Bindings for protocols::antibody::grafting namespace

Classes
		builtins.object AntibodyChain AntibodyChainNumbering AntibodyFramework AntibodyNumbering AntibodySequence CDR_Bounds Chothia_Numberer FRH_FRL Numberer SCS_Functor SCS_BlastFilter_by_OCD SCS_BlastFilter_by_alignment_length SCS_BlastFilter_by_outlier SCS_BlastFilter_by_sequence_identity SCS_BlastFilter_by_sequence_length SCS_BlastFilter_by_template_bfactor SCS_BlastFilter_by_template_resolution SCS_Comparator SCS_BlastComparator SCS_BlastComparator_BitScore_Resolution SCS_Result SCS_Antibody_Database_Result SCS_BlastResult SCS_SubstitutionMatrixResult SCS_ResultSet SCS_Results rosetta.basic.Reporter(builtins.object) CDR_Detector RegEx_based_CDR_Detector SCS_Base SCS_LoopOverSCs SCS_BlastPlus SCS_SubstitutionMatrix SCS_MultiTemplate rosetta.utility.SingletonBase_protocols_antibody_grafting_SCS_Helper_t(builtins.object) SCS_Helper rosetta.utility.vector0_std_shared_ptr_protocols_antibody_grafting_SCS_Result_t(builtins.object) SCS_ResultVector rosetta.utility.excn.EXCN_Msg_Exception(rosetta.utility.excn.EXCN_Exception) Grafting_Base_Exception   class AntibodyChain(builtins.object)     Hold information about heavy or light antibody chain. This include:     - loop info (though CDR_Bounds cdr*)     - sequnce     Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(self : rosetta.protocols.antibody.grafting.AntibodyChain, sequence_ : str) -> NoneType   2. __init__(self : rosetta.protocols.antibody.grafting.AntibodyChain,  : rosetta.protocols.antibody.grafting.AntibodyChain) -> 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.antibody.grafting.AntibodyChain,  : rosetta.protocols.antibody.grafting.AntibodyChain) -> rosetta.protocols.antibody.grafting.AntibodyChain cdr1_sequence(...) from builtins.PyCapsule cdr1_sequence(rosetta.protocols.antibody.grafting.AntibodyChain) -> str   Calculate CDR sequence      _AE_cdr_undefined_ if reuested CDR regions is not defined.      _AE_invalid_cdr_region_ if CDR sequence out of bound of Chain sequence cdr2_sequence(...) from builtins.PyCapsule cdr2_sequence(rosetta.protocols.antibody.grafting.AntibodyChain) -> str cdr3_sequence(...) from builtins.PyCapsule cdr3_sequence(rosetta.protocols.antibody.grafting.AntibodyChain) -> str validate(...) from builtins.PyCapsule validate(rosetta.protocols.antibody.grafting.AntibodyChain) -> NoneType   validate CDR sequence's      _AE_cdr_undefined_ if reuested CDR regions is not defined.      _AE_invalid_cdr_region_ if CDR sequence out of bound of Chain sequence Data descriptors defined here: cdr1 cdr2 cdr3 sequence   class AntibodyChainNumbering(builtins.object)       Methods defined here: __init__(...) from builtins.PyCapsule __init__(rosetta.protocols.antibody.grafting.AntibodyChainNumbering) -> 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.antibody.grafting.AntibodyChainNumbering) -> str all(...) from builtins.PyCapsule all(rosetta.protocols.antibody.grafting.AntibodyChainNumbering) -> rosetta.utility.vector0_std_string validate(...) from builtins.PyCapsule validate(self : rosetta.protocols.antibody.grafting.AntibodyChainNumbering,  : rosetta.protocols.antibody.grafting.AntibodyChain,  : rosetta.protocols.antibody.grafting.AntibodyFramework, chain_id : str) -> NoneType   Check if numbering array length match content of AntibodyChain and AntibodyFramework      throws _AE_unexpected_region_length_ if mismatch detected Data descriptors defined here: cdr1 cdr2 cdr3 fr1 fr2 fr3 fr4   class AntibodyFramework(builtins.object)       Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.protocols.antibody.grafting.AntibodyFramework) -> NoneType   2. __init__(self : rosetta.protocols.antibody.grafting.AntibodyFramework,  : rosetta.protocols.antibody.grafting.AntibodyFramework) -> 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.antibody.grafting.AntibodyFramework) -> str assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.antibody.grafting.AntibodyFramework,  : rosetta.protocols.antibody.grafting.AntibodyFramework) -> rosetta.protocols.antibody.grafting.AntibodyFramework update_sequences(...) from builtins.PyCapsule update_sequences(self : rosetta.protocols.antibody.grafting.AntibodyFramework, chain_sequence : str) -> NoneType   update fr1/4 sequences.      _AE_invalid_cdr_region_ if CDR sequence out of bound of Chain sequence Data descriptors defined here: fr1 fr1_begin fr1_end fr2 fr2_begin fr2_end fr3 fr3_begin fr3_end fr4 fr4_begin fr4_end   class AntibodyNumbering(builtins.object)       Methods defined here: __init__(...) from builtins.PyCapsule __init__(rosetta.protocols.antibody.grafting.AntibodyNumbering) -> 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.antibody.grafting.AntibodyNumbering) -> str Data descriptors defined here: heavy light   class AntibodySequence(builtins.object)     Hold info about whole antibody sequence: heavy and light chains. This is basially a convenience class     Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.protocols.antibody.grafting.AntibodySequence) -> NoneType   2. __init__(self : rosetta.protocols.antibody.grafting.AntibodySequence, heavy_ : str, light_ : str) -> NoneType   3. __init__(self : rosetta.protocols.antibody.grafting.AntibodySequence,  : rosetta.protocols.antibody.grafting.AntibodySequence) -> 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.antibody.grafting.AntibodySequence,  : rosetta.protocols.antibody.grafting.AntibodySequence) -> rosetta.protocols.antibody.grafting.AntibodySequence h1_sequence(...) from builtins.PyCapsule h1_sequence(rosetta.protocols.antibody.grafting.AntibodySequence) -> str   Calculate CDR sequence      _AE_cdr_undefined_ if reuested CDR regions is not defined.      _AE_invalid_cdr_region_ if CDR sequence out of bound of Chain sequence h2_sequence(...) from builtins.PyCapsule h2_sequence(rosetta.protocols.antibody.grafting.AntibodySequence) -> str h3_sequence(...) from builtins.PyCapsule h3_sequence(rosetta.protocols.antibody.grafting.AntibodySequence) -> str heavy_framework(...) from builtins.PyCapsule heavy_framework(rosetta.protocols.antibody.grafting.AntibodySequence) -> rosetta.protocols.antibody.grafting.AntibodyFramework   Calculate Framework sequence's by using CDR's CDR_Bounds info      _AE_cdr_undefined_ if reuested CDR regions is not defined.      _AE_invalid_cdr_region_ if CDR sequence out of bound of Chain sequence l1_sequence(...) from builtins.PyCapsule l1_sequence(rosetta.protocols.antibody.grafting.AntibodySequence) -> str l2_sequence(...) from builtins.PyCapsule l2_sequence(rosetta.protocols.antibody.grafting.AntibodySequence) -> str l3_sequence(...) from builtins.PyCapsule l3_sequence(rosetta.protocols.antibody.grafting.AntibodySequence) -> str light_framework(...) from builtins.PyCapsule light_framework(rosetta.protocols.antibody.grafting.AntibodySequence) -> rosetta.protocols.antibody.grafting.AntibodyFramework Data descriptors defined here: heavy light   class CDR_Bounds(builtins.object)       Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.protocols.antibody.grafting.CDR_Bounds) -> NoneType   2. __init__(self : rosetta.protocols.antibody.grafting.CDR_Bounds,  : rosetta.protocols.antibody.grafting.CDR_Bounds) -> 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.antibody.grafting.CDR_Bounds) -> str assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.antibody.grafting.CDR_Bounds,  : rosetta.protocols.antibody.grafting.CDR_Bounds) -> rosetta.protocols.antibody.grafting.CDR_Bounds defined(...) from builtins.PyCapsule defined(rosetta.protocols.antibody.grafting.CDR_Bounds) -> bool   Check if current value of begin/end could be valid for some sequence size(...) from builtins.PyCapsule size(rosetta.protocols.antibody.grafting.CDR_Bounds) -> int   return size of region valid(...) from builtins.PyCapsule valid(self : rosetta.protocols.antibody.grafting.CDR_Bounds, sequence : str) -> bool   Check if current value of begin/end if valid for given sequence. Always return true if CDR undefined. validate(...) from builtins.PyCapsule validate(self : rosetta.protocols.antibody.grafting.CDR_Bounds, sequence : str) -> NoneType   validate CDR sequence      _AE_cdr_undefined_ if reuested CDR regions is not defined.      _AE_invalid_cdr_region_ if CDR sequence out of bound of Chain sequence Data descriptors defined here: begin end   class CDR_Detector(rosetta.basic.Reporter)     Base class for antibody CDR detector. Sub-class it to implement particular detection methods     Method resolution order: CDR_Detector rosetta.basic.Reporter builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(self : rosetta.protocols.antibody.grafting.CDR_Detector,  : rosetta.basic.Report) -> NoneType   2. __init__(rosetta.protocols.antibody.grafting.CDR_Detector) -> NoneType   3. __init__(rosetta.protocols.antibody.grafting.CDR_Detector, rosetta.protocols.antibody.grafting.CDR_Detector) -> 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.antibody.grafting.CDR_Detector,  : rosetta.protocols.antibody.grafting.CDR_Detector) -> rosetta.protocols.antibody.grafting.CDR_Detector detect(...) from builtins.PyCapsule detect(self : rosetta.protocols.antibody.grafting.CDR_Detector,  : rosetta.protocols.antibody.grafting.AntibodySequence) -> NoneType   Detect CDR's      _AE_cdr_detection_failed_ if for some of the loops detection failed   class Chothia_Numberer(builtins.object)     Use RegEx and antibody sequence information to detect CDR's     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.antibody.grafting.Chothia_Numberer,  : rosetta.protocols.antibody.grafting.Chothia_Numberer) -> rosetta.protocols.antibody.grafting.Chothia_Numberer number(...) from builtins.PyCapsule number(self : rosetta.protocols.antibody.grafting.Chothia_Numberer,  : rosetta.protocols.antibody.grafting.AntibodySequence, heavy_fr : rosetta.protocols.antibody.grafting.AntibodyFramework, light_fr : rosetta.protocols.antibody.grafting.AntibodyFramework) -> rosetta.protocols.antibody.grafting.AntibodyNumbering   Detect CDR's      _AE_unexpected_cdr_region_ (sub-class of _AE_numbering_failed_) if numbering is fails      _AE_cdr_undefined_ if reuested CDR regions is not defined.      _AE_invalid_cdr_region_ if CDR sequence out of bound of Chain sequence number_heavy_chain(...) from builtins.PyCapsule number_heavy_chain(self : rosetta.protocols.antibody.grafting.Chothia_Numberer,  : rosetta.protocols.antibody.grafting.AntibodySequence, heavy_fr : rosetta.protocols.antibody.grafting.AntibodyFramework) -> rosetta.protocols.antibody.grafting.AntibodyChainNumbering number_light_chain(...) from builtins.PyCapsule number_light_chain(self : rosetta.protocols.antibody.grafting.Chothia_Numberer,  : rosetta.protocols.antibody.grafting.AntibodySequence, light_fr : rosetta.protocols.antibody.grafting.AntibodyFramework) -> rosetta.protocols.antibody.grafting.AntibodyChainNumbering   class FRH_FRL(builtins.object)       Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.protocols.antibody.grafting.FRH_FRL) -> NoneType   2. __init__(self : rosetta.protocols.antibody.grafting.FRH_FRL,  : rosetta.protocols.antibody.grafting.FRH_FRL) -> 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.antibody.grafting.FRH_FRL,  : rosetta.protocols.antibody.grafting.FRH_FRL) -> rosetta.protocols.antibody.grafting.FRH_FRL Data descriptors defined here: frh1 frh2 frh3 frh4 frl1 frl2 frl3 frl4   class Grafting_Base_Exception(rosetta.utility.excn.EXCN_Msg_Exception)       Method resolution order: Grafting_Base_Exception rosetta.utility.excn.EXCN_Msg_Exception rosetta.utility.excn.EXCN_Exception rosetta.utility.excn.EXCN_Base builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle) -> NoneType   2. __init__(self : handle, msg : str) -> NoneType   3. __init__(handle, rosetta.protocols.antibody.grafting.Grafting_Base_Exception) -> 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.antibody.grafting.Grafting_Base_Exception,  : rosetta.protocols.antibody.grafting.Grafting_Base_Exception) -> rosetta.protocols.antibody.grafting.Grafting_Base_Exception Methods inherited from rosetta.utility.excn.EXCN_Msg_Exception: add_msg(...) from builtins.PyCapsule add_msg(self : rosetta.utility.excn.EXCN_Msg_Exception, str : str) -> NoneType msg(...) from builtins.PyCapsule msg(rosetta.utility.excn.EXCN_Msg_Exception) -> str Methods inherited from rosetta.utility.excn.EXCN_Base: __str__(...) from builtins.PyCapsule __str__(rosetta.utility.excn.EXCN_Base) -> str   class Numberer(builtins.object)     Base class for antibody CDR detector. Sub-class it to implement particular detection methods     Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.protocols.antibody.grafting.Numberer) -> NoneType   2. __init__(rosetta.protocols.antibody.grafting.Numberer, rosetta.protocols.antibody.grafting.Numberer) -> 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.antibody.grafting.Numberer,  : rosetta.protocols.antibody.grafting.Numberer) -> rosetta.protocols.antibody.grafting.Numberer number(...) from builtins.PyCapsule number(self : rosetta.protocols.antibody.grafting.Numberer,  : rosetta.protocols.antibody.grafting.AntibodySequence, heavy_fr : rosetta.protocols.antibody.grafting.AntibodyFramework, light_fr : rosetta.protocols.antibody.grafting.AntibodyFramework) -> rosetta.protocols.antibody.grafting.AntibodyNumbering   Number CDR's      _AE_unexpected_cdr_region_ (or it sub-class) if numbering is fails      _AE_cdr_undefined_ if reuested CDR regions is not defined.      _AE_invalid_cdr_region_ if CDR sequence out of bound of Chain sequence   class RegEx_based_CDR_Detector(CDR_Detector)     Use RegEx and antibody sequence information to detect CDR's     Method resolution order: RegEx_based_CDR_Detector CDR_Detector rosetta.basic.Reporter builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle) -> NoneType   2. __init__(self : handle,  : rosetta.basic.Report) -> 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.antibody.grafting.RegEx_based_CDR_Detector,  : rosetta.protocols.antibody.grafting.RegEx_based_CDR_Detector) -> rosetta.protocols.antibody.grafting.RegEx_based_CDR_Detector detect(...) from builtins.PyCapsule detect(self : rosetta.protocols.antibody.grafting.RegEx_based_CDR_Detector,  : rosetta.protocols.antibody.grafting.AntibodySequence) -> NoneType   Detect CDR's      _AE_cdr_detection_failed_ if for some of the loops detection failed detect_heavy_chain(...) from builtins.PyCapsule detect_heavy_chain(self : rosetta.protocols.antibody.grafting.RegEx_based_CDR_Detector,  : rosetta.protocols.antibody.grafting.AntibodySequence) -> NoneType detect_light_chain(...) from builtins.PyCapsule detect_light_chain(self : rosetta.protocols.antibody.grafting.RegEx_based_CDR_Detector,  : rosetta.protocols.antibody.grafting.AntibodySequence) -> NoneType   class SCS_Antibody_Database_Result(SCS_Result)       Method resolution order: SCS_Antibody_Database_Result SCS_Result builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.protocols.antibody.grafting.SCS_Antibody_Database_Result) -> NoneType   2. __init__(self : rosetta.protocols.antibody.grafting.SCS_Antibody_Database_Result,  : rosetta.protocols.antibody.grafting.SCS_Antibody_Database_Result) -> 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.antibody.grafting.SCS_Antibody_Database_Result,  : rosetta.protocols.antibody.grafting.SCS_Antibody_Database_Result) -> rosetta.protocols.antibody.grafting.SCS_Antibody_Database_Result Data descriptors defined here: bio_type frh frl h1 h2 h3 l1 l2 l3 light_type resolution struct_source Data descriptors inherited from SCS_Result: padded pdb   class SCS_Base(rosetta.basic.Reporter)       Method resolution order: SCS_Base rosetta.basic.Reporter builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(self : rosetta.protocols.antibody.grafting.SCS_Base,  : rosetta.basic.Report) -> NoneType   2. __init__(rosetta.protocols.antibody.grafting.SCS_Base) -> NoneType   3. __init__(rosetta.protocols.antibody.grafting.SCS_Base, rosetta.protocols.antibody.grafting.SCS_Base) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. add_filter(...) from builtins.PyCapsule add_filter(self : rosetta.protocols.antibody.grafting.SCS_Base, filter : protocols::antibody::grafting::SCS_Functor) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.antibody.grafting.SCS_Base,  : rosetta.protocols.antibody.grafting.SCS_Base) -> rosetta.protocols.antibody.grafting.SCS_Base pad_results(...) from builtins.PyCapsule pad_results(self : rosetta.protocols.antibody.grafting.SCS_Base, n : int,  : rosetta.protocols.antibody.grafting.AntibodySequence,  : rosetta.protocols.antibody.grafting.SCS_Results) -> NoneType   Pad results vectors for each region (if possible) by adding arbitraty but compatible templates so at least n templates for each region is avalible raw_select(...) from builtins.PyCapsule raw_select(self : rosetta.protocols.antibody.grafting.SCS_Base,  : rosetta.protocols.antibody.grafting.AntibodySequence) -> rosetta.protocols.antibody.grafting.SCS_Results   Select CDR's template without filtering or sorting. In general you probably need to call select(...) instead      _AE_scs_failed_ on failure select(...) from builtins.PyCapsule select(self : rosetta.protocols.antibody.grafting.SCS_Base, n : int,  : rosetta.protocols.antibody.grafting.AntibodySequence) -> rosetta.protocols.antibody.grafting.SCS_Results   Select CDR's template, filter it and sort. Try to provide at least 'n' templates if possible      _AE_scs_failed_ on failure set_sorter(...) from builtins.PyCapsule set_sorter(self : rosetta.protocols.antibody.grafting.SCS_Base, sorter : protocols::antibody::grafting::SCS_Functor) -> NoneType   class SCS_BlastComparator(SCS_Comparator)       Method resolution order: SCS_BlastComparator SCS_Comparator SCS_Functor builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(rosetta.protocols.antibody.grafting.SCS_BlastComparator) -> 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.antibody.grafting.SCS_BlastComparator,  : rosetta.protocols.antibody.grafting.SCS_BlastComparator) -> rosetta.protocols.antibody.grafting.SCS_BlastComparator compare(...) from builtins.PyCapsule compare(*args, **kwargs) Overloaded function.   1. compare(self : rosetta.protocols.antibody.grafting.SCS_BlastComparator, antibody_sequence : rosetta.protocols.antibody.grafting.AntibodySequence, a : rosetta.protocols.antibody.grafting.SCS_Result, b : rosetta.protocols.antibody.grafting.SCS_Result) -> bool   2. compare(self : rosetta.protocols.antibody.grafting.SCS_BlastComparator, antibody_sequence : rosetta.protocols.antibody.grafting.AntibodySequence, a : rosetta.protocols.antibody.grafting.SCS_BlastResult, b : rosetta.protocols.antibody.grafting.SCS_BlastResult) -> bool Methods inherited from SCS_Comparator: apply(...) from builtins.PyCapsule apply(self : rosetta.protocols.antibody.grafting.SCS_Comparator, antibody_sequence : rosetta.protocols.antibody.grafting.AntibodySequence, results : rosetta.protocols.antibody.grafting.SCS_Results) -> NoneType   class SCS_BlastComparator_BitScore_Resolution(SCS_BlastComparator)       Method resolution order: SCS_BlastComparator_BitScore_Resolution SCS_BlastComparator SCS_Comparator SCS_Functor 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.antibody.grafting.SCS_BlastComparator_BitScore_Resolution,  : rosetta.protocols.antibody.grafting.SCS_BlastComparator_BitScore_Resolution) -> rosetta.protocols.antibody.grafting.SCS_BlastComparator_BitScore_Resolution compare(...) from builtins.PyCapsule compare(self : rosetta.protocols.antibody.grafting.SCS_BlastComparator_BitScore_Resolution,  : rosetta.protocols.antibody.grafting.AntibodySequence, a : rosetta.protocols.antibody.grafting.SCS_BlastResult, b : rosetta.protocols.antibody.grafting.SCS_BlastResult) -> bool Methods inherited from SCS_Comparator: apply(...) from builtins.PyCapsule apply(self : rosetta.protocols.antibody.grafting.SCS_Comparator, antibody_sequence : rosetta.protocols.antibody.grafting.AntibodySequence, results : rosetta.protocols.antibody.grafting.SCS_Results) -> NoneType   class SCS_BlastFilter_by_OCD(SCS_Functor)       Method resolution order: SCS_BlastFilter_by_OCD SCS_Functor 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. apply(...) from builtins.PyCapsule apply(self : rosetta.protocols.antibody.grafting.SCS_BlastFilter_by_OCD, antibody_sequence : rosetta.protocols.antibody.grafting.AntibodySequence, results : rosetta.protocols.antibody.grafting.SCS_Results) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.antibody.grafting.SCS_BlastFilter_by_OCD,  : rosetta.protocols.antibody.grafting.SCS_BlastFilter_by_OCD) -> rosetta.protocols.antibody.grafting.SCS_BlastFilter_by_OCD get_n_orientational_templates(...) from builtins.PyCapsule get_n_orientational_templates(rosetta.protocols.antibody.grafting.SCS_BlastFilter_by_OCD) -> int get_ocd_cutoff(...) from builtins.PyCapsule get_ocd_cutoff(rosetta.protocols.antibody.grafting.SCS_BlastFilter_by_OCD) -> float init_from_options(...) from builtins.PyCapsule init_from_options(rosetta.protocols.antibody.grafting.SCS_BlastFilter_by_OCD) -> NoneType set_n_orientational_templates(...) from builtins.PyCapsule set_n_orientational_templates(self : rosetta.protocols.antibody.grafting.SCS_BlastFilter_by_OCD, n : int) -> NoneType set_ocd_cutoff(...) from builtins.PyCapsule set_ocd_cutoff(self : rosetta.protocols.antibody.grafting.SCS_BlastFilter_by_OCD, cutoff : float) -> NoneType   class SCS_BlastFilter_by_alignment_length(SCS_Functor)       Method resolution order: SCS_BlastFilter_by_alignment_length SCS_Functor 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. apply(...) from builtins.PyCapsule apply(self : rosetta.protocols.antibody.grafting.SCS_BlastFilter_by_alignment_length, antibody_sequence : rosetta.protocols.antibody.grafting.AntibodySequence, results : rosetta.protocols.antibody.grafting.SCS_Results) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.antibody.grafting.SCS_BlastFilter_by_alignment_length,  : rosetta.protocols.antibody.grafting.SCS_BlastFilter_by_alignment_length) -> rosetta.protocols.antibody.grafting.SCS_BlastFilter_by_alignment_length   class SCS_BlastFilter_by_outlier(SCS_Functor)       Method resolution order: SCS_BlastFilter_by_outlier SCS_Functor 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. apply(...) from builtins.PyCapsule apply(self : rosetta.protocols.antibody.grafting.SCS_BlastFilter_by_outlier, antibody_sequence : rosetta.protocols.antibody.grafting.AntibodySequence, results : rosetta.protocols.antibody.grafting.SCS_Results) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.antibody.grafting.SCS_BlastFilter_by_outlier,  : rosetta.protocols.antibody.grafting.SCS_BlastFilter_by_outlier) -> rosetta.protocols.antibody.grafting.SCS_BlastFilter_by_outlier   class SCS_BlastFilter_by_sequence_identity(SCS_Functor)       Method resolution order: SCS_BlastFilter_by_sequence_identity SCS_Functor 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. apply(...) from builtins.PyCapsule apply(self : rosetta.protocols.antibody.grafting.SCS_BlastFilter_by_sequence_identity, antibody_sequence : rosetta.protocols.antibody.grafting.AntibodySequence, results : rosetta.protocols.antibody.grafting.SCS_Results) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.antibody.grafting.SCS_BlastFilter_by_sequence_identity,  : rosetta.protocols.antibody.grafting.SCS_BlastFilter_by_sequence_identity) -> rosetta.protocols.antibody.grafting.SCS_BlastFilter_by_sequence_identity get_sid_cutoff_cdr(...) from builtins.PyCapsule get_sid_cutoff_cdr(rosetta.protocols.antibody.grafting.SCS_BlastFilter_by_sequence_identity) -> float get_sid_cutoff_fr(...) from builtins.PyCapsule get_sid_cutoff_fr(rosetta.protocols.antibody.grafting.SCS_BlastFilter_by_sequence_identity) -> float init_from_options(...) from builtins.PyCapsule init_from_options(rosetta.protocols.antibody.grafting.SCS_BlastFilter_by_sequence_identity) -> NoneType set_sid_cutoff_cdr(...) from builtins.PyCapsule set_sid_cutoff_cdr(self : rosetta.protocols.antibody.grafting.SCS_BlastFilter_by_sequence_identity, cutoff : float) -> NoneType set_sid_cutoff_fr(...) from builtins.PyCapsule set_sid_cutoff_fr(self : rosetta.protocols.antibody.grafting.SCS_BlastFilter_by_sequence_identity, cutoff : float) -> NoneType   class SCS_BlastFilter_by_sequence_length(SCS_Functor)       Method resolution order: SCS_BlastFilter_by_sequence_length SCS_Functor 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. apply(...) from builtins.PyCapsule apply(self : rosetta.protocols.antibody.grafting.SCS_BlastFilter_by_sequence_length, antibody_sequence : rosetta.protocols.antibody.grafting.AntibodySequence, results : rosetta.protocols.antibody.grafting.SCS_Results) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.antibody.grafting.SCS_BlastFilter_by_sequence_length,  : rosetta.protocols.antibody.grafting.SCS_BlastFilter_by_sequence_length) -> rosetta.protocols.antibody.grafting.SCS_BlastFilter_by_sequence_length   class SCS_BlastFilter_by_template_bfactor(SCS_Functor)       Method resolution order: SCS_BlastFilter_by_template_bfactor SCS_Functor 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. apply(...) from builtins.PyCapsule apply(self : rosetta.protocols.antibody.grafting.SCS_BlastFilter_by_template_bfactor, antibody_sequence : rosetta.protocols.antibody.grafting.AntibodySequence, results : rosetta.protocols.antibody.grafting.SCS_Results) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.antibody.grafting.SCS_BlastFilter_by_template_bfactor,  : rosetta.protocols.antibody.grafting.SCS_BlastFilter_by_template_bfactor) -> rosetta.protocols.antibody.grafting.SCS_BlastFilter_by_template_bfactor   class SCS_BlastFilter_by_template_resolution(SCS_Functor)       Method resolution order: SCS_BlastFilter_by_template_resolution SCS_Functor 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. apply(...) from builtins.PyCapsule apply(self : rosetta.protocols.antibody.grafting.SCS_BlastFilter_by_template_resolution, antibody_sequence : rosetta.protocols.antibody.grafting.AntibodySequence, results : rosetta.protocols.antibody.grafting.SCS_Results) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.antibody.grafting.SCS_BlastFilter_by_template_resolution,  : rosetta.protocols.antibody.grafting.SCS_BlastFilter_by_template_resolution) -> rosetta.protocols.antibody.grafting.SCS_BlastFilter_by_template_resolution get_resolution_cutoff(...) from builtins.PyCapsule get_resolution_cutoff(rosetta.protocols.antibody.grafting.SCS_BlastFilter_by_template_resolution) -> float