Bindings for protocols::frag_picker namespace

Modules
		rosetta.protocols.frag_picker.frag_movers rosetta.protocols.frag_picker.nonlocal rosetta.protocols.frag_picker.quota rosetta.protocols.frag_picker.scores

Classes
		builtins.object CS2ndShift CSTalosIO CandidatesCollector BoundedCollector_protocols_frag_picker_CompareTotalScore_t BoundedCollector_CompareTotalScore GrabAllCollector Contact ContactCounts ContactType FragmentCandidate FragmentComparatorBase CompareByScoreCombination CompareQueryPosition CompareScoreComponent CompareTotalScore FragmentPicker FragmentSelectingRule BestTotalScoreSelector CompositeFragmentSelector CustomScoreSelector DiversifyCrmsdByClustering DiversifyCrmsdSelector DiversifyDihedralsSelector JCouplingIO LAMBEGO_IO PhiPsiTalosIO SidechainContactDistCutoff TorsionBinIO VallChunk VallChunkFilter PdbIdChunkFilter AllowPdbIdFilter DenyPdbIdFilter VallProvider VallResidue rosetta.std.basic_ostringstream_char_std_char_traits_char_std_allocator_char_t(builtins.object) QuotaDebug   class AllowPdbIdFilter(PdbIdChunkFilter)     Accepts a chunk based on the pdb id of the source protein     If a given chunk comes from a registered pdb file then it will PASS the test. Otherwise it will be rejected     Method resolution order: AllowPdbIdFilter PdbIdChunkFilter VallChunkFilter 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.protocols.frag_picker.AllowPdbIdFilter,  : rosetta.protocols.frag_picker.AllowPdbIdFilter) -> rosetta.protocols.frag_picker.AllowPdbIdFilter test_chunk(...) from builtins.PyCapsule test_chunk(self : rosetta.protocols.frag_picker.AllowPdbIdFilter, a_chunk : rosetta.protocols.frag_picker.VallChunk) -> bool   say if a given chunk looks promising.      Simply if its pdb id is on a list then it will pass the test Methods inherited from PdbIdChunkFilter: add_pdb_id(...) from builtins.PyCapsule add_pdb_id(self : rosetta.protocols.frag_picker.PdbIdChunkFilter, pdb_ids : str) -> NoneType   Adds  a pdb id to the filter.      What that PDB id means it depends on the filter implementation add_pdb_ids(...) from builtins.PyCapsule add_pdb_ids(self : rosetta.protocols.frag_picker.PdbIdChunkFilter, list_of_pdb_ids : rosetta.utility.vector1_std_string) -> NoneType   Adds a bunch of pdb ids to the filter load_pdb_id_from_file(...) from builtins.PyCapsule load_pdb_id_from_file(self : rosetta.protocols.frag_picker.PdbIdChunkFilter,  : str) -> NoneType   class BestTotalScoreSelector(FragmentSelectingRule)     selects a given number of fragments using a quota scheme     Method resolution order: BestTotalScoreSelector FragmentSelectingRule builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(self : handle, frags_per_pos : int, scoring_scheme : rosetta.protocols.frag_picker.scores.FragmentScoreManager) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.frag_picker.BestTotalScoreSelector,  : rosetta.protocols.frag_picker.BestTotalScoreSelector) -> rosetta.protocols.frag_picker.BestTotalScoreSelector select_fragments(...) from builtins.PyCapsule select_fragments(self : rosetta.protocols.frag_picker.BestTotalScoreSelector,  : rosetta.utility.vector1_std_pair_std_shared_ptr_protocols_frag_picker_FragmentCandidate_std_shared_ptr_protocols_frag_picker_scores_FragmentScoreMap_t,  : rosetta.utility.vector1_std_pair_std_shared_ptr_protocols_frag_picker_FragmentCandidate_std_shared_ptr_protocols_frag_picker_scores_FragmentScoreMap_t) -> NoneType   Selects desired number of fragments from a given candidates Methods inherited from FragmentSelectingRule: frags_per_pos(...) from builtins.PyCapsule frags_per_pos(rosetta.protocols.frag_picker.FragmentSelectingRule) -> int   Says how many fragments will be selected for each position in a query sequence   class BoundedCollector_CompareTotalScore(BoundedCollector_protocols_frag_picker_CompareTotalScore_t)       Method resolution order: BoundedCollector_CompareTotalScore BoundedCollector_protocols_frag_picker_CompareTotalScore_t CandidatesCollector builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle, int, int, rosetta.protocols.frag_picker.CompareTotalScore, int) -> NoneType   doc   2. __init__(self : handle, query_size : int, max_frags_per_pos : int, fragment_comparator : rosetta.protocols.frag_picker.CompareTotalScore, n_score_terms : int, buffer_factor : int) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.frag_picker.BoundedCollector_CompareTotalScore,  : rosetta.protocols.frag_picker.BoundedCollector_CompareTotalScore) -> rosetta.protocols.frag_picker.BoundedCollector_CompareTotalScore Methods inherited from BoundedCollector_protocols_frag_picker_CompareTotalScore_t: add(...) from builtins.PyCapsule add(*args, **kwargs) Overloaded function.   1. add(self : rosetta.protocols.frag_picker.BoundedCollector_protocols_frag_picker_CompareTotalScore_t, new_canditate : (rosetta.protocols.frag_picker.FragmentCandidate, rosetta.protocols.frag_picker.scores.FragmentScoreMap)) -> bool   2. add(self : rosetta.protocols.frag_picker.CandidatesCollector,  : (rosetta.protocols.frag_picker.FragmentCandidate, rosetta.protocols.frag_picker.scores.FragmentScoreMap)) -> bool   Insert a fragment candidate to the container clear(...) from builtins.PyCapsule clear(*args, **kwargs) Overloaded function.   1. clear(rosetta.protocols.frag_picker.BoundedCollector_protocols_frag_picker_CompareTotalScore_t) -> NoneType   2. clear(rosetta.protocols.frag_picker.CandidatesCollector) -> NoneType   removes all candidates from the container count_candidates(...) from builtins.PyCapsule count_candidates(*args, **kwargs) Overloaded function.   1. count_candidates(self : rosetta.protocols.frag_picker.BoundedCollector_protocols_frag_picker_CompareTotalScore_t, seq_pos : int) -> int   2. count_candidates(rosetta.protocols.frag_picker.BoundedCollector_protocols_frag_picker_CompareTotalScore_t) -> int   3. count_candidates(self : rosetta.protocols.frag_picker.CandidatesCollector,  : int) -> int   Check how many candidates have been already collected for a given position   4. count_candidates(rosetta.protocols.frag_picker.CandidatesCollector) -> int   Check how many candidates have been already collected for all positions get_candidates(...) from builtins.PyCapsule get_candidates(*args, **kwargs) Overloaded function.   1. get_candidates(self : rosetta.protocols.frag_picker.BoundedCollector_protocols_frag_picker_CompareTotalScore_t, position_in_query : int) -> rosetta.utility.vector1_std_pair_std_shared_ptr_protocols_frag_picker_FragmentCandidate_std_shared_ptr_protocols_frag_picker_scores_FragmentScoreMap_t   2. get_candidates(self : rosetta.protocols.frag_picker.CandidatesCollector, position_in_query : int) -> rosetta.utility.vector1_std_pair_std_shared_ptr_protocols_frag_picker_FragmentCandidate_std_shared_ptr_protocols_frag_picker_scores_FragmentScoreMap_t insert(...) from builtins.PyCapsule insert(*args, **kwargs) Overloaded function.   1. insert(self : rosetta.protocols.frag_picker.BoundedCollector_protocols_frag_picker_CompareTotalScore_t, pos : int, collector : rosetta.protocols.frag_picker.CandidatesCollector) -> NoneType   2. insert(self : rosetta.protocols.frag_picker.CandidatesCollector,  : int,  : rosetta.protocols.frag_picker.CandidatesCollector) -> NoneType   inserts candidates from another collector  Candidates may or may not get inserted depending on the candidate and type of storage query_length(...) from builtins.PyCapsule query_length(*args, **kwargs) Overloaded function.   1. query_length(rosetta.protocols.frag_picker.BoundedCollector_protocols_frag_picker_CompareTotalScore_t) -> int   2. query_length(rosetta.protocols.frag_picker.CandidatesCollector) -> int   Check the size of query sequence that this object knows.  This is mainly to be ale to check if it is the same as in the other parts of  fragment picking machinery.   class BoundedCollector_protocols_frag_picker_CompareTotalScore_t(CandidatesCollector)       Method resolution order: BoundedCollector_protocols_frag_picker_CompareTotalScore_t CandidatesCollector builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle, int, int, rosetta.protocols.frag_picker.CompareTotalScore, int) -> NoneType   doc   2. __init__(self : handle, query_size : int, max_frags_per_pos : int, fragment_comparator : rosetta.protocols.frag_picker.CompareTotalScore, n_score_terms : int, buffer_factor : int) -> NoneType   3. __init__(handle, rosetta.protocols.frag_picker.BoundedCollector_protocols_frag_picker_CompareTotalScore_t) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. add(...) from builtins.PyCapsule add(*args, **kwargs) Overloaded function.   1. add(self : rosetta.protocols.frag_picker.BoundedCollector_protocols_frag_picker_CompareTotalScore_t, new_canditate : (rosetta.protocols.frag_picker.FragmentCandidate, rosetta.protocols.frag_picker.scores.FragmentScoreMap)) -> bool   2. add(self : rosetta.protocols.frag_picker.CandidatesCollector,  : (rosetta.protocols.frag_picker.FragmentCandidate, rosetta.protocols.frag_picker.scores.FragmentScoreMap)) -> bool   Insert a fragment candidate to the container assign(...) from builtins.PyCapsule assign(*args, **kwargs) Overloaded function.   1. assign(self : rosetta.protocols.frag_picker.BoundedCollector_protocols_frag_picker_CompareTotalScore_t,  : rosetta.protocols.frag_picker.BoundedCollector_protocols_frag_picker_CompareTotalScore_t) -> rosetta.protocols.frag_picker.BoundedCollector_protocols_frag_picker_CompareTotalScore_t   2. assign(self : rosetta.protocols.frag_picker.CandidatesCollector,  : rosetta.protocols.frag_picker.CandidatesCollector) -> rosetta.protocols.frag_picker.CandidatesCollector clear(...) from builtins.PyCapsule clear(*args, **kwargs) Overloaded function.   1. clear(rosetta.protocols.frag_picker.BoundedCollector_protocols_frag_picker_CompareTotalScore_t) -> NoneType   2. clear(rosetta.protocols.frag_picker.CandidatesCollector) -> NoneType   removes all candidates from the container count_candidates(...) from builtins.PyCapsule count_candidates(*args, **kwargs) Overloaded function.   1. count_candidates(self : rosetta.protocols.frag_picker.BoundedCollector_protocols_frag_picker_CompareTotalScore_t, seq_pos : int) -> int   2. count_candidates(rosetta.protocols.frag_picker.BoundedCollector_protocols_frag_picker_CompareTotalScore_t) -> int   3. count_candidates(self : rosetta.protocols.frag_picker.CandidatesCollector,  : int) -> int   Check how many candidates have been already collected for a given position   4. count_candidates(rosetta.protocols.frag_picker.CandidatesCollector) -> int   Check how many candidates have been already collected for all positions get_candidates(...) from builtins.PyCapsule get_candidates(*args, **kwargs) Overloaded function.   