protocols::splice Namespace Reference

Classes
class	AlignEndsMover
class	AlignEndsMoverCreator
class	DesignInterfacesOperation
class	DesignInterfacesOperationCreator
class	FindEndpointsOperation
class	FindEndpointsOperationCreator
class	RBInMover
class	RBInMoverCreator
class	RBOutMover
class	RBOutMoverCreator
class	RotLibOut
class	RotLibOutCreator
struct	ROT
class	RotLibdb
class	SampleRotamersFromPDB_RotamerSetOperation
class	SampleRotamersFromPDB
class	SampleRotamersFromPDBCreator
class	BBMatching
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	BBDofs
class	ResidueBBDofs
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::Size >	find_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

AlignEndsMoverCOP

typedef utility::pointer::shared_ptr< AlignEndsMover const > protocols::splice::AlignEndsMoverCOP

AlignEndsMoverOP

typedef utility::pointer::shared_ptr< AlignEndsMover > protocols::splice::AlignEndsMoverOP

BBMatchingCOP

typedef utility::pointer::shared_ptr< BBMatching const > protocols::splice::BBMatchingCOP

BBMatchingOP

typedef utility::pointer::shared_ptr< BBMatching > protocols::splice::BBMatchingOP

DataccacheBoolDataOP

typedef utility::pointer::shared_ptr< basic::datacache::DataMapObj< bool > > protocols::splice::DataccacheBoolDataOP

DesignInterfacesOperationCOP

typedef utility::pointer::shared_ptr< DesignInterfacesOperation const > protocols::splice::DesignInterfacesOperationCOP

DesignInterfacesOperationOP

typedef utility::pointer::shared_ptr< DesignInterfacesOperation > protocols::splice::DesignInterfacesOperationOP

FindEndpointsOperationCOP

typedef utility::pointer::shared_ptr< FindEndpointsOperation const > protocols::splice::FindEndpointsOperationCOP

FindEndpointsOperationOP

typedef utility::pointer::shared_ptr< FindEndpointsOperation > protocols::splice::FindEndpointsOperationOP

RBInMoverCOP

typedef utility::pointer::shared_ptr< RBInMover const > protocols::splice::RBInMoverCOP

RBInMoverOP

typedef utility::pointer::shared_ptr< RBInMover > protocols::splice::RBInMoverOP

RBOutMoverCOP

typedef utility::pointer::shared_ptr< RBOutMover const > protocols::splice::RBOutMoverCOP

RBOutMoverOP

typedef utility::pointer::shared_ptr< RBOutMover > protocols::splice::RBOutMoverOP

res_matrix

typedef utility::vector1< utility::vector1< core::conformation::ResidueOP > > protocols::splice::res_matrix

rot_matrix

typedef utility::vector1< utility::vector1< ROT > > protocols::splice::rot_matrix

RotLibdbCOP

typedef utility::pointer::shared_ptr< RotLibdb const > protocols::splice::RotLibdbCOP

RotLibdbOP

typedef utility::pointer::shared_ptr< RotLibdb > protocols::splice::RotLibdbOP

RotLibOutCOP

typedef utility::pointer::shared_ptr< RotLibOut const > protocols::splice::RotLibOutCOP

RotLibOutOP

typedef utility::pointer::shared_ptr< RotLibOut > protocols::splice::RotLibOutOP

SampleRotamersFromPDB_RotamerSetOperationCOP

typedef utility::pointer::shared_ptr< SampleRotamersFromPDB_RotamerSetOperation const > protocols::splice::SampleRotamersFromPDB_RotamerSetOperationCOP

SampleRotamersFromPDB_RotamerSetOperationOP

typedef utility::pointer::shared_ptr< SampleRotamersFromPDB_RotamerSetOperation > protocols::splice::SampleRotamersFromPDB_RotamerSetOperationOP

SampleRotamersFromPDBCOP

typedef utility::pointer::shared_ptr< SampleRotamersFromPDB const > protocols::splice::SampleRotamersFromPDBCOP

