Bindings for core::io::silent namespace

Classes
		builtins.object SharedSilentData EnergyNames SimpleSequenceData SharedSilentDataType SilentEnergy SilentFileData SilentStruct BinarySilentStruct RNA_SilentStruct RigidBodySilentStruct ScoreFileSilentStruct ScoreJumpFileSilentStruct SilentStructCreator BinarySilentStructCreator ProteinSilentStructCreator ProteinSilentStruct_SinglePrecCreator RNA_SilentStructCreator RigidBodySilentStructCreator ScoreFileSilentStructCreator ScoreJumpFileSilentStructCreator rosetta.basic.resource_manager.ResourceLoader(builtins.object) SilentFileLoader rosetta.basic.resource_manager.ResourceLoaderCreator(builtins.object) SilentFileLoaderCreator rosetta.basic.resource_manager.ResourceOptions(builtins.object) SilentFileOptions rosetta.basic.resource_manager.ResourceOptionsCreator(builtins.object) SilentFileOptionsCreator rosetta.utility.SingletonBase_core_io_silent_SilentStructFactory_t(builtins.object) SilentStructFactory   class BinarySilentStruct(SilentStruct)       Method resolution order: BinarySilentStruct SilentStruct builtins.object Methods defined here: CA_rmsd(...) from builtins.PyCapsule CA_rmsd(self : rosetta.core.io.silent.BinarySilentStruct, other_pss : rosetta.core.io.silent.BinarySilentStruct) -> float __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(self : handle, nres_in : int) -> NoneType   2. __init__(handle) -> NoneType   3. __init__(handle, rosetta.core.pose.Pose) -> NoneType   doc   4. __init__(self : handle, pose : rosetta.core.pose.Pose, tag : str) -> NoneType   5. __init__(handle, rosetta.core.io.silent.BinarySilentStruct) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. add_chain_ending(...) from builtins.PyCapsule add_chain_ending(self : rosetta.core.io.silent.BinarySilentStruct, seqpos : int) -> NoneType add_jump(...) from builtins.PyCapsule add_jump(self : rosetta.core.io.silent.BinarySilentStruct, jump : rosetta.core.kinematics.Jump) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.core.io.silent.BinarySilentStruct, src : rosetta.core.io.silent.BinarySilentStruct) -> rosetta.core.io.silent.BinarySilentStruct   Test if this BinarySilentStruct is equal to the given  BinarySilentStruct in terms of conformation.  Doesn't check  energies. chain_endings(...) from builtins.PyCapsule chain_endings(*args, **kwargs) Overloaded function.   1. chain_endings(self : rosetta.core.io.silent.BinarySilentStruct, endings : rosetta.utility.vector1_unsigned_long) -> NoneType   2. chain_endings(rosetta.core.io.silent.BinarySilentStruct) -> rosetta.utility.vector1_unsigned_long chain_endings_str(...) from builtins.PyCapsule chain_endings_str(rosetta.core.io.silent.BinarySilentStruct) -> str clone(...) from builtins.PyCapsule clone(rosetta.core.io.silent.BinarySilentStruct) -> rosetta.core.io.silent.SilentStruct fill_pose(...) from builtins.PyCapsule fill_pose(*args, **kwargs) Overloaded function.   1. fill_pose(self : rosetta.core.io.silent.BinarySilentStruct, pose : rosetta.core.pose.Pose) -> NoneType   Configure the conformation of the given Pose with the  conformational data within this BinarySilentStruct. Calls  pose.clear() and rebuilds Pose from scratch using FA_STANDARD residue  types.   2. fill_pose(self : rosetta.core.io.silent.BinarySilentStruct, pose : rosetta.core.pose.Pose, residue_set : rosetta.core.chemical.ResidueTypeSet) -> NoneType   Configure the conformation of the given Pose with the  conformational data within this BinarySilentStruct. Calls  pose.clear() and rebuilds Pose from scratch using the user-specified  residue types. fill_struct(...) from builtins.PyCapsule fill_struct(self : rosetta.core.io.silent.BinarySilentStruct, pose : rosetta.core.pose.Pose, tag : str) -> NoneType   opposite of fill_pose fold_tree(...) from builtins.PyCapsule fold_tree(*args, **kwargs) Overloaded function.   1. fold_tree(self : rosetta.core.io.silent.BinarySilentStruct, f : rosetta.core.kinematics.FoldTree) -> NoneType   2. fold_tree(rosetta.core.io.silent.BinarySilentStruct) -> rosetta.core.kinematics.FoldTree fullatom(...) from builtins.PyCapsule fullatom(*args, **kwargs) Overloaded function.   1. fullatom(rosetta.core.io.silent.BinarySilentStruct) -> bool   2. fullatom(self : rosetta.core.io.silent.BinarySilentStruct, fullatom : bool) -> NoneType get_CA_xyz(...) from builtins.PyCapsule get_CA_xyz(rosetta.core.io.silent.BinarySilentStruct) -> ObjexxFCL::FArray2D<double>   returns the positions of the CA atoms get_debug_rmsd(...) from builtins.PyCapsule get_debug_rmsd(rosetta.core.io.silent.BinarySilentStruct) -> float   calculates the RMSD between the C-alpha atoms of a Pose built from  the torsions in this ProteinSilentStruct and the C-alpha atoms from this  ProteinSilentStruct. init_from_lines(...) from builtins.PyCapsule init_from_lines(self : rosetta.core.io.silent.BinarySilentStruct, lines : rosetta.utility.vector1_std_string, container : rosetta.core.io.silent.SilentFileData) -> bool   Initialize object from a set of lines is_symmetric(...) from builtins.PyCapsule is_symmetric(rosetta.core.io.silent.BinarySilentStruct) -> bool jump(...) from builtins.PyCapsule jump(self : rosetta.core.io.silent.BinarySilentStruct, jump_num : int) -> rosetta.core.kinematics.RT resize(...) from builtins.PyCapsule resize(self : rosetta.core.io.silent.BinarySilentStruct, nres_in : int) -> NoneType   Re-dimension the storage capacity of this BinarySilentStruct to the given number of residues. secstruct(...) from builtins.PyCapsule secstruct(*args, **kwargs) Overloaded function.   1. secstruct(self : rosetta.core.io.silent.BinarySilentStruct, seqpos : int) -> str   2. secstruct(self : rosetta.core.io.silent.BinarySilentStruct, seqpos : int, ss : str) -> NoneType setup_other_poses(...) from builtins.PyCapsule setup_other_poses(self : rosetta.core.io.silent.BinarySilentStruct, pose : rosetta.core.pose.Pose, residue_set : rosetta.core.chemical.ResidueTypeSet) -> NoneType   for stepwise modeling, setup other_poses inside full_model_info shared_from_this(...) from builtins.PyCapsule shared_from_this(rosetta.core.io.silent.BinarySilentStruct) -> rosetta.core.io.silent.BinarySilentStruct symmetry_info(...) from builtins.PyCapsule symmetry_info(*args, **kwargs) Overloaded function.   1. symmetry_info(self : rosetta.core.io.silent.BinarySilentStruct, s : rosetta.core.conformation.symmetry.SymmetryInfo) -> NoneType   2. symmetry_info(rosetta.core.io.silent.BinarySilentStruct) -> rosetta.core.conformation.symmetry.SymmetryInfo Methods inherited from SilentStruct: add_comment(...) from builtins.PyCapsule add_comment(self : rosetta.core.io.silent.SilentStruct, name : str, value : str) -> NoneType   add a named comment to this SilentStruct object.  Similar to methods for playing with energies, but  mapping is string => string rather than string => Real. add_energy(...) from builtins.PyCapsule add_energy(*args, **kwargs) Overloaded function.   1. add_energy(self : rosetta.core.io.silent.SilentStruct, scorename : str, value : float) -> NoneType   add a score of a given name and value to this SilentStruct.  Takes an optional weight that defaults to 1.0.   2. add_energy(self : rosetta.core.io.silent.SilentStruct, scorename : str, value : float, weight : float) -> NoneType   add a score of a given name and value to this SilentStruct.  Takes an optional weight that defaults to 1.0. add_other_struct(...) from builtins.PyCapsule add_other_struct(self : rosetta.core.io.silent.SilentStruct, silent_struct : rosetta.core.io.silent.SilentStruct) -> NoneType add_parent_remark(...) from builtins.PyCapsule add_parent_remark(self : rosetta.core.io.silent.SilentStruct, name : str, value : str) -> NoneType add_string_value(...) from builtins.PyCapsule add_string_value(self : rosetta.core.io.silent.SilentStruct, scorename : str, value : str) -> NoneType   add a non-floating point score of a given name and value to this  SilentStruct. clear_comments(...) from builtins.PyCapsule clear_comments(rosetta.core.io.silent.SilentStruct) -> NoneType clear_energies(...) from builtins.PyCapsule clear_energies(rosetta.core.io.silent.SilentStruct) -> NoneType   Clear all of the energies in the SilentStruct. Doesn't just  zero the energies, it entirely removes all knowledge of all energies  from this SilentStruct. comment_from_line(...) from builtins.PyCapsule comment_from_line(self : rosetta.core.io.silent.SilentStruct, line : str) -> NoneType copy_scores(...) from builtins.PyCapsule copy_scores(self : rosetta.core.io.silent.SilentStruct, src_ss : rosetta.core.io.silent.SilentStruct) -> NoneType   Copy the score information in the given SilentStruct into  this SilentStruct. decoy_tag(...) from builtins.PyCapsule decoy_tag(*args, **kwargs) Overloaded function.   1. decoy_tag(rosetta.core.io.silent.SilentStruct) -> str   returns the tag associated with this SilentStruct.   2. decoy_tag(self : rosetta.core.io.silent.SilentStruct, tag : str) -> NoneType   sets the tag associated with this SilentStruct. energies(...) from builtins.PyCapsule energies(rosetta.core.io.silent.SilentStruct) -> rosetta.utility.vector1_core_io_silent_SilentEnergy   Returns the vector of SilentEnergy objects associated with  this SilentStruct object. energies_from_pose(...) from builtins.PyCapsule energies_from_pose(self : rosetta.core.io.silent.SilentStruct, pose : rosetta.core.pose.Pose) -> NoneType   Initialize this SilentStruct's energies from the given Pose.  This sets energies, energy weights, and the output widths for the  energies. energies_into_pose(...) from builtins.PyCapsule energies_into_pose(self : rosetta.core.io.silent.SilentStruct, pose : rosetta.core.pose.Pose) -> NoneType   Put the energy information from this SilentStruct into the  pose. Energies that correspond to a ScoreType are put into the  pose.energies().total_energies() EnergyMap, all other energies are  put into the ARBITRARY_FLOAT_DATA map in the pose DataCache. Also  sets the scorefxn_weights in the Energies object using the  information from this SilentStruct. energy_names(...) from builtins.PyCapsule energy_names(rosetta.core.io.silent.SilentStruct) -> core::io::silent::EnergyNames   Returns the EnergyNames that this SilentStruct contains. erase_comment(...) from builtins.PyCapsule erase_comment(self : rosetta.core.io.silent.SilentStruct, name : str) -> NoneType fill_other_struct_list(...) from builtins.PyCapsule fill_other_struct_list(self : rosetta.core.io.silent.SilentStruct, pose : rosetta.core.pose.Pose) -> NoneType fill_struct_with_residue_numbers(...) from builtins.PyCapsule fill_struct_with_residue_numbers(self : rosetta.core.io.silent.SilentStruct, pose : rosetta.core.pose.Pose) -> NoneType fill_struct_with_submotif_info_list(...) from builtins.PyCapsule fill_struct_with_submotif_info_list(self : rosetta.core.io.silent.SilentStruct, pose : rosetta.core.pose.Pose) -> NoneType finish_pose(...) from builtins.PyCapsule finish_pose(self : rosetta.core.io.silent.SilentStruct, pose : rosetta.core.pose.Pose) -> NoneType   calls optH if command line requests optH.  must be called by derived classes. force_bitflip(...) from builtins.PyCapsule force_bitflip(rosetta.core.io.silent.SilentStruct) -> bool   Gets whether conversion from big-endian to little-endian (or the converse) should be forced  when a binary silent structure is initialized from lines. full_model_info_into_pose(...) from builtins.PyCapsule full_model_info_into_pose(self : rosetta.core.io.silent.SilentStruct, pose : rosetta.core.pose.Pose) -> NoneType full_model_parameters(...) from builtins.PyCapsule full_model_parameters(rosetta.core.io.silent.SilentStruct) -> rosetta.core.pose.full_model_info.FullModelParameters get_all_comments(...) from builtins.PyCapsule get_all_comments(rosetta.core.io.silent.SilentStruct) -> rosetta.std.map_std_string_std_string get_comment(...) from builtins.PyCapsule get_comment(self : rosetta.core.io.silent.SilentStruct, name : str) -> str get_energy(...) from builtins.PyCapsule get_energy(self : rosetta.core.io.silent.SilentStruct, scorename : str) -> float   Returns the energy associated with the given scorename if this  SilentStruct has an energy for that scorename. Otherwise returns 0. get_parent_remark(...) from builtins.PyCapsule get_parent_remark(self : rosetta.core.io.silent.SilentStruct, name : str) -> str get_parent_remark_from_line(...) from builtins.PyCapsule get_parent_remark_from_line(self : rosetta.core.io.silent.SilentStruct, line : str) -> NoneType get_self_ptr(...) from builtins.PyCapsule get_self_ptr(*args, **kwargs) Overloaded function.   1. get_self_ptr(rosetta.core.io.silent.SilentStruct) -> rosetta.core.io.silent.SilentStruct   self pointers   2. get_self_ptr(rosetta.core.io.silent.SilentStruct) -> rosetta.core.io.silent.SilentStruct get_silent_energies(...) from builtins.PyCapsule get_silent_energies(rosetta.core.io.silent.SilentStruct) -> rosetta.utility.vector1_core_io_silent_SilentEnergy get_silent_energy(...) from builtins.PyCapsule get_silent_energy(self : rosetta.core.io.silent.SilentStruct, scorename : str) -> rosetta.core.io.silent.SilentEnergy   Returns the SilentEnergy associated with this scorename. get_string_value(...) from builtins.PyCapsule get_string_value(self : rosetta.core.io.silent.SilentStruct, scorename : str) -> str   Returns the energy associated with the given scorename if this  SilentStruct has an energy for that scorename. Otherwise returns 0. has_comment(...) from builtins.PyCapsule has_comment(self : rosetta.core.io.silent.SilentStruct, name : str) -> bool has_energy(...) from builtins.PyCapsule has_energy(self : rosetta.core.io.silent.SilentStruct, scorename : str) -> bool   returns true if this SilentStruct has an energy for the given  scorename, returns false otherwise. has_parent_remark(...) from builtins.PyCapsule has_parent_remark(self : rosetta.core.io.silent.SilentStruct, name : str) -> bool mem_footprint(...) from builtins.PyCapsule mem_footprint(rosetta.core.io.silent.SilentStruct) -> int nonconst_other_struct_list(...) from builtins.PyCapsule nonconst_other_struct_list(rosetta.core.io.silent.SilentStruct) -> rosetta.utility.vector1_std_shared_ptr_core_io_silent_SilentStruct_t nres(...) from builtins.PyCapsule nres(*args, **kwargs) Overloaded function.   1. nres(rosetta.core.io.silent.SilentStruct) -> int   returns the number of residues contained by this  SilentStruct.   2. nres(self : rosetta.core.io.silent.SilentStruct, nres : int) -> NoneType   returns the number of residues in this SilentStruct. one_letter_sequence(...) from builtins.PyCapsule one_letter_sequence(rosetta.core.io.silent.SilentStruct) -> str   strip [...] comment from seqeunce_ and return pure  one-letter sequence other_struct_list(...) from builtins.PyCapsule other_struct_list(rosetta.core.io.silent.SilentStruct) -> rosetta.utility.vector1_std_shared_ptr_core_io_silent_SilentStruct_t precision(...) from builtins.PyCapsule precision(*args, **kwargs) Overloaded function.   1. precision(self : rosetta.core.io.silent.SilentStruct, precision : int) -> NoneType   2. precision(rosetta.core.io.silent.SilentStruct) -> int read_score_headers(...) from builtins.PyCapsule read_score_headers(self : rosetta.core.io.silent.SilentStruct, line : str, enames : rosetta.utility.vector1_std_string, container : rosetta.core.io.silent.SilentFileData) -> NoneType read_sequence(...) from builtins.PyCapsule read_sequence(self : rosetta.core.io.silent.SilentStruct, line : str) -> bool rename_energies(...) from builtins.PyCapsule rename_energies(rosetta.core.io.silent.SilentStruct) -> NoneType residue_numbers_into_pose(...) from builtins.PyCapsule residue_numbers_into_pose(self : rosetta.core.io.silent.SilentStruct, pose : rosetta.core.pose.Pose) -> NoneType scoreline_prefix(...) from builtins.PyCapsule scoreline_prefix(*args, **kwargs) Overloaded function.   