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protocols::splice Namespace Reference

Classes

class  AlignEndsMover
 
class  AlignEndsMoverCreator
 
class  BBDofs
 
class  BBMatching
 
class  DesignInterfacesOperation
 
class  DesignInterfacesOperationCreator
 
class  FindEndpointsOperation
 
class  FindEndpointsOperationCreator
 
class  RBInMover
 
class  RBInMoverCreator
 
class  RBOutMover
 
class  RBOutMoverCreator
 
class  ResidueBBDofs
 
struct  ROT
 
class  RotLibdb
 
class  RotLibOut
 
class  RotLibOutCreator
 
class  SampleRotamersFromPDB
 
class  SampleRotamersFromPDB_RotamerSetOperation
 
class  SampleRotamersFromPDBCreator
 
class  Splice
 container for BBDofs, providing a convenient operator [], size, other methods and iterators that allow splice to treat ResidueBBDofs as a simple vector (even though it contains other elements as well) More...
 
class  SpliceCreator
 
class  SpliceIn
 
class  SpliceInAntibody
 
class  SpliceInAntibodyCreator
 
class  SpliceInCreator
 
class  SpliceInTail
 
class  SpliceInTailCreator
 
class  SpliceManager
 
class  SpliceOut
 
class  SpliceOutAntibody
 
class  SpliceOutAntibodyCreator
 
class  SpliceOutCreator
 
class  SpliceOutTail
 
class  SpliceOutTailCreator
 
class  SpliceSegment
 utility class and functions for dealing with sequence profiles for varying segments in Splice More...
 
class  TailSegmentMover
 FloppyTail mover. More...
 
class  TailSegmentMoverCreator
 

Typedefs

typedef
utility::pointer::shared_ptr
< AlignEndsMover
AlignEndsMoverOP
 
typedef
utility::pointer::shared_ptr
< AlignEndsMover const > 
AlignEndsMoverCOP
 
typedef
utility::pointer::shared_ptr
< DesignInterfacesOperation
DesignInterfacesOperationOP
 
typedef
utility::pointer::shared_ptr
< DesignInterfacesOperation
const > 
DesignInterfacesOperationCOP
 
typedef
utility::pointer::shared_ptr
< FindEndpointsOperation
FindEndpointsOperationOP
 
typedef
utility::pointer::shared_ptr
< FindEndpointsOperation const > 
FindEndpointsOperationCOP
 
typedef
utility::pointer::shared_ptr
< RBInMover
RBInMoverOP
 
typedef
utility::pointer::shared_ptr
< RBInMover const > 
RBInMoverCOP
 
typedef
utility::pointer::shared_ptr
< RBOutMover
RBOutMoverOP
 
typedef
utility::pointer::shared_ptr
< RBOutMover const > 
RBOutMoverCOP
 
typedef
utility::pointer::shared_ptr
< RotLibOut
RotLibOutOP
 
typedef
utility::pointer::shared_ptr
< RotLibOut const > 
RotLibOutCOP
 
typedef utility::vector1
< utility::vector1
< core::conformation::ResidueOP > > 
res_matrix
 
typedef utility::vector1
< utility::vector1< ROT > > 
rot_matrix
 
typedef
utility::pointer::shared_ptr
< SampleRotamersFromPDB_RotamerSetOperation
SampleRotamersFromPDB_RotamerSetOperationOP
 
typedef
utility::pointer::shared_ptr
< SampleRotamersFromPDB_RotamerSetOperation
const > 
SampleRotamersFromPDB_RotamerSetOperationCOP
 
typedef
utility::pointer::shared_ptr
< SampleRotamersFromPDB
SampleRotamersFromPDBOP
 
typedef
utility::pointer::shared_ptr
< SampleRotamersFromPDB const > 
SampleRotamersFromPDBCOP
 
typedef
utility::pointer::shared_ptr
< RotLibdb
RotLibdbOP
 
typedef
utility::pointer::shared_ptr
< RotLibdb const > 
RotLibdbCOP
 
typedef
utility::pointer::shared_ptr
< Splice
SpliceOP
 
typedef
utility::pointer::shared_ptr
< Splice const > 
SpliceCOP
 
typedef
utility::pointer::shared_ptr
< BBMatching
BBMatchingOP
 
typedef
utility::pointer::shared_ptr
< BBMatching const > 
BBMatchingCOP
 
typedef
utility::pointer::shared_ptr
< SpliceIn
SpliceInOP
 
typedef
utility::pointer::shared_ptr
< SpliceIn const > 
SpliceInCOP
 
typedef
utility::pointer::shared_ptr
< SpliceInAntibody
SpliceInAntibodyOP
 
typedef
utility::pointer::shared_ptr
< SpliceInAntibody const > 
SpliceInAntibodyCOP
 