SampleRotamersFromPDBOP

typedef utility::pointer::shared_ptr< SampleRotamersFromPDB > protocols::splice::SampleRotamersFromPDBOP

SpliceCOP

typedef utility::pointer::shared_ptr< Splice const > protocols::splice::SpliceCOP

SpliceInAntibodyCOP

typedef utility::pointer::shared_ptr< SpliceInAntibody const > protocols::splice::SpliceInAntibodyCOP

SpliceInAntibodyOP

typedef utility::pointer::shared_ptr< SpliceInAntibody > protocols::splice::SpliceInAntibodyOP

SpliceInCOP

typedef utility::pointer::shared_ptr< SpliceIn const > protocols::splice::SpliceInCOP

SpliceInOP

typedef utility::pointer::shared_ptr< SpliceIn > protocols::splice::SpliceInOP

SpliceInTailCOP

typedef utility::pointer::shared_ptr< SpliceInTail const > protocols::splice::SpliceInTailCOP

SpliceInTailOP

typedef utility::pointer::shared_ptr< SpliceInTail > protocols::splice::SpliceInTailOP

SpliceManagerCOP

typedef utility::pointer::shared_ptr< SpliceManager const > protocols::splice::SpliceManagerCOP

SpliceManagerOP

typedef utility::pointer::shared_ptr< SpliceManager > protocols::splice::SpliceManagerOP

SpliceOP

typedef utility::pointer::shared_ptr< Splice > protocols::splice::SpliceOP

SpliceOutAntibodyCOP

typedef utility::pointer::shared_ptr< SpliceOutAntibody const > protocols::splice::SpliceOutAntibodyCOP

SpliceOutAntibodyOP

typedef utility::pointer::shared_ptr< SpliceOutAntibody > protocols::splice::SpliceOutAntibodyOP

SpliceOutCOP

typedef utility::pointer::shared_ptr< SpliceOut const > protocols::splice::SpliceOutCOP

SpliceOutOP

typedef utility::pointer::shared_ptr< SpliceOut > protocols::splice::SpliceOutOP

SpliceOutTailCOP

typedef utility::pointer::shared_ptr< SpliceOutTail const > protocols::splice::SpliceOutTailCOP

SpliceOutTailOP

typedef utility::pointer::shared_ptr< SpliceOutTail > protocols::splice::SpliceOutTailOP

SpliceSegmentCOP

typedef utility::pointer::shared_ptr< SpliceSegment const > protocols::splice::SpliceSegmentCOP

SpliceSegmentOP

typedef utility::pointer::shared_ptr< SpliceSegment > protocols::splice::SpliceSegmentOP

TagCOP

typedef utility::tag::TagCOP protocols::splice::TagCOP

TailSegmentMoverCOP

typedef utility::pointer::shared_ptr< TailSegmentMover const > protocols::splice::TailSegmentMoverCOP

TailSegmentMoverOP

typedef utility::pointer::shared_ptr< TailSegmentMover > protocols::splice::TailSegmentMoverOP

Function Documentation

atom_dist_with_zero()

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
	)

References core::pose::Pose::phi(), core::pose::Pose::psi(), core::pose::Pose::residue(), TR(), and core::conformation::Residue::xyz().

Referenced by protocols::splice::RotLibOut::find_matching_res().

Ca_coords()

utility::vector1< numeric::xyzVector< core::Real > > protocols::splice::Ca_coords	(	core::pose::Pose const &	pose,
		utility::vector1< core::Size > const	positions
	)

References coords(), core::pose::Pose::residue(), and core::conformation::Residue::xyz().

Referenced by protocols::splice::AlignEndsMover::apply().

calculate_rmsd()

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
	)

References core::pose::add_comment(), protocols::simple_filters::dssp(), core::pose::Pose::residue(), core::scoring::rms, TR(), and core::conformation::Residue::xyz().