1. scoreline_prefix(self : rosetta.core.io.silent.SilentStruct, prefix : str) -> NoneType   2. scoreline_prefix(rosetta.core.io.silent.SilentStruct) -> str sequence(...) from builtins.PyCapsule sequence(*args, **kwargs) Overloaded function.   1. sequence(rosetta.core.io.silent.SilentStruct) -> rosetta.core.sequence.AnnotatedSequence   returns the sequence associated with this SilentStruct.   2. sequence(self : rosetta.core.io.silent.SilentStruct, sequence : rosetta.core.sequence.AnnotatedSequence) -> NoneType   sets the sequence for this SilentStruct. set_chains(...) from builtins.PyCapsule set_chains(self : rosetta.core.io.silent.SilentStruct, chains : rosetta.utility.vector1_char) -> NoneType set_decoy_tag(...) from builtins.PyCapsule set_decoy_tag(self : rosetta.core.io.silent.SilentStruct, tag : str) -> NoneType   set the tag associate with this SilentStruct set_force_bitflip(...) from builtins.PyCapsule set_force_bitflip(self : rosetta.core.io.silent.SilentStruct, setting : bool) -> NoneType   Sets whether conversion from big-endian to little-endian (or the converse) should be forced  when a binary silent structure is initialized from lines. set_full_model_parameters(...) from builtins.PyCapsule set_full_model_parameters(self : rosetta.core.io.silent.SilentStruct, setting : rosetta.core.pose.full_model_info.FullModelParameters) -> NoneType set_residue_numbers(...) from builtins.PyCapsule set_residue_numbers(self : rosetta.core.io.silent.SilentStruct, residue_numbers : rosetta.utility.vector1_unsigned_long) -> NoneType set_segment_IDs(...) from builtins.PyCapsule set_segment_IDs(self : rosetta.core.io.silent.SilentStruct, segids : rosetta.utility.vector1_std_string) -> NoneType set_tag_from_pose(...) from builtins.PyCapsule set_tag_from_pose(self : rosetta.core.io.silent.SilentStruct, pose : rosetta.core.pose.Pose) -> NoneType   Sets the tag from the Pose DataCache. set_valid_energies(...) from builtins.PyCapsule set_valid_energies(self : rosetta.core.io.silent.SilentStruct, valid : rosetta.utility.vector1_std_string) -> NoneType silent_energies(...) from builtins.PyCapsule silent_energies(self : rosetta.core.io.silent.SilentStruct, new_se : rosetta.utility.vector1_core_io_silent_SilentEnergy) -> NoneType   sets the silent_energies for this SilentStruct. sort_silent_scores(...) from builtins.PyCapsule sort_silent_scores(rosetta.core.io.silent.SilentStruct) -> NoneType   sort all the silent energies by their name.   class BinarySilentStructCreator(SilentStructCreator)     creator for the BinarySilentStruct class     Method resolution order: BinarySilentStructCreator SilentStructCreator 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.io.silent.BinarySilentStructCreator,  : rosetta.core.io.silent.BinarySilentStructCreator) -> rosetta.core.io.silent.BinarySilentStructCreator create_silent_struct(...) from builtins.PyCapsule create_silent_struct(rosetta.core.io.silent.BinarySilentStructCreator) -> rosetta.core.io.silent.SilentStruct keyname(...) from builtins.PyCapsule keyname(rosetta.core.io.silent.BinarySilentStructCreator) -> str   class EnergyNames(SharedSilentData)       Method resolution order: EnergyNames SharedSilentData builtins.object Methods defined here: __eq__(...) from builtins.PyCapsule __eq__(self : rosetta.core.io.silent.EnergyNames, other : rosetta.core.io.silent.EnergyNames) -> bool __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.core.io.silent.EnergyNames) -> NoneType   2. __init__(self : rosetta.core.io.silent.EnergyNames, line : str) -> 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.io.silent.EnergyNames,  : rosetta.core.io.silent.EnergyNames) -> rosetta.core.io.silent.EnergyNames energy_names(...) from builtins.PyCapsule energy_names(*args, **kwargs) Overloaded function.   1. energy_names(self : rosetta.core.io.silent.EnergyNames, new_e_names : rosetta.utility.vector1_std_string) -> NoneType   2. energy_names(rosetta.core.io.silent.EnergyNames) -> rosetta.utility.vector1_std_string   class ProteinSilentStructCreator(SilentStructCreator)     creator for the ProteinSilentStruct class     Method resolution order: ProteinSilentStructCreator SilentStructCreator 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.io.silent.ProteinSilentStructCreator,  : rosetta.core.io.silent.ProteinSilentStructCreator) -> rosetta.core.io.silent.ProteinSilentStructCreator create_silent_struct(...) from builtins.PyCapsule create_silent_struct(rosetta.core.io.silent.ProteinSilentStructCreator) -> rosetta.core.io.silent.SilentStruct keyname(...) from builtins.PyCapsule keyname(rosetta.core.io.silent.ProteinSilentStructCreator) -> str   class ProteinSilentStruct_SinglePrecCreator(SilentStructCreator)     creator for the ProteinSilentStruct_SinglePrec class     Method resolution order: ProteinSilentStruct_SinglePrecCreator SilentStructCreator 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.io.silent.ProteinSilentStruct_SinglePrecCreator,  : rosetta.core.io.silent.ProteinSilentStruct_SinglePrecCreator) -> rosetta.core.io.silent.ProteinSilentStruct_SinglePrecCreator create_silent_struct(...) from builtins.PyCapsule create_silent_struct(rosetta.core.io.silent.ProteinSilentStruct_SinglePrecCreator) -> rosetta.core.io.silent.SilentStruct keyname(...) from builtins.PyCapsule keyname(rosetta.core.io.silent.ProteinSilentStruct_SinglePrecCreator) -> str   class RNA_SilentStruct(SilentStruct)       Method resolution order: RNA_SilentStruct SilentStruct builtins.object Methods defined here: CA_rmsd(...) from builtins.PyCapsule CA_rmsd(self : rosetta.core.io.silent.RNA_SilentStruct, other_pss : rosetta.core.io.silent.RNA_SilentStruct) -> float __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(self : handle, nres_in : int) -> NoneType   2. __init__(handle) -> NoneType   3. __init__(handle, rosetta.core.pose.Pose) -> NoneType   doc   4. __init__(handle, rosetta.core.pose.Pose, str) -> NoneType   doc   5. __init__(self : handle, pose : rosetta.core.pose.Pose, tag : str, fa : bool) -> NoneType   6. __init__(handle, rosetta.core.io.silent.RNA_SilentStruct) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. add_jump(...) from builtins.PyCapsule add_jump(self : rosetta.core.io.silent.RNA_SilentStruct, jump : rosetta.core.kinematics.Jump) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.core.io.silent.RNA_SilentStruct, src : rosetta.core.io.silent.RNA_SilentStruct) -> rosetta.core.io.silent.RNA_SilentStruct   Test if this RNA_SilentStruct is equal to the given RNA_SilentStruct in terms of conformation.  Doesn't check energies. chi(...) from builtins.PyCapsule chi(self : rosetta.core.io.silent.RNA_SilentStruct, seqpos : int, torsion_num : int) -> float chi_torsions(...) from builtins.PyCapsule chi_torsions(self : rosetta.core.io.silent.RNA_SilentStruct, seqpos : int) -> rosetta.utility.vector1_double clone(...) from builtins.PyCapsule clone(rosetta.core.io.silent.RNA_SilentStruct) -> rosetta.core.io.silent.SilentStruct coords(...) from builtins.PyCapsule coords(*args, **kwargs) Overloaded function.   1. coords(self : rosetta.core.io.silent.RNA_SilentStruct, seqpos : int) -> rosetta.numeric.xyzVector_double_t   2. coords(rosetta.core.io.silent.RNA_SilentStruct) -> rosetta.utility.vector1_numeric_xyzVector_double_t fill_pose(...) from builtins.PyCapsule fill_pose(*args, **kwargs) Overloaded function.   1. fill_pose(self : rosetta.core.io.silent.RNA_SilentStruct, pose : rosetta.core.pose.Pose) -> NoneType   Configure the conformation of the given Pose with the conformational data within this RNA_SilentStruct.  Calls pose.clear() and rebuilds Pose from scratch using FA_STANDARD residue types.   2. fill_pose(self : rosetta.core.io.silent.RNA_SilentStruct, pose : rosetta.core.pose.Pose, residue_set : rosetta.core.chemical.ResidueTypeSet) -> NoneType   Configure the conformation of the given Pose with the conformational data within  this RNA_SilentStruct. Calls pose.clear() and rebuilds Pose from scratch using the  user-specified residue types. fill_struct(...) from builtins.PyCapsule fill_struct(self : rosetta.core.io.silent.RNA_SilentStruct, pose : rosetta.core.pose.Pose, tag : str) -> NoneType   opposite of fill_pose fold_tree(...) from builtins.PyCapsule fold_tree(rosetta.core.io.silent.RNA_SilentStruct) -> rosetta.core.kinematics.FoldTree fullatom(...) from builtins.PyCapsule fullatom(*args, **kwargs) Overloaded function.   1. fullatom(rosetta.core.io.silent.RNA_SilentStruct) -> bool   data getters/setters   2. fullatom(self : rosetta.core.io.silent.RNA_SilentStruct, fullatom : bool) -> NoneType get_CA_xyz(...) from builtins.PyCapsule get_CA_xyz(rosetta.core.io.silent.RNA_SilentStruct) -> ObjexxFCL::FArray2D<double>   returns the positions of the CA atoms in this RNA_SilentStruct.  Useful for RMS calculations. get_debug_rmsd(...) from builtins.PyCapsule get_debug_rmsd(rosetta.core.io.silent.RNA_SilentStruct) -> float   calculates the RMSD between the C-alpha atoms of a Pose built from the torsions in this  RNA_SilentStruct and the C-alpha atoms from this RNA_SilentStruct. init_from_lines(...) from builtins.PyCapsule init_from_lines(self : rosetta.core.io.silent.RNA_SilentStruct, lines : rosetta.utility.vector1_std_string, container : rosetta.core.io.silent.SilentFileData) -> bool   Tells this RNA_SilentStruct object to initialize itself from the given set of lines. Lines should  be of the format jump(...) from builtins.PyCapsule jump(self : rosetta.core.io.silent.RNA_SilentStruct, jump_num : int) -> rosetta.core.kinematics.Jump mainchain_torsion(...) from builtins.PyCapsule mainchain_torsion(self : rosetta.core.io.silent.RNA_SilentStruct, seqpos : int, torsion_num : int) -> float mainchain_torsions(...) from builtins.PyCapsule mainchain_torsions(self : rosetta.core.io.silent.RNA_SilentStruct, seqpos : int) -> rosetta.utility.vector1_double resize(...) from builtins.PyCapsule resize(self : rosetta.core.io.silent.RNA_SilentStruct, nres_in : int) -> NoneType   Re-dimension the storage capacity of this RNA_SilentStruct to the given number of residues. secstruct(...) from builtins.PyCapsule secstruct(self : rosetta.core.io.silent.RNA_SilentStruct, seqpos : int) -> str set_chi_torsions(...) from builtins.PyCapsule set_chi_torsions(self : rosetta.core.io.silent.RNA_SilentStruct, seqpos : int, torsions : rosetta.utility.vector1_double) -> NoneType set_coords(...) from builtins.PyCapsule set_coords(self : rosetta.core.io.silent.RNA_SilentStruct, seqpos : int, coords : rosetta.numeric.xyzVector_double_t) -> NoneType set_fold_tree(...) from builtins.PyCapsule set_fold_tree(self : rosetta.core.io.silent.RNA_SilentStruct, f : rosetta.core.kinematics.FoldTree) -> NoneType set_mainchain_torsions(...) from builtins.PyCapsule set_mainchain_torsions(self : rosetta.core.io.silent.RNA_SilentStruct, seqpos : int, torsions : rosetta.utility.vector1_double) -> NoneType set_non_main_chain_sugar_coords(...) from builtins.PyCapsule set_non_main_chain_sugar_coords(self : rosetta.core.io.silent.RNA_SilentStruct, seqpos : int, vecs : rosetta.utility.vector1_numeric_xyzVector_double_t) -> NoneType set_secstruct(...) from builtins.PyCapsule set_secstruct(self : rosetta.core.io.silent.RNA_SilentStruct, seqpos : int, ss : str) -> NoneType Methods inherited from SilentStruct: add_comment(...) from builtins.PyCapsule add_comment(self : rosetta.core.io.silent.SilentStruct, name : str, value : str) -> NoneType   add a named comment to this SilentStruct object.  Similar to methods for playing with energies, but  mapping is string => string rather than string => Real. add_energy(...) from builtins.PyCapsule add_energy(*args, **kwargs) Overloaded function.   1. add_energy(self : rosetta.core.io.silent.SilentStruct, scorename : str, value : float) -> NoneType   add a score of a given name and value to this SilentStruct.  Takes an optional weight that defaults to 1.0.   2. add_energy(self : rosetta.core.io.silent.SilentStruct, scorename : str, value : float, weight : float) -> NoneType   add a score of a given name and value to this SilentStruct.  Takes an optional weight that defaults to 1.0. add_other_struct(...) from builtins.PyCapsule add_other_struct(self : rosetta.core.io.silent.SilentStruct, silent_struct : rosetta.core.io.silent.SilentStruct) -> NoneType add_parent_remark(...) from builtins.PyCapsule add_parent_remark(self : rosetta.core.io.silent.SilentStruct, name : str, value : str) -> NoneType add_string_value(...) from builtins.PyCapsule add_string_value(self : rosetta.core.io.silent.SilentStruct, scorename : str, value : str) -> NoneType   add a non-floating point score of a given name and value to this  SilentStruct. clear_comments(...) from builtins.PyCapsule clear_comments(rosetta.core.io.silent.SilentStruct) -> NoneType clear_energies(...) from builtins.PyCapsule clear_energies(rosetta.core.io.silent.SilentStruct) -> NoneType   Clear all of the energies in the SilentStruct. Doesn't just  zero the energies, it entirely removes all knowledge of all energies  from this SilentStruct. comment_from_line(...) from builtins.PyCapsule comment_from_line(self : rosetta.core.io.silent.SilentStruct, line : str) -> NoneType copy_scores(...) from builtins.PyCapsule copy_scores(self : rosetta.core.io.silent.SilentStruct, src_ss : rosetta.core.io.silent.SilentStruct) -> NoneType   Copy the score information in the given SilentStruct into  this SilentStruct. decoy_tag(...) from builtins.PyCapsule decoy_tag(*args, **kwargs) Overloaded function.   1. decoy_tag(rosetta.core.io.silent.SilentStruct) -> str   returns the tag associated with this SilentStruct.   2. decoy_tag(self : rosetta.core.io.silent.SilentStruct, tag : str) -> NoneType   sets the tag associated with this SilentStruct. energies(...) from builtins.PyCapsule energies(rosetta.core.io.silent.SilentStruct) -> rosetta.utility.vector1_core_io_silent_SilentEnergy   Returns the vector of SilentEnergy objects associated with  this SilentStruct object. energies_from_pose(...) from builtins.PyCapsule energies_from_pose(self : rosetta.core.io.silent.SilentStruct, pose : rosetta.core.pose.Pose) -> NoneType   Initialize this SilentStruct's energies from the given Pose.  