1. get_candidates(self : rosetta.protocols.frag_picker.BoundedCollector_protocols_frag_picker_CompareTotalScore_t, position_in_query : int) -> rosetta.utility.vector1_std_pair_std_shared_ptr_protocols_frag_picker_FragmentCandidate_std_shared_ptr_protocols_frag_picker_scores_FragmentScoreMap_t   2. get_candidates(self : rosetta.protocols.frag_picker.CandidatesCollector, position_in_query : int) -> rosetta.utility.vector1_std_pair_std_shared_ptr_protocols_frag_picker_FragmentCandidate_std_shared_ptr_protocols_frag_picker_scores_FragmentScoreMap_t insert(...) from builtins.PyCapsule insert(*args, **kwargs) Overloaded function.   1. insert(self : rosetta.protocols.frag_picker.BoundedCollector_protocols_frag_picker_CompareTotalScore_t, pos : int, collector : rosetta.protocols.frag_picker.CandidatesCollector) -> NoneType   2. insert(self : rosetta.protocols.frag_picker.CandidatesCollector,  : int,  : rosetta.protocols.frag_picker.CandidatesCollector) -> NoneType   inserts candidates from another collector  Candidates may or may not get inserted depending on the candidate and type of storage query_length(...) from builtins.PyCapsule query_length(*args, **kwargs) Overloaded function.   1. query_length(rosetta.protocols.frag_picker.BoundedCollector_protocols_frag_picker_CompareTotalScore_t) -> int   2. query_length(rosetta.protocols.frag_picker.CandidatesCollector) -> int   Check the size of query sequence that this object knows.  This is mainly to be ale to check if it is the same as in the other parts of  fragment picking machinery.   class CS2ndShift(builtins.object)       Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.protocols.frag_picker.CS2ndShift) -> NoneType   2. __init__(self : rosetta.protocols.frag_picker.CS2ndShift, input_data : rosetta.protocols.frag_picker.CSTalosIO, use_sslimit : bool) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. shifts(...) from builtins.PyCapsule shifts(rosetta.protocols.frag_picker.CS2ndShift) -> rosetta.utility.vector1_utility_vector1_std_pair_unsigned_long_double_std_allocator_std_pair_unsigned_long_double_t   class CSTalosIO(builtins.object)       Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.protocols.frag_picker.CSTalosIO) -> NoneType   2. __init__(self : rosetta.protocols.frag_picker.CSTalosIO, file_name : str) -> NoneType   3. __init__(self : rosetta.protocols.frag_picker.CSTalosIO,  : rosetta.protocols.frag_picker.CSTalosIO) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.frag_picker.CSTalosIO,  : rosetta.protocols.frag_picker.CSTalosIO) -> rosetta.protocols.frag_picker.CSTalosIO get_first_residue_id(...) from builtins.PyCapsule get_first_residue_id(rosetta.protocols.frag_picker.CSTalosIO) -> int get_last_residue_id(...) from builtins.PyCapsule get_last_residue_id(rosetta.protocols.frag_picker.CSTalosIO) -> int get_sequence(...) from builtins.PyCapsule get_sequence(rosetta.protocols.frag_picker.CSTalosIO) -> str get_shift(...) from builtins.PyCapsule get_shift(self : rosetta.protocols.frag_picker.CSTalosIO,  : int,  : str) -> float has_atom(...) from builtins.PyCapsule has_atom(self : rosetta.protocols.frag_picker.CSTalosIO,  : int,  : str) -> bool has_entry(...) from builtins.PyCapsule has_entry(self : rosetta.protocols.frag_picker.CSTalosIO, residue_id : int) -> bool read(...) from builtins.PyCapsule read(self : rosetta.protocols.frag_picker.CSTalosIO,  : str) -> NoneType repack_to_matrix(...) from builtins.PyCapsule repack_to_matrix(rosetta.protocols.frag_picker.CSTalosIO) -> rosetta.utility.vector1_utility_vector1_std_pair_unsigned_long_double_std_allocator_std_pair_unsigned_long_double_t   class CandidatesCollector(builtins.object)     TODO write collector for mixed fragment lengths     A base class for collecting fragments.     The purpose of a collector is to keep fragment candidates to the end of vall processing. Then a selector will go through all the candidates stored in a collector and select the final fragments     GrabAll collector for a possible implementation     Methods defined here: __init__(self, /, *args, **kwargs) Initialize self.  See help(type(self)) for accurate signature. __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. add(...) from builtins.PyCapsule add(self : rosetta.protocols.frag_picker.CandidatesCollector,  : (rosetta.protocols.frag_picker.FragmentCandidate, rosetta.protocols.frag_picker.scores.FragmentScoreMap)) -> bool   Insert a fragment candidate to the container assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.frag_picker.CandidatesCollector,  : rosetta.protocols.frag_picker.CandidatesCollector) -> rosetta.protocols.frag_picker.CandidatesCollector clear(...) from builtins.PyCapsule clear(rosetta.protocols.frag_picker.CandidatesCollector) -> NoneType   removes all candidates from the container count_candidates(...) from builtins.PyCapsule count_candidates(*args, **kwargs) Overloaded function.   1. count_candidates(self : rosetta.protocols.frag_picker.CandidatesCollector,  : int) -> int   Check how many candidates have been already collected for a given position   2. count_candidates(rosetta.protocols.frag_picker.CandidatesCollector) -> int   Check how many candidates have been already collected for all positions get_candidates(...) from builtins.PyCapsule get_candidates(self : rosetta.protocols.frag_picker.CandidatesCollector, position_in_query : int) -> rosetta.utility.vector1_std_pair_std_shared_ptr_protocols_frag_picker_FragmentCandidate_std_shared_ptr_protocols_frag_picker_scores_FragmentScoreMap_t insert(...) from builtins.PyCapsule insert(self : rosetta.protocols.frag_picker.CandidatesCollector,  : int,  : rosetta.protocols.frag_picker.CandidatesCollector) -> NoneType   inserts candidates from another collector  Candidates may or may not get inserted depending on the candidate and type of storage query_length(...) from builtins.PyCapsule query_length(rosetta.protocols.frag_picker.CandidatesCollector) -> int   Check the size of query sequence that this object knows.  This is mainly to be ale to check if it is the same as in the other parts of  fragment picking machinery.   class CompareByScoreCombination(FragmentComparatorBase)     comparator based on the linear combination of some score components     returns true if first pair has lower weighted score than the second one     Method resolution order: CompareByScoreCombination FragmentComparatorBase builtins.object Methods defined here: __call__(...) from builtins.PyCapsule __call__(self : rosetta.protocols.frag_picker.CompareByScoreCombination, first_candidate : (rosetta.protocols.frag_picker.FragmentCandidate, rosetta.protocols.frag_picker.scores.FragmentScoreMap), second_candidate : (rosetta.protocols.frag_picker.FragmentCandidate, rosetta.protocols.frag_picker.scores.FragmentScoreMap)) -> bool   compares two fragment candidates      returns true if second pair has greater total score than the first one.  Using this comparator to sort fragment candidates order them descending according  to their total score __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(self : handle, which_components : rosetta.utility.vector1_unsigned_long, weights : rosetta.utility.vector1_double) -> NoneType   2. __init__(handle, rosetta.protocols.frag_picker.CompareByScoreCombination) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.frag_picker.CompareByScoreCombination,  : rosetta.protocols.frag_picker.CompareByScoreCombination) -> rosetta.protocols.frag_picker.CompareByScoreCombination   class CompareQueryPosition(FragmentComparatorBase)     comparator based on a sequence position in a query     Method resolution order: CompareQueryPosition FragmentComparatorBase builtins.object Methods defined here: __call__(...) from builtins.PyCapsule __call__(self : rosetta.protocols.frag_picker.CompareQueryPosition, first_candidate : (rosetta.protocols.frag_picker.FragmentCandidate, rosetta.protocols.frag_picker.scores.FragmentScoreMap), second_candidate : (rosetta.protocols.frag_picker.FragmentCandidate, rosetta.protocols.frag_picker.scores.FragmentScoreMap)) -> bool   compares two fragment candidates      returns true if second_candidate starts on the later residue than first_candidate  Using this comparator to sort fragment candidates orders them ascending by their sequence position __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.protocols.frag_picker.CompareQueryPosition,  : rosetta.protocols.frag_picker.CompareQueryPosition) -> rosetta.protocols.frag_picker.CompareQueryPosition   class CompareScoreComponent(FragmentComparatorBase)     comparator based on one of the score components calculated for  fragments     returns true if first pair has lower score component than the second one     Method resolution order: CompareScoreComponent FragmentComparatorBase builtins.object Methods defined here: __call__(...) from builtins.PyCapsule __call__(self : rosetta.protocols.frag_picker.CompareScoreComponent, first_candidate : (rosetta.protocols.frag_picker.FragmentCandidate, rosetta.protocols.frag_picker.scores.FragmentScoreMap), second_candidate : (rosetta.protocols.frag_picker.FragmentCandidate, rosetta.protocols.frag_picker.scores.FragmentScoreMap)) -> bool   compares two fragment candidates      returns true if second pair has greater total score than the first one.  Using this comparator to sort fragment candidates order them ascending according  to their total score __init__(...) from builtins.PyCapsule __init__(self : handle, component_id : int) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.frag_picker.CompareScoreComponent,  : rosetta.protocols.frag_picker.CompareScoreComponent) -> rosetta.protocols.frag_picker.CompareScoreComponent   class CompareTotalScore(FragmentComparatorBase)     comparator based on the total score of fragments     returns true if first pair has lower total score than the second one     Method resolution order: CompareTotalScore FragmentComparatorBase builtins.object Methods defined here: __call__(...) from builtins.PyCapsule __call__(self : rosetta.protocols.frag_picker.CompareTotalScore, first_candidate : (rosetta.protocols.frag_picker.FragmentCandidate, rosetta.protocols.frag_picker.scores.FragmentScoreMap), second_candidate : (rosetta.protocols.frag_picker.FragmentCandidate, rosetta.protocols.frag_picker.scores.FragmentScoreMap)) -> bool   compares two fragment candidates      returns true if second pair has greater total score than the first one.  