Bindings for core::sequence namespace

Classes
		builtins.object ABEGO ABEGOManager AlignMove Aligner MCAligner NWAligner SWAligner AlignerFactory AnnotatedSequence Cell DP_Matrix Line ScoringScheme ChemicalShiftScoringScheme CompassScoringScheme CompositeScoringScheme DPScoringScheme L1ScoringScheme MatrixScoringScheme PairScoringScheme ProfSimScoringScheme SimpleScoringScheme ScoringSchemeFactory Sequence CompositeSequence SequenceProfile ChemicalShiftSequence SequenceCoupling SequenceAlignment SequenceCreator ChemicalShiftSequenceCreator CompositeSequenceCreator SequenceCouplingCreator SequenceProfileCreator SimpleSequenceCreator rosetta.core.id.SequenceMapping(builtins.object) DerivedSequenceMapping rosetta.std.unary_function_core_sequence_SequenceAlignment_unsigned_long_t(builtins.object) SequenceAlignmentHasher rosetta.utility.SingletonBase_core_sequence_SequenceFactory_t(builtins.object) SequenceFactory   class ABEGO(builtins.object)     abego elments     Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.core.sequence.ABEGO) -> NoneType   2. __init__(self : rosetta.core.sequence.ABEGO, name : str, phi_min : float, phi_max : float, psi_min : float, psi_max : float, cis_omega : bool) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. add_line(...) from builtins.PyCapsule add_line(self : rosetta.core.sequence.ABEGO, slope : float, intercept : float, region : bool) -> NoneType check_rama(...) from builtins.PyCapsule check_rama(self : rosetta.core.sequence.ABEGO, phi : float, psi : float, omega : float) -> bool   check input torsion angle are in a given abego region check_rama2(...) from builtins.PyCapsule check_rama2(self : rosetta.core.sequence.ABEGO, phi : float, psi : float) -> bool   check input torsion angle are in a given abego region cis_omega(...) from builtins.PyCapsule cis_omega(rosetta.core.sequence.ABEGO) -> bool name(...) from builtins.PyCapsule name(rosetta.core.sequence.ABEGO) -> str phi_max(...) from builtins.PyCapsule phi_max(rosetta.core.sequence.ABEGO) -> float phi_min(...) from builtins.PyCapsule phi_min(rosetta.core.sequence.ABEGO) -> float psi_max(...) from builtins.PyCapsule psi_max(rosetta.core.sequence.ABEGO) -> float psi_min(...) from builtins.PyCapsule psi_min(rosetta.core.sequence.ABEGO) -> float   class ABEGOManager(builtins.object)     manager for abego     Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.core.sequence.ABEGOManager) -> NoneType   2. __init__(self : rosetta.core.sequence.ABEGOManager, rval : rosetta.core.sequence.ABEGOManager) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. alllevel(...) from builtins.PyCapsule alllevel(rosetta.core.sequence.ABEGOManager) -> int   all output level in current setup assign(...) from builtins.PyCapsule assign(self : rosetta.core.sequence.ABEGOManager,  : rosetta.core.sequence.ABEGOManager) -> rosetta.core.sequence.ABEGOManager base5index2symbolString(...) from builtins.PyCapsule base5index2symbolString(self : rosetta.core.sequence.ABEGOManager, base5index : int, length : int) -> str   transform abego string to abego base5 index check_rama(...) from builtins.PyCapsule check_rama(self : rosetta.core.sequence.ABEGOManager, symbol : str, phi : float, psi : float, omega : float) -> bool   check input torsion angle are in a given abego region get_abego_string(...) from builtins.PyCapsule get_abego_string(self : rosetta.core.sequence.ABEGOManager, abego : rosetta.utility.vector1_std_string) -> str   get abego string get_symbols(...) from builtins.PyCapsule get_symbols(*args, **kwargs) Overloaded function.   1. get_symbols(self : rosetta.core.sequence.ABEGOManager, pose : rosetta.core.pose.Pose) -> rosetta.utility.vector1_std_string   get abego sequence from pose   2. get_symbols(self : rosetta.core.sequence.ABEGOManager, pose : rosetta.core.pose.Pose, level : int) -> rosetta.utility.vector1_std_string   get abego sequence from pose   3. get_symbols(self : rosetta.core.sequence.ABEGOManager, pose : rosetta.core.pose.Pose, begin : int, end : int, level : int) -> rosetta.utility.vector1_std_string   get abego sequence from pose index2symbol(...) from builtins.PyCapsule index2symbol(self : rosetta.core.sequence.ABEGOManager, idx : int) -> str   transform abego index to symbol initialize(...) from builtins.PyCapsule initialize(rosetta.core.sequence.ABEGOManager) -> NoneType   initialize symbol2index(...) from builtins.PyCapsule symbol2index(self : rosetta.core.sequence.ABEGOManager, symbol : str) -> int   transform abego symbol to index symbolString2base5index(...) from builtins.PyCapsule symbolString2base5index(self : rosetta.core.sequence.ABEGOManager, symbolString : str) -> int   transform abego symbol string to base5 index torsion2index(...) from builtins.PyCapsule torsion2index(*args, **kwargs) Overloaded function.   1. torsion2index(self : rosetta.core.sequence.ABEGOManager, phi : float, psi : float, omega : float) -> int   get abego index from torsion angles   2. torsion2index(self : rosetta.core.sequence.ABEGOManager, phi : float, psi : float, omega : float, level : int) -> int   get abego index from torsion angles torsion2index_level1(...) from builtins.PyCapsule torsion2index_level1(self : rosetta.core.sequence.ABEGOManager, phi : float, psi : float, omega : float) -> int   get abego index from torsion angles at level 1 torsion2index_level2(...) from builtins.PyCapsule torsion2index_level2(self : rosetta.core.sequence.ABEGOManager, phi : float, psi : float, omega : float) -> int   get abego index from torsion angles at level 2 torsion2index_level3(...) from builtins.PyCapsule torsion2index_level3(self : rosetta.core.sequence.ABEGOManager, phi : float, psi : float, omega : float) -> int   get abego index from torsion angles at level 3 torsion2index_level4(...) from builtins.PyCapsule torsion2index_level4(self : rosetta.core.sequence.ABEGOManager, phi : float, psi : float, omega : float) -> int   get abego index from torsion angles at level 3 total_number_abego(...) from builtins.PyCapsule total_number_abego(rosetta.core.sequence.ABEGOManager) -> int   total number of abego definition   class AlignMove(builtins.object)       Methods defined here: __eq__(...) from builtins.PyCapsule __eq__(rosetta.core.sequence.AlignMove, rosetta.core.sequence.AlignMove) -> bool __hash__(...) from builtins.PyCapsule __hash__(rosetta.core.sequence.AlignMove) -> int __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.core.sequence.AlignMove, int) -> NoneType   2. __init__(rosetta.core.sequence.AlignMove, int) -> NoneType __int__(...) from builtins.PyCapsule __int__(rosetta.core.sequence.AlignMove) -> int __ne__(...) from builtins.PyCapsule __ne__(rosetta.core.sequence.AlignMove, rosetta.core.sequence.AlignMove) -> 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.sequence.AlignMove) -> str Data and other attributes defined here: above = AlignMove.above diagonal = AlignMove.diagonal end = AlignMove.end left = AlignMove.left   class Aligner(builtins.object)       Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.core.sequence.Aligner) -> NoneType   2. __init__(rosetta.core.sequence.Aligner, rosetta.core.sequence.Aligner) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. align(...) from builtins.PyCapsule align(self : rosetta.core.sequence.Aligner, seq_y : rosetta.core.sequence.Sequence, seq_x : rosetta.core.sequence.Sequence, ss : core::sequence::ScoringScheme) -> core::sequence::SequenceAlignment assign(...) from builtins.PyCapsule assign(self : rosetta.core.sequence.Aligner,  : rosetta.core.sequence.Aligner) -> rosetta.core.sequence.Aligner traceback(...) from builtins.PyCapsule traceback(self : rosetta.core.sequence.Aligner, seq_x : rosetta.core.sequence.Sequence, seq_y : rosetta.core.sequence.Sequence, matrix : rosetta.core.sequence.DP_Matrix, start : rosetta.core.sequence.Cell) -> core::sequence::SequenceAlignment validate_input(...) from builtins.PyCapsule validate_input(self : rosetta.core.sequence.Aligner, seq_y : rosetta.core.sequence.Sequence, seq_x : rosetta.core.sequence.Sequence, ss : core::sequence::ScoringScheme) -> NoneType   class AlignerFactory(builtins.object)       Methods defined here: __init__(...) from builtins.PyCapsule __init__(rosetta.core.sequence.AlignerFactory) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. get_aligner(...) from builtins.PyCapsule get_aligner(type : str) -> rosetta.core.sequence.Aligner   returns an AlignerOP   class AnnotatedSequence(builtins.object)       Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.core.sequence.AnnotatedSequence) -> NoneType   2. __init__(self : rosetta.core.sequence.AnnotatedSequence,  : str) -> NoneType   3. __init__(self : rosetta.core.sequence.AnnotatedSequence, other : rosetta.core.sequence.AnnotatedSequence) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. aa(...) from builtins.PyCapsule aa(self : rosetta.core.sequence.AnnotatedSequence, seqpos : int) -> rosetta.core.chemical.AA assign(...) from builtins.PyCapsule assign(*args, **kwargs) Overloaded function.   1. assign(self : rosetta.core.sequence.AnnotatedSequence,  : str) -> NoneType   2. assign(self : rosetta.core.sequence.AnnotatedSequence, other : rosetta.core.sequence.AnnotatedSequence) -> rosetta.core.sequence.AnnotatedSequence is_patched(...) from builtins.PyCapsule is_patched(self : rosetta.core.sequence.AnnotatedSequence, seqpos : int) -> bool length(...) from builtins.PyCapsule length(rosetta.core.sequence.AnnotatedSequence) -> int one_letter(...) from builtins.PyCapsule one_letter(self : rosetta.core.sequence.AnnotatedSequence, seqpos : int) -> str one_letter_sequence(...) from builtins.PyCapsule one_letter_sequence(rosetta.core.sequence.AnnotatedSequence) -> str patch_str(...) from builtins.PyCapsule patch_str(self : rosetta.core.sequence.AnnotatedSequence, seqpos : int) -> str   class Cell(builtins.object)       Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.core.sequence.Cell) -> NoneType   2. __init__(rosetta.core.sequence.Cell, float) -> NoneType   doc   3. __init__(self : rosetta.core.sequence.Cell, sc : float, ty : rosetta.core.sequence.AlignMove) -> NoneType   4. __init__(self : rosetta.core.sequence.Cell,  : rosetta.core.sequence.Cell) -> 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.sequence.Cell, c : rosetta.core.sequence.Cell) -> rosetta.core.sequence.Cell came_from(...) from builtins.PyCapsule came_from(*args, **kwargs) Overloaded function.   1. came_from(rosetta.core.sequence.Cell) -> rosetta.core.sequence.AlignMove   2. came_from(self : rosetta.core.sequence.Cell, type : rosetta.core.sequence.AlignMove) -> NoneType next(...) from builtins.PyCapsule next(*args, **kwargs) Overloaded function.   1. next(self : rosetta.core.sequence.Cell, n : rosetta.core.sequence.Cell) -> NoneType   2. next(rosetta.core.sequence.Cell) -> rosetta.core.sequence.Cell score(...) from builtins.PyCapsule score(*args, **kwargs) Overloaded function.   1. score(self : rosetta.core.sequence.Cell, score : float) -> NoneType   2. score(rosetta.core.sequence.Cell) -> float x(...) from builtins.PyCapsule x(*args, **kwargs) Overloaded function.   1. x(self : rosetta.core.sequence.Cell, s : int) -> NoneType   2. x(rosetta.core.sequence.Cell) -> int y(...) from builtins.PyCapsule y(*args, **kwargs) Overloaded function.   1. y(self : rosetta.core.sequence.Cell, s : int) -> NoneType   2. y(rosetta.core.sequence.Cell) -> int   class ChemicalShiftScoringScheme(ScoringScheme)       Method resolution order: ChemicalShiftScoringScheme ScoringScheme builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle) -> NoneType   doc   2. __init__(handle, float) -> NoneType   doc   3. __init__(self : handle, open : float, extend : float) -> NoneType   4. __init__(handle, rosetta.core.sequence.ChemicalShiftScoringScheme) -> 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.sequence.ChemicalShiftScoringScheme,  : rosetta.core.sequence.ChemicalShiftScoringScheme) -> rosetta.core.sequence.ChemicalShiftScoringScheme clone(...) from builtins.PyCapsule clone(rosetta.core.sequence.ChemicalShiftScoringScheme) -> rosetta.core.sequence.ScoringScheme score(...) from builtins.PyCapsule score(self : rosetta.core.sequence.ChemicalShiftScoringScheme, seq1 : rosetta.core.sequence.Sequence, seq2 : rosetta.core.sequence.Sequence, pos1 : int, pos2 : int) -> float Methods inherited from ScoringScheme: gap_extend(...) from builtins.PyCapsule gap_extend(*args, **kwargs) Overloaded function.   1. gap_extend(rosetta.core.sequence.ScoringScheme) -> float   Gets the gap extension penalty.   2. gap_extend(self : rosetta.core.sequence.ScoringScheme, gap_extend : float) -> NoneType   Sets the gap extension penalty. gap_open(...) from builtins.PyCapsule gap_open(*args, **kwargs) Overloaded function.   1. gap_open(rosetta.core.sequence.ScoringScheme) -> float   Gets the gap opening penalty.   2. gap_open(self : rosetta.core.sequence.ScoringScheme, gap_open : float) -> NoneType   Sets the gap opening penalty. is_good(...) from builtins.PyCapsule is_good(self : rosetta.core.sequence.ScoringScheme, num : float) -> bool read_data(...) from builtins.PyCapsule read_data(self : rosetta.core.sequence.ScoringScheme,  : rosetta.utility.io.izstream) -> NoneType read_from_file(...) from builtins.PyCapsule read_from_file(self : rosetta.core.sequence.ScoringScheme,  : rosetta.utility.file.FileName) -> NoneType   Initialize from a file. type(...) from builtins.PyCapsule type(*args, **kwargs) Overloaded function.   1. type(rosetta.core.sequence.ScoringScheme) -> str   getters for type, which is a unique string name for this object.   2. type(self : rosetta.core.sequence.ScoringScheme, new_type : str) -> NoneType   getters for type, which is a unique string name for this object. unimplemented_method_error(...) from builtins.PyCapsule unimplemented_method_error(self : rosetta.core.sequence.ScoringScheme, method_name : str) -> NoneType   Utility method for producing useful error messages and exiting  from program. Declared const which is funny, because exiting the program  certainly changes the state of this object! This might be replaced with  exception handling if we ever start using those.   