Bindings for core::conformation::symmetry namespace

Classes
		builtins.object SlideCriteriaType SlideType SymDof SymSlideInfo SymmData SymmetryInfo SymmetryTransform VirtualCoordinate dof_type rosetta.basic.resource_manager.ResourceLoader(builtins.object) SymmDataLoader rosetta.basic.resource_manager.ResourceLoaderCreator(builtins.object) SymmDataLoaderCreator rosetta.basic.resource_manager.ResourceOptions(builtins.object) SymmDataOptions rosetta.basic.resource_manager.ResourceOptionsCreator(builtins.object) SymmDataOptionsCreator rosetta.core.conformation.Conformation(builtins.object) SymmetricConformation MirrorSymmetricConformation   class MirrorSymmetricConformation(SymmetricConformation)     Mirror symmetric conformation contains the same symminfo logic, but also includes special logic for mirror symmetries     Method resolution order: MirrorSymmetricConformation SymmetricConformation rosetta.core.conformation.Conformation builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle) -> NoneType   2. __init__(self : handle, conf : rosetta.core.conformation.Conformation, symm_info : core::conformation::symmetry::SymmetryInfo) -> NoneType   3. __init__(handle, rosetta.core.conformation.symmetry.MirrorSymmetricConformation) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. append_residue_by_jump(...) from builtins.PyCapsule append_residue_by_jump(*args, **kwargs) Overloaded function.   1. append_residue_by_jump(self : rosetta.core.conformation.symmetry.MirrorSymmetricConformation, new_rsd : rosetta.core.conformation.Residue, anchor_residue : int) -> NoneType   Append a new residue by a jump; clones this append to all copies   2. append_residue_by_jump(self : rosetta.core.conformation.symmetry.MirrorSymmetricConformation, new_rsd : rosetta.core.conformation.Residue, anchor_residue : int, anchor_atom : str) -> NoneType   Append a new residue by a jump; clones this append to all copies   3. append_residue_by_jump(self : rosetta.core.conformation.symmetry.MirrorSymmetricConformation, new_rsd : rosetta.core.conformation.Residue, anchor_residue : int, anchor_atom : str, root_atom : str) -> NoneType   Append a new residue by a jump; clones this append to all copies   4. append_residue_by_jump(self : rosetta.core.conformation.symmetry.MirrorSymmetricConformation, new_rsd : rosetta.core.conformation.Residue, anchor_residue : int, anchor_atom : str, root_atom : str, start_new_chain : bool) -> NoneType   Append a new residue by a jump; clones this append to all copies assign(...) from builtins.PyCapsule assign(*args, **kwargs) Overloaded function.   1. assign(self : rosetta.core.conformation.symmetry.MirrorSymmetricConformation, src : rosetta.core.conformation.Conformation) -> rosetta.core.conformation.Conformation   virtual assignment operator   2. assign(self : rosetta.core.conformation.symmetry.MirrorSymmetricConformation,  : rosetta.core.conformation.symmetry.MirrorSymmetricConformation) -> rosetta.core.conformation.symmetry.MirrorSymmetricConformation clone(...) from builtins.PyCapsule clone(rosetta.core.conformation.symmetry.MirrorSymmetricConformation) -> rosetta.core.conformation.Conformation detached_copy(...) from builtins.PyCapsule detached_copy(self : rosetta.core.conformation.symmetry.MirrorSymmetricConformation, src : rosetta.core.conformation.Conformation) -> NoneType detect_disulfides(...) from builtins.PyCapsule detect_disulfides(*args, **kwargs) Overloaded function.   1. detect_disulfides(rosetta.core.conformation.symmetry.MirrorSymmetricConformation) -> NoneType   2. detect_disulfides(self : rosetta.core.conformation.symmetry.MirrorSymmetricConformation, disulf_one : rosetta.utility.vector1_unsigned_long) -> NoneType   3. detect_disulfides(self : rosetta.core.conformation.symmetry.MirrorSymmetricConformation, disulf_one : rosetta.utility.vector1_unsigned_long, disulf_two : rosetta.utility.vector1_unsigned_long) -> NoneType fold_tree(...) from builtins.PyCapsule fold_tree(self : rosetta.core.conformation.symmetry.MirrorSymmetricConformation, fold_tree_in : rosetta.core.kinematics.FoldTree) -> NoneType   set the fold_tree get_residue_weight(...) from builtins.PyCapsule get_residue_weight(self : rosetta.core.conformation.symmetry.MirrorSymmetricConformation, resid1 : int, resid2 : int) -> float insert_conformation_by_jump(...) from builtins.PyCapsule insert_conformation_by_jump(*args, **kwargs) Overloaded function.   1. insert_conformation_by_jump(self : rosetta.core.conformation.symmetry.MirrorSymmetricConformation, conf : rosetta.core.conformation.Conformation, insert_seqpos : int, insert_jumppos : int, anchor_pos : int) -> NoneType   Append a new conformation by a jump; clones this append to all copies   2. insert_conformation_by_jump(self : rosetta.core.conformation.symmetry.MirrorSymmetricConformation, conf : rosetta.core.conformation.Conformation, insert_seqpos : int, insert_jumppos : int, anchor_pos : int, anchor_jump_number : int) -> NoneType   Append a new conformation by a jump; clones this append to all copies   3. insert_conformation_by_jump(self : rosetta.core.conformation.symmetry.MirrorSymmetricConformation, conf : rosetta.core.conformation.Conformation, insert_seqpos : int, insert_jumppos : int, anchor_pos : int, anchor_jump_number : int, anchor_atom : str) -> NoneType   Append a new conformation by a jump; clones this append to all copies   4. insert_conformation_by_jump(self : rosetta.core.conformation.symmetry.MirrorSymmetricConformation, conf : rosetta.core.conformation.Conformation, insert_seqpos : int, insert_jumppos : int, anchor_pos : int, anchor_jump_number : int, anchor_atom : str, root_atom : str) -> NoneType   Append a new conformation by a jump; clones this append to all copies recalculate_transforms(...) from builtins.PyCapsule recalculate_transforms(rosetta.core.conformation.symmetry.MirrorSymmetricConformation) -> NoneType replace_residue(...) from builtins.PyCapsule replace_residue(*args, **kwargs) Overloaded function.   1. replace_residue(self : rosetta.core.conformation.symmetry.MirrorSymmetricConformation, seqpos : int, new_rsd : rosetta.core.conformation.Residue, orient_backbone : bool) -> NoneType   replace residue   2. replace_residue(self : rosetta.core.conformation.symmetry.MirrorSymmetricConformation, seqpos : int, new_rsd : rosetta.core.conformation.Residue, atom_pairs : rosetta.utility.vector1_std_pair_std_string_std_string_t) -> NoneType res_is_mirrored(...) from builtins.PyCapsule res_is_mirrored(self : rosetta.core.conformation.symmetry.MirrorSymmetricConformation, seqpos : int) -> bool   Is this residue mirrored relative to the asymmetric unit?      Vikram K. Mulligan (vmullig.edu). same_type_as_me(...) from builtins.PyCapsule same_type_as_me(self : rosetta.core.conformation.symmetry.MirrorSymmetricConformation, other : rosetta.core.conformation.Conformation, recurse : bool) -> bool set_dof(...) from builtins.PyCapsule set_dof(self : rosetta.core.conformation.symmetry.MirrorSymmetricConformation, id : rosetta.core.id.DOF_ID, setting : float) -> NoneType   DOF set_jump(...) from builtins.PyCapsule set_jump(*args, **kwargs) Overloaded function.   1. set_jump(self : rosetta.core.conformation.symmetry.MirrorSymmetricConformation, jump_number : int, new_jump : rosetta.core.kinematics.Jump) -> NoneType   JUMPS      set a jump   2. set_jump(self : rosetta.core.conformation.symmetry.MirrorSymmetricConformation, id : rosetta.core.id.AtomID, new_jump : rosetta.core.kinematics.Jump) -> NoneType   set a jump set_torsion(...) from builtins.PyCapsule set_torsion(self : rosetta.core.conformation.symmetry.MirrorSymmetricConformation, id : core::id::TorsionID, setting : float) -> NoneType   BONDS/TORSIONS set_torsion_angle(...) from builtins.PyCapsule set_torsion_angle(*args, **kwargs) Overloaded function.   1. set_torsion_angle(self : rosetta.core.conformation.symmetry.MirrorSymmetricConformation, atom1 : rosetta.core.id.AtomID, atom2 : rosetta.core.id.AtomID, atom3 : rosetta.core.id.AtomID, atom4 : rosetta.core.id.AtomID, setting : float) -> NoneType   2. set_torsion_angle(self : rosetta.core.conformation.symmetry.MirrorSymmetricConformation, atom1 : rosetta.core.id.AtomID, atom2 : rosetta.core.id.AtomID, atom3 : rosetta.core.id.AtomID, atom4 : rosetta.core.id.AtomID, setting : float, quiet : bool) -> NoneType update_residue_identities(...) from builtins.PyCapsule update_residue_identities(rosetta.core.conformation.symmetry.MirrorSymmetricConformation) -> NoneType   Updates residue identities in symmetric subunits, ensuring that they are mirrored relative to the ASU in mirrored subunits  and identical to the ASU in non-mirrored subunits.      Assumes that the residue identities and variants (aside from D/L variants) already match.  That is, if I have ASN at position  5 in my asymmetric unit, I either have ASN or DASN at the equivalent position in each symmetry copy.  Safe to call repeatedly.      Vikram K. Mulligan (vmullig.edu). Methods inherited from SymmetricConformation: Symmetry_Info(...) from builtins.PyCapsule Symmetry_Info(*args, **kwargs) Overloaded function.   1. Symmetry_Info(rosetta.core.conformation.symmetry.SymmetricConformation) -> core::conformation::symmetry::SymmetryInfo   2. Symmetry_Info(rosetta.core.conformation.symmetry.SymmetricConformation) -> core::conformation::symmetry::SymmetryInfo apply_transform_Rx_plus_v(...) from builtins.PyCapsule apply_transform_Rx_plus_v(self : rosetta.core.conformation.symmetry.SymmetricConformation, R : rosetta.numeric.xyzMatrix_double_t, v : rosetta.numeric.xyzVector_double_t) -> NoneType apply_transformation(...) from builtins.PyCapsule apply_transformation(*args, **kwargs) Overloaded function.   1. apply_transformation(self : rosetta.core.conformation.symmetry.SymmetricConformation, Xin : rosetta.numeric.xyzVector_double_t, residfrom : int, residto : int) -> rosetta.numeric.xyzVector_double_t   Remap coordinate X from resid i's frame to resid j's frame   2. apply_transformation(self : rosetta.core.conformation.symmetry.SymmetricConformation, Xin : rosetta.numeric.xyzVector_double_t, residfrom : int, residto : int, rotationonly : bool) -> rosetta.numeric.xyzVector_double_t   Remap coordinate X from resid i's frame to resid j's frame apply_transformation_norecompute(...) from builtins.PyCapsule apply_transformation_norecompute(*args, **kwargs) Overloaded function.   1. apply_transformation_norecompute(self : rosetta.core.conformation.symmetry.SymmetricConformation, Xin : rosetta.numeric.xyzVector_double_t, residfrom : int, residto : int) -> rosetta.numeric.xyzVector_double_t   Remap coordinate X from resid i's frame to resid j's frame    assumes that the transformations are already computed (thus can be const)   2. apply_transformation_norecompute(self : rosetta.core.conformation.symmetry.SymmetricConformation, Xin : rosetta.numeric.xyzVector_double_t, residfrom : int, residto : int, rotationonly : bool) -> rosetta.numeric.xyzVector_double_t   Remap coordinate X from resid i's frame to resid j's frame    assumes that the transformations are already computed (thus can be const) batch_set_xyz(...) from builtins.PyCapsule batch_set_xyz(self : rosetta.core.conformation.symmetry.SymmetricConformation, ids : rosetta.utility.vector1_core_id_AtomID, positions : rosetta.utility.vector1_numeric_xyzVector_double_t) -> NoneType   Symmetric batch_set_xyz declare_chemical_bond(...) from builtins.PyCapsule declare_chemical_bond(self : rosetta.core.conformation.symmetry.SymmetricConformation, seqpos1 : int, atom_name1 : str, seqpos2 : int, atom_name2 : str) -> NoneType   Declare that a chemical bond exists between two residues      This updates all symmetry copies, so that each one has a chemical  bond between the residues in question.      Frank DiMaio.      Rewritten by Vikram K. Mulligan (vmullig.edu). get_residue_mask(...) from builtins.PyCapsule get_residue_mask(rosetta.core.conformation.symmetry.SymmetricConformation) -> rosetta.utility.vector1_bool get_transformation(...) from builtins.PyCapsule get_transformation(self : rosetta.core.conformation.symmetry.SymmetricConformation, resid : int) -> rosetta.numeric.HomogeneousTransform_double_t   Get the transformation controlling resid i set_bond_angle(...) from builtins.PyCapsule set_bond_angle(self : rosetta.core.conformation.symmetry.SymmetricConformation, atom1 : rosetta.core.id.AtomID, atom2 : rosetta.core.id.AtomID, atom3 : rosetta.core.id.AtomID, setting : float) -> NoneType set_bond_length(...) from builtins.PyCapsule set_bond_length(self : rosetta.core.conformation.symmetry.SymmetricConformation, atom1 : rosetta.core.id.AtomID, atom2 : rosetta.core.id.AtomID, setting : float) -> NoneType set_secstruct(...) from builtins.PyCapsule set_secstruct(self : rosetta.core.conformation.symmetry.SymmetricConformation, seqpos : int, setting : str) -> NoneType set_xyz(...) from builtins.PyCapsule set_xyz(self : rosetta.core.conformation.symmetry.SymmetricConformation, id : rosetta.core.id.AtomID, position : rosetta.numeric.xyzVector_double_t) -> NoneType   Symmetric set_xyz Methods inherited from rosetta.core.conformation.Conformation: __str__(...) from builtins.PyCapsule __str__(rosetta.core.conformation.Conformation) -> str aa(...) from builtins.PyCapsule aa(self : rosetta.core.conformation.Conformation, seqpos : int) -> rosetta.core.chemical.AA   Returns the AA enum for position  <seqpos> add_parameters_set(...) from builtins.PyCapsule add_parameters_set(self : rosetta.core.conformation.Conformation, newset : rosetta.core.conformation.parametric.ParametersSet) -> NoneType   Add a (predefined) ParametersSet object (via its owning pointer)  to the current Conformation object.      Vikram K. Mulligan (vmullig.edu) annotated_sequence(...) from builtins.PyCapsule annotated_sequence(self : rosetta.core.conformation.Conformation, show_all_variants : bool) -> str   Returns the variant-tagged string representing the  residue types that make up a conformation; e.g.  M[MET:N-Terminus-Variant]CDH[HIS_D]LLR[ARG:C-Terminus-Variant] append_polymer_residue_after_seqpos(...) from builtins.PyCapsule append_polymer_residue_after_seqpos(self : rosetta.core.conformation.Conformation, new_rsd : rosetta.core.conformation.Residue, seqpos : int, build_ideal_geometry : bool) -> NoneType   glues to seqpos and perhaps also seqpos+1 append_residue_by_bond(...) from builtins.PyCapsule append_residue_by_bond(*args, **kwargs) Overloaded function.   1. append_residue_by_bond(self : rosetta.core.conformation.Conformation, new_rsd : rosetta.core.conformation.Residue) -> NoneType   Append a new residue by a bond.   2. append_residue_by_bond(self : rosetta.core.conformation.Conformation, new_rsd : rosetta.core.conformation.Residue, build_ideal_geometry : bool) -> NoneType   Append a new residue by a bond.   3. append_residue_by_bond(self : rosetta.core.conformation.Conformation, new_rsd : rosetta.core.conformation.Residue, build_ideal_geometry : bool, connection_index : int) -> NoneType   Append a new residue by a bond.   4. append_residue_by_bond(self : rosetta.core.conformation.Conformation, new_rsd : rosetta.core.conformation.Residue, build_ideal_geometry : bool, connection_index : int, anchor_residue : int) -> NoneType   Append a new residue by a bond.   5. append_residue_by_bond(self : rosetta.core.conformation.Conformation, new_rsd : rosetta.core.conformation.Residue, build_ideal_geometry : bool, connection_index : int, anchor_residue : int, anchor_connection_index : int) -> NoneType   Append a new residue by a bond.   6. append_residue_by_bond(self : rosetta.core.conformation.Conformation, new_rsd : rosetta.core.conformation.Residue, build_ideal_geometry : bool, connection_index : int, anchor_residue : int, anchor_connection_index : int, start_new_chain : bool) -> NoneType   Append a new residue by a bond.   7. append_residue_by_bond(self : rosetta.core.conformation.Conformation, new_rsd : rosetta.core.conformation.Residue, build_ideal_geometry : bool, connection_index : int, anchor_residue : int, anchor_connection_index : int, start_new_chain : bool, lookup_bond_length : bool) -> NoneType   Append a new residue by a bond. atom_is_backbone_norefold(...) from builtins.PyCapsule atom_is_backbone_norefold(self : rosetta.core.conformation.Conformation, pos : int, atomno : int) -> bool   returns true if atom is part of backbone. atom_tree(...) from builtins.PyCapsule atom_tree(rosetta.core.conformation.Conformation) -> core::kinematics::AtomTree   Returns the conformation's AtomTree batch_get_xyz(...) from builtins.PyCapsule batch_get_xyz(self : rosetta.core.conformation.Conformation, id : rosetta.utility.vector1_core_id_AtomID, position : rosetta.utility.vector1_numeric_xyzVector_double_t) -> NoneType block_signals(...) from builtins.PyCapsule block_signals(rosetta.core.conformation.Conformation) -> NoneType   block signals from being sent blocking_signals(...) from builtins.PyCapsule blocking_signals(rosetta.core.conformation.Conformation) -> bool   are signals being blocked? bond_angle(...) from builtins.PyCapsule bond_angle(self : rosetta.core.conformation.Conformation, atom1 : rosetta.core.id.AtomID, atom2 : rosetta.core.id.AtomID, atom3 : rosetta.core.id.AtomID) -> float   Returns the bond angle defined by  <atom[1-3]> through the AtomTree bond_length(...) from builtins.PyCapsule bond_length(self : rosetta.core.conformation.Conformation, atom1 : rosetta.core.id.AtomID, atom2 : rosetta.core.id.AtomID) -> float   Returns the bond length between  <atom1>  and  <atom2> through the AtomTree bonded_neighbor_all_res(...) from builtins.PyCapsule bonded_neighbor_all_res(*args, **kwargs) Overloaded function.   