protocols::dna Namespace Reference

Classes
class	DesignProteinBackboneAroundDNA
class	DesignProteinBackboneAroundDNACreator
class	DNABase
class	DNABasepair
class	DNABasestep
class	DnaChains
class	DnaDesignDef
	command-line dna_defs are of the format "C.501.ADE" they are parsed here into this little class for convenience More...
class	DnaInterfaceFinder
class	DnaInterfaceMinMover
class	DnaInterfaceMinMoverCreator
class	DnaInterfaceMultiStateDesign
	wraps DNA-interface specific considerations around the general multistate design / genetic algorithm framework More...
class	DnaInterfaceMultiStateDesignCreator
class	DnaInterfacePacker
class	DnaInterfacePackerCreator
class	DnaNeighbor
class	DNAParameters
class	DnaPosition
class	PDBOutput
class	PositionType
	basic struct for remembering position/type information before/during/after design More...
class	RestrictDesignToProteinDNAInterface
class	RestrictDesignToProteinDNAInterfaceCreator
class	ResTypeSequence_lt
class	Reversion
class	RotamerDNAHBondFilter
class	SeparateDnaFromNonDna
class	SeparateDnaFromNonDnaCreator
class	WatsonCrickRotamerCouplings
class	WatsonCrickRotamerCouplingsCreator

Typedefs
typedef utility::pointer::shared_ptr < DnaChains >	DnaChainsOP
typedef utility::pointer::shared_ptr < DnaChains const >	DnaChainsCOP
typedef std::map< core::Size, DnaPosition >	DnaPositions
typedef utility::pointer::shared_ptr < DnaDesignDef >	DnaDesignDefOP
typedef utility::pointer::shared_ptr < DnaDesignDef const >	DnaDesignDefCOP
typedef utility::vector1 < DnaDesignDef >	DnaDesignDefs
typedef utility::vector1 < DnaDesignDefOP >	DnaDesignDefOPs
typedef utility::pointer::shared_ptr < DnaInterfaceFinder >	DnaInterfaceFinderOP
typedef utility::pointer::shared_ptr < DnaInterfaceFinder const >	DnaInterfaceFinderCOP
typedef std::map< core::Size, DnaNeighbor >	DnaNeighbors
typedef utility::pointer::shared_ptr < DnaInterfaceMinMover >	DnaInterfaceMinMoverOP
typedef utility::pointer::shared_ptr < DnaInterfaceMinMover const >	DnaInterfaceMinMoverCOP
typedef utility::pointer::shared_ptr < DnaInterfaceMultiStateDesign >	DnaInterfaceMultiStateDesignOP
typedef utility::pointer::shared_ptr < DnaInterfaceMultiStateDesign const >	DnaInterfaceMultiStateDesignCOP
typedef vector1< Reversion >	Reversions
typedef utility::pointer::shared_ptr < DnaInterfacePacker >	DnaInterfacePackerOP
typedef utility::pointer::shared_ptr < DnaInterfacePacker const >	DnaInterfacePackerCOP
typedef std::map < ResTypeSequence, core::Real, ResTypeSequence_lt >	SequenceScores
typedef utility::pointer::shared_ptr < DNAParameters >	DNAParametersOP
typedef utility::pointer::shared_ptr < DNAParameters const >	DNAParametersCOP
typedef utility::pointer::shared_ptr < PDBOutput >	PDBOutputOP
typedef utility::pointer::shared_ptr < PDBOutput const >	PDBOutputCOP
typedef utility::pointer::shared_ptr < RestrictDesignToProteinDNAInterface >	RestrictDesignToProteinDNAInterfaceOP
typedef utility::pointer::shared_ptr < RotamerDNAHBondFilter >	RotamerDNAHBondFilterOP
typedef utility::pointer::shared_ptr < SeparateDnaFromNonDna >	SeparateDnaFromNonDnaOP
typedef utility::pointer::shared_ptr < SeparateDnaFromNonDna const >	SeparateDnaFromNonDnaCOP
typedef std::map< core::Size, core::chemical::ResidueTypeCOP >	ResTypeSequence
typedef utility::vector1 < ResTypeSequence >	ResTypeSequences
typedef std::map< core::Size, core::chemical::ResidueTypeCOPs >	TypesMap
typedef utility::vector1 < core::Size >	Positions
typedef utility::vector1 < std::string >	Strings
typedef utility::vector1 < PositionType >	PositionTypes
typedef utility::pointer::shared_ptr < WatsonCrickRotamerCouplings >	WatsonCrickRotamerCouplingsOP
typedef utility::pointer::shared_ptr < ProteinInterfaceMultiStateDesignMover >	ProteinInterfaceMultiStateDesignMoverOP
typedef utility::pointer::shared_ptr < ProteinInterfaceMultiStateDesignMover const >	ProteinInterfaceMultiStateDesignMoverCOP

