NamedAtomID_Map_NamedAtomID,  : rosetta.core.id.NamedAtomID_Map_NamedAtomID) -> 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.core.id.NamedAtomID_Map_NamedAtomID,  : rosetta.core.id.NamedAtomID_Map_NamedAtomID) -> rosetta.core.id.NamedAtomID_Map_NamedAtomID Methods inherited from NamedAtomID_Map_core_id_NamedAtomID_t: __call__(...) from builtins.PyCapsule __call__(*args, **kwargs) Overloaded function.   1. __call__(self : rosetta.core.id.NamedAtomID_Map_core_id_NamedAtomID_t, id : rosetta.core.id.NamedAtomID) -> rosetta.core.id.NamedAtomID   2. __call__(self : rosetta.core.id.NamedAtomID_Map_core_id_NamedAtomID_t, id : rosetta.core.id.NamedAtomID) -> rosetta.core.id.NamedAtomID   3. __call__(self : rosetta.core.id.NamedAtomID_Map_core_id_NamedAtomID_t, i_res : int, atom : str) -> rosetta.core.id.NamedAtomID   4. __call__(self : rosetta.core.id.NamedAtomID_Map_core_id_NamedAtomID_t, i_res : int, atom : str) -> rosetta.core.id.NamedAtomID   5. __call__(self : rosetta.core.id.NamedAtomID_Map_core_id_NamedAtomID_t, i_res : int) -> rosetta.std.map_std_string_core_id_NamedAtomID   6. __call__(self : rosetta.core.id.NamedAtomID_Map_core_id_NamedAtomID_t, i_res : int) -> rosetta.std.map_std_string_core_id_NamedAtomID __getitem__(...) from builtins.PyCapsule __getitem__(*args, **kwargs) Overloaded function.   1. __getitem__(self : rosetta.core.id.NamedAtomID_Map_core_id_NamedAtomID_t, id : rosetta.core.id.NamedAtomID) -> rosetta.core.id.NamedAtomID   2. __getitem__(self : rosetta.core.id.NamedAtomID_Map_core_id_NamedAtomID_t, id : rosetta.core.id.NamedAtomID) -> rosetta.core.id.NamedAtomID   3. __getitem__(self : rosetta.core.id.NamedAtomID_Map_core_id_NamedAtomID_t, i_res : int) -> rosetta.std.map_std_string_core_id_NamedAtomID   4. __getitem__(self : rosetta.core.id.NamedAtomID_Map_core_id_NamedAtomID_t, i_res : int) -> rosetta.std.map_std_string_core_id_NamedAtomID clear(...) from builtins.PyCapsule clear(*args, **kwargs) Overloaded function.   1. clear(rosetta.core.id.NamedAtomID_Map_core_id_NamedAtomID_t) -> NoneType   2. clear(self : rosetta.core.id.NamedAtomID_Map_core_id_NamedAtomID_t, default_value_a : rosetta.core.id.NamedAtomID) -> NoneType default_value(...) from builtins.PyCapsule default_value(*args, **kwargs) Overloaded function.   1. default_value(rosetta.core.id.NamedAtomID_Map_core_id_NamedAtomID_t) -> rosetta.core.id.NamedAtomID   2. default_value(self : rosetta.core.id.NamedAtomID_Map_core_id_NamedAtomID_t, default_value_a : rosetta.core.id.NamedAtomID) -> NoneType empty(...) from builtins.PyCapsule empty(rosetta.core.id.NamedAtomID_Map_core_id_NamedAtomID_t) -> bool fill(...) from builtins.PyCapsule fill(rosetta.core.id.NamedAtomID_Map_core_id_NamedAtomID_t) -> NoneType finalize(...) from builtins.PyCapsule finalize(rosetta.core.id.NamedAtomID_Map_core_id_NamedAtomID_t) -> NoneType get(...) from builtins.PyCapsule get(self : rosetta.core.id.NamedAtomID_Map_core_id_NamedAtomID_t, id : rosetta.core.id.NamedAtomID) -> rosetta.core.id.NamedAtomID has(...) from builtins.PyCapsule has(self : rosetta.core.id.NamedAtomID_Map_core_id_NamedAtomID_t, id : rosetta.core.id.NamedAtomID) -> bool n_atom(...) from builtins.PyCapsule n_atom(self : rosetta.core.id.NamedAtomID_Map_core_id_NamedAtomID_t, i_res : int) -> int n_residue(...) from builtins.PyCapsule n_residue(rosetta.core.id.NamedAtomID_Map_core_id_NamedAtomID_t) -> int resize(...) from builtins.PyCapsule resize(*args, **kwargs) Overloaded function.   