This sets energies, energy weights, and the output widths for the  energies. energies_into_pose(...) from builtins.PyCapsule energies_into_pose(self : rosetta.core.io.silent.SilentStruct, pose : rosetta.core.pose.Pose) -> NoneType   Put the energy information from this SilentStruct into the  pose. Energies that correspond to a ScoreType are put into the  pose.energies().total_energies() EnergyMap, all other energies are  put into the ARBITRARY_FLOAT_DATA map in the pose DataCache. Also  sets the scorefxn_weights in the Energies object using the  information from this SilentStruct. energy_names(...) from builtins.PyCapsule energy_names(rosetta.core.io.silent.SilentStruct) -> core::io::silent::EnergyNames   Returns the EnergyNames that this SilentStruct contains. erase_comment(...) from builtins.PyCapsule erase_comment(self : rosetta.core.io.silent.SilentStruct, name : str) -> NoneType fill_other_struct_list(...) from builtins.PyCapsule fill_other_struct_list(self : rosetta.core.io.silent.SilentStruct, pose : rosetta.core.pose.Pose) -> NoneType fill_struct_with_residue_numbers(...) from builtins.PyCapsule fill_struct_with_residue_numbers(self : rosetta.core.io.silent.SilentStruct, pose : rosetta.core.pose.Pose) -> NoneType fill_struct_with_submotif_info_list(...) from builtins.PyCapsule fill_struct_with_submotif_info_list(self : rosetta.core.io.silent.SilentStruct, pose : rosetta.core.pose.Pose) -> NoneType finish_pose(...) from builtins.PyCapsule finish_pose(self : rosetta.core.io.silent.SilentStruct, pose : rosetta.core.pose.Pose) -> NoneType   calls optH if command line requests optH.  must be called by derived classes. force_bitflip(...) from builtins.PyCapsule force_bitflip(rosetta.core.io.silent.SilentStruct) -> bool   Gets whether conversion from big-endian to little-endian (or the converse) should be forced  when a binary silent structure is initialized from lines. full_model_info_into_pose(...) from builtins.PyCapsule full_model_info_into_pose(self : rosetta.core.io.silent.SilentStruct, pose : rosetta.core.pose.Pose) -> NoneType full_model_parameters(...) from builtins.PyCapsule full_model_parameters(rosetta.core.io.silent.SilentStruct) -> rosetta.core.pose.full_model_info.FullModelParameters get_all_comments(...) from builtins.PyCapsule get_all_comments(rosetta.core.io.silent.SilentStruct) -> rosetta.std.map_std_string_std_string get_comment(...) from builtins.PyCapsule get_comment(self : rosetta.core.io.silent.SilentStruct, name : str) -> str get_energy(...) from builtins.PyCapsule get_energy(self : rosetta.core.io.silent.SilentStruct, scorename : str) -> float   Returns the energy associated with the given scorename if this  SilentStruct has an energy for that scorename. Otherwise returns 0. get_parent_remark(...) from builtins.PyCapsule get_parent_remark(self : rosetta.core.io.silent.SilentStruct, name : str) -> str get_parent_remark_from_line(...) from builtins.PyCapsule get_parent_remark_from_line(self : rosetta.core.io.silent.SilentStruct, line : str) -> NoneType get_self_ptr(...) from builtins.PyCapsule get_self_ptr(*args, **kwargs) Overloaded function.   1. get_self_ptr(rosetta.core.io.silent.SilentStruct) -> rosetta.core.io.silent.SilentStruct   self pointers   2. get_self_ptr(rosetta.core.io.silent.SilentStruct) -> rosetta.core.io.silent.SilentStruct get_silent_energies(...) from builtins.PyCapsule get_silent_energies(rosetta.core.io.silent.SilentStruct) -> rosetta.utility.vector1_core_io_silent_SilentEnergy get_silent_energy(...) from builtins.PyCapsule get_silent_energy(self : rosetta.core.io.silent.SilentStruct, scorename : str) -> rosetta.core.io.silent.SilentEnergy   Returns the SilentEnergy associated with this scorename. get_string_value(...) from builtins.PyCapsule get_string_value(self : rosetta.core.io.silent.SilentStruct, scorename : str) -> str   Returns the energy associated with the given scorename if this  SilentStruct has an energy for that scorename. Otherwise returns 0. has_comment(...) from builtins.PyCapsule has_comment(self : rosetta.core.io.silent.SilentStruct, name : str) -> bool has_energy(...) from builtins.PyCapsule has_energy(self : rosetta.core.io.silent.SilentStruct, scorename : str) -> bool   returns true if this SilentStruct has an energy for the given  scorename, returns false otherwise. has_parent_remark(...) from builtins.PyCapsule has_parent_remark(self : rosetta.core.io.silent.SilentStruct, name : str) -> bool mem_footprint(...) from builtins.PyCapsule mem_footprint(rosetta.core.io.silent.SilentStruct) -> int nonconst_other_struct_list(...) from builtins.PyCapsule nonconst_other_struct_list(rosetta.core.io.silent.SilentStruct) -> rosetta.utility.vector1_std_shared_ptr_core_io_silent_SilentStruct_t nres(...) from builtins.PyCapsule nres(*args, **kwargs) Overloaded function.   1. nres(rosetta.core.io.silent.SilentStruct) -> int   returns the number of residues contained by this  SilentStruct.   2. nres(self : rosetta.core.io.silent.SilentStruct, nres : int) -> NoneType   returns the number of residues in this SilentStruct. one_letter_sequence(...) from builtins.PyCapsule one_letter_sequence(rosetta.core.io.silent.SilentStruct) -> str   strip [...] comment from seqeunce_ and return pure  one-letter sequence other_struct_list(...) from builtins.PyCapsule other_struct_list(rosetta.core.io.silent.SilentStruct) -> rosetta.utility.vector1_std_shared_ptr_core_io_silent_SilentStruct_t precision(...) from builtins.PyCapsule precision(*args, **kwargs) Overloaded function.   1. precision(self : rosetta.core.io.silent.SilentStruct, precision : int) -> NoneType   2. precision(rosetta.core.io.silent.SilentStruct) -> int read_score_headers(...) from builtins.PyCapsule read_score_headers(self : rosetta.core.io.silent.SilentStruct, line : str, enames : rosetta.utility.vector1_std_string, container : rosetta.core.io.silent.SilentFileData) -> NoneType read_sequence(...) from builtins.PyCapsule read_sequence(self : rosetta.core.io.silent.SilentStruct, line : str) -> bool rename_energies(...) from builtins.PyCapsule rename_energies(rosetta.core.io.silent.SilentStruct) -> NoneType residue_numbers_into_pose(...) from builtins.PyCapsule residue_numbers_into_pose(self : rosetta.core.io.silent.SilentStruct, pose : rosetta.core.pose.Pose) -> NoneType scoreline_prefix(...) from builtins.PyCapsule scoreline_prefix(*args, **kwargs) Overloaded function.   1. scoreline_prefix(self : rosetta.core.io.silent.SilentStruct, prefix : str) -> NoneType   2. scoreline_prefix(rosetta.core.io.silent.SilentStruct) -> str sequence(...) from builtins.PyCapsule sequence(*args, **kwargs) Overloaded function.   1. sequence(rosetta.core.io.silent.SilentStruct) -> rosetta.core.sequence.AnnotatedSequence   returns the sequence associated with this SilentStruct.   2. sequence(self : rosetta.core.io.silent.SilentStruct, sequence : rosetta.core.sequence.AnnotatedSequence) -> NoneType   sets the sequence for this SilentStruct. set_chains(...) from builtins.PyCapsule set_chains(self : rosetta.core.io.silent.SilentStruct, chains : rosetta.utility.vector1_char) -> NoneType set_decoy_tag(...) from builtins.PyCapsule set_decoy_tag(self : rosetta.core.io.silent.SilentStruct, tag : str) -> NoneType   set the tag associate with this SilentStruct set_force_bitflip(...) from builtins.PyCapsule set_force_bitflip(self : rosetta.core.io.silent.SilentStruct, setting : bool) -> NoneType   Sets whether conversion from big-endian to little-endian (or the converse) should be forced  when a binary silent structure is initialized from lines. set_full_model_parameters(...) from builtins.PyCapsule set_full_model_parameters(self : rosetta.core.io.silent.SilentStruct, setting : rosetta.core.pose.full_model_info.FullModelParameters) -> NoneType set_residue_numbers(...) from builtins.PyCapsule set_residue_numbers(self : rosetta.core.io.silent.SilentStruct, residue_numbers : rosetta.utility.vector1_unsigned_long) -> NoneType set_segment_IDs(...) from builtins.PyCapsule set_segment_IDs(self : rosetta.core.io.silent.SilentStruct, segids : rosetta.utility.vector1_std_string) -> NoneType set_tag_from_pose(...) from builtins.PyCapsule set_tag_from_pose(self : rosetta.core.io.silent.SilentStruct, pose : rosetta.core.pose.Pose) -> NoneType   Sets the tag from the Pose DataCache. set_valid_energies(...) from builtins.PyCapsule set_valid_energies(self : rosetta.core.io.silent.SilentStruct, valid : rosetta.utility.vector1_std_string) -> NoneType silent_energies(...) from builtins.PyCapsule silent_energies(self : rosetta.core.io.silent.SilentStruct, new_se : rosetta.utility.vector1_core_io_silent_SilentEnergy) -> NoneType   sets the silent_energies for this SilentStruct. sort_silent_scores(...) from builtins.PyCapsule sort_silent_scores(rosetta.core.io.silent.SilentStruct) -> NoneType   sort all the silent energies by their name.   class RNA_SilentStructCreator(SilentStructCreator)     creator for the RNA_SilentStruct class     Method resolution order: RNA_SilentStructCreator SilentStructCreator 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.io.silent.RNA_SilentStructCreator,  : rosetta.core.io.silent.RNA_SilentStructCreator) -> rosetta.core.io.silent.RNA_SilentStructCreator create_silent_struct(...) from builtins.PyCapsule create_silent_struct(rosetta.core.io.silent.RNA_SilentStructCreator) -> rosetta.core.io.silent.SilentStruct keyname(...) from builtins.PyCapsule keyname(rosetta.core.io.silent.RNA_SilentStructCreator) -> str   class RigidBodySilentStruct(SilentStruct)       Method resolution order: RigidBodySilentStruct SilentStruct builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle, rosetta.core.pose.Pose) -> NoneType   doc   2. __init__(self : handle, pose : rosetta.core.pose.Pose, tag : str) -> NoneType   3. __init__(handle) -> NoneType   4. __init__(handle, rosetta.core.io.silent.RigidBodySilentStruct) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. add_jump(...) from builtins.PyCapsule add_jump(self : rosetta.core.io.silent.RigidBodySilentStruct, jump : rosetta.core.kinematics.Jump) -> NoneType add_rt(...) from builtins.PyCapsule add_rt(self : rosetta.core.io.silent.RigidBodySilentStruct, rt : rosetta.core.kinematics.RT) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.core.io.silent.RigidBodySilentStruct, src : rosetta.core.io.silent.RigidBodySilentStruct) -> rosetta.core.io.silent.RigidBodySilentStruct   Test if this RigidBodySilentStruct is equal to the given  RigidBodySilentStruct in terms of conformation. Doesn't check energies. clone(...) from builtins.PyCapsule clone(rosetta.core.io.silent.RigidBodySilentStruct) -> rosetta.core.io.silent.SilentStruct   Returns a new RigidBodySilentStruct with a copy of the information  in this RigidBodySilentStruct. fill_pose(...) from builtins.PyCapsule fill_pose(*args, **kwargs) Overloaded function.   1. fill_pose(self : rosetta.core.io.silent.RigidBodySilentStruct, pose : rosetta.core.pose.Pose) -> NoneType   Configure the conformation of the given Pose with the  conformational data within this RigidBodySilentStruct.  sets the jump stored in the RigidBodySilentStruct   2. fill_pose(self : rosetta.core.io.silent.RigidBodySilentStruct, pose : rosetta.core.pose.Pose, residue_set : rosetta.core.chemical.ResidueTypeSet) -> NoneType   Configure the conformation of the given Pose with the  conformational data within this RigidBodySilentStruct. fill_struct(...) from builtins.PyCapsule fill_struct(*args, **kwargs) Overloaded function.   1. fill_struct(self : rosetta.core.io.silent.RigidBodySilentStruct, pose : rosetta.core.pose.Pose) -> NoneType   opposite of fill_pose   2. fill_struct(self : rosetta.core.io.silent.RigidBodySilentStruct, pose : rosetta.core.pose.Pose, tag : str) -> NoneType   opposite of fill_pose fold_tree(...) from builtins.PyCapsule fold_tree(*args, **kwargs) Overloaded function.   1. fold_tree(self : rosetta.core.io.silent.RigidBodySilentStruct,  : rosetta.core.kinematics.FoldTree) -> NoneType   2. fold_tree(rosetta.core.io.silent.RigidBodySilentStruct) -> rosetta.core.kinematics.FoldTree get_CA_xyz(...) from builtins.PyCapsule get_CA_xyz(rosetta.core.io.silent.RigidBodySilentStruct) -> ObjexxFCL::FArray2D<double> get_debug_rmsd(...) from builtins.PyCapsule get_debug_rmsd(rosetta.core.io.silent.RigidBodySilentStruct) -> float   calculates the RMSD between the C-alpha atoms of a Pose built from  the torsions in this RigidBodySilentStruct and the C-alpha atoms from this  RigidBodySilentStruct. init_from_lines(...) from builtins.PyCapsule init_from_lines(self : rosetta.core.io.silent.RigidBodySilentStruct, lines : rosetta.utility.vector1_std_string, container : rosetta.core.io.silent.SilentFileData) -> bool   Tells this RigidBodySilentStruct object to initialize itself from is_symmetric(...) from builtins.PyCapsule is_symmetric(rosetta.core.io.silent.RigidBodySilentStruct) -> bool jump(...) from builtins.PyCapsule jump(self : rosetta.core.io.silent.RigidBodySilentStruct, jump_num : int) -> rosetta.core.kinematics.RT njumps(...) from builtins.PyCapsule njumps(rosetta.core.io.silent.RigidBodySilentStruct) -> int   returns the number of jumps held in this container. symmetry_info(...) from builtins.PyCapsule symmetry_info(*args, **kwargs) Overloaded function.   1. symmetry_info(self : rosetta.core.io.silent.RigidBodySilentStruct, s : rosetta.core.conformation.symmetry.SymmetryInfo) -> NoneType   2. symmetry_info(rosetta.core.io.silent.RigidBodySilentStruct) -> rosetta.core.conformation.symmetry.SymmetryInfo Methods inherited from SilentStruct: add_comment(...) from builtins.PyCapsule add_comment(self : rosetta.core.io.silent.SilentStruct, name : str, value : str) -> NoneType   add a named comment to this SilentStruct object.  Similar to methods for playing with energies, but  mapping is string => string rather than string => Real. add_energy(...) from builtins.PyCapsule add_energy(*args, **kwargs) Overloaded function.   1. add_energy(self : rosetta.core.io.silent.SilentStruct, scorename : str, value : float) -> NoneType   add a score of a given name and value to this SilentStruct.  Takes an optional weight that defaults to 1.0.   2. add_energy(self : rosetta.core.io.silent.SilentStruct, scorename : str, value : float, weight : float) -> NoneType   add a score of a given name and value to this SilentStruct.  Takes an optional weight that defaults to 1.0. add_other_struct(...) from builtins.PyCapsule add_other_struct(self : rosetta.core.io.silent.SilentStruct, silent_struct : rosetta.core.io.silent.SilentStruct) -> NoneType add_parent_remark(...) from builtins.PyCapsule add_parent_remark(self : rosetta.core.io.silent.SilentStruct, name : str, value : str) -> NoneType add_string_value(...) from builtins.PyCapsule add_string_value(self : rosetta.core.io.silent.SilentStruct, scorename : str, value : str) -> NoneType   add a non-floating point score of a given name and value to this  SilentStruct. clear_comments(...) from builtins.PyCapsule clear_comments(rosetta.core.io.silent.SilentStruct) -> NoneType clear_energies(...) from builtins.PyCapsule clear_energies(rosetta.core.io.silent.SilentStruct) -> NoneType   Clear all of the energies in the SilentStruct. Doesn't just  zero the energies, it entirely removes all knowledge of all energies  from this SilentStruct. comment_from_line(...) from builtins.PyCapsule comment_from_line(self : rosetta.core.io.silent.SilentStruct, line : str) -> NoneType copy_scores(...) from builtins.PyCapsule copy_scores(self : rosetta.core.io.silent.SilentStruct, src_ss : rosetta.core.io.silent.SilentStruct) -> NoneType   Copy the score information in the given SilentStruct into  this SilentStruct. decoy_tag(...) from builtins.PyCapsule decoy_tag(*args, **kwargs) Overloaded function.   1. decoy_tag(rosetta.core.io.silent.SilentStruct) -> str   returns the tag associated with this SilentStruct.   2. decoy_tag(self : rosetta.core.io.silent.SilentStruct, tag : str) -> NoneType   sets the tag associated with this SilentStruct. energies(...) from builtins.PyCapsule energies(rosetta.core.io.silent.SilentStruct) -> rosetta.utility.vector1_core_io_silent_SilentEnergy   Returns the vector of SilentEnergy objects associated with  this SilentStruct object. energies_from_pose(...) from builtins.PyCapsule energies_from_pose(self : rosetta.core.io.silent.SilentStruct, pose : rosetta.core.pose.Pose) -> NoneType   Initialize this SilentStruct's energies from the given Pose.  