class ChemicalShiftSequence(SequenceProfile)       Method resolution order: ChemicalShiftSequence SequenceProfile Sequence builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle) -> NoneType   2. __init__(self : handle, fn : rosetta.utility.file.FileName) -> NoneType   3. __init__(handle, rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t, str, str) -> NoneType   doc   4. __init__(self : handle, cs_prof : rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t, seq : str, ident : str, start_idx : int) -> NoneType   5. __init__(handle, rosetta.core.sequence.ChemicalShiftSequence) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. __str__(...) from builtins.PyCapsule __str__(rosetta.core.sequence.ChemicalShiftSequence) -> str alphabet(...) from builtins.PyCapsule alphabet(*args, **kwargs) Overloaded function.   1. alphabet(rosetta.core.sequence.ChemicalShiftSequence) -> rosetta.utility.vector1_std_string   Return the alphabet used by this sequence profile. This is an  N-dimensional vector1 where N is the width of the profile, and the ith  entry of any row in the profile represents the probability of ith  character at that row in the sequence.   2. alphabet(self : rosetta.core.sequence.ChemicalShiftSequence, new_alphabet : rosetta.utility.vector1_std_string) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.core.sequence.ChemicalShiftSequence, rhs : rosetta.core.sequence.ChemicalShiftSequence) -> rosetta.core.sequence.ChemicalShiftSequence   assignment operator. clone(...) from builtins.PyCapsule clone(rosetta.core.sequence.ChemicalShiftSequence) -> rosetta.core.sequence.Sequence   Returns an owning pointer to a new ChemicalShiftSequence object,  with data that is a deep copy of the information in this object. read_from_file(...) from builtins.PyCapsule read_from_file(self : rosetta.core.sequence.ChemicalShiftSequence, fn : rosetta.utility.file.FileName) -> NoneType   Read an profile matrix from the given filename using the  2nd_inCS.tab format. sigma(...) from builtins.PyCapsule sigma(self : rosetta.core.sequence.ChemicalShiftSequence,  : int, idx : int) -> float Methods inherited from SequenceProfile: __eq__(...) from builtins.PyCapsule __eq__(self : rosetta.core.sequence.SequenceProfile, other : rosetta.core.sequence.SequenceProfile) -> bool convert_profile_to_probs(...) from builtins.PyCapsule convert_profile_to_probs(*args, **kwargs) Overloaded function.   1. convert_profile_to_probs(rosetta.core.sequence.SequenceProfile) -> NoneType   Use boltzman scaling on a per-residue basis to convert the current profile values to probabilities ( range 0.0-1.0 )   2. convert_profile_to_probs(self : rosetta.core.sequence.SequenceProfile, temp : float) -> NoneType   Use boltzman scaling on a per-residue basis to convert the current profile values to probabilities ( range 0.0-1.0 ) delete_position(...) from builtins.PyCapsule delete_position(self : rosetta.core.sequence.SequenceProfile, pos : int) -> NoneType   Deletes the given position from the Sequence and shifts  everything else back by one. generate_from_sequence(...) from builtins.PyCapsule generate_from_sequence(*args, **kwargs) Overloaded function.   1. generate_from_sequence(self : rosetta.core.sequence.SequenceProfile, seq : rosetta.core.sequence.Sequence) -> NoneType   Generate the profile matrix from a sequence and a given substitution matrix   2. generate_from_sequence(self : rosetta.core.sequence.SequenceProfile, seq : rosetta.core.sequence.Sequence, matrix : str) -> NoneType   Generate the profile matrix from a sequence and a given substitution matrix global_auto_rescale(...) from builtins.PyCapsule global_auto_rescale(rosetta.core.sequence.SequenceProfile) -> NoneType   Use linear rescaling (with a fixed zero) to fit the values within the range -1.0 to 1.0 insert_char(...) from builtins.PyCapsule insert_char(self : rosetta.core.sequence.SequenceProfile, pos : int, new_char : str) -> NoneType   Inserts a character at the given position. negative_better(...) from builtins.PyCapsule negative_better(*args, **kwargs) Overloaded function.   1. negative_better(rosetta.core.sequence.SequenceProfile) -> bool   Returns true if negative values are better identities.      The "default" use case is for storing log likelihood values  where positive is better. If you're using this class to store energy-like  values, set negative_better to true.   2. negative_better(self : rosetta.core.sequence.SequenceProfile, negbet : bool) -> NoneType   Set whether negative identities are better. occurrence_data(...) from builtins.PyCapsule occurrence_data(*args, **kwargs) Overloaded function.   1. occurrence_data(rosetta.core.sequence.SequenceProfile) -> rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t   Returns the 2D vector1 of Real values of the probabilties of each aa.   2. occurrence_data(self : rosetta.core.sequence.SequenceProfile, new_occurrence_data : rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t) -> NoneType   Sets the 2D vector1 of Real values of the probabilties of each aa. probability_row(...) from builtins.PyCapsule probability_row(self : rosetta.core.sequence.SequenceProfile, pos : int) -> rosetta.utility.vector1_double probabilty_row(...) from builtins.PyCapsule probabilty_row(self : rosetta.core.sequence.SequenceProfile, new_prob_row : rosetta.utility.vector1_double, pos : int) -> NoneType prof_row(...) from builtins.PyCapsule prof_row(*args, **kwargs) Overloaded function.   1. prof_row(self : rosetta.core.sequence.SequenceProfile, pos : int) -> rosetta.utility.vector1_double   Returns the vector1 of values at this position.   2. prof_row(self : rosetta.core.sequence.SequenceProfile, new_prof_row : rosetta.utility.vector1_double, pos : int) -> NoneType   Sets the 1D vector1 of Real values representing this profile at pos X. profile(...) from builtins.PyCapsule profile(*args, **kwargs) Overloaded function.   1. profile(rosetta.core.sequence.SequenceProfile) -> rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t   Returns the 2D vector1 of Real values representing this profile.   2. profile(self : rosetta.core.sequence.SequenceProfile, new_profile : rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t) -> NoneType   Sets the 2D vector1 of Real values representing this profile. read_from_binary_chk(...) from builtins.PyCapsule read_from_binary_chk(self : rosetta.core.sequence.SequenceProfile, fn : rosetta.utility.file.FileName) -> NoneType   Read profile matrix from the given filename in the legacy BLAST binary format read_from_checkpoint(...) from builtins.PyCapsule read_from_checkpoint(*args, **kwargs) Overloaded function.   1. read_from_checkpoint(self : rosetta.core.sequence.SequenceProfile, fn : rosetta.utility.file.FileName) -> NoneType   Read profile matrix from the given filename using the NNMAKE  .checkpoint format.  For compatability, negative_better defaults to true. Set manually if necessary.   2. read_from_checkpoint(self : rosetta.core.sequence.SequenceProfile, fn : rosetta.utility.file.FileName, negative_better : bool) -> NoneType   Read profile matrix from the given filename using the NNMAKE  .checkpoint format.  For compatability, negative_better defaults to true. Set manually if necessary. rescale(...) from builtins.PyCapsule rescale(*args, **kwargs) Overloaded function.   1. rescale(rosetta.core.sequence.SequenceProfile) -> NoneType   Multiply all profile weights by factor   2. rescale(self : rosetta.core.sequence.SequenceProfile, factor : float) -> NoneType   Multiply all profile weights by factor size(...) from builtins.PyCapsule size(rosetta.core.sequence.SequenceProfile) -> int temp(...) from builtins.PyCapsule temp(rosetta.core.sequence.SequenceProfile) -> float   returns the temperature used in computing profile probabilities type(...) from builtins.PyCapsule type(rosetta.core.sequence.SequenceProfile) -> str width(...) from builtins.PyCapsule width(rosetta.core.sequence.SequenceProfile) -> int   Returns the number of distinct values at each position in this  profile. Methods inherited from Sequence: __getitem__(...) from builtins.PyCapsule __getitem__(self : rosetta.core.sequence.Sequence, pos : int) -> str   Returns the character at the given sequence position. append_char(...) from builtins.PyCapsule append_char(self : rosetta.core.sequence.Sequence, new_char : str) -> NoneType   Append a character append_gap(...) from builtins.PyCapsule append_gap(rosetta.core.sequence.Sequence) -> NoneType   Append a gap at(...) from builtins.PyCapsule at(self : rosetta.core.sequence.Sequence, pos : int) -> str gap_char(...) from builtins.PyCapsule gap_char(*args, **kwargs) Overloaded function.   1. gap_char(self : rosetta.core.sequence.Sequence, gap_char : str) -> NoneType   sets gap_char to the given value.   2. gap_char(rosetta.core.sequence.Sequence) -> str   Returns the character used to represent a gap for this object. id(...) from builtins.PyCapsule id(*args, **kwargs) Overloaded function.   1. id(self : rosetta.core.sequence.Sequence, new_id : str) -> NoneType   sets id to the given value.   2. id(rosetta.core.sequence.Sequence) -> str   Returns the id of this object. insert_gap(...) from builtins.PyCapsule insert_gap(self : rosetta.core.sequence.Sequence, pos : int) -> NoneType   Inserts a gap at the given position, where insert_gap( 0 )  inserts the character at the beginning of the sequence, and  insert_gap( length() ) inserts the character at the end of the  sequence. is_gap(...) from builtins.PyCapsule is_gap(self : rosetta.core.sequence.Sequence, pos : int) -> bool   Returns true if this position in the sequence represents a gap,  returns false otherwise. length(...) from builtins.PyCapsule length(rosetta.core.sequence.Sequence) -> int   Returns the number of characters in this object. resnum(...) from builtins.PyCapsule resnum(self : rosetta.core.sequence.Sequence, idx : int) -> int   Returns the index of the given sequence position, which is the  position in the sequence minus any gaps that occur earlier in the  sequence. For example, if the sequence is ---AT, resnum(5) will return 2.  Returns 0 for unaligned positions. sequence(...) from builtins.PyCapsule sequence(*args, **kwargs) Overloaded function.   1. sequence(self : rosetta.core.sequence.Sequence, sequence : str) -> NoneType   sets sequence to the given value.   2. sequence(rosetta.core.sequence.Sequence) -> str   Returns the full sequence, which may include gaps. spacer_positions(...) from builtins.PyCapsule spacer_positions(*args, **kwargs) Overloaded function.   1. spacer_positions(self : rosetta.core.sequence.Sequence, spacer_positions : rosetta.utility.vector1_unsigned_long) -> NoneType   sets spacer_positions to the given value.   2. spacer_positions(rosetta.core.sequence.Sequence) -> rosetta.utility.vector1_unsigned_long   Returns the spacer positions (chain breaks, e.g., from spaces or commas in original sequence text) start(...) from builtins.PyCapsule start(*args, **kwargs) Overloaded function.   1. start(self : rosetta.core.sequence.Sequence, new_start : int) -> NoneType   sets starting index to the given value.   2. start(rosetta.core.sequence.Sequence) -> int   Returns the start of this object. to_string(...) from builtins.PyCapsule to_string(rosetta.core.sequence.Sequence) -> str ungapped_length(...) from builtins.PyCapsule ungapped_length(rosetta.core.sequence.Sequence) -> int   Returns the number of characters in this object, ignoring gaps. ungapped_sequence(...) from builtins.PyCapsule ungapped_sequence(rosetta.core.sequence.Sequence) -> str   Returns the string representing this sequence without gaps.   class ChemicalShiftSequenceCreator(SequenceCreator)       Method resolution order: ChemicalShiftSequenceCreator SequenceCreator 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.sequence.ChemicalShiftSequenceCreator,  : rosetta.core.sequence.ChemicalShiftSequenceCreator) -> rosetta.core.sequence.ChemicalShiftSequenceCreator create_sequence(...) from builtins.PyCapsule create_sequence(rosetta.core.sequence.ChemicalShiftSequenceCreator) -> rosetta.core.sequence.Sequence keyname(...) from builtins.PyCapsule keyname(rosetta.core.sequence.ChemicalShiftSequenceCreator) -> str   class CompassScoringScheme(ScoringScheme)       Method resolution order: CompassScoringScheme ScoringScheme builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle) -> NoneType   doc   2. __init__(handle, float) -> NoneType   doc   3. __init__(self : handle, open : float, extend : float) -> NoneType   4. __init__(handle, rosetta.core.sequence.CompassScoringScheme) -> 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.sequence.CompassScoringScheme,  : rosetta.core.sequence.CompassScoringScheme) -> rosetta.core.sequence.CompassScoringScheme clone(...) from builtins.PyCapsule clone(rosetta.core.sequence.CompassScoringScheme) -> rosetta.core.sequence.ScoringScheme score(...) from builtins.PyCapsule score(self : rosetta.core.sequence.CompassScoringScheme, seq1 : rosetta.core.sequence.Sequence, seq2 : rosetta.core.sequence.Sequence, pos1 : int, pos2 : int) -> float Methods inherited from ScoringScheme: gap_extend(...) from builtins.PyCapsule gap_extend(*args, **kwargs) Overloaded function.   1. gap_extend(rosetta.core.sequence.ScoringScheme) -> float   Gets the gap extension penalty.   2. gap_extend(self : rosetta.core.sequence.ScoringScheme, gap_extend : float) -> NoneType   Sets the gap extension penalty. gap_open(...) from builtins.PyCapsule gap_open(*args, **kwargs) Overloaded function.   1. gap_open(rosetta.core.sequence.ScoringScheme) -> float   Gets the gap opening penalty.   2. gap_open(self : rosetta.core.sequence.ScoringScheme, gap_open : float) -> NoneType   Sets the gap opening penalty. is_good(...) from builtins.PyCapsule is_good(self : rosetta.core.sequence.ScoringScheme, num : float) -> bool read_data(...) from builtins.PyCapsule read_data(self : rosetta.core.sequence.ScoringScheme,  : rosetta.utility.io.izstream) -> NoneType read_from_file(...) from builtins.PyCapsule read_from_file(self : rosetta.core.sequence.ScoringScheme,  : rosetta.utility.file.FileName) -> NoneType   Initialize from a file. type(...) from builtins.PyCapsule type(*args, **kwargs) Overloaded function.   