Functions
static thread_local basic::Tracer	TR ("protocols.dna.DesignProteinBackboneAroundDNA", t_info)
std::ostream &	operator<< (std::ostream &os, DnaDesignDef const &def)
std::ostream &	operator<< (std::ostream &os, DnaDesignDefs const &defs)
std::ostream &	operator<< (std::ostream &os, DnaDesignDefOPs const &defs)
static thread_local basic::Tracer	TR ("protocols.dna.DnaInterfaceMinMover", t_info)
static thread_local basic::Tracer	TR ("protocols.dna.DnaInterfaceMultiStateDesign", t_info)
static thread_local basic::Tracer	TR ("protocols.dna.DnaInterfacePacker")
static thread_local basic::Tracer	TR_spec ("protocols.dna.Specificity")
static thread_local basic::Tracer	TR ("protocols.dna.PDBOutput", t_info)
std::string	string_join (PDBOutput::Strings const &list, std::string sep=", ")
void	make_subdirs (std::string const &name)
static thread_local basic::Tracer	TR ("protocols.dna.RestrictDesignToProteinDNAInterface", t_info)
static thread_local basic::Tracer	TR ("protocols.dna.SeparateDnaFromNonDna", basic::t_info)
static thread_local basic::Tracer	TR ("protocols.dna.util", basic::t_info)
bool	close_to_dna (Residue const &pres, Residue const &dres, Real threshold, bool base_only)
Real	argrot_dna_dis2 (pose::Pose const &pose, Size presid, Residue const &pres, Residue const &dres, Real threshold, bool base_only)
Real	contact_distance2 (Atoms::const_iterator a_begin, Atoms::const_iterator a_end, Atoms::const_iterator b_begin, Atoms::const_iterator b_end, Real threshold)
Real	z_axis_dist (Residue const &pres, Residue const &dres)
std::string	dna_comp_name_str (std::string const &dna)
	also consider using the dna_base_partner function below More...
std::string	dna_full_name3 (std::string const &name3)
	intended to convert any DNA "threeletter code" into the full three-letter code. Note that this does not (necessarily) return the same thing as residue_type::name3 (which returns " N" format as of Dec 2008) More...
chemical::AA	dna_base_partner (chemical::AA const &na)
	helper function More...
void	find_basepairs (pose::Pose const &pose, DnaChains &dna_chains, bool include_unpaired)
void	make_sequence_combinations (utility::vector1< Size >::const_iterator seqset_iter, utility::vector1< Size > const &seq_indices, task::PackerTaskCOP ptask, ResTypeSequence &sequence, ResTypeSequences &sequences)
void	make_single_mutants (ResTypeSequence const &sequence, task::PackerTaskCOP ptask, ResTypeSequences &sequences)
	make a list of all single mutants from a base sequence More...
void	design_residues_list (std::list< PositionType > &design_residues, pose::Pose const &pose, task::PackerTask const &ptask)
std::ostream &	operator<< (std::ostream &os, ResTypeSequence const &seq)
std::string	seq_to_str (ResTypeSequence const &seq)
std::ostream &	operator<< (std::ostream &os, ResTypeSequences const &seqs)
std::string	seq_pdb_str (ResTypeSequence const &seq, pose::Pose const &pose)
void	print_sequence_pdb_nums (ResTypeSequence const &seq, pose::Pose const &pose, std::ostream &os)
void	print_sequences_pdb_nums (ResTypeSequences const &seqs, pose::Pose const &pose, std::ostream &os)
void	restrict_dna_rotamers (RotamerSetsCOP rotamer_sets, ResTypeSequence const &seq, utility::vector0< int > &rot_to_pack)
void	restrict_to_single_sequence (rotamer_set::RotamerSetsCOP rotamer_sets, vector1< ResidueTypeCOP > const &single_sequence, utility::vector0< int > &rot_to_pack)
void	substitute_residue (pose::Pose &pose, Size index, ResidueType const &new_type)
void	write_checkpoint (pose::Pose &pose, Size iter)
void	load_checkpoint (pose::Pose &pose, Size &iter)
void	checkpoint_cleanup ()
void	load_dna_design_defs_from_strings (DnaDesignDefOPs &defs, Strings const &str_defs)
	loads command-line dna design definitions (shorthand alternative to using resfile) option value is string vector i.e. -dna_defs C.-6 C.-5 or -dna_defs C.-6.GUA C.-5.CYT More...
void	load_dna_design_defs_from_file (DnaDesignDefOPs &defs, std::string const &filename, std::string const &pdb_prefix)
void	load_dna_design_defs_from_options (DnaDesignDefOPs &defs, std::string pdb_prefix)
void	add_constraints_from_file (pose::Pose &pose)
kinematics::FoldTree	make_base_pair_aware_fold_tree (pose::Pose const &pose)
bool	not_already_connected (pose::Pose const &pose, Size const num_jumps, char const this_chain, char const other_chain, ObjexxFCL::FArray2D_int &jump_pairs)
void	set_base_segment_chainbreak_constraints (pose::Pose &pose, core::Size const start_base, core::Size const end_base)
void	design_residues_list (std::list< PositionType > &design_residues, core::pose::Pose const &pose, core::pack::task::PackerTask const &ptask)
void	load_dna_design_defs_from_strings (DnaDesignDefOPs &defs, utility::vector1< std::string > const &str_defs)
	loads command-line dna design definitions (shorthand alternative to using resfile) option value is string vector i.e. -dna_defs C.-6 C.-5 or -dna_defs C.-6.GUA C.-5.CYT More...
static thread_local basic::Tracer	TR ("protocols.dna.WatsonCrickRotamerCouplings", t_info)