Referenced by protocols::splice::Splice::apply(), and protocols::splice::SpliceOut::SpliceOutRMSDFilter().

compare()

bool protocols::splice::compare	(	std::pair< core::Size, core::Size >	p1,
		std::pair< core::Size, core::Size >	p2
	)

Referenced by find_disulfs_in_range().

complex_type_name_for_subsubtag()

std::string protocols::splice::complex_type_name_for_subsubtag

(

std::string const &

foo

)

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

complex_type_name_for_subtag()

std::string protocols::splice::complex_type_name_for_subtag

(

std::string const &

foo

)

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

concatenate_profiles() [1/2]

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

concatenate_profiles() [2/2]

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

coords()

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

References core::pose::Pose::residue(), and core::conformation::Residue::xyz().

Referenced by protocols::drug_design::align_residues(), core::conformation::all_atom_center(), core::pose::all_atom_center(), Ca_coords(), core::pose::center_of_mass(), core::conformation::symmetry::setup_symmetric_conformation(), protocols::splice::Splice::superimpose_source_on_pose(), protocols::splice::SpliceOut::superimpose_source_on_pose(), protocols::splice::SpliceOutTail::superimpose_source_on_pose(), and protocols::splice::RBOutMover::superimpose_source_on_pose().

find_disulfs_in_range()

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(), protocols::loops::start, and core::conformation::Residue::xyz().

find_residues_on_chain1_inside_interface()

utility::vector1< core::Size > protocols::splice::find_residues_on_chain1_inside_interface	(	core::pose::Pose const &	pose,
		core::Size	chainNum
	)

References core::pose::Pose::conformation(), core::conformation::Conformation::num_chains(), and protocols::rosetta_scripts::residue_packer_states().

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

fix_chain_break_residue()

void protocols::splice::fix_chain_break_residue	(	core::pose::Pose &	pose,
		SpliceManager	splicemanager
	)

References core::conformation::Residue::atom_index(), core::conformation::Residue::build_atom_ideal(), core::pose::Pose::conformation(), protocols::splice::SpliceManager::cut_site(), protocols::splice::SpliceManager::debug(), core::pose::Pose::replace_residue(), core::pose::Pose::residue(), core::conformation::Residue::set_xyz(), TR(), and core::conformation::Residue::xyz().

Referenced by protocols::splice::SpliceIn::apply().

is_identical_rotamer()

bool protocols::splice::is_identical_rotamer	(	ROT const	existing_res,
		ROT const	new_res
	)

References protocols::splice::ROT::AA, and protocols::splice::ROT::chi_vec.

Referenced by protocols::splice::SampleRotamersFromPDB_RotamerSetOperation::fill_rotamer_matrix_from_db_file(), and protocols::splice::RotLibdb::fill_rotamer_matrix_from_db_file().

load_pdb_segments_from_pose_comments()

void protocols::splice::load_pdb_segments_from_pose_comments	(	core::pose::Pose const &	pose,
		std::map< std::string, std::string > &	pdb_segments
	)

References core::pose::get_all_comments(), TR(), and protocols::hybridization::val.

Referenced by protocols::splice::Splice::apply(), protocols::splice::SpliceIn::apply(), protocols::splice::SpliceInTail::apply(), protocols::splice::SampleRotamersFromPDB::combine_rot_dbs(), protocols::splice::Splice::find_dbase_entry(), protocols::splice::Splice::generate_sequence_profile(), and protocols::splice::SpliceManager::generate_sequence_profile().

min_seg()

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
	)

References protocols::minimization_packing::MinMover::apply(), protocols::protein_interface_design::movers::AddChainBreak::apply(), core::conformation::Conformation::chain_end(), core::scoring::chainbreak, protocols::protein_interface_design::movers::AddChainBreak::change_foldtree(), core::kinematics::FoldTree::clone(), core::pose::Pose::conformation(), core::pack::interaction_graph::debug, core::pose::Pose::dump_pdb(), protocols::protein_interface_design::movers::AddChainBreak::find_automatically(), protocols::rosetta_scripts::find_nearest_disulfide(), core::pose::Pose::fold_tree(), core::pose::Pose::remove_constraints(), protocols::protein_interface_design::movers::AddChainBreak::resnum(), protocols::splice::ResidueBBDofs::size(), core::id::to_string(), and TR().