1. type(rosetta.core.sequence.ScoringScheme) -> str   getters for type, which is a unique string name for this object.   2. type(self : rosetta.core.sequence.ScoringScheme, new_type : str) -> NoneType   getters for type, which is a unique string name for this object. unimplemented_method_error(...) from builtins.PyCapsule unimplemented_method_error(self : rosetta.core.sequence.ScoringScheme, method_name : str) -> NoneType   Utility method for producing useful error messages and exiting  from program. Declared const which is funny, because exiting the program  certainly changes the state of this object! This might be replaced with  exception handling if we ever start using those.   class CompositeScoringScheme(ScoringScheme)       Method resolution order: CompositeScoringScheme ScoringScheme builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle) -> NoneType   2. __init__(self : handle, gap_open_in : float, gap_extend_in : float, schemes : rosetta.utility.vector1_std_shared_ptr_core_sequence_ScoringScheme_t) -> NoneType   3. __init__(handle, rosetta.core.sequence.CompositeScoringScheme) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. add_scoring_scheme(...) from builtins.PyCapsule add_scoring_scheme(self : rosetta.core.sequence.CompositeScoringScheme, scheme : rosetta.core.sequence.ScoringScheme) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.core.sequence.CompositeScoringScheme,  : rosetta.core.sequence.CompositeScoringScheme) -> rosetta.core.sequence.CompositeScoringScheme clone(...) from builtins.PyCapsule clone(rosetta.core.sequence.CompositeScoringScheme) -> rosetta.core.sequence.ScoringScheme count(...) from builtins.PyCapsule count(rosetta.core.sequence.CompositeScoringScheme) -> int read_from_file(...) from builtins.PyCapsule read_from_file(self : rosetta.core.sequence.CompositeScoringScheme, fn : rosetta.utility.file.FileName) -> NoneType score(...) from builtins.PyCapsule score(self : rosetta.core.sequence.CompositeScoringScheme, seq1 : rosetta.core.sequence.Sequence, seq2 : rosetta.core.sequence.Sequence, pos1 : int, pos2 : int) -> float scoring_schemes(...) from builtins.PyCapsule scoring_schemes(rosetta.core.sequence.CompositeScoringScheme) -> rosetta.utility.vector1_std_shared_ptr_core_sequence_ScoringScheme_t Methods inherited from ScoringScheme: gap_extend(...) from builtins.PyCapsule gap_extend(*args, **kwargs) Overloaded function.   1. gap_extend(rosetta.core.sequence.ScoringScheme) -> float   Gets the gap extension penalty.   2. gap_extend(self : rosetta.core.sequence.ScoringScheme, gap_extend : float) -> NoneType   Sets the gap extension penalty. gap_open(...) from builtins.PyCapsule gap_open(*args, **kwargs) Overloaded function.   1. gap_open(rosetta.core.sequence.ScoringScheme) -> float   Gets the gap opening penalty.   2. gap_open(self : rosetta.core.sequence.ScoringScheme, gap_open : float) -> NoneType   Sets the gap opening penalty. is_good(...) from builtins.PyCapsule is_good(self : rosetta.core.sequence.ScoringScheme, num : float) -> bool read_data(...) from builtins.PyCapsule read_data(self : rosetta.core.sequence.ScoringScheme,  : rosetta.utility.io.izstream) -> NoneType type(...) from builtins.PyCapsule type(*args, **kwargs) Overloaded function.   1. type(rosetta.core.sequence.ScoringScheme) -> str   getters for type, which is a unique string name for this object.   2. type(self : rosetta.core.sequence.ScoringScheme, new_type : str) -> NoneType   getters for type, which is a unique string name for this object. unimplemented_method_error(...) from builtins.PyCapsule unimplemented_method_error(self : rosetta.core.sequence.ScoringScheme, method_name : str) -> NoneType   Utility method for producing useful error messages and exiting  from program. Declared const which is funny, because exiting the program  certainly changes the state of this object! This might be replaced with  exception handling if we ever start using those.   class CompositeSequence(Sequence)       Method resolution order: CompositeSequence Sequence builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle) -> NoneType   2. __init__(handle, rosetta.core.sequence.CompositeSequence) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. add_sequence(...) from builtins.PyCapsule add_sequence(self : rosetta.core.sequence.CompositeSequence, seq : rosetta.core.sequence.Sequence) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.core.sequence.CompositeSequence, rhs : rosetta.core.sequence.CompositeSequence) -> rosetta.core.sequence.CompositeSequence   assignment operator. clone(...) from builtins.PyCapsule clone(rosetta.core.sequence.CompositeSequence) -> rosetta.core.sequence.Sequence   Returns an owning pointer to a new CompositeSequence object,  with data that is a deep copy of the information in this object. delete_position(...) from builtins.PyCapsule delete_position(self : rosetta.core.sequence.CompositeSequence, pos : int) -> NoneType insert_char(...) from builtins.PyCapsule insert_char(self : rosetta.core.sequence.CompositeSequence, pos : int, new_char : str) -> NoneType length(...) from builtins.PyCapsule length(rosetta.core.sequence.CompositeSequence) -> int n_seqs(...) from builtins.PyCapsule n_seqs(rosetta.core.sequence.CompositeSequence) -> int seq(...) from builtins.PyCapsule seq(self : rosetta.core.sequence.CompositeSequence, idx : int) -> rosetta.core.sequence.Sequence seqs(...) from builtins.PyCapsule seqs(rosetta.core.sequence.CompositeSequence) -> rosetta.utility.vector1_std_shared_ptr_core_sequence_Sequence_t to_string(...) from builtins.PyCapsule to_string(rosetta.core.sequence.CompositeSequence) -> str type(...) from builtins.PyCapsule type(rosetta.core.sequence.CompositeSequence) -> str Methods inherited from Sequence: __eq__(...) from builtins.PyCapsule __eq__(self : rosetta.core.sequence.Sequence, s : rosetta.core.sequence.Sequence) -> bool   Returns true if the given Sequence object is equal to this  Sequence object. Tests for string equality of id(), start(), and  sequence(), and returns false if any of these are not equal. __getitem__(...) from builtins.PyCapsule __getitem__(self : rosetta.core.sequence.Sequence, pos : int) -> str   Returns the character at the given sequence position. __str__(...) from builtins.PyCapsule __str__(rosetta.core.sequence.Sequence) -> str append_char(...) from builtins.PyCapsule append_char(self : rosetta.core.sequence.Sequence, new_char : str) -> NoneType   Append a character append_gap(...) from builtins.PyCapsule append_gap(rosetta.core.sequence.Sequence) -> NoneType   Append a gap at(...) from builtins.PyCapsule at(self : rosetta.core.sequence.Sequence, pos : int) -> str gap_char(...) from builtins.PyCapsule gap_char(*args, **kwargs) Overloaded function.   1. gap_char(self : rosetta.core.sequence.Sequence, gap_char : str) -> NoneType   sets gap_char to the given value.   2. gap_char(rosetta.core.sequence.Sequence) -> str   Returns the character used to represent a gap for this object. id(...) from builtins.PyCapsule id(*args, **kwargs) Overloaded function.   1. id(self : rosetta.core.sequence.Sequence, new_id : str) -> NoneType   sets id to the given value.   2. id(rosetta.core.sequence.Sequence) -> str   Returns the id of this object. insert_gap(...) from builtins.PyCapsule insert_gap(self : rosetta.core.sequence.Sequence, pos : int) -> NoneType   Inserts a gap at the given position, where insert_gap( 0 )  inserts the character at the beginning of the sequence, and  insert_gap( length() ) inserts the character at the end of the  sequence. is_gap(...) from builtins.PyCapsule is_gap(self : rosetta.core.sequence.Sequence, pos : int) -> bool   Returns true if this position in the sequence represents a gap,  returns false otherwise. read_from_file(...) from builtins.PyCapsule read_from_file(self : rosetta.core.sequence.Sequence,  : rosetta.utility.file.FileName) -> NoneType   initializes this sequence object from a file. resnum(...) from builtins.PyCapsule resnum(self : rosetta.core.sequence.Sequence, idx : int) -> int   Returns the index of the given sequence position, which is the  position in the sequence minus any gaps that occur earlier in the  sequence. For example, if the sequence is ---AT, resnum(5) will return 2.  Returns 0 for unaligned positions. sequence(...) from builtins.PyCapsule sequence(*args, **kwargs) Overloaded function.   1. sequence(self : rosetta.core.sequence.Sequence, sequence : str) -> NoneType   sets sequence to the given value.   2. sequence(rosetta.core.sequence.Sequence) -> str   Returns the full sequence, which may include gaps. spacer_positions(...) from builtins.PyCapsule spacer_positions(*args, **kwargs) Overloaded function.   1. spacer_positions(self : rosetta.core.sequence.Sequence, spacer_positions : rosetta.utility.vector1_unsigned_long) -> NoneType   sets spacer_positions to the given value.   2. spacer_positions(rosetta.core.sequence.Sequence) -> rosetta.utility.vector1_unsigned_long   Returns the spacer positions (chain breaks, e.g., from spaces or commas in original sequence text) start(...) from builtins.PyCapsule start(*args, **kwargs) Overloaded function.   1. start(self : rosetta.core.sequence.Sequence, new_start : int) -> NoneType   sets starting index to the given value.   2. start(rosetta.core.sequence.Sequence) -> int   Returns the start of this object. ungapped_length(...) from builtins.PyCapsule ungapped_length(rosetta.core.sequence.Sequence) -> int   Returns the number of characters in this object, ignoring gaps. ungapped_sequence(...) from builtins.PyCapsule ungapped_sequence(rosetta.core.sequence.Sequence) -> str   Returns the string representing this sequence without gaps.   class CompositeSequenceCreator(SequenceCreator)       Method resolution order: CompositeSequenceCreator SequenceCreator 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.sequence.CompositeSequenceCreator,  : rosetta.core.sequence.CompositeSequenceCreator) -> rosetta.core.sequence.CompositeSequenceCreator create_sequence(...) from builtins.PyCapsule create_sequence(rosetta.core.sequence.CompositeSequenceCreator) -> rosetta.core.sequence.Sequence keyname(...) from builtins.PyCapsule keyname(rosetta.core.sequence.CompositeSequenceCreator) -> str   class DPScoringScheme(ScoringScheme)       Method resolution order: DPScoringScheme ScoringScheme builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle) -> NoneType   doc   2. __init__(handle, float) -> NoneType   doc   3. __init__(self : handle, open : float, extend : float) -> NoneType   4. __init__(handle, rosetta.core.sequence.DPScoringScheme) -> 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.sequence.DPScoringScheme,  : rosetta.core.sequence.DPScoringScheme) -> rosetta.core.sequence.DPScoringScheme clone(...) from builtins.PyCapsule clone(rosetta.core.sequence.DPScoringScheme) -> rosetta.core.sequence.ScoringScheme score(...) from builtins.PyCapsule score(self : rosetta.core.sequence.DPScoringScheme, seq1 : rosetta.core.sequence.Sequence, seq2 : rosetta.core.sequence.Sequence, pos1 : int, pos2 : int) -> float Methods inherited from ScoringScheme: gap_extend(...) from builtins.PyCapsule gap_extend(*args, **kwargs) Overloaded function.   1. gap_extend(rosetta.core.sequence.ScoringScheme) -> float   Gets the gap extension penalty.   2. gap_extend(self : rosetta.core.sequence.ScoringScheme, gap_extend : float) -> NoneType   Sets the gap extension penalty. gap_open(...) from builtins.PyCapsule gap_open(*args, **kwargs) Overloaded function.   1. gap_open(rosetta.core.sequence.ScoringScheme) -> float   Gets the gap opening penalty.   2. gap_open(self : rosetta.core.sequence.ScoringScheme, gap_open : float) -> NoneType   Sets the gap opening penalty. is_good(...) from builtins.PyCapsule is_good(self : rosetta.core.sequence.ScoringScheme, num : float) -> bool read_data(...) from builtins.PyCapsule read_data(self : rosetta.core.sequence.ScoringScheme,  : rosetta.utility.io.izstream) -> NoneType read_from_file(...) from builtins.PyCapsule read_from_file(self : rosetta.core.sequence.ScoringScheme,  : rosetta.utility.file.FileName) -> NoneType   Initialize from a file. type(...) from builtins.PyCapsule type(*args, **kwargs) Overloaded function.   1. type(rosetta.core.sequence.ScoringScheme) -> str   getters for type, which is a unique string name for this object.   2. type(self : rosetta.core.sequence.ScoringScheme, new_type : str) -> NoneType   getters for type, which is a unique string name for this object. unimplemented_method_error(...) from builtins.PyCapsule unimplemented_method_error(self : rosetta.core.sequence.ScoringScheme, method_name : str) -> NoneType   Utility method for producing useful error messages and exiting  from program. Declared const which is funny, because exiting the program  certainly changes the state of this object! This might be replaced with  exception handling if we ever start using those.   class DP_Matrix(builtins.object)       Methods defined here: __call__(...) from builtins.PyCapsule __call__(self : rosetta.core.sequence.DP_Matrix, row : int, col : int) -> rosetta.core.sequence.Cell __init__(...) from builtins.PyCapsule __init__(self : rosetta.core.sequence.DP_Matrix, rs : int, cs : int) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. __str__(...) from builtins.PyCapsule __str__(rosetta.core.sequence.DP_Matrix) -> str assign(...) from builtins.PyCapsule assign(self : rosetta.core.sequence.DP_Matrix,  : rosetta.core.sequence.DP_Matrix) -> rosetta.core.sequence.DP_Matrix clear(...) from builtins.PyCapsule clear(rosetta.core.sequence.DP_Matrix) -> NoneType cols(...) from builtins.PyCapsule cols(rosetta.core.sequence.DP_Matrix) -> int rows(...) from builtins.PyCapsule rows(rosetta.core.sequence.DP_Matrix) -> int xlab(...) from builtins.PyCapsule xlab(*args, **kwargs) Overloaded function.   1. xlab(self : rosetta.core.sequence.DP_Matrix, xs : rosetta.utility.vector1_char) -> NoneType   2. xlab(rosetta.core.sequence.DP_Matrix) -> rosetta.utility.vector1_char ylab(...) from builtins.PyCapsule ylab(*args, **kwargs) Overloaded function.   