1. bonded_neighbor_all_res(self : rosetta.core.conformation.Conformation, atomid : rosetta.core.id.AtomID) -> rosetta.utility.vector1_core_id_AtomID   get all atoms bonded to another   2. bonded_neighbor_all_res(self : rosetta.core.conformation.Conformation, atomid : rosetta.core.id.AtomID, virt : bool) -> rosetta.utility.vector1_core_id_AtomID   get all atoms bonded to another buffer_signals(...) from builtins.PyCapsule buffer_signals(rosetta.core.conformation.Conformation) -> NoneType   block signals from being sent and buffer them to be sent after unblocking buffering_signals(...) from builtins.PyCapsule buffering_signals(rosetta.core.conformation.Conformation) -> bool   are signals being blocked and buffered? chain_begin(...) from builtins.PyCapsule chain_begin(self : rosetta.core.conformation.Conformation, chain : int) -> int   Returns the position number of the first residue in  <chain> chain_end(...) from builtins.PyCapsule chain_end(self : rosetta.core.conformation.Conformation, chain : int) -> int   Returns the position number of the last residue in  <chain> chain_endings(...) from builtins.PyCapsule chain_endings(*args, **kwargs) Overloaded function.   1. chain_endings(rosetta.core.conformation.Conformation) -> rosetta.utility.vector1_unsigned_long   Returns the list of chain endings   2. chain_endings(self : rosetta.core.conformation.Conformation, endings : rosetta.utility.vector1_unsigned_long) -> NoneType   Sets the list of chain endings chains_from_termini(...) from builtins.PyCapsule chains_from_termini(rosetta.core.conformation.Conformation) -> NoneType   Rederive the chains from the termini/polymer status check_valid_membrane(...) from builtins.PyCapsule check_valid_membrane(rosetta.core.conformation.Conformation) -> NoneType   Check that a new membrane position is valid      Given a new membrane normal/center pair, check that the newly constructed stub represents  an orthogonal coordinate frame clear(...) from builtins.PyCapsule clear(rosetta.core.conformation.Conformation) -> NoneType   clear data clear_observers(...) from builtins.PyCapsule clear_observers(rosetta.core.conformation.Conformation) -> NoneType   clear all observers clear_parameters_set_list(...) from builtins.PyCapsule clear_parameters_set_list(rosetta.core.conformation.Conformation) -> NoneType   Delete the list of ParametersSetOP objects.      Vikram K. Mulligan (vmullig.edu) const_residues(...) from builtins.PyCapsule const_residues(rosetta.core.conformation.Conformation) -> rosetta.utility.vector1_std_shared_ptr_const_core_conformation_Residue_t   Inefficient -- constructs copy of residues_ contains_carbohydrate_residues(...) from builtins.PyCapsule contains_carbohydrate_residues(*args, **kwargs) Overloaded function.   1. contains_carbohydrate_residues(rosetta.core.conformation.Conformation) -> bool   Return true if this conformation contains any carbohydrate residues.   2. contains_carbohydrate_residues(self : rosetta.core.conformation.Conformation, setting : bool) -> NoneType   Set whether this conformation contains any carbohydrate residues. copy_segment(...) from builtins.PyCapsule copy_segment(self : rosetta.core.conformation.Conformation, size : int, src : rosetta.core.conformation.Conformation, begin : int, src_begin : int) -> NoneType   copy a stretch of coordinates/torsions from another Conformation create_new_parameters_set(...) from builtins.PyCapsule create_new_parameters_set(rosetta.core.conformation.Conformation) -> NoneType   Create a new (empty) ParametersSet object and add its owning pointer  to the current Conformation object.      Vikram K. Mulligan (vmullig.edu) debug_pause(...) from builtins.PyCapsule debug_pause(*args, **kwargs) Overloaded function.   1. debug_pause(self : rosetta.core.conformation.Conformation, flag : bool) -> NoneType   wait for stdin after sending a GeneralEvent signal   2. debug_pause(rosetta.core.conformation.Conformation) -> bool   waiting for stdin after sending a GeneralEvent signal? debug_residue_torsions(...) from builtins.PyCapsule debug_residue_torsions(*args, **kwargs) Overloaded function.   1. debug_residue_torsions(rosetta.core.conformation.Conformation) -> NoneType   debugging   2. debug_residue_torsions(self : rosetta.core.conformation.Conformation, verbose : bool) -> NoneType   debugging delete_chain_ending(...) from builtins.PyCapsule delete_chain_ending(self : rosetta.core.conformation.Conformation, seqpos : int) -> NoneType   Deletes  <seqpos>  from the list of chain endings delete_polymer_residue(...) from builtins.PyCapsule delete_polymer_residue(self : rosetta.core.conformation.Conformation, seqpos : int) -> NoneType   Delete polymer residue at the given sequence position delete_residue_range_slow(...) from builtins.PyCapsule delete_residue_range_slow(self : rosetta.core.conformation.Conformation, range_begin : int, range_end : int) -> NoneType   Slow method that relies on FoldTree::delete_seqpos, rebuilds atomtree, can handle jumps/root residue delete_residue_slow(...) from builtins.PyCapsule delete_residue_slow(self : rosetta.core.conformation.Conformation, seqpos : int) -> NoneType   Slow method that relies on FoldTree::delete_seqpos, rebuilds atomtree, can handle jumps/root residue detect_bonds(...) from builtins.PyCapsule detect_bonds(rosetta.core.conformation.Conformation) -> NoneType detect_pseudobonds(...) from builtins.PyCapsule detect_pseudobonds(rosetta.core.conformation.Conformation) -> NoneType dof(...) from builtins.PyCapsule dof(self : rosetta.core.conformation.Conformation, id : rosetta.core.id.DOF_ID) -> float   Returns the AtomTree degree of freedom (DOF)  <id> dof_id_from_torsion_id(...) from builtins.PyCapsule dof_id_from_torsion_id(self : rosetta.core.conformation.Conformation, id : core::id::TorsionID) -> rosetta.core.id.DOF_ID downstream_jump_stub(...) from builtins.PyCapsule downstream_jump_stub(self : rosetta.core.conformation.Conformation, jump_number : int) -> rosetta.core.kinematics.Stub   The upstream and downstream Stubs are the coordinate frames between which this jump is transforming empty(...) from builtins.PyCapsule empty(rosetta.core.conformation.Conformation) -> bool   Returns true if this conformation does not have any residues fill_missing_atoms(...) from builtins.PyCapsule fill_missing_atoms(self : rosetta.core.conformation.Conformation, missing : rosetta.core.id.AtomID_Map_bool_t) -> NoneType fix_disulfides(...) from builtins.PyCapsule fix_disulfides(self : rosetta.core.conformation.Conformation, disulf_bonds : rosetta.utility.vector1_std_pair_unsigned_long_unsigned_long_t) -> NoneType   Assigns disulfide bonds based on a pre-determined list get_jump_atom_ids(...) from builtins.PyCapsule get_jump_atom_ids(self : rosetta.core.conformation.Conformation, jump_number : int, upstream_id : rosetta.core.id.AtomID, downstream_id : rosetta.core.id.AtomID) -> bool   get two atoms connect by jump get_self_ptr(...) from builtins.PyCapsule get_self_ptr(*args, **kwargs) Overloaded function.   1. get_self_ptr(rosetta.core.conformation.Conformation) -> rosetta.core.conformation.Conformation   self pointers   2. get_self_ptr(rosetta.core.conformation.Conformation) -> rosetta.core.conformation.Conformation get_self_weak_ptr(...) from builtins.PyCapsule get_self_weak_ptr(*args, **kwargs) Overloaded function.   1. get_self_weak_ptr(rosetta.core.conformation.Conformation) -> rosetta.std.weak_ptr_const_core_conformation_Conformation_t   2. get_self_weak_ptr(rosetta.core.conformation.Conformation) -> rosetta.std.weak_ptr_core_conformation_Conformation_t get_stub_transform(...) from builtins.PyCapsule get_stub_transform(self : rosetta.core.conformation.Conformation, stub_id1 : rosetta.core.id.StubID, stub_id2 : rosetta.core.id.StubID) -> rosetta.core.kinematics.RT   get the transform between two stubs get_torsion_angle_atom_ids(...) from builtins.PyCapsule get_torsion_angle_atom_ids(self : rosetta.core.conformation.Conformation, tor_id : core::id::TorsionID, id1 : rosetta.core.id.AtomID, id2 : rosetta.core.id.AtomID, id3 : rosetta.core.id.AtomID, id4 : rosetta.core.id.AtomID) -> bool   get four atoms which defined this torsion has_passport(...) from builtins.PyCapsule has_passport(rosetta.core.conformation.Conformation) -> bool insert_chain_ending(...) from builtins.PyCapsule insert_chain_ending(self : rosetta.core.conformation.Conformation, seqpos : int) -> NoneType   Marks  <seqpos>  as the end of a new chain insert_ideal_geometry_at_polymer_bond(...) from builtins.PyCapsule insert_ideal_geometry_at_polymer_bond(self : rosetta.core.conformation.Conformation, seqpos : int) -> NoneType insert_ideal_geometry_at_residue_connection(...) from builtins.PyCapsule insert_ideal_geometry_at_residue_connection(self : rosetta.core.conformation.Conformation, pos1 : int, connid1 : int) -> NoneType insert_residue_by_bond(...) from builtins.PyCapsule insert_residue_by_bond(*args, **kwargs) Overloaded function.   1. insert_residue_by_bond(self : rosetta.core.conformation.Conformation, new_rsd_in : rosetta.core.conformation.Residue, seqpos : int, anchor_pos : int) -> NoneType   Insert a new residue by jump.  If new_chain is "true", then seqpos must be the last  residue of one chain (i.e. residue(seqpos).chain() != residue(seqpos+1).chain() )   2. insert_residue_by_bond(self : rosetta.core.conformation.Conformation, new_rsd_in : rosetta.core.conformation.Residue, seqpos : int, anchor_pos : int, build_ideal_geometry : bool) -> NoneType   Insert a new residue by jump.  If new_chain is "true", then seqpos must be the last  residue of one chain (i.e. residue(seqpos).chain() != residue(seqpos+1).chain() )   3. insert_residue_by_bond(self : rosetta.core.conformation.Conformation, new_rsd_in : rosetta.core.conformation.Residue, seqpos : int, anchor_pos : int, build_ideal_geometry : bool, anchor_atom : str) -> NoneType   Insert a new residue by jump.  If new_chain is "true", then seqpos must be the last  residue of one chain (i.e. residue(seqpos).chain() != residue(seqpos+1).chain() )   4. insert_residue_by_bond(self : rosetta.core.conformation.Conformation, new_rsd_in : rosetta.core.conformation.Residue, seqpos : int, anchor_pos : int, build_ideal_geometry : bool, anchor_atom : str, root_atom : str) -> NoneType   Insert a new residue by jump.  If new_chain is "true", then seqpos must be the last  residue of one chain (i.e. residue(seqpos).chain() != residue(seqpos+1).chain() )   5. insert_residue_by_bond(self : rosetta.core.conformation.Conformation, new_rsd_in : rosetta.core.conformation.Residue, seqpos : int, anchor_pos : int, build_ideal_geometry : bool, anchor_atom : str, root_atom : str, new_chain : bool) -> NoneType   Insert a new residue by jump.  If new_chain is "true", then seqpos must be the last  residue of one chain (i.e. residue(seqpos).chain() != residue(seqpos+1).chain() )   6. insert_residue_by_bond(self : rosetta.core.conformation.Conformation, new_rsd_in : rosetta.core.conformation.Residue, seqpos : int, anchor_pos : int, build_ideal_geometry : bool, anchor_atom : str, root_atom : str, new_chain : bool, lookup_bond_length : bool) -> NoneType   Insert a new residue by jump.  If new_chain is "true", then seqpos must be the last  residue of one chain (i.e. residue(seqpos).chain() != residue(seqpos+1).chain() ) insert_residue_by_jump(...) from builtins.PyCapsule insert_residue_by_jump(*args, **kwargs) Overloaded function.   1. insert_residue_by_jump(self : rosetta.core.conformation.Conformation, new_rsd_in : rosetta.core.conformation.Residue, seqpos : int, anchor_pos : int) -> NoneType   Insert a new residue by jump.  If new_chain is "true", then seqpos must be the last  residue of one chain (i.e. residue(seqpos).chain() != residue(seqpos+1).chain() )   2. insert_residue_by_jump(self : rosetta.core.conformation.Conformation, new_rsd_in : rosetta.core.conformation.Residue, seqpos : int, anchor_pos : int, anchor_atom : str) -> NoneType   Insert a new residue by jump.  If new_chain is "true", then seqpos must be the last  residue of one chain (i.e. residue(seqpos).chain() != residue(seqpos+1).chain() )   3. insert_residue_by_jump(self : rosetta.core.conformation.Conformation, new_rsd_in : rosetta.core.conformation.Residue, seqpos : int, anchor_pos : int, anchor_atom : str, root_atom : str) -> NoneType   Insert a new residue by jump.  If new_chain is "true", then seqpos must be the last  residue of one chain (i.e. residue(seqpos).chain() != residue(seqpos+1).chain() )   4. insert_residue_by_jump(self : rosetta.core.conformation.Conformation, new_rsd_in : rosetta.core.conformation.Residue, seqpos : int, anchor_pos : int, anchor_atom : str, root_atom : str, new_chain : bool) -> NoneType   Insert a new residue by jump.  If new_chain is "true", then seqpos must be the last  residue of one chain (i.e. residue(seqpos).chain() != residue(seqpos+1).chain() ) inter_residue_connection_partner(...) from builtins.PyCapsule inter_residue_connection_partner(self : rosetta.core.conformation.Conformation, seqpos : int, connection_index : int) -> rosetta.core.id.AtomID   This returns the AtomID of the atom in the other residue to which the "connection_index"-th  connection of residue seqpos is connected to. is_centroid(...) from builtins.PyCapsule is_centroid(rosetta.core.conformation.Conformation) -> bool   convenience test for residue_type_set ( based on two middle residue -- to avoid hitting on ligands or pseudos ) is_fullatom(...) from builtins.PyCapsule is_fullatom(rosetta.core.conformation.Conformation) -> bool   convenience test for residue_type_set ( based on two middle residue -- to avoid hitting on ligands or pseudos ) is_membrane(...) from builtins.PyCapsule is_membrane(rosetta.core.conformation.Conformation) -> bool   convenience test for if the conformation contains information for a membrane protein is_protected(...) from builtins.PyCapsule is_protected(rosetta.core.conformation.Conformation) -> bool is_residue_typeset(...) from builtins.PyCapsule is_residue_typeset(self : rosetta.core.conformation.Conformation, tag : str) -> bool   convenience test for residue_type_set ( based on two middle residue -- to avoid hitting on ligands or pseudos ) jump(...) from builtins.PyCapsule jump(*args, **kwargs) Overloaded function.   1. jump(self : rosetta.core.conformation.Conformation, jump_number : int) -> rosetta.core.kinematics.Jump   Returns the Jump with jump number  <jump_number>   2. jump(self : rosetta.core.conformation.Conformation, id : rosetta.core.id.AtomID) -> rosetta.core.kinematics.Jump   access a jump jump_atom_id(...) from builtins.PyCapsule jump_atom_id(self : rosetta.core.conformation.Conformation, jump_number : int) -> rosetta.core.id.AtomID membrane_info(...) from builtins.PyCapsule membrane_info(rosetta.core.conformation.Conformation) -> core::conformation::membrane::MembraneInfo   Returns the const MembraneInfo object in conformation      Membrane Info contains information describing location of the  membrane virtual residue in the pose sequence, membrane spanning region definitions  and lipid exposure/burial data n_parameters_sets(...) from builtins.PyCapsule n_parameters_sets(rosetta.core.conformation.Conformation) -> int   Get the number of parameters sets defined for this Conformation.      Vikram K. Mulligan (vmullig.edu) num_chains(...) from builtins.PyCapsule num_chains(rosetta.core.conformation.Conformation) -> int   Returns the number of chains parameters_set(...) from builtins.PyCapsule parameters_set(*args, **kwargs) Overloaded function.   1. parameters_set(self : rosetta.core.conformation.Conformation, index : int) -> rosetta.core.conformation.parametric.ParametersSet   Access one of the ParametersSets objects linked to this Conformation.      