Variables
int const	PRECISION (3)

Typedef Documentation

typedef utility::pointer::shared_ptr< DnaChains const > protocols::dna::DnaChainsCOP

typedef utility::pointer::shared_ptr< DnaChains > protocols::dna::DnaChainsOP

typedef utility::pointer::shared_ptr< DnaDesignDef const > protocols::dna::DnaDesignDefCOP

typedef utility::pointer::shared_ptr< DnaDesignDef > protocols::dna::DnaDesignDefOP

typedef utility::vector1< DnaDesignDefOP > protocols::dna::DnaDesignDefOPs

typedef utility::vector1< DnaDesignDef > protocols::dna::DnaDesignDefs

typedef utility::pointer::shared_ptr< DnaInterfaceFinder const > protocols::dna::DnaInterfaceFinderCOP

typedef utility::pointer::shared_ptr< DnaInterfaceFinder > protocols::dna::DnaInterfaceFinderOP

typedef utility::pointer::shared_ptr< DnaInterfaceMinMover const > protocols::dna::DnaInterfaceMinMoverCOP

typedef utility::pointer::shared_ptr< DnaInterfaceMinMover > protocols::dna::DnaInterfaceMinMoverOP

typedef utility::pointer::shared_ptr< DnaInterfaceMultiStateDesign const > protocols::dna::DnaInterfaceMultiStateDesignCOP

typedef utility::pointer::shared_ptr< DnaInterfaceMultiStateDesign > protocols::dna::DnaInterfaceMultiStateDesignOP

typedef utility::pointer::shared_ptr< DnaInterfacePacker const > protocols::dna::DnaInterfacePackerCOP

typedef utility::pointer::shared_ptr< DnaInterfacePacker > protocols::dna::DnaInterfacePackerOP

typedef std::map< core::Size, DnaNeighbor > protocols::dna::DnaNeighbors

typedef utility::pointer::shared_ptr< DNAParameters const > protocols::dna::DNAParametersCOP

typedef utility::pointer::shared_ptr< DNAParameters > protocols::dna::DNAParametersOP

typedef std::map< core::Size, DnaPosition > protocols::dna::DnaPositions

typedef utility::pointer::shared_ptr< PDBOutput const > protocols::dna::PDBOutputCOP

typedef utility::pointer::shared_ptr< PDBOutput > protocols::dna::PDBOutputOP

typedef utility::vector1< core::Size > protocols::dna::Positions

typedef utility::vector1< PositionType > protocols::dna::PositionTypes

typedef utility::pointer::shared_ptr< ProteinInterfaceMultiStateDesignMover const > protocols::dna::ProteinInterfaceMultiStateDesignMoverCOP