1. ylab(self : rosetta.core.sequence.DP_Matrix, ys : rosetta.utility.vector1_char) -> NoneType   2. ylab(rosetta.core.sequence.DP_Matrix) -> rosetta.utility.vector1_char   class DerivedSequenceMapping(rosetta.core.id.SequenceMapping)     This is quite possibly the laziest form of class naming ever.  What does the name of this class tell you about it? It's a SequenceMapping, and it's derived from SequenceMapping.  Oops, it said it twice. What is different about this sequence mapping from the parent class? Who knows!  When should you use it? Who knows!</snark>     Method resolution order: DerivedSequenceMapping rosetta.core.id.SequenceMapping builtins.object Methods defined here: __eq__(...) from builtins.PyCapsule __eq__(self : rosetta.core.sequence.DerivedSequenceMapping, rhs : rosetta.core.id.SequenceMapping) -> bool __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle) -> NoneType   2. __init__(self : handle, s1 : int, s2 : int) -> NoneType   3. __init__(handle, rosetta.core.sequence.DerivedSequenceMapping) -> 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.sequence.DerivedSequenceMapping, src : rosetta.core.sequence.DerivedSequenceMapping) -> rosetta.core.sequence.DerivedSequenceMapping same_type_as_me(...) from builtins.PyCapsule same_type_as_me(self : rosetta.core.sequence.DerivedSequenceMapping, other : rosetta.core.id.SequenceMapping) -> bool seq1(...) from builtins.PyCapsule seq1(*args, **kwargs) Overloaded function.   1. seq1(rosetta.core.sequence.DerivedSequenceMapping) -> str   2. seq1(rosetta.core.sequence.DerivedSequenceMapping) -> str   3. seq1(self : rosetta.core.sequence.DerivedSequenceMapping, s : str) -> NoneType seq2(...) from builtins.PyCapsule seq2(*args, **kwargs) Overloaded function.   1. seq2(rosetta.core.sequence.DerivedSequenceMapping) -> str   2. seq2(rosetta.core.sequence.DerivedSequenceMapping) -> str   3. seq2(self : rosetta.core.sequence.DerivedSequenceMapping, s : str) -> NoneType start_seq2(...) from builtins.PyCapsule start_seq2(*args, **kwargs) Overloaded function.   1. start_seq2(rosetta.core.sequence.DerivedSequenceMapping) -> int   2. start_seq2(self : rosetta.core.sequence.DerivedSequenceMapping, s : int) -> NoneType Methods inherited from rosetta.core.id.SequenceMapping: __getitem__(...) from builtins.PyCapsule __getitem__(*args, **kwargs) Overloaded function.   1. __getitem__(self : rosetta.core.id.SequenceMapping, pos1 : int) -> int   2. __getitem__(self : rosetta.core.id.SequenceMapping, pos1 : int) -> int __str__(...) from builtins.PyCapsule __str__(rosetta.core.id.SequenceMapping) -> str all_aligned(...) from builtins.PyCapsule all_aligned(rosetta.core.id.SequenceMapping) -> bool clear(...) from builtins.PyCapsule clear(rosetta.core.id.SequenceMapping) -> NoneType delete_source_residue(...) from builtins.PyCapsule delete_source_residue(self : rosetta.core.id.SequenceMapping, pos1 : int) -> NoneType delete_target_residue(...) from builtins.PyCapsule delete_target_residue(self : rosetta.core.id.SequenceMapping, pos : int) -> NoneType downstream_combine(...) from builtins.PyCapsule downstream_combine(self : rosetta.core.id.SequenceMapping, smap_to_add : rosetta.core.id.SequenceMapping) -> NoneType   Apply a B->C mapping to the current A->B mapping to get an A->C mapping  i.e. smap[j] becomes smap_to_add[ smap[j] ] identity(...) from builtins.PyCapsule identity(size : int) -> rosetta.core.id.SequenceMapping   Construct an identity mapping, which means that for all positions,  i in seq1 maps to i in seq2. insert_aligned_residue(...) from builtins.PyCapsule insert_aligned_residue(self : rosetta.core.id.SequenceMapping, pos1 : int, pos2 : int) -> NoneType insert_aligned_residue_safe(...) from builtins.PyCapsule insert_aligned_residue_safe(self : rosetta.core.id.SequenceMapping, pos1 : int, pos2 : int) -> NoneType   same as insert_aligned_residue, but a couple of extra checks on size1 and size2. insert_source_residue(...) from builtins.PyCapsule insert_source_residue(self : rosetta.core.id.SequenceMapping, pos1 : int) -> NoneType insert_target_residue(...) from builtins.PyCapsule insert_target_residue(self : rosetta.core.id.SequenceMapping, pos : int) -> NoneType is_identity(...) from builtins.PyCapsule is_identity(rosetta.core.id.SequenceMapping) -> bool is_identity_ignore_gaps(...) from builtins.PyCapsule is_identity_ignore_gaps(rosetta.core.id.SequenceMapping) -> bool mapping(...) from builtins.PyCapsule mapping(*args, **kwargs) Overloaded function.   1. mapping(rosetta.core.id.SequenceMapping) -> rosetta.utility.vector1_unsigned_long   2. mapping(self : rosetta.core.id.SequenceMapping, mapping : rosetta.utility.vector1_unsigned_long) -> NoneType push_back(...) from builtins.PyCapsule push_back(self : rosetta.core.id.SequenceMapping, al : int) -> NoneType resize(...) from builtins.PyCapsule resize(self : rosetta.core.id.SequenceMapping, s1 : int, s2 : int) -> NoneType   resize reverse(...) from builtins.PyCapsule reverse(rosetta.core.id.SequenceMapping) -> NoneType   go from an A->B mapping to a B->A mapping set_offset(...) from builtins.PyCapsule set_offset(self : rosetta.core.id.SequenceMapping, setting : int) -> NoneType show(...) from builtins.PyCapsule show(rosetta.core.id.SequenceMapping) -> NoneType size1(...) from builtins.PyCapsule size1(rosetta.core.id.SequenceMapping) -> int   size of target sequence size2(...) from builtins.PyCapsule size2(*args, **kwargs) Overloaded function.   1. size2(rosetta.core.id.SequenceMapping) -> int   size of aligned sequence ???   2. size2(self : rosetta.core.id.SequenceMapping, s2 : int) -> NoneType to_string(...) from builtins.PyCapsule to_string(rosetta.core.id.SequenceMapping) -> str upstream_combine(...) from builtins.PyCapsule upstream_combine(self : rosetta.core.id.SequenceMapping, smap_to_add : rosetta.core.id.SequenceMapping) -> NoneType   Apply a C->A mapping to the current A->B mapping to get a C->B mapping  i.e. smap[j] becomes smap[ smap_to_add[ j ] ]   class L1ScoringScheme(ScoringScheme)       Method resolution order: L1ScoringScheme ScoringScheme builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle) -> NoneType   doc   2. __init__(handle, float) -> NoneType   doc   3. __init__(self : handle, open : float, extend : float) -> NoneType   4. __init__(handle, rosetta.core.sequence.L1ScoringScheme) -> 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.sequence.L1ScoringScheme,  : rosetta.core.sequence.L1ScoringScheme) -> rosetta.core.sequence.L1ScoringScheme clone(...) from builtins.PyCapsule clone(rosetta.core.sequence.L1ScoringScheme) -> rosetta.core.sequence.ScoringScheme score(...) from builtins.PyCapsule score(self : rosetta.core.sequence.L1ScoringScheme, seq1 : rosetta.core.sequence.Sequence, seq2 : rosetta.core.sequence.Sequence, pos1 : int, pos2 : int) -> float Methods inherited from ScoringScheme: gap_extend(...) from builtins.PyCapsule gap_extend(*args, **kwargs) Overloaded function.   1. gap_extend(rosetta.core.sequence.ScoringScheme) -> float   Gets the gap extension penalty.   2. gap_extend(self : rosetta.core.sequence.ScoringScheme, gap_extend : float) -> NoneType   Sets the gap extension penalty. gap_open(...) from builtins.PyCapsule gap_open(*args, **kwargs) Overloaded function.   1. gap_open(rosetta.core.sequence.ScoringScheme) -> float   Gets the gap opening penalty.   2. gap_open(self : rosetta.core.sequence.ScoringScheme, gap_open : float) -> NoneType   Sets the gap opening penalty. is_good(...) from builtins.PyCapsule is_good(self : rosetta.core.sequence.ScoringScheme, num : float) -> bool read_data(...) from builtins.PyCapsule read_data(self : rosetta.core.sequence.ScoringScheme,  : rosetta.utility.io.izstream) -> NoneType read_from_file(...) from builtins.PyCapsule read_from_file(self : rosetta.core.sequence.ScoringScheme,  : rosetta.utility.file.FileName) -> NoneType   Initialize from a file. type(...) from builtins.PyCapsule type(*args, **kwargs) Overloaded function.   1. type(rosetta.core.sequence.ScoringScheme) -> str   getters for type, which is a unique string name for this object.   2. type(self : rosetta.core.sequence.ScoringScheme, new_type : str) -> NoneType   getters for type, which is a unique string name for this object. unimplemented_method_error(...) from builtins.PyCapsule unimplemented_method_error(self : rosetta.core.sequence.ScoringScheme, method_name : str) -> NoneType   Utility method for producing useful error messages and exiting  from program. Declared const which is funny, because exiting the program  certainly changes the state of this object! This might be replaced with  exception handling if we ever start using those.   class Line(builtins.object)     struct     Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.core.sequence.Line) -> NoneType   2. __init__(self : rosetta.core.sequence.Line, r1 : float, r2 : float, b : bool) -> NoneType   3. __init__(self : rosetta.core.sequence.Line, rval : rosetta.core.sequence.Line) -> 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.sequence.Line, rval : rosetta.core.sequence.Line) -> rosetta.core.sequence.Line   copy assignment Data descriptors defined here: intercept region slope   class MCAligner(Aligner)       Method resolution order: MCAligner Aligner builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle) -> NoneType   2. __init__(self : handle, kT : float) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. align(...) from builtins.PyCapsule align(self : rosetta.core.sequence.MCAligner, seq_y : rosetta.core.sequence.Sequence, seq_x : rosetta.core.sequence.Sequence, ss : rosetta.core.sequence.ScoringScheme) -> core::sequence::SequenceAlignment   Align these two Sequences using the given ScoringScheme. Rather  than finding an optimal alignment, MCAligner uses a stochastic algorithm  to generate an alignment at a given kT.      The Needleman-Wunsch algorithm uses dynamic programming to  generate an optimal alignment between two scoring sequences under a given  scoring scheme.  Rather than making the best decision at each element of  the dynamic programming matrix, MCAligner makes a stochastic decision  between introducing a gap in seq_y, introducing a gap in seq_x, or aligning two  characters between the two sequences. The decision is made by transforming the  scores for each of the three possible decisions into probabilities using  Boltzmann weighting of the scores for each possibility at a given kT. The kT  is stored as a member variable of the MCAligner class, and accessor methods  are provided above. assign(...) from builtins.PyCapsule assign(self : rosetta.core.sequence.MCAligner,  : rosetta.core.sequence.MCAligner) -> rosetta.core.sequence.MCAligner kT(...) from builtins.PyCapsule kT(*args, **kwargs) Overloaded function.   1. kT(self : rosetta.core.sequence.MCAligner, new_kT : float) -> NoneType   Sets the kT used in the align method. A optimal value of kT means  acceptance of less optimal decisions along the dynamic programming matrix.   2. kT(rosetta.core.sequence.MCAligner) -> float   Returns the kT used in the align method. Methods inherited from Aligner: traceback(...) from builtins.PyCapsule traceback(self : rosetta.core.sequence.Aligner, seq_x : rosetta.core.sequence.Sequence, seq_y : rosetta.core.sequence.Sequence, matrix : rosetta.core.sequence.DP_Matrix, start : rosetta.core.sequence.Cell) -> core::sequence::SequenceAlignment validate_input(...) from builtins.PyCapsule validate_input(self : rosetta.core.sequence.Aligner, seq_y : rosetta.core.sequence.Sequence, seq_x : rosetta.core.sequence.Sequence, ss : core::sequence::ScoringScheme) -> NoneType   class MatrixScoringScheme(ScoringScheme)       Method resolution order: MatrixScoringScheme ScoringScheme builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle) -> NoneType   2. __init__(self : handle, open : float, extend : float, fn : rosetta.utility.file.FileName) -> NoneType   3. __init__(self : handle, open : float, extend : float, matrix : rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t) -> NoneType   4. __init__(handle, rosetta.core.sequence.MatrixScoringScheme) -> 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.sequence.MatrixScoringScheme,  : rosetta.core.sequence.MatrixScoringScheme) -> rosetta.core.sequence.MatrixScoringScheme clone(...) from builtins.PyCapsule clone(rosetta.core.sequence.MatrixScoringScheme) -> rosetta.core.sequence.ScoringScheme   returns owning pointer to a new object with a deep copy of  this object's values. read_data(...) from builtins.PyCapsule read_data(self : rosetta.core.sequence.MatrixScoringScheme, input : rosetta.utility.io.izstream) -> NoneType read_from_database(...) from builtins.PyCapsule read_from_database(*args, **kwargs) Overloaded function.   1. read_from_database(rosetta.core.sequence.MatrixScoringScheme) -> NoneType   Read an alignment matrix from the given database filename using the  NCBI BLOSUM format for matrices.   2. read_from_database(self : rosetta.core.sequence.MatrixScoringScheme, name : str) -> NoneType   Read an alignment matrix from the given database filename using the  NCBI BLOSUM format for matrices. read_from_file(...) from builtins.PyCapsule read_from_file(self : rosetta.core.sequence.MatrixScoringScheme, fn : rosetta.utility.file.FileName) -> NoneType   Read an alignment matrix from the given filename using the  NCBI BLOSUM format for matrices. score(...) from builtins.PyCapsule score(self : rosetta.core.sequence.MatrixScoringScheme, seq1 : rosetta.core.sequence.Sequence, seq2 : rosetta.core.sequence.Sequence, pos1 : int, pos2 : int) -> float scoring_matrix(...) from builtins.PyCapsule scoring_matrix(rosetta.core.sequence.MatrixScoringScheme) -> rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t values_for_aa(...) from builtins.PyCapsule values_for_aa(*args, **kwargs) Overloaded function.   1. values_for_aa(self : rosetta.core.sequence.MatrixScoringScheme, aa : str) -> rosetta.utility.vector1_double   Get the values for amino acid aa, in Rosetta aa order.   2. values_for_aa(self : rosetta.core.sequence.MatrixScoringScheme, aa : rosetta.core.chemical.AA) -> rosetta.utility.vector1_double   Get the values for amino acid aa, in Rosetta aa order. Methods inherited from ScoringScheme: gap_extend(...) from builtins.PyCapsule gap_extend(*args, **kwargs) Overloaded function.   