This sets energies, energy weights, and the output widths for the  energies. energies_into_pose(...) from builtins.PyCapsule energies_into_pose(self : rosetta.core.io.silent.SilentStruct, pose : rosetta.core.pose.Pose) -> NoneType   Put the energy information from this SilentStruct into the  pose. Energies that correspond to a ScoreType are put into the  pose.energies().total_energies() EnergyMap, all other energies are  put into the ARBITRARY_FLOAT_DATA map in the pose DataCache. Also  sets the scorefxn_weights in the Energies object using the  information from this SilentStruct. energy_names(...) from builtins.PyCapsule energy_names(rosetta.core.io.silent.SilentStruct) -> core::io::silent::EnergyNames   Returns the EnergyNames that this SilentStruct contains. erase_comment(...) from builtins.PyCapsule erase_comment(self : rosetta.core.io.silent.SilentStruct, name : str) -> NoneType fill_other_struct_list(...) from builtins.PyCapsule fill_other_struct_list(self : rosetta.core.io.silent.SilentStruct, pose : rosetta.core.pose.Pose) -> NoneType fill_struct_with_residue_numbers(...) from builtins.PyCapsule fill_struct_with_residue_numbers(self : rosetta.core.io.silent.SilentStruct, pose : rosetta.core.pose.Pose) -> NoneType fill_struct_with_submotif_info_list(...) from builtins.PyCapsule fill_struct_with_submotif_info_list(self : rosetta.core.io.silent.SilentStruct, pose : rosetta.core.pose.Pose) -> NoneType finish_pose(...) from builtins.PyCapsule finish_pose(self : rosetta.core.io.silent.SilentStruct, pose : rosetta.core.pose.Pose) -> NoneType   calls optH if command line requests optH.  must be called by derived classes. force_bitflip(...) from builtins.PyCapsule force_bitflip(rosetta.core.io.silent.SilentStruct) -> bool   Gets whether conversion from big-endian to little-endian (or the converse) should be forced  when a binary silent structure is initialized from lines. full_model_info_into_pose(...) from builtins.PyCapsule full_model_info_into_pose(self : rosetta.core.io.silent.SilentStruct, pose : rosetta.core.pose.Pose) -> NoneType full_model_parameters(...) from builtins.PyCapsule full_model_parameters(rosetta.core.io.silent.SilentStruct) -> rosetta.core.pose.full_model_info.FullModelParameters get_all_comments(...) from builtins.PyCapsule get_all_comments(rosetta.core.io.silent.SilentStruct) -> rosetta.std.map_std_string_std_string get_comment(...) from builtins.PyCapsule get_comment(self : rosetta.core.io.silent.SilentStruct, name : str) -> str get_energy(...) from builtins.PyCapsule get_energy(self : rosetta.core.io.silent.SilentStruct, scorename : str) -> float   Returns the energy associated with the given scorename if this  SilentStruct has an energy for that scorename. Otherwise returns 0. get_parent_remark(...) from builtins.PyCapsule get_parent_remark(self : rosetta.core.io.silent.SilentStruct, name : str) -> str get_parent_remark_from_line(...) from builtins.PyCapsule get_parent_remark_from_line(self : rosetta.core.io.silent.SilentStruct, line : str) -> NoneType get_self_ptr(...) from builtins.PyCapsule get_self_ptr(*args, **kwargs) Overloaded function.   1. get_self_ptr(rosetta.core.io.silent.SilentStruct) -> rosetta.core.io.silent.SilentStruct   self pointers   2. get_self_ptr(rosetta.core.io.silent.SilentStruct) -> rosetta.core.io.silent.SilentStruct get_silent_energies(...) from builtins.PyCapsule get_silent_energies(rosetta.core.io.silent.SilentStruct) -> rosetta.utility.vector1_core_io_silent_SilentEnergy get_silent_energy(...) from builtins.PyCapsule get_silent_energy(self : rosetta.core.io.silent.SilentStruct, scorename : str) -> rosetta.core.io.silent.SilentEnergy   Returns the SilentEnergy associated with this scorename. get_string_value(...) from builtins.PyCapsule get_string_value(self : rosetta.core.io.silent.SilentStruct, scorename : str) -> str   Returns the energy associated with the given scorename if this  SilentStruct has an energy for that scorename. Otherwise returns 0. has_comment(...) from builtins.PyCapsule has_comment(self : rosetta.core.io.silent.SilentStruct, name : str) -> bool has_energy(...) from builtins.PyCapsule has_energy(self : rosetta.core.io.silent.SilentStruct, scorename : str) -> bool   returns true if this SilentStruct has an energy for the given  scorename, returns false otherwise. has_parent_remark(...) from builtins.PyCapsule has_parent_remark(self : rosetta.core.io.silent.SilentStruct, name : str) -> bool mem_footprint(...) from builtins.PyCapsule mem_footprint(rosetta.core.io.silent.SilentStruct) -> int nonconst_other_struct_list(...) from builtins.PyCapsule nonconst_other_struct_list(rosetta.core.io.silent.SilentStruct) -> rosetta.utility.vector1_std_shared_ptr_core_io_silent_SilentStruct_t nres(...) from builtins.PyCapsule nres(*args, **kwargs) Overloaded function.   1. nres(rosetta.core.io.silent.SilentStruct) -> int   returns the number of residues contained by this  SilentStruct.   2. nres(self : rosetta.core.io.silent.SilentStruct, nres : int) -> NoneType   returns the number of residues in this SilentStruct. one_letter_sequence(...) from builtins.PyCapsule one_letter_sequence(rosetta.core.io.silent.SilentStruct) -> str   strip [...] comment from seqeunce_ and return pure  one-letter sequence other_struct_list(...) from builtins.PyCapsule other_struct_list(rosetta.core.io.silent.SilentStruct) -> rosetta.utility.vector1_std_shared_ptr_core_io_silent_SilentStruct_t precision(...) from builtins.PyCapsule precision(*args, **kwargs) Overloaded function.   1. precision(self : rosetta.core.io.silent.SilentStruct, precision : int) -> NoneType   2. precision(rosetta.core.io.silent.SilentStruct) -> int read_score_headers(...) from builtins.PyCapsule read_score_headers(self : rosetta.core.io.silent.SilentStruct, line : str, enames : rosetta.utility.vector1_std_string, container : rosetta.core.io.silent.SilentFileData) -> NoneType read_sequence(...) from builtins.PyCapsule read_sequence(self : rosetta.core.io.silent.SilentStruct, line : str) -> bool rename_energies(...) from builtins.PyCapsule rename_energies(rosetta.core.io.silent.SilentStruct) -> NoneType residue_numbers_into_pose(...) from builtins.PyCapsule residue_numbers_into_pose(self : rosetta.core.io.silent.SilentStruct, pose : rosetta.core.pose.Pose) -> NoneType scoreline_prefix(...) from builtins.PyCapsule scoreline_prefix(*args, **kwargs) Overloaded function.   1. scoreline_prefix(self : rosetta.core.io.silent.SilentStruct, prefix : str) -> NoneType   2. scoreline_prefix(rosetta.core.io.silent.SilentStruct) -> str sequence(...) from builtins.PyCapsule sequence(*args, **kwargs) Overloaded function.   1. sequence(rosetta.core.io.silent.SilentStruct) -> rosetta.core.sequence.AnnotatedSequence   returns the sequence associated with this SilentStruct.   2. sequence(self : rosetta.core.io.silent.SilentStruct, sequence : rosetta.core.sequence.AnnotatedSequence) -> NoneType   sets the sequence for this SilentStruct. set_chains(...) from builtins.PyCapsule set_chains(self : rosetta.core.io.silent.SilentStruct, chains : rosetta.utility.vector1_char) -> NoneType set_decoy_tag(...) from builtins.PyCapsule set_decoy_tag(self : rosetta.core.io.silent.SilentStruct, tag : str) -> NoneType   set the tag associate with this SilentStruct set_force_bitflip(...) from builtins.PyCapsule set_force_bitflip(self : rosetta.core.io.silent.SilentStruct, setting : bool) -> NoneType   Sets whether conversion from big-endian to little-endian (or the converse) should be forced  when a binary silent structure is initialized from lines. set_full_model_parameters(...) from builtins.PyCapsule set_full_model_parameters(self : rosetta.core.io.silent.SilentStruct, setting : rosetta.core.pose.full_model_info.FullModelParameters) -> NoneType set_residue_numbers(...) from builtins.PyCapsule set_residue_numbers(self : rosetta.core.io.silent.SilentStruct, residue_numbers : rosetta.utility.vector1_unsigned_long) -> NoneType set_segment_IDs(...) from builtins.PyCapsule set_segment_IDs(self : rosetta.core.io.silent.SilentStruct, segids : rosetta.utility.vector1_std_string) -> NoneType set_tag_from_pose(...) from builtins.PyCapsule set_tag_from_pose(self : rosetta.core.io.silent.SilentStruct, pose : rosetta.core.pose.Pose) -> NoneType   Sets the tag from the Pose DataCache. set_valid_energies(...) from builtins.PyCapsule set_valid_energies(self : rosetta.core.io.silent.SilentStruct, valid : rosetta.utility.vector1_std_string) -> NoneType silent_energies(...) from builtins.PyCapsule silent_energies(self : rosetta.core.io.silent.SilentStruct, new_se : rosetta.utility.vector1_core_io_silent_SilentEnergy) -> NoneType   sets the silent_energies for this SilentStruct. sort_silent_scores(...) from builtins.PyCapsule sort_silent_scores(rosetta.core.io.silent.SilentStruct) -> NoneType   sort all the silent energies by their name.   class RigidBodySilentStructCreator(SilentStructCreator)     creator for the RigidBodySilentStruct class     Method resolution order: RigidBodySilentStructCreator SilentStructCreator 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.io.silent.RigidBodySilentStructCreator,  : rosetta.core.io.silent.RigidBodySilentStructCreator) -> rosetta.core.io.silent.RigidBodySilentStructCreator create_silent_struct(...) from builtins.PyCapsule create_silent_struct(rosetta.core.io.silent.RigidBodySilentStructCreator) -> rosetta.core.io.silent.SilentStruct keyname(...) from builtins.PyCapsule keyname(rosetta.core.io.silent.RigidBodySilentStructCreator) -> str   class ScoreFileSilentStruct(SilentStruct)       Method resolution order: ScoreFileSilentStruct SilentStruct builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle) -> NoneType   2. __init__(handle, rosetta.core.pose.Pose) -> NoneType   doc   3. __init__(self : handle, pose : rosetta.core.pose.Pose, tag : str) -> NoneType   4. __init__(handle, rosetta.core.io.silent.ScoreFileSilentStruct) -> 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.io.silent.ScoreFileSilentStruct, src : rosetta.core.io.silent.ScoreFileSilentStruct) -> rosetta.core.io.silent.ScoreFileSilentStruct   Test if this ScoreFileSilentStruct is equal to the given ScoreFileSilentStruct in  terms of conformation. Doesn't check energies. clone(...) from builtins.PyCapsule clone(rosetta.core.io.silent.ScoreFileSilentStruct) -> rosetta.core.io.silent.SilentStruct fill_pose(...) from builtins.PyCapsule fill_pose(self : rosetta.core.io.silent.ScoreFileSilentStruct, pose : rosetta.core.pose.Pose, residue_set : rosetta.core.chemical.ResidueTypeSet) -> NoneType   Configure the conformation of the given Pose with the  conformational data within this ScoreFileSilentStruct. Calls pose.clear() and  rebuilds Pose from scratch using the / user-specified residue types. fill_struct(...) from builtins.PyCapsule fill_struct(self : rosetta.core.io.silent.ScoreFileSilentStruct, pose : rosetta.core.pose.Pose, tag : str) -> NoneType   opposite of fill_pose get_CA_xyz(...) from builtins.PyCapsule get_CA_xyz(rosetta.core.io.silent.ScoreFileSilentStruct) -> ObjexxFCL::FArray2D<double>   returns the positions of the CA atoms in this ScoreFileSilentStruct.  Useful for RMS calculations. get_debug_rmsd(...) from builtins.PyCapsule get_debug_rmsd(rosetta.core.io.silent.ScoreFileSilentStruct) -> float   calculates the RMSD between the C-alpha atoms of a Pose built from the torsions in this  ScoreFileSilentStruct and the C-alpha atoms from this ScoreFileSilentStruct. init_from_lines(...) from builtins.PyCapsule init_from_lines(self : rosetta.core.io.silent.ScoreFileSilentStruct, lines : rosetta.utility.vector1_std_string, container : rosetta.core.io.silent.SilentFileData) -> bool   Tells this ScoreFileSilentStruct object to initialize itself from the given set of lines.  Only initializes energies. Methods inherited from SilentStruct: add_comment(...) from builtins.PyCapsule add_comment(self : rosetta.core.io.silent.SilentStruct, name : str, value : str) -> NoneType   add a named comment to this SilentStruct object.  Similar to methods for playing with energies, but  mapping is string => string rather than string => Real. add_energy(...) from builtins.PyCapsule add_energy(*args, **kwargs) Overloaded function.   1. add_energy(self : rosetta.core.io.silent.SilentStruct, scorename : str, value : float) -> NoneType   add a score of a given name and value to this SilentStruct.  Takes an optional weight that defaults to 1.0.   2. add_energy(self : rosetta.core.io.silent.SilentStruct, scorename : str, value : float, weight : float) -> NoneType   add a score of a given name and value to this SilentStruct.  Takes an optional weight that defaults to 1.0. add_other_struct(...) from builtins.PyCapsule add_other_struct(self : rosetta.core.io.silent.SilentStruct, silent_struct : rosetta.core.io.silent.SilentStruct) -> NoneType add_parent_remark(...) from builtins.PyCapsule add_parent_remark(self : rosetta.core.io.silent.SilentStruct, name : str, value : str) -> NoneType add_string_value(...) from builtins.PyCapsule add_string_value(self : rosetta.core.io.silent.SilentStruct, scorename : str, value : str) -> NoneType   add a non-floating point score of a given name and value to this  SilentStruct. clear_comments(...) from builtins.PyCapsule clear_comments(rosetta.core.io.silent.SilentStruct) -> NoneType clear_energies(...) from builtins.PyCapsule clear_energies(rosetta.core.io.silent.SilentStruct) -> NoneType   Clear all of the energies in the SilentStruct. Doesn't just  zero the energies, it entirely removes all knowledge of all energies  from this SilentStruct. comment_from_line(...) from builtins.PyCapsule comment_from_line(self : rosetta.core.io.silent.SilentStruct, line : str) -> NoneType copy_scores(...) from builtins.PyCapsule copy_scores(self : rosetta.core.io.silent.SilentStruct, src_ss : rosetta.core.io.silent.SilentStruct) -> NoneType   Copy the score information in the given SilentStruct into  this SilentStruct. decoy_tag(...) from builtins.PyCapsule decoy_tag(*args, **kwargs) Overloaded function.   1. decoy_tag(rosetta.core.io.silent.SilentStruct) -> str   returns the tag associated with this SilentStruct.   2. decoy_tag(self : rosetta.core.io.silent.SilentStruct, tag : str) -> NoneType   sets the tag associated with this SilentStruct. energies(...) from builtins.PyCapsule energies(rosetta.core.io.silent.SilentStruct) -> rosetta.utility.vector1_core_io_silent_SilentEnergy   Returns the vector of SilentEnergy objects associated with  this SilentStruct object. energies_from_pose(...) from builtins.PyCapsule energies_from_pose(self : rosetta.core.io.silent.SilentStruct, pose : rosetta.core.pose.Pose) -> NoneType   Initialize this SilentStruct's energies from the given Pose.  