set_resolution_cutoff(...) from builtins.PyCapsule set_resolution_cutoff(self : rosetta.protocols.antibody.grafting.SCS_BlastFilter_by_template_resolution, cutoff : float) -> NoneType   class SCS_BlastPlus(SCS_LoopOverSCs)       Method resolution order: SCS_BlastPlus SCS_LoopOverSCs SCS_Base rosetta.basic.Reporter builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle) -> NoneType   2. __init__(handle, rosetta.protocols.antibody.grafting.SCS_BlastPlus) -> NoneType   3. __init__(self : handle,  : rosetta.basic.Report) -> 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.antibody.grafting.SCS_BlastPlus,  : rosetta.protocols.antibody.grafting.SCS_BlastPlus) -> rosetta.protocols.antibody.grafting.SCS_BlastPlus init_from_options(...) from builtins.PyCapsule init_from_options(rosetta.protocols.antibody.grafting.SCS_BlastPlus) -> NoneType   set working dir/output-prefix for intermediate files based on command-line options pad_results(...) from builtins.PyCapsule pad_results(self : rosetta.protocols.antibody.grafting.SCS_BlastPlus, n : int,  : rosetta.protocols.antibody.grafting.AntibodySequence,  : rosetta.protocols.antibody.grafting.SCS_Results) -> NoneType   Pad results vectors for each region (if possible) by adding arbitraty but compatible templates so at least n templates for each region is avalible set_blastp_executable(...) from builtins.PyCapsule set_blastp_executable(self : rosetta.protocols.antibody.grafting.SCS_BlastPlus, blastp : str) -> NoneType   set path to NCBI-Blast+ executable set_output_prefix(...) from builtins.PyCapsule set_output_prefix(self : rosetta.protocols.antibody.grafting.SCS_BlastPlus, prefix : str) -> NoneType   set custom working dir/output-prefix for intermediate files Methods inherited from SCS_LoopOverSCs: raw_select(...) from builtins.PyCapsule raw_select(self : rosetta.protocols.antibody.grafting.SCS_LoopOverSCs,  : rosetta.protocols.antibody.grafting.AntibodySequence) -> rosetta.protocols.antibody.grafting.SCS_Results   Select CDR's template      _AE_scs_failed_ on failure set_database_path(...) from builtins.PyCapsule set_database_path(self : rosetta.protocols.antibody.grafting.SCS_LoopOverSCs, database : str) -> NoneType   set path to antibody grafting database root, should point to tools/antibody Methods inherited from SCS_Base: add_filter(...) from builtins.PyCapsule add_filter(self : rosetta.protocols.antibody.grafting.SCS_Base, filter : protocols::antibody::grafting::SCS_Functor) -> NoneType select(...) from builtins.PyCapsule select(self : rosetta.protocols.antibody.grafting.SCS_Base, n : int,  : rosetta.protocols.antibody.grafting.AntibodySequence) -> rosetta.protocols.antibody.grafting.SCS_Results   Select CDR's template, filter it and sort. Try to provide at least 'n' templates if possible      _AE_scs_failed_ on failure set_sorter(...) from builtins.PyCapsule set_sorter(self : rosetta.protocols.antibody.grafting.SCS_Base, sorter : protocols::antibody::grafting::SCS_Functor) -> NoneType   class SCS_BlastResult(SCS_Antibody_Database_Result)       Method resolution order: SCS_BlastResult SCS_Antibody_Database_Result SCS_Result builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.protocols.antibody.grafting.SCS_BlastResult) -> NoneType   2. __init__(self : rosetta.protocols.antibody.grafting.SCS_BlastResult,  : rosetta.protocols.antibody.grafting.SCS_BlastResult) -> 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.antibody.grafting.SCS_BlastResult,  : rosetta.protocols.antibody.grafting.SCS_BlastResult) -> rosetta.protocols.antibody.grafting.SCS_BlastResult Data descriptors defined here: alignment_length bit_score identity Data descriptors inherited from SCS_Antibody_Database_Result: bio_type frh frl h1 h2 h3 l1 l2 l3 light_type resolution struct_source Data descriptors inherited from SCS_Result: padded pdb   class SCS_Comparator(SCS_Functor)       Method resolution order: SCS_Comparator SCS_Functor builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(rosetta.protocols.antibody.grafting.SCS_Comparator) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. apply(...) from builtins.PyCapsule apply(self : rosetta.protocols.antibody.grafting.SCS_Comparator, antibody_sequence : rosetta.protocols.antibody.grafting.AntibodySequence, results : rosetta.protocols.antibody.grafting.SCS_Results) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.antibody.grafting.SCS_Comparator,  : rosetta.protocols.antibody.grafting.SCS_Comparator) -> rosetta.protocols.antibody.grafting.SCS_Comparator compare(...) from builtins.PyCapsule compare(self : rosetta.protocols.antibody.grafting.SCS_Comparator, antibody_sequence : rosetta.protocols.antibody.grafting.AntibodySequence, a : rosetta.protocols.antibody.grafting.SCS_Result, b : rosetta.protocols.antibody.grafting.SCS_Result) -> bool   class SCS_Functor(builtins.object)       Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.protocols.antibody.grafting.SCS_Functor) -> NoneType   2. __init__(rosetta.protocols.antibody.grafting.SCS_Functor, rosetta.protocols.antibody.grafting.SCS_Functor) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. apply(...) from builtins.PyCapsule apply(self : rosetta.protocols.antibody.grafting.SCS_Functor, antibody_sequence : rosetta.protocols.antibody.grafting.AntibodySequence, results : rosetta.protocols.antibody.grafting.SCS_Results) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.antibody.grafting.SCS_Functor,  : rosetta.protocols.antibody.grafting.SCS_Functor) -> rosetta.protocols.antibody.grafting.SCS_Functor   class SCS_Helper(rosetta.utility.SingletonBase_protocols_antibody_grafting_SCS_Helper_t)     This class is a singleton and manages data that is necessary for SCS filters and should be read only once     Method resolution order: SCS_Helper rosetta.utility.SingletonBase_protocols_antibody_grafting_SCS_Helper_t builtins.object Methods defined here: __init__(self, /, *args, **kwargs) Initialize self.  