1. resize(self : rosetta.core.id.NamedAtomID_Map_core_id_NamedAtomID_t, n_res : int) -> NoneType   2. resize(self : rosetta.core.id.NamedAtomID_Map_core_id_NamedAtomID_t,  : int,  : int) -> NoneType   3. resize(self : rosetta.core.id.NamedAtomID_Map_core_id_NamedAtomID_t,  : int,  : int,  : rosetta.core.id.NamedAtomID) -> NoneType set(...) from builtins.PyCapsule set(self : rosetta.core.id.NamedAtomID_Map_core_id_NamedAtomID_t, id : rosetta.core.id.NamedAtomID, value : rosetta.core.id.NamedAtomID) -> NoneType shrink(...) from builtins.PyCapsule shrink(rosetta.core.id.NamedAtomID_Map_core_id_NamedAtomID_t) -> NoneType size(...) from builtins.PyCapsule size(rosetta.core.id.NamedAtomID_Map_core_id_NamedAtomID_t) -> int swap(...) from builtins.PyCapsule swap(self : rosetta.core.id.NamedAtomID_Map_core_id_NamedAtomID_t, s : rosetta.core.id.NamedAtomID_Map_core_id_NamedAtomID_t) -> NoneType update_sequence_numbering(...) from builtins.PyCapsule update_sequence_numbering(self : rosetta.core.id.NamedAtomID_Map_core_id_NamedAtomID_t, new_size : int, old2new : rosetta.utility.vector1_unsigned_long) -> NoneType   class NamedAtomID_Map_core_id_NamedAtomID_t(builtins.object)       Methods defined here: __call__(...) from builtins.PyCapsule __call__(*args, **kwargs) Overloaded function.   1. __call__(self : rosetta.core.id.NamedAtomID_Map_core_id_NamedAtomID_t, id : rosetta.core.id.NamedAtomID) -> rosetta.core.id.NamedAtomID   2. __call__(self : rosetta.core.id.NamedAtomID_Map_core_id_NamedAtomID_t, id : rosetta.core.id.NamedAtomID) -> rosetta.core.id.NamedAtomID   3. __call__(self : rosetta.core.id.NamedAtomID_Map_core_id_NamedAtomID_t, i_res : int, atom : str) -> rosetta.core.id.NamedAtomID   4. __call__(self : rosetta.core.id.NamedAtomID_Map_core_id_NamedAtomID_t, i_res : int, atom : str) -> rosetta.core.id.NamedAtomID   5. __call__(self : rosetta.core.id.NamedAtomID_Map_core_id_NamedAtomID_t, i_res : int) -> rosetta.std.map_std_string_core_id_NamedAtomID   6. __call__(self : rosetta.core.id.NamedAtomID_Map_core_id_NamedAtomID_t, i_res : int) -> rosetta.std.map_std_string_core_id_NamedAtomID __getitem__(...) from builtins.PyCapsule __getitem__(*args, **kwargs) Overloaded function.   1. __getitem__(self : rosetta.core.id.NamedAtomID_Map_core_id_NamedAtomID_t, id : rosetta.core.id.NamedAtomID) -> rosetta.core.id.NamedAtomID   2. __getitem__(self : rosetta.core.id.NamedAtomID_Map_core_id_NamedAtomID_t, id : rosetta.core.id.NamedAtomID) -> rosetta.core.id.NamedAtomID   3. __getitem__(self : rosetta.core.id.NamedAtomID_Map_core_id_NamedAtomID_t, i_res : int) -> rosetta.std.map_std_string_core_id_NamedAtomID   4. __getitem__(self : rosetta.core.id.NamedAtomID_Map_core_id_NamedAtomID_t, i_res : int) -> rosetta.std.map_std_string_core_id_NamedAtomID __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.core.id.NamedAtomID_Map_core_id_NamedAtomID_t) -> NoneType   2. __init__(self : rosetta.core.id.NamedAtomID_Map_core_id_NamedAtomID_t, default_value_a : rosetta.core.id.NamedAtomID) -> NoneType   3. __init__(self : rosetta.core.id.NamedAtomID_Map_core_id_NamedAtomID_t, n_res : int) -> NoneType   4. __init__(self : rosetta.core.id.NamedAtomID_Map_core_id_NamedAtomID_t, n_res : int, default_value_a : rosetta.core.id.NamedAtomID) -> NoneType   5. __init__(self : rosetta.core.id.NamedAtomID_Map_core_id_NamedAtomID_t,  : rosetta.core.id.NamedAtomID_Map_core_id_NamedAtomID_t) -> 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.core.id.NamedAtomID_Map_core_id_NamedAtomID_t,  : rosetta.core.id.NamedAtomID_Map_core_id_NamedAtomID_t) -> rosetta.core.id.NamedAtomID_Map_core_id_NamedAtomID_t clear(...) from builtins.PyCapsule clear(*args, **kwargs) Overloaded function.   