This sets energies, energy weights, and the output widths for the  energies. energies_into_pose(...) from builtins.PyCapsule energies_into_pose(self : rosetta.core.io.silent.SilentStruct, pose : rosetta.core.pose.Pose) -> NoneType   Put the energy information from this SilentStruct into the  pose. Energies that correspond to a ScoreType are put into the  pose.energies().total_energies() EnergyMap, all other energies are  put into the ARBITRARY_FLOAT_DATA map in the pose DataCache. Also  sets the scorefxn_weights in the Energies object using the  information from this SilentStruct. energy_names(...) from builtins.PyCapsule energy_names(rosetta.core.io.silent.SilentStruct) -> core::io::silent::EnergyNames   Returns the EnergyNames that this SilentStruct contains. erase_comment(...) from builtins.PyCapsule erase_comment(self : rosetta.core.io.silent.SilentStruct, name : str) -> NoneType fill_other_struct_list(...) from builtins.PyCapsule fill_other_struct_list(self : rosetta.core.io.silent.SilentStruct, pose : rosetta.core.pose.Pose) -> NoneType fill_struct_with_residue_numbers(...) from builtins.PyCapsule fill_struct_with_residue_numbers(self : rosetta.core.io.silent.SilentStruct, pose : rosetta.core.pose.Pose) -> NoneType fill_struct_with_submotif_info_list(...) from builtins.PyCapsule fill_struct_with_submotif_info_list(self : rosetta.core.io.silent.SilentStruct, pose : rosetta.core.pose.Pose) -> NoneType finish_pose(...) from builtins.PyCapsule finish_pose(self : rosetta.core.io.silent.SilentStruct, pose : rosetta.core.pose.Pose) -> NoneType   calls optH if command line requests optH.  must be called by derived classes. force_bitflip(...) from builtins.PyCapsule force_bitflip(rosetta.core.io.silent.SilentStruct) -> bool   Gets whether conversion from big-endian to little-endian (or the converse) should be forced  when a binary silent structure is initialized from lines. full_model_info_into_pose(...) from builtins.PyCapsule full_model_info_into_pose(self : rosetta.core.io.silent.SilentStruct, pose : rosetta.core.pose.Pose) -> NoneType full_model_parameters(...) from builtins.PyCapsule full_model_parameters(rosetta.core.io.silent.SilentStruct) -> rosetta.core.pose.full_model_info.FullModelParameters get_all_comments(...) from builtins.PyCapsule get_all_comments(rosetta.core.io.silent.SilentStruct) -> rosetta.std.map_std_string_std_string get_comment(...) from builtins.PyCapsule get_comment(self : rosetta.core.io.silent.SilentStruct, name : str) -> str get_energy(...) from builtins.PyCapsule get_energy(self : rosetta.core.io.silent.SilentStruct, scorename : str) -> float   Returns the energy associated with the given scorename if this  SilentStruct has an energy for that scorename. Otherwise returns 0. get_parent_remark(...) from builtins.PyCapsule get_parent_remark(self : rosetta.core.io.silent.SilentStruct, name : str) -> str get_parent_remark_from_line(...) from builtins.PyCapsule get_parent_remark_from_line(self : rosetta.core.io.silent.SilentStruct, line : str) -> NoneType get_self_ptr(...) from builtins.PyCapsule get_self_ptr(*args, **kwargs) Overloaded function.   1. get_self_ptr(rosetta.core.io.silent.SilentStruct) -> rosetta.core.io.silent.SilentStruct   self pointers   2. get_self_ptr(rosetta.core.io.silent.SilentStruct) -> rosetta.core.io.silent.SilentStruct get_silent_energies(...) from builtins.PyCapsule get_silent_energies(rosetta.core.io.silent.SilentStruct) -> rosetta.utility.vector1_core_io_silent_SilentEnergy get_silent_energy(...) from builtins.PyCapsule get_silent_energy(self : rosetta.core.io.silent.SilentStruct, scorename : str) -> rosetta.core.io.silent.SilentEnergy   Returns the SilentEnergy associated with this scorename. get_string_value(...) from builtins.PyCapsule get_string_value(self : rosetta.core.io.silent.SilentStruct, scorename : str) -> str   Returns the energy associated with the given scorename if this  SilentStruct has an energy for that scorename. Otherwise returns 0. has_comment(...) from builtins.PyCapsule has_comment(self : rosetta.core.io.silent.SilentStruct, name : str) -> bool has_energy(...) from builtins.PyCapsule has_energy(self : rosetta.core.io.silent.SilentStruct, scorename : str) -> bool   returns true if this SilentStruct has an energy for the given  scorename, returns false otherwise. has_parent_remark(...) from builtins.PyCapsule has_parent_remark(self : rosetta.core.io.silent.SilentStruct, name : str) -> bool mem_footprint(...) from builtins.PyCapsule mem_footprint(rosetta.core.io.silent.SilentStruct) -> int nonconst_other_struct_list(...) from builtins.PyCapsule nonconst_other_struct_list(rosetta.core.io.silent.SilentStruct) -> rosetta.utility.vector1_std_shared_ptr_core_io_silent_SilentStruct_t nres(...) from builtins.PyCapsule nres(*args, **kwargs) Overloaded function.   1. nres(rosetta.core.io.silent.SilentStruct) -> int   returns the number of residues contained by this  SilentStruct.   2. nres(self : rosetta.core.io.silent.SilentStruct, nres : int) -> NoneType   returns the number of residues in this SilentStruct. one_letter_sequence(...) from builtins.PyCapsule one_letter_sequence(rosetta.core.io.silent.SilentStruct) -> str   strip [...] comment from seqeunce_ and return pure  one-letter sequence other_struct_list(...) from builtins.PyCapsule other_struct_list(rosetta.core.io.silent.SilentStruct) -> rosetta.utility.vector1_std_shared_ptr_core_io_silent_SilentStruct_t precision(...) from builtins.PyCapsule precision(*args, **kwargs) Overloaded function.   1. precision(self : rosetta.core.io.silent.SilentStruct, precision : int) -> NoneType   2. precision(rosetta.core.io.silent.SilentStruct) -> int read_score_headers(...) from builtins.PyCapsule read_score_headers(self : rosetta.core.io.silent.SilentStruct, line : str, enames : rosetta.utility.vector1_std_string, container : rosetta.core.io.silent.SilentFileData) -> NoneType read_sequence(...) from builtins.PyCapsule read_sequence(self : rosetta.core.io.silent.SilentStruct, line : str) -> bool rename_energies(...) from builtins.PyCapsule rename_energies(rosetta.core.io.silent.SilentStruct) -> NoneType residue_numbers_into_pose(...) from builtins.PyCapsule residue_numbers_into_pose(self : rosetta.core.io.silent.SilentStruct, pose : rosetta.core.pose.Pose) -> NoneType scoreline_prefix(...) from builtins.PyCapsule scoreline_prefix(*args, **kwargs) Overloaded function.   1. scoreline_prefix(self : rosetta.core.io.silent.SilentStruct, prefix : str) -> NoneType   2. scoreline_prefix(rosetta.core.io.silent.SilentStruct) -> str sequence(...) from builtins.PyCapsule sequence(*args, **kwargs) Overloaded function.   1. sequence(rosetta.core.io.silent.SilentStruct) -> rosetta.core.sequence.AnnotatedSequence   returns the sequence associated with this SilentStruct.   2. sequence(self : rosetta.core.io.silent.SilentStruct, sequence : rosetta.core.sequence.AnnotatedSequence) -> NoneType   sets the sequence for this SilentStruct. set_chains(...) from builtins.PyCapsule set_chains(self : rosetta.core.io.silent.SilentStruct, chains : rosetta.utility.vector1_char) -> NoneType set_decoy_tag(...) from builtins.PyCapsule set_decoy_tag(self : rosetta.core.io.silent.SilentStruct, tag : str) -> NoneType   set the tag associate with this SilentStruct set_force_bitflip(...) from builtins.PyCapsule set_force_bitflip(self : rosetta.core.io.silent.SilentStruct, setting : bool) -> NoneType   Sets whether conversion from big-endian to little-endian (or the converse) should be forced  when a binary silent structure is initialized from lines. set_full_model_parameters(...) from builtins.PyCapsule set_full_model_parameters(self : rosetta.core.io.silent.SilentStruct, setting : rosetta.core.pose.full_model_info.FullModelParameters) -> NoneType set_residue_numbers(...) from builtins.PyCapsule set_residue_numbers(self : rosetta.core.io.silent.SilentStruct, residue_numbers : rosetta.utility.vector1_unsigned_long) -> NoneType set_segment_IDs(...) from builtins.PyCapsule set_segment_IDs(self : rosetta.core.io.silent.SilentStruct, segids : rosetta.utility.vector1_std_string) -> NoneType set_tag_from_pose(...) from builtins.PyCapsule set_tag_from_pose(self : rosetta.core.io.silent.SilentStruct, pose : rosetta.core.pose.Pose) -> NoneType   Sets the tag from the Pose DataCache. set_valid_energies(...) from builtins.PyCapsule set_valid_energies(self : rosetta.core.io.silent.SilentStruct, valid : rosetta.utility.vector1_std_string) -> NoneType silent_energies(...) from builtins.PyCapsule silent_energies(self : rosetta.core.io.silent.SilentStruct, new_se : rosetta.utility.vector1_core_io_silent_SilentEnergy) -> NoneType   sets the silent_energies for this SilentStruct. sort_silent_scores(...) from builtins.PyCapsule sort_silent_scores(rosetta.core.io.silent.SilentStruct) -> NoneType   sort all the silent energies by their name.   class ScoreFileSilentStructCreator(SilentStructCreator)     creator for the ScoreFileSilentStruct class     Method resolution order: ScoreFileSilentStructCreator SilentStructCreator 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.io.silent.ScoreFileSilentStructCreator,  : rosetta.core.io.silent.ScoreFileSilentStructCreator) -> rosetta.core.io.silent.ScoreFileSilentStructCreator create_silent_struct(...) from builtins.PyCapsule create_silent_struct(rosetta.core.io.silent.ScoreFileSilentStructCreator) -> rosetta.core.io.silent.SilentStruct keyname(...) from builtins.PyCapsule keyname(rosetta.core.io.silent.ScoreFileSilentStructCreator) -> str   class ScoreJumpFileSilentStruct(SilentStruct)       Method resolution order: ScoreJumpFileSilentStruct SilentStruct builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle) -> NoneType   2. __init__(handle, rosetta.core.pose.Pose) -> NoneType   doc   3. __init__(self : handle, pose : rosetta.core.pose.Pose, tag : str) -> NoneType   4. __init__(handle, rosetta.core.io.silent.ScoreJumpFileSilentStruct) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. add_jump(...) from builtins.PyCapsule add_jump(self : rosetta.core.io.silent.ScoreJumpFileSilentStruct, jump : rosetta.core.kinematics.Jump) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.core.io.silent.ScoreJumpFileSilentStruct, src : rosetta.core.io.silent.ScoreJumpFileSilentStruct) -> rosetta.core.io.silent.ScoreJumpFileSilentStruct   Test if this ScoreJumpFileSilentStruct is equal to the given ScoreJumpFileSilentStruct in  terms of conformation. Doesn't check energies. clone(...) from builtins.PyCapsule clone(rosetta.core.io.silent.ScoreJumpFileSilentStruct) -> rosetta.core.io.silent.SilentStruct fill_pose(...) from builtins.PyCapsule fill_pose(self : rosetta.core.io.silent.ScoreJumpFileSilentStruct, pose : rosetta.core.pose.Pose, residue_set : rosetta.core.chemical.ResidueTypeSet) -> NoneType   Configure the conformation of the given Pose with the  conformational data within this ScoreJumpFileSilentStruct. Calls pose.clear() and  rebuilds Pose from scratch using the / user-specified residue types. fill_struct(...) from builtins.PyCapsule fill_struct(self : rosetta.core.io.silent.ScoreJumpFileSilentStruct, pose : rosetta.core.pose.Pose, tag : str) -> NoneType   opposite of fill_pose fold_tree(...) from builtins.PyCapsule fold_tree(*args, **kwargs) Overloaded function.   1. fold_tree(self : rosetta.core.io.silent.ScoreJumpFileSilentStruct, f : rosetta.core.kinematics.FoldTree) -> NoneType   2. fold_tree(rosetta.core.io.silent.ScoreJumpFileSilentStruct) -> rosetta.core.kinematics.FoldTree get_CA_xyz(...) from builtins.PyCapsule get_CA_xyz(rosetta.core.io.silent.ScoreJumpFileSilentStruct) -> ObjexxFCL::FArray2D<double>   returns the positions of the CA atoms in this ScoreJumpFileSilentStruct.  Useful for RMS calculations. get_debug_rmsd(...) from builtins.PyCapsule get_debug_rmsd(rosetta.core.io.silent.ScoreJumpFileSilentStruct) -> float   calculates the RMSD between the C-alpha atoms of a Pose built from the torsions in this  ScoreJumpFileSilentStruct and the C-alpha atoms from this ScoreJumpFileSilentStruct. init_from_lines(...) from builtins.PyCapsule init_from_lines(self : rosetta.core.io.silent.ScoreJumpFileSilentStruct, lines : rosetta.utility.vector1_std_string, container : rosetta.core.io.silent.SilentFileData) -> bool   Tells this ScoreJumpFileSilentStruct object to initialize itself from the given set of lines.  Only initializes energies. jump(...) from builtins.PyCapsule jump(self : rosetta.core.io.silent.ScoreJumpFileSilentStruct, jump_num : int) -> rosetta.core.kinematics.RT shared_from_this(...) from builtins.PyCapsule shared_from_this(rosetta.core.io.silent.ScoreJumpFileSilentStruct) -> rosetta.core.io.silent.ScoreJumpFileSilentStruct Methods inherited from SilentStruct: add_comment(...) from builtins.PyCapsule add_comment(self : rosetta.core.io.silent.SilentStruct, name : str, value : str) -> NoneType   add a named comment to this SilentStruct object.  Similar to methods for playing with energies, but  mapping is string => string rather than string => Real. add_energy(...) from builtins.PyCapsule add_energy(*args, **kwargs) Overloaded function.   1. add_energy(self : rosetta.core.io.silent.SilentStruct, scorename : str, value : float) -> NoneType   add a score of a given name and value to this SilentStruct.  Takes an optional weight that defaults to 1.0.   2. add_energy(self : rosetta.core.io.silent.SilentStruct, scorename : str, value : float, weight : float) -> NoneType   add a score of a given name and value to this SilentStruct.  Takes an optional weight that defaults to 1.0. add_other_struct(...) from builtins.PyCapsule add_other_struct(self : rosetta.core.io.silent.SilentStruct, silent_struct : rosetta.core.io.silent.SilentStruct) -> NoneType add_parent_remark(...) from builtins.PyCapsule add_parent_remark(self : rosetta.core.io.silent.SilentStruct, name : str, value : str) -> NoneType add_string_value(...) from builtins.PyCapsule add_string_value(self : rosetta.core.io.silent.SilentStruct, scorename : str, value : str) -> NoneType   add a non-floating point score of a given name and value to this  SilentStruct. clear_comments(...) from builtins.PyCapsule clear_comments(rosetta.core.io.silent.SilentStruct) -> NoneType clear_energies(...) from builtins.PyCapsule clear_energies(rosetta.core.io.silent.SilentStruct) -> NoneType   Clear all of the energies in the SilentStruct. Doesn't just  zero the energies, it entirely removes all knowledge of all energies  from this SilentStruct. comment_from_line(...) from builtins.PyCapsule comment_from_line(self : rosetta.core.io.silent.SilentStruct, line : str) -> NoneType copy_scores(...) from builtins.PyCapsule copy_scores(self : rosetta.core.io.silent.SilentStruct, src_ss : rosetta.core.io.silent.SilentStruct) -> NoneType   Copy the score information in the given SilentStruct into  this SilentStruct. decoy_tag(...) from builtins.PyCapsule decoy_tag(*args, **kwargs) Overloaded function.   1. decoy_tag(rosetta.core.io.silent.SilentStruct) -> str   returns the tag associated with this SilentStruct.   2. decoy_tag(self : rosetta.core.io.silent.SilentStruct, tag : str) -> NoneType   sets the tag associated with this SilentStruct. energies(...) from builtins.PyCapsule energies(rosetta.core.io.silent.SilentStruct) -> rosetta.utility.vector1_core_io_silent_SilentEnergy   Returns the vector of SilentEnergy objects associated with  this SilentStruct object. energies_from_pose(...) from builtins.PyCapsule energies_from_pose(self : rosetta.core.io.silent.SilentStruct, pose : rosetta.core.pose.Pose) -> NoneType   Initialize this SilentStruct's energies from the given Pose.  