See help(type(self)) for accurate signature. __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. get_ab_OCDs(...) from builtins.PyCapsule get_ab_OCDs() -> rosetta.std.map_std_string_std_map_std_string_double_std_less_std_string_std_allocator_std_pair_const_std_string_double_t   Return a map of pdb to map of pdb to a float (OCD distance between the two pdbs) get_ab_cdr_bfactors(...) from builtins.PyCapsule get_ab_cdr_bfactors() -> rosetta.std.map_std_string_std_map_std_string_bool_std_less_std_string_std_allocator_std_pair_const_std_string_bool_t   Return a map of pdb to map of CDR to bool (true if bfactor cutoff is NOT met) get_ab_region_outliers(...) from builtins.PyCapsule get_ab_region_outliers() -> rosetta.std.map_std_string_std_map_std_string_bool_std_less_std_string_std_allocator_std_pair_const_std_string_bool_t   Return a map of pdb to map of CDR to bool (true if region is outlier) Methods inherited from rosetta.utility.SingletonBase_protocols_antibody_grafting_SCS_Helper_t: get_instance(...) from builtins.PyCapsule get_instance() -> protocols::antibody::grafting::SCS_Helper   class SCS_LoopOverSCs(SCS_Base)       Method resolution order: SCS_LoopOverSCs SCS_Base rosetta.basic.Reporter builtins.object Methods defined here: __init__(self, /, *args, **kwargs) Initialize self.  See help(type(self)) for accurate signature. __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.antibody.grafting.SCS_LoopOverSCs,  : rosetta.protocols.antibody.grafting.SCS_LoopOverSCs) -> rosetta.protocols.antibody.grafting.SCS_LoopOverSCs init_from_options(...) from builtins.PyCapsule init_from_options(rosetta.protocols.antibody.grafting.SCS_LoopOverSCs) -> NoneType   set working dir/output-prefix for intermediate files based on command-line options raw_select(...) from builtins.PyCapsule raw_select(self : rosetta.protocols.antibody.grafting.SCS_LoopOverSCs,  : rosetta.protocols.antibody.grafting.AntibodySequence) -> rosetta.protocols.antibody.grafting.SCS_Results   Select CDR's template      _AE_scs_failed_ on failure set_database_path(...) from builtins.PyCapsule set_database_path(self : rosetta.protocols.antibody.grafting.SCS_LoopOverSCs, database : str) -> NoneType   set path to antibody grafting database root, should point to tools/antibody Methods inherited from SCS_Base: add_filter(...) from builtins.PyCapsule add_filter(self : rosetta.protocols.antibody.grafting.SCS_Base, filter : protocols::antibody::grafting::SCS_Functor) -> NoneType pad_results(...) from builtins.PyCapsule pad_results(self : rosetta.protocols.antibody.grafting.SCS_Base, n : int,  : rosetta.protocols.antibody.grafting.AntibodySequence,  : rosetta.protocols.antibody.grafting.SCS_Results) -> NoneType   Pad results vectors for each region (if possible) by adding arbitraty but compatible templates so at least n templates for each region is avalible select(...) from builtins.PyCapsule select(self : rosetta.protocols.antibody.grafting.SCS_Base, n : int,  : rosetta.protocols.antibody.grafting.AntibodySequence) -> rosetta.protocols.antibody.grafting.SCS_Results   Select CDR's template, filter it and sort. Try to provide at least 'n' templates if possible      _AE_scs_failed_ on failure set_sorter(...) from builtins.PyCapsule set_sorter(self : rosetta.protocols.antibody.grafting.SCS_Base, sorter : protocols::antibody::grafting::SCS_Functor) -> NoneType   class SCS_MultiTemplate(SCS_Base)     Proxy-like class for SCS_Base that alter SCS results: - for results not in 'regions_' return top result obtained from source_ - for results in 'regions_' return N best results     Method resolution order: SCS_MultiTemplate SCS_Base rosetta.basic.Reporter builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle, rosetta.protocols.antibody.grafting.SCS_Base) -> NoneType   doc   2. __init__(handle, rosetta.protocols.antibody.grafting.SCS_Base, rosetta.utility.vector0_std_string) -> NoneType   doc   3. __init__(self : handle, source : rosetta.protocols.antibody.grafting.SCS_Base, regions : rosetta.utility.vector0_std_string, report : rosetta.basic.Report) -> 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.antibody.grafting.SCS_MultiTemplate,  : rosetta.protocols.antibody.grafting.SCS_MultiTemplate) -> rosetta.protocols.antibody.grafting.SCS_MultiTemplate pad_results(...) from builtins.PyCapsule pad_results(self : rosetta.protocols.antibody.grafting.SCS_MultiTemplate,  : int,  : rosetta.protocols.antibody.grafting.AntibodySequence,  : rosetta.protocols.antibody.grafting.SCS_Results) -> NoneType   Pad results vectors for each region (if possible) by adding arbitraty but compatible templates so at least n templates for each region is avalible raw_select(...) from builtins.PyCapsule raw_select(self : rosetta.protocols.antibody.grafting.SCS_MultiTemplate,  : rosetta.protocols.antibody.grafting.AntibodySequence) -> rosetta.protocols.antibody.grafting.SCS_Results   Select CDR's template without filtering or sorting. In general you probably need to call select(...) instead      _AE_scs_failed_ on failure select(...) from builtins.PyCapsule select(self : rosetta.protocols.antibody.grafting.SCS_MultiTemplate, n : int,  : rosetta.protocols.antibody.grafting.AntibodySequence) -> rosetta.protocols.antibody.grafting.SCS_Results   Select CDR's template, filter it and sort. Try to provide at least 'n' templates if possible      _AE_scs_failed_ on failure set_multi_template_regions(...) from builtins.PyCapsule set_multi_template_regions(self : rosetta.protocols.antibody.grafting.SCS_MultiTemplate, regions : rosetta.utility.vector0_std_string) -> NoneType   specify mutable regions for multi-template selection mode. Methods inherited from SCS_Base: add_filter(...) from builtins.PyCapsule add_filter(self : rosetta.protocols.antibody.grafting.SCS_Base, filter : protocols::antibody::grafting::SCS_Functor) -> NoneType set_sorter(...) from builtins.PyCapsule set_sorter(self : rosetta.protocols.antibody.grafting.SCS_Base, sorter : protocols::antibody::grafting::SCS_Functor) -> NoneType   class SCS_Result(builtins.object)     Base struct for any SCS single result. Hold information of selected template     Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.protocols.antibody.grafting.SCS_Result) -> NoneType   2. __init__(self : rosetta.protocols.antibody.grafting.SCS_Result,  : rosetta.protocols.antibody.grafting.SCS_Result) -> 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.antibody.grafting.SCS_Result,  : rosetta.protocols.antibody.grafting.SCS_Result) -> rosetta.protocols.antibody.grafting.SCS_Result Data descriptors defined here: padded pdb   class SCS_ResultSet(builtins.object)       Methods defined here: __init__(...) from builtins.PyCapsule __init__(rosetta.protocols.antibody.grafting.SCS_ResultSet) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. Data descriptors defined here: frh frl h1 h2 h3 l1 l2 l3 orientation   class SCS_ResultVector(rosetta.utility.vector0_std_shared_ptr_protocols_antibody_grafting_SCS_Result_t)       Method resolution order: SCS_ResultVector rosetta.utility.vector0_std_shared_ptr_protocols_antibody_grafting_SCS_Result_t builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(rosetta.protocols.antibody.grafting.SCS_ResultVector) -> 