Referenced by protocols::splice::Splice::apply(), protocols::frags::get_min_and_max_contigs(), and protocols::frags::insert_random_fragments_in_flexible_protein_regions().

modify_dbase_with_compatible_backbones()

void protocols::splice::modify_dbase_with_compatible_backbones	(	utility::vector1< ResidueBBDofs >	torsion_database,
		utility::vector1< core::Size > &	dbase,
		utility::vector1< std::string >	intersect_pdbs
	)

References TR().

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

nearest_to_entry_stop_on_pose()

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
	)

References protocols::simple_moves::CutChainMover::chain_cut(), core::conformation::Conformation::chain_end(), core::pose::Pose::conformation(), and protocols::rosetta_scripts::find_nearest_res().

Referenced by protocols::splice::Splice::find_dbase_entry(), protocols::splice::SpliceIn::find_dbase_entry(), and protocols::splice::SpliceInTail::find_dbase_entry().

neighbors_in_vector()

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
	)

compute the number of residue neighbours target_res has within neighbours vector

References core::kinematics::distance(), protocols::simple_filters::dssp(), protocols::mean_field::max(), protocols::mean_field::min(), protocols::sic_dock::neighbor_count(), core::pose::Pose::residue(), and core::conformation::Residue::xyz().

Referenced by protocols::splice::FindEndpointsOperation::apply(), and protocols::splice::AlignEndsMover::reference_positions().

parse_pdb_code()

std::string protocols::splice::parse_pdb_code

(

std::string

pdb_file_name

)

Referenced by protocols::splice::RBOutMover::apply(), protocols::splice::SpliceOut::apply(), and protocols::splice::SpliceOut::find_non_active_site_cut_site().

printChi()

void protocols::splice::printChi

(

core::conformation::Residue const

res

)

References core::conformation::Residue::chi(), core::conformation::Residue::name3(), and TR().

Referenced by protocols::splice::SampleRotamersFromPDB_RotamerSetOperation::alter_rotamer_set_from_db(), and protocols::splice::SampleRotamersFromPDB_RotamerSetOperation::alter_rotamer_set_from_pdb().

read_H3_seq()

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().

read_pdb_seq()

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().

report_coordinate_constraints()

core::Size protocols::splice::report_coordinate_constraints

(

core::pose::Pose const &

pose

)

References core::pose::Pose::constraint_set(), and TR().

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

report_des_pack_res()

void protocols::splice::report_des_pack_res	(	core::pose::Pose const &	pose,
		core::pack::task::TaskFactoryOP	tf
	)

References protocols::rosetta_scripts::residue_packer_states(), and TR().

Referenced by protocols::splice::SpliceIn::rtmin().

report_designable_packable_residues()

void protocols::splice::report_designable_packable_residues	(	core::pack::task::TaskFactoryOP const	tf,
		core::pose::Pose	pose
	)

References protocols::rosetta_scripts::residue_packer_states(), and TR().

SpliceIn_complex_type_name_for_subsubtag()

std::string protocols::splice::SpliceIn_complex_type_name_for_subsubtag

(

std::string const &

foo

)

Referenced by protocols::splice::SpliceIn::provide_xml_schema().

SpliceIn_complex_type_name_for_subtag()

std::string protocols::splice::SpliceIn_complex_type_name_for_subtag

(

std::string const &

foo

)

Referenced by protocols::splice::SpliceIn::provide_xml_schema().