This sets energies, energy weights, and the output widths for the  energies. energies_into_pose(...) from builtins.PyCapsule energies_into_pose(self : rosetta.core.io.silent.SilentStruct, pose : rosetta.core.pose.Pose) -> NoneType   Put the energy information from this SilentStruct into the  pose. Energies that correspond to a ScoreType are put into the  pose.energies().total_energies() EnergyMap, all other energies are  put into the ARBITRARY_FLOAT_DATA map in the pose DataCache. Also  sets the scorefxn_weights in the Energies object using the  information from this SilentStruct. energy_names(...) from builtins.PyCapsule energy_names(rosetta.core.io.silent.SilentStruct) -> core::io::silent::EnergyNames   Returns the EnergyNames that this SilentStruct contains. erase_comment(...) from builtins.PyCapsule erase_comment(self : rosetta.core.io.silent.SilentStruct, name : str) -> NoneType fill_other_struct_list(...) from builtins.PyCapsule fill_other_struct_list(self : rosetta.core.io.silent.SilentStruct, pose : rosetta.core.pose.Pose) -> NoneType fill_struct_with_residue_numbers(...) from builtins.PyCapsule fill_struct_with_residue_numbers(self : rosetta.core.io.silent.SilentStruct, pose : rosetta.core.pose.Pose) -> NoneType fill_struct_with_submotif_info_list(...) from builtins.PyCapsule fill_struct_with_submotif_info_list(self : rosetta.core.io.silent.SilentStruct, pose : rosetta.core.pose.Pose) -> NoneType finish_pose(...) from builtins.PyCapsule finish_pose(self : rosetta.core.io.silent.SilentStruct, pose : rosetta.core.pose.Pose) -> NoneType   calls optH if command line requests optH.  must be called by derived classes. force_bitflip(...) from builtins.PyCapsule force_bitflip(rosetta.core.io.silent.SilentStruct) -> bool   Gets whether conversion from big-endian to little-endian (or the converse) should be forced  when a binary silent structure is initialized from lines. full_model_info_into_pose(...) from builtins.PyCapsule full_model_info_into_pose(self : rosetta.core.io.silent.SilentStruct, pose : rosetta.core.pose.Pose) -> NoneType full_model_parameters(...) from builtins.PyCapsule full_model_parameters(rosetta.core.io.silent.SilentStruct) -> rosetta.core.pose.full_model_info.FullModelParameters get_all_comments(...) from builtins.PyCapsule get_all_comments(rosetta.core.io.silent.SilentStruct) -> rosetta.std.map_std_string_std_string get_comment(...) from builtins.PyCapsule get_comment(self : rosetta.core.io.silent.SilentStruct, name : str) -> str get_energy(...) from builtins.PyCapsule get_energy(self : rosetta.core.io.silent.SilentStruct, scorename : str) -> float   Returns the energy associated with the given scorename if this  SilentStruct has an energy for that scorename. Otherwise returns 0. get_parent_remark(...) from builtins.PyCapsule get_parent_remark(self : rosetta.core.io.silent.SilentStruct, name : str) -> str get_parent_remark_from_line(...) from builtins.PyCapsule get_parent_remark_from_line(self : rosetta.core.io.silent.SilentStruct, line : str) -> NoneType get_self_ptr(...) from builtins.PyCapsule get_self_ptr(*args, **kwargs) Overloaded function.   1. get_self_ptr(rosetta.core.io.silent.SilentStruct) -> rosetta.core.io.silent.SilentStruct   self pointers   2. get_self_ptr(rosetta.core.io.silent.SilentStruct) -> rosetta.core.io.silent.SilentStruct get_silent_energies(...) from builtins.PyCapsule get_silent_energies(rosetta.core.io.silent.SilentStruct) -> rosetta.utility.vector1_core_io_silent_SilentEnergy get_silent_energy(...) from builtins.PyCapsule get_silent_energy(self : rosetta.core.io.silent.SilentStruct, scorename : str) -> rosetta.core.io.silent.SilentEnergy   Returns the SilentEnergy associated with this scorename. get_string_value(...) from builtins.PyCapsule get_string_value(self : rosetta.core.io.silent.SilentStruct, scorename : str) -> str   Returns the energy associated with the given scorename if this  SilentStruct has an energy for that scorename. Otherwise returns 0. has_comment(...) from builtins.PyCapsule has_comment(self : rosetta.core.io.silent.SilentStruct, name : str) -> bool has_energy(...) from builtins.PyCapsule has_energy(self : rosetta.core.io.silent.SilentStruct, scorename : str) -> bool   returns true if this SilentStruct has an energy for the given  scorename, returns false otherwise. has_parent_remark(...) from builtins.PyCapsule has_parent_remark(self : rosetta.core.io.silent.SilentStruct, name : str) -> bool mem_footprint(...) from builtins.PyCapsule mem_footprint(rosetta.core.io.silent.SilentStruct) -> int nonconst_other_struct_list(...) from builtins.PyCapsule nonconst_other_struct_list(rosetta.core.io.silent.SilentStruct) -> rosetta.utility.vector1_std_shared_ptr_core_io_silent_SilentStruct_t nres(...) from builtins.PyCapsule nres(*args, **kwargs) Overloaded function.   1. nres(rosetta.core.io.silent.SilentStruct) -> int   returns the number of residues contained by this  SilentStruct.   2. nres(self : rosetta.core.io.silent.SilentStruct, nres : int) -> NoneType   returns the number of residues in this SilentStruct. one_letter_sequence(...) from builtins.PyCapsule one_letter_sequence(rosetta.core.io.silent.SilentStruct) -> str   strip [...] comment from seqeunce_ and return pure  one-letter sequence other_struct_list(...) from builtins.PyCapsule other_struct_list(rosetta.core.io.silent.SilentStruct) -> rosetta.utility.vector1_std_shared_ptr_core_io_silent_SilentStruct_t precision(...) from builtins.PyCapsule precision(*args, **kwargs) Overloaded function.   1. precision(self : rosetta.core.io.silent.SilentStruct, precision : int) -> NoneType   2. precision(rosetta.core.io.silent.SilentStruct) -> int read_score_headers(...) from builtins.PyCapsule read_score_headers(self : rosetta.core.io.silent.SilentStruct, line : str, enames : rosetta.utility.vector1_std_string, container : rosetta.core.io.silent.SilentFileData) -> NoneType read_sequence(...) from builtins.PyCapsule read_sequence(self : rosetta.core.io.silent.SilentStruct, line : str) -> bool rename_energies(...) from builtins.PyCapsule rename_energies(rosetta.core.io.silent.SilentStruct) -> NoneType residue_numbers_into_pose(...) from builtins.PyCapsule residue_numbers_into_pose(self : rosetta.core.io.silent.SilentStruct, pose : rosetta.core.pose.Pose) -> NoneType scoreline_prefix(...) from builtins.PyCapsule scoreline_prefix(*args, **kwargs) Overloaded function.   1. scoreline_prefix(self : rosetta.core.io.silent.SilentStruct, prefix : str) -> NoneType   2. scoreline_prefix(rosetta.core.io.silent.SilentStruct) -> str sequence(...) from builtins.PyCapsule sequence(*args, **kwargs) Overloaded function.   1. sequence(rosetta.core.io.silent.SilentStruct) -> rosetta.core.sequence.AnnotatedSequence   returns the sequence associated with this SilentStruct.   2. sequence(self : rosetta.core.io.silent.SilentStruct, sequence : rosetta.core.sequence.AnnotatedSequence) -> NoneType   sets the sequence for this SilentStruct. set_chains(...) from builtins.PyCapsule set_chains(self : rosetta.core.io.silent.SilentStruct, chains : rosetta.utility.vector1_char) -> NoneType set_decoy_tag(...) from builtins.PyCapsule set_decoy_tag(self : rosetta.core.io.silent.SilentStruct, tag : str) -> NoneType   set the tag associate with this SilentStruct set_force_bitflip(...) from builtins.PyCapsule set_force_bitflip(self : rosetta.core.io.silent.SilentStruct, setting : bool) -> NoneType   Sets whether conversion from big-endian to little-endian (or the converse) should be forced  when a binary silent structure is initialized from lines. set_full_model_parameters(...) from builtins.PyCapsule set_full_model_parameters(self : rosetta.core.io.silent.SilentStruct, setting : rosetta.core.pose.full_model_info.FullModelParameters) -> NoneType set_residue_numbers(...) from builtins.PyCapsule set_residue_numbers(self : rosetta.core.io.silent.SilentStruct, residue_numbers : rosetta.utility.vector1_unsigned_long) -> NoneType set_segment_IDs(...) from builtins.PyCapsule set_segment_IDs(self : rosetta.core.io.silent.SilentStruct, segids : rosetta.utility.vector1_std_string) -> NoneType set_tag_from_pose(...) from builtins.PyCapsule set_tag_from_pose(self : rosetta.core.io.silent.SilentStruct, pose : rosetta.core.pose.Pose) -> NoneType   Sets the tag from the Pose DataCache. set_valid_energies(...) from builtins.PyCapsule set_valid_energies(self : rosetta.core.io.silent.SilentStruct, valid : rosetta.utility.vector1_std_string) -> NoneType silent_energies(...) from builtins.PyCapsule silent_energies(self : rosetta.core.io.silent.SilentStruct, new_se : rosetta.utility.vector1_core_io_silent_SilentEnergy) -> NoneType   sets the silent_energies for this SilentStruct. sort_silent_scores(...) from builtins.PyCapsule sort_silent_scores(rosetta.core.io.silent.SilentStruct) -> NoneType   sort all the silent energies by their name.   class ScoreJumpFileSilentStructCreator(SilentStructCreator)     creator for the ScoreJumpFileSilentStruct class     Method resolution order: ScoreJumpFileSilentStructCreator SilentStructCreator 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.io.silent.ScoreJumpFileSilentStructCreator,  : rosetta.core.io.silent.ScoreJumpFileSilentStructCreator) -> rosetta.core.io.silent.ScoreJumpFileSilentStructCreator create_silent_struct(...) from builtins.PyCapsule create_silent_struct(rosetta.core.io.silent.ScoreJumpFileSilentStructCreator) -> rosetta.core.io.silent.SilentStruct keyname(...) from builtins.PyCapsule keyname(rosetta.core.io.silent.ScoreJumpFileSilentStructCreator) -> str   class SharedSilentData(builtins.object)       Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.core.io.silent.SharedSilentData) -> NoneType   2. __init__(self : rosetta.core.io.silent.SharedSilentData,  : rosetta.core.io.silent.SharedSilentData) -> 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.io.silent.SharedSilentData,  : rosetta.core.io.silent.SharedSilentData) -> rosetta.core.io.silent.SharedSilentData   class SharedSilentDataType(builtins.object)       Methods defined here: __eq__(...) from builtins.PyCapsule __eq__(rosetta.core.io.silent.SharedSilentDataType, rosetta.core.io.silent.SharedSilentDataType) -> bool __hash__(...) from builtins.PyCapsule __hash__(rosetta.core.io.silent.SharedSilentDataType) -> int __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.core.io.silent.SharedSilentDataType, int) -> NoneType   2. __init__(rosetta.core.io.silent.SharedSilentDataType, int) -> NoneType __int__(...) from builtins.PyCapsule __int__(rosetta.core.io.silent.SharedSilentDataType) -> int __ne__(...) from builtins.PyCapsule __ne__(rosetta.core.io.silent.SharedSilentDataType, rosetta.core.io.silent.SharedSilentDataType) -> 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.io.silent.SharedSilentDataType) -> str Data and other attributes defined here: energynames = SharedSilentDataType.energynames simplesequencedata = SharedSilentDataType.simplesequencedata   class SilentEnergy(builtins.object)     Helper class for silent-file classes to keep track of energy information.     Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.core.io.silent.SilentEnergy) -> NoneType   2. __init__(self : rosetta.core.io.silent.SilentEnergy, name : str, value : float, weight : float, width : int) -> NoneType   3. __init__(self : rosetta.core.io.silent.SilentEnergy, name : str, value : str, width : int) -> NoneType   4. __init__(self : rosetta.core.io.silent.SilentEnergy,  : rosetta.core.io.silent.SilentEnergy) -> 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.io.silent.SilentEnergy,  : rosetta.core.io.silent.SilentEnergy) -> rosetta.core.io.silent.SilentEnergy name(...) from builtins.PyCapsule name(*args, **kwargs) Overloaded function.   1. name(rosetta.core.io.silent.SilentEnergy) -> str   2. name(self : rosetta.core.io.silent.SilentEnergy, new_name : str) -> NoneType string_value(...) from builtins.PyCapsule string_value(rosetta.core.io.silent.SilentEnergy) -> str value(...) from builtins.PyCapsule value(*args, **kwargs) Overloaded function.   1. value(rosetta.core.io.silent.SilentEnergy) -> float   2. value(self : rosetta.core.io.silent.SilentEnergy, new_value : float) -> NoneType   3. value(self : rosetta.core.io.silent.SilentEnergy, new_string_value : str) -> NoneType weight(...) from builtins.PyCapsule weight(*args, **kwargs) Overloaded function.   1. weight(rosetta.core.io.silent.SilentEnergy) -> float   2. weight(self : rosetta.core.io.silent.SilentEnergy, new_weight : float) -> NoneType width(...) from builtins.PyCapsule width(*args, **kwargs) Overloaded function.   1. width(rosetta.core.io.silent.SilentEnergy) -> int   2. width(self : rosetta.core.io.silent.SilentEnergy, new_width : int) -> NoneType   class SilentFileData(builtins.object)     Abstract base class for classes that read and write different types of silent-files. Silent-files can contain SilentStruct objects which are expected, to be uniquely identified by some sort of string-based tag inside the file.     Methods defined here: __getitem__(...) from builtins.PyCapsule __getitem__(self : rosetta.core.io.silent.SilentFileData, tag : str) -> core::io::silent::SilentStruct __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.core.io.silent.SilentFileData) -> NoneType   2. __init__(self : rosetta.core.io.silent.SilentFileData, filename : str) -> NoneType   3. __init__(self : rosetta.core.io.silent.SilentFileData, filename : str, store_argv_in_file : bool, strict_column_mode : bool, silent_struct_type : str) -> NoneType   4. __init__(self : rosetta.core.io.silent.SilentFileData,  : rosetta.core.io.silent.SilentFileData) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. add_as_other_struct_if_relevant(...) from builtins.PyCapsule add_as_other_struct_if_relevant(self : rosetta.core.io.silent.SilentFileData, new_struct : core::io::silent::SilentStruct) -> bool   In stepwise modeling, sometimes poses carry refs to 'other poses' add_structure(...) from builtins.PyCapsule add_structure(*args, **kwargs) Overloaded function.   1. add_structure(self : rosetta.core.io.silent.SilentFileData, new_struct : core::io::silent::SilentStruct) -> NoneType   Adds a SilentStructOP to the structure_map_. If the SilentStruct's  tag already exists in the structure_map_, a new tag is assigned. Careful  with this method, as it stores an owning pointer. If you change the  SilentStruct later, it will change your already stored structures.   2. add_structure(self : rosetta.core.io.silent.SilentFileData, new_struct : core::io::silent::SilentStruct) -> NoneType   Saves a copy of the silent struct. This method is:  - SAFE! in the sense that it actually copies the SilentStruct object, not  just the pointer to the object.  - SLOW! in the sense that copying the object takes a small amount of time. add_structure_replace_tag_if_necessary(...) from builtins.PyCapsule add_structure_replace_tag_if_necessary(self : rosetta.core.io.silent.SilentFileData, new_struct : core::io::silent::SilentStruct) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.core.io.silent.SilentFileData,  : rosetta.core.io.silent.SilentFileData) -> rosetta.core.io.silent.SilentFileData begin(...) from builtins.PyCapsule begin(*args, **kwargs) Overloaded function.   1. begin(rosetta.core.io.silent.SilentFileData) -> core::io::silent::SilentFileData::iterator   Returns an iterator to the start of the members of this container.   2. begin(rosetta.core.io.silent.SilentFileData) -> core::io::silent::SilentFileData::const_iterator   Returns an iterator to the start of the members of this container. clear(...) from builtins.PyCapsule clear(rosetta.core.io.silent.SilentFileData) -> NoneType   Clears all of the data associated with this object. clear_shared_silent_data(...) from builtins.PyCapsule clear_shared_silent_data(rosetta.core.io.silent.SilentFileData) -> NoneType   Clears all of the data associated with this object. clear_structure_map(...) from builtins.PyCapsule clear_structure_map(rosetta.core.io.silent.SilentFileData) -> NoneType   Remove all of the SilentStruct objects from this object. comment_line(...) from builtins.PyCapsule comment_line(self : rosetta.core.io.silent.SilentFileData, line : str) -> NoneType   Adds a comment-line that will be printed in write_all method.  