1. clear(rosetta.core.id.NamedAtomID_Map_core_id_NamedAtomID_t) -> NoneType   2. clear(self : rosetta.core.id.NamedAtomID_Map_core_id_NamedAtomID_t, default_value_a : rosetta.core.id.NamedAtomID) -> NoneType default_value(...) from builtins.PyCapsule default_value(*args, **kwargs) Overloaded function.   1. default_value(rosetta.core.id.NamedAtomID_Map_core_id_NamedAtomID_t) -> rosetta.core.id.NamedAtomID   2. default_value(self : rosetta.core.id.NamedAtomID_Map_core_id_NamedAtomID_t, default_value_a : rosetta.core.id.NamedAtomID) -> NoneType empty(...) from builtins.PyCapsule empty(rosetta.core.id.NamedAtomID_Map_core_id_NamedAtomID_t) -> bool fill(...) from builtins.PyCapsule fill(rosetta.core.id.NamedAtomID_Map_core_id_NamedAtomID_t) -> NoneType finalize(...) from builtins.PyCapsule finalize(rosetta.core.id.NamedAtomID_Map_core_id_NamedAtomID_t) -> NoneType get(...) from builtins.PyCapsule get(self : rosetta.core.id.NamedAtomID_Map_core_id_NamedAtomID_t, id : rosetta.core.id.NamedAtomID) -> rosetta.core.id.NamedAtomID has(...) from builtins.PyCapsule has(self : rosetta.core.id.NamedAtomID_Map_core_id_NamedAtomID_t, id : rosetta.core.id.NamedAtomID) -> bool n_atom(...) from builtins.PyCapsule n_atom(self : rosetta.core.id.NamedAtomID_Map_core_id_NamedAtomID_t, i_res : int) -> int n_residue(...) from builtins.PyCapsule n_residue(rosetta.core.id.NamedAtomID_Map_core_id_NamedAtomID_t) -> int resize(...) from builtins.PyCapsule resize(*args, **kwargs) Overloaded function.   1. resize(self : rosetta.core.id.NamedAtomID_Map_core_id_NamedAtomID_t, n_res : int) -> NoneType   2. resize(self : rosetta.core.id.NamedAtomID_Map_core_id_NamedAtomID_t,  : int,  : int) -> NoneType   3. resize(self : rosetta.core.id.NamedAtomID_Map_core_id_NamedAtomID_t,  : int,  : int,  : rosetta.core.id.NamedAtomID) -> NoneType set(...) from builtins.PyCapsule set(self : rosetta.core.id.NamedAtomID_Map_core_id_NamedAtomID_t, id : rosetta.core.id.NamedAtomID, value : rosetta.core.id.NamedAtomID) -> NoneType shrink(...) from builtins.PyCapsule shrink(rosetta.core.id.NamedAtomID_Map_core_id_NamedAtomID_t) -> NoneType size(...) from builtins.PyCapsule size(rosetta.core.id.NamedAtomID_Map_core_id_NamedAtomID_t) -> int swap(...) from builtins.PyCapsule swap(self : rosetta.core.id.NamedAtomID_Map_core_id_NamedAtomID_t, s : rosetta.core.id.NamedAtomID_Map_core_id_NamedAtomID_t) -> NoneType update_sequence_numbering(...) from builtins.PyCapsule update_sequence_numbering(self : rosetta.core.id.NamedAtomID_Map_core_id_NamedAtomID_t, new_size : int, old2new : rosetta.utility.vector1_unsigned_long) -> NoneType   class NamedStubID(builtins.object)     ////////////////////////////////////////////////////////////////////////////     Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(self : rosetta.core.id.NamedStubID, a1 : rosetta.core.id.NamedAtomID, a2 : rosetta.core.id.NamedAtomID, a3 : rosetta.core.id.NamedAtomID) -> NoneType   