1. gap_extend(rosetta.core.sequence.ScoringScheme) -> float   Gets the gap extension penalty.   2. gap_extend(self : rosetta.core.sequence.ScoringScheme, gap_extend : float) -> NoneType   Sets the gap extension penalty. gap_open(...) from builtins.PyCapsule gap_open(*args, **kwargs) Overloaded function.   1. gap_open(rosetta.core.sequence.ScoringScheme) -> float   Gets the gap opening penalty.   2. gap_open(self : rosetta.core.sequence.ScoringScheme, gap_open : float) -> NoneType   Sets the gap opening penalty. is_good(...) from builtins.PyCapsule is_good(self : rosetta.core.sequence.ScoringScheme, num : float) -> bool type(...) from builtins.PyCapsule type(*args, **kwargs) Overloaded function.   1. type(rosetta.core.sequence.ScoringScheme) -> str   getters for type, which is a unique string name for this object.   2. type(self : rosetta.core.sequence.ScoringScheme, new_type : str) -> NoneType   getters for type, which is a unique string name for this object. unimplemented_method_error(...) from builtins.PyCapsule unimplemented_method_error(self : rosetta.core.sequence.ScoringScheme, method_name : str) -> NoneType   Utility method for producing useful error messages and exiting  from program. Declared const which is funny, because exiting the program  certainly changes the state of this object! This might be replaced with  exception handling if we ever start using those.   class NWAligner(Aligner)       Method resolution order: NWAligner Aligner 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. align(...) from builtins.PyCapsule align(self : rosetta.core.sequence.NWAligner, seq_y : rosetta.core.sequence.Sequence, seq_x : rosetta.core.sequence.Sequence, ss : rosetta.core.sequence.ScoringScheme) -> core::sequence::SequenceAlignment assign(...) from builtins.PyCapsule assign(self : rosetta.core.sequence.NWAligner,  : rosetta.core.sequence.NWAligner) -> rosetta.core.sequence.NWAligner init_matrix(...) from builtins.PyCapsule init_matrix(y_len : int, x_len : int, ss : rosetta.core.sequence.ScoringScheme, scores : rosetta.core.sequence.DP_Matrix) -> NoneType Methods inherited from Aligner: traceback(...) from builtins.PyCapsule traceback(self : rosetta.core.sequence.Aligner, seq_x : rosetta.core.sequence.Sequence, seq_y : rosetta.core.sequence.Sequence, matrix : rosetta.core.sequence.DP_Matrix, start : rosetta.core.sequence.Cell) -> core::sequence::SequenceAlignment validate_input(...) from builtins.PyCapsule validate_input(self : rosetta.core.sequence.Aligner, seq_y : rosetta.core.sequence.Sequence, seq_x : rosetta.core.sequence.Sequence, ss : core::sequence::ScoringScheme) -> NoneType   class PairScoringScheme(ScoringScheme)       Method resolution order: PairScoringScheme ScoringScheme builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle) -> NoneType   2. __init__(self : handle, gap_open_in : float, gap_extend_in : float, pairs : rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t) -> NoneType   3. __init__(handle, rosetta.core.sequence.PairScoringScheme) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. add_scored_pair(...) from builtins.PyCapsule add_scored_pair(self : rosetta.core.sequence.PairScoringScheme, res1 : int, res2 : int, score : float) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.core.sequence.PairScoringScheme,  : rosetta.core.sequence.PairScoringScheme) -> rosetta.core.sequence.PairScoringScheme clone(...) from builtins.PyCapsule clone(rosetta.core.sequence.PairScoringScheme) -> rosetta.core.sequence.ScoringScheme pairs(...) from builtins.PyCapsule pairs(rosetta.core.sequence.PairScoringScheme) -> rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t read_from_file(...) from builtins.PyCapsule read_from_file(self : rosetta.core.sequence.PairScoringScheme, fn : rosetta.utility.file.FileName) -> NoneType score(...) from builtins.PyCapsule score(self : rosetta.core.sequence.PairScoringScheme, seq1 : rosetta.core.sequence.Sequence, seq2 : rosetta.core.sequence.Sequence, pos1 : int, pos2 : int) -> float Methods inherited from ScoringScheme: gap_extend(...) from builtins.PyCapsule gap_extend(*args, **kwargs) Overloaded function.   1. gap_extend(rosetta.core.sequence.ScoringScheme) -> float   Gets the gap extension penalty.   2. gap_extend(self : rosetta.core.sequence.ScoringScheme, gap_extend : float) -> NoneType   Sets the gap extension penalty. gap_open(...) from builtins.PyCapsule gap_open(*args, **kwargs) Overloaded function.   1. gap_open(rosetta.core.sequence.ScoringScheme) -> float   Gets the gap opening penalty.   2. gap_open(self : rosetta.core.sequence.ScoringScheme, gap_open : float) -> NoneType   Sets the gap opening penalty. is_good(...) from builtins.PyCapsule is_good(self : rosetta.core.sequence.ScoringScheme, num : float) -> bool read_data(...) from builtins.PyCapsule read_data(self : rosetta.core.sequence.ScoringScheme,  : rosetta.utility.io.izstream) -> NoneType type(...) from builtins.PyCapsule type(*args, **kwargs) Overloaded function.   1. type(rosetta.core.sequence.ScoringScheme) -> str   getters for type, which is a unique string name for this object.   2. type(self : rosetta.core.sequence.ScoringScheme, new_type : str) -> NoneType   getters for type, which is a unique string name for this object. unimplemented_method_error(...) from builtins.PyCapsule unimplemented_method_error(self : rosetta.core.sequence.ScoringScheme, method_name : str) -> NoneType   Utility method for producing useful error messages and exiting  from program. Declared const which is funny, because exiting the program  certainly changes the state of this object! This might be replaced with  exception handling if we ever start using those.   class ProfSimScoringScheme(ScoringScheme)       Method resolution order: ProfSimScoringScheme ScoringScheme builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle) -> NoneType   doc   2. __init__(handle, float) -> NoneType   doc   3. __init__(self : handle, open : float, extend : float) -> NoneType   4. __init__(handle, rosetta.core.sequence.ProfSimScoringScheme) -> 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.sequence.ProfSimScoringScheme,  : rosetta.core.sequence.ProfSimScoringScheme) -> rosetta.core.sequence.ProfSimScoringScheme clone(...) from builtins.PyCapsule clone(rosetta.core.sequence.ProfSimScoringScheme) -> rosetta.core.sequence.ScoringScheme   returns owning pointer to a new object with a deep copy of this  object's values. initialize_parameters(...) from builtins.PyCapsule initialize_parameters(rosetta.core.sequence.ProfSimScoringScheme) -> NoneType   Initialize log-probabilities of occurence for each amino acid. score(...) from builtins.PyCapsule score(self : rosetta.core.sequence.ProfSimScoringScheme, seq1 : rosetta.core.sequence.Sequence, seq2 : rosetta.core.sequence.Sequence, pos1 : int, pos2 : int) -> float   ProfSim profile-profile similarity metric based on information theory.  Published by Yona and Levitt in JMB, 2002 in a paper titled "Within the  Twilight Zone: A Sensitive Profile-Profile Comparison Tool Based on  Information Theory."      The basic idea for this score is that it incorporates both  divergence of probability distributions at each position and the significance  of that divergence in order to construct a position-specific  profile-profile score. The divergence score is the J-S divergence between  the two probability distributions at probability position, and the  significance score is the J-S divergence between:  1. the average of the two probability distributions at this position  2. a prior probability distribution over all allowed characters at this  position.  J-S divergence between two distributions is defined as:  D( p1, p2 ) = 0.5 * sum( p1[i] * log( p1[i] / p2[i] ) ) +                0.5 * sum( p2[i] * log( p2[i] / p1[i] ) ) Methods inherited from ScoringScheme: gap_extend(...) from builtins.PyCapsule gap_extend(*args, **kwargs) Overloaded function.   1. gap_extend(rosetta.core.sequence.ScoringScheme) -> float   Gets the gap extension penalty.   2. gap_extend(self : rosetta.core.sequence.ScoringScheme, gap_extend : float) -> NoneType   Sets the gap extension penalty. gap_open(...) from builtins.PyCapsule gap_open(*args, **kwargs) Overloaded function.   1. gap_open(rosetta.core.sequence.ScoringScheme) -> float   Gets the gap opening penalty.   2. gap_open(self : rosetta.core.sequence.ScoringScheme, gap_open : float) -> NoneType   Sets the gap opening penalty. is_good(...) from builtins.PyCapsule is_good(self : rosetta.core.sequence.ScoringScheme, num : float) -> bool read_data(...) from builtins.PyCapsule read_data(self : rosetta.core.sequence.ScoringScheme,  : rosetta.utility.io.izstream) -> NoneType read_from_file(...) from builtins.PyCapsule read_from_file(self : rosetta.core.sequence.ScoringScheme,  : rosetta.utility.file.FileName) -> NoneType   Initialize from a file. type(...) from builtins.PyCapsule type(*args, **kwargs) Overloaded function.   1. type(rosetta.core.sequence.ScoringScheme) -> str   getters for type, which is a unique string name for this object.   2. type(self : rosetta.core.sequence.ScoringScheme, new_type : str) -> NoneType   getters for type, which is a unique string name for this object. unimplemented_method_error(...) from builtins.PyCapsule unimplemented_method_error(self : rosetta.core.sequence.ScoringScheme, method_name : str) -> NoneType   Utility method for producing useful error messages and exiting  from program. Declared const which is funny, because exiting the program  certainly changes the state of this object! This might be replaced with  exception handling if we ever start using those.   class SWAligner(Aligner)       Method resolution order: SWAligner Aligner 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. align(...) from builtins.PyCapsule align(self : rosetta.core.sequence.SWAligner, seq_y : rosetta.core.sequence.Sequence, seq_x : rosetta.core.sequence.Sequence, ss : rosetta.core.sequence.ScoringScheme) -> core::sequence::SequenceAlignment assign(...) from builtins.PyCapsule assign(self : rosetta.core.sequence.SWAligner,  : rosetta.core.sequence.SWAligner) -> rosetta.core.sequence.SWAligner Methods inherited from Aligner: traceback(...) from builtins.PyCapsule traceback(self : rosetta.core.sequence.Aligner, seq_x : rosetta.core.sequence.Sequence, seq_y : rosetta.core.sequence.Sequence, matrix : rosetta.core.sequence.DP_Matrix, start : rosetta.core.sequence.Cell) -> core::sequence::SequenceAlignment validate_input(...) from builtins.PyCapsule validate_input(self : rosetta.core.sequence.Aligner, seq_y : rosetta.core.sequence.Sequence, seq_x : rosetta.core.sequence.Sequence, ss : core::sequence::ScoringScheme) -> NoneType   class ScoringScheme(builtins.object)       Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.core.sequence.ScoringScheme) -> NoneType   2. __init__(rosetta.core.sequence.ScoringScheme, rosetta.core.sequence.ScoringScheme) -> 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.sequence.ScoringScheme,  : rosetta.core.sequence.ScoringScheme) -> rosetta.core.sequence.ScoringScheme clone(...) from builtins.PyCapsule clone(rosetta.core.sequence.ScoringScheme) -> rosetta.core.sequence.ScoringScheme   clone method. gap_extend(...) from builtins.PyCapsule gap_extend(*args, **kwargs) Overloaded function.   1. gap_extend(rosetta.core.sequence.ScoringScheme) -> float   Gets the gap extension penalty.   2. gap_extend(self : rosetta.core.sequence.ScoringScheme, gap_extend : float) -> NoneType   Sets the gap extension penalty. gap_open(...) from builtins.PyCapsule gap_open(*args, **kwargs) Overloaded function.   1. gap_open(rosetta.core.sequence.ScoringScheme) -> float   Gets the gap opening penalty.   2. gap_open(self : rosetta.core.sequence.ScoringScheme, gap_open : float) -> NoneType   Sets the gap opening penalty. is_good(...) from builtins.PyCapsule is_good(self : rosetta.core.sequence.ScoringScheme, num : float) -> bool read_data(...) from builtins.PyCapsule read_data(self : rosetta.core.sequence.ScoringScheme,  : rosetta.utility.io.izstream) -> NoneType read_from_file(...) from builtins.PyCapsule read_from_file(self : rosetta.core.sequence.ScoringScheme,  : rosetta.utility.file.FileName) -> NoneType   Initialize from a file. score(...) from builtins.PyCapsule score(self : rosetta.core.sequence.ScoringScheme, seq1 : rosetta.core.sequence.Sequence, seq2 : rosetta.core.sequence.Sequence, pos1 : int, pos2 : int) -> float type(...) from builtins.PyCapsule type(*args, **kwargs) Overloaded function.   1. type(rosetta.core.sequence.ScoringScheme) -> str   getters for type, which is a unique string name for this object.   2. type(self : rosetta.core.sequence.ScoringScheme, new_type : str) -> NoneType   getters for type, which is a unique string name for this object. unimplemented_method_error(...) from builtins.PyCapsule unimplemented_method_error(self : rosetta.core.sequence.ScoringScheme, method_name : str) -> NoneType   Utility method for producing useful error messages and exiting  from program. Declared const which is funny, because exiting the program  certainly changes the state of this object! This might be replaced with  exception handling if we ever start using those.   