Comment lines are simply lines in the silent-file that begin with the #  character, and are printed in the write_all method. comment_lines(...) from builtins.PyCapsule comment_lines(rosetta.core.io.silent.SilentFileData) -> rosetta.utility.vector1_std_string   Returns a vector1 of the comment lines read in from  a silent-file. Comment lines are any lines in the silent-file  beginning with a # character. create_SilentStructOP(...) from builtins.PyCapsule create_SilentStructOP(rosetta.core.io.silent.SilentFileData) -> core::io::silent::SilentStruct end(...) from builtins.PyCapsule end(*args, **kwargs) Overloaded function.   1. end(rosetta.core.io.silent.SilentFileData) -> core::io::silent::SilentFileData::iterator   Returns an iterator to the end of the members of this container.   2. end(rosetta.core.io.silent.SilentFileData) -> core::io::silent::SilentFileData::const_iterator   Returns an iterator to the end of the members of this container. filename(...) from builtins.PyCapsule filename(rosetta.core.io.silent.SilentFileData) -> str   Gets the filename that this SilentFileData object will  write to. get_iterator_for_tag(...) from builtins.PyCapsule get_iterator_for_tag(*args, **kwargs) Overloaded function.   1. get_iterator_for_tag(self : rosetta.core.io.silent.SilentFileData, tag : str) -> core::io::silent::SilentFileData::iterator   2. get_iterator_for_tag(self : rosetta.core.io.silent.SilentFileData, tag : str) -> core::io::silent::SilentFileData::const_iterator get_sequence(...) from builtins.PyCapsule get_sequence(self : rosetta.core.io.silent.SilentFileData, filename : str) -> str get_shared_silent_data(...) from builtins.PyCapsule get_shared_silent_data(self : rosetta.core.io.silent.SilentFileData, ssdt : rosetta.core.io.silent.SharedSilentDataType) -> rosetta.core.io.silent.SharedSilentData   SharedSilentData methods get_structure(...) from builtins.PyCapsule get_structure(self : rosetta.core.io.silent.SilentFileData, tag : str) -> core::io::silent::SilentStruct   Return a SilentStruct referred to by the given tag. Assumes that  we have checked the tag!! has_shared_silent_data(...) from builtins.PyCapsule has_shared_silent_data(self : rosetta.core.io.silent.SilentFileData, ssdt : rosetta.core.io.silent.SharedSilentDataType) -> bool has_tag(...) from builtins.PyCapsule has_tag(self : rosetta.core.io.silent.SilentFileData, tag : str) -> bool   Returns true if we have a SilentStruct matching the given tag,  false otherwise. matched_tags(...) from builtins.PyCapsule matched_tags(self : rosetta.core.io.silent.SilentFileData, expression : str, mode : str, tags_in_file : rosetta.utility.vector1_std_string) -> bool   return mode=first,last,all matched tags -- currently matching 'expression*' to tags in file, boost::regexp possible later nres(...) from builtins.PyCapsule nres(rosetta.core.io.silent.SilentFileData) -> int   Returns the number of residues in the first structure in  this object. Not guaranteed to be fixed for all structures in  this container. order_by_energy(...) from builtins.PyCapsule order_by_energy(rosetta.core.io.silent.SilentFileData) -> NoneType   Orders silent structs by energy. push_back(...) from builtins.PyCapsule push_back(self : rosetta.core.io.silent.SilentFileData, new_struct : core::io::silent::SilentStruct) -> NoneType   push_back to provide compatibility with other std containers. read_file(...) from builtins.PyCapsule read_file(*args, **kwargs) Overloaded function.   1. read_file(self : rosetta.core.io.silent.SilentFileData, filename : str) -> bool   Read in the SilentStruct objects contained in the given filename.  this version will throw an exception if things go wrong (boolean return value is thus always true)   2. read_file(self : rosetta.core.io.silent.SilentFileData, filename : str, tags : rosetta.utility.vector1_std_string) -> bool   Read in the SilentStruct objects contained in the given filename.  Ignore any SilentStruct with a tag not in the tags vector.  throw an exception if things go wrong (returned boolean always true) read_tags_fast(...) from builtins.PyCapsule read_tags_fast(*args, **kwargs) Overloaded function.   1. read_tags_fast(self : rosetta.core.io.silent.SilentFileData, filename : str) -> rosetta.utility.vector1_std_string   quickly read a list of tags from a silent-input file. Only checks  lines beginning with SCORE: strings.   2. read_tags_fast(self : rosetta.core.io.silent.SilentFileData, filename : str,  : rosetta.utility.vector1_std_string) -> bool   quickly read a list of tags from a silent-input file. Only checks  lines beginning with SCORE: strings. renumber_all_decoys(...) from builtins.PyCapsule renumber_all_decoys(rosetta.core.io.silent.SilentFileData) -> NoneType   renumber all of the decoys in this SilentFileData object. This  obliterates decoy tag associated with every SilentStruct object, and tries  to sensibly number the decoys with similar and increasingly numbered decoy  tags. reverse_score_filter(...) from builtins.PyCapsule reverse_score_filter(self : rosetta.core.io.silent.SilentFileData, score_fraction : float) -> NoneType score_filter(...) from builtins.PyCapsule score_filter(self : rosetta.core.io.silent.SilentFileData, score_fraction : float) -> NoneType   Removes the worst ( 1 - score_fraction ) percent of the decoys by  score. The value of score_fraction should be between 0 and 1.0. set_filename(...) from builtins.PyCapsule set_filename(self : rosetta.core.io.silent.SilentFileData, filename : str) -> NoneType   Sets the filename that this SilentFileData object will  write to. set_record_source(...) from builtins.PyCapsule set_record_source(self : rosetta.core.io.silent.SilentFileData, new_mode : bool) -> NoneType   ///////////////////////////////////////////////// set_shared_silent_data(...) from builtins.PyCapsule set_shared_silent_data(self : rosetta.core.io.silent.SilentFileData, ssdt : rosetta.core.io.silent.SharedSilentDataType, ssd_op : rosetta.core.io.silent.SharedSilentData) -> NoneType set_verbose(...) from builtins.PyCapsule set_verbose(self : rosetta.core.io.silent.SilentFileData, setting : bool) -> NoneType   Sets the filename that this SilentFileData object will  write to. setup_extra_patches(...) from builtins.PyCapsule setup_extra_patches(self : rosetta.core.io.silent.SilentFileData, all_patches : rosetta.utility.vector1_std_string) -> NoneType setup_extra_res(...) from builtins.PyCapsule setup_extra_res(self : rosetta.core.io.silent.SilentFileData, all_res : rosetta.utility.vector1_std_string) -> NoneType setup_include_patches(...) from builtins.PyCapsule setup_include_patches(self : rosetta.core.io.silent.SilentFileData, filename : str) -> bool size(...) from builtins.PyCapsule size(rosetta.core.io.silent.SilentFileData) -> int   Returns the number of structures contained in this container. store_argv_in_file(...) from builtins.PyCapsule store_argv_in_file(*args, **kwargs) Overloaded function.   1. store_argv_in_file(rosetta.core.io.silent.SilentFileData) -> bool   Returns true if this silent-file plans on storing  option.get_argv() as a comment in the silent-file, false  otherwise.   2. store_argv_in_file(self : rosetta.core.io.silent.SilentFileData, new_setting : bool) -> NoneType   Sets a boolean variable governing if this silent-file  plans on storing option.get_argv() as a comment in the  silent-file. strict_column_mode(...) from builtins.PyCapsule strict_column_mode(*args, **kwargs) Overloaded function.   1. strict_column_mode(rosetta.core.io.silent.SilentFileData) -> bool   Returns a boolean indicating whether or not the strict_column_mode  is turned on when printing scores.      If strict_column_mode() is true, then the first SilentStruct  printed to this SilentFileData object sets the EnergyNames that will be  printed for all other SilentStruct objects. Extra EnergyNames in  subsequent SilentStruct objects are ignored. If new objects are missing  energies that should be printed in strict_column_mode, missing energy  values are set to zero. In !strict_column_mode(), when each SilentStruct  is printed, a new SCORE: header is printed if energies differ from last  printed SilentStruct.   2. strict_column_mode(self : rosetta.core.io.silent.SilentFileData, new_mode : bool) -> NoneType   Sets value for strict column mode. See strict_column_mode() for  more information. structure_list(...) from builtins.PyCapsule structure_list(rosetta.core.io.silent.SilentFileData) -> rosetta.utility.vector1_std_shared_ptr_core_io_silent_SilentStruct_t   Function to access the vector of silent structure owning pointers  ordered as they were in the input file. tags(...) from builtins.PyCapsule tags(rosetta.core.io.silent.SilentFileData) -> rosetta.utility.vector1_std_string   Return all tags in this container. write_all(...) from builtins.PyCapsule write_all(*args, **kwargs) Overloaded function.   1. write_all(self : rosetta.core.io.silent.SilentFileData, filename : str) -> NoneType   write all SilentStruct objects in the structure_map_ to the given  filename.   2. write_all(self : rosetta.core.io.silent.SilentFileData, filename : str, bWriteScoreOnly : bool) -> NoneType   write all SilentStruct objects in the structure_map_ to the given  filename. write_silent_struct(...) from builtins.PyCapsule write_silent_struct(*args, **kwargs) Overloaded function.   1. write_silent_struct(self : rosetta.core.io.silent.SilentFileData, s : core::io::silent::SilentStruct, filename : str) -> bool   Write the given silent-struct to the given outfile.   2. write_silent_struct(self : rosetta.core.io.silent.SilentFileData, s : core::io::silent::SilentStruct, filename : str, bWriteScoreOnly : bool) -> bool   Write the given silent-struct to the given outfile.   class SilentFileLoader(rosetta.basic.resource_manager.ResourceLoader)       Method resolution order: SilentFileLoader rosetta.basic.resource_manager.ResourceLoader builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle) -> NoneType   2. __init__(handle, rosetta.core.io.silent.SilentFileLoader) -> 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.io.silent.SilentFileLoader,  : rosetta.core.io.silent.SilentFileLoader) -> rosetta.core.io.silent.SilentFileLoader default_options(...) from builtins.PyCapsule default_options(rosetta.core.io.silent.SilentFileLoader) -> rosetta.basic.resource_manager.ResourceOptions   class SilentFileLoaderCreator(rosetta.basic.resource_manager.ResourceLoaderCreator)     creator for the SilentFileLoader class     Method resolution order: SilentFileLoaderCreator 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.io.silent.SilentFileLoaderCreator,  : rosetta.core.io.silent.SilentFileLoaderCreator) -> rosetta.core.io.silent.SilentFileLoaderCreator create_resource_loader(...) from builtins.PyCapsule create_resource_loader(rosetta.core.io.silent.SilentFileLoaderCreator) -> rosetta.basic.resource_manager.ResourceLoader loader_type(...) from builtins.PyCapsule loader_type(rosetta.core.io.silent.SilentFileLoaderCreator) -> str   class SilentFileOptions(rosetta.basic.resource_manager.ResourceOptions)       Method resolution order: SilentFileOptions 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.io.silent.SilentFileOptions) -> 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.io.silent.SilentFileOptions,  : rosetta.core.io.silent.SilentFileOptions) -> rosetta.core.io.silent.SilentFileOptions get_silent_struct_type(...) from builtins.PyCapsule get_silent_struct_type(rosetta.core.io.silent.SilentFileOptions) -> str parse_my_tag(...) from builtins.PyCapsule parse_my_tag(self : rosetta.core.io.silent.SilentFileOptions, tag : utility::tag::Tag) -> NoneType set_silent_struct_type(...) from builtins.PyCapsule set_silent_struct_type(self : rosetta.core.io.silent.SilentFileOptions, silent_struct_type : str) -> NoneType type(...) from builtins.PyCapsule type(rosetta.core.io.silent.SilentFileOptions) -> str   The class name for a particular ResourceOptions instance.  This function allows for better error message delivery 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 SilentFileOptionsCreator(rosetta.basic.resource_manager.ResourceOptionsCreator)     creator for the SilentFileOptions class     Method resolution order: SilentFileOptionsCreator 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.io.silent.SilentFileOptionsCreator,  : rosetta.core.io.silent.SilentFileOptionsCreator) -> rosetta.core.io.silent.SilentFileOptionsCreator create_options(...) from builtins.PyCapsule create_options(rosetta.core.io.silent.SilentFileOptionsCreator) -> rosetta.basic.resource_manager.ResourceOptions options_type(...) from builtins.PyCapsule options_type(rosetta.core.io.silent.SilentFileOptionsCreator) -> str   class SilentStruct(builtins.object)     ///////////////////////////////////////////////////////////////////     Methods defined here: __init__(self, /, *args, **kwargs) Initialize self.  See help(type(self)) for accurate signature. __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. add_comment(...) from builtins.PyCapsule add_comment(self : rosetta.core.io.silent.SilentStruct, name : str, value : str) -> NoneType   add a named comment to this SilentStruct object.  Similar to methods for playing with energies, but  mapping is string => string rather than string => Real. add_energy(...) from builtins.PyCapsule add_energy(*args, **kwargs) Overloaded function.   1. add_energy(self : rosetta.core.io.silent.SilentStruct, scorename : str, value : float) -> NoneType   add a score of a given name and value to this SilentStruct.  Takes an optional weight that defaults to 1.0.   2. add_energy(self : rosetta.core.io.silent.SilentStruct, scorename : str, value : float, weight : float) -> NoneType   add a score of a given name and value to this SilentStruct.  Takes an optional weight that defaults to 1.0. add_other_struct(...) from builtins.PyCapsule add_other_struct(self : rosetta.core.io.silent.SilentStruct, silent_struct : rosetta.core.io.silent.SilentStruct) -> NoneType add_parent_remark(...) from builtins.PyCapsule add_parent_remark(self : rosetta.core.io.silent.SilentStruct, name : str, value : str) -> NoneType add_string_value(...) from builtins.PyCapsule add_string_value(self : rosetta.core.io.silent.SilentStruct, scorename : str, value : str) -> NoneType   add a non-floating point score of a given name and value to this  SilentStruct. assign(...) from builtins.PyCapsule assign(self : rosetta.core.io.silent.SilentStruct,  : rosetta.core.io.silent.SilentStruct) -> rosetta.core.io.silent.SilentStruct clear_comments(...) from builtins.PyCapsule clear_comments(rosetta.core.io.silent.SilentStruct) -> NoneType clear_energies(...) from builtins.PyCapsule clear_energies(rosetta.core.io.silent.SilentStruct) -> NoneType   Clear all of the energies in the SilentStruct. Doesn't just  zero the energies, it entirely removes all knowledge of all energies  from this SilentStruct. clone(...) from builtins.PyCapsule clone(rosetta.core.io.silent.SilentStruct) -> rosetta.core.io.silent.SilentStruct comment_from_line(...) from builtins.PyCapsule comment_from_line(self : rosetta.core.io.silent.SilentStruct, line : str) -> NoneType copy_scores(...) from builtins.PyCapsule copy_scores(self : rosetta.core.io.silent.SilentStruct, src_ss : rosetta.core.io.silent.SilentStruct) -> NoneType   Copy the score information in the given SilentStruct into  this SilentStruct. decoy_tag(...) from builtins.PyCapsule decoy_tag(*args, **kwargs) Overloaded function.   1. decoy_tag(rosetta.core.io.silent.SilentStruct) -> str   returns the tag associated with this SilentStruct.   