Using this comparator to sort fragment candidates order them descending according  to their total score __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(self : handle, scoring : rosetta.protocols.frag_picker.scores.FragmentScoreManager) -> NoneType   2. __init__(handle, rosetta.protocols.frag_picker.CompareTotalScore) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.frag_picker.CompareTotalScore,  : rosetta.protocols.frag_picker.CompareTotalScore) -> rosetta.protocols.frag_picker.CompareTotalScore   class CompositeFragmentSelector(FragmentSelectingRule)     selects fragments by running several selectors     Method resolution order: CompositeFragmentSelector FragmentSelectingRule builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(self : handle, frags_per_pos : int) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. add_selector(...) from builtins.PyCapsule add_selector(self : rosetta.protocols.frag_picker.CompositeFragmentSelector, new_selector : rosetta.protocols.frag_picker.FragmentSelectingRule) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.frag_picker.CompositeFragmentSelector,  : rosetta.protocols.frag_picker.CompositeFragmentSelector) -> rosetta.protocols.frag_picker.CompositeFragmentSelector select_fragments(...) from builtins.PyCapsule select_fragments(self : rosetta.protocols.frag_picker.CompositeFragmentSelector,  : rosetta.utility.vector1_std_pair_std_shared_ptr_protocols_frag_picker_FragmentCandidate_std_shared_ptr_protocols_frag_picker_scores_FragmentScoreMap_t,  : rosetta.utility.vector1_std_pair_std_shared_ptr_protocols_frag_picker_FragmentCandidate_std_shared_ptr_protocols_frag_picker_scores_FragmentScoreMap_t) -> NoneType   Selects desired number of fragments from a given set of candidates Methods inherited from FragmentSelectingRule: frags_per_pos(...) from builtins.PyCapsule frags_per_pos(rosetta.protocols.frag_picker.FragmentSelectingRule) -> int   Says how many fragments will be selected for each position in a query sequence   class Contact(builtins.object)       Methods defined here: __init__(...) from builtins.PyCapsule __init__(self : rosetta.protocols.frag_picker.Contact, i : int, j : int, dist_squared : float, type : rosetta.protocols.frag_picker.ContactType) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.frag_picker.Contact,  : rosetta.protocols.frag_picker.Contact) -> rosetta.protocols.frag_picker.Contact dist(...) from builtins.PyCapsule dist(rosetta.protocols.frag_picker.Contact) -> float dist_squared(...) from builtins.PyCapsule dist_squared(rosetta.protocols.frag_picker.Contact) -> float i(...) from builtins.PyCapsule i(rosetta.protocols.frag_picker.Contact) -> int j(...) from builtins.PyCapsule j(rosetta.protocols.frag_picker.Contact) -> int type(...) from builtins.PyCapsule type(rosetta.protocols.frag_picker.Contact) -> rosetta.protocols.frag_picker.ContactType type_name(...) from builtins.PyCapsule type_name(rosetta.protocols.frag_picker.Contact) -> str   class ContactCounts(builtins.object)       Methods defined here: __init__(...) from builtins.PyCapsule __init__(rosetta.protocols.frag_picker.ContactCounts) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.frag_picker.ContactCounts,  : rosetta.protocols.frag_picker.ContactCounts) -> rosetta.protocols.frag_picker.ContactCounts counts(...) from builtins.PyCapsule counts(rosetta.protocols.frag_picker.ContactCounts) -> rosetta.std.map_std_pair_unsigned_long_unsigned_long_t_unsigned_long   class ContactType(builtins.object)       Methods defined here: __eq__(...) from builtins.PyCapsule __eq__(rosetta.protocols.frag_picker.ContactType, rosetta.protocols.frag_picker.ContactType) -> bool __hash__(...) from builtins.PyCapsule __hash__(rosetta.protocols.frag_picker.ContactType) -> int __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.protocols.frag_picker.ContactType, int) -> NoneType   2. __init__(rosetta.protocols.frag_picker.ContactType, int) -> NoneType __int__(...) from builtins.PyCapsule __int__(rosetta.protocols.frag_picker.ContactType) -> int __ne__(...) from builtins.PyCapsule __ne__(rosetta.protocols.frag_picker.ContactType, rosetta.protocols.frag_picker.ContactType) -> 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.protocols.frag_picker.ContactType) -> str Data and other attributes defined here: CA = ContactType.CA CB = ContactType.CB CEN = ContactType.CEN UNK = ContactType.num_contact_types num_contact_types = ContactType.num_contact_types   class CustomScoreSelector(FragmentSelectingRule)     selects a given number of fragments using a quota scheme     Method resolution order: CustomScoreSelector FragmentSelectingRule builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(self : handle, frags_per_pos : int, scoring_scheme : rosetta.protocols.frag_picker.scores.FragmentScoreManager) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.frag_picker.CustomScoreSelector,  : rosetta.protocols.frag_picker.CustomScoreSelector) -> rosetta.protocols.frag_picker.CustomScoreSelector select_fragments(...) from builtins.PyCapsule select_fragments(self : rosetta.protocols.frag_picker.CustomScoreSelector,  : rosetta.utility.vector1_std_pair_std_shared_ptr_protocols_frag_picker_FragmentCandidate_std_shared_ptr_protocols_frag_picker_scores_FragmentScoreMap_t,  : rosetta.utility.vector1_std_pair_std_shared_ptr_protocols_frag_picker_FragmentCandidate_std_shared_ptr_protocols_frag_picker_scores_FragmentScoreMap_t) -> NoneType   Selects desired number of fragments from a given candidates Methods inherited from FragmentSelectingRule: frags_per_pos(...) from builtins.PyCapsule frags_per_pos(rosetta.protocols.frag_picker.FragmentSelectingRule) -> int   Says how many fragments will be selected for each position in a query sequence   class DenyPdbIdFilter(PdbIdChunkFilter)     Denies a chunk based on the pdb id of the source protein     If a given chunk comes from a registered pdb file then it will FAIL the test. Otherwise it will be accepted     Method resolution order: DenyPdbIdFilter PdbIdChunkFilter VallChunkFilter 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.protocols.frag_picker.DenyPdbIdFilter,  : rosetta.protocols.frag_picker.DenyPdbIdFilter) -> rosetta.protocols.frag_picker.DenyPdbIdFilter test_chunk(...) from builtins.PyCapsule test_chunk(self : rosetta.protocols.frag_picker.DenyPdbIdFilter, a_chunk : rosetta.protocols.frag_picker.VallChunk) -> bool   say if a given chunk looks promising.      Simply if its pdb id is on a list then it will be rejected Methods inherited from PdbIdChunkFilter: add_pdb_id(...) from builtins.PyCapsule add_pdb_id(self : rosetta.protocols.frag_picker.PdbIdChunkFilter, pdb_ids : str) -> NoneType   Adds  a pdb id to the filter.      What that PDB id means it depends on the filter implementation add_pdb_ids(...) from builtins.PyCapsule add_pdb_ids(self : rosetta.protocols.frag_picker.PdbIdChunkFilter, list_of_pdb_ids : rosetta.utility.vector1_std_string) -> NoneType   Adds a bunch of pdb ids to the filter load_pdb_id_from_file(...) from builtins.PyCapsule load_pdb_id_from_file(self : rosetta.protocols.frag_picker.PdbIdChunkFilter,  : str) -> NoneType   class DiversifyCrmsdByClustering(FragmentSelectingRule)     selects fragments by running several selectors     Method resolution order: DiversifyCrmsdByClustering FragmentSelectingRule builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(self : handle, frags_per_pos : int) -> NoneType   2. __init__(handle, rosetta.protocols.frag_picker.DiversifyCrmsdByClustering) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.frag_picker.DiversifyCrmsdByClustering,  : rosetta.protocols.frag_picker.DiversifyCrmsdByClustering) -> rosetta.protocols.frag_picker.DiversifyCrmsdByClustering select_fragments(...) from builtins.PyCapsule select_fragments(self : rosetta.protocols.frag_picker.DiversifyCrmsdByClustering,  : rosetta.utility.vector1_std_pair_std_shared_ptr_protocols_frag_picker_FragmentCandidate_std_shared_ptr_protocols_frag_picker_scores_FragmentScoreMap_t,  : rosetta.utility.vector1_std_pair_std_shared_ptr_protocols_frag_picker_FragmentCandidate_std_shared_ptr_protocols_frag_picker_scores_FragmentScoreMap_t) -> NoneType   Selects desired number of fragments from a given set of candidates Methods inherited from FragmentSelectingRule: frags_per_pos(...) from builtins.PyCapsule frags_per_pos(rosetta.protocols.frag_picker.FragmentSelectingRule) -> int   Says how many fragments will be selected for each position in a query sequence   class DiversifyCrmsdSelector(FragmentSelectingRule)     selects fragments by running several selectors     Method resolution order: DiversifyCrmsdSelector FragmentSelectingRule builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(self : handle, frags_per_pos : int, cutoff : float) -> NoneType   2. __init__(handle, rosetta.protocols.frag_picker.DiversifyCrmsdSelector) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.frag_picker.DiversifyCrmsdSelector,  : rosetta.protocols.frag_picker.DiversifyCrmsdSelector) -> rosetta.protocols.frag_picker.DiversifyCrmsdSelector select_fragments(...) from builtins.PyCapsule select_fragments(self : rosetta.protocols.frag_picker.DiversifyCrmsdSelector,  : rosetta.utility.vector1_std_pair_std_shared_ptr_protocols_frag_picker_FragmentCandidate_std_shared_ptr_protocols_frag_picker_scores_FragmentScoreMap_t,  : rosetta.utility.vector1_std_pair_std_shared_ptr_protocols_frag_picker_FragmentCandidate_std_shared_ptr_protocols_frag_picker_scores_FragmentScoreMap_t) -> NoneType   Selects desired number of fragments from a given set of candidates Methods inherited from FragmentSelectingRule: frags_per_pos(...) from builtins.PyCapsule frags_per_pos(rosetta.protocols.frag_picker.FragmentSelectingRule) -> int   Says how many fragments will be selected for each position in a query sequence   class DiversifyDihedralsSelector(FragmentSelectingRule)     selects fragments by running several selectors     Method resolution order: DiversifyDihedralsSelector FragmentSelectingRule builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(self : handle, frags_per_pos : int, cutoff : float) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.frag_picker.DiversifyDihedralsSelector,  : rosetta.protocols.frag_picker.DiversifyDihedralsSelector) -> rosetta.protocols.frag_picker.DiversifyDihedralsSelector dihedral_rmsd(...) from builtins.PyCapsule dihedral_rmsd(self : rosetta.protocols.frag_picker.DiversifyDihedralsSelector,  : rosetta.protocols.frag_picker.FragmentCandidate,  : rosetta.protocols.frag_picker.FragmentCandidate) -> float select_fragments(...) from builtins.PyCapsule select_fragments(self : rosetta.protocols.frag_picker.DiversifyDihedralsSelector,  : rosetta.utility.vector1_std_pair_std_shared_ptr_protocols_frag_picker_FragmentCandidate_std_shared_ptr_protocols_frag_picker_scores_FragmentScoreMap_t,  : rosetta.utility.vector1_std_pair_std_shared_ptr_protocols_frag_picker_FragmentCandidate_std_shared_ptr_protocols_frag_picker_scores_FragmentScoreMap_t) -> NoneType   