class ScoringSchemeFactory(builtins.object)       Methods defined here: __init__(...) from builtins.PyCapsule __init__(rosetta.core.sequence.ScoringSchemeFactory) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. add_type(...) from builtins.PyCapsule add_type(self : rosetta.core.sequence.ScoringSchemeFactory, new_scheme : rosetta.core.sequence.ScoringScheme) -> NoneType   adds a ScoringSchemeOP get_scoring_scheme(...) from builtins.PyCapsule get_scoring_scheme(self : rosetta.core.sequence.ScoringSchemeFactory, type : str) -> rosetta.core.sequence.ScoringScheme Data descriptors defined here: scheme_types_   class Sequence(builtins.object)       Methods defined here: __eq__(...) from builtins.PyCapsule __eq__(self : rosetta.core.sequence.Sequence, s : rosetta.core.sequence.Sequence) -> bool   Returns true if the given Sequence object is equal to this  Sequence object. Tests for string equality of id(), start(), and  sequence(), and returns false if any of these are not equal. __getitem__(...) from builtins.PyCapsule __getitem__(self : rosetta.core.sequence.Sequence, pos : int) -> str   Returns the character at the given sequence position. __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle) -> NoneType   2. __init__(handle, str, str) -> NoneType   doc   3. __init__(self : handle, seq : str, id : str, start : int) -> NoneType   4. __init__(self : handle, pose : rosetta.core.pose.Pose) -> NoneType   5. __init__(handle, rosetta.core.sequence.Sequence) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. __str__(...) from builtins.PyCapsule __str__(rosetta.core.sequence.Sequence) -> str append_char(...) from builtins.PyCapsule append_char(self : rosetta.core.sequence.Sequence, new_char : str) -> NoneType   Append a character append_gap(...) from builtins.PyCapsule append_gap(rosetta.core.sequence.Sequence) -> NoneType   Append a gap assign(...) from builtins.PyCapsule assign(self : rosetta.core.sequence.Sequence, rhs : rosetta.core.sequence.Sequence) -> rosetta.core.sequence.Sequence   assignment operator. at(...) from builtins.PyCapsule at(self : rosetta.core.sequence.Sequence, pos : int) -> str clone(...) from builtins.PyCapsule clone(rosetta.core.sequence.Sequence) -> rosetta.core.sequence.Sequence   Returns an owning pointer to a copy of this sequence. delete_position(...) from builtins.PyCapsule delete_position(self : rosetta.core.sequence.Sequence, pos : int) -> NoneType   Deletes the given position from the Sequence and shifts  everything else back by one. gap_char(...) from builtins.PyCapsule gap_char(*args, **kwargs) Overloaded function.   1. gap_char(self : rosetta.core.sequence.Sequence, gap_char : str) -> NoneType   sets gap_char to the given value.   2. gap_char(rosetta.core.sequence.Sequence) -> str   Returns the character used to represent a gap for this object. id(...) from builtins.PyCapsule id(*args, **kwargs) Overloaded function.   1. id(self : rosetta.core.sequence.Sequence, new_id : str) -> NoneType   sets id to the given value.   2. id(rosetta.core.sequence.Sequence) -> str   Returns the id of this object. insert_char(...) from builtins.PyCapsule insert_char(self : rosetta.core.sequence.Sequence, pos : int, new_char : str) -> NoneType   Inserts a character at the given position. insert_gap(...) from builtins.PyCapsule insert_gap(self : rosetta.core.sequence.Sequence, pos : int) -> NoneType   Inserts a gap at the given position, where insert_gap( 0 )  inserts the character at the beginning of the sequence, and  insert_gap( length() ) inserts the character at the end of the  sequence. is_gap(...) from builtins.PyCapsule is_gap(self : rosetta.core.sequence.Sequence, pos : int) -> bool   Returns true if this position in the sequence represents a gap,  returns false otherwise. length(...) from builtins.PyCapsule length(rosetta.core.sequence.Sequence) -> int   Returns the number of characters in this object. read_from_file(...) from builtins.PyCapsule read_from_file(self : rosetta.core.sequence.Sequence,  : rosetta.utility.file.FileName) -> NoneType   initializes this sequence object from a file. resnum(...) from builtins.PyCapsule resnum(self : rosetta.core.sequence.Sequence, idx : int) -> int   Returns the index of the given sequence position, which is the  position in the sequence minus any gaps that occur earlier in the  sequence. For example, if the sequence is ---AT, resnum(5) will return 2.  Returns 0 for unaligned positions. sequence(...) from builtins.PyCapsule sequence(*args, **kwargs) Overloaded function.   1. sequence(self : rosetta.core.sequence.Sequence, sequence : str) -> NoneType   sets sequence to the given value.   2. sequence(rosetta.core.sequence.Sequence) -> str   Returns the full sequence, which may include gaps. spacer_positions(...) from builtins.PyCapsule spacer_positions(*args, **kwargs) Overloaded function.   1. spacer_positions(self : rosetta.core.sequence.Sequence, spacer_positions : rosetta.utility.vector1_unsigned_long) -> NoneType   sets spacer_positions to the given value.   2. spacer_positions(rosetta.core.sequence.Sequence) -> rosetta.utility.vector1_unsigned_long   Returns the spacer positions (chain breaks, e.g., from spaces or commas in original sequence text) start(...) from builtins.PyCapsule start(*args, **kwargs) Overloaded function.   1. start(self : rosetta.core.sequence.Sequence, new_start : int) -> NoneType   sets starting index to the given value.   2. start(rosetta.core.sequence.Sequence) -> int   Returns the start of this object. to_string(...) from builtins.PyCapsule to_string(rosetta.core.sequence.Sequence) -> str type(...) from builtins.PyCapsule type(rosetta.core.sequence.Sequence) -> str ungapped_length(...) from builtins.PyCapsule ungapped_length(rosetta.core.sequence.Sequence) -> int   Returns the number of characters in this object, ignoring gaps. ungapped_sequence(...) from builtins.PyCapsule ungapped_sequence(rosetta.core.sequence.Sequence) -> str   Returns the string representing this sequence without gaps.   class SequenceAlignment(builtins.object)       Methods defined here: __eq__(...) from builtins.PyCapsule __eq__(self : rosetta.core.sequence.SequenceAlignment, other : rosetta.core.sequence.SequenceAlignment) -> bool   Equality operator __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.core.sequence.SequenceAlignment) -> NoneType   2. __init__(self : rosetta.core.sequence.SequenceAlignment, src : rosetta.core.sequence.SequenceAlignment) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. __str__(...) from builtins.PyCapsule __str__(rosetta.core.sequence.SequenceAlignment) -> str add_sequence(...) from builtins.PyCapsule add_sequence(self : rosetta.core.sequence.SequenceAlignment, myseq : rosetta.core.sequence.Sequence) -> NoneType alignment_id(...) from builtins.PyCapsule alignment_id(rosetta.core.sequence.SequenceAlignment) -> str   this gives the id of the second sequence  --- in a typical alignment it is 1) query, 2) template assign(...) from builtins.PyCapsule assign(self : rosetta.core.sequence.SequenceAlignment, src : rosetta.core.sequence.SequenceAlignment) -> rosetta.core.sequence.SequenceAlignment   assignment operator calculate_per_position_scores(...) from builtins.PyCapsule calculate_per_position_scores(self : rosetta.core.sequence.SequenceAlignment, ss : rosetta.core.sequence.ScoringScheme) -> rosetta.utility.vector1_double   calculates pairwise scores similar to  calculate_score_sum_of_pairs. calculate_score_sum_of_pairs(...) from builtins.PyCapsule calculate_score_sum_of_pairs(self : rosetta.core.sequence.SequenceAlignment, ss : rosetta.core.sequence.ScoringScheme) -> float   calculates the score of this alignment under  the given ScoringScheme by summing up all of pairwise  alignment scores between all pairs of sequence. clear(...) from builtins.PyCapsule clear(rosetta.core.sequence.SequenceAlignment) -> NoneType clone(...) from builtins.PyCapsule clone(rosetta.core.sequence.SequenceAlignment) -> rosetta.core.sequence.SequenceAlignment comment(...) from builtins.PyCapsule comment(self : rosetta.core.sequence.SequenceAlignment, comment : str) -> NoneType   getter/setters for comments comments(...) from builtins.PyCapsule comments(rosetta.core.sequence.SequenceAlignment) -> rosetta.utility.vector1_std_string data_integrity_check(...) from builtins.PyCapsule data_integrity_check(rosetta.core.sequence.SequenceAlignment) -> NoneType gapped_positions(...) from builtins.PyCapsule gapped_positions(rosetta.core.sequence.SequenceAlignment) -> int   Returns the number of positions in the  SequenceAlignment with at least one gap. identities(...) from builtins.PyCapsule identities(rosetta.core.sequence.SequenceAlignment) -> int   Returns the number of positions at which all is_gapped(...) from builtins.PyCapsule is_gapped(self : rosetta.core.sequence.SequenceAlignment, col_idx : int) -> bool   Returns true if the given alignment column index is gapped,  false otherwise. length(...) from builtins.PyCapsule length(rosetta.core.sequence.SequenceAlignment) -> int   Returns the length of all sequences in this SequenceAlignment. max_gap_percentage(...) from builtins.PyCapsule max_gap_percentage(rosetta.core.sequence.SequenceAlignment) -> float   Returns the number of gaps contained by  the sequence in the alignment with the most gaps. read_from_file(...) from builtins.PyCapsule read_from_file(self : rosetta.core.sequence.SequenceAlignment, filename : str) -> NoneType   initialize this SequenceAlignment object from the  given file. remove_gapped_positions(...) from builtins.PyCapsule remove_gapped_positions(rosetta.core.sequence.SequenceAlignment) -> NoneType   Removes positions that are gapped in all  columns of the alignment. score(...) from builtins.PyCapsule score(*args, **kwargs) Overloaded function.   1. score(self : rosetta.core.sequence.SequenceAlignment, sc : float) -> NoneType   Accessors for the score of this SequenceAlignment.   2. score(rosetta.core.sequence.SequenceAlignment) -> float   3. score(self : rosetta.core.sequence.SequenceAlignment, name : str) -> float   4. score(self : rosetta.core.sequence.SequenceAlignment, name : str, value : float) -> NoneType scores(...) from builtins.PyCapsule scores(*args, **kwargs) Overloaded function.   1. scores(rosetta.core.sequence.SequenceAlignment) -> rosetta.std.map_std_string_double   2. scores(self : rosetta.core.sequence.SequenceAlignment, new_scores : rosetta.std.map_std_string_double) -> NoneType sequence(...) from builtins.PyCapsule sequence(self : rosetta.core.sequence.SequenceAlignment, idx : int) -> rosetta.core.sequence.Sequence sequence_indices(...) from builtins.PyCapsule sequence_indices(self : rosetta.core.sequence.SequenceAlignment, column : int) -> rosetta.utility.vector1_unsigned_long   Returns a vector1 of the sequence indices in  the given column of the SequenceAlignment that are  calculated using the Sequence resnum() method. sequence_mapping(...) from builtins.PyCapsule sequence_mapping(self : rosetta.core.sequence.SequenceAlignment, idx1 : int, idx2 : int) -> rosetta.core.id.SequenceMapping   returns a SequenceMapping of the sequence at index  idx1 mapped to the sequence at idx2. sequences_are_in_frame(...) from builtins.PyCapsule sequences_are_in_frame(rosetta.core.sequence.SequenceAlignment) -> bool   Returns true if all of the sequences are  "in-frame," which means that residue x in the first  sequence maps to residue x in all other sequences.  This method intentionally ignores any sequence at the  position where that sequence has a gap. size(...) from builtins.PyCapsule size(rosetta.core.sequence.SequenceAlignment) -> int   Returns the number of sequences. to_string(...) from builtins.PyCapsule to_string(rosetta.core.sequence.SequenceAlignment) -> str   class SequenceAlignmentHasher(rosetta.std.unary_function_core_sequence_SequenceAlignment_unsigned_long_t)     Allows SequenceAlignment's to be used as keys in unordered_{set|map}.     Method resolution order: SequenceAlignmentHasher rosetta.std.unary_function_core_sequence_SequenceAlignment_unsigned_long_t builtins.object Methods defined here: __call__(...) from builtins.PyCapsule __call__(self : rosetta.core.sequence.SequenceAlignmentHasher, alignment : rosetta.core.sequence.SequenceAlignment) -> int __init__(...) from builtins.PyCapsule __init__(rosetta.core.sequence.SequenceAlignmentHasher) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature.   class SequenceCoupling(SequenceProfile)       Method resolution order: SequenceCoupling SequenceProfile Sequence builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle) -> NoneType   2. __init__(handle, rosetta.core.sequence.SequenceCoupling) -> 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.sequence.SequenceCoupling, rhs : rosetta.core.sequence.SequenceCoupling) -> rosetta.core.sequence.SequenceCoupling   assignment operator. delete_position(...) from builtins.PyCapsule delete_position(self : rosetta.core.sequence.SequenceCoupling, pos : int) -> NoneType   Deletes the given position from the Sequence and shifts  everything else back by one. edgeList(...) from builtins.PyCapsule edgeList(*args, **kwargs) Overloaded function.   1. edgeList(rosetta.core.sequence.SequenceCoupling) -> rosetta.utility.vector1_utility_vector1_unsigned_long_std_allocator_unsigned_long_t   Print this SequenceCoupling object to the given std::ostream.  Commenting out to fix PyRosetta build  friend std::ostream & operator<<( std::ostream & out, const SequenceCoupling & p );   2. edgeList(self : rosetta.core.sequence.SequenceCoupling, eList : rosetta.utility.vector1_utility_vector1_unsigned_long_std_allocator_unsigned_long_t) -> NoneType edgePotBetween(...) from builtins.PyCapsule edgePotBetween(*args, **kwargs) Overloaded function.   1. edgePotBetween(self : rosetta.core.sequence.SequenceCoupling, vert1 : int, vert2 : int) -> rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t   2. edgePotBetween(self : rosetta.core.sequence.SequenceCoupling, edgeId : int) -> rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t edgePots(...) from builtins.PyCapsule edgePots(*args, **kwargs) Overloaded function.   1. edgePots(rosetta.core.sequence.SequenceCoupling) -> rosetta.utility.vector1_utility_vector1_utility_vector1_double_std_allocator_double_std_allocator_utility_vector1_double_std_allocator_double_t   2. edgePots(self : rosetta.core.sequence.SequenceCoupling, ePots : rosetta.utility.vector1_utility_vector1_utility_vector1_double_std_allocator_double_std_allocator_utility_vector1_double_std_allocator_double_t) -> NoneType findEdgeId(...) from builtins.PyCapsule findEdgeId(self : rosetta.core.sequence.SequenceCoupling, vert1 : int, vert2 : int) -> int insert_char(...) from builtins.PyCapsule insert_char(self : rosetta.core.sequence.SequenceCoupling, pos : int, new_char : str) -> NoneType   Read profile matrix from the given filename using the NNMAKE  .checkpoint format. void read_from_checkpoint( FileName const & fn ); npos(...) from builtins.PyCapsule npos(rosetta.core.sequence.SequenceCoupling) -> int read_from_file(...) from builtins.PyCapsule read_from_file(*args, **kwargs) Overloaded function.   