Vikram K. Mulligan (vmullig.edu)   2. parameters_set(self : rosetta.core.conformation.Conformation, index : int) -> rosetta.core.conformation.parametric.ParametersSet   Const access to one of the ParametersSets objects linked to this Conformation.      Vikram K. Mulligan (vmullig.edu) pop_passport(...) from builtins.PyCapsule pop_passport(rosetta.core.conformation.Conformation) -> core::environment::DofPassport prepend_polymer_residue_before_seqpos(...) from builtins.PyCapsule prepend_polymer_residue_before_seqpos(self : rosetta.core.conformation.Conformation, new_rsd : rosetta.core.conformation.Residue, seqpos : int, build_ideal_geometry : bool) -> NoneType   glues to seqpos and perhaps also seqpos-1 push_passport(...) from builtins.PyCapsule push_passport(self : rosetta.core.conformation.Conformation,  : core::environment::DofPassport) -> NoneType rebuild_polymer_bond_dependent_atoms(...) from builtins.PyCapsule rebuild_polymer_bond_dependent_atoms(self : rosetta.core.conformation.Conformation, seqpos : int) -> NoneType   Rebuild the atoms ( like HN(seqpos), OC(seqpos+1) ) that are dependent on the polymer bond between seqpos and seqpos+1 rebuild_polymer_bond_dependent_atoms_this_residue_only(...) from builtins.PyCapsule rebuild_polymer_bond_dependent_atoms_this_residue_only(self : rosetta.core.conformation.Conformation, seqpos : int) -> NoneType   Rebuilds the atoms that are depenent on polymer bonds for the specified residue only.      Vikram K. Mulligan (vmullig.edu) rebuild_residue_connection_dependent_atoms(...) from builtins.PyCapsule rebuild_residue_connection_dependent_atoms(self : rosetta.core.conformation.Conformation, seqpos : int, connid : int) -> NoneType receive_observers_from(...) from builtins.PyCapsule receive_observers_from(self : rosetta.core.conformation.Conformation, src : rosetta.core.conformation.Conformation) -> NoneType   fire a ConnectionEvent::TRANSFER to transfer observers from some source Conformation reset_chain_endings(...) from builtins.PyCapsule reset_chain_endings(rosetta.core.conformation.Conformation) -> NoneType   Resets chain data so that the Conformation is marked as a single chain reset_move_data(...) from builtins.PyCapsule reset_move_data(rosetta.core.conformation.Conformation) -> NoneType   forget all the structure modifications reset_structure_moved(...) from builtins.PyCapsule reset_structure_moved(rosetta.core.conformation.Conformation) -> NoneType   reset the structure_moved_ bool residue(...) from builtins.PyCapsule residue(self : rosetta.core.conformation.Conformation, seqpos : int) -> rosetta.core.conformation.Residue   access one of the residues      this access is inlined, since otherwise it  shows up in the profiler.  This will call non-inlined refold methods if necessary.      update coordinates and torsions for this and all other residues before  allowing read access residue_cop(...) from builtins.PyCapsule residue_cop(self : rosetta.core.conformation.Conformation, seqpos : int) -> rosetta.core.conformation.Residue   access one of the residues, using COP residue_op(...) from builtins.PyCapsule residue_op(self : rosetta.core.conformation.Conformation, seqpos : int) -> rosetta.core.conformation.Residue   Access one of the residues, using OP      Non-const access. residue_type(...) from builtins.PyCapsule residue_type(self : rosetta.core.conformation.Conformation, seqpos : int) -> rosetta.core.chemical.ResidueType   access one of the residue's types -- avoids coord/torsion update safely_append_polymer_residue_after_seqpos(...) from builtins.PyCapsule safely_append_polymer_residue_after_seqpos(self : rosetta.core.conformation.Conformation, new_rsd : rosetta.core.conformation.Residue, seqpos : int, build_ideal_geometry : bool) -> NoneType   glues to seqpos and perhaps also seqpos+1, removes termini variants if necessary safely_prepend_polymer_residue_before_seqpos(...) from builtins.PyCapsule safely_prepend_polymer_residue_before_seqpos(self : rosetta.core.conformation.Conformation, new_rsd : rosetta.core.conformation.Residue, seqpos : int, build_ideal_geometry : bool) -> NoneType   glues to seqpos and perhaps also seqpos-1, removes termini variants if necessary secstruct(...) from builtins.PyCapsule secstruct(self : rosetta.core.conformation.Conformation, seqpos : int) -> str   Returns the secondary structure the position  <seqpos>      character representing secondary structure; returns 'L' if the  requested sequence position is larger than the length in the  secondary structure array sequence_matches(...) from builtins.PyCapsule sequence_matches(self : rosetta.core.conformation.Conformation, other : rosetta.core.conformation.Conformation) -> bool   do the names of all residues in this and src match? set_jump_atom_stub_id(...) from builtins.PyCapsule set_jump_atom_stub_id(self : rosetta.core.conformation.Conformation, id : rosetta.core.id.StubID) -> NoneType set_membrane_info(...) from builtins.PyCapsule set_membrane_info(self : rosetta.core.conformation.Conformation, mem_info : core::conformation::membrane::MembraneInfo) -> NoneType   Setup a Membrane Info object in Conformation - pos & topology      Add a MembraneInfo object - describes the position of the  membrane virtual residue, information on membrane spanning regions,  lipid exposure/burial of residues in the pose, and fullatom steepness  and thickness parameters. At construction, specify membrane position  and list of spanning topology objects by chain. set_noncanonical_connection(...) from builtins.PyCapsule set_noncanonical_connection(self : rosetta.core.conformation.Conformation, res_id_lower : int, lr_conn_id : int, res_id_upper : int, ur_conn_id : int) -> NoneType   Create an arbitrary covalent connection between two residues. set_polymeric_connection(...) from builtins.PyCapsule set_polymeric_connection(self : rosetta.core.conformation.Conformation, res_id_lower : int, res_id_upper : int) -> NoneType   identify polymeric connections set_stub_transform(...) from builtins.PyCapsule set_stub_transform(self : rosetta.core.conformation.Conformation, stub_id1 : rosetta.core.id.StubID, stub_id2 : rosetta.core.id.StubID, target_rt : rosetta.core.kinematics.RT) -> NoneType   Set the transform between two stubs -- only works if there's a jump between the two sets of stubatoms show_residue_connections(...) from builtins.PyCapsule show_residue_connections(rosetta.core.conformation.Conformation) -> NoneType   Show residue connections for debugging purposes. size(...) from builtins.PyCapsule size(rosetta.core.conformation.Conformation) -> int   Returns the number of residues in the Conformation structure_moved(...) from builtins.PyCapsule structure_moved(rosetta.core.conformation.Conformation) -> bool   has the structure moved since the last call to reset_move_data or reset_structure_moved stub_from_id(...) from builtins.PyCapsule stub_from_id(self : rosetta.core.conformation.Conformation, id : rosetta.core.id.StubID) -> rosetta.core.kinematics.Stub torsion(...) from builtins.PyCapsule torsion(self : rosetta.core.conformation.Conformation, id : core::id::TorsionID) -> float   Return the torsion angle OR rigid-body offset for  <id> torsion_angle(...) from builtins.PyCapsule torsion_angle(self : rosetta.core.conformation.Conformation, atom1 : rosetta.core.id.AtomID, atom2 : rosetta.core.id.AtomID, atom3 : rosetta.core.id.AtomID, atom4 : rosetta.core.id.AtomID) -> float   Returns the torsion angle defined by  <atom[1-4]> unblock_signals(...) from builtins.PyCapsule unblock_signals(rosetta.core.conformation.Conformation) -> NoneType   allow signals to be sent update_actcoord(...) from builtins.PyCapsule update_actcoord(self : rosetta.core.conformation.Conformation, resid : int) -> NoneType update_actcoords(...) from builtins.PyCapsule update_actcoords(rosetta.core.conformation.Conformation) -> NoneType update_domain_map(...) from builtins.PyCapsule update_domain_map(self : rosetta.core.conformation.Conformation, domain_map : ObjexxFCL::FArray1D<int>) -> NoneType   Generate a domain_map from the current dof/xyz moved data update_membrane_position(...) from builtins.PyCapsule update_membrane_position(self : rosetta.core.conformation.Conformation, center : rosetta.numeric.xyzVector_double_t, normal : rosetta.numeric.xyzVector_double_t) -> NoneType   Update Normal, Center in the Membrane      Sets the center and normal coordinates to the appropriate  parameters and checks for a valid stub prior to returning. update_noncanonical_connection(...) from builtins.PyCapsule update_noncanonical_connection(self : rosetta.core.conformation.Conformation, lower_seqpos : int, lr_conn_id : int, upper_seqpos : int, ur_conn_id : int) -> NoneType   Update the connection status between the lower_seqpos residue's lr_conn_id connection ID and  the upper_seqpos residue's ur_conn_id connection ID. update_orbital_coords(...) from builtins.PyCapsule update_orbital_coords(*args, **kwargs) Overloaded function.   1. update_orbital_coords(self : rosetta.core.conformation.Conformation, rsd : rosetta.core.conformation.Residue) -> NoneType   2. update_orbital_coords(self : rosetta.core.conformation.Conformation, resid : int) -> NoneType update_polymeric_connection(...) from builtins.PyCapsule update_polymeric_connection(*args, **kwargs) Overloaded function.   1. update_polymeric_connection(self : rosetta.core.conformation.Conformation, lower_seqpos : int) -> NoneType   Update the polymer connection status between lower_seqpos and lower_seqpos+1  based on chainID's and termini.  If update_connection_dep_atoms is true, positions of  atoms dependent on the polymer connection are updated.   2. update_polymeric_connection(self : rosetta.core.conformation.Conformation, lower_seqpos : int, update_connection_dep_atoms : bool) -> NoneType   Update the polymer connection status between lower_seqpos and lower_seqpos+1  based on chainID's and termini.  If update_connection_dep_atoms is true, positions of  atoms dependent on the polymer connection are updated. upstream_jump_stub(...) from builtins.PyCapsule upstream_jump_stub(self : rosetta.core.conformation.Conformation, jump_number : int) -> rosetta.core.kinematics.Stub   The upstream and downstream Stubs are the coordinate frames between which this jump is transforming xyz(...) from builtins.PyCapsule xyz(self : rosetta.core.conformation.Conformation, id : rosetta.core.id.AtomID) -> rosetta.numeric.xyzVector_double_t   access xyz coordinates of an atom   class SlideCriteriaType(builtins.object)       Methods defined here: __eq__(...) from builtins.PyCapsule __eq__(rosetta.core.conformation.symmetry.SlideCriteriaType, rosetta.core.conformation.symmetry.SlideCriteriaType) -> bool __hash__(...) from builtins.PyCapsule __hash__(rosetta.core.conformation.symmetry.SlideCriteriaType) -> int __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.core.conformation.symmetry.SlideCriteriaType, int) -> NoneType   2. __init__(rosetta.core.conformation.symmetry.SlideCriteriaType, int) -> NoneType __int__(...) from builtins.PyCapsule __int__(rosetta.core.conformation.symmetry.SlideCriteriaType) -> int __ne__(...) from builtins.PyCapsule __ne__(rosetta.core.conformation.symmetry.SlideCriteriaType, rosetta.core.conformation.symmetry.SlideCriteriaType) -> 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.conformation.symmetry.SlideCriteriaType) -> str Data and other attributes defined here: CEN_DOCK_SCORE = SlideCriteriaType.CEN_DOCK_SCORE CONTACTS = SlideCriteriaType.CONTACTS FA_REP_SCORE = SlideCriteriaType.FA_REP_SCORE TOTAL_NUM_CRITERIA = SlideCriteriaType.TOTAL_NUM_CRITERIA   class SlideType(builtins.object)       Methods defined here: __eq__(...) from builtins.PyCapsule __eq__(rosetta.core.conformation.symmetry.SlideType, rosetta.core.conformation.symmetry.SlideType) -> bool __hash__(...) from builtins.PyCapsule __hash__(rosetta.core.conformation.symmetry.SlideType) -> int __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.core.conformation.symmetry.SlideType, int) -> NoneType   2. __init__(rosetta.core.conformation.symmetry.SlideType, int) -> NoneType __int__(...) from builtins.PyCapsule __int__(rosetta.core.conformation.symmetry.SlideType) -> int __ne__(...) from builtins.PyCapsule __ne__(rosetta.core.conformation.symmetry.SlideType, rosetta.core.conformation.symmetry.SlideType) -> 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.conformation.symmetry.SlideType) -> str Data and other attributes defined here: ORDERED_SEQUENTIAL = SlideType.ORDERED_SEQUENTIAL RANDOM = SlideType.RANDOM SEQUENTIAL = SlideType.SEQUENTIAL   class SymDof(builtins.object)       Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.core.conformation.symmetry.SymDof) -> NoneType   2. __init__(self : rosetta.core.conformation.symmetry.SymDof, src : rosetta.core.conformation.symmetry.SymDof) -> 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.conformation.symmetry.SymDof) -> str add_dof_from_string(...) from builtins.PyCapsule add_dof_from_string(self : rosetta.core.conformation.symmetry.SymDof, dof_string : rosetta.utility.vector1_std_string) -> NoneType allow_dof(...) from builtins.PyCapsule allow_dof(self : rosetta.core.conformation.symmetry.SymDof, df : int) -> bool assign(...) from builtins.PyCapsule assign(self : rosetta.core.conformation.symmetry.SymDof, src : rosetta.core.conformation.symmetry.SymDof) -> rosetta.core.conformation.symmetry.SymDof has_dof(...) from builtins.PyCapsule has_dof(rosetta.core.conformation.symmetry.SymDof) -> bool has_range1(...) from builtins.PyCapsule has_range1(self : rosetta.core.conformation.symmetry.SymDof, df : int) -> bool has_range1_lower(...) from builtins.PyCapsule has_range1_lower(self : rosetta.core.conformation.symmetry.SymDof, df : int) -> bool has_range1_upper(...) from builtins.PyCapsule has_range1_upper(self : rosetta.core.conformation.symmetry.SymDof, df : int) -> bool has_range2(...) from builtins.PyCapsule has_range2(self : rosetta.core.conformation.symmetry.SymDof, df : int) -> bool has_range2_lower(...) from builtins.PyCapsule has_range2_lower(self : rosetta.core.conformation.symmetry.SymDof, df : int) -> bool has_range2_upper(...) from builtins.PyCapsule has_range2_upper(self : rosetta.core.conformation.symmetry.SymDof, df : int) -> bool jump_direction(...) from builtins.PyCapsule jump_direction(self : rosetta.core.conformation.symmetry.SymDof, df : int) -> int range1_lower(...) from builtins.PyCapsule range1_lower(self : rosetta.core.conformation.symmetry.SymDof, df : int) -> float range1_upper(...) from builtins.PyCapsule range1_upper(self : rosetta.core.conformation.symmetry.SymDof, df : int) -> float range2_is_bound(...) from builtins.PyCapsule range2_is_bound(self : rosetta.core.conformation.symmetry.SymDof, df : int) -> bool range2_lower(...) from builtins.PyCapsule range2_lower(self : rosetta.core.conformation.symmetry.SymDof, df : int) -> float range2_upper(...) from builtins.PyCapsule range2_upper(self : rosetta.core.conformation.symmetry.SymDof, df : int) -> float read(...) from builtins.PyCapsule read(self : rosetta.core.conformation.symmetry.SymDof, dof_line : str) -> NoneType set_allow_dof(...) from builtins.PyCapsule set_allow_dof(self : rosetta.core.conformation.symmetry.SymDof, df : int, newval : bool) -> NoneType   class SymSlideInfo(builtins.object)       Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.core.conformation.symmetry.SymSlideInfo) -> NoneType   2. __init__(self : rosetta.core.conformation.symmetry.SymSlideInfo, src : rosetta.core.conformation.symmetry.SymSlideInfo) -> 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.conformation.symmetry.SymSlideInfo, src : rosetta.core.conformation.symmetry.SymSlideInfo) -> rosetta.core.conformation.symmetry.SymSlideInfo get_SlideCriteriaType(...) from builtins.PyCapsule get_SlideCriteriaType(rosetta.core.conformation.symmetry.SymSlideInfo) -> rosetta.core.conformation.symmetry.SlideCriteriaType get_SlideCriteriaVal(...) from builtins.PyCapsule get_SlideCriteriaVal(rosetta.core.conformation.symmetry.SymSlideInfo) -> str get_slide_order(...) from builtins.PyCapsule get_slide_order(rosetta.core.conformation.symmetry.SymSlideInfo) -> rosetta.std.vector_unsigned_long get_slide_type(...) from builtins.PyCapsule get_slide_type(rosetta.core.conformation.symmetry.SymSlideInfo) -> rosetta.core.conformation.symmetry.SlideType set_SlideCriteriaType(...) from builtins.PyCapsule set_SlideCriteriaType(self : rosetta.core.conformation.symmetry.SymSlideInfo, score_criteria : rosetta.core.conformation.symmetry.SlideCriteriaType) -> NoneType set_SlideCriteriaVal(...) from builtins.PyCapsule