Selects desired number of fragments from a given set of candidates Methods inherited from FragmentSelectingRule: frags_per_pos(...) from builtins.PyCapsule frags_per_pos(rosetta.protocols.frag_picker.FragmentSelectingRule) -> int   Says how many fragments will be selected for each position in a query sequence   class FragmentCandidate(builtins.object)     Vector candidate says which X-mer from vall fits to a query sequence     Scores for a given fragment are stored separately in a FragmentScoreMap object Therefore fragment containers hold std::pair<FragmentCandidateOP,FragmentScoreMapOP>     Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(self : rosetta.protocols.frag_picker.FragmentCandidate, queryPosition : int, inChunkPosition : int, chunk : rosetta.protocols.frag_picker.VallChunk, fragmentLength : int) -> NoneType   2. __init__(self : rosetta.protocols.frag_picker.FragmentCandidate,  : rosetta.protocols.frag_picker.FragmentCandidate) -> 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.protocols.frag_picker.FragmentCandidate) -> str assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.frag_picker.FragmentCandidate,  : rosetta.protocols.frag_picker.FragmentCandidate) -> rosetta.protocols.frag_picker.FragmentCandidate get_chain_id(...) from builtins.PyCapsule get_chain_id(rosetta.protocols.frag_picker.FragmentCandidate) -> str   returns a chain id of a protein from which the fragment has been extracted get_chunk(...) from builtins.PyCapsule get_chunk(rosetta.protocols.frag_picker.FragmentCandidate) -> rosetta.protocols.frag_picker.VallChunk   returns a pointer to the original chunk from vall the fragment comes from get_first_index_in_query(...) from builtins.PyCapsule get_first_index_in_query(rosetta.protocols.frag_picker.FragmentCandidate) -> int   returns the index of a very first residue in a query sequence that is covered by this fragment get_first_index_in_vall(...) from builtins.PyCapsule get_first_index_in_vall(rosetta.protocols.frag_picker.FragmentCandidate) -> int   returns the index of a very first residue in a Vall chunk that is covered by this fragment get_frag_data(...) from builtins.PyCapsule get_frag_data(rosetta.protocols.frag_picker.FragmentCandidate) -> rosetta.core.fragment.FragData get_length(...) from builtins.PyCapsule get_length(rosetta.protocols.frag_picker.FragmentCandidate) -> int   returns the length of this fragment get_middle_residue(...) from builtins.PyCapsule get_middle_residue(rosetta.protocols.frag_picker.FragmentCandidate) -> rosetta.protocols.frag_picker.VallResidue   returns the middle residue of this fragment candidate get_middle_ss(...) from builtins.PyCapsule get_middle_ss(rosetta.protocols.frag_picker.FragmentCandidate) -> str   returns secondary structure assigned to the middle residue of this fragment candidate      secondary structure of the middle residue of this fragment, as extracted from Vall data get_pdb_id(...) from builtins.PyCapsule get_pdb_id(rosetta.protocols.frag_picker.FragmentCandidate) -> str   returns a PDB id of a protein from which the fragment has been extracted get_pool_name(...) from builtins.PyCapsule get_pool_name(rosetta.protocols.frag_picker.FragmentCandidate) -> str get_query_middle_res_id(...) from builtins.PyCapsule get_query_middle_res_id(rosetta.protocols.frag_picker.FragmentCandidate) -> int   returns a query index of a middle residue in this fragment      a position of the middle residue of this fragment in the query sequence get_residue(...) from builtins.PyCapsule get_residue(self : rosetta.protocols.frag_picker.FragmentCandidate, whichOne : int) -> rosetta.protocols.frag_picker.VallResidue   returns a given residue from this fragment      the irgument is in the range [1,fragmentLength] get_vall_middle_res_id(...) from builtins.PyCapsule get_vall_middle_res_id(rosetta.protocols.frag_picker.FragmentCandidate) -> int   returns a vall index of a middle residue in this fragment      a position of the middle residue of this fragment in the vall sequence key(...) from builtins.PyCapsule key(rosetta.protocols.frag_picker.FragmentCandidate) -> int   returns an integer key identifying a fragment output_silent(...) from builtins.PyCapsule output_silent(self : rosetta.protocols.frag_picker.FragmentCandidate, sfd : rosetta.core.io.silent.SilentFileData, sequence : str, silent_file_name : str, tag : str, sc : rosetta.protocols.frag_picker.scores.FragmentScoreMap, ms : rosetta.protocols.frag_picker.scores.FragmentScoreManager) -> NoneType   Prints fragment to silent struct same_chain(...) from builtins.PyCapsule same_chain(self : rosetta.protocols.frag_picker.FragmentCandidate, fr : rosetta.protocols.frag_picker.FragmentCandidate) -> bool sequence(...) from builtins.PyCapsule sequence(rosetta.protocols.frag_picker.FragmentCandidate) -> str   creates a new string object that contains a sequence of this fragment set_pool_name(...) from builtins.PyCapsule set_pool_name(self : rosetta.protocols.frag_picker.FragmentCandidate, pool_name : str) -> NoneType   class FragmentComparatorBase(builtins.object)       Methods defined here: __call__(...) from builtins.PyCapsule __call__(self : rosetta.protocols.frag_picker.FragmentComparatorBase, first_candidate : (rosetta.protocols.frag_picker.FragmentCandidate, rosetta.protocols.frag_picker.scores.FragmentScoreMap), second_candidate : (rosetta.protocols.frag_picker.FragmentCandidate, rosetta.protocols.frag_picker.scores.FragmentScoreMap)) -> bool __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.protocols.frag_picker.FragmentComparatorBase) -> NoneType   2. __init__(rosetta.protocols.frag_picker.FragmentComparatorBase, rosetta.protocols.frag_picker.FragmentComparatorBase) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.frag_picker.FragmentComparatorBase,  : rosetta.protocols.frag_picker.FragmentComparatorBase) -> rosetta.protocols.frag_picker.FragmentComparatorBase   class FragmentPicker(builtins.object)     The core of the fragment picking machinery     FragmentPicker class does:    - know about query data: sequence, sequence profile, secondary structure.      All other query data must be loaded directly to the relevant scoring methods    - provide slots for 'plugable' parts of the machinery, like chunk filters, scoring methods and so on.    - pick fragments     Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.protocols.frag_picker.FragmentPicker) -> NoneType   2. __init__(self : rosetta.protocols.frag_picker.FragmentPicker, fragment_score_manager_type : str) -> NoneType   3. __init__(self : rosetta.protocols.frag_picker.FragmentPicker,  : rosetta.protocols.frag_picker.FragmentPicker) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. add_chunk_filter(...) from builtins.PyCapsule add_chunk_filter(self : rosetta.protocols.frag_picker.FragmentPicker, filter : rosetta.protocols.frag_picker.VallChunkFilter) -> NoneType   adds a chunk filter that will be used to screen chunks before they are cut into fragments add_query_ss(...) from builtins.PyCapsule add_query_ss(self : rosetta.protocols.frag_picker.FragmentPicker,  : str,  : str) -> NoneType   Sets the query secondary structure add_scoring_method(...) from builtins.PyCapsule add_scoring_method(*args, **kwargs) Overloaded function.   1. add_scoring_method(self : rosetta.protocols.frag_picker.FragmentPicker, scoring_term : rosetta.protocols.frag_picker.scores.FragmentScoringMethod, weight : float) -> NoneType   adds a new scoring method to the scoring scheme   2. add_scoring_method(self : rosetta.protocols.frag_picker.FragmentPicker, scoring_term : rosetta.protocols.frag_picker.scores.FragmentScoringMethod, weight : float, index : int) -> NoneType   adds a new scoring method to the scoring scheme assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.frag_picker.FragmentPicker,  : rosetta.protocols.frag_picker.FragmentPicker) -> rosetta.protocols.frag_picker.FragmentPicker bounded_protocol(...) from builtins.PyCapsule bounded_protocol(rosetta.protocols.frag_picker.FragmentPicker) -> NoneType   Picks fragments and saves them into proper files - uses bounded queue.      This protocol scores all vall data against all query positions  and keeps a limited number of candidates per position using a bounded queue.  When all candidates for all positions are scored, it selects final fragments. count_query_ss(...) from builtins.PyCapsule count_query_ss(rosetta.protocols.frag_picker.FragmentPicker) -> int   Sets the query secondary structure fragment_contacts(...) from builtins.PyCapsule fragment_contacts(self : rosetta.protocols.frag_picker.FragmentPicker, fragment_size : int, fragment_set : rosetta.utility.vector1_utility_vector1_std_pair_std_shared_ptr_protocols_frag_picker_FragmentCandidate_std_shared_ptr_protocols_frag_picker_scores_FragmentScoreMap_std_allocator_std_pair_std_shared_ptr_protocols_frag_picker_FragmentCandidate_std_shared_ptr_protocols_frag_picker_scores_FragmentScoreMap_t) -> NoneType get_candidates_collector(...) from builtins.PyCapsule get_candidates_collector(*args, **kwargs) Overloaded function.   1. get_candidates_collector(self : rosetta.protocols.frag_picker.FragmentPicker, frag_size : int) -> rosetta.protocols.frag_picker.CandidatesCollector   returns a pointer to the candidates collector currently used      one may need this instance to access the candidates that have been found by the picker   2. get_candidates_collector(self : rosetta.protocols.frag_picker.FragmentPicker, frag_size : int, index : int) -> rosetta.protocols.frag_picker.CandidatesCollector   returns a pointer to the candidates collector currently used      one may need this instance to access the candidates that have been found by the picker get_query_phi_prediction(...) from builtins.PyCapsule get_query_phi_prediction(rosetta.protocols.frag_picker.FragmentPicker) -> rosetta.utility.vector1_double   Returns the phi prediction get_query_phi_prediction_conf(...) from builtins.PyCapsule get_query_phi_prediction_conf(rosetta.protocols.frag_picker.FragmentPicker) -> rosetta.utility.vector1_double   Returns the phi prediction confidence get_query_psi_prediction(...) from builtins.PyCapsule get_query_psi_prediction(rosetta.protocols.frag_picker.FragmentPicker) -> rosetta.utility.vector1_double   Returns the psi prediction get_query_psi_prediction_conf(...) from builtins.PyCapsule get_query_psi_prediction_conf(rosetta.protocols.frag_picker.FragmentPicker) -> rosetta.utility.vector1_double   Returns the psi prediction confidence get_query_residue_depth(...) from builtins.PyCapsule get_query_residue_depth(rosetta.protocols.frag_picker.FragmentPicker) -> rosetta.utility.vector1_double   Returns residue depth values get_query_sa_prediction(...) from builtins.PyCapsule get_query_sa_prediction(rosetta.protocols.frag_picker.FragmentPicker) -> rosetta.utility.vector1_double   Returns the solvent accessibility prediction get_query_seq(...) from builtins.PyCapsule get_query_seq(rosetta.protocols.frag_picker.FragmentPicker) -> rosetta.core.sequence.SequenceProfile get_query_seq_string(...) from builtins.PyCapsule get_query_seq_string(rosetta.protocols.frag_picker.FragmentPicker) -> str   Returns the sequence we are picking fragments for (as a string) get_query_ss(...) from builtins.PyCapsule get_query_ss(self : rosetta.protocols.frag_picker.FragmentPicker, prediction_name : str) -> rosetta.core.fragment.SecondaryStructure   Returns the query secondary structure as a SecondaryStructure object get_query_ss_string(...) from builtins.PyCapsule get_query_ss_string(self : rosetta.protocols.frag_picker.FragmentPicker, prediction_name : str) -> str   Returns the query secondary structure as a string get_score_manager(...) from builtins.PyCapsule get_score_manager(*args, **kwargs) Overloaded function.   