typedef
utility::pointer::shared_ptr
< SpliceInTail
SpliceInTailOP
 
typedef
utility::pointer::shared_ptr
< SpliceInTail const > 
SpliceInTailCOP
 
typedef
utility::pointer::shared_ptr
< SpliceManager
SpliceManagerOP
 
typedef
utility::pointer::shared_ptr
< SpliceManager const > 
SpliceManagerCOP
 
typedef utility::tag::TagCOP TagCOP
 
typedef
utility::pointer::shared_ptr
< basic::datacache::DataMapObj
< bool > > 
DataccacheBoolDataOP
 
typedef
utility::pointer::shared_ptr
< SpliceOut
SpliceOutOP
 
typedef
utility::pointer::shared_ptr
< SpliceOut const > 
SpliceOutCOP
 
typedef
utility::pointer::shared_ptr
< SpliceOutAntibody
SpliceOutAntibodyOP
 
typedef
utility::pointer::shared_ptr
< SpliceOutAntibody const > 
SpliceOutAntibodyCOP
 
typedef
utility::pointer::shared_ptr
< SpliceOutTail
SpliceOutTailOP
 
typedef
utility::pointer::shared_ptr
< SpliceOutTail const > 
SpliceOutTailCOP
 
typedef
utility::pointer::shared_ptr
< SpliceSegment
SpliceSegmentOP
 
typedef
utility::pointer::shared_ptr
< SpliceSegment const > 
SpliceSegmentCOP
 
typedef
utility::pointer::shared_ptr
< TailSegmentMover
TailSegmentMoverOP
 
typedef
utility::pointer::shared_ptr
< TailSegmentMover const > 
TailSegmentMoverCOP
 

Functions

utility::vector1
< numeric::xyzVector
< core::Real > > 
Ca_coords (core::pose::Pose const &pose, utility::vector1< core::Size > const positions)
 
core::Size neighbors_in_vector (core::pose::Pose const &pose, core::Size const target_res, utility::vector1< core::Size > const &neighbors, core::Real const dist_threshold, core::scoring::dssp::Dssp &dssp, core::Size const sequence_separation)
 compute the number of residue neighbours target_res has within neighbours vector More...
 
bool compare (std::pair< core::Size, core::Size > p1, std::pair< core::Size, core::Size > p2)
 
utility::vector1< std::pair
< core::Size, core::Size > > 
find_disulfs_in_range (core::pose::Pose const &pose, core::Size const start, core::Size const end)
 find disulfide pairs. Simply look for pairs of SG atoms on residues that are disulfide variants and within 3.0A More...
 
bool atom_dist_with_zero (core::pose::Pose &pose, core::pose::Pose &hit_pose, core::Size cur_target, core::Size cur_nearest, core::Size min_dist)
 
static basic::Tracer TR ("core.pack.rotamer_set.SampleRotamersFromPDB_RotamerSetOperation")
 
void printChi (core::conformation::Residue const res)
 
bool is_identical_rotamer (ROT const existing_res, ROT const new_res)
 
std::string Srfp_complex_type_name_for_subsubtag (std::string const &foo)
 
std::string Srfp_complex_type_name_for_subtag (std::string const &foo)
 
static basic::Tracer TR ("protocols.splice.Splice")
 
static basic::Tracer TR_ccd ("protocols.splice.Splice_ccd")
 
static basic::Tracer TR_constraints ("protocols.splice.Splice_constraints")
 
static basic::Tracer TR_pssm ("protocols.splice.Splice_pssm")
 
static basic::Tracer TR_min ("protocols.splice.Splice_min")
 
std::string complex_type_name_for_subsubtag (std::string const &foo)
 
std::string complex_type_name_for_subtag (std::string const &foo)
 
static basic::Tracer TR_constraints ("protocols.splice.Splice_constraints")
 
static basic::Tracer TR ("protocols.splice.SpliceIn")
 
static basic::Tracer TR_pssm ("protocols.splice.Splice_pssm")
 
std::string SpliceIn_complex_type_name_for_subsubtag (std::string const &foo)
 
std::string SpliceIn_complex_type_name_for_subtag (std::string const &foo)
 
static basic::Tracer TR_constraints ("protocols.splice.Splice_constraints")
 
static basic::Tracer TR ("protocols.splice.SpliceInAntibody")
 
static basic::Tracer TR_pssm ("protocols.splice.Splice_pssm")
 