set_SlideCriteriaVal(self : rosetta.core.conformation.symmetry.SymSlideInfo, SlideCriteriaVal : str) -> NoneType set_slide_order(...) from builtins.PyCapsule set_slide_order(self : rosetta.core.conformation.symmetry.SymSlideInfo, slide_order : rosetta.std.vector_unsigned_long) -> NoneType set_slide_type(...) from builtins.PyCapsule set_slide_type(self : rosetta.core.conformation.symmetry.SymSlideInfo, slide_type : rosetta.core.conformation.symmetry.SlideType) -> NoneType   class SymmData(builtins.object)       Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.core.conformation.symmetry.SymmData) -> NoneType   2. __init__(self : rosetta.core.conformation.symmetry.SymmData, nres : int, njump : int) -> NoneType   3. __init__(self : rosetta.core.conformation.symmetry.SymmData,  : rosetta.core.conformation.symmetry.SymmData) -> 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.conformation.symmetry.SymmData,  : rosetta.core.conformation.symmetry.SymmData) -> rosetta.core.conformation.symmetry.SymmData clone(...) from builtins.PyCapsule clone(rosetta.core.conformation.symmetry.SymmData) -> rosetta.core.conformation.symmetry.SymmData components_moved_by_jump(...) from builtins.PyCapsule components_moved_by_jump(self : rosetta.core.conformation.symmetry.SymmData, jname : str) -> rosetta.utility.vector1_char get_anchor_residue(...) from builtins.PyCapsule get_anchor_residue(rosetta.core.conformation.symmetry.SymmData) -> str get_components(...) from builtins.PyCapsule get_components(rosetta.core.conformation.symmetry.SymmData) -> rosetta.utility.vector1_char get_dofs(...) from builtins.PyCapsule get_dofs(rosetta.core.conformation.symmetry.SymmData) -> rosetta.std.map_unsigned_long_core_conformation_symmetry_SymDof get_include_subunit(...) from builtins.PyCapsule get_include_subunit(rosetta.core.conformation.symmetry.SymmData) -> rosetta.utility.vector1_unsigned_long get_interfaces(...) from builtins.PyCapsule get_interfaces(rosetta.core.conformation.symmetry.SymmData) -> int get_jump_clones(...) from builtins.PyCapsule get_jump_clones(rosetta.core.conformation.symmetry.SymmData) -> rosetta.std.map_unsigned_long_utility_vector1_std_pair_unsigned_long_double_std_allocator_std_pair_unsigned_long_double_t get_jump_name_to_components(...) from builtins.PyCapsule get_jump_name_to_components(rosetta.core.conformation.symmetry.SymmData) -> rosetta.std.map_std_string_utility_vector1_char_std_allocator_char_t get_jump_name_to_subunits(...) from builtins.PyCapsule get_jump_name_to_subunits(rosetta.core.conformation.symmetry.SymmData) -> rosetta.std.map_std_string_utility_vector1_unsigned_long_std_allocator_unsigned_long_t get_jump_string_to_jump_num(...) from builtins.PyCapsule get_jump_string_to_jump_num(rosetta.core.conformation.symmetry.SymmData) -> rosetta.std.map_std_string_unsigned_long get_least_common_ancertor_jump(...) from builtins.PyCapsule get_least_common_ancertor_jump(self : rosetta.core.conformation.symmetry.SymmData, jname1 : str, jname2 : str) -> str get_least_common_ancertor_virtual(...) from builtins.PyCapsule get_least_common_ancertor_virtual(self : rosetta.core.conformation.symmetry.SymmData, vname1 : str, vname2 : str) -> str get_num_components(...) from builtins.PyCapsule get_num_components(rosetta.core.conformation.symmetry.SymmData) -> int get_num_virtual(...) from builtins.PyCapsule get_num_virtual(rosetta.core.conformation.symmetry.SymmData) -> int get_output_subunit(...) from builtins.PyCapsule get_output_subunit(rosetta.core.conformation.symmetry.SymmData) -> rosetta.utility.vector1_unsigned_long get_parent_jump(...) from builtins.PyCapsule get_parent_jump(self : rosetta.core.conformation.symmetry.SymmData, jname : str) -> str get_parent_virtual(...) from builtins.PyCapsule get_parent_virtual(self : rosetta.core.conformation.symmetry.SymmData, vname : str) -> str get_recenter(...) from builtins.PyCapsule get_recenter(rosetta.core.conformation.symmetry.SymmData) -> bool get_root(...) from builtins.PyCapsule get_root(rosetta.core.conformation.symmetry.SymmData) -> int get_rotation_matrix(...) from builtins.PyCapsule get_rotation_matrix(rosetta.core.conformation.symmetry.SymmData) -> rosetta.std.vector_numeric_xyzMatrix_double_t get_score_multiply_subunit(...) from builtins.PyCapsule get_score_multiply_subunit(rosetta.core.conformation.symmetry.SymmData) -> rosetta.utility.vector1_unsigned_long get_score_subunit(...) from builtins.PyCapsule get_score_subunit(rosetta.core.conformation.symmetry.SymmData) -> int get_slide_info(...) from builtins.PyCapsule get_slide_info(rosetta.core.conformation.symmetry.SymmData) -> rosetta.core.conformation.symmetry.SymSlideInfo get_subunit_name_to_component(...) from builtins.PyCapsule get_subunit_name_to_component(rosetta.core.conformation.symmetry.SymmData) -> rosetta.std.map_std_string_char get_subunit_num_to_virt_id(...) from builtins.PyCapsule get_subunit_num_to_virt_id(rosetta.core.conformation.symmetry.SymmData) -> rosetta.std.map_unsigned_long_std_string get_subunits(...) from builtins.PyCapsule get_subunits(rosetta.core.conformation.symmetry.SymmData) -> int get_symmetry_name(...) from builtins.PyCapsule get_symmetry_name(rosetta.core.conformation.symmetry.SymmData) -> str get_symmetry_type(...) from builtins.PyCapsule get_symmetry_type(rosetta.core.conformation.symmetry.SymmData) -> str get_translation_matrix(...) from builtins.PyCapsule get_translation_matrix(rosetta.core.conformation.symmetry.SymmData) -> rosetta.std.vector_numeric_xyzMatrix_double_t get_virt_id_to_subunit_chain(...) from builtins.PyCapsule get_virt_id_to_subunit_chain(rosetta.core.conformation.symmetry.SymmData) -> rosetta.std.map_std_string_char get_virt_id_to_subunit_num(...) from builtins.PyCapsule get_virt_id_to_subunit_num(rosetta.core.conformation.symmetry.SymmData) -> rosetta.std.map_std_string_unsigned_long get_virt_id_to_subunit_residue(...) from builtins.PyCapsule get_virt_id_to_subunit_residue(rosetta.core.conformation.symmetry.SymmData) -> rosetta.std.map_std_string_std_string get_virtual_connects(...) from builtins.PyCapsule get_virtual_connects(rosetta.core.conformation.symmetry.SymmData) -> rosetta.std.map_std_string_std_pair_std_string_std_string_t get_virtual_coordinates(...) from builtins.PyCapsule get_virtual_coordinates(rosetta.core.conformation.symmetry.SymmData) -> rosetta.std.map_std_string_core_conformation_symmetry_VirtualCoordinate get_virtual_id_to_num(...) from builtins.PyCapsule get_virtual_id_to_num(rosetta.core.conformation.symmetry.SymmData) -> rosetta.std.map_std_string_unsigned_long get_virtual_num_to_id(...) from builtins.PyCapsule get_virtual_num_to_id(rosetta.core.conformation.symmetry.SymmData) -> rosetta.std.map_unsigned_long_std_string is_ancestor_virtual(...) from builtins.PyCapsule is_ancestor_virtual(self : rosetta.core.conformation.symmetry.SymmData, ancestor : str, child : str) -> bool read_symmetry_data_from_file(...) from builtins.PyCapsule read_symmetry_data_from_file(self : rosetta.core.conformation.symmetry.SymmData, filename : str) -> NoneType sanity_check(...) from builtins.PyCapsule sanity_check(rosetta.core.conformation.symmetry.SymmData) -> NoneType set_anchor_residue(...) from builtins.PyCapsule set_anchor_residue(self : rosetta.core.conformation.symmetry.SymmData, anchor : str) -> NoneType set_interfaces(...) from builtins.PyCapsule set_interfaces(self : rosetta.core.conformation.symmetry.SymmData, interfaces : int) -> NoneType set_rotation_matrix(...) from builtins.PyCapsule set_rotation_matrix(self : rosetta.core.conformation.symmetry.SymmData, rotation_matrices : rosetta.std.vector_numeric_xyzMatrix_double_t) -> NoneType set_score_multiply_subunit(...) from builtins.PyCapsule set_score_multiply_subunit(self : rosetta.core.conformation.symmetry.SymmData, score_multiply_vector : rosetta.utility.vector1_double) -> NoneType set_slide_info(...) from builtins.PyCapsule set_slide_info(self : rosetta.core.conformation.symmetry.SymmData, slide_info : rosetta.core.conformation.symmetry.SymSlideInfo) -> NoneType set_subunits(...) from builtins.PyCapsule set_subunits(self : rosetta.core.conformation.symmetry.SymmData, num_subunits : int) -> NoneType set_symm_transforms(...) from builtins.PyCapsule set_symm_transforms(self : rosetta.core.conformation.symmetry.SymmData, symm_transforms : rosetta.std.vector_std_vector_std_string_std_allocator_std_string_t) -> NoneType set_symmetry_name(...) from builtins.PyCapsule set_symmetry_name(self : rosetta.core.conformation.symmetry.SymmData, symm_name : str) -> NoneType set_symmetry_type(...) from builtins.PyCapsule set_symmetry_type(self : rosetta.core.conformation.symmetry.SymmData, symm_type : str) -> NoneType set_translation_matrix(...) from builtins.PyCapsule set_translation_matrix(self : rosetta.core.conformation.symmetry.SymmData, translation_matrices : rosetta.std.vector_numeric_xyzMatrix_double_t) -> NoneType show(...) from builtins.PyCapsule show(rosetta.core.conformation.symmetry.SymmData) -> NoneType subunits_moved_by_jump(...) from builtins.PyCapsule subunits_moved_by_jump(self : rosetta.core.conformation.symmetry.SymmData, jname : str) -> rosetta.utility.vector1_unsigned_long   class SymmDataLoader(rosetta.basic.resource_manager.ResourceLoader)       Method resolution order: SymmDataLoader rosetta.basic.resource_manager.ResourceLoader builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(handle) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. assign(...) from builtins.PyCapsule assign(self : rosetta.core.conformation.symmetry.SymmDataLoader,  : rosetta.core.conformation.symmetry.SymmDataLoader) -> rosetta.core.conformation.symmetry.SymmDataLoader default_options(...) from builtins.PyCapsule default_options(rosetta.core.conformation.symmetry.SymmDataLoader) -> rosetta.basic.resource_manager.ResourceOptions   class SymmDataLoaderCreator(rosetta.basic.resource_manager.ResourceLoaderCreator)       Method resolution order: SymmDataLoaderCreator rosetta.basic.resource_manager.ResourceLoaderCreator builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(handle) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. assign(...) from builtins.PyCapsule assign(self : rosetta.core.conformation.symmetry.SymmDataLoaderCreator,  : rosetta.core.conformation.symmetry.SymmDataLoaderCreator) -> rosetta.core.conformation.symmetry.SymmDataLoaderCreator create_resource_loader(...) from builtins.PyCapsule create_resource_loader(rosetta.core.conformation.symmetry.SymmDataLoaderCreator) -> rosetta.basic.resource_manager.ResourceLoader loader_type(...) from builtins.PyCapsule loader_type(rosetta.core.conformation.symmetry.SymmDataLoaderCreator) -> str   class SymmDataOptions(rosetta.basic.resource_manager.ResourceOptions)       Method resolution order: SymmDataOptions rosetta.basic.resource_manager.ResourceOptions builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle) -> NoneType   2. __init__(self : handle, name : str) -> NoneType   3. __init__(handle, rosetta.core.conformation.symmetry.SymmDataOptions) -> 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.conformation.symmetry.SymmDataOptions,  : rosetta.core.conformation.symmetry.SymmDataOptions) -> rosetta.core.conformation.symmetry.SymmDataOptions parse_my_tag(...) from builtins.PyCapsule parse_my_tag(self : rosetta.core.conformation.symmetry.SymmDataOptions,  : utility::tag::Tag) -> NoneType type(...) from builtins.PyCapsule type(rosetta.core.conformation.symmetry.SymmDataOptions) -> str Methods inherited from rosetta.basic.resource_manager.ResourceOptions: __str__(...) from builtins.PyCapsule __str__(rosetta.basic.resource_manager.ResourceOptions) -> str name(...) from builtins.PyCapsule name(*args, **kwargs) Overloaded function.   1. name(rosetta.basic.resource_manager.ResourceOptions) -> str   A name given to a particular ResourceOptions instance.  This function allows for better error message delivery.   2. name(self : rosetta.basic.resource_manager.ResourceOptions, setting : str) -> NoneType   Set the name for this %ResoureOptions instance.   class SymmDataOptionsCreator(rosetta.basic.resource_manager.ResourceOptionsCreator)       Method resolution order: SymmDataOptionsCreator rosetta.basic.resource_manager.ResourceOptionsCreator builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(handle) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. assign(...) from builtins.PyCapsule assign(self : rosetta.core.conformation.symmetry.SymmDataOptionsCreator,  : rosetta.core.conformation.symmetry.SymmDataOptionsCreator) -> rosetta.core.conformation.symmetry.SymmDataOptionsCreator create_options(...) from builtins.PyCapsule create_options(rosetta.core.conformation.symmetry.SymmDataOptionsCreator) -> rosetta.basic.resource_manager.ResourceOptions options_type(...) from builtins.PyCapsule options_type(rosetta.core.conformation.symmetry.SymmDataOptionsCreator) -> str   class SymmetricConformation(rosetta.core.conformation.Conformation)     A symmetric conformation: has an additional data member "SymmetryInfo" class     Handles symmetrizing of *some* of the conformation-changing methods of Conformation     Method resolution order: SymmetricConformation rosetta.core.conformation.Conformation builtins.object Methods defined here: Symmetry_Info(...) from builtins.PyCapsule Symmetry_Info(*args, **kwargs) Overloaded function.   1. Symmetry_Info(rosetta.core.conformation.symmetry.SymmetricConformation) -> core::conformation::symmetry::SymmetryInfo   2. Symmetry_Info(rosetta.core.conformation.symmetry.SymmetricConformation) -> core::conformation::symmetry::SymmetryInfo __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle) -> NoneType   2. __init__(self : handle, conf : rosetta.core.conformation.Conformation, symm_info : core::conformation::symmetry::SymmetryInfo) -> NoneType   3. __init__(handle, rosetta.core.conformation.symmetry.SymmetricConformation) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. append_residue_by_jump(...) from builtins.PyCapsule append_residue_by_jump(*args, **kwargs) Overloaded function.   1. append_residue_by_jump(self : rosetta.core.conformation.symmetry.SymmetricConformation, new_rsd : rosetta.core.conformation.Residue, anchor_residue : int) -> NoneType   Append a new residue by a jump; clones this append to all copies   2. append_residue_by_jump(self : rosetta.core.conformation.symmetry.SymmetricConformation, new_rsd : rosetta.core.conformation.Residue, anchor_residue : int, anchor_atom : str) -> NoneType   Append a new residue by a jump; clones this append to all copies   3. append_residue_by_jump(self : rosetta.core.conformation.symmetry.SymmetricConformation, new_rsd : rosetta.core.conformation.Residue, anchor_residue : int, anchor_atom : str, root_atom : str) -> NoneType   Append a new residue by a jump; clones this append to all copies   4. append_residue_by_jump(self : rosetta.core.conformation.symmetry.SymmetricConformation, new_rsd : rosetta.core.conformation.Residue, anchor_residue : int, anchor_atom : str, root_atom : str, start_new_chain : bool) -> NoneType   Append a new residue by a jump; clones this append to all copies apply_transform_Rx_plus_v(...) from builtins.PyCapsule apply_transform_Rx_plus_v(self : rosetta.core.conformation.symmetry.SymmetricConformation, R : rosetta.numeric.xyzMatrix_double_t, v : rosetta.numeric.xyzVector_double_t) -> NoneType apply_transformation(...) from builtins.PyCapsule apply_transformation(*args, **kwargs) Overloaded function.   1. apply_transformation(self : rosetta.core.conformation.symmetry.SymmetricConformation, Xin : rosetta.numeric.xyzVector_double_t, residfrom : int, residto : int) -> rosetta.numeric.xyzVector_double_t   Remap coordinate X from resid i's frame to resid j's frame   2. apply_transformation(self : rosetta.core.conformation.symmetry.SymmetricConformation, Xin : rosetta.numeric.xyzVector_double_t, residfrom : int, residto : int, rotationonly : bool) -> rosetta.numeric.xyzVector_double_t   Remap coordinate X from resid i's frame to resid j's frame apply_transformation_norecompute(...) from builtins.PyCapsule apply_transformation_norecompute(*args, **kwargs) Overloaded function.   1. apply_transformation_norecompute(self : rosetta.core.conformation.symmetry.SymmetricConformation, Xin : rosetta.numeric.xyzVector_double_t, residfrom : int, residto : int) -> rosetta.numeric.xyzVector_double_t   Remap coordinate X from resid i's frame to resid j's frame    assumes that the transformations are already computed (thus can be const)   2. apply_transformation_norecompute(self : rosetta.core.conformation.symmetry.SymmetricConformation, Xin : rosetta.numeric.xyzVector_double_t, residfrom : int, residto : int, rotationonly : bool) -> rosetta.numeric.xyzVector_double_t   Remap coordinate X from resid i's frame to resid j's frame    assumes that the transformations are already computed (thus can be const) assign(...) from builtins.PyCapsule assign(*args, **kwargs) Overloaded function.   