2. __init__(self : rosetta.core.id.NamedStubID, c : rosetta.core.id.NamedAtomID, a1 : rosetta.core.id.NamedAtomID, a2 : rosetta.core.id.NamedAtomID, a3 : rosetta.core.id.NamedAtomID) -> NoneType   3. __init__(self : rosetta.core.id.NamedStubID, a1 : str, a2 : str, a3 : str, rsd : int) -> NoneType   4. __init__(self : rosetta.core.id.NamedStubID, c : str, a1 : str, a2 : str, a3 : str, rsd : int) -> NoneType   5. __init__(self : rosetta.core.id.NamedStubID, a1 : str, rsd1 : int, a2 : str, rsd2 : int, a3 : str, rsd3 : int) -> NoneType   6. __init__(self : rosetta.core.id.NamedStubID,  : rosetta.utility.vector1_std_string, rsd : int) -> NoneType   7. __init__(rosetta.core.id.NamedStubID) -> NoneType   8. __init__(self : rosetta.core.id.NamedStubID,  : rosetta.core.id.NamedStubID) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. __str__(...) from builtins.PyCapsule __str__(rosetta.core.id.NamedStubID) -> str assign(...) from builtins.PyCapsule assign(self : rosetta.core.id.NamedStubID,  : rosetta.core.id.NamedStubID) -> rosetta.core.id.NamedStubID atom(...) from builtins.PyCapsule atom(self : rosetta.core.id.NamedStubID, index : int) -> rosetta.core.id.NamedAtomID center(...) from builtins.PyCapsule center(rosetta.core.id.NamedStubID) -> rosetta.core.id.NamedAtomID valid(...) from builtins.PyCapsule valid(rosetta.core.id.NamedStubID) -> bool Data descriptors defined here: atom1 atom2 atom3 center_   class SequenceMapping(builtins.object)       Methods defined here: __eq__(...) from builtins.PyCapsule __eq__(self : rosetta.core.id.SequenceMapping, rhs : rosetta.core.id.SequenceMapping) -> bool   Equality operator. __getitem__(...) from builtins.PyCapsule __getitem__(*args, **kwargs) Overloaded function.   1. __getitem__(self : rosetta.core.id.SequenceMapping, pos1 : int) -> int   2. __getitem__(self : rosetta.core.id.SequenceMapping, pos1 : int) -> int __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle) -> NoneType   2. __init__(self : handle, s1 : int, s2 : int) -> NoneType   3. __init__(self : handle, mapping : rosetta.utility.vector1_unsigned_long) -> NoneType   4. __init__(self : handle, event : core::conformation::signals::LengthEvent) -> NoneType   5. __init__(handle, rosetta.core.id.SequenceMapping) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. __str__(...) from builtins.PyCapsule __str__(rosetta.core.id.SequenceMapping) -> str all_aligned(...) from builtins.PyCapsule all_aligned(rosetta.core.id.SequenceMapping) -> bool assign(...) from builtins.PyCapsule assign(self : rosetta.core.id.SequenceMapping, src : rosetta.core.id.SequenceMapping) -> rosetta.core.id.SequenceMapping clear(...) from builtins.PyCapsule clear(rosetta.core.id.SequenceMapping) -> NoneType delete_source_residue(...) from builtins.PyCapsule delete_source_residue(self : rosetta.core.id.SequenceMapping, pos1 : int) -> NoneType delete_target_residue(...) from builtins.PyCapsule delete_target_residue(self : rosetta.core.id.SequenceMapping, pos : int) -> NoneType downstream_combine(...) from builtins.PyCapsule downstream_combine(self : rosetta.core.id.SequenceMapping, smap_to_add : rosetta.core.id.SequenceMapping) -> NoneType   Apply a B->C mapping to the current A->B mapping to get an A->C mapping  i.e. smap[j] becomes smap_to_add[ smap[j] ] identity(...) from builtins.PyCapsule identity(size : int) -> rosetta.core.id.SequenceMapping   Construct an identity mapping, which means that for all positions,  i in seq1 maps to i in seq2. insert_aligned_residue(...) from builtins.PyCapsule insert_aligned_residue(self : rosetta.core.id.SequenceMapping, pos1 : int, pos2 : int) -> NoneType insert_aligned_residue_safe(...) from builtins.PyCapsule insert_aligned_residue_safe(self : rosetta.core.id.SequenceMapping, pos1 : int, pos2 : int) -> NoneType   same as insert_aligned_residue, but a couple of extra checks on size1 and size2. insert_source_residue(...) from builtins.PyCapsule insert_source_residue(self : rosetta.core.id.SequenceMapping, pos1 : int) -> NoneType insert_target_residue(...) from builtins.PyCapsule insert_target_residue(self : rosetta.core.id.SequenceMapping, pos : int) -> NoneType is_identity(...) from builtins.PyCapsule is_identity(rosetta.core.id.SequenceMapping) -> bool is_identity_ignore_gaps(...) from builtins.PyCapsule is_identity_ignore_gaps(rosetta.core.id.SequenceMapping) -> bool mapping(...) from builtins.PyCapsule mapping(*args, **kwargs) Overloaded function.   1. mapping(rosetta.core.id.SequenceMapping) -> rosetta.utility.vector1_unsigned_long   2. mapping(self : rosetta.core.id.SequenceMapping, mapping : rosetta.utility.vector1_unsigned_long) -> NoneType push_back(...) from builtins.PyCapsule push_back(self : rosetta.core.id.SequenceMapping, al : int) -> NoneType resize(...) from builtins.PyCapsule resize(self : rosetta.core.id.SequenceMapping, s1 : int, s2 : int) -> NoneType   resize reverse(...) from builtins.PyCapsule reverse(rosetta.core.id.SequenceMapping) -> NoneType   go from an A->B mapping to a B->A mapping same_type_as_me(...) from builtins.PyCapsule same_type_as_me(self : rosetta.core.id.SequenceMapping, other : rosetta.core.id.SequenceMapping) -> bool   virtual function for ensuring both sequence mappings are the same type;  essential for a valid equality operator. set_offset(...) from builtins.PyCapsule set_offset(self : rosetta.core.id.SequenceMapping, setting : int) -> NoneType show(...) from builtins.PyCapsule show(rosetta.core.id.SequenceMapping) -> NoneType size1(...) from builtins.PyCapsule size1(rosetta.core.id.SequenceMapping) -> int   size of target sequence size2(...) from builtins.PyCapsule size2(*args, **kwargs) Overloaded function.   1. size2(rosetta.core.id.SequenceMapping) -> int   size of aligned sequence ???   2. size2(self : rosetta.core.id.SequenceMapping, s2 : int) -> NoneType to_string(...) from builtins.PyCapsule to_string(rosetta.core.id.SequenceMapping) -> str upstream_combine(...) from builtins.PyCapsule upstream_combine(self : rosetta.core.id.SequenceMapping, smap_to_add : rosetta.core.id.SequenceMapping) -> NoneType   Apply a C->A mapping to the current A->B mapping to get a C->B mapping  i.e. smap[j] becomes smap[ smap_to_add[ j ] ]   class StubID(builtins.object)     ////////////////////////////////////////////////////////////////////////////     Methods defined here: __eq__(...) from builtins.PyCapsule __eq__(self : rosetta.core.id.StubID, rhs : rosetta.core.id.StubID) -> bool __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(self : rosetta.core.id.StubID, a1 : rosetta.core.id.AtomID, a2 : rosetta.core.id.AtomID, a3 : rosetta.core.id.AtomID) -> NoneType   2. __init__(self : rosetta.core.id.StubID, c : rosetta.core.id.AtomID, a1 : rosetta.core.id.AtomID, a2 : rosetta.core.id.AtomID, a3 : rosetta.core.id.AtomID) -> NoneType   3. __init__(rosetta.core.id.StubID) -> NoneType   4. __init__(self : rosetta.core.id.StubID,  : rosetta.core.id.StubID) -> NoneType __ne__(...) from builtins.PyCapsule __ne__(self : rosetta.core.id.StubID, rhs : rosetta.core.id.StubID) -> bool __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. __str__(...) from builtins.PyCapsule __str__(rosetta.core.id.StubID) -> str assign(...) from builtins.PyCapsule assign(self : rosetta.core.id.StubID,  : rosetta.core.id.StubID) -> rosetta.core.id.StubID atom(...) from builtins.PyCapsule atom(self : rosetta.core.id.StubID, index : int) -> rosetta.core.id.AtomID center(...) from builtins.PyCapsule center(rosetta.core.id.StubID) -> rosetta.core.id.AtomID valid(...) from builtins.PyCapsule valid(rosetta.core.id.StubID) -> bool Data descriptors defined here: atom1 atom2 atom3 center_   class TorsionID(builtins.object)     Torsion identifier class     Consider a few examples to get a better picture for how torsions are uniquely identified:                   Note the order of the elements in construction calls (residue, type, torsion) go from least to most specific.   TorsionIDs are very different for JUMP TorsionTypes. In such a case, they are interpreted as follows: TorsionID(1, JUMP, 2)  // RB2 of jump #1 for the Pose.     Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.core.id.TorsionID) -> NoneType   2. __init__(self : rosetta.core.id.TorsionID, src : rosetta.core.id.TorsionID) -> NoneType   3. __init__(self : rosetta.core.id.TorsionID, rsd_in : int, type_in : rosetta.core.id.TorsionType, torsion_in : int) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. __str__(...) from builtins.PyCapsule __str__(rosetta.core.id.TorsionID) -> str assign(...) from builtins.PyCapsule assign(self : rosetta.core.id.TorsionID,  : rosetta.core.id.TorsionID) -> rosetta.core.id.TorsionID rsd(...) from builtins.PyCapsule rsd(*args, **kwargs) Overloaded function.   1. rsd(rosetta.core.id.TorsionID) -> int   For this TorsionID, return the Residue number within the complex OR the Jump number for the Pose.   2. rsd(rosetta.core.id.TorsionID) -> int   For this TorsionID, set the Residue number within the complex OR the Jump number for the Pose. torsion(...) from builtins.PyCapsule torsion(*args, **kwargs) Overloaded function.   1. torsion(rosetta.core.id.TorsionID) -> int   Return the torsion number of the given type within the residue OR  the rigid-body identifier for a JUMP TorsionType.   2. torsion(rosetta.core.id.TorsionID) -> int   Set the torsion number of the given type within the residue OR  the rigid-body identifier for a JUMP TorsionType. type(...) from builtins.PyCapsule type(*args, **kwargs) Overloaded function.   1. type(rosetta.core.id.TorsionID) -> rosetta.core.id.TorsionType   Return the type (BB, CHI,NU, BRANCH, JUMP) of this torsion.   2. type(rosetta.core.id.TorsionID) -> rosetta.core.id.TorsionType   Set the type (BB, CHI,NU, BRANCH, JUMP) of this torsion. valid(...) from builtins.PyCapsule valid(rosetta.core.id.TorsionID) -> bool   Is this id valid?      