1. get_score_manager(rosetta.protocols.frag_picker.FragmentPicker) -> rosetta.protocols.frag_picker.scores.FragmentScoreManager   returns a pointer to a scoring manager   2. get_score_manager(self : rosetta.protocols.frag_picker.FragmentPicker, index : int) -> rosetta.protocols.frag_picker.scores.FragmentScoreManager   returns a pointer to a scoring manager get_self_ptr(...) from builtins.PyCapsule get_self_ptr(*args, **kwargs) Overloaded function.   1. get_self_ptr(rosetta.protocols.frag_picker.FragmentPicker) -> rosetta.protocols.frag_picker.FragmentPicker   2. get_self_ptr(rosetta.protocols.frag_picker.FragmentPicker) -> rosetta.protocols.frag_picker.FragmentPicker get_self_weak_ptr(...) from builtins.PyCapsule get_self_weak_ptr(*args, **kwargs) Overloaded function.   1. get_self_weak_ptr(rosetta.protocols.frag_picker.FragmentPicker) -> rosetta.std.weak_ptr_const_protocols_frag_picker_FragmentPicker_t   2. get_self_weak_ptr(rosetta.protocols.frag_picker.FragmentPicker) -> rosetta.std.weak_ptr_protocols_frag_picker_FragmentPicker_t get_vall(...) from builtins.PyCapsule get_vall(rosetta.protocols.frag_picker.FragmentPicker) -> rosetta.protocols.frag_picker.VallProvider   a pointer to Vall provider is_valid_chunk(...) from builtins.PyCapsule is_valid_chunk(*args, **kwargs) Overloaded function.   1. is_valid_chunk(self : rosetta.protocols.frag_picker.FragmentPicker, chunk : rosetta.protocols.frag_picker.VallChunk) -> bool   2. is_valid_chunk(self : rosetta.protocols.frag_picker.FragmentPicker, frag_len : int, chunk : rosetta.protocols.frag_picker.VallChunk) -> bool keep_all_protocol(...) from builtins.PyCapsule keep_all_protocol(rosetta.protocols.frag_picker.FragmentPicker) -> NoneType   Picks fragments and saves them into proper files - independently for each query position.      This protocol scores all vall data against a given position  and keeps all the candidates unless they fail an energy filter  When all candidates for a positions are scored, it selects fragments  for the position and proceeds to the next position. Bounded queue is not used max_frag_len(...) from builtins.PyCapsule max_frag_len(rosetta.protocols.frag_picker.FragmentPicker) -> int   How long is the longest fragment? nonlocal_pairs(...) from builtins.PyCapsule nonlocal_pairs(self : rosetta.protocols.frag_picker.FragmentPicker, fragment_size : int, fragment_set : rosetta.utility.vector1_utility_vector1_std_pair_std_shared_ptr_protocols_frag_picker_FragmentCandidate_std_shared_ptr_protocols_frag_picker_scores_FragmentScoreMap_std_allocator_std_pair_std_shared_ptr_protocols_frag_picker_FragmentCandidate_std_shared_ptr_protocols_frag_picker_scores_FragmentScoreMap_t) -> NoneType output_fragments(...) from builtins.PyCapsule output_fragments(self : rosetta.protocols.frag_picker.FragmentPicker, fragment_size : int, final_fragments : rosetta.utility.vector1_utility_vector1_std_pair_std_shared_ptr_protocols_frag_picker_FragmentCandidate_std_shared_ptr_protocols_frag_picker_scores_FragmentScoreMap_std_allocator_std_pair_std_shared_ptr_protocols_frag_picker_FragmentCandidate_std_shared_ptr_protocols_frag_picker_scores_FragmentScoreMap_t) -> NoneType parse_command_line(...) from builtins.PyCapsule parse_command_line(rosetta.protocols.frag_picker.FragmentPicker) -> NoneType parse_quota_command_line(...) from builtins.PyCapsule parse_quota_command_line(rosetta.protocols.frag_picker.FragmentPicker) -> NoneType pick_candidates(...) from builtins.PyCapsule pick_candidates(*args, **kwargs) Overloaded function.   1. pick_candidates(rosetta.protocols.frag_picker.FragmentPicker) -> NoneType   2. pick_candidates(self : rosetta.protocols.frag_picker.FragmentPicker, i_pos : int, frag_len : int) -> NoneType pick_chunk_candidates(...) from builtins.PyCapsule pick_chunk_candidates(self : rosetta.protocols.frag_picker.FragmentPicker, chunks : rosetta.utility.vector1_std_shared_ptr_protocols_frag_picker_VallChunk_t, index : int) -> NoneType   multi-threaded task quota_protocol(...) from builtins.PyCapsule quota_protocol(rosetta.protocols.frag_picker.FragmentPicker) -> NoneType read_depth(...) from builtins.PyCapsule read_depth(self : rosetta.protocols.frag_picker.FragmentPicker, file_name : str) -> NoneType   Reads DEPTH residue depth values read_psipred_ss2(...) from builtins.PyCapsule read_psipred_ss2(self : rosetta.protocols.frag_picker.FragmentPicker,  : str,  : str) -> NoneType   Reads query secondary structure prediction from a PsiPred file read_spine_x(...) from builtins.PyCapsule read_spine_x(self : rosetta.protocols.frag_picker.FragmentPicker, file_name : str) -> NoneType   Reads spine-x phi, psi, and solvent accessibility predictions read_ss_file(...) from builtins.PyCapsule read_ss_file(self : rosetta.protocols.frag_picker.FragmentPicker,  : str,  : str) -> NoneType   Identifies if the ss file is psipred or talos, calls appropriate reader read_ss_files(...) from builtins.PyCapsule read_ss_files(self : rosetta.protocols.frag_picker.FragmentPicker, sec_str_input : rosetta.utility.vector1_std_string) -> NoneType   Reads a bunch of ss predicitons from files and plugs them into the picker read_talos_ss(...) from builtins.PyCapsule read_talos_ss(self : rosetta.protocols.frag_picker.FragmentPicker,  : str,  : str) -> NoneType   Reads query secondary structure prediction from a Talos+ file read_vall(...) from builtins.PyCapsule read_vall(*args, **kwargs) Overloaded function.   1. read_vall(self : rosetta.protocols.frag_picker.FragmentPicker, fn : str) -> NoneType   reads a vall file   2. read_vall(self : rosetta.protocols.frag_picker.FragmentPicker, fns : rosetta.utility.vector1_std_string) -> NoneType save_candidates(...) from builtins.PyCapsule save_candidates(rosetta.protocols.frag_picker.FragmentPicker) -> NoneType save_fragments(...) from builtins.PyCapsule save_fragments(rosetta.protocols.frag_picker.FragmentPicker) -> NoneType set_candidates_collector(...) from builtins.PyCapsule set_candidates_collector(*args, **kwargs) Overloaded function.   1. set_candidates_collector(self : rosetta.protocols.frag_picker.FragmentPicker, frag_size : int, sink : rosetta.protocols.frag_picker.CandidatesCollector) -> NoneType   sets a collector where fragment candidates will be kept until final selection   2. set_candidates_collector(self : rosetta.protocols.frag_picker.FragmentPicker, frag_size : int, sink : rosetta.protocols.frag_picker.CandidatesCollector, index : int) -> NoneType   sets a collector where fragment candidates will be kept until final selection set_picked_positions(...) from builtins.PyCapsule set_picked_positions(*args, **kwargs) Overloaded function.   1. set_picked_positions(self : rosetta.protocols.frag_picker.FragmentPicker,  : int,  : int) -> NoneType   Asks the picker to pick fragments from a given range in a query sequence   2. set_picked_positions(self : rosetta.protocols.frag_picker.FragmentPicker,  : rosetta.utility.vector1_unsigned_long) -> NoneType   Asks the picker to pick fragments for given positions in a query sequence set_query_profile(...) from builtins.PyCapsule set_query_profile(self : rosetta.protocols.frag_picker.FragmentPicker, profile : rosetta.core.sequence.SequenceProfile) -> NoneType   Sets the sequence object we are picking fragments for set_query_seq(...) from builtins.PyCapsule set_query_seq(*args, **kwargs) Overloaded function.   1. set_query_seq(self : rosetta.protocols.frag_picker.FragmentPicker, query_sequence : rosetta.core.sequence.SequenceProfile) -> NoneType   sets the query sequence      Well, it is a sequence profile, but the sequence can be extracted from it   2. set_query_seq(self : rosetta.protocols.frag_picker.FragmentPicker, query_sequence : str) -> NoneType   sets the query sequence set_up_quota_nnmake_style(...) from builtins.PyCapsule set_up_quota_nnmake_style(rosetta.protocols.frag_picker.FragmentPicker) -> NoneType set_up_ss_abego_quota(...) from builtins.PyCapsule set_up_ss_abego_quota(rosetta.protocols.frag_picker.FragmentPicker) -> NoneType set_vall(...) from builtins.PyCapsule set_vall(self : rosetta.protocols.frag_picker.FragmentPicker, vall_chunks : rosetta.protocols.frag_picker.VallProvider) -> NoneType   sets vall data size_of_query(...) from builtins.PyCapsule size_of_query(rosetta.protocols.frag_picker.FragmentPicker) -> int total_score(...) from builtins.PyCapsule total_score(*args, **kwargs) Overloaded function.   