1. assign(self : rosetta.core.conformation.symmetry.SymmetricConformation, src : rosetta.core.conformation.Conformation) -> rosetta.core.conformation.Conformation   virtual assignment operator   2. assign(self : rosetta.core.conformation.symmetry.SymmetricConformation,  : rosetta.core.conformation.symmetry.SymmetricConformation) -> rosetta.core.conformation.symmetry.SymmetricConformation batch_set_xyz(...) from builtins.PyCapsule batch_set_xyz(self : rosetta.core.conformation.symmetry.SymmetricConformation, ids : rosetta.utility.vector1_core_id_AtomID, positions : rosetta.utility.vector1_numeric_xyzVector_double_t) -> NoneType   Symmetric batch_set_xyz clone(...) from builtins.PyCapsule clone(rosetta.core.conformation.symmetry.SymmetricConformation) -> rosetta.core.conformation.Conformation declare_chemical_bond(...) from builtins.PyCapsule declare_chemical_bond(self : rosetta.core.conformation.symmetry.SymmetricConformation, seqpos1 : int, atom_name1 : str, seqpos2 : int, atom_name2 : str) -> NoneType   Declare that a chemical bond exists between two residues      This updates all symmetry copies, so that each one has a chemical  bond between the residues in question.      Frank DiMaio.      Rewritten by Vikram K. Mulligan (vmullig.edu). detached_copy(...) from builtins.PyCapsule detached_copy(self : rosetta.core.conformation.symmetry.SymmetricConformation, src : rosetta.core.conformation.Conformation) -> NoneType detect_disulfides(...) from builtins.PyCapsule detect_disulfides(*args, **kwargs) Overloaded function.   1. detect_disulfides(rosetta.core.conformation.symmetry.SymmetricConformation) -> NoneType   2. detect_disulfides(self : rosetta.core.conformation.symmetry.SymmetricConformation, disulf_one : rosetta.utility.vector1_unsigned_long) -> NoneType   3. detect_disulfides(self : rosetta.core.conformation.symmetry.SymmetricConformation, disulf_one : rosetta.utility.vector1_unsigned_long, disulf_two : rosetta.utility.vector1_unsigned_long) -> NoneType fold_tree(...) from builtins.PyCapsule fold_tree(*args, **kwargs) Overloaded function.   1. fold_tree(self : rosetta.core.conformation.symmetry.SymmetricConformation, fold_tree_in : rosetta.core.kinematics.FoldTree) -> NoneType   set the fold_tree .. update symminfo if jump numbering changed   2. fold_tree(rosetta.core.conformation.symmetry.SymmetricConformation) -> rosetta.core.kinematics.FoldTree   FoldTree access get_residue_mask(...) from builtins.PyCapsule get_residue_mask(rosetta.core.conformation.symmetry.SymmetricConformation) -> rosetta.utility.vector1_bool get_residue_weight(...) from builtins.PyCapsule get_residue_weight(self : rosetta.core.conformation.symmetry.SymmetricConformation, resid1 : int, resid2 : int) -> float get_transformation(...) from builtins.PyCapsule get_transformation(self : rosetta.core.conformation.symmetry.SymmetricConformation, resid : int) -> rosetta.numeric.HomogeneousTransform_double_t   Get the transformation controlling resid i insert_conformation_by_jump(...) from builtins.PyCapsule insert_conformation_by_jump(*args, **kwargs) Overloaded function.   1. insert_conformation_by_jump(self : rosetta.core.conformation.symmetry.SymmetricConformation, conf : rosetta.core.conformation.Conformation, insert_seqpos : int, insert_jumppos : int, anchor_pos : int) -> NoneType   Append a new conformation by a jump; clones this append to all copies   2. insert_conformation_by_jump(self : rosetta.core.conformation.symmetry.SymmetricConformation, conf : rosetta.core.conformation.Conformation, insert_seqpos : int, insert_jumppos : int, anchor_pos : int, anchor_jump_number : int) -> NoneType   Append a new conformation by a jump; clones this append to all copies   3. insert_conformation_by_jump(self : rosetta.core.conformation.symmetry.SymmetricConformation, conf : rosetta.core.conformation.Conformation, insert_seqpos : int, insert_jumppos : int, anchor_pos : int, anchor_jump_number : int, anchor_atom : str) -> NoneType   Append a new conformation by a jump; clones this append to all copies   4. insert_conformation_by_jump(self : rosetta.core.conformation.symmetry.SymmetricConformation, conf : rosetta.core.conformation.Conformation, insert_seqpos : int, insert_jumppos : int, anchor_pos : int, anchor_jump_number : int, anchor_atom : str, root_atom : str) -> NoneType   Append a new conformation by a jump; clones this append to all copies recalculate_transforms(...) from builtins.PyCapsule recalculate_transforms(rosetta.core.conformation.symmetry.SymmetricConformation) -> NoneType replace_residue(...) from builtins.PyCapsule replace_residue(*args, **kwargs) Overloaded function.   1. replace_residue(self : rosetta.core.conformation.symmetry.SymmetricConformation, seqpos : int, new_rsd : rosetta.core.conformation.Residue, orient_backbone : bool) -> NoneType   replace residue   2. replace_residue(self : rosetta.core.conformation.symmetry.SymmetricConformation, seqpos : int, new_rsd : rosetta.core.conformation.Residue, atom_pairs : rosetta.utility.vector1_std_pair_std_string_std_string_t) -> NoneType same_type_as_me(...) from builtins.PyCapsule same_type_as_me(self : rosetta.core.conformation.symmetry.SymmetricConformation, other : rosetta.core.conformation.Conformation, recurse : bool) -> bool set_bond_angle(...) from builtins.PyCapsule set_bond_angle(self : rosetta.core.conformation.symmetry.SymmetricConformation, atom1 : rosetta.core.id.AtomID, atom2 : rosetta.core.id.AtomID, atom3 : rosetta.core.id.AtomID, setting : float) -> NoneType set_bond_length(...) from builtins.PyCapsule set_bond_length(self : rosetta.core.conformation.symmetry.SymmetricConformation, atom1 : rosetta.core.id.AtomID, atom2 : rosetta.core.id.AtomID, setting : float) -> NoneType set_dof(...) from builtins.PyCapsule set_dof(self : rosetta.core.conformation.symmetry.SymmetricConformation, id : rosetta.core.id.DOF_ID, setting : float) -> NoneType   DOF set_jump(...) from builtins.PyCapsule set_jump(*args, **kwargs) Overloaded function.   1. set_jump(self : rosetta.core.conformation.symmetry.SymmetricConformation, jump_number : int, new_jump : rosetta.core.kinematics.Jump) -> NoneType   JUMPS      set a jump   2. set_jump(self : rosetta.core.conformation.symmetry.SymmetricConformation, id : rosetta.core.id.AtomID, new_jump : rosetta.core.kinematics.Jump) -> NoneType   set a jump set_secstruct(...) from builtins.PyCapsule set_secstruct(self : rosetta.core.conformation.symmetry.SymmetricConformation, seqpos : int, setting : str) -> NoneType set_torsion(...) from builtins.PyCapsule set_torsion(self : rosetta.core.conformation.symmetry.SymmetricConformation, id : core::id::TorsionID, setting : float) -> NoneType   BONDS/TORSIONS set_torsion_angle(...) from builtins.PyCapsule set_torsion_angle(*args, **kwargs) Overloaded function.   1. set_torsion_angle(self : rosetta.core.conformation.symmetry.SymmetricConformation, atom1 : rosetta.core.id.AtomID, atom2 : rosetta.core.id.AtomID, atom3 : rosetta.core.id.AtomID, atom4 : rosetta.core.id.AtomID, setting : float) -> NoneType   2. set_torsion_angle(self : rosetta.core.conformation.symmetry.SymmetricConformation, atom1 : rosetta.core.id.AtomID, atom2 : rosetta.core.id.AtomID, atom3 : rosetta.core.id.AtomID, atom4 : rosetta.core.id.AtomID, setting : float, quiet : bool) -> NoneType set_xyz(...) from builtins.PyCapsule set_xyz(self : rosetta.core.conformation.symmetry.SymmetricConformation, id : rosetta.core.id.AtomID, position : rosetta.numeric.xyzVector_double_t) -> NoneType   Symmetric set_xyz Methods inherited from rosetta.core.conformation.Conformation: __str__(...) from builtins.PyCapsule __str__(rosetta.core.conformation.Conformation) -> str aa(...) from builtins.PyCapsule aa(self : rosetta.core.conformation.Conformation, seqpos : int) -> rosetta.core.chemical.AA   Returns the AA enum for position  <seqpos> add_parameters_set(...) from builtins.PyCapsule add_parameters_set(self : rosetta.core.conformation.Conformation, newset : rosetta.core.conformation.parametric.ParametersSet) -> NoneType   Add a (predefined) ParametersSet object (via its owning pointer)  to the current Conformation object.      Vikram K. Mulligan (vmullig.edu) annotated_sequence(...) from builtins.PyCapsule annotated_sequence(self : rosetta.core.conformation.Conformation, show_all_variants : bool) -> str   Returns the variant-tagged string representing the  residue types that make up a conformation; e.g.  M[MET:N-Terminus-Variant]CDH[HIS_D]LLR[ARG:C-Terminus-Variant] append_polymer_residue_after_seqpos(...) from builtins.PyCapsule append_polymer_residue_after_seqpos(self : rosetta.core.conformation.Conformation, new_rsd : rosetta.core.conformation.Residue, seqpos : int, build_ideal_geometry : bool) -> NoneType   glues to seqpos and perhaps also seqpos+1 append_residue_by_bond(...) from builtins.PyCapsule append_residue_by_bond(*args, **kwargs) Overloaded function.   1. append_residue_by_bond(self : rosetta.core.conformation.Conformation, new_rsd : rosetta.core.conformation.Residue) -> NoneType   Append a new residue by a bond.   2. append_residue_by_bond(self : rosetta.core.conformation.Conformation, new_rsd : rosetta.core.conformation.Residue, build_ideal_geometry : bool) -> NoneType   Append a new residue by a bond.   3. append_residue_by_bond(self : rosetta.core.conformation.Conformation, new_rsd : rosetta.core.conformation.Residue, build_ideal_geometry : bool, connection_index : int) -> NoneType   Append a new residue by a bond.   4. append_residue_by_bond(self : rosetta.core.conformation.Conformation, new_rsd : rosetta.core.conformation.Residue, build_ideal_geometry : bool, connection_index : int, anchor_residue : int) -> NoneType   Append a new residue by a bond.   5. append_residue_by_bond(self : rosetta.core.conformation.Conformation, new_rsd : rosetta.core.conformation.Residue, build_ideal_geometry : bool, connection_index : int, anchor_residue : int, anchor_connection_index : int) -> NoneType   Append a new residue by a bond.   6. append_residue_by_bond(self : rosetta.core.conformation.Conformation, new_rsd : rosetta.core.conformation.Residue, build_ideal_geometry : bool, connection_index : int, anchor_residue : int, anchor_connection_index : int, start_new_chain : bool) -> NoneType   Append a new residue by a bond.   7. append_residue_by_bond(self : rosetta.core.conformation.Conformation, new_rsd : rosetta.core.conformation.Residue, build_ideal_geometry : bool, connection_index : int, anchor_residue : int, anchor_connection_index : int, start_new_chain : bool, lookup_bond_length : bool) -> NoneType   Append a new residue by a bond. atom_is_backbone_norefold(...) from builtins.PyCapsule atom_is_backbone_norefold(self : rosetta.core.conformation.Conformation, pos : int, atomno : int) -> bool   returns true if atom is part of backbone. atom_tree(...) from builtins.PyCapsule atom_tree(rosetta.core.conformation.Conformation) -> core::kinematics::AtomTree   Returns the conformation's AtomTree batch_get_xyz(...) from builtins.PyCapsule batch_get_xyz(self : rosetta.core.conformation.Conformation, id : rosetta.utility.vector1_core_id_AtomID, position : rosetta.utility.vector1_numeric_xyzVector_double_t) -> NoneType block_signals(...) from builtins.PyCapsule block_signals(rosetta.core.conformation.Conformation) -> NoneType   block signals from being sent blocking_signals(...) from builtins.PyCapsule blocking_signals(rosetta.core.conformation.Conformation) -> bool   are signals being blocked? bond_angle(...) from builtins.PyCapsule bond_angle(self : rosetta.core.conformation.Conformation, atom1 : rosetta.core.id.AtomID, atom2 : rosetta.core.id.AtomID, atom3 : rosetta.core.id.AtomID) -> float   Returns the bond angle defined by  <atom[1-3]> through the AtomTree bond_length(...) from builtins.PyCapsule bond_length(self : rosetta.core.conformation.Conformation, atom1 : rosetta.core.id.AtomID, atom2 : rosetta.core.id.AtomID) -> float   Returns the bond length between  <atom1>  and  <atom2> through the AtomTree bonded_neighbor_all_res(...) from builtins.PyCapsule bonded_neighbor_all_res(*args, **kwargs) Overloaded function.   1. bonded_neighbor_all_res(self : rosetta.core.conformation.Conformation, atomid : rosetta.core.id.AtomID) -> rosetta.utility.vector1_core_id_AtomID   get all atoms bonded to another   2. bonded_neighbor_all_res(self : rosetta.core.conformation.Conformation, atomid : rosetta.core.id.AtomID, virt : bool) -> rosetta.utility.vector1_core_id_AtomID   get all atoms bonded to another buffer_signals(...) from builtins.PyCapsule buffer_signals(rosetta.core.conformation.Conformation) -> NoneType   block signals from being sent and buffer them to be sent after unblocking buffering_signals(...) from builtins.PyCapsule buffering_signals(rosetta.core.conformation.Conformation) -> bool   are signals being blocked and buffered? chain_begin(...) from builtins.PyCapsule chain_begin(self : rosetta.core.conformation.Conformation, chain : int) -> int   Returns the position number of the first residue in  <chain> chain_end(...) from builtins.PyCapsule chain_end(self : rosetta.core.conformation.Conformation, chain : int) -> int   Returns the position number of the last residue in  <chain> chain_endings(...) from builtins.PyCapsule chain_endings(*args, **kwargs) Overloaded function.   1. chain_endings(rosetta.core.conformation.Conformation) -> rosetta.utility.vector1_unsigned_long   Returns the list of chain endings   2. chain_endings(self : rosetta.core.conformation.Conformation, endings : rosetta.utility.vector1_unsigned_long) -> NoneType   Sets the list of chain endings chains_from_termini(...) from builtins.PyCapsule chains_from_termini(rosetta.core.conformation.Conformation) -> NoneType   Rederive the chains from the termini/polymer status check_valid_membrane(...) from builtins.PyCapsule check_valid_membrane(rosetta.core.conformation.Conformation) -> NoneType   Check that a new membrane position is valid      Given a new membrane normal/center pair, check that the newly constructed stub represents  an orthogonal coordinate frame clear(...) from builtins.PyCapsule clear(rosetta.core.conformation.Conformation) -> NoneType   clear data clear_observers(...) from builtins.PyCapsule clear_observers(rosetta.core.conformation.Conformation) -> NoneType   clear all observers clear_parameters_set_list(...) from builtins.PyCapsule clear_parameters_set_list(rosetta.core.conformation.Conformation) -> NoneType   Delete the list of ParametersSetOP objects.      Vikram K. Mulligan (vmullig.edu) const_residues(...) from builtins.PyCapsule const_residues(rosetta.core.conformation.Conformation) -> rosetta.utility.vector1_std_shared_ptr_const_core_conformation_Residue_t   Inefficient -- constructs copy of residues_ contains_carbohydrate_residues(...) from builtins.PyCapsule contains_carbohydrate_residues(*args, **kwargs) Overloaded function.   1. contains_carbohydrate_residues(rosetta.core.conformation.Conformation) -> bool   Return true if this conformation contains any carbohydrate residues.   2. contains_carbohydrate_residues(self : rosetta.core.conformation.Conformation, setting : bool) -> NoneType   Set whether this conformation contains any carbohydrate residues. copy_segment(...) from builtins.PyCapsule copy_segment(self : rosetta.core.conformation.Conformation, size : int, src : rosetta.core.conformation.Conformation, begin : int, src_begin : int) -> NoneType   copy a stretch of coordinates/torsions from another Conformation create_new_parameters_set(...) from builtins.PyCapsule create_new_parameters_set(rosetta.core.conformation.Conformation) -> NoneType   Create a new (empty) ParametersSet object and add its owning pointer  to the current Conformation object.      Vikram K. Mulligan (vmullig.edu) debug_pause(...) from builtins.PyCapsule debug_pause(*args, **kwargs) Overloaded function.   1. debug_pause(self : rosetta.core.conformation.Conformation, flag : bool) -> NoneType   wait for stdin after sending a GeneralEvent signal   2. debug_pause(rosetta.core.conformation.Conformation) -> bool   waiting for stdin after sending a GeneralEvent signal? debug_residue_torsions(...) from builtins.PyCapsule debug_residue_torsions(*args, **kwargs) Overloaded function.   