Must return false for BOGUS_TORSION_ID   class TorsionID_Range(builtins.object)     Kinematics DOF identifier (with range) class     Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.core.id.TorsionID_Range) -> NoneType   2. __init__(self : rosetta.core.id.TorsionID_Range, torsion_id : rosetta.core.id.TorsionID, min : float, max : float) -> NoneType   3. __init__(self : rosetta.core.id.TorsionID_Range,  : rosetta.core.id.TorsionID_Range) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. __str__(...) from builtins.PyCapsule __str__(rosetta.core.id.TorsionID_Range) -> str max(...) from builtins.PyCapsule max(rosetta.core.id.TorsionID_Range) -> float min(...) from builtins.PyCapsule min(rosetta.core.id.TorsionID_Range) -> float torsion_id(...) from builtins.PyCapsule torsion_id(rosetta.core.id.TorsionID_Range) -> rosetta.core.id.TorsionID   class TorsionType(builtins.object)     Torsion type -- used in the TorsionID class       - BB     : "backbone" torsion (Actually, this is a main-chain torsion.) - CHI    : sidechain torsion - NU     : internal ring torsion - BRANCH : torsions at branch connection points which are CHEMICAL edges of the FoldTree - JUMP   : rigid-body transformation     Methods defined here: __eq__(...) from builtins.PyCapsule __eq__(rosetta.core.id.TorsionType, rosetta.core.id.TorsionType) -> bool __hash__(...) from builtins.PyCapsule __hash__(rosetta.core.id.TorsionType) -> int __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.core.id.TorsionType, int) -> NoneType   2. __init__(rosetta.core.id.TorsionType, int) -> NoneType __int__(...) from builtins.PyCapsule __int__(rosetta.core.id.TorsionType) -> int __ne__(...) from builtins.PyCapsule __ne__(rosetta.core.id.TorsionType, rosetta.core.id.TorsionType) -> bool __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. __repr__(...) from builtins.PyCapsule __repr__(rosetta.core.id.TorsionType) -> str Data and other attributes defined here: BB = TorsionType.BB BRANCH = TorsionType.BRANCH CHI = TorsionType.CHI JUMP = TorsionType.JUMP NU = TorsionType.NU

Functions
		DOF_type_is_rb(...) method of builtins.PyCapsule instance DOF_type_is_rb(t : rosetta.core.id.DOF_Type) -> bool   ////////////////////////////////////////////////////////////////////////// combine_sequence_mappings(...) method of builtins.PyCapsule instance combine_sequence_mappings(smap : rosetta.core.id.SequenceMapping, smap_to_add : rosetta.core.id.SequenceMapping) -> NoneType   combine the input sequence mappings into one  utility function added by flo, feb 2011 get_rb_number(...) method of builtins.PyCapsule instance get_rb_number(t : rosetta.core.id.DOF_Type) -> int   ////////////////////////////////////////////////////////////////////////// get_rb_type(...) method of builtins.PyCapsule instance get_rb_type(k : int) -> rosetta.core.id.DOF_Type to_string(...) method of builtins.PyCapsule instance to_string(*args, **kwargs) Overloaded function.   1. to_string(type : rosetta.core.id.DOF_Type) -> str   2. to_string(type : rosetta.core.id.TorsionType) -> str

Data
		BB = TorsionType.BB BRANCH = TorsionType.BRANCH CHI = TorsionType.CHI D = DOF_Type.D JUMP = TorsionType.JUMP NU = TorsionType.NU PHI = DOF_Type.PHI RB1 = DOF_Type.RB1 RB2 = DOF_Type.RB2 RB3 = DOF_Type.RB3 RB4 = DOF_Type.RB4 RB5 = DOF_Type.RB5 RB6 = DOF_Type.RB6 THETA = DOF_Type.THETA omega2_dihedral = MainchainTorsionType.omega2_dihedral omega3_dihedral = MainchainTorsionType.omega3_dihedral omega_dihedral = MainchainTorsionType.omega_dihedral phi_dihedral = MainchainTorsionType.phi_dihedral psi_dihedral = MainchainTorsionType.psi_dihedral