2. decoy_tag(self : rosetta.core.io.silent.SilentStruct, tag : str) -> NoneType   sets the tag associated with this SilentStruct. energies(...) from builtins.PyCapsule energies(rosetta.core.io.silent.SilentStruct) -> rosetta.utility.vector1_core_io_silent_SilentEnergy   Returns the vector of SilentEnergy objects associated with  this SilentStruct object. energies_from_pose(...) from builtins.PyCapsule energies_from_pose(self : rosetta.core.io.silent.SilentStruct, pose : rosetta.core.pose.Pose) -> NoneType   Initialize this SilentStruct's energies from the given Pose.  This sets energies, energy weights, and the output widths for the  energies. energies_into_pose(...) from builtins.PyCapsule energies_into_pose(self : rosetta.core.io.silent.SilentStruct, pose : rosetta.core.pose.Pose) -> NoneType   Put the energy information from this SilentStruct into the  pose. Energies that correspond to a ScoreType are put into the  pose.energies().total_energies() EnergyMap, all other energies are  put into the ARBITRARY_FLOAT_DATA map in the pose DataCache. Also  sets the scorefxn_weights in the Energies object using the  information from this SilentStruct. energy_names(...) from builtins.PyCapsule energy_names(rosetta.core.io.silent.SilentStruct) -> core::io::silent::EnergyNames   Returns the EnergyNames that this SilentStruct contains. erase_comment(...) from builtins.PyCapsule erase_comment(self : rosetta.core.io.silent.SilentStruct, name : str) -> NoneType fill_other_struct_list(...) from builtins.PyCapsule fill_other_struct_list(self : rosetta.core.io.silent.SilentStruct, pose : rosetta.core.pose.Pose) -> NoneType fill_pose(...) from builtins.PyCapsule fill_pose(*args, **kwargs) Overloaded function.   1. fill_pose(self : rosetta.core.io.silent.SilentStruct, pose : rosetta.core.pose.Pose) -> NoneType   2. fill_pose(self : rosetta.core.io.silent.SilentStruct, pose : rosetta.core.pose.Pose, residue_set : rosetta.core.chemical.ResidueTypeSet) -> NoneType   non-virtual interface that takes a ResidueTypeSetCOP (instead of a const & to one)  and invokes the virtual method that takes the const &.   3. fill_pose(self : rosetta.core.io.silent.SilentStruct, pose : rosetta.core.pose.Pose, residue_set : rosetta.core.chemical.ResidueTypeSet) -> NoneType   Fill a Pose with the conformation information in this  SilentStruct and the ResidueTypeSet provided by the caller. This is  a virtual method which should be implemented by classes derived from  SilentStruct. fill_struct(...) from builtins.PyCapsule fill_struct(*args, **kwargs) Overloaded function.   1. fill_struct(self : rosetta.core.io.silent.SilentStruct, pose : rosetta.core.pose.Pose) -> NoneType   opposite of fill_pose -- superclass provides  functionality used by most SilentStruct types, and is  optionally called at the beginning of the subclass's  fill_struct method. As of this writing, used only by  protein SilentStructs   2. fill_struct(self : rosetta.core.io.silent.SilentStruct, pose : rosetta.core.pose.Pose, tag : str) -> NoneType   opposite of fill_pose -- superclass provides  functionality used by most SilentStruct types, and is  optionally called at the beginning of the subclass's  fill_struct method. As of this writing, used only by  protein SilentStructs fill_struct_with_residue_numbers(...) from builtins.PyCapsule fill_struct_with_residue_numbers(self : rosetta.core.io.silent.SilentStruct, pose : rosetta.core.pose.Pose) -> NoneType fill_struct_with_submotif_info_list(...) from builtins.PyCapsule fill_struct_with_submotif_info_list(self : rosetta.core.io.silent.SilentStruct, pose : rosetta.core.pose.Pose) -> NoneType finish_pose(...) from builtins.PyCapsule finish_pose(self : rosetta.core.io.silent.SilentStruct, pose : rosetta.core.pose.Pose) -> NoneType   calls optH if command line requests optH.  must be called by derived classes. force_bitflip(...) from builtins.PyCapsule force_bitflip(rosetta.core.io.silent.SilentStruct) -> bool   Gets whether conversion from big-endian to little-endian (or the converse) should be forced  when a binary silent structure is initialized from lines. full_model_info_into_pose(...) from builtins.PyCapsule full_model_info_into_pose(self : rosetta.core.io.silent.SilentStruct, pose : rosetta.core.pose.Pose) -> NoneType full_model_parameters(...) from builtins.PyCapsule full_model_parameters(rosetta.core.io.silent.SilentStruct) -> rosetta.core.pose.full_model_info.FullModelParameters get_CA_xyz(...) from builtins.PyCapsule get_CA_xyz(rosetta.core.io.silent.SilentStruct) -> ObjexxFCL::FArray2D<double>   returns the positions of the CA atoms in this  ProteinSilentStruct.  Useful for RMS calculations. get_all_comments(...) from builtins.PyCapsule get_all_comments(rosetta.core.io.silent.SilentStruct) -> rosetta.std.map_std_string_std_string get_comment(...) from builtins.PyCapsule get_comment(self : rosetta.core.io.silent.SilentStruct, name : str) -> str get_debug_rmsd(...) from builtins.PyCapsule get_debug_rmsd(rosetta.core.io.silent.SilentStruct) -> float   Do some sort of comparison between the actual RMSD of this  silent-struct and the cached coordinates. Used for SilentStruct  objects that are rebuild from torsions or other reduced  representations of data. get_energy(...) from builtins.PyCapsule get_energy(self : rosetta.core.io.silent.SilentStruct, scorename : str) -> float   Returns the energy associated with the given scorename if this  SilentStruct has an energy for that scorename. Otherwise returns 0. get_parent_remark(...) from builtins.PyCapsule get_parent_remark(self : rosetta.core.io.silent.SilentStruct, name : str) -> str get_parent_remark_from_line(...) from builtins.PyCapsule get_parent_remark_from_line(self : rosetta.core.io.silent.SilentStruct, line : str) -> NoneType get_self_ptr(...) from builtins.PyCapsule get_self_ptr(*args, **kwargs) Overloaded function.   1. get_self_ptr(rosetta.core.io.silent.SilentStruct) -> rosetta.core.io.silent.SilentStruct   self pointers   2. get_self_ptr(rosetta.core.io.silent.SilentStruct) -> rosetta.core.io.silent.SilentStruct get_silent_energies(...) from builtins.PyCapsule get_silent_energies(rosetta.core.io.silent.SilentStruct) -> rosetta.utility.vector1_core_io_silent_SilentEnergy get_silent_energy(...) from builtins.PyCapsule get_silent_energy(self : rosetta.core.io.silent.SilentStruct, scorename : str) -> rosetta.core.io.silent.SilentEnergy   Returns the SilentEnergy associated with this scorename. get_string_value(...) from builtins.PyCapsule get_string_value(self : rosetta.core.io.silent.SilentStruct, scorename : str) -> str   Returns the energy associated with the given scorename if this  SilentStruct has an energy for that scorename. Otherwise returns 0. has_comment(...) from builtins.PyCapsule has_comment(self : rosetta.core.io.silent.SilentStruct, name : str) -> bool has_energy(...) from builtins.PyCapsule has_energy(self : rosetta.core.io.silent.SilentStruct, scorename : str) -> bool   returns true if this SilentStruct has an energy for the given  scorename, returns false otherwise. has_parent_remark(...) from builtins.PyCapsule has_parent_remark(self : rosetta.core.io.silent.SilentStruct, name : str) -> bool init_from_lines(...) from builtins.PyCapsule init_from_lines(self : rosetta.core.io.silent.SilentStruct, lines : rosetta.utility.vector1_std_string, container : rosetta.core.io.silent.SilentFileData) -> bool   Create a new SilentStruct object from the provided set of  lines. This abstract method should be overwritten by derived  classes. Returns false if the init_from_lines routine encounters a  problem with the lines provided. mem_footprint(...) from builtins.PyCapsule mem_footprint(rosetta.core.io.silent.SilentStruct) -> int nonconst_other_struct_list(...) from builtins.PyCapsule nonconst_other_struct_list(rosetta.core.io.silent.SilentStruct) -> rosetta.utility.vector1_std_shared_ptr_core_io_silent_SilentStruct_t nres(...) from builtins.PyCapsule nres(*args, **kwargs) Overloaded function.   1. nres(rosetta.core.io.silent.SilentStruct) -> int   returns the number of residues contained by this  SilentStruct.   2. nres(self : rosetta.core.io.silent.SilentStruct, nres : int) -> NoneType   returns the number of residues in this SilentStruct. one_letter_sequence(...) from builtins.PyCapsule one_letter_sequence(rosetta.core.io.silent.SilentStruct) -> str   strip [...] comment from seqeunce_ and return pure  one-letter sequence other_struct_list(...) from builtins.PyCapsule other_struct_list(rosetta.core.io.silent.SilentStruct) -> rosetta.utility.vector1_std_shared_ptr_core_io_silent_SilentStruct_t precision(...) from builtins.PyCapsule precision(*args, **kwargs) Overloaded function.   1. precision(self : rosetta.core.io.silent.SilentStruct, precision : int) -> NoneType   2. precision(rosetta.core.io.silent.SilentStruct) -> int read_score_headers(...) from builtins.PyCapsule read_score_headers(self : rosetta.core.io.silent.SilentStruct, line : str, enames : rosetta.utility.vector1_std_string, container : rosetta.core.io.silent.SilentFileData) -> NoneType read_sequence(...) from builtins.PyCapsule read_sequence(self : rosetta.core.io.silent.SilentStruct, line : str) -> bool rename_energies(...) from builtins.PyCapsule rename_energies(rosetta.core.io.silent.SilentStruct) -> NoneType residue_numbers_into_pose(...) from builtins.PyCapsule residue_numbers_into_pose(self : rosetta.core.io.silent.SilentStruct, pose : rosetta.core.pose.Pose) -> NoneType scoreline_prefix(...) from builtins.PyCapsule scoreline_prefix(*args, **kwargs) Overloaded function.   1. scoreline_prefix(self : rosetta.core.io.silent.SilentStruct, prefix : str) -> NoneType   2. scoreline_prefix(rosetta.core.io.silent.SilentStruct) -> str sequence(...) from builtins.PyCapsule sequence(*args, **kwargs) Overloaded function.   1. sequence(rosetta.core.io.silent.SilentStruct) -> rosetta.core.sequence.AnnotatedSequence   returns the sequence associated with this SilentStruct.   2. sequence(self : rosetta.core.io.silent.SilentStruct, sequence : rosetta.core.sequence.AnnotatedSequence) -> NoneType   sets the sequence for this SilentStruct. set_chains(...) from builtins.PyCapsule set_chains(self : rosetta.core.io.silent.SilentStruct, chains : rosetta.utility.vector1_char) -> NoneType set_decoy_tag(...) from builtins.PyCapsule set_decoy_tag(self : rosetta.core.io.silent.SilentStruct, tag : str) -> NoneType   set the tag associate with this SilentStruct set_force_bitflip(...) from builtins.PyCapsule set_force_bitflip(self : rosetta.core.io.silent.SilentStruct, setting : bool) -> NoneType   Sets whether conversion from big-endian to little-endian (or the converse) should be forced  when a binary silent structure is initialized from lines. set_full_model_parameters(...) from builtins.PyCapsule set_full_model_parameters(self : rosetta.core.io.silent.SilentStruct, setting : rosetta.core.pose.full_model_info.FullModelParameters) -> NoneType set_residue_numbers(...) from builtins.PyCapsule set_residue_numbers(self : rosetta.core.io.silent.SilentStruct, residue_numbers : rosetta.utility.vector1_unsigned_long) -> NoneType set_segment_IDs(...) from builtins.PyCapsule set_segment_IDs(self : rosetta.core.io.silent.SilentStruct, segids : rosetta.utility.vector1_std_string) -> NoneType set_tag_from_pose(...) from builtins.PyCapsule set_tag_from_pose(self : rosetta.core.io.silent.SilentStruct, pose : rosetta.core.pose.Pose) -> NoneType   Sets the tag from the Pose DataCache. set_valid_energies(...) from builtins.PyCapsule set_valid_energies(self : rosetta.core.io.silent.SilentStruct, valid : rosetta.utility.vector1_std_string) -> NoneType silent_energies(...) from builtins.PyCapsule silent_energies(self : rosetta.core.io.silent.SilentStruct, new_se : rosetta.utility.vector1_core_io_silent_SilentEnergy) -> NoneType   sets the silent_energies for this SilentStruct. sort_silent_scores(...) from builtins.PyCapsule sort_silent_scores(rosetta.core.io.silent.SilentStruct) -> NoneType   sort all the silent energies by their name.   class SilentStructCreator(builtins.object)     Abstract base class for a Mover factory; the Creator class is responsible for creating a particular mover class.     Methods defined here: __init__(...) from builtins.PyCapsule __init__(rosetta.core.io.silent.SilentStructCreator) -> 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.io.silent.SilentStructCreator,  : rosetta.core.io.silent.SilentStructCreator) -> rosetta.core.io.silent.SilentStructCreator create_silent_struct(...) from builtins.PyCapsule create_silent_struct(rosetta.core.io.silent.SilentStructCreator) -> rosetta.core.io.silent.SilentStruct keyname(...) from builtins.PyCapsule keyname(rosetta.core.io.silent.SilentStructCreator) -> str   class SilentStructFactory(rosetta.utility.SingletonBase_core_io_silent_SilentStructFactory_t)       Method resolution order: SilentStructFactory rosetta.utility.SingletonBase_core_io_silent_SilentStructFactory_t builtins.object Methods defined here: __init__(self, /, *args, **kwargs) Initialize self.  See help(type(self)) for accurate signature. __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. factory_register(...) from builtins.PyCapsule factory_register(self : rosetta.core.io.silent.SilentStructFactory, creator : rosetta.core.io.silent.SilentStructCreator) -> NoneType get_creator(...) from builtins.PyCapsule get_creator(self : rosetta.core.io.silent.SilentStructFactory, type_name : str) -> rosetta.core.io.silent.SilentStructCreator get_silent_struct(...) from builtins.PyCapsule get_silent_struct(self : rosetta.core.io.silent.SilentStructFactory, type_name : str) -> rosetta.core.io.silent.SilentStruct get_silent_struct_in(...) from builtins.PyCapsule get_silent_struct_in(rosetta.core.io.silent.SilentStructFactory) -> rosetta.core.io.silent.SilentStruct get_silent_struct_out(...) from builtins.PyCapsule get_silent_struct_out(*args, **kwargs) Overloaded function.   1. get_silent_struct_out(rosetta.core.io.silent.SilentStructFactory) -> rosetta.core.io.silent.SilentStruct   2. get_silent_struct_out(self : rosetta.core.io.silent.SilentStructFactory, pose : rosetta.core.pose.Pose) -> rosetta.core.io.silent.SilentStruct get_ss_names(...) from builtins.PyCapsule get_ss_names(rosetta.core.io.silent.SilentStructFactory) -> rosetta.utility.vector1_std_string has_silent_struct_type(...) from builtins.PyCapsule has_silent_struct_type(self : rosetta.core.io.silent.SilentStructFactory, type_name : str) -> bool   test if the specified silent struct type name is associated with a registered silent struct type. Methods inherited from rosetta.utility.SingletonBase_core_io_silent_SilentStructFactory_t: get_instance(...) from builtins.PyCapsule get_instance() -> core::io::silent::SilentStructFactory   class SimpleSequenceData(SharedSilentData)       Method resolution order: SimpleSequenceData SharedSilentData builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.core.io.silent.SimpleSequenceData) -> NoneType   2. __init__(self : rosetta.core.io.silent.SimpleSequenceData,  : rosetta.core.io.silent.SimpleSequenceData) -> 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.io.silent.SimpleSequenceData,  : rosetta.core.io.silent.SimpleSequenceData) -> rosetta.core.io.silent.SimpleSequenceData sequence(...) from builtins.PyCapsule sequence(rosetta.core.io.silent.SimpleSequenceData) -> str set_sequence(...) from builtins.PyCapsule set_sequence(self : rosetta.core.io.silent.SimpleSequenceData, sequence : str) -> NoneType