1. read_from_file(self : rosetta.core.sequence.SequenceCoupling, fn : rosetta.utility.file.FileName) -> NoneType   Read a SequenceCoupling model in GREMLIN format .   2. read_from_file(self : rosetta.core.sequence.SequenceCoupling, fn : rosetta.utility.file.FileName, temp : float) -> NoneType   virtual SequenceOP clone() const {  SequenceOP new_seq_op( new SequenceProfile( *this ) );  return new_seq_op; } temp(...) from builtins.PyCapsule temp(*args, **kwargs) Overloaded function.   1. temp(rosetta.core.sequence.SequenceCoupling) -> float   2. temp(self : rosetta.core.sequence.SequenceCoupling, t : float) -> NoneType type(...) from builtins.PyCapsule type(rosetta.core.sequence.SequenceCoupling) -> str Methods inherited from SequenceProfile: __eq__(...) from builtins.PyCapsule __eq__(self : rosetta.core.sequence.SequenceProfile, other : rosetta.core.sequence.SequenceProfile) -> bool __str__(...) from builtins.PyCapsule __str__(rosetta.core.sequence.SequenceProfile) -> str alphabet(...) from builtins.PyCapsule alphabet(*args, **kwargs) Overloaded function.   1. alphabet(rosetta.core.sequence.SequenceProfile) -> rosetta.utility.vector1_std_string   Return the alphabet used by this sequence profile. This is an  N-dimensional vector1 where N is the width of the profile, and the ith  entry of any row in the profile represents the probability of ith  character at that row in the sequence.   2. alphabet(self : rosetta.core.sequence.SequenceProfile, new_alphabet : rosetta.utility.vector1_std_string) -> NoneType clone(...) from builtins.PyCapsule clone(rosetta.core.sequence.SequenceProfile) -> rosetta.core.sequence.Sequence   Returns an owning pointer to a new SequenceProfile object,  with data that is a deep copy of the information in this object. convert_profile_to_probs(...) from builtins.PyCapsule convert_profile_to_probs(*args, **kwargs) Overloaded function.   1. convert_profile_to_probs(rosetta.core.sequence.SequenceProfile) -> NoneType   Use boltzman scaling on a per-residue basis to convert the current profile values to probabilities ( range 0.0-1.0 )   2. convert_profile_to_probs(self : rosetta.core.sequence.SequenceProfile, temp : float) -> NoneType   Use boltzman scaling on a per-residue basis to convert the current profile values to probabilities ( range 0.0-1.0 ) generate_from_sequence(...) from builtins.PyCapsule generate_from_sequence(*args, **kwargs) Overloaded function.   1. generate_from_sequence(self : rosetta.core.sequence.SequenceProfile, seq : rosetta.core.sequence.Sequence) -> NoneType   Generate the profile matrix from a sequence and a given substitution matrix   2. generate_from_sequence(self : rosetta.core.sequence.SequenceProfile, seq : rosetta.core.sequence.Sequence, matrix : str) -> NoneType   Generate the profile matrix from a sequence and a given substitution matrix global_auto_rescale(...) from builtins.PyCapsule global_auto_rescale(rosetta.core.sequence.SequenceProfile) -> NoneType   Use linear rescaling (with a fixed zero) to fit the values within the range -1.0 to 1.0 negative_better(...) from builtins.PyCapsule negative_better(*args, **kwargs) Overloaded function.   1. negative_better(rosetta.core.sequence.SequenceProfile) -> bool   Returns true if negative values are better identities.      The "default" use case is for storing log likelihood values  where positive is better. If you're using this class to store energy-like  values, set negative_better to true.   2. negative_better(self : rosetta.core.sequence.SequenceProfile, negbet : bool) -> NoneType   Set whether negative identities are better. occurrence_data(...) from builtins.PyCapsule occurrence_data(*args, **kwargs) Overloaded function.   1. occurrence_data(rosetta.core.sequence.SequenceProfile) -> rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t   Returns the 2D vector1 of Real values of the probabilties of each aa.   2. occurrence_data(self : rosetta.core.sequence.SequenceProfile, new_occurrence_data : rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t) -> NoneType   Sets the 2D vector1 of Real values of the probabilties of each aa. probability_row(...) from builtins.PyCapsule probability_row(self : rosetta.core.sequence.SequenceProfile, pos : int) -> rosetta.utility.vector1_double probabilty_row(...) from builtins.PyCapsule probabilty_row(self : rosetta.core.sequence.SequenceProfile, new_prob_row : rosetta.utility.vector1_double, pos : int) -> NoneType prof_row(...) from builtins.PyCapsule prof_row(*args, **kwargs) Overloaded function.   1. prof_row(self : rosetta.core.sequence.SequenceProfile, pos : int) -> rosetta.utility.vector1_double   Returns the vector1 of values at this position.   2. prof_row(self : rosetta.core.sequence.SequenceProfile, new_prof_row : rosetta.utility.vector1_double, pos : int) -> NoneType   Sets the 1D vector1 of Real values representing this profile at pos X. profile(...) from builtins.PyCapsule profile(*args, **kwargs) Overloaded function.   1. profile(rosetta.core.sequence.SequenceProfile) -> rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t   Returns the 2D vector1 of Real values representing this profile.   2. profile(self : rosetta.core.sequence.SequenceProfile, new_profile : rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t) -> NoneType   Sets the 2D vector1 of Real values representing this profile. read_from_binary_chk(...) from builtins.PyCapsule read_from_binary_chk(self : rosetta.core.sequence.SequenceProfile, fn : rosetta.utility.file.FileName) -> NoneType   Read profile matrix from the given filename in the legacy BLAST binary format read_from_checkpoint(...) from builtins.PyCapsule read_from_checkpoint(*args, **kwargs) Overloaded function.   1. read_from_checkpoint(self : rosetta.core.sequence.SequenceProfile, fn : rosetta.utility.file.FileName) -> NoneType   Read profile matrix from the given filename using the NNMAKE  .checkpoint format.  For compatability, negative_better defaults to true. Set manually if necessary.   2. read_from_checkpoint(self : rosetta.core.sequence.SequenceProfile, fn : rosetta.utility.file.FileName, negative_better : bool) -> NoneType   Read profile matrix from the given filename using the NNMAKE  .checkpoint format.  For compatability, negative_better defaults to true. Set manually if necessary. rescale(...) from builtins.PyCapsule rescale(*args, **kwargs) Overloaded function.   1. rescale(rosetta.core.sequence.SequenceProfile) -> NoneType   Multiply all profile weights by factor   2. rescale(self : rosetta.core.sequence.SequenceProfile, factor : float) -> NoneType   Multiply all profile weights by factor size(...) from builtins.PyCapsule size(rosetta.core.sequence.SequenceProfile) -> int width(...) from builtins.PyCapsule width(rosetta.core.sequence.SequenceProfile) -> int   Returns the number of distinct values at each position in this  profile. Methods inherited from Sequence: __getitem__(...) from builtins.PyCapsule __getitem__(self : rosetta.core.sequence.Sequence, pos : int) -> str   Returns the character at the given sequence position. append_char(...) from builtins.PyCapsule append_char(self : rosetta.core.sequence.Sequence, new_char : str) -> NoneType   Append a character append_gap(...) from builtins.PyCapsule append_gap(rosetta.core.sequence.Sequence) -> NoneType   Append a gap at(...) from builtins.PyCapsule at(self : rosetta.core.sequence.Sequence, pos : int) -> str gap_char(...) from builtins.PyCapsule gap_char(*args, **kwargs) Overloaded function.   1. gap_char(self : rosetta.core.sequence.Sequence, gap_char : str) -> NoneType   sets gap_char to the given value.   2. gap_char(rosetta.core.sequence.Sequence) -> str   Returns the character used to represent a gap for this object. id(...) from builtins.PyCapsule id(*args, **kwargs) Overloaded function.   1. id(self : rosetta.core.sequence.Sequence, new_id : str) -> NoneType   sets id to the given value.   2. id(rosetta.core.sequence.Sequence) -> str   Returns the id of this object. insert_gap(...) from builtins.PyCapsule insert_gap(self : rosetta.core.sequence.Sequence, pos : int) -> NoneType   Inserts a gap at the given position, where insert_gap( 0 )  inserts the character at the beginning of the sequence, and  insert_gap( length() ) inserts the character at the end of the  sequence. is_gap(...) from builtins.PyCapsule is_gap(self : rosetta.core.sequence.Sequence, pos : int) -> bool   Returns true if this position in the sequence represents a gap,  returns false otherwise. length(...) from builtins.PyCapsule length(rosetta.core.sequence.Sequence) -> int   Returns the number of characters in this object. resnum(...) from builtins.PyCapsule resnum(self : rosetta.core.sequence.Sequence, idx : int) -> int   Returns the index of the given sequence position, which is the  position in the sequence minus any gaps that occur earlier in the  sequence. For example, if the sequence is ---AT, resnum(5) will return 2.  Returns 0 for unaligned positions. sequence(...) from builtins.PyCapsule sequence(*args, **kwargs) Overloaded function.   1. sequence(self : rosetta.core.sequence.Sequence, sequence : str) -> NoneType   sets sequence to the given value.   2. sequence(rosetta.core.sequence.Sequence) -> str   Returns the full sequence, which may include gaps. spacer_positions(...) from builtins.PyCapsule spacer_positions(*args, **kwargs) Overloaded function.   1. spacer_positions(self : rosetta.core.sequence.Sequence, spacer_positions : rosetta.utility.vector1_unsigned_long) -> NoneType   sets spacer_positions to the given value.   2. spacer_positions(rosetta.core.sequence.Sequence) -> rosetta.utility.vector1_unsigned_long   Returns the spacer positions (chain breaks, e.g., from spaces or commas in original sequence text) start(...) from builtins.PyCapsule start(*args, **kwargs) Overloaded function.   1. start(self : rosetta.core.sequence.Sequence, new_start : int) -> NoneType   sets starting index to the given value.   2. start(rosetta.core.sequence.Sequence) -> int   Returns the start of this object. to_string(...) from builtins.PyCapsule to_string(rosetta.core.sequence.Sequence) -> str ungapped_length(...) from builtins.PyCapsule ungapped_length(rosetta.core.sequence.Sequence) -> int   Returns the number of characters in this object, ignoring gaps. ungapped_sequence(...) from builtins.PyCapsule ungapped_sequence(rosetta.core.sequence.Sequence) -> str   Returns the string representing this sequence without gaps.   class SequenceCouplingCreator(SequenceCreator)       Method resolution order: SequenceCouplingCreator SequenceCreator 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.sequence.SequenceCouplingCreator,  : rosetta.core.sequence.SequenceCouplingCreator) -> rosetta.core.sequence.SequenceCouplingCreator create_sequence(...) from builtins.PyCapsule create_sequence(rosetta.core.sequence.SequenceCouplingCreator) -> rosetta.core.sequence.Sequence keyname(...) from builtins.PyCapsule keyname(rosetta.core.sequence.SequenceCouplingCreator) -> str   class SequenceCreator(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.sequence.SequenceCreator) -> 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.sequence.SequenceCreator,  : rosetta.core.sequence.SequenceCreator) -> rosetta.core.sequence.SequenceCreator create_sequence(...) from builtins.PyCapsule create_sequence(rosetta.core.sequence.SequenceCreator) -> rosetta.core.sequence.Sequence keyname(...) from builtins.PyCapsule keyname(rosetta.core.sequence.SequenceCreator) -> str   class SequenceFactory(rosetta.utility.SingletonBase_core_sequence_SequenceFactory_t)       Method resolution order: SequenceFactory rosetta.utility.SingletonBase_core_sequence_SequenceFactory_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.sequence.SequenceFactory, creator : rosetta.core.sequence.SequenceCreator) -> NoneType get_creator(...) from builtins.PyCapsule get_creator(self : rosetta.core.sequence.SequenceFactory, type_name : str) -> rosetta.core.sequence.SequenceCreator get_seq_names(...) from builtins.PyCapsule get_seq_names(rosetta.core.sequence.SequenceFactory) -> rosetta.utility.vector1_std_string get_sequence(...) from builtins.PyCapsule get_sequence(self : rosetta.core.sequence.SequenceFactory, type_name : str) -> rosetta.core.sequence.Sequence seq_from_file(...) from builtins.PyCapsule seq_from_file(self : rosetta.core.sequence.SequenceFactory, fn : str, type_name : str) -> rosetta.core.sequence.Sequence Methods inherited from rosetta.utility.SingletonBase_core_sequence_SequenceFactory_t: get_instance(...) from builtins.PyCapsule get_instance() -> core::sequence::SequenceFactory   class SequenceProfile(Sequence)       Method resolution order: SequenceProfile Sequence builtins.object Methods defined here: __eq__(...) from builtins.PyCapsule __eq__(self : rosetta.core.sequence.SequenceProfile, other : rosetta.core.sequence.SequenceProfile) -> bool __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle) -> NoneType   2. __init__(self : handle, fn : rosetta.utility.file.FileName) -> NoneType   3. __init__(handle, rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t, str, str) -> NoneType   doc   4. __init__(handle, rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t, str, str, int) -> NoneType   doc   5. __init__(self : handle, prof : rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t, sequence : str, id : str, start : int, negative_better : bool) -> NoneType   6. __init__(handle, rosetta.core.sequence.SequenceProfile) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. __str__(...) from builtins.PyCapsule __str__(rosetta.core.sequence.SequenceProfile) -> str alphabet(...) from builtins.PyCapsule alphabet(*args, **kwargs) Overloaded function.   1. alphabet(rosetta.core.sequence.SequenceProfile) -> rosetta.utility.vector1_std_string   Return the alphabet used by this sequence profile. This is an  N-dimensional vector1 where N is the width of the profile, and the ith  entry of any row in the profile represents the probability of ith  character at that row in the sequence.   