typedef utility::pointer::shared_ptr< ProteinInterfaceMultiStateDesignMover > protocols::dna::ProteinInterfaceMultiStateDesignMoverOP

typedef utility::pointer::shared_ptr< RestrictDesignToProteinDNAInterface > protocols::dna::RestrictDesignToProteinDNAInterfaceOP

typedef std::map< core::Size, core::chemical::ResidueTypeCOP > protocols::dna::ResTypeSequence

typedef utility::vector1< ResTypeSequence > protocols::dna::ResTypeSequences

typedef vector1< Reversion > protocols::dna::Reversions

typedef utility::pointer::shared_ptr< RotamerDNAHBondFilter > protocols::dna::RotamerDNAHBondFilterOP

typedef utility::pointer::shared_ptr< SeparateDnaFromNonDna const > protocols::dna::SeparateDnaFromNonDnaCOP

typedef utility::pointer::shared_ptr< SeparateDnaFromNonDna > protocols::dna::SeparateDnaFromNonDnaOP

typedef std::map< ResTypeSequence, core::Real, ResTypeSequence_lt > protocols::dna::SequenceScores

typedef utility::vector1< std::string > protocols::dna::Strings

typedef std::map< core::Size, core::chemical::ResidueTypeCOPs > protocols::dna::TypesMap

typedef utility::pointer::shared_ptr< WatsonCrickRotamerCouplings > protocols::dna::WatsonCrickRotamerCouplingsOP

Function Documentation

void protocols::dna::add_constraints_from_file

(

pose::Pose &

pose

)

References core::pose::Pose::constraint_set(), option, and user.

core::Real protocols::dna::argrot_dna_dis2	(	pose::Pose const &	pose,
		Size	presid,
		Residue const &	pres,
		Residue const &	dres,
		Real	threshold,
		bool	base_only
	)

argrot_dna_dis2

arginine rotamer sweep at a protein residue to see if it should be considered a (potentially) 'dna-contacting' residue

Authors

ashworth

arginine rotamer sweep at a protein residue to see if it should be considered a (potentially) 'dna-contacting' residue

Authors

ashworth

References aa_arg, core::conformation::Residue::atom_begin(), contact_distance2(), core::pack::task::TaskFactory::create_packer_task(), core::scoring::ScoreFunctionFactory::create_score_function(), core::conformation::Residue::heavyAtoms_end(), num_canonical_aas, option, core::pack::task::ResidueLevelTask::or_ex1(), runtime_assert, core::conformation::Residue::sidechainAtoms_begin(), core::pose::Pose::total_residue(), and user.

Referenced by protocols::dna::DnaInterfaceFinder::determine_dna_interface(), protocols::dna::DnaInterfaceFinder::determine_protein_interface(), and protocols::enzdes::DetectProteinLigandInterface::find_design_interface_arg_sweep().

void protocols::dna::checkpoint_cleanup

(

)

References utility::file::file_exists(), filename(), option, and user.

bool protocols::dna::close_to_dna	(	Residue const &	pres,
		Residue const &	dres,
		Real	threshold,
		bool	base_only
	)

close_to_dna

checks c-beta (except glycine) to base atom-atom distances, not including ribose or phosphate backbone.

Authors

ashworth

checks c-beta (except glycine) to base atom-atom distances, not including ribose or phosphate backbone.

Authors

ashworth

References core::conformation::Residue::atom_begin(), end, core::conformation::Residue::heavyAtoms_end(), core::conformation::Residue::nbr_atom_xyz(), and core::conformation::Residue::sidechainAtoms_begin().