1. total_score(self : rosetta.protocols.frag_picker.FragmentPicker, f : rosetta.protocols.frag_picker.scores.FragmentScoreMap) -> float   Calculates total score for a given vector of small scores  (FragmentScoreMap object pointer)      FragmentScoreManager that is stored inside the picker is used  for this calculation. It particular it provides weights   2. total_score(self : rosetta.protocols.frag_picker.FragmentPicker, f : rosetta.protocols.frag_picker.scores.FragmentScoreMap, index : int) -> float   Calculates total score for a given vector of small scores  (FragmentScoreMap object pointer)      FragmentScoreManager that is stored inside the picker is used  for this calculation. It particular it provides weights Data descriptors defined here: frag_sizes_ n_candidates_ n_frags_ prefix_ selector_   class FragmentSelectingRule(builtins.object)     selects a given number of fragments just by selecting the best ones     Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(self : rosetta.protocols.frag_picker.FragmentSelectingRule, frags_per_pos : int) -> NoneType   2. __init__(rosetta.protocols.frag_picker.FragmentSelectingRule, rosetta.protocols.frag_picker.FragmentSelectingRule) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.frag_picker.FragmentSelectingRule,  : rosetta.protocols.frag_picker.FragmentSelectingRule) -> rosetta.protocols.frag_picker.FragmentSelectingRule frags_per_pos(...) from builtins.PyCapsule frags_per_pos(rosetta.protocols.frag_picker.FragmentSelectingRule) -> int   Says how many fragments will be selected for each position in a query sequence select_fragments(...) from builtins.PyCapsule select_fragments(self : rosetta.protocols.frag_picker.FragmentSelectingRule,  : rosetta.utility.vector1_std_pair_std_shared_ptr_protocols_frag_picker_FragmentCandidate_std_shared_ptr_protocols_frag_picker_scores_FragmentScoreMap_t,  : rosetta.utility.vector1_std_pair_std_shared_ptr_protocols_frag_picker_FragmentCandidate_std_shared_ptr_protocols_frag_picker_scores_FragmentScoreMap_t) -> NoneType   Selects desired number of fragments from a given candidates   class GrabAllCollector(CandidatesCollector)     Keeps all fragments candidates for the final selection     The purpose of a collector is to keep fragment candidates to the end of vall processing. This simple implementation keeps all candidates which might use huge memory     Method resolution order: GrabAllCollector CandidatesCollector builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(self : handle, query_size : int) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. add(...) from builtins.PyCapsule add(self : rosetta.protocols.frag_picker.GrabAllCollector, new_canditate : (rosetta.protocols.frag_picker.FragmentCandidate, rosetta.protocols.frag_picker.scores.FragmentScoreMap)) -> bool   Insert a fragment candidate to the container assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.frag_picker.GrabAllCollector,  : rosetta.protocols.frag_picker.GrabAllCollector) -> rosetta.protocols.frag_picker.GrabAllCollector clear(...) from builtins.PyCapsule clear(rosetta.protocols.frag_picker.GrabAllCollector) -> NoneType count_candidates(...) from builtins.PyCapsule count_candidates(*args, **kwargs) Overloaded function.   1. count_candidates(self : rosetta.protocols.frag_picker.GrabAllCollector, seq_pos : int) -> int   Check how many candidates have been already collected for a given position   2. count_candidates(rosetta.protocols.frag_picker.GrabAllCollector) -> int   Check how many candidates have been already collected for all positions get_candidates(...) from builtins.PyCapsule get_candidates(self : rosetta.protocols.frag_picker.GrabAllCollector, position_in_query : int) -> rosetta.utility.vector1_std_pair_std_shared_ptr_protocols_frag_picker_FragmentCandidate_std_shared_ptr_protocols_frag_picker_scores_FragmentScoreMap_t   returns all stored fragment candidates that begins at a given position in a query insert(...) from builtins.PyCapsule insert(self : rosetta.protocols.frag_picker.GrabAllCollector, pos : int, collector : rosetta.protocols.frag_picker.CandidatesCollector) -> NoneType   Inserts candidates from another Collector for a give position in the query query_length(...) from builtins.PyCapsule query_length(rosetta.protocols.frag_picker.GrabAllCollector) -> int   Check the size of query sequence that this object knows.  This is mainly to be able to check if it is the same as in the other parts of  fragment picking machinery.   class JCouplingIO(builtins.object)       Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.protocols.frag_picker.JCouplingIO) -> NoneType   2. __init__(self : rosetta.protocols.frag_picker.JCouplingIO, file_name : str) -> NoneType   3. __init__(self : rosetta.protocols.frag_picker.JCouplingIO,  : rosetta.protocols.frag_picker.JCouplingIO) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.frag_picker.JCouplingIO,  : rosetta.protocols.frag_picker.JCouplingIO) -> rosetta.protocols.frag_picker.JCouplingIO get_data(...) from builtins.PyCapsule get_data(self : rosetta.protocols.frag_picker.JCouplingIO, res_num : int, has_data : bool) -> (float, float) get_length(...) from builtins.PyCapsule get_length(rosetta.protocols.frag_picker.JCouplingIO) -> int get_parameters(...) from builtins.PyCapsule get_parameters(rosetta.protocols.frag_picker.JCouplingIO) -> rosetta.utility.vector1_double read(...) from builtins.PyCapsule read(self : rosetta.protocols.frag_picker.JCouplingIO,  : str) -> NoneType   class LAMBEGO_IO(builtins.object)       Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.protocols.frag_picker.LAMBEGO_IO) -> NoneType   2. __init__(self : rosetta.protocols.frag_picker.LAMBEGO_IO,  : rosetta.protocols.frag_picker.LAMBEGO_IO) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.frag_picker.LAMBEGO_IO,  : rosetta.protocols.frag_picker.LAMBEGO_IO) -> rosetta.protocols.frag_picker.LAMBEGO_IO matrix(...) from builtins.PyCapsule matrix(rosetta.protocols.frag_picker.LAMBEGO_IO) -> rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t nrows(...) from builtins.PyCapsule nrows(rosetta.protocols.frag_picker.LAMBEGO_IO) -> int prof_row(...) from builtins.PyCapsule prof_row(self : rosetta.protocols.frag_picker.LAMBEGO_IO, idx : int) -> rosetta.utility.vector1_double   class PdbIdChunkFilter(VallChunkFilter)       Method resolution order: PdbIdChunkFilter VallChunkFilter builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(rosetta.protocols.frag_picker.PdbIdChunkFilter) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. add_pdb_id(...) from builtins.PyCapsule add_pdb_id(self : rosetta.protocols.frag_picker.PdbIdChunkFilter, pdb_ids : str) -> NoneType   Adds  a pdb id to the filter.      What that PDB id means it depends on the filter implementation add_pdb_ids(...) from builtins.PyCapsule add_pdb_ids(self : rosetta.protocols.frag_picker.PdbIdChunkFilter, list_of_pdb_ids : rosetta.utility.vector1_std_string) -> NoneType   Adds a bunch of pdb ids to the filter assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.frag_picker.PdbIdChunkFilter,  : rosetta.protocols.frag_picker.PdbIdChunkFilter) -> rosetta.protocols.frag_picker.PdbIdChunkFilter load_pdb_id_from_file(...) from builtins.PyCapsule load_pdb_id_from_file(self : rosetta.protocols.frag_picker.PdbIdChunkFilter,  : str) -> NoneType Methods inherited from VallChunkFilter: test_chunk(...) from builtins.PyCapsule test_chunk(self : rosetta.protocols.frag_picker.VallChunkFilter,  : rosetta.protocols.frag_picker.VallChunk) -> bool   if a chunk seems to be interesting, return true. Otherwise say false   class PhiPsiTalosIO(builtins.object)       Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.protocols.frag_picker.PhiPsiTalosIO) -> NoneType   2. __init__(self : rosetta.protocols.frag_picker.PhiPsiTalosIO, file_name : str) -> NoneType   3. __init__(self : rosetta.protocols.frag_picker.PhiPsiTalosIO,  : rosetta.protocols.frag_picker.PhiPsiTalosIO) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.frag_picker.PhiPsiTalosIO,  : rosetta.protocols.frag_picker.PhiPsiTalosIO) -> rosetta.protocols.frag_picker.PhiPsiTalosIO d_phi(...) from builtins.PyCapsule d_phi(self : rosetta.protocols.frag_picker.PhiPsiTalosIO, res_id : int) -> float d_psi(...) from builtins.PyCapsule d_psi(self : rosetta.protocols.frag_picker.PhiPsiTalosIO, res_id : int) -> float dist(...) from builtins.PyCapsule dist(self : rosetta.protocols.frag_picker.PhiPsiTalosIO, res_id : int) -> float get_first_residue_id(...) from builtins.PyCapsule get_first_residue_id(rosetta.protocols.frag_picker.PhiPsiTalosIO) -> int get_last_residue_id(...) from builtins.PyCapsule get_last_residue_id(rosetta.protocols.frag_picker.PhiPsiTalosIO) -> int get_sequence(...) from builtins.PyCapsule get_sequence(rosetta.protocols.frag_picker.PhiPsiTalosIO) -> str has_entry(...) from builtins.PyCapsule has_entry(self : rosetta.protocols.frag_picker.PhiPsiTalosIO, residue_id : int) -> bool phi(...) from builtins.PyCapsule phi(self : rosetta.protocols.frag_picker.PhiPsiTalosIO, res_id : int) -> float psi(...) from builtins.PyCapsule psi(self : rosetta.protocols.frag_picker.PhiPsiTalosIO, res_id : int) -> float quality(...) from builtins.PyCapsule quality(self : rosetta.protocols.frag_picker.PhiPsiTalosIO, res_id : int) -> str read(...) from builtins.PyCapsule read(self : rosetta.protocols.frag_picker.PhiPsiTalosIO,  : str) -> NoneType s2(...) from builtins.PyCapsule s2(self : rosetta.protocols.frag_picker.PhiPsiTalosIO, res_id : int) -> float   class QuotaDebug(rosetta.std.basic_ostringstream_char_std_char_traits_char_std_allocator_char_t)       Method resolution order: QuotaDebug rosetta.std.basic_ostringstream_char_std_char_traits_char_std_allocator_char_t builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(self : rosetta.protocols.frag_picker.QuotaDebug, nFrags : int) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. log(...) from builtins.PyCapsule log(self : rosetta.protocols.frag_picker.QuotaDebug,  : int,  : int,  : rosetta.utility.vector1_double) -> NoneType max_pools(...) from builtins.PyCapsule max_pools(rosetta.protocols.frag_picker.QuotaDebug) -> int setup_summary(...) from builtins.PyCapsule setup_summary(self : rosetta.protocols.frag_picker.QuotaDebug, collector_ : protocols::frag_picker::quota::QuotaCollector) -> NoneType write_summary(...) from builtins.PyCapsule write_summary(rosetta.protocols.frag_picker.QuotaDebug) -> NoneType Data descriptors defined here: nFrags_ tag_map_ tags_ Methods inherited from rosetta.std.basic_ostringstream_char_std_char_traits_char_std_allocator_char_t: rdbuf(...) from builtins.PyCapsule rdbuf(rosetta.std.basic_ostringstream_char_std_char_traits_char_std_allocator_char_t) -> std::basic_stringbuf<char, std::char_traits<char>, std::allocator<char> > str(...) from builtins.PyCapsule str(*args, **kwargs) Overloaded function.   1. str(rosetta.std.basic_ostringstream_char_std_char_traits_char_std_allocator_char_t) -> str   2. str(self : rosetta.std.basic_ostringstream_char_std_char_traits_char_std_allocator_char_t, __s : str) -> NoneType   class SidechainContactDistCutoff(builtins.object)     defines sidechain contact distance cutoffs.     provides amino acid pair specific distance cutoffs.     Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.protocols.frag_picker.SidechainContactDistCutoff) -> NoneType   2. __init__(self : rosetta.protocols.frag_picker.SidechainContactDistCutoff, scale_factor : float) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.frag_picker.SidechainContactDistCutoff,  : rosetta.protocols.frag_picker.SidechainContactDistCutoff) -> rosetta.protocols.frag_picker.SidechainContactDistCutoff get_cutoff(...) from builtins.PyCapsule get_cutoff(self : rosetta.protocols.frag_picker.SidechainContactDistCutoff, aa_i : str, aa_j : str) -> float get_cutoff_squared(...) from builtins.PyCapsule get_cutoff_squared(self : rosetta.protocols.frag_picker.SidechainContactDistCutoff, aa_i : str, aa_j : str) -> float scale_factor(...) from builtins.PyCapsule scale_factor(rosetta.protocols.frag_picker.SidechainContactDistCutoff) -> float   class TorsionBinIO(builtins.object)       Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.protocols.frag_picker.TorsionBinIO) -> NoneType   2. __init__(self : rosetta.protocols.frag_picker.TorsionBinIO,  : rosetta.protocols.frag_picker.TorsionBinIO) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.frag_picker.TorsionBinIO,  : rosetta.protocols.frag_picker.TorsionBinIO) -> rosetta.protocols.frag_picker.TorsionBinIO matrix(...) from builtins.PyCapsule matrix(rosetta.protocols.frag_picker.TorsionBinIO) -> rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t nrows(...) from builtins.PyCapsule nrows(rosetta.protocols.frag_picker.TorsionBinIO) -> int prof_row(...) from builtins.PyCapsule prof_row(self : rosetta.protocols.frag_picker.TorsionBinIO, idx : int) -> rosetta.utility.vector1_double   class VallChunk(builtins.object)     represents a chunk of residues extracted from a vall.     VallChunk contains a vector of VallResidue objects and provides a basic ways to access them     Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(self : rosetta.protocols.frag_picker.VallChunk, provider : rosetta.std.weak_ptr_protocols_frag_picker_VallProvider_t) -> NoneType   2. __init__(self : rosetta.protocols.frag_picker.VallChunk,  : rosetta.protocols.frag_picker.VallChunk) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.frag_picker.VallChunk,  : rosetta.protocols.frag_picker.VallChunk) -> rosetta.protocols.frag_picker.VallChunk at(...) from builtins.PyCapsule at(self : rosetta.protocols.frag_picker.VallChunk, index : int) -> rosetta.protocols.frag_picker.VallResidue   returns i-th residue form this chunk. The first residue has index 1 chunk_key(...) from builtins.PyCapsule chunk_key(rosetta.protocols.frag_picker.VallChunk) -> str   returns a string that is unique for each chunk in vall get_chain_id(...) from builtins.PyCapsule get_chain_id(rosetta.protocols.frag_picker.VallChunk) -> str   returns protein chain ID get_pdb_id(...) from builtins.PyCapsule get_pdb_id(rosetta.protocols.frag_picker.VallChunk) -> str   returns a PDB id (a string of four letters, e.g. "4mba") get_pose(...) from builtins.PyCapsule get_pose(rosetta.protocols.frag_picker.VallChunk) -> rosetta.core.pose.Pose   returns a pose created for this chunk      the pose object is created when this function is called for the first time  and then cached within a VallProvider object  Every time this method is called for a new chunk, VallProvider caches new data get_profile(...) from builtins.PyCapsule get_profile(rosetta.protocols.frag_picker.VallChunk) -> rosetta.core.sequence.SequenceProfile   returns amino acid profile of this chunk      the profile object is created when this function is called for the first time  and then cached within a VallProvider object.  Every time this method is called for a new chunk, VallProvider caches new data get_self_ptr(...) from builtins.PyCapsule get_self_ptr(*args, **kwargs) Overloaded function.   1. get_self_ptr(rosetta.protocols.frag_picker.VallChunk) -> rosetta.protocols.frag_picker.VallChunk   2. get_self_ptr(rosetta.protocols.frag_picker.VallChunk) -> rosetta.protocols.frag_picker.VallChunk get_self_weak_ptr(...) from builtins.PyCapsule get_self_weak_ptr(*args, **kwargs) Overloaded function.   1. get_self_weak_ptr(rosetta.protocols.frag_picker.VallChunk) -> rosetta.std.weak_ptr_const_protocols_frag_picker_VallChunk_t   2. get_self_weak_ptr(rosetta.protocols.frag_picker.VallChunk) -> rosetta.std.weak_ptr_protocols_frag_picker_VallChunk_t get_sequence(...) from builtins.PyCapsule get_sequence(rosetta.protocols.frag_picker.VallChunk) -> str   returns amino acid sequence of this chunk get_vall_filename(...) from builtins.PyCapsule get_vall_filename(rosetta.protocols.frag_picker.VallChunk) -> str   returns the Vall file used for this chunk get_vall_provider(...) from builtins.PyCapsule get_vall_provider(rosetta.protocols.frag_picker.VallChunk) -> protocols::frag_picker::VallProvider   returns the Vall Provider key(...) from builtins.PyCapsule key(rosetta.protocols.frag_picker.VallChunk) -> int   returns integer key of this chunk, which is the key of this chunk's first residue push_back(...) from builtins.PyCapsule push_back(self : rosetta.protocols.frag_picker.VallChunk, what : rosetta.protocols.frag_picker.VallResidue) -> NoneType   appends a residue to this chunk size(...) from builtins.PyCapsule size(rosetta.protocols.frag_picker.VallChunk) -> int   returns the size of this chunk i.e. the number of residues stored in there vall_key(...) from builtins.PyCapsule vall_key(*args, **kwargs) Overloaded function.   1. vall_key(rosetta.protocols.frag_picker.VallChunk) -> int   2. vall_key(self : rosetta.protocols.frag_picker.VallChunk, key : int) -> NoneType   class VallChunkFilter(builtins.object)     a base class for a chunk filtering mechanism     Chunk filtering is used to screen chunks before any fragment is evaluated Therefore it is the fastest way to excluded unwanted proteins     AllowPdbIdFilter and DenyPdbIdFilter for implementations     Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.protocols.frag_picker.VallChunkFilter) -> NoneType   2. __init__(rosetta.protocols.frag_picker.VallChunkFilter, rosetta.protocols.frag_picker.VallChunkFilter) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.frag_picker.VallChunkFilter,  : rosetta.protocols.frag_picker.VallChunkFilter) -> rosetta.protocols.frag_picker.VallChunkFilter test_chunk(...) from builtins.PyCapsule test_chunk(self : rosetta.protocols.frag_picker.VallChunkFilter,  : rosetta.protocols.frag_picker.VallChunk) -> bool   if a chunk seems to be interesting, return true. Otherwise say false   class VallProvider(builtins.object)     a vector of vall chunks     Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.protocols.frag_picker.VallProvider) -> NoneType   2. __init__(self : rosetta.protocols.frag_picker.VallProvider,  : rosetta.protocols.frag_picker.VallProvider) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.frag_picker.VallProvider,  : rosetta.protocols.frag_picker.VallProvider) -> rosetta.protocols.frag_picker.VallProvider at(...) from builtins.PyCapsule at(self : rosetta.protocols.frag_picker.VallProvider, index : int) -> rosetta.protocols.frag_picker.VallChunk   returns a certain chunk (starts from 1) cache_pose(...) from builtins.PyCapsule cache_pose(self : rosetta.protocols.frag_picker.VallProvider, source_chunk : rosetta.protocols.frag_picker.VallChunk) -> rosetta.core.pose.Pose   cache a pose for a given chunk cache_profile(...) from builtins.PyCapsule cache_profile(self : rosetta.protocols.frag_picker.VallProvider, source_chunk : rosetta.protocols.frag_picker.VallChunk) -> rosetta.core.sequence.SequenceProfile   cache a sequence profile for a given chunk find_chunk(...) from builtins.PyCapsule find_chunk(self : rosetta.protocols.frag_picker.VallProvider,  : str,  : str,  : int) -> rosetta.protocols.frag_picker.VallChunk   tries to find a chunk defined by PDB id, chain id and a residue  sequence id     If this VallProvider does not contain a desired  chunk, 0 is returned. get_largest_chunk_size(...) from builtins.PyCapsule get_largest_chunk_size(rosetta.protocols.frag_picker.VallProvider) -> int   says what is the length of the largest chunk known to this  provider get_self_ptr(...) from builtins.PyCapsule get_self_ptr(*args, **kwargs) Overloaded function.   1. get_self_ptr(rosetta.protocols.frag_picker.VallProvider) -> rosetta.protocols.frag_picker.VallProvider   2. get_self_ptr(rosetta.protocols.frag_picker.VallProvider) -> rosetta.protocols.frag_picker.VallProvider get_self_weak_ptr(...) from builtins.PyCapsule get_self_weak_ptr(*args, **kwargs) Overloaded function.   1. get_self_weak_ptr(rosetta.protocols.frag_picker.VallProvider) -> rosetta.std.weak_ptr_const_protocols_frag_picker_VallProvider_t   2. get_self_weak_ptr(rosetta.protocols.frag_picker.VallProvider) -> rosetta.std.weak_ptr_protocols_frag_picker_VallProvider_t get_vall_by_key(...) from builtins.PyCapsule get_vall_by_key(self : rosetta.protocols.frag_picker.VallProvider, index : int) -> str get_vall_count(...) from builtins.PyCapsule get_vall_count(rosetta.protocols.frag_picker.VallProvider) -> int get_vall_end_line_by_key(...) from builtins.PyCapsule get_vall_end_line_by_key(self : rosetta.protocols.frag_picker.VallProvider, index : int) -> int get_vall_last_residue_key_by_key(...) from builtins.PyCapsule get_vall_last_residue_key_by_key(self : rosetta.protocols.frag_picker.VallProvider, index : int) -> int get_vall_start_line_by_key(...) from builtins.PyCapsule get_vall_start_line_by_key(self : rosetta.protocols.frag_picker.VallProvider, index : int) -> int push_back(...) from builtins.PyCapsule push_back(self : rosetta.protocols.frag_picker.VallProvider, what : rosetta.protocols.frag_picker.VallChunk) -> NoneType   adds a new chunk to this provider size(...) from builtins.PyCapsule size(rosetta.protocols.frag_picker.VallProvider) -> int   says how many chunks do we have vallChunksFromLibraries(...) from builtins.PyCapsule vallChunksFromLibraries(self : rosetta.protocols.frag_picker.VallProvider, fns : rosetta.utility.vector1_std_string) -> int vallChunksFromLibrary(...) from builtins.PyCapsule vallChunksFromLibrary(*args, **kwargs) Overloaded function.   1. vallChunksFromLibrary(self : rosetta.protocols.frag_picker.VallProvider, filename : str) -> int   Vall reader  THe defaults should ensure that the file is fully read if startline and endline ar not specified. endline = 0 means read to the end.   2. vallChunksFromLibrary(self : rosetta.protocols.frag_picker.VallProvider, filename : str, startline : int) -> int   Vall reader  THe defaults should ensure that the file is fully read if startline and endline ar not specified. endline = 0 means read to the end.   3. vallChunksFromLibrary(self : rosetta.protocols.frag_picker.VallProvider, filename : str, startline : int, endline : int) -> int   Vall reader  THe defaults should ensure that the file is fully read if startline and endline ar not specified. endline = 0 means read to the end. vallNumLines(...) from builtins.PyCapsule vallNumLines(self : rosetta.protocols.frag_picker.VallProvider, filename : str) -> int   Runs through the Vall and stores number of lines   class VallResidue(builtins.object)     class for managing a line of the Vall fragment library     Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.protocols.frag_picker.VallResidue) -> NoneType   2. __init__(self : rosetta.protocols.frag_picker.VallResidue, line : str) -> NoneType   3. __init__(self : rosetta.protocols.frag_picker.VallResidue, rval : rosetta.protocols.frag_picker.VallResidue) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. aa(...) from builtins.PyCapsule aa(*args, **kwargs) Overloaded function.   