SpliceInAntibody_complex_type_name_for_subsubtag()

std::string protocols::splice::SpliceInAntibody_complex_type_name_for_subsubtag

(

std::string const &

foo

)

SpliceInAntibody_complex_type_name_for_subtag()

std::string protocols::splice::SpliceInAntibody_complex_type_name_for_subtag

(

std::string const &

foo

)

SpliceInTail_complex_type_name_for_subsubtag()

std::string protocols::splice::SpliceInTail_complex_type_name_for_subsubtag

(

std::string const &

foo

)

Referenced by protocols::splice::SpliceInTail::provide_xml_schema().

SpliceInTail_complex_type_name_for_subtag()

std::string protocols::splice::SpliceInTail_complex_type_name_for_subtag

(

std::string const &

foo

)

Referenced by protocols::splice::SpliceInTail::provide_xml_schema().

SpliceOut_complex_type_name_for_subsubtag()

std::string protocols::splice::SpliceOut_complex_type_name_for_subsubtag

(

std::string const &

foo

)

Referenced by protocols::splice::SpliceOut::provide_xml_schema().

SpliceOut_complex_type_name_for_subtag()

std::string protocols::splice::SpliceOut_complex_type_name_for_subtag

(

std::string const &

foo

)

Referenced by protocols::splice::SpliceOut::provide_xml_schema().

SpliceOutAntibody_complex_type_name_for_subsubtag()

std::string protocols::splice::SpliceOutAntibody_complex_type_name_for_subsubtag

(

std::string const &

foo

)

SpliceOutAntibody_complex_type_name_for_subtag()

std::string protocols::splice::SpliceOutAntibody_complex_type_name_for_subtag

(

std::string const &

foo

)

SpliceOutTail_complex_type_name_for_subsubtag()

std::string protocols::splice::SpliceOutTail_complex_type_name_for_subsubtag

(

std::string const &

foo

)

Referenced by protocols::splice::SpliceOutTail::provide_xml_schema().

SpliceOutTail_complex_type_name_for_subtag()

std::string protocols::splice::SpliceOutTail_complex_type_name_for_subtag

(

std::string const &

foo

)

Referenced by protocols::splice::SpliceOutTail::provide_xml_schema().

Srfp_complex_type_name_for_subsubtag()

std::string protocols::splice::Srfp_complex_type_name_for_subsubtag

(

std::string const &

foo

)

Referenced by protocols::splice::SampleRotamersFromPDB::provide_xml_schema().

Srfp_complex_type_name_for_subtag()

std::string protocols::splice::Srfp_complex_type_name_for_subtag

(

std::string const &

foo

)

Referenced by protocols::splice::SampleRotamersFromPDB::provide_xml_schema().

TR() [1/10]