2. alphabet(self : rosetta.core.sequence.SequenceProfile, new_alphabet : rosetta.utility.vector1_std_string) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.core.sequence.SequenceProfile, rhs : rosetta.core.sequence.SequenceProfile) -> rosetta.core.sequence.SequenceProfile   assignment operator. clone(...) from builtins.PyCapsule clone(rosetta.core.sequence.SequenceProfile) -> rosetta.core.sequence.Sequence   Returns an owning pointer to a new SequenceProfile object,  with data that is a deep copy of the information in this object. convert_profile_to_probs(...) from builtins.PyCapsule convert_profile_to_probs(*args, **kwargs) Overloaded function.   1. convert_profile_to_probs(rosetta.core.sequence.SequenceProfile) -> NoneType   Use boltzman scaling on a per-residue basis to convert the current profile values to probabilities ( range 0.0-1.0 )   2. convert_profile_to_probs(self : rosetta.core.sequence.SequenceProfile, temp : float) -> NoneType   Use boltzman scaling on a per-residue basis to convert the current profile values to probabilities ( range 0.0-1.0 ) delete_position(...) from builtins.PyCapsule delete_position(self : rosetta.core.sequence.SequenceProfile, pos : int) -> NoneType   Deletes the given position from the Sequence and shifts  everything else back by one. generate_from_sequence(...) from builtins.PyCapsule generate_from_sequence(*args, **kwargs) Overloaded function.   1. generate_from_sequence(self : rosetta.core.sequence.SequenceProfile, seq : rosetta.core.sequence.Sequence) -> NoneType   Generate the profile matrix from a sequence and a given substitution matrix   2. generate_from_sequence(self : rosetta.core.sequence.SequenceProfile, seq : rosetta.core.sequence.Sequence, matrix : str) -> NoneType   Generate the profile matrix from a sequence and a given substitution matrix global_auto_rescale(...) from builtins.PyCapsule global_auto_rescale(rosetta.core.sequence.SequenceProfile) -> NoneType   Use linear rescaling (with a fixed zero) to fit the values within the range -1.0 to 1.0 insert_char(...) from builtins.PyCapsule insert_char(self : rosetta.core.sequence.SequenceProfile, pos : int, new_char : str) -> NoneType   Inserts a character at the given position. negative_better(...) from builtins.PyCapsule negative_better(*args, **kwargs) Overloaded function.   1. negative_better(rosetta.core.sequence.SequenceProfile) -> bool   Returns true if negative values are better identities.      The "default" use case is for storing log likelihood values  where positive is better. If you're using this class to store energy-like  values, set negative_better to true.   2. negative_better(self : rosetta.core.sequence.SequenceProfile, negbet : bool) -> NoneType   Set whether negative identities are better. occurrence_data(...) from builtins.PyCapsule occurrence_data(*args, **kwargs) Overloaded function.   1. occurrence_data(rosetta.core.sequence.SequenceProfile) -> rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t   Returns the 2D vector1 of Real values of the probabilties of each aa.   2. occurrence_data(self : rosetta.core.sequence.SequenceProfile, new_occurrence_data : rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t) -> NoneType   Sets the 2D vector1 of Real values of the probabilties of each aa. probability_row(...) from builtins.PyCapsule probability_row(self : rosetta.core.sequence.SequenceProfile, pos : int) -> rosetta.utility.vector1_double probabilty_row(...) from builtins.PyCapsule probabilty_row(self : rosetta.core.sequence.SequenceProfile, new_prob_row : rosetta.utility.vector1_double, pos : int) -> NoneType prof_row(...) from builtins.PyCapsule prof_row(*args, **kwargs) Overloaded function.   1. prof_row(self : rosetta.core.sequence.SequenceProfile, pos : int) -> rosetta.utility.vector1_double   Returns the vector1 of values at this position.   2. prof_row(self : rosetta.core.sequence.SequenceProfile, new_prof_row : rosetta.utility.vector1_double, pos : int) -> NoneType   Sets the 1D vector1 of Real values representing this profile at pos X. profile(...) from builtins.PyCapsule profile(*args, **kwargs) Overloaded function.   1. profile(rosetta.core.sequence.SequenceProfile) -> rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t   Returns the 2D vector1 of Real values representing this profile.   2. profile(self : rosetta.core.sequence.SequenceProfile, new_profile : rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t) -> NoneType   Sets the 2D vector1 of Real values representing this profile. read_from_binary_chk(...) from builtins.PyCapsule read_from_binary_chk(self : rosetta.core.sequence.SequenceProfile, fn : rosetta.utility.file.FileName) -> NoneType   Read profile matrix from the given filename in the legacy BLAST binary format read_from_checkpoint(...) from builtins.PyCapsule read_from_checkpoint(*args, **kwargs) Overloaded function.   1. read_from_checkpoint(self : rosetta.core.sequence.SequenceProfile, fn : rosetta.utility.file.FileName) -> NoneType   Read profile matrix from the given filename using the NNMAKE  .checkpoint format.  For compatability, negative_better defaults to true. Set manually if necessary.   2. read_from_checkpoint(self : rosetta.core.sequence.SequenceProfile, fn : rosetta.utility.file.FileName, negative_better : bool) -> NoneType   Read profile matrix from the given filename using the NNMAKE  .checkpoint format.  For compatability, negative_better defaults to true. Set manually if necessary. read_from_file(...) from builtins.PyCapsule read_from_file(self : rosetta.core.sequence.SequenceProfile, fn : rosetta.utility.file.FileName) -> NoneType   Read an profile matrix from the given filename using the NCBI  PSSM format for a position-specific scoring matrix. rescale(...) from builtins.PyCapsule rescale(*args, **kwargs) Overloaded function.   1. rescale(rosetta.core.sequence.SequenceProfile) -> NoneType   Multiply all profile weights by factor   2. rescale(self : rosetta.core.sequence.SequenceProfile, factor : float) -> NoneType   Multiply all profile weights by factor size(...) from builtins.PyCapsule size(rosetta.core.sequence.SequenceProfile) -> int temp(...) from builtins.PyCapsule temp(rosetta.core.sequence.SequenceProfile) -> float   returns the temperature used in computing profile probabilities type(...) from builtins.PyCapsule type(rosetta.core.sequence.SequenceProfile) -> str width(...) from builtins.PyCapsule width(rosetta.core.sequence.SequenceProfile) -> int   Returns the number of distinct values at each position in this  profile. Methods inherited from Sequence: __getitem__(...) from builtins.PyCapsule __getitem__(self : rosetta.core.sequence.Sequence, pos : int) -> str   Returns the character at the given sequence position. append_char(...) from builtins.PyCapsule append_char(self : rosetta.core.sequence.Sequence, new_char : str) -> NoneType   Append a character append_gap(...) from builtins.PyCapsule append_gap(rosetta.core.sequence.Sequence) -> NoneType   Append a gap at(...) from builtins.PyCapsule at(self : rosetta.core.sequence.Sequence, pos : int) -> str gap_char(...) from builtins.PyCapsule gap_char(*args, **kwargs) Overloaded function.   1. gap_char(self : rosetta.core.sequence.Sequence, gap_char : str) -> NoneType   sets gap_char to the given value.   2. gap_char(rosetta.core.sequence.Sequence) -> str   Returns the character used to represent a gap for this object. id(...) from builtins.PyCapsule id(*args, **kwargs) Overloaded function.   1. id(self : rosetta.core.sequence.Sequence, new_id : str) -> NoneType   sets id to the given value.   2. id(rosetta.core.sequence.Sequence) -> str   Returns the id of this object. insert_gap(...) from builtins.PyCapsule insert_gap(self : rosetta.core.sequence.Sequence, pos : int) -> NoneType   Inserts a gap at the given position, where insert_gap( 0 )  inserts the character at the beginning of the sequence, and  insert_gap( length() ) inserts the character at the end of the  sequence. is_gap(...) from builtins.PyCapsule is_gap(self : rosetta.core.sequence.Sequence, pos : int) -> bool   Returns true if this position in the sequence represents a gap,  returns false otherwise. length(...) from builtins.PyCapsule length(rosetta.core.sequence.Sequence) -> int   Returns the number of characters in this object. resnum(...) from builtins.PyCapsule resnum(self : rosetta.core.sequence.Sequence, idx : int) -> int   Returns the index of the given sequence position, which is the  position in the sequence minus any gaps that occur earlier in the  sequence. For example, if the sequence is ---AT, resnum(5) will return 2.  Returns 0 for unaligned positions. sequence(...) from builtins.PyCapsule sequence(*args, **kwargs) Overloaded function.   1. sequence(self : rosetta.core.sequence.Sequence, sequence : str) -> NoneType   sets sequence to the given value.   2. sequence(rosetta.core.sequence.Sequence) -> str   Returns the full sequence, which may include gaps. spacer_positions(...) from builtins.PyCapsule spacer_positions(*args, **kwargs) Overloaded function.   1. spacer_positions(self : rosetta.core.sequence.Sequence, spacer_positions : rosetta.utility.vector1_unsigned_long) -> NoneType   sets spacer_positions to the given value.   2. spacer_positions(rosetta.core.sequence.Sequence) -> rosetta.utility.vector1_unsigned_long   Returns the spacer positions (chain breaks, e.g., from spaces or commas in original sequence text) start(...) from builtins.PyCapsule start(*args, **kwargs) Overloaded function.   1. start(self : rosetta.core.sequence.Sequence, new_start : int) -> NoneType   sets starting index to the given value.   2. start(rosetta.core.sequence.Sequence) -> int   Returns the start of this object. to_string(...) from builtins.PyCapsule to_string(rosetta.core.sequence.Sequence) -> str ungapped_length(...) from builtins.PyCapsule ungapped_length(rosetta.core.sequence.Sequence) -> int   Returns the number of characters in this object, ignoring gaps. ungapped_sequence(...) from builtins.PyCapsule ungapped_sequence(rosetta.core.sequence.Sequence) -> str   Returns the string representing this sequence without gaps.   class SequenceProfileCreator(SequenceCreator)       Method resolution order: SequenceProfileCreator SequenceCreator 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.sequence.SequenceProfileCreator,  : rosetta.core.sequence.SequenceProfileCreator) -> rosetta.core.sequence.SequenceProfileCreator create_sequence(...) from builtins.PyCapsule create_sequence(rosetta.core.sequence.SequenceProfileCreator) -> rosetta.core.sequence.Sequence keyname(...) from builtins.PyCapsule keyname(rosetta.core.sequence.SequenceProfileCreator) -> str   class SimpleScoringScheme(ScoringScheme)       Method resolution order: SimpleScoringScheme ScoringScheme builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle) -> NoneType   doc   2. __init__(handle, float) -> NoneType   doc   3. __init__(handle, float, float) -> NoneType   doc   4. __init__(handle, float, float, float) -> NoneType   doc   5. __init__(self : handle, match_score : float, mismatch_score : float, gap_open_in : float, gap_extend_in : float) -> NoneType   6. __init__(handle, rosetta.core.sequence.SimpleScoringScheme) -> 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.sequence.SimpleScoringScheme,  : rosetta.core.sequence.SimpleScoringScheme) -> rosetta.core.sequence.SimpleScoringScheme clone(...) from builtins.PyCapsule clone(rosetta.core.sequence.SimpleScoringScheme) -> rosetta.core.sequence.ScoringScheme match_score(...) from builtins.PyCapsule match_score(rosetta.core.sequence.SimpleScoringScheme) -> float mismatch_score(...) from builtins.PyCapsule mismatch_score(rosetta.core.sequence.SimpleScoringScheme) -> float read_from_file(...) from builtins.PyCapsule read_from_file(self : rosetta.core.sequence.SimpleScoringScheme, fn : rosetta.utility.file.FileName) -> NoneType score(...) from builtins.PyCapsule score(self : rosetta.core.sequence.SimpleScoringScheme, seq1 : rosetta.core.sequence.Sequence, seq2 : rosetta.core.sequence.Sequence, pos1 : int, pos2 : int) -> float Methods inherited from ScoringScheme: gap_extend(...) from builtins.PyCapsule gap_extend(*args, **kwargs) Overloaded function.   1. gap_extend(rosetta.core.sequence.ScoringScheme) -> float   Gets the gap extension penalty.   2. gap_extend(self : rosetta.core.sequence.ScoringScheme, gap_extend : float) -> NoneType   Sets the gap extension penalty. gap_open(...) from builtins.PyCapsule gap_open(*args, **kwargs) Overloaded function.   1. gap_open(rosetta.core.sequence.ScoringScheme) -> float   Gets the gap opening penalty.   2. gap_open(self : rosetta.core.sequence.ScoringScheme, gap_open : float) -> NoneType   Sets the gap opening penalty. is_good(...) from builtins.PyCapsule is_good(self : rosetta.core.sequence.ScoringScheme, num : float) -> bool read_data(...) from builtins.PyCapsule read_data(self : rosetta.core.sequence.ScoringScheme,  : rosetta.utility.io.izstream) -> NoneType type(...) from builtins.PyCapsule type(*args, **kwargs) Overloaded function.   1. type(rosetta.core.sequence.ScoringScheme) -> str   getters for type, which is a unique string name for this object.   2. type(self : rosetta.core.sequence.ScoringScheme, new_type : str) -> NoneType   getters for type, which is a unique string name for this object. unimplemented_method_error(...) from builtins.PyCapsule unimplemented_method_error(self : rosetta.core.sequence.ScoringScheme, method_name : str) -> NoneType   Utility method for producing useful error messages and exiting  from program. Declared const which is funny, because exiting the program  certainly changes the state of this object! This might be replaced with  exception handling if we ever start using those.   class SimpleSequenceCreator(SequenceCreator)       Method resolution order: SimpleSequenceCreator SequenceCreator 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.sequence.SimpleSequenceCreator,  : rosetta.core.sequence.SimpleSequenceCreator) -> rosetta.core.sequence.SimpleSequenceCreator create_sequence(...) from builtins.PyCapsule create_sequence(rosetta.core.sequence.SimpleSequenceCreator) -> rosetta.core.sequence.Sequence keyname(...) from builtins.PyCapsule keyname(rosetta.core.sequence.SimpleSequenceCreator) -> str