1. aa(rosetta.protocols.frag_picker.VallResidue) -> str   one letter amino acid code   2. aa(self : rosetta.protocols.frag_picker.VallResidue, c : str) -> NoneType   one letter amino acid code assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.frag_picker.VallResidue, rval : rosetta.protocols.frag_picker.VallResidue) -> rosetta.protocols.frag_picker.VallResidue   copy assignment bF(...) from builtins.PyCapsule bF(*args, **kwargs) Overloaded function.   1. bF(rosetta.protocols.frag_picker.VallResidue) -> float   b factor average for backbone   2. bF(self : rosetta.protocols.frag_picker.VallResidue, val : float) -> NoneType   b factor average for backbone bbtorsion_srfd(...) from builtins.PyCapsule bbtorsion_srfd(rosetta.protocols.frag_picker.VallResidue) -> rosetta.core.fragment.BBTorsionSRFD   build a BBTorsionSRFD from this page cbx(...) from builtins.PyCapsule cbx(*args, **kwargs) Overloaded function.   1. cbx(rosetta.protocols.frag_picker.VallResidue) -> float   x-coordinate of C-beta   2. cbx(self : rosetta.protocols.frag_picker.VallResidue, val : float) -> NoneType   x-coordinate of C-beta cby(...) from builtins.PyCapsule cby(*args, **kwargs) Overloaded function.   1. cby(rosetta.protocols.frag_picker.VallResidue) -> float   y-coordinate of C-beta   2. cby(self : rosetta.protocols.frag_picker.VallResidue, val : float) -> NoneType   y-coordinate of C-beta cbz(...) from builtins.PyCapsule cbz(*args, **kwargs) Overloaded function.   1. cbz(rosetta.protocols.frag_picker.VallResidue) -> float   z-coordinate of C-beta   2. cbz(self : rosetta.protocols.frag_picker.VallResidue, val : float) -> NoneType   z-coordinate of C-beta cenx(...) from builtins.PyCapsule cenx(*args, **kwargs) Overloaded function.   1. cenx(rosetta.protocols.frag_picker.VallResidue) -> float   x-coordinate of centroid   2. cenx(self : rosetta.protocols.frag_picker.VallResidue, val : float) -> NoneType   x-coordinate of centroid ceny(...) from builtins.PyCapsule ceny(*args, **kwargs) Overloaded function.   1. ceny(rosetta.protocols.frag_picker.VallResidue) -> float   y-coordinate of centroid   2. ceny(self : rosetta.protocols.frag_picker.VallResidue, val : float) -> NoneType   y-coordinate of centroid cenz(...) from builtins.PyCapsule cenz(*args, **kwargs) Overloaded function.   1. cenz(rosetta.protocols.frag_picker.VallResidue) -> float   z-coordinate of centroid   2. cenz(self : rosetta.protocols.frag_picker.VallResidue, val : float) -> NoneType   z-coordinate of centroid depth(...) from builtins.PyCapsule depth(*args, **kwargs) Overloaded function.   1. depth(rosetta.protocols.frag_picker.VallResidue) -> float   all-atom residue depth   2. depth(self : rosetta.protocols.frag_picker.VallResidue, depth : float) -> NoneType   all-atom residue depth distance_squared(...) from builtins.PyCapsule distance_squared(*args, **kwargs) Overloaded function.   1. distance_squared(self : rosetta.protocols.frag_picker.VallResidue, r : rosetta.protocols.frag_picker.VallResidue) -> float   2. distance_squared(self : rosetta.protocols.frag_picker.VallResidue, r : rosetta.protocols.frag_picker.VallResidue, type : rosetta.protocols.frag_picker.ContactType) -> float distance_squared_cb(...) from builtins.PyCapsule distance_squared_cb(self : rosetta.protocols.frag_picker.VallResidue, r : rosetta.protocols.frag_picker.VallResidue) -> float distance_squared_cen(...) from builtins.PyCapsule distance_squared_cen(self : rosetta.protocols.frag_picker.VallResidue, r : rosetta.protocols.frag_picker.VallResidue) -> float dssp_phi(...) from builtins.PyCapsule dssp_phi(rosetta.protocols.frag_picker.VallResidue) -> float   phi backbone torsion in degrees from DSSP dssp_psi(...) from builtins.PyCapsule dssp_psi(rosetta.protocols.frag_picker.VallResidue) -> float   psi backbone torsion in degrees from DSSP fill_from_string(...) from builtins.PyCapsule fill_from_string(self : rosetta.protocols.frag_picker.VallResidue, line : str) -> NoneType   fill internal data from string fill_from_string_cs(...) from builtins.PyCapsule fill_from_string_cs(self : rosetta.protocols.frag_picker.VallResidue, line : str) -> NoneType   fill internal data from string fill_from_string_residue_depth_version1(...) from builtins.PyCapsule fill_from_string_residue_depth_version1(self : rosetta.protocols.frag_picker.VallResidue, line : str) -> NoneType fill_from_string_version1(...) from builtins.PyCapsule fill_from_string_version1(self : rosetta.protocols.frag_picker.VallResidue, line : str) -> NoneType   fill internal data from string has_chemical_shifts(...) from builtins.PyCapsule has_chemical_shifts(rosetta.protocols.frag_picker.VallResidue) -> bool has_profile(...) from builtins.PyCapsule has_profile(rosetta.protocols.frag_picker.VallResidue) -> bool   has profile info? has_profile_struct(...) from builtins.PyCapsule has_profile_struct(rosetta.protocols.frag_picker.VallResidue) -> bool   has structure profile info? id(...) from builtins.PyCapsule id(*args, **kwargs) Overloaded function.   1. id(rosetta.protocols.frag_picker.VallResidue) -> str   id of fragment source (e.g. pdb name)   2. id(self : rosetta.protocols.frag_picker.VallResidue, s : str) -> NoneType   id of fragment source (e.g. pdb name) key(...) from builtins.PyCapsule key(*args, **kwargs) Overloaded function.   1. key(self : rosetta.protocols.frag_picker.VallResidue, key : int) -> NoneType   sets the key id   2. key(rosetta.protocols.frag_picker.VallResidue) -> int   sets the key id nali(...) from builtins.PyCapsule nali(*args, **kwargs) Overloaded function.   1. nali(rosetta.protocols.frag_picker.VallResidue) -> int   number of alignments   2. nali(self : rosetta.protocols.frag_picker.VallResidue, val : int) -> NoneType   number of alignments omega(...) from builtins.PyCapsule omega(*args, **kwargs) Overloaded function.   1. omega(rosetta.protocols.frag_picker.VallResidue) -> float   omega backbone torsion in degrees   2. omega(self : rosetta.protocols.frag_picker.VallResidue, val : float) -> NoneType   omega backbone torsion in degrees phi(...) from builtins.PyCapsule phi(*args, **kwargs) Overloaded function.   1. phi(rosetta.protocols.frag_picker.VallResidue) -> float   phi backbone torsion in degrees   2. phi(self : rosetta.protocols.frag_picker.VallResidue, val : float) -> NoneType   phi backbone torsion in degrees profile(...) from builtins.PyCapsule profile(*args, **kwargs) Overloaded function.   1. profile(rosetta.protocols.frag_picker.VallResidue) -> rosetta.utility.vector1_double   per amino acid profile data   2. profile(self : rosetta.protocols.frag_picker.VallResidue, v : rosetta.utility.vector1_double) -> NoneType   per amino acid profile data profile_struct(...) from builtins.PyCapsule profile_struct(*args, **kwargs) Overloaded function.   1. profile_struct(rosetta.protocols.frag_picker.VallResidue) -> rosetta.utility.vector1_double   per amino acid structure profile data   2. profile_struct(self : rosetta.protocols.frag_picker.VallResidue, v : rosetta.utility.vector1_double) -> NoneType   per amino acid structure profile data psi(...) from builtins.PyCapsule psi(*args, **kwargs) Overloaded function.   1. psi(rosetta.protocols.frag_picker.VallResidue) -> float   psi backbone torsion in degrees   2. psi(self : rosetta.protocols.frag_picker.VallResidue, val : float) -> NoneType   psi backbone torsion in degrees resi(...) from builtins.PyCapsule resi(*args, **kwargs) Overloaded function.   1. resi(rosetta.protocols.frag_picker.VallResidue) -> int   residue sequence number in source   2. resi(self : rosetta.protocols.frag_picker.VallResidue, i : int) -> NoneType   residue sequence number in source sa(...) from builtins.PyCapsule sa(*args, **kwargs) Overloaded function.   1. sa(rosetta.protocols.frag_picker.VallResidue) -> float   solvent accessible area   2. sa(self : rosetta.protocols.frag_picker.VallResidue, val : float) -> NoneType   solvent accessible area sa_norm(...) from builtins.PyCapsule sa_norm(rosetta.protocols.frag_picker.VallResidue) -> float   solvent accessible area normalized secondary_shifts(...) from builtins.PyCapsule secondary_shifts(rosetta.protocols.frag_picker.VallResidue) -> rosetta.utility.vector1_double   secondary chemical shifts set_ss_from_str(...) from builtins.PyCapsule set_ss_from_str(rosetta.protocols.frag_picker.VallResidue) -> NoneType ss(...) from builtins.PyCapsule ss(*args, **kwargs) Overloaded function.   1. ss(rosetta.protocols.frag_picker.VallResidue) -> str   one letter secondary structure code   2. ss(self : rosetta.protocols.frag_picker.VallResidue, c : str) -> NoneType   one letter secondary structure code ss_str(...) from builtins.PyCapsule ss_str(*args, **kwargs) Overloaded function.   1. ss_str(rosetta.protocols.frag_picker.VallResidue) -> str   one letter secondary structure STR code   2. ss_str(self : rosetta.protocols.frag_picker.VallResidue, c : str) -> NoneType   one letter secondary structure STR code x(...) from builtins.PyCapsule x(*args, **kwargs) Overloaded function.   1. x(rosetta.protocols.frag_picker.VallResidue) -> float   x-coordinate of C-alpha   2. x(self : rosetta.protocols.frag_picker.VallResidue, val : float) -> NoneType   x-coordinate of C-alpha y(...) from builtins.PyCapsule y(*args, **kwargs) Overloaded function.   1. y(rosetta.protocols.frag_picker.VallResidue) -> float   y-coordinate of C-alpha   2. y(self : rosetta.protocols.frag_picker.VallResidue, val : float) -> NoneType   y-coordinate of C-alpha z(...) from builtins.PyCapsule z(*args, **kwargs) Overloaded function.   1. z(rosetta.protocols.frag_picker.VallResidue) -> float   z-coordinate of C-alpha   2. z(self : rosetta.protocols.frag_picker.VallResidue, val : float) -> NoneType   z-coordinate of C-alpha

Functions
		contact_name(...) method of builtins.PyCapsule instance contact_name(type : rosetta.protocols.frag_picker.ContactType) -> str   ////////////////////////////////////////////////////      give an enum type and return the string name //////////////////////////////////////////////////// contact_type(...) method of builtins.PyCapsule instance contact_type(name : str) -> rosetta.protocols.frag_picker.ContactType   ///////////////////////////////////////////////////////      give a string name and return its enum type /////////////////////////////////////////////////////// sa_faraggi_max(...) method of builtins.PyCapsule instance sa_faraggi_max(aa : str) -> float

Data
		CA = ContactType.CA CB = ContactType.CB CEN = ContactType.CEN UNK = ContactType.num_contact_types num_contact_types = ContactType.num_contact_types