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::Splice::add_sequence_constraints(), protocols::splice::SpliceManager::add_sequence_constraints(), protocols::splice::SpliceInAntibody::adjust_n_ter_tail_length(), protocols::splice::SpliceOutAntibody::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::TailSegmentMover::apply(), protocols::splice::DesignInterfacesOperation::apply(), protocols::splice::FindEndpointsOperation::apply(), protocols::splice::Splice::apply(), protocols::splice::SpliceIn::apply(), protocols::splice::SpliceInAntibody::apply(), protocols::splice::SpliceInTail::apply(), protocols::splice::SpliceOut::apply(), protocols::splice::SpliceOutAntibody::apply(), protocols::splice::SpliceIn::assign_from_res_to_res(), protocols::splice::SpliceInTail::assign_from_res_to_res(), atom_dist_with_zero(), protocols::splice::SpliceOut::build_ideal_segment(), protocols::splice::SpliceIn::build_ideal_segment(), protocols::splice::SpliceInTail::build_ideal_segment(), protocols::splice::SpliceOutTail::build_ideal_segment(), calculate_rmsd(), protocols::splice::SpliceOut::ccd_mover(), protocols::splice::Splice::chainbreak_check(), protocols::splice::SpliceManager::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::Splice::find_dbase_entry(), protocols::splice::SpliceIn::find_dbase_entry(), protocols::splice::SpliceInTail::find_dbase_entry(), protocols::splice::RotLibOut::find_matching_res(), protocols::splice::Splice::find_non_active_site_cut_site(), protocols::splice::SpliceOut::find_non_active_site_cut_site(), protocols::splice::SpliceInAntibody::find_vl_vh_cut(), protocols::splice::SpliceOutAntibody::find_vl_vh_cut(), fix_chain_break_residue(), protocols::splice::Splice::fold_tree(), protocols::splice::SpliceManager::fold_tree(), protocols::splice::Splice::generate_sequence_profile(), protocols::splice::SpliceManager::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::Splice::load_from_checkpoint(), protocols::splice::SpliceIn::load_from_checkpoint(), protocols::splice::Splice::load_pdb_segments_from_pose_comments(), protocols::splice::SpliceOut::load_pdb_segments_from_pose_comments(), 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::Splice::parse_my_tag(), protocols::splice::SpliceIn::parse_my_tag(), protocols::splice::SpliceInAntibody::parse_my_tag(), protocols::splice::SpliceInTail::parse_my_tag(), protocols::splice::SpliceOutAntibody::parse_my_tag(), protocols::splice::AlignEndsMover::parse_my_tag(), protocols::splice::RBOutMover::parse_my_tag(), protocols::splice::SpliceManager::parse_segments(), protocols::splice::SpliceOut::parse_SpliceOut_tags(), protocols::splice::SampleRotamersFromPDB::parse_tag(), protocols::splice::DesignInterfacesOperation::parse_tag(), protocols::splice::FindEndpointsOperation::parse_tag(), protocols::splice::SpliceManager::parse_tags(), protocols::splice::SpliceOut::place_cut_site_in_segment(), printChi(), protocols::splice::Splice::rb_adjust_template(), protocols::splice::SpliceManager::rb_adjust_template(), read_H3_seq(), read_pdb_seq(), protocols::splice::Splice::read_splice_segments(), protocols::splice::Splice::read_torsion_database(), protocols::splice::SpliceIn::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::SpliceIn::set_loop_length_change(), protocols::splice::SpliceInTail::set_loop_length_change(), protocols::splice::SpliceOut::set_source_from_to_res(), protocols::splice::SpliceOut::SpliceOutFilter(), protocols::splice::Splice::superimpose_source_on_pose(), protocols::splice::SpliceOut::superimpose_source_on_pose(), protocols::splice::SpliceOutTail::superimpose_source_on_pose(), protocols::splice::RBOutMover::superimpose_source_on_pose(), protocols::splice::Splice::tail_fold_tree(), protocols::splice::SpliceOut::write_database_to_file(), and protocols::splice::SpliceOutTail::write_database_to_file().

TR() [2/10]

static basic::Tracer protocols::splice::TR ( "protocols.splice.Splice"  )

static

TR() [3/10]

static basic::Tracer protocols::splice::TR ( "protocols.splice.SpliceIn"  )

static

TR() [4/10]

static basic::Tracer protocols::splice::TR ( "protocols.splice.SpliceInAntibody"  )

static

TR() [5/10]

static basic::Tracer protocols::splice::TR ( "protocols.splice.SpliceInTail"  )

static

TR() [6/10]

static basic::Tracer protocols::splice::TR ( "protocols.splice.SpliceManager"  )

static

TR() [7/10]

static basic::Tracer protocols::splice::TR ( "protocols.splice.SpliceOut"  )

static

TR() [8/10]

static basic::Tracer protocols::splice::TR ( "protocols.splice.SpliceOutAntibody"  )

static

TR() [9/10]

static basic::Tracer protocols::splice::TR ( "protocols.splice.SpliceOutTail"  )

static

TR() [10/10]

static basic::Tracer protocols::splice::TR ( "protocols.splice.SpliceSegment"  )

static

TR_ccd() [1/4]

static basic::Tracer protocols::splice::TR_ccd ( "protocols.splice.Splice_ccd"  )

static

Referenced by protocols::splice::Splice::apply(), and protocols::splice::SpliceOut::ccd_mover().