Referenced by protocols::dna::DnaInterfaceFinder::determine_dna_interface(), protocols::dna::DnaInterfaceFinder::determine_protein_interface(), protocols::enzdes::DetectProteinLigandInterface::find_design_interface_arg_sweep(), and protocols::dna::RotamerDNAHBondFilter::operator()().

core::Real protocols::dna::contact_distance2	(	Atoms::const_iterator	a_begin,
		Atoms::const_iterator	a_end,
		Atoms::const_iterator	b_begin,
		Atoms::const_iterator	b_end,
		Real	threshold
	)

contact_distance2

distance check for contact between two sets of atoms

Authors

ashworth

distance check for contact between two sets of atoms

Authors

ashworth

Referenced by argrot_dna_dis2().

void protocols::dna::design_residues_list	(	std::list< PositionType > &	design_residues,
		core::pose::Pose const &	pose,
		core::pack::task::PackerTask const &	ptask
	)

void protocols::dna::design_residues_list	(	std::list< PositionType > &	design_residues,
		pose::Pose const &	pose,
		task::PackerTask const &	ptask
	)

References core::chemical::ResidueType::get_self_ptr(), core::chemical::ResidueType::is_DNA(), core::pose::Pose::residue_type(), and core::pose::Pose::total_residue().

core::chemical::AA protocols::dna::dna_base_partner

(

chemical::AA const &

na

)

helper function

References aa_unk, na_ade, na_cyt, na_gua, na_thy, and utility_exit_with_message.

Referenced by protocols::dna::DnaInterfacePacker::add_complementary_sequence(), and protocols::motifs::make_base_pair_mutation().

std::string protocols::dna::dna_comp_name_str

(

std::string const &

dna

)

also consider using the dna_base_partner function below

dna_comp_name_str

Authors

ashworth

ashworth

References utility_exit_with_message.

Referenced by protocols::dna::DnaInterfaceMultiStateDesign::add_dna_states(), and protocols::dna::RestrictDesignToProteinDNAInterface::apply().

std::string protocols::dna::dna_full_name3

(

std::string const &

name3

)

intended to convert any DNA "threeletter code" into the full three-letter code. Note that this does not (necessarily) return the same thing as residue_type::name3 (which returns " N" format as of Dec 2008)

dna_full_name3

Referenced by protocols::dna::WatsonCrickRotamerCouplings::apply(), protocols::motifs::Motif::apply_check(), protocols::dna::DnaInterfacePacker::calculate_specificity(), protocols::dna::DnaInterfacePacker::dna_seq_tag(), protocols::motifs::MotifSearch::incorporate_motifs(), protocols::motifs::LigandMotifSearch::incorporate_motifs(), protocols::motifs::MotifSearch::initialize(), protocols::motifs::make_dna_mutations(), protocols::motifs::Motif::Motif(), protocols::dna::PDBOutput::output_buried_unsatisfied_hbonds(), protocols::motifs::Motif::place_atoms(), protocols::motifs::Motif::place_residue(), protocols::motifs::MotifSearch::protein_dna_motif(), protocols::motifs::LigandMotifSearch::protein_dna_motif(), protocols::dna::DnaInterfacePacker::protein_scan(), and seq_pdb_str().

void protocols::dna::find_basepairs	(	pose::Pose const &	pose,
		DnaChains &	dna_chains,
		bool	include_unpaired
	)

find_basepairs

DnaChains version, adapted from pbradley's code. More paranoid geometry checks, in order to allow highly distorted basepairs without making mistakes

Authors

ashworth

DnaChains version, adapted from pbradley's code. More paranoid geometry checks, in order to allow highly distorted basepairs without making mistakes

Authors

ashworth

References protocols::dna::DnaChains::clear(), protocols::dna::DnaChains::contains(), dot(), protocols::dna::DnaChains::empty(), get_y_axis(), get_z_axis(), na_ade, na_cyt, na_gua, na_rad, na_rcy, na_rgu, na_thy, na_ura, core::pose::Pose::pdb_info(), protocols::dna::DnaChains::print(), core::pose::Pose::residue(), runtime_assert, and core::pose::Pose::total_residue().

Referenced by protocols::dna::WatsonCrickRotamerCouplings::apply(), protocols::dna::RestrictDesignToProteinDNAInterface::apply(), protocols::dna::DnaInterfacePacker::init_standard(), and protocols::dna::DnaInterfaceMultiStateDesign::initialize().

void protocols::dna::load_checkpoint	(	pose::Pose &	pose,
		Size &	iter
	)

References utility::io::izstream::close(), filename(), utility::io::izstream::open(), option, core::import_pose::pose_from_pdb(), skip(), and user.

void protocols::dna::load_dna_design_defs_from_file	(	DnaDesignDefOPs &	defs,
		std::string const &	filename,
		std::string const &	pdb_prefix
	)

References getline(), load_dna_design_defs_from_strings(), and string_split().

Referenced by load_dna_design_defs_from