1. debug_residue_torsions(rosetta.core.conformation.Conformation) -> NoneType   debugging   2. debug_residue_torsions(self : rosetta.core.conformation.Conformation, verbose : bool) -> NoneType   debugging delete_chain_ending(...) from builtins.PyCapsule delete_chain_ending(self : rosetta.core.conformation.Conformation, seqpos : int) -> NoneType   Deletes  <seqpos>  from the list of chain endings delete_polymer_residue(...) from builtins.PyCapsule delete_polymer_residue(self : rosetta.core.conformation.Conformation, seqpos : int) -> NoneType   Delete polymer residue at the given sequence position delete_residue_range_slow(...) from builtins.PyCapsule delete_residue_range_slow(self : rosetta.core.conformation.Conformation, range_begin : int, range_end : int) -> NoneType   Slow method that relies on FoldTree::delete_seqpos, rebuilds atomtree, can handle jumps/root residue delete_residue_slow(...) from builtins.PyCapsule delete_residue_slow(self : rosetta.core.conformation.Conformation, seqpos : int) -> NoneType   Slow method that relies on FoldTree::delete_seqpos, rebuilds atomtree, can handle jumps/root residue detect_bonds(...) from builtins.PyCapsule detect_bonds(rosetta.core.conformation.Conformation) -> NoneType detect_pseudobonds(...) from builtins.PyCapsule detect_pseudobonds(rosetta.core.conformation.Conformation) -> NoneType dof(...) from builtins.PyCapsule dof(self : rosetta.core.conformation.Conformation, id : rosetta.core.id.DOF_ID) -> float   Returns the AtomTree degree of freedom (DOF)  <id> dof_id_from_torsion_id(...) from builtins.PyCapsule dof_id_from_torsion_id(self : rosetta.core.conformation.Conformation, id : core::id::TorsionID) -> rosetta.core.id.DOF_ID downstream_jump_stub(...) from builtins.PyCapsule downstream_jump_stub(self : rosetta.core.conformation.Conformation, jump_number : int) -> rosetta.core.kinematics.Stub   The upstream and downstream Stubs are the coordinate frames between which this jump is transforming empty(...) from builtins.PyCapsule empty(rosetta.core.conformation.Conformation) -> bool   Returns true if this conformation does not have any residues fill_missing_atoms(...) from builtins.PyCapsule fill_missing_atoms(self : rosetta.core.conformation.Conformation, missing : rosetta.core.id.AtomID_Map_bool_t) -> NoneType fix_disulfides(...) from builtins.PyCapsule fix_disulfides(self : rosetta.core.conformation.Conformation, disulf_bonds : rosetta.utility.vector1_std_pair_unsigned_long_unsigned_long_t) -> NoneType   Assigns disulfide bonds based on a pre-determined list get_jump_atom_ids(...) from builtins.PyCapsule get_jump_atom_ids(self : rosetta.core.conformation.Conformation, jump_number : int, upstream_id : rosetta.core.id.AtomID, downstream_id : rosetta.core.id.AtomID) -> bool   get two atoms connect by jump get_self_ptr(...) from builtins.PyCapsule get_self_ptr(*args, **kwargs) Overloaded function.   1. get_self_ptr(rosetta.core.conformation.Conformation) -> rosetta.core.conformation.Conformation   self pointers   2. get_self_ptr(rosetta.core.conformation.Conformation) -> rosetta.core.conformation.Conformation get_self_weak_ptr(...) from builtins.PyCapsule get_self_weak_ptr(*args, **kwargs) Overloaded function.   1. get_self_weak_ptr(rosetta.core.conformation.Conformation) -> rosetta.std.weak_ptr_const_core_conformation_Conformation_t   2. get_self_weak_ptr(rosetta.core.conformation.Conformation) -> rosetta.std.weak_ptr_core_conformation_Conformation_t get_stub_transform(...) from builtins.PyCapsule get_stub_transform(self : rosetta.core.conformation.Conformation, stub_id1 : rosetta.core.id.StubID, stub_id2 : rosetta.core.id.StubID) -> rosetta.core.kinematics.RT   get the transform between two stubs get_torsion_angle_atom_ids(...) from builtins.PyCapsule get_torsion_angle_atom_ids(self : rosetta.core.conformation.Conformation, tor_id : core::id::TorsionID, id1 : rosetta.core.id.AtomID, id2 : rosetta.core.id.AtomID, id3 : rosetta.core.id.AtomID, id4 : rosetta.core.id.AtomID) -> bool   get four atoms which defined this torsion has_passport(...) from builtins.PyCapsule has_passport(rosetta.core.conformation.Conformation) -> bool insert_chain_ending(...) from builtins.PyCapsule insert_chain_ending(self : rosetta.core.conformation.Conformation, seqpos : int) -> NoneType   Marks  <seqpos>  as the end of a new chain insert_ideal_geometry_at_polymer_bond(...) from builtins.PyCapsule insert_ideal_geometry_at_polymer_bond(self : rosetta.core.conformation.Conformation, seqpos : int) -> NoneType insert_ideal_geometry_at_residue_connection(...) from builtins.PyCapsule insert_ideal_geometry_at_residue_connection(self : rosetta.core.conformation.Conformation, pos1 : int, connid1 : int) -> NoneType insert_residue_by_bond(...) from builtins.PyCapsule insert_residue_by_bond(*args, **kwargs) Overloaded function.   1. insert_residue_by_bond(self : rosetta.core.conformation.Conformation, new_rsd_in : rosetta.core.conformation.Residue, seqpos : int, anchor_pos : int) -> NoneType   Insert a new residue by jump.  If new_chain is "true", then seqpos must be the last  residue of one chain (i.e. residue(seqpos).chain() != residue(seqpos+1).chain() )   2. insert_residue_by_bond(self : rosetta.core.conformation.Conformation, new_rsd_in : rosetta.core.conformation.Residue, seqpos : int, anchor_pos : int, build_ideal_geometry : bool) -> NoneType   Insert a new residue by jump.  If new_chain is "true", then seqpos must be the last  residue of one chain (i.e. residue(seqpos).chain() != residue(seqpos+1).chain() )   3. insert_residue_by_bond(self : rosetta.core.conformation.Conformation, new_rsd_in : rosetta.core.conformation.Residue, seqpos : int, anchor_pos : int, build_ideal_geometry : bool, anchor_atom : str) -> NoneType   Insert a new residue by jump.  If new_chain is "true", then seqpos must be the last  residue of one chain (i.e. residue(seqpos).chain() != residue(seqpos+1).chain() )   4. insert_residue_by_bond(self : rosetta.core.conformation.Conformation, new_rsd_in : rosetta.core.conformation.Residue, seqpos : int, anchor_pos : int, build_ideal_geometry : bool, anchor_atom : str, root_atom : str) -> NoneType   Insert a new residue by jump.  If new_chain is "true", then seqpos must be the last  residue of one chain (i.e. residue(seqpos).chain() != residue(seqpos+1).chain() )   5. insert_residue_by_bond(self : rosetta.core.conformation.Conformation, new_rsd_in : rosetta.core.conformation.Residue, seqpos : int, anchor_pos : int, build_ideal_geometry : bool, anchor_atom : str, root_atom : str, new_chain : bool) -> NoneType   Insert a new residue by jump.  If new_chain is "true", then seqpos must be the last  residue of one chain (i.e. residue(seqpos).chain() != residue(seqpos+1).chain() )   6. insert_residue_by_bond(self : rosetta.core.conformation.Conformation, new_rsd_in : rosetta.core.conformation.Residue, seqpos : int, anchor_pos : int, build_ideal_geometry : bool, anchor_atom : str, root_atom : str, new_chain : bool, lookup_bond_length : bool) -> NoneType   Insert a new residue by jump.  If new_chain is "true", then seqpos must be the last  residue of one chain (i.e. residue(seqpos).chain() != residue(seqpos+1).chain() ) insert_residue_by_jump(...) from builtins.PyCapsule insert_residue_by_jump(*args, **kwargs) Overloaded function.   1. insert_residue_by_jump(self : rosetta.core.conformation.Conformation, new_rsd_in : rosetta.core.conformation.Residue, seqpos : int, anchor_pos : int) -> NoneType   Insert a new residue by jump.  If new_chain is "true", then seqpos must be the last  residue of one chain (i.e. residue(seqpos).chain() != residue(seqpos+1).chain() )   2. insert_residue_by_jump(self : rosetta.core.conformation.Conformation, new_rsd_in : rosetta.core.conformation.Residue, seqpos : int, anchor_pos : int, anchor_atom : str) -> NoneType   Insert a new residue by jump.  If new_chain is "true", then seqpos must be the last  residue of one chain (i.e. residue(seqpos).chain() != residue(seqpos+1).chain() )   3. insert_residue_by_jump(self : rosetta.core.conformation.Conformation, new_rsd_in : rosetta.core.conformation.Residue, seqpos : int, anchor_pos : int, anchor_atom : str, root_atom : str) -> NoneType   Insert a new residue by jump.  If new_chain is "true", then seqpos must be the last  residue of one chain (i.e. residue(seqpos).chain() != residue(seqpos+1).chain() )   4. insert_residue_by_jump(self : rosetta.core.conformation.Conformation, new_rsd_in : rosetta.core.conformation.Residue, seqpos : int, anchor_pos : int, anchor_atom : str, root_atom : str, new_chain : bool) -> NoneType   Insert a new residue by jump.  If new_chain is "true", then seqpos must be the last  residue of one chain (i.e. residue(seqpos).chain() != residue(seqpos+1).chain() ) inter_residue_connection_partner(...) from builtins.PyCapsule inter_residue_connection_partner(self : rosetta.core.conformation.Conformation, seqpos : int, connection_index : int) -> rosetta.core.id.AtomID   This returns the AtomID of the atom in the other residue to which the "connection_index"-th  connection of residue seqpos is connected to. is_centroid(...) from builtins.PyCapsule is_centroid(rosetta.core.conformation.Conformation) -> bool   convenience test for residue_type_set ( based on two middle residue -- to avoid hitting on ligands or pseudos ) is_fullatom(...) from builtins.PyCapsule is_fullatom(rosetta.core.conformation.Conformation) -> bool   convenience test for residue_type_set ( based on two middle residue -- to avoid hitting on ligands or pseudos ) is_membrane(...) from builtins.PyCapsule is_membrane(rosetta.core.conformation.Conformation) -> bool   convenience test for if the conformation contains information for a membrane protein is_protected(...) from builtins.PyCapsule is_protected(rosetta.core.conformation.Conformation) -> bool is_residue_typeset(...) from builtins.PyCapsule is_residue_typeset(self : rosetta.core.conformation.Conformation, tag : str) -> bool   convenience test for residue_type_set ( based on two middle residue -- to avoid hitting on ligands or pseudos ) jump(...) from builtins.PyCapsule jump(*args, **kwargs) Overloaded function.   1. jump(self : rosetta.core.conformation.Conformation, jump_number : int) -> rosetta.core.kinematics.Jump   Returns the Jump with jump number  <jump_number>   2. jump(self : rosetta.core.conformation.Conformation, id : rosetta.core.id.AtomID) -> rosetta.core.kinematics.Jump   access a jump jump_atom_id(...) from builtins.PyCapsule jump_atom_id(self : rosetta.core.conformation.Conformation, jump_number : int) -> rosetta.core.id.AtomID membrane_info(...) from builtins.PyCapsule membrane_info(rosetta.core.conformation.Conformation) -> core::conformation::membrane::MembraneInfo   Returns the const MembraneInfo object in conformation      Membrane Info contains information describing location of the  membrane virtual residue in the pose sequence, membrane spanning region definitions  and lipid exposure/burial data n_parameters_sets(...) from builtins.PyCapsule n_parameters_sets(rosetta.core.conformation.Conformation) -> int   Get the number of parameters sets defined for this Conformation.      Vikram K. Mulligan (vmullig.edu) num_chains(...) from builtins.PyCapsule num_chains(rosetta.core.conformation.Conformation) -> int   Returns the number of chains parameters_set(...) from builtins.PyCapsule parameters_set(*args, **kwargs) Overloaded function.   1. parameters_set(self : rosetta.core.conformation.Conformation, index : int) -> rosetta.core.conformation.parametric.ParametersSet   Access one of the ParametersSets objects linked to this Conformation.      Vikram K. Mulligan (vmullig.edu)   2. parameters_set(self : rosetta.core.conformation.Conformation, index : int) -> rosetta.core.conformation.parametric.ParametersSet   Const access to one of the ParametersSets objects linked to this Conformation.      Vikram K. Mulligan (vmullig.edu) pop_passport(...) from builtins.PyCapsule pop_passport(rosetta.core.conformation.Conformation) -> core::environment::DofPassport prepend_polymer_residue_before_seqpos(...) from builtins.PyCapsule prepend_polymer_residue_before_seqpos(self : rosetta.core.conformation.Conformation, new_rsd : rosetta.core.conformation.Residue, seqpos : int, build_ideal_geometry : bool) -> NoneType   glues to seqpos and perhaps also seqpos-1 push_passport(...) from builtins.PyCapsule push_passport(self : rosetta.core.conformation.Conformation,  : core::environment::DofPassport) -> NoneType rebuild_polymer_bond_dependent_atoms(...) from builtins.PyCapsule rebuild_polymer_bond_dependent_atoms(self : rosetta.core.conformation.Conformation, seqpos : int) -> NoneType   Rebuild the atoms ( like HN(seqpos), OC(seqpos+1) ) that are dependent on the polymer bond between seqpos and seqpos+1 rebuild_polymer_bond_dependent_atoms_this_residue_only(...) from builtins.PyCapsule rebuild_polymer_bond_dependent_atoms_this_residue_only(self : rosetta.core.conformation.Conformation, seqpos : int) -> NoneType   Rebuilds the atoms that are depenent on polymer bonds for the specified residue only.      Vikram K. Mulligan (vmullig.edu) rebuild_residue_connection_dependent_atoms(...) from builtins.PyCapsule rebuild_residue_connection_dependent_atoms(self : rosetta.core.conformation.Conformation, seqpos : int, connid : int) -> NoneType receive_observers_from(...) from builtins.PyCapsule receive_observers_from(self : rosetta.core.conformation.Conformation, src : rosetta.core.conformation.Conformation) -> NoneType   fire a ConnectionEvent::TRANSFER to transfer observers from some source Conformation reset_chain_endings(...) from builtins.PyCapsule reset_chain_endings(rosetta.core.conformation.Conformation) -> NoneType   Resets chain data so that the Conformation is marked as a single chain reset_move_data(...) from builtins.PyCapsule reset_move_data(rosetta.core.conformation.Conformation) -> NoneType   forget all the structure modifications reset_structure_moved(...) from builtins.PyCapsule reset_structure_moved(rosetta.core.conformation.Conformation) -> NoneType   reset the structure_moved_ bool residue(...) from builtins.PyCapsule residue(self : rosetta.core.conformation.Conformation, seqpos : int) -> rosetta.core.conformation.Residue   access one of the residues      this access is inlined, since otherwise it  shows up in the profiler.  This will call non-inlined refold methods if necessary.      