TR_ccd() [2/4]

static basic::Tracer protocols::splice::TR_ccd ( "protocols.splice.Splice_ccd"  )

static

TR_ccd() [3/4]

static basic::Tracer protocols::splice::TR_ccd ( "protocols.splice.Splice_ccd"  )

static

TR_ccd() [4/4]

static basic::Tracer protocols::splice::TR_ccd ( "protocols.splice.Splice_ccd"  )

static

TR_constraints() [1/8]

static basic::Tracer protocols::splice::TR_constraints ( "protocols.splice.Splice_constraints"  )

static

Referenced by protocols::splice::Splice::add_coordinate_constraints(), protocols::splice::SpliceManager::add_coordinate_constraints(), protocols::splice::Splice::add_dihedral_constraints(), protocols::splice::SpliceManager::add_dihedral_constraints(), protocols::splice::Splice::apply(), and protocols::splice::SpliceOut::apply().

TR_constraints() [2/8]

static basic::Tracer protocols::splice::TR_constraints ( "protocols.splice.Splice_constraints"  )

static

TR_constraints() [3/8]

static basic::Tracer protocols::splice::TR_constraints ( "protocols.splice.Splice_constraints"  )

static

TR_constraints() [4/8]

static basic::Tracer protocols::splice::TR_constraints ( "protocols.splice.Splice_constraints"  )

static

TR_constraints() [5/8]

static basic::Tracer protocols::splice::TR_constraints ( "protocols.splice.Splice_constraints"  )

static

TR_constraints() [6/8]

static basic::Tracer protocols::splice::TR_constraints ( "protocols.splice.Splice_constraints"  )

static

TR_constraints() [7/8]

static basic::Tracer protocols::splice::TR_constraints ( "protocols.splice.Splice_constraints"  )

static

TR_constraints() [8/8]

static basic::Tracer protocols::splice::TR_constraints ( "protocols.splice.Splice_constraints"  )

static

TR_min() [1/4]

static basic::Tracer protocols::splice::TR_min ( "protocols.splice.Splice_min"  )

static

Referenced by protocols::splice::SpliceOut::min_mover().

TR_min() [2/4]

static basic::Tracer protocols::splice::TR_min ( "protocols.splice.Splice_min"  )

static

TR_min() [3/4]

static basic::Tracer protocols::splice::TR_min ( "protocols.splice.Splice_min"  )

static

TR_min() [4/4]

static basic::Tracer protocols::splice::TR_min ( "protocols.splice.Splice_min"  )

static

TR_pssm() [1/7]

static basic::Tracer protocols::splice::TR_pssm ( "protocols.splice.Splice_pssm"  )

static

Referenced by protocols::splice::SpliceOut::check_pose_pssm_match(), protocols::splice::Splice::find_non_active_site_cut_site(), protocols::splice::SpliceOut::find_non_active_site_cut_site(), and protocols::splice::Splice::generate_sequence_profile().

TR_pssm() [2/7]

static basic::Tracer protocols::splice::TR_pssm ( "protocols.splice.Splice_pssm"  )

static

TR_pssm() [3/7]

static basic::Tracer protocols::splice::TR_pssm ( "protocols.splice.Splice_pssm"  )

static

TR_pssm() [4/7]

static basic::Tracer protocols::splice::TR_pssm ( "protocols.splice.Splice_pssm"  )

static

TR_pssm() [5/7]

static basic::Tracer protocols::splice::TR_pssm ( "protocols.splice.Splice_pssm"  )

static

TR_pssm() [6/7]

static basic::Tracer protocols::splice::TR_pssm ( "protocols.splice.Splice_pssm"  )

static

TR_pssm() [7/7]

static basic::Tracer protocols::splice::TR_pssm ( "protocols.splice.Splice_pssm"  )

static

TR_tail()

static basic::Tracer protocols::splice::TR_tail ( "protocols.splice.Splice_Tail"  )

static

Referenced by protocols::splice::SpliceOut::tail_mover().