std::string SpliceInAntibody_complex_type_name_for_subsubtag (std::string const &foo)
 
std::string SpliceInAntibody_complex_type_name_for_subtag (std::string const &foo)
 
static basic::Tracer TR_constraints ("protocols.splice.Splice_constraints")
 
static basic::Tracer TR ("protocols.splice.SpliceInTail")
 
static basic::Tracer TR_pssm ("protocols.splice.Splice_pssm")
 
std::string SpliceInTail_complex_type_name_for_subsubtag (std::string const &foo)
 
std::string SpliceInTail_complex_type_name_for_subtag (std::string const &foo)
 
static basic::Tracer TR ("protocols.splice.SpliceManager")
 
static basic::Tracer TR_constraints ("protocols.splice.Splice_constraints")
 
static basic::Tracer TR ("protocols.splice.SpliceOut")
 
static basic::Tracer TR_ccd ("protocols.splice.Splice_ccd")
 
static basic::Tracer TR_constraints ("protocols.splice.Splice_constraints")
 
static basic::Tracer TR_pssm ("protocols.splice.Splice_pssm")
 
static basic::Tracer TR_min ("protocols.splice.Splice_min")
 
static basic::Tracer TR_tail ("protocols.splice.Splice_Tail")
 
std::string SpliceOut_complex_type_name_for_subsubtag (std::string const &foo)
 
std::string SpliceOut_complex_type_name_for_subtag (std::string const &foo)
 
static basic::Tracer TR ("protocols.splice.SpliceOutAntibody")
 
static basic::Tracer TR_ccd ("protocols.splice.Splice_ccd")
 
static basic::Tracer TR_constraints ("protocols.splice.Splice_constraints")
 
static basic::Tracer TR_pssm ("protocols.splice.Splice_pssm")
 
static basic::Tracer TR_min ("protocols.splice.Splice_min")
 
std::string SpliceOutAntibody_complex_type_name_for_subsubtag (std::string const &foo)
 
std::string SpliceOutAntibody_complex_type_name_for_subtag (std::string const &foo)
 
static basic::Tracer TR ("protocols.splice.SpliceOutTail")
 
static basic::Tracer TR_ccd ("protocols.splice.Splice_ccd")
 
static basic::Tracer TR_constraints ("protocols.splice.Splice_constraints")
 
static basic::Tracer TR_pssm ("protocols.splice.Splice_pssm")
 
static basic::Tracer TR_min ("protocols.splice.Splice_min")
 
std::string SpliceOutTail_complex_type_name_for_subsubtag (std::string const &foo)
 
std::string SpliceOutTail_complex_type_name_for_subtag (std::string const &foo)
 
static basic::Tracer TR ("protocols.splice.SpliceSegment")
 
SequenceProfileOP concatenate_profiles (utility::vector1< SequenceProfileOP > const &profiles, utility::vector1< std::string > segment_names_ordered, std::string H3_seq)
 generate one long sequence profile out of several sequence-profile segments. More...
 
std::map< std::string,
std::string > 
read_H3_seq (std::string const &Protein_family_path)
 Reads from given file the H3 sequences from all PDBs in the db. More...
 
std::map< std::string,
std::string > 
read_pdb_seq (std::string const &Protein_family_path)
 in cases where we have only one sequence per pdb we store the sequences in a seperate map we can later use them to create pssms using blosum More...
 
core::sequence::SequenceProfileOP concatenate_profiles (utility::vector1< core::sequence::SequenceProfileOP > const &profiles, utility::vector1< std::string > segment_names_ordered, std::string H3_seq)
 generate one long sequence profile out of several sequence-profile segments. More...
 
core::Size nearest_to_entry_stop_on_pose (core::pose::Pose const &pose, core::pose::Pose const &template_pose, core::Size residue, std::string tail_segment, std::string protein_family, core::Size chain, std::string segment)
 
void modify_dbase_with_compatible_backbones (utility::vector1< ResidueBBDofs > torsion_database, utility::vector1< core::Size > &dbase, utility::vector1< std::string > intersect_pdbs)
 
void load_pdb_segments_from_pose_comments (core::pose::Pose const &pose, std::map< std::string, std::string > &pdb_segments)
 
core::Size report_coordinate_constraints (core::pose::Pose const &pose)
 
void report_designable_packable_residues (core::pack::task::TaskFactoryOP const tf, core::pose::Pose pose)
 
bool calculate_rmsd (core::pose::Pose &pose, core::pose::Pose const &source_pose, core::Size total_residue_new, core::Size nearest_to_from, core::Size from_res, core::Real rms_A, core::Real rms_B)
 