update coordinates and torsions for this and all other residues before  allowing read access residue_cop(...) from builtins.PyCapsule residue_cop(self : rosetta.core.conformation.Conformation, seqpos : int) -> rosetta.core.conformation.Residue   access one of the residues, using COP residue_op(...) from builtins.PyCapsule residue_op(self : rosetta.core.conformation.Conformation, seqpos : int) -> rosetta.core.conformation.Residue   Access one of the residues, using OP      Non-const access. residue_type(...) from builtins.PyCapsule residue_type(self : rosetta.core.conformation.Conformation, seqpos : int) -> rosetta.core.chemical.ResidueType   access one of the residue's types -- avoids coord/torsion update safely_append_polymer_residue_after_seqpos(...) from builtins.PyCapsule safely_append_polymer_residue_after_seqpos(self : rosetta.core.conformation.Conformation, new_rsd : rosetta.core.conformation.Residue, seqpos : int, build_ideal_geometry : bool) -> NoneType   glues to seqpos and perhaps also seqpos+1, removes termini variants if necessary safely_prepend_polymer_residue_before_seqpos(...) from builtins.PyCapsule safely_prepend_polymer_residue_before_seqpos(self : rosetta.core.conformation.Conformation, new_rsd : rosetta.core.conformation.Residue, seqpos : int, build_ideal_geometry : bool) -> NoneType   glues to seqpos and perhaps also seqpos-1, removes termini variants if necessary secstruct(...) from builtins.PyCapsule secstruct(self : rosetta.core.conformation.Conformation, seqpos : int) -> str   Returns the secondary structure the position  <seqpos>      character representing secondary structure; returns 'L' if the  requested sequence position is larger than the length in the  secondary structure array sequence_matches(...) from builtins.PyCapsule sequence_matches(self : rosetta.core.conformation.Conformation, other : rosetta.core.conformation.Conformation) -> bool   do the names of all residues in this and src match? set_jump_atom_stub_id(...) from builtins.PyCapsule set_jump_atom_stub_id(self : rosetta.core.conformation.Conformation, id : rosetta.core.id.StubID) -> NoneType set_membrane_info(...) from builtins.PyCapsule set_membrane_info(self : rosetta.core.conformation.Conformation, mem_info : core::conformation::membrane::MembraneInfo) -> NoneType   Setup a Membrane Info object in Conformation - pos & topology      Add a MembraneInfo object - describes the position of the  membrane virtual residue, information on membrane spanning regions,  lipid exposure/burial of residues in the pose, and fullatom steepness  and thickness parameters. At construction, specify membrane position  and list of spanning topology objects by chain. set_noncanonical_connection(...) from builtins.PyCapsule set_noncanonical_connection(self : rosetta.core.conformation.Conformation, res_id_lower : int, lr_conn_id : int, res_id_upper : int, ur_conn_id : int) -> NoneType   Create an arbitrary covalent connection between two residues. set_polymeric_connection(...) from builtins.PyCapsule set_polymeric_connection(self : rosetta.core.conformation.Conformation, res_id_lower : int, res_id_upper : int) -> NoneType   identify polymeric connections set_stub_transform(...) from builtins.PyCapsule set_stub_transform(self : rosetta.core.conformation.Conformation, stub_id1 : rosetta.core.id.StubID, stub_id2 : rosetta.core.id.StubID, target_rt : rosetta.core.kinematics.RT) -> NoneType   Set the transform between two stubs -- only works if there's a jump between the two sets of stubatoms show_residue_connections(...) from builtins.PyCapsule show_residue_connections(rosetta.core.conformation.Conformation) -> NoneType   Show residue connections for debugging purposes. size(...) from builtins.PyCapsule size(rosetta.core.conformation.Conformation) -> int   Returns the number of residues in the Conformation structure_moved(...) from builtins.PyCapsule structure_moved(rosetta.core.conformation.Conformation) -> bool   has the structure moved since the last call to reset_move_data or reset_structure_moved stub_from_id(...) from builtins.PyCapsule stub_from_id(self : rosetta.core.conformation.Conformation, id : rosetta.core.id.StubID) -> rosetta.core.kinematics.Stub torsion(...) from builtins.PyCapsule torsion(self : rosetta.core.conformation.Conformation, id : core::id::TorsionID) -> float   Return the torsion angle OR rigid-body offset for  <id> torsion_angle(...) from builtins.PyCapsule torsion_angle(self : rosetta.core.conformation.Conformation, atom1 : rosetta.core.id.AtomID, atom2 : rosetta.core.id.AtomID, atom3 : rosetta.core.id.AtomID, atom4 : rosetta.core.id.AtomID) -> float   Returns the torsion angle defined by  <atom[1-4]> unblock_signals(...) from builtins.PyCapsule unblock_signals(rosetta.core.conformation.Conformation) -> NoneType   allow signals to be sent update_actcoord(...) from builtins.PyCapsule update_actcoord(self : rosetta.core.conformation.Conformation, resid : int) -> NoneType update_actcoords(...) from builtins.PyCapsule update_actcoords(rosetta.core.conformation.Conformation) -> NoneType update_domain_map(...) from builtins.PyCapsule update_domain_map(self : rosetta.core.conformation.Conformation, domain_map : ObjexxFCL::FArray1D<int>) -> NoneType   Generate a domain_map from the current dof/xyz moved data update_membrane_position(...) from builtins.PyCapsule update_membrane_position(self : rosetta.core.conformation.Conformation, center : rosetta.numeric.xyzVector_double_t, normal : rosetta.numeric.xyzVector_double_t) -> NoneType   Update Normal, Center in the Membrane      Sets the center and normal coordinates to the appropriate  parameters and checks for a valid stub prior to returning. update_noncanonical_connection(...) from builtins.PyCapsule update_noncanonical_connection(self : rosetta.core.conformation.Conformation, lower_seqpos : int, lr_conn_id : int, upper_seqpos : int, ur_conn_id : int) -> NoneType   Update the connection status between the lower_seqpos residue's lr_conn_id connection ID and  the upper_seqpos residue's ur_conn_id connection ID. update_orbital_coords(...) from builtins.PyCapsule update_orbital_coords(*args, **kwargs) Overloaded function.   1. update_orbital_coords(self : rosetta.core.conformation.Conformation, rsd : rosetta.core.conformation.Residue) -> NoneType   2. update_orbital_coords(self : rosetta.core.conformation.Conformation, resid : int) -> NoneType update_polymeric_connection(...) from builtins.PyCapsule update_polymeric_connection(*args, **kwargs) Overloaded function.   1. update_polymeric_connection(self : rosetta.core.conformation.Conformation, lower_seqpos : int) -> NoneType   Update the polymer connection status between lower_seqpos and lower_seqpos+1  based on chainID's and termini.  If update_connection_dep_atoms is true, positions of  atoms dependent on the polymer connection are updated.   2. update_polymeric_connection(self : rosetta.core.conformation.Conformation, lower_seqpos : int, update_connection_dep_atoms : bool) -> NoneType   Update the polymer connection status between lower_seqpos and lower_seqpos+1  based on chainID's and termini.  If update_connection_dep_atoms is true, positions of  atoms dependent on the polymer connection are updated. upstream_jump_stub(...) from builtins.PyCapsule upstream_jump_stub(self : rosetta.core.conformation.Conformation, jump_number : int) -> rosetta.core.kinematics.Stub   The upstream and downstream Stubs are the coordinate frames between which this jump is transforming xyz(...) from builtins.PyCapsule xyz(self : rosetta.core.conformation.Conformation, id : rosetta.core.id.AtomID) -> rosetta.numeric.xyzVector_double_t   access xyz coordinates of an atom   class SymmetryInfo(builtins.object)       Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.core.conformation.symmetry.SymmetryInfo) -> NoneType   2. __init__(self : rosetta.core.conformation.symmetry.SymmetryInfo, symmdata : rosetta.core.conformation.symmetry.SymmData, nres_subunit : int, njump_subunit : int) -> NoneType   3. __init__(rosetta.core.conformation.symmetry.SymmetryInfo, int, int, int, rosetta.std.map_unsigned_long_core_conformation_symmetry_SymDof, int, rosetta.utility.vector1_double, rosetta.core.conformation.symmetry.SymSlideInfo) -> NoneType   doc   4. __init__(rosetta.core.conformation.symmetry.SymmetryInfo, int, int, int, rosetta.std.map_unsigned_long_core_conformation_symmetry_SymDof, int, rosetta.utility.vector1_double, rosetta.core.conformation.symmetry.SymSlideInfo, int) -> NoneType   doc   5. __init__(self : rosetta.core.conformation.symmetry.SymmetryInfo, nres_monomer : int, njump_monomer : int, N : int, dofs : rosetta.std.map_unsigned_long_core_conformation_symmetry_SymDof, score_subunit : int, score_multiply : rosetta.utility.vector1_double, slide_info : rosetta.core.conformation.symmetry.SymSlideInfo, num_interfaces : int, type : str) -> NoneType   6. __init__(self : rosetta.core.conformation.symmetry.SymmetryInfo,  : rosetta.core.conformation.symmetry.SymmetryInfo) -> 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.conformation.symmetry.SymmetryInfo) -> str add_bb_clone(...) from builtins.PyCapsule add_bb_clone(self : rosetta.core.conformation.symmetry.SymmetryInfo, base_pos : int, clone_pos : int) -> NoneType add_chi_clone(...) from builtins.PyCapsule add_chi_clone(self : rosetta.core.conformation.symmetry.SymmetryInfo, base_pos : int, clone_pos : int) -> NoneType add_jump_clone(...) from builtins.PyCapsule add_jump_clone(self : rosetta.core.conformation.symmetry.SymmetryInfo, base_pos : int, clone_jump : int, wt : float) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.core.conformation.symmetry.SymmetryInfo,  : rosetta.core.conformation.symmetry.SymmetryInfo) -> rosetta.core.conformation.symmetry.SymmetryInfo atom_is_independent(...) from builtins.PyCapsule atom_is_independent(self : rosetta.core.conformation.symmetry.SymmetryInfo, id : rosetta.core.id.AtomID) -> bool bb_clones(...) from builtins.PyCapsule bb_clones(self : rosetta.core.conformation.symmetry.SymmetryInfo, seqpos : int) -> rosetta.utility.vector1_unsigned_long bb_follows(...) from builtins.PyCapsule bb_follows(self : rosetta.core.conformation.symmetry.SymmetryInfo, seqpos : int) -> int bb_is_independent(...) from builtins.PyCapsule bb_is_independent(self : rosetta.core.conformation.symmetry.SymmetryInfo, seqpos : int) -> bool chi_clones(...) from builtins.PyCapsule chi_clones(self : rosetta.core.conformation.symmetry.SymmetryInfo, seqpos : int) -> rosetta.utility.vector1_unsigned_long chi_follows(...) from builtins.PyCapsule chi_follows(self : rosetta.core.conformation.symmetry.SymmetryInfo, seqpos : int) -> int chi_is_independent(...) from builtins.PyCapsule chi_is_independent(self : rosetta.core.conformation.symmetry.SymmetryInfo, seqpos : int) -> bool clone(...) from builtins.PyCapsule clone(rosetta.core.conformation.symmetry.SymmetryInfo) -> rosetta.core.conformation.symmetry.SymmetryInfo contiguous_monomers(...) from builtins.PyCapsule contiguous_monomers(rosetta.core.conformation.symmetry.SymmetryInfo) -> bool dependent_atoms(...) from builtins.PyCapsule dependent_atoms(self : rosetta.core.conformation.symmetry.SymmetryInfo, id : rosetta.core.id.AtomID) -> rosetta.utility.vector1_core_id_AtomID dependent_dofs(...) from builtins.PyCapsule dependent_dofs(self : rosetta.core.conformation.symmetry.SymmetryInfo, id : rosetta.core.id.DOF_ID, conf : rosetta.core.conformation.Conformation) -> rosetta.utility.vector1_core_id_DOF_ID   Returns a list of dofs that depend on id. Inefficient -- creates list anew each time. dependent_torsions(...) from builtins.PyCapsule dependent_torsions(self : rosetta.core.conformation.symmetry.SymmetryInfo, id : core::id::TorsionID) -> rosetta.utility.vector1_core_id_TorsionID   Returns a list of dofs that depend on id. Inefficient -- creates list anew each time. deriv_multiply(...) from builtins.PyCapsule deriv_multiply(self : rosetta.core.conformation.symmetry.SymmetryInfo, res1 : int, res2 : int) -> float dof_is_independent(...) from builtins.PyCapsule dof_is_independent(self : rosetta.core.conformation.symmetry.SymmetryInfo, id : rosetta.core.id.DOF_ID, conf : rosetta.core.conformation.Conformation) -> bool equivalent_residue_on_subunit(...) from builtins.PyCapsule equivalent_residue_on_subunit(self : rosetta.core.conformation.symmetry.SymmetryInfo, subunit_index : int, residue_id : int) -> int   What is the equivalent residue on a particular subunit for the given residue? The  logic here mimics the logic in subunit index in terms of subunit numbering. fa_is_independent(...) from builtins.PyCapsule fa_is_independent(self : rosetta.core.conformation.symmetry.SymmetryInfo, seqpos : int) -> bool get_asymmetric_seqpos(...) from builtins.PyCapsule get_asymmetric_seqpos(self : rosetta.core.conformation.symmetry.SymmetryInfo, res : int) -> int get_component(...) from builtins.PyCapsule get_component(self : rosetta.core.conformation.symmetry.SymmetryInfo, i : int) -> str get_component_bounds(...) from builtins.PyCapsule get_component_bounds(*args, **kwargs) Overloaded function.   1. get_component_bounds(rosetta.core.conformation.symmetry.SymmetryInfo) -> rosetta.std.map_char_std_pair_unsigned_long_unsigned_long_t   2. get_component_bounds(self : rosetta.core.conformation.symmetry.SymmetryInfo, c : str) -> (int, int) get_component_lower_bound(...) from builtins.PyCapsule get_component_lower_bound(self : rosetta.core.conformation.symmetry.SymmetryInfo, c : str) -> int get_component_of_residue(...) from builtins.PyCapsule get_component_of_residue(self : rosetta.core.conformation.symmetry.SymmetryInfo, ir : int) -> str get_component_upper_bound(...) from builtins.PyCapsule get_component_upper_bound(self : rosetta.core.conformation.symmetry.SymmetryInfo, c : str) -> int get_components(...) from builtins.PyCapsule get_components(rosetta.core.conformation.symmetry.SymmetryInfo) -> rosetta.utility.vector1_char get_dof_derivative_weight(...) from builtins.PyCapsule get_dof_derivative_weight(self : rosetta.core.conformation.symmetry.SymmetryInfo, id : rosetta.core.id.DOF_ID, conf : rosetta.core.conformation.Conformation) -> float get_dofs(...) from builtins.PyCapsule get_dofs(rosetta.core.conformation.symmetry.SymmetryInfo) -> rosetta.std.map_unsigned_long_core_conformation_symmetry_SymDof get_jump_name(...) from builtins.PyCapsule get_jump_name(self : rosetta.core.conformation.symmetry.SymmetryInfo, i : int) -> str get_jump_name_to_components(...) from builtins.PyCapsule get_jump_name_to_components(*args, **kwargs) Overloaded function.   1. get_jump_name_to_components(rosetta.core.conformation.symmetry.SymmetryInfo) -> rosetta.std.map_std_string_utility_vector1_char_std_allocator_char_t   2. get_jump_name_to_components(self : rosetta.core.conformation.symmetry.SymmetryInfo, jname : str) -> rosetta.utility.vector1_char get_jump_name_to_subunits(...) from builtins.PyCapsule get_jump_name_to_subunits(*args, **kwargs) Overloaded function.   1. get_jump_name_to_subunits(rosetta.core.conformation.symmetry.SymmetryInfo) -> rosetta.std.map_std_string_utility_vector1_unsigned_long_std_allocator_unsigned_long_t   2. get_jump_name_to_subunits(self : rosetta.core.conformation.symmetry.SymmetryInfo, jname : str) -> rosetta.utility.vector1_unsigned_long get_jump_num(...) from builtins.PyCapsule get_jump_num(self : rosetta.core.conformation.symmetry.SymmetryInfo, i : str) -> int get_njumps_subunit(...) from builtins.PyCapsule get_njumps_subunit(rosetta.core.conformation.symmetry.SymmetryInfo) -> int get_nres_subunit(...) from builtins.PyCapsule get_nres_subunit(rosetta.core.conformation.symmetry.SymmetryInfo) -> int get_num_components(...) from builtins.PyCapsule get_num_components(rosetta.core.conformation.symmetry.SymmetryInfo) -> int get_slide_info(...) from builtins.PyCapsule get_slide_info(rosetta.core.conformation.symmetry.SymmetryInfo) -> rosetta.core.conformation.symmetry.SymSlideInfo get_subunit_name_to_component(...) from builtins.PyCapsule get_subunit_name_to_component(*args, **kwargs) Overloaded function.   1. get_subunit_name_to_component(rosetta.core.conformation.symmetry.SymmetryInfo) -> rosetta.std.map_std_string_char   2. get_subunit_name_to_component(self : rosetta.core.conformation.symmetry.SymmetryInfo, vname : str) -> str get_use_symmetry(...) from builtins.PyCapsule get_use_symmetry(rosetta.core.conformation.symmetry.SymmetryInfo) -> bool independent_residues(...) from builtins.PyCapsule independent_residues(rosetta.core.conformation.symmetry.SymmetryInfo) -> rosetta.utility.vector1_bool init_defaults(...) from builtins.PyCapsule init_defaults(rosetta.core.conformation.symmetry.SymmetryInfo) -> NoneType initialize(...) from builtins.PyCapsule initialize(*args, **kwargs) Overloaded function.   