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.antibody.grafting.SCS_ResultVector,  : rosetta.protocols.antibody.grafting.SCS_ResultVector) -> rosetta.protocols.antibody.grafting.SCS_ResultVector Methods inherited from rosetta.utility.vector0_std_shared_ptr_protocols_antibody_grafting_SCS_Result_t: __bool__(...) from builtins.PyCapsule __bool__(rosetta.utility.vector0_std_shared_ptr_protocols_antibody_grafting_SCS_Result_t) -> bool   Check whether the list is nonempty __contains__(...) from builtins.PyCapsule __contains__(rosetta.utility.vector0_std_shared_ptr_protocols_antibody_grafting_SCS_Result_t, protocols::antibody::grafting::SCS_Result) -> bool   return true if item in the container __eq__(...) from builtins.PyCapsule __eq__(rosetta.utility.vector0_std_shared_ptr_protocols_antibody_grafting_SCS_Result_t, rosetta.utility.vector0_std_shared_ptr_protocols_antibody_grafting_SCS_Result_t) -> bool __getitem__(...) from builtins.PyCapsule __getitem__(rosetta.utility.vector0_std_shared_ptr_protocols_antibody_grafting_SCS_Result_t, int) -> protocols::antibody::grafting::SCS_Result __iter__(...) from builtins.PyCapsule __iter__(rosetta.utility.vector0_std_shared_ptr_protocols_antibody_grafting_SCS_Result_t) -> iterator __len__(...) from builtins.PyCapsule __len__(rosetta.utility.vector0_std_shared_ptr_protocols_antibody_grafting_SCS_Result_t) -> int __ne__(...) from builtins.PyCapsule __ne__(rosetta.utility.vector0_std_shared_ptr_protocols_antibody_grafting_SCS_Result_t, rosetta.utility.vector0_std_shared_ptr_protocols_antibody_grafting_SCS_Result_t) -> bool __repr__(...) from builtins.PyCapsule __repr__(rosetta.utility.vector0_std_shared_ptr_protocols_antibody_grafting_SCS_Result_t) -> str __setitem__(...) from builtins.PyCapsule __setitem__(rosetta.utility.vector0_std_shared_ptr_protocols_antibody_grafting_SCS_Result_t, int, protocols::antibody::grafting::SCS_Result) -> NoneType append(...) from builtins.PyCapsule append(rosetta.utility.vector0_std_shared_ptr_protocols_antibody_grafting_SCS_Result_t, protocols::antibody::grafting::SCS_Result) -> NoneType   adds an element to the end back(...) from builtins.PyCapsule back(rosetta.utility.vector0_std_shared_ptr_protocols_antibody_grafting_SCS_Result_t) -> protocols::antibody::grafting::SCS_Result   access the last element capacity(...) from builtins.PyCapsule capacity(std::vector<std::shared_ptr<protocols::antibody::grafting::SCS_Result>, std::allocator<std::shared_ptr<protocols::antibody::grafting::SCS_Result> > >) -> int   returns the number of elements that can be held in currently allocated storage clear(...) from builtins.PyCapsule clear(std::vector<std::shared_ptr<protocols::antibody::grafting::SCS_Result>, std::allocator<std::shared_ptr<protocols::antibody::grafting::SCS_Result> > >) -> NoneType   clears the contents count(...) from builtins.PyCapsule count(rosetta.utility.vector0_std_shared_ptr_protocols_antibody_grafting_SCS_Result_t, protocols::antibody::grafting::SCS_Result) -> int   counts the elements that are equal to value erase(...) from builtins.PyCapsule erase(rosetta.utility.vector0_std_shared_ptr_protocols_antibody_grafting_SCS_Result_t, int) -> NoneType   erases element at index extend = _vector_extend_func(vec, othervec) # Vector compatibility: Adding 'extend' to all utility.vector* functions front(...) from builtins.PyCapsule front(rosetta.utility.vector0_std_shared_ptr_protocols_antibody_grafting_SCS_Result_t) -> protocols::antibody::grafting::SCS_Result   access the first element l(...) from builtins.PyCapsule l(rosetta.utility.vector0_std_shared_ptr_protocols_antibody_grafting_SCS_Result_t) -> int   lower index max_size(...) from builtins.PyCapsule max_size(std::vector<std::shared_ptr<protocols::antibody::grafting::SCS_Result>, std::allocator<std::shared_ptr<protocols::antibody::grafting::SCS_Result> > >) -> int   returns the maximum possible number of elements pop(...) from builtins.PyCapsule pop(*args, **kwargs) Overloaded function.   1. pop(rosetta.utility.vector0_std_shared_ptr_protocols_antibody_grafting_SCS_Result_t) -> protocols::antibody::grafting::SCS_Result   remove and return last item   2. pop(rosetta.utility.vector0_std_shared_ptr_protocols_antibody_grafting_SCS_Result_t, int) -> protocols::antibody::grafting::SCS_Result   remove and return item at index remove(...) from builtins.PyCapsule remove(rosetta.utility.vector0_std_shared_ptr_protocols_antibody_grafting_SCS_Result_t, protocols::antibody::grafting::SCS_Result) -> NoneType   Remove the first item from the list whose value is x. It is an error if there is no such item. reserve(...) from builtins.PyCapsule reserve(std::vector<std::shared_ptr<protocols::antibody::grafting::SCS_Result>, std::allocator<std::shared_ptr<protocols::antibody::grafting::SCS_Result> > >, int) -> NoneType   reserves storage resize(...) from builtins.PyCapsule resize(rosetta.utility.vector0_std_shared_ptr_protocols_antibody_grafting_SCS_Result_t, int) -> NoneType   changes the number of elements stored shrink_to_fit(...) from builtins.PyCapsule shrink_to_fit(std::vector<std::shared_ptr<protocols::antibody::grafting::SCS_Result>, std::allocator<std::shared_ptr<protocols::antibody::grafting::SCS_Result> > >) -> NoneType   reduces memory usage by freeing unused memory u(...) from builtins.PyCapsule u(rosetta.utility.vector0_std_shared_ptr_protocols_antibody_grafting_SCS_Result_t) -> int   upper index   class SCS_Results(builtins.object)       Methods defined here: __init__(...) from builtins.PyCapsule __init__(rosetta.protocols.antibody.grafting.SCS_Results) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. get_result_set(...) from builtins.PyCapsule get_result_set(*args, **kwargs) Overloaded function.   1. get_result_set(self : rosetta.protocols.antibody.grafting.SCS_Results, row : int) -> protocols::antibody::grafting::SCS_ResultSet   Create result set from 'row' element of each SCS_ResultVector vector         if strict is true the throw if no resuls found otherwise use empty OP      std::out_of_range if for some of the row is not present and strict==true   2. get_result_set(self : rosetta.protocols.antibody.grafting.SCS_Results, row : int, strict : bool) -> protocols::antibody::grafting::SCS_ResultSet   Create result set from 'row' element of each SCS_ResultVector vector         if strict is true the throw if no resuls found otherwise use empty OP      std::out_of_range if for some of the row is not present and strict==true Data descriptors defined here: frh frl h1 h2 h3 l1 l2 l3 orientation   class SCS_SubstitutionMatrix(SCS_LoopOverSCs)       Method resolution order: SCS_SubstitutionMatrix SCS_LoopOverSCs SCS_Base rosetta.basic.Reporter builtins.object Methods defined here: __init__(self, /, *args, **kwargs) Initialize self.  See help(type(self)) for accurate signature. __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.antibody.grafting.SCS_SubstitutionMatrix,  : rosetta.protocols.antibody.grafting.SCS_SubstitutionMatrix) -> rosetta.protocols.antibody.grafting.SCS_SubstitutionMatrix init_from_options(...) from builtins.PyCapsule init_from_options(rosetta.protocols.antibody.grafting.SCS_SubstitutionMatrix) -> NoneType   set working dir/output-prefix for intermediate files based on command-line options Methods inherited from SCS_LoopOverSCs: raw_select(...) from builtins.PyCapsule raw_select(self : rosetta.protocols.antibody.grafting.SCS_LoopOverSCs,  : rosetta.protocols.antibody.grafting.AntibodySequence) -> rosetta.protocols.antibody.grafting.SCS_Results   Select CDR's template      _AE_scs_failed_ on failure set_database_path(...) from builtins.PyCapsule set_database_path(self : rosetta.protocols.antibody.grafting.SCS_LoopOverSCs, database : str) -> NoneType   set path to antibody grafting database root, should point to tools/antibody Methods inherited from SCS_Base: add_filter(...) from builtins.PyCapsule add_filter(self : rosetta.protocols.antibody.grafting.SCS_Base, filter : protocols::antibody::grafting::SCS_Functor) -> NoneType pad_results(...) from builtins.PyCapsule pad_results(self : rosetta.protocols.antibody.grafting.SCS_Base, n : int,  : rosetta.protocols.antibody.grafting.AntibodySequence,  : rosetta.protocols.antibody.grafting.SCS_Results) -> NoneType   Pad results vectors for each region (if possible) by adding arbitraty but compatible templates so at least n templates for each region is avalible select(...) from builtins.PyCapsule select(self : rosetta.protocols.antibody.grafting.SCS_Base, n : int,  : rosetta.protocols.antibody.grafting.AntibodySequence) -> rosetta.protocols.antibody.grafting.SCS_Results   Select CDR's template, filter it and sort. Try to provide at least 'n' templates if possible      _AE_scs_failed_ on failure set_sorter(...) from builtins.PyCapsule set_sorter(self : rosetta.protocols.antibody.grafting.SCS_Base, sorter : protocols::antibody::grafting::SCS_Functor) -> NoneType   class SCS_SubstitutionMatrixResult(SCS_Antibody_Database_Result)       Method resolution order: SCS_SubstitutionMatrixResult SCS_Antibody_Database_Result SCS_Result builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.protocols.antibody.grafting.SCS_SubstitutionMatrixResult) -> NoneType   2. __init__(self : rosetta.protocols.antibody.grafting.SCS_SubstitutionMatrixResult,  : rosetta.protocols.antibody.grafting.SCS_SubstitutionMatrixResult) -> 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.antibody.grafting.SCS_SubstitutionMatrixResult,  : rosetta.protocols.antibody.grafting.SCS_SubstitutionMatrixResult) -> rosetta.protocols.antibody.grafting.SCS_SubstitutionMatrixResult Data descriptors defined here: frh frl h1 h2 h3 l1 l2 l3 score sid Data descriptors inherited from SCS_Antibody_Database_Result: bio_type light_type resolution struct_source Data descriptors inherited from SCS_Result: padded pdb

Functions
		antibody_grafting_usable(...) method of builtins.PyCapsule instance antibody_grafting_usable() -> bool   Check if regex library is functional calculate_frh_frl(...) method of builtins.PyCapsule instance calculate_frh_frl( : rosetta.protocols.antibody.grafting.AntibodySequence) -> rosetta.protocols.antibody.grafting.FRH_FRL   Calculate frh+frl pair by trimming fr* and removing 'less-preserved' regions graft_cdr_loops(...) method of builtins.PyCapsule instance graft_cdr_loops(A : rosetta.protocols.antibody.grafting.AntibodySequence,  : rosetta.protocols.antibody.grafting.SCS_ResultSet, output_prefix : str, suffix : str, database : str) -> rosetta.core.pose.Pose   graft cdr-loops using best scs-results and write results into specified output_prefix parse_plain_text_with_columns(...) method of builtins.PyCapsule instance parse_plain_text_with_columns(*args, **kwargs) Overloaded function.   1. parse_plain_text_with_columns(file_name : str) -> rosetta.utility.vector0_std_map_std_string_std_string_std_less_std_string_std_allocator_std_pair_const_std_string_std_string_t   helper function to parse plain text for BLAST result and filter data   2. parse_plain_text_with_columns(file_name : str, legend_prefix : str) -> rosetta.utility.vector0_std_map_std_string_std_string_std_less_std_string_std_allocator_std_pair_const_std_string_std_string_t   helper function to parse plain text for BLAST result and filter data   3. parse_plain_text_with_columns(file_name : str, legend_prefix : str, legend_separator : str) -> rosetta.utility.vector0_std_map_std_string_std_string_std_less_std_string_std_allocator_std_pair_const_std_string_std_string_t   helper function to parse plain text for BLAST result and filter data   4. parse_plain_text_with_columns(file_name : str, legend_prefix : str, legend_separator : str, data_prefix : str) -> rosetta.utility.vector0_std_map_std_string_std_string_std_less_std_string_std_allocator_std_pair_const_std_string_std_string_t   helper function to parse plain text for BLAST result and filter data   5. parse_plain_text_with_columns(file_name : str, legend_prefix : str, legend_separator : str, data_prefix : str, data_separator : str) -> rosetta.utility.vector0_std_map_std_string_std_string_std_less_std_string_std_allocator_std_pair_const_std_string_std_string_t   helper function to parse plain text for BLAST result and filter data populate_results_from_db(...) method of builtins.PyCapsule instance populate_results_from_db(result : rosetta.protocols.antibody.grafting.SCS_Antibody_Database_Result, db : rosetta.std.map_std_string_std_map_std_string_std_string_std_less_std_string_std_allocator_std_pair_const_std_string_std_string_t) -> NoneType result_sizes(...) method of builtins.PyCapsule instance result_sizes(*args, **kwargs) Overloaded function.   1. result_sizes(r : rosetta.protocols.antibody.grafting.SCS_Results) -> str   filter helper function: generate string with results sizes   2. result_sizes(r : rosetta.protocols.antibody.grafting.SCS_Results, width : int) -> str   filter helper function: generate string with results sizes trim_framework(...) method of builtins.PyCapsule instance trim_framework(A : rosetta.protocols.antibody.grafting.AntibodySequence, heavy_fr : rosetta.protocols.antibody.grafting.AntibodyFramework, light_fr : rosetta.protocols.antibody.grafting.AntibodyFramework) -> NoneType   Calculate antibody framework regions (frh1...frl4) and Trim it by removing less-preserved elements