void min_seg (core::pose::Pose &pose, ResidueBBDofs dofs, bool debug, core::Size from_res, std::string tail_segment, core::Size cut_site, core::Size cut_vl_vh_after_llc, ResidueBBDofs tail_dofs, core::scoring::ScoreFunctionOP scorefxn, std::string segment_type)
 
utility::vector1
< numeric::xyzVector
< core::Real > > 
coords (core::pose::Pose const &pose, utility::vector1< core::Size > const positions)
 
utility::vector1< core::Sizefind_residues_on_chain1_inside_interface (core::pose::Pose const &pose, core::Size chainNum)
 
std::string parse_pdb_code (std::string pdb_file_name)
 
void fix_chain_break_residue (core::pose::Pose &pose, SpliceManager splicemanager)
 
void report_des_pack_res (core::pose::Pose const &pose, core::pack::task::TaskFactoryOP tf)
 

Typedef Documentation

typedef utility::pointer::shared_ptr< AlignEndsMover const > protocols::splice::AlignEndsMoverCOP
typedef utility::pointer::shared_ptr< AlignEndsMover > protocols::splice::AlignEndsMoverOP
typedef utility::pointer::shared_ptr< BBMatching const > protocols::splice::BBMatchingCOP
typedef utility::pointer::shared_ptr< BBMatching > protocols::splice::BBMatchingOP
typedef utility::pointer::shared_ptr< basic::datacache::DataMapObj< bool > > protocols::splice::DataccacheBoolDataOP
typedef utility::pointer::shared_ptr< DesignInterfacesOperation const > protocols::splice::DesignInterfacesOperationCOP
typedef utility::pointer::shared_ptr< FindEndpointsOperation const > protocols::splice::FindEndpointsOperationCOP
typedef utility::pointer::shared_ptr< RBInMover const > protocols::splice::RBInMoverCOP
typedef utility::pointer::shared_ptr< RBInMover > protocols::splice::RBInMoverOP
typedef utility::pointer::shared_ptr< RBOutMover const > protocols::splice::RBOutMoverCOP
typedef utility::pointer::shared_ptr< RBOutMover > protocols::splice::RBOutMoverOP
typedef utility::vector1< utility::vector1< core::conformation::ResidueOP > > protocols::splice::res_matrix
typedef utility::vector1< utility::vector1< ROT > > protocols::splice::rot_matrix
typedef utility::pointer::shared_ptr< RotLibdb const > protocols::splice::RotLibdbCOP
typedef utility::pointer::shared_ptr< RotLibdb > protocols::splice::RotLibdbOP
typedef utility::pointer::shared_ptr< RotLibOut const > protocols::splice::RotLibOutCOP
typedef utility::pointer::shared_ptr< RotLibOut > protocols::splice::RotLibOutOP
typedef utility::pointer::shared_ptr< SampleRotamersFromPDB const > protocols::splice::SampleRotamersFromPDBCOP
typedef utility::pointer::shared_ptr< SampleRotamersFromPDB > protocols::splice::SampleRotamersFromPDBOP
typedef utility::pointer::shared_ptr< Splice const > protocols::splice::SpliceCOP
typedef utility::pointer::shared_ptr< SpliceInAntibody const > protocols::splice::SpliceInAntibodyCOP
typedef utility::pointer::shared_ptr< SpliceInAntibody > protocols::splice::SpliceInAntibodyOP
typedef utility::pointer::shared_ptr< SpliceIn const > protocols::splice::SpliceInCOP
typedef utility::pointer::shared_ptr< SpliceIn > protocols::splice::SpliceInOP
typedef utility::pointer::shared_ptr< SpliceInTail const > protocols::splice::SpliceInTailCOP
typedef utility::pointer::shared_ptr< SpliceInTail > protocols::splice::SpliceInTailOP
typedef utility::pointer::shared_ptr< SpliceManager const > protocols::splice::SpliceManagerCOP
typedef utility::pointer::shared_ptr< SpliceManager > protocols::splice::SpliceManagerOP
typedef utility::pointer::shared_ptr< Splice > protocols::splice::SpliceOP
typedef utility::pointer::shared_ptr< SpliceOutAntibody const > protocols::splice::SpliceOutAntibodyCOP
typedef utility::pointer::shared_ptr< SpliceOutAntibody > protocols::splice::SpliceOutAntibodyOP
typedef utility::pointer::shared_ptr< SpliceOut const > protocols::splice::SpliceOutCOP
typedef utility::pointer::shared_ptr< SpliceOut > protocols::splice::SpliceOutOP
typedef utility::pointer::shared_ptr< SpliceOutTail const > protocols::splice::SpliceOutTailCOP
typedef utility::pointer::shared_ptr< SpliceOutTail > protocols::splice::SpliceOutTailOP
typedef utility::pointer::shared_ptr< SpliceSegment const > protocols::splice::SpliceSegmentCOP
typedef utility::pointer::shared_ptr< SpliceSegment > protocols::splice::SpliceSegmentOP
typedef utility::tag::TagCOP protocols::splice::TagCOP
typedef utility::pointer::shared_ptr< TailSegmentMover const > protocols::splice::TailSegmentMoverCOP
typedef utility::pointer::shared_ptr< TailSegmentMover > protocols::splice::TailSegmentMoverOP

Function Documentation

bool protocols::splice::atom_dist_with_zero ( core::pose::Pose pose,
core::pose::Pose hit_pose,
core::Size  cur_target,
core::Size  cur_nearest,
core::Size  min_dist 
)
utility::vector1< numeric::xyzVector< core::Real > > protocols::splice::Ca_coords ( core::pose::Pose const &  pose,
utility::vector1< core::Size > const  positions 
)
bool protocols::splice::calculate_rmsd ( core::pose::Pose pose,
core::pose::Pose const &  source_pose,
core::Size  total_residue_new,
core::Size  nearest_to_from,
core::Size  from_res,
core::Real  rms_A,
core::Real  rms_B 
)
bool protocols::splice::compare ( std::pair< core::Size, core::Size p1,
std::pair< core::Size, core::Size p2 
)

Referenced by find_disulfs_in_range().

std::string protocols::splice::complex_type_name_for_subsubtag ( std::string const &  foo)
std::string protocols::splice::complex_type_name_for_subtag ( std::string const &  foo)
core::sequence::SequenceProfileOP protocols::splice::concatenate_profiles ( utility::vector1< core::sequence::SequenceProfileOP > const &  profiles,
utility::vector1< std::string >  segment_names_ordered,
std::string  H3_seq 
)

generate one long sequence profile out of several sequence-profile segments.

References core::sequence::Sequence::sequence(), and TR().

Referenced by protocols::splice::SpliceManager::generate_sequence_profile(), and protocols::splice::Splice::generate_sequence_profile().

SequenceProfileOP protocols::splice::concatenate_profiles ( utility::vector1< SequenceProfileOP > const &  profiles,
utility::vector1< std::string >  segment_names_ordered,
std::string  H3_seq 
)

generate one long sequence profile out of several sequence-profile segments.

References core::sequence::Sequence::sequence(), and TR().

Referenced by protocols::splice::SpliceManager::generate_sequence_profile(), and protocols::splice::Splice::generate_sequence_profile().

utility::vector1< numeric::xyzVector< core::Real > > protocols::splice::coords ( core::pose::Pose const &  pose,
utility::vector1< core::Size > const  positions 
)
utility::vector1< std::pair< core::Size, core::Size > > protocols::splice::find_disulfs_in_range ( core::pose::Pose const &  pose,
core::Size const  start,
core::Size const  end 
)

find disulfide pairs. Simply look for pairs of SG atoms on residues that are disulfide variants and within 3.0A

utility function for finding disulfide bonded pairs

References compare(), core::kinematics::distance(), core::chemical::DISULFIDE, core::sequence::end, core::conformation::Residue::has_variant_type(), core::pose::Pose::residue(), core::pose::Pose::size(), and core::conformation::Residue::xyz().

utility::vector1< core::Size > protocols::splice::find_residues_on_chain1_inside_interface ( core::pose::Pose const &  pose,
core::Size  chainNum 
)
void protocols::splice::fix_chain_break_residue ( core::pose::Pose pose,
SpliceManager  splicemanager 
)
bool protocols::splice::is_identical_rotamer ( ROT const  existing_res,
ROT const  new_res 
)
void protocols::splice::load_pdb_segments_from_pose_comments ( core::pose::Pose const &  pose,
std::map< std::string, std::string > &  pdb_segments 
)
void protocols::splice::min_seg ( core::pose::Pose pose,
ResidueBBDofs  dofs,
bool  debug,
core::Size  from_res,
std::string  tail_segment,
core::Size  cut_site,
core::Size  cut_vl_vh_after_llc,
ResidueBBDofs  tail_dofs,
core::scoring::ScoreFunctionOP  scorefxn,
std::string  segment_type 
)
void protocols::splice::modify_dbase_with_compatible_backbones ( utility::vector1< ResidueBBDofs >  torsion_database,
utility::vector1< core::Size > &  dbase,
utility::vector1< std::string >  intersect_pdbs 
)
core::Size protocols::splice::nearest_to_entry_stop_on_pose ( core::pose::Pose const &  pose,
core::pose::Pose const &  template_pose,
core::Size  residue,
std::string  tail_segment,
std::string  protein_family,
core::Size  chain,
std::string  segment 
)
core::Size protocols::splice::neighbors_in_vector ( core::pose::Pose const &  pose,
core::Size const  target_res,
utility::vector1< core::Size > const &  neighbors,
core::Real const  dist_threshold,
core::scoring::dssp::Dssp dssp,
core::Size const  sequence_separation 
)
std::string protocols::splice::parse_pdb_code ( std::string  pdb_file_name)
void protocols::splice::printChi ( core::conformation::Residue const  res)
std::map< std::string, std::string > protocols::splice::read_H3_seq ( std::string const &  Protein_family_path)

Reads from given file the H3 sequences from all PDBs in the db.

References TR().

Referenced by protocols::splice::Splice::parse_my_tag().

std::map< std::string, std::string > protocols::splice::read_pdb_seq ( std::string const &  Protein_family_path)

in cases where we have only one sequence per pdb we store the sequences in a seperate map we can later use them to create pssms using blosum

References TR().

Referenced by protocols::splice::SpliceOutAntibody::parse_my_tag().

core::Size protocols::splice::report_coordinate_constraints ( core::pose::Pose const &  pose)
void protocols::splice::report_des_pack_res ( core::pose::Pose const &  pose,
core::pack::task::TaskFactoryOP  tf 
)
void protocols::splice::report_designable_packable_residues ( core::pack::task::TaskFactoryOP const  tf,
core::pose::Pose  pose 
)
std::string protocols::splice::SpliceIn_complex_type_name_for_subsubtag ( std::string const &  foo)
std::string protocols::splice::SpliceIn_complex_type_name_for_subtag ( std::string const &  foo)
std::string protocols::splice::SpliceInAntibody_complex_type_name_for_subsubtag ( std::string const &  foo)
std::string protocols::splice::SpliceInAntibody_complex_type_name_for_subtag ( std::string const &  foo)
std::string protocols::splice::SpliceInTail_complex_type_name_for_subsubtag ( std::string const &  foo)
std::string protocols::splice::SpliceInTail_complex_type_name_for_subtag ( std::string const &  foo)
std::string protocols::splice::SpliceOut_complex_type_name_for_subsubtag ( std::string const &  foo)
std::string protocols::splice::SpliceOut_complex_type_name_for_subtag ( std::string const &  foo)
std::string protocols::splice::SpliceOutAntibody_complex_type_name_for_subsubtag ( std::string const &  foo)
std::string protocols::splice::SpliceOutAntibody_complex_type_name_for_subtag ( std::string const &  foo)
std::string protocols::splice::SpliceOutTail_complex_type_name_for_subsubtag ( std::string const &  foo)
std::string protocols::splice::SpliceOutTail_complex_type_name_for_subtag ( std::string const &  foo)
std::string protocols::splice::Srfp_complex_type_name_for_subsubtag ( std::string const &  foo)
std::string protocols::splice::Srfp_complex_type_name_for_subtag ( std::string const &  foo)
static basic::Tracer protocols::splice::TR ( "protocols.splice.SpliceSegment"  )
static
static basic::Tracer protocols::splice::TR ( "protocols.splice.SpliceManager"  )
static
static basic::Tracer protocols::splice::TR ( "core.pack.rotamer_set.SampleRotamersFromPDB_RotamerSetOperation"  )
static

Referenced by protocols::splice::SpliceOutTail::abstract_parse_tag(), protocols::splice::Splice::add_coordinate_constraints(), protocols::splice::SpliceManager::add_coordinate_constraints(), protocols::splice::SpliceManager::add_dihedral_constraints(), protocols::splice::SampleRotamersFromPDB_RotamerSetOperation::add_rotamer_to_rotamer_set(), protocols::splice::SpliceManager::add_sequence_constraints(), protocols::splice::Splice::add_sequence_constraints(), protocols::splice::SpliceOutAntibody::adjust_n_ter_tail_length(), protocols::splice::SpliceInAntibody::adjust_n_ter_tail_length(), protocols::splice::SpliceManager::adjust_stem_positions_by_template(), protocols::splice::SpliceInAntibody::adjust_template_jump(), protocols::splice::SampleRotamersFromPDB_RotamerSetOperation::alter_rotamer_set_from_db(), protocols::splice::SampleRotamersFromPDB_RotamerSetOperation::alter_rotamer_set_from_pdb(), protocols::splice::AlignEndsMover::apply(), protocols::splice::RBInMover::apply(), protocols::splice::RBOutMover::apply(), protocols::splice::RotLibOut::apply(), protocols::splice::FindEndpointsOperation::apply(), protocols::splice::SpliceOutAntibody::apply(), protocols::splice::SpliceInAntibody::apply(), protocols::splice::SpliceIn::apply(), protocols::splice::SpliceInTail::apply(), protocols::splice::SpliceOut::apply(), protocols::splice::DesignInterfacesOperation::apply(), protocols::splice::TailSegmentMover::apply(), protocols::splice::Splice::apply(), protocols::splice::SpliceIn::assign_from_res_to_res(), protocols::splice::SpliceInTail::assign_from_res_to_res(), atom_dist_with_zero(), protocols::splice::SpliceOutTail::build_ideal_segment(), protocols::splice::SpliceInTail::build_ideal_segment(), protocols::splice::SpliceIn::build_ideal_segment(), protocols::splice::SpliceOut::build_ideal_segment(), calculate_rmsd(), protocols::splice::SpliceOut::ccd_mover(), protocols::splice::SpliceManager::chainbreak_check(), protocols::splice::Splice::chainbreak_check(), protocols::splice::SpliceManager::check_sequence_profile(), protocols::splice::SpliceOut::check_source_segment(), protocols::splice::RBInMover::checkpoint(), protocols::splice::SampleRotamersFromPDB::combine_rot_dbs(), concatenate_profiles(), protocols::splice::SampleRotamersFromPDB::concatenate_rot_matrix(), protocols::splice::Splice::copy_stretch(), protocols::splice::SampleRotamersFromPDB_RotamerSetOperation::fill_rotamer_matrix_from_db_file(), protocols::splice::SpliceIn::find_dbase_entry(), protocols::splice::SpliceInTail::find_dbase_entry(), protocols::splice::Splice::find_dbase_entry(), protocols::splice::RotLibOut::find_matching_res(), protocols::splice::SpliceOut::find_non_active_site_cut_site(), protocols::splice::Splice::find_non_active_site_cut_site(), protocols::splice::SpliceOutAntibody::find_vl_vh_cut(), protocols::splice::SpliceInAntibody::find_vl_vh_cut(), fix_chain_break_residue(), protocols::splice::SpliceManager::fold_tree(), protocols::splice::Splice::fold_tree(), protocols::splice::SpliceManager::generate_sequence_profile(), protocols::splice::Splice::generate_sequence_profile(), protocols::splice::RBOutMover::get_disulf_jump(), protocols::splice::SpliceOut::handle_mover_tag(), protocols::splice::SpliceOutAntibody::handle_tail_mover_tag(), protocols::splice::RBInMover::init(), protocols::splice::SampleRotamersFromPDB_RotamerSetOperation::initialize_from_command_line(), protocols::splice::SpliceIn::load_from_checkpoint(), protocols::splice::Splice::load_from_checkpoint(), load_pdb_segments_from_pose_comments(), protocols::splice::SpliceOut::load_pdb_segments_from_pose_comments(), protocols::splice::Splice::load_pdb_segments_from_pose_comments(), min_seg(), protocols::splice::SpliceIn::minimize_segment(), protocols::splice::SpliceOut::minimize_segment(), modify_dbase_with_compatible_backbones(), protocols::splice::AlignEndsMover::parse_my_tag(), protocols::splice::RBOutMover::parse_my_tag(), protocols::splice::SpliceOutAntibody::parse_my_tag(), protocols::splice::SpliceInAntibody::parse_my_tag(), protocols::splice::SpliceIn::parse_my_tag(), protocols::splice::SpliceInTail::parse_my_tag(), protocols::splice::Splice::parse_my_tag(), protocols::splice::SpliceManager::parse_segments(), protocols::splice::SpliceOut::parse_SpliceOut_tags(), protocols::splice::FindEndpointsOperation::parse_tag(), protocols::splice::DesignInterfacesOperation::parse_tag(), protocols::splice::SampleRotamersFromPDB::parse_tag(), protocols::splice::SpliceManager::parse_tags(), protocols::splice::SpliceOut::place_cut_site_in_segment(), printChi(), protocols::splice::SpliceManager::rb_adjust_template(), protocols::splice::Splice::rb_adjust_template(), read_H3_seq(), read_pdb_seq(), protocols::splice::Splice::read_splice_segments(), protocols::splice::SpliceIn::read_torsion_database(), protocols::splice::Splice::read_torsion_database(), protocols::splice::AlignEndsMover::reference_positions(), report_coordinate_constraints(), report_des_pack_res(), report_designable_packable_residues(), protocols::splice::SpliceIn::rtmin(), protocols::splice::Splice::save_to_checkpoint(), protocols::splice::SpliceManager::set_BB_dofs(), protocols::splice::RBInMover::set_fold_tree(), protocols::splice::Splice::set_fold_tree(), protocols::splice::SpliceInTail::set_fold_tree_nodes(), protocols::splice::SpliceOutTail::set_fold_tree_nodes(), protocols::splice::SpliceInTail::set_loop_length_change(), protocols::splice::SpliceIn::set_loop_length_change(), protocols::splice::SpliceOut::set_source_from_to_res(), protocols::splice::SpliceOut::SpliceOutFilter(), protocols::splice::RBOutMover::superimpose_source_on_pose(), protocols::splice::SpliceOutTail::superimpose_source_on_pose(), protocols::splice::SpliceOut::superimpose_source_on_pose(), protocols::splice::Splice::superimpose_source_on_pose(), protocols::splice::Splice::tail_fold_tree(), protocols::splice::SpliceOutTail::write_database_to_file(), and protocols::splice::SpliceOut::write_database_to_file().

static basic::Tracer protocols::splice::TR ( "protocols.splice.SpliceOut"  )
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static basic::Tracer protocols::splice::TR ( "protocols.splice.SpliceInAntibody"  )
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static basic::Tracer protocols::splice::TR ( "protocols.splice.SpliceInTail"  )
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static basic::Tracer protocols::splice::TR ( "protocols.splice.SpliceIn"  )
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static basic::Tracer protocols::splice::TR ( "protocols.splice.SpliceOutAntibody"  )
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static basic::Tracer protocols::splice::TR ( "protocols.splice.SpliceOutTail"  )
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static basic::Tracer protocols::splice::TR ( "protocols.splice.Splice"  )
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static basic::Tracer protocols::splice::TR_ccd ( "protocols.splice.Splice_ccd"  )
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static basic::Tracer protocols::splice::TR_ccd ( "protocols.splice.Splice_ccd"  )
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static basic::Tracer protocols::splice::TR_ccd ( "protocols.splice.Splice_ccd"  )
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static basic::Tracer protocols::splice::TR_ccd ( "protocols.splice.Splice_ccd"  )
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static basic::Tracer protocols::splice::TR_constraints ( "protocols.splice.Splice_constraints"  )
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static basic::Tracer protocols::splice::TR_constraints ( "protocols.splice.Splice_constraints"  )
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static basic::Tracer protocols::splice::TR_constraints ( "protocols.splice.Splice_constraints"  )
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static basic::Tracer protocols::splice::TR_constraints ( "protocols.splice.Splice_constraints"  )
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static basic::Tracer protocols::splice::TR_constraints ( "protocols.splice.Splice_constraints"  )
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static basic::Tracer protocols::splice::TR_constraints ( "protocols.splice.Splice_constraints"  )
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static basic::Tracer protocols::splice::TR_constraints ( "protocols.splice.Splice_constraints"  )
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static basic::Tracer protocols::splice::TR_constraints ( "protocols.splice.Splice_constraints"  )
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static basic::Tracer protocols::splice::TR_min ( "protocols.splice.Splice_min"  )
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static basic::Tracer protocols::splice::TR_min ( "protocols.splice.Splice_min"  )
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static basic::Tracer protocols::splice::TR_min ( "protocols.splice.Splice_min"  )
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static basic::Tracer protocols::splice::TR_min ( "protocols.splice.Splice_min"  )
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static basic::Tracer protocols::splice::TR_pssm ( "protocols.splice.Splice_pssm"  )
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static basic::Tracer protocols::splice::TR_pssm ( "protocols.splice.Splice_pssm"  )
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static basic::Tracer protocols::splice::TR_pssm ( "protocols.splice.Splice_pssm"  )
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static basic::Tracer protocols::splice::TR_pssm ( "protocols.splice.Splice_pssm"  )
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static basic::Tracer protocols::splice::TR_pssm ( "protocols.splice.Splice_pssm"  )
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static basic::Tracer protocols::splice::TR_pssm ( "protocols.splice.Splice_pssm"  )
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static basic::Tracer protocols::splice::TR_pssm ( "protocols.splice.Splice_pssm"  )
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static basic::Tracer protocols::splice::TR_tail ( "protocols.splice.Splice_Tail"  )
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