1. initialize(self : rosetta.core.conformation.symmetry.SymmetryInfo, nres_monomer : int, njump_monomer : int, N : int, num_virtual : int, dofs : rosetta.std.map_unsigned_long_core_conformation_symmetry_SymDof, score_subunit : int, score_multiply : rosetta.utility.vector1_double, slide_info : rosetta.core.conformation.symmetry.SymSlideInfo) -> NoneType   2. initialize(self : rosetta.core.conformation.symmetry.SymmetryInfo, nres_monomer : int, njump_monomer : int, N : int, num_virtual : int, dofs : rosetta.std.map_unsigned_long_core_conformation_symmetry_SymDof, score_subunit : int, score_multiply : rosetta.utility.vector1_double, slide_info : rosetta.core.conformation.symmetry.SymSlideInfo, num_interfaces : int) -> NoneType   3. initialize(self : rosetta.core.conformation.symmetry.SymmetryInfo, nres_monomer : int, njump_monomer : int, N : int, num_virtual : int, dofs : rosetta.std.map_unsigned_long_core_conformation_symmetry_SymDof, score_subunit : int, score_multiply : rosetta.utility.vector1_double, slide_info : rosetta.core.conformation.symmetry.SymSlideInfo, num_interfaces : int, type : str) -> NoneType   4. initialize(self : rosetta.core.conformation.symmetry.SymmetryInfo, nres_monomer : int, njump_monomer : int, N : int, num_virtual : int, jump_clones : rosetta.std.map_unsigned_long_utility_vector1_std_pair_unsigned_long_double_std_allocator_std_pair_unsigned_long_double_t, dofs : rosetta.std.map_unsigned_long_core_conformation_symmetry_SymDof, score_subunit : int, score_multiply : rosetta.utility.vector1_double, slide_info : rosetta.core.conformation.symmetry.SymSlideInfo) -> NoneType   5. initialize(self : rosetta.core.conformation.symmetry.SymmetryInfo, nres_monomer : int, njump_monomer : int, N : int, num_virtual : int, jump_clones : rosetta.std.map_unsigned_long_utility_vector1_std_pair_unsigned_long_double_std_allocator_std_pair_unsigned_long_double_t, dofs : rosetta.std.map_unsigned_long_core_conformation_symmetry_SymDof, score_subunit : int, score_multiply : rosetta.utility.vector1_double, slide_info : rosetta.core.conformation.symmetry.SymSlideInfo, num_interfaces : int) -> NoneType   6. initialize(self : rosetta.core.conformation.symmetry.SymmetryInfo, nres_monomer : int, njump_monomer : int, N : int, num_virtual : int, jump_clones : rosetta.std.map_unsigned_long_utility_vector1_std_pair_unsigned_long_double_std_allocator_std_pair_unsigned_long_double_t, dofs : rosetta.std.map_unsigned_long_core_conformation_symmetry_SymDof, score_subunit : int, score_multiply : rosetta.utility.vector1_double, slide_info : rosetta.core.conformation.symmetry.SymSlideInfo, num_interfaces : int, type : str) -> NoneType interface_number(...) from builtins.PyCapsule interface_number(self : rosetta.core.conformation.symmetry.SymmetryInfo, res1 : int, res2 : int) -> int is_asymmetric_seqpos(...) from builtins.PyCapsule is_asymmetric_seqpos(self : rosetta.core.conformation.symmetry.SymmetryInfo, res : int) -> bool is_virtual(...) from builtins.PyCapsule is_virtual(self : rosetta.core.conformation.symmetry.SymmetryInfo, seqpos : int) -> bool jump_clones(...) from builtins.PyCapsule jump_clones(self : rosetta.core.conformation.symmetry.SymmetryInfo, base_jump : int) -> rosetta.utility.vector1_unsigned_long jump_follows(...) from builtins.PyCapsule jump_follows(self : rosetta.core.conformation.symmetry.SymmetryInfo, seqpos : int) -> int jump_is_independent(...) from builtins.PyCapsule jump_is_independent(self : rosetta.core.conformation.symmetry.SymmetryInfo, seqpos : int) -> bool last_independent_residue(...) from builtins.PyCapsule last_independent_residue(rosetta.core.conformation.symmetry.SymmetryInfo) -> int map_symmetric_res_pairs(...) from builtins.PyCapsule map_symmetric_res_pairs(self : rosetta.core.conformation.symmetry.SymmetryInfo, res1 : int, res2 : int) -> rosetta.std.vector_std_pair_unsigned_long_unsigned_long_t num_bb_clones(...) from builtins.PyCapsule num_bb_clones(rosetta.core.conformation.symmetry.SymmetryInfo) -> int num_chi_clones(...) from builtins.PyCapsule num_chi_clones(rosetta.core.conformation.symmetry.SymmetryInfo) -> int num_independent_residues(...) from builtins.PyCapsule num_independent_residues(rosetta.core.conformation.symmetry.SymmetryInfo) -> int num_interfaces(...) from builtins.PyCapsule num_interfaces(rosetta.core.conformation.symmetry.SymmetryInfo) -> int num_jump_clones(...) from builtins.PyCapsule num_jump_clones(rosetta.core.conformation.symmetry.SymmetryInfo) -> int num_slidablejumps(...) from builtins.PyCapsule num_slidablejumps(rosetta.core.conformation.symmetry.SymmetryInfo) -> int num_total_residues(...) from builtins.PyCapsule num_total_residues(rosetta.core.conformation.symmetry.SymmetryInfo) -> int num_total_residues_with_pseudo(...) from builtins.PyCapsule num_total_residues_with_pseudo(rosetta.core.conformation.symmetry.SymmetryInfo) -> int num_total_residues_without_pseudo(...) from builtins.PyCapsule num_total_residues_without_pseudo(rosetta.core.conformation.symmetry.SymmetryInfo) -> int num_virtuals(...) from builtins.PyCapsule num_virtuals(*args, **kwargs) Overloaded function.   1. num_virtuals(rosetta.core.conformation.symmetry.SymmetryInfo) -> int   2. num_virtuals(self : rosetta.core.conformation.symmetry.SymmetryInfo, setting : int) -> NoneType read_silent_struct(...) from builtins.PyCapsule read_silent_struct(self : rosetta.core.conformation.symmetry.SymmetryInfo, filename : str) -> bool reset_score_multiply_to_reasonable_default(...) from builtins.PyCapsule reset_score_multiply_to_reasonable_default(rosetta.core.conformation.symmetry.SymmetryInfo) -> bool resize_asu(...) from builtins.PyCapsule resize_asu(self : rosetta.core.conformation.symmetry.SymmetryInfo, nres_new : int) -> NoneType score_multiply(...) from builtins.PyCapsule score_multiply(self : rosetta.core.conformation.symmetry.SymmetryInfo, res1 : int, res2 : int) -> float score_multiply_factor(...) from builtins.PyCapsule score_multiply_factor(rosetta.core.conformation.symmetry.SymmetryInfo) -> int set_dofs(...) from builtins.PyCapsule set_dofs(self : rosetta.core.conformation.symmetry.SymmetryInfo, dofs : rosetta.std.map_unsigned_long_core_conformation_symmetry_SymDof) -> NoneType set_flat_score_multiply(...) from builtins.PyCapsule set_flat_score_multiply(self : rosetta.core.conformation.symmetry.SymmetryInfo, nres : int, factor : int) -> NoneType set_jump_name(...) from builtins.PyCapsule set_jump_name(self : rosetta.core.conformation.symmetry.SymmetryInfo, i : int,  : str) -> NoneType set_multicomponent_info(...) from builtins.PyCapsule set_multicomponent_info(self : rosetta.core.conformation.symmetry.SymmetryInfo, num_components : int, components : rosetta.utility.vector1_char, component_bounds : rosetta.std.map_char_std_pair_unsigned_long_unsigned_long_t, name2component : rosetta.std.map_std_string_char, jname2component : rosetta.std.map_std_string_utility_vector1_char_std_allocator_char_t, jname2subunits : rosetta.std.map_std_string_utility_vector1_unsigned_long_std_allocator_unsigned_long_t) -> NoneType set_nres_subunit(...) from builtins.PyCapsule set_nres_subunit(self : rosetta.core.conformation.symmetry.SymmetryInfo, setting : int) -> NoneType set_score_multiply(...) from builtins.PyCapsule set_score_multiply(self : rosetta.core.conformation.symmetry.SymmetryInfo, res : int, factor : int) -> NoneType set_score_multiply_from_subunit_factors(...) from builtins.PyCapsule set_score_multiply_from_subunit_factors(self : rosetta.core.conformation.symmetry.SymmetryInfo, score_multiply_vector_subunit : rosetta.utility.vector1_double, nres_subunit : int, n_subunits : int) -> NoneType set_use_symmetry(...) from builtins.PyCapsule set_use_symmetry(self : rosetta.core.conformation.symmetry.SymmetryInfo, setting : bool) -> NoneType subunit_index(...) from builtins.PyCapsule subunit_index(self : rosetta.core.conformation.symmetry.SymmetryInfo, seqpos : int) -> int   What subunit does a particular residue come from? subunits(...) from builtins.PyCapsule subunits(rosetta.core.conformation.symmetry.SymmetryInfo) -> int torsion_changes_move_other_monomers(...) from builtins.PyCapsule torsion_changes_move_other_monomers(*args, **kwargs) Overloaded function.   1. torsion_changes_move_other_monomers(rosetta.core.conformation.symmetry.SymmetryInfo) -> bool   2. torsion_changes_move_other_monomers(self : rosetta.core.conformation.symmetry.SymmetryInfo, setting : bool) -> NoneType torsion_is_independent(...) from builtins.PyCapsule torsion_is_independent(self : rosetta.core.conformation.symmetry.SymmetryInfo, id : core::id::TorsionID) -> bool update_nmonomer_jumps(...) from builtins.PyCapsule update_nmonomer_jumps(self : rosetta.core.conformation.symmetry.SymmetryInfo, nmonomer_new : int) -> NoneType update_score_multiply_factor(...) from builtins.PyCapsule update_score_multiply_factor(rosetta.core.conformation.symmetry.SymmetryInfo) -> NoneType write_silent_struct(...) from builtins.PyCapsule write_silent_struct(self : rosetta.core.conformation.symmetry.SymmetryInfo, filename : str) -> bool   class SymmetryTransform(builtins.object)       Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.core.conformation.symmetry.SymmetryTransform) -> NoneType   2. __init__(rosetta.core.conformation.symmetry.SymmetryTransform, rosetta.numeric.xyzVector_double_t, rosetta.numeric.xyzVector_double_t, rosetta.numeric.xyzVector_double_t) -> NoneType   doc   3. __init__(self : rosetta.core.conformation.symmetry.SymmetryTransform, p1 : rosetta.numeric.xyzVector_double_t, p2 : rosetta.numeric.xyzVector_double_t, p3 : rosetta.numeric.xyzVector_double_t, mirror_z : bool) -> 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.conformation.symmetry.SymmetryTransform,  : rosetta.core.conformation.symmetry.SymmetryTransform) -> rosetta.core.conformation.symmetry.SymmetryTransform clone(...) from builtins.PyCapsule clone(rosetta.core.conformation.symmetry.SymmetryTransform) -> rosetta.core.conformation.symmetry.SymmetryTransform   Clone operator.      Copy this object and return an owning pointer to the copy. ht(...) from builtins.PyCapsule ht(rosetta.core.conformation.symmetry.SymmetryTransform) -> rosetta.numeric.HomogeneousTransform_double_t   Get the HomogeneousTransform matrix. mirror_z(...) from builtins.PyCapsule mirror_z(rosetta.core.conformation.symmetry.SymmetryTransform) -> bool   Get whether this HomogeneousTransform mirrors aout the z-axis or not. set_mirror_z(...) from builtins.PyCapsule set_mirror_z(self : rosetta.core.conformation.symmetry.SymmetryTransform, val : bool) -> NoneType   Set whether this HomogeneousTransform mirrors about the z-axis or not.   class VirtualCoordinate(builtins.object)       Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.core.conformation.symmetry.VirtualCoordinate) -> NoneType   2. __init__(self : rosetta.core.conformation.symmetry.VirtualCoordinate, src : rosetta.core.conformation.symmetry.VirtualCoordinate) -> NoneType   3. __init__(self : rosetta.core.conformation.symmetry.VirtualCoordinate, axis_x : rosetta.numeric.xyzVector_double_t, axis_y : rosetta.numeric.xyzVector_double_t, axis_origin : rosetta.numeric.xyzVector_double_t) -> NoneType   4. __init__(self : rosetta.core.conformation.symmetry.VirtualCoordinate, axis_x : rosetta.numeric.xyzVector_double_t, axis_y : rosetta.numeric.xyzVector_double_t, axis_origin : rosetta.numeric.xyzVector_double_t, mirror_z : bool) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. add_coordinate_from_string(...) from builtins.PyCapsule add_coordinate_from_string(*args, **kwargs) Overloaded function.   1. add_coordinate_from_string(self : rosetta.core.conformation.symmetry.VirtualCoordinate, coords : rosetta.utility.vector1_std_string) -> NoneType   2. add_coordinate_from_string(self : rosetta.core.conformation.symmetry.VirtualCoordinate, coords : rosetta.utility.vector1_std_string, coord_start : int) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.core.conformation.symmetry.VirtualCoordinate, src : rosetta.core.conformation.symmetry.VirtualCoordinate) -> rosetta.core.conformation.symmetry.VirtualCoordinate get_mirror_z(...) from builtins.PyCapsule get_mirror_z(rosetta.core.conformation.symmetry.VirtualCoordinate) -> bool get_origin(...) from builtins.PyCapsule get_origin(*args, **kwargs) Overloaded function.   1. get_origin(rosetta.core.conformation.symmetry.VirtualCoordinate) -> rosetta.numeric.xyzVector_double_t   2. get_origin(rosetta.core.conformation.symmetry.VirtualCoordinate) -> rosetta.numeric.xyzVector_double_t get_x(...) from builtins.PyCapsule get_x(*args, **kwargs) Overloaded function.   1. get_x(rosetta.core.conformation.symmetry.VirtualCoordinate) -> rosetta.numeric.xyzVector_double_t   2. get_x(rosetta.core.conformation.symmetry.VirtualCoordinate) -> rosetta.numeric.xyzVector_double_t get_y(...) from builtins.PyCapsule get_y(*args, **kwargs) Overloaded function.   1. get_y(rosetta.core.conformation.symmetry.VirtualCoordinate) -> rosetta.numeric.xyzVector_double_t   2. get_y(rosetta.core.conformation.symmetry.VirtualCoordinate) -> rosetta.numeric.xyzVector_double_t set_mirror_z(...) from builtins.PyCapsule set_mirror_z(self : rosetta.core.conformation.symmetry.VirtualCoordinate, val : bool) -> NoneType   class dof_type(builtins.object)       Methods defined here: __eq__(...) from builtins.PyCapsule __eq__(rosetta.core.conformation.symmetry.dof_type, rosetta.core.conformation.symmetry.dof_type) -> bool __hash__(...) from builtins.PyCapsule __hash__(rosetta.core.conformation.symmetry.dof_type) -> int __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.core.conformation.symmetry.dof_type, int) -> NoneType   2. __init__(rosetta.core.conformation.symmetry.dof_type, int) -> NoneType __int__(...) from builtins.PyCapsule __int__(rosetta.core.conformation.symmetry.dof_type) -> int __ne__(...) from builtins.PyCapsule __ne__(rosetta.core.conformation.symmetry.dof_type, rosetta.core.conformation.symmetry.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.conformation.symmetry.dof_type) -> str Data and other attributes defined here: X_ANGLE_DOF = dof_type.X_ANGLE_DOF X_DOF = dof_type.X_DOF Y_ANGLE_DOF = dof_type.Y_ANGLE_DOF Y_DOF = dof_type.Y_DOF Z_ANGLE_DOF = dof_type.Z_ANGLE_DOF Z_DOF = dof_type.Z_DOF

Functions
		calculate_inverting_virtuals(...) method of builtins.PyCapsule instance calculate_inverting_virtuals(ft : rosetta.core.kinematics.FoldTree, conf : rosetta.core.conformation.Conformation, symm_info : rosetta.core.conformation.symmetry.SymmetryInfo, mirrored_subs : rosetta.utility.vector1_bool, mirrored_jumps : rosetta.utility.vector1_std_pair_bool_bool_t) -> NoneType   A very specific helper function that counts the number of mirror ops from root->each subunit get_asymm_unit_fold_tree(...) method of builtins.PyCapsule instance get_asymm_unit_fold_tree(conf : rosetta.core.conformation.Conformation) -> rosetta.core.kinematics.FoldTree is_mirror_symmetric(...) method of builtins.PyCapsule instance is_mirror_symmetric(conf : rosetta.core.conformation.Conformation) -> bool is_symmetric(...) method of builtins.PyCapsule instance is_symmetric(*args, **kwargs) Overloaded function.   1. is_symmetric(conf : rosetta.core.conformation.Conformation) -> bool   2. is_symmetric(symminfo : rosetta.core.conformation.symmetry.SymmetryInfo) -> bool recenter(...) method of builtins.PyCapsule instance recenter(src_conformation : rosetta.core.conformation.Conformation, symmdata : rosetta.core.conformation.symmetry.SymmData) -> NoneType replaced_symmetric_foldtree_with_new_monomer(...) method of builtins.PyCapsule instance replaced_symmetric_foldtree_with_new_monomer(symm_f : rosetta.core.kinematics.FoldTree, symmetry_info : rosetta.core.conformation.symmetry.SymmetryInfo, monomer_f : rosetta.core.kinematics.FoldTree) -> rosetta.core.kinematics.FoldTree residue_center_of_mass(...) method of builtins.PyCapsule instance residue_center_of_mass(conformation : rosetta.core.conformation.Conformation, start : int, stop : int) -> int return_nearest_residue(...) method of builtins.PyCapsule instance return_nearest_residue(conformation : rosetta.core.conformation.Conformation, begin : int, end : int, center : rosetta.numeric.xyzVector_double_t) -> int set_asymm_unit_fold_tree(...) method of builtins.PyCapsule instance set_asymm_unit_fold_tree(p : rosetta.core.conformation.Conformation, f : rosetta.core.kinematics.FoldTree) -> NoneType set_fold_tree_from_symm_data(...) method of builtins.PyCapsule instance set_fold_tree_from_symm_data(*args, **kwargs) Overloaded function.   1. set_fold_tree_from_symm_data(src_conformation : rosetta.core.conformation.Conformation, symmdata : rosetta.core.conformation.symmetry.SymmData) -> rosetta.core.kinematics.FoldTree   2. set_fold_tree_from_symm_data(src_conformation : rosetta.core.conformation.Conformation, symmdata : rosetta.core.conformation.symmetry.SymmData, conf2pdb_chain : rosetta.std.map_int_char) -> rosetta.core.kinematics.FoldTree setup_symmetric_conformation(...) method of builtins.PyCapsule instance setup_symmetric_conformation(*args, **kwargs) Overloaded function.   1. setup_symmetric_conformation(src_conformation : rosetta.core.conformation.Conformation, symmdata : rosetta.core.conformation.symmetry.SymmData) -> rosetta.core.conformation.symmetry.SymmetricConformation   2. setup_symmetric_conformation(src_conformation : rosetta.core.conformation.Conformation, symmdata : rosetta.core.conformation.symmetry.SymmData, conf2pdb_chain : rosetta.std.map_int_char) -> rosetta.core.conformation.symmetry.SymmetricConformation shift_jump_numbers_in_dofs(...) method of builtins.PyCapsule instance shift_jump_numbers_in_dofs(src_conformation : rosetta.core.conformation.Conformation, shift : int) -> NoneType show_foldtree(...) method of builtins.PyCapsule instance show_foldtree(symm_conf : rosetta.core.conformation.symmetry.SymmetricConformation, symdata : rosetta.core.conformation.symmetry.SymmData, chain2range : rosetta.std.map_char_std_pair_unsigned_long_unsigned_long_t) -> str symmetrize_fold_tree(...) method of builtins.PyCapsule instance symmetrize_fold_tree(conf : rosetta.core.conformation.Conformation, f : rosetta.core.kinematics.FoldTree) -> NoneType   Converts an asymmetric foldtree (f) with virtual root into a            symmetric foldtree compatible with symmetric conformation (conf)      - A symmetric conformation      - An asymmetric foldtree. This foldtree MUST have a virtual root       This function does not require the symm data

Data
		CEN_DOCK_SCORE = SlideCriteriaType.CEN_DOCK_SCORE CONTACTS = SlideCriteriaType.CONTACTS FA_REP_SCORE = SlideCriteriaType.FA_REP_SCORE ORDERED_SEQUENTIAL = SlideType.ORDERED_SEQUENTIAL RANDOM = SlideType.RANDOM SEQUENTIAL = SlideType.SEQUENTIAL TOTAL_NUM_CRITERIA = SlideCriteriaType.TOTAL_NUM_CRITERIA X_ANGLE_DOF = dof_type.X_ANGLE_DOF X_DOF = dof_type.X_DOF Y_ANGLE_DOF = dof_type.Y_ANGLE_DOF Y_DOF = dof_type.Y_DOF Z_ANGLE_DOF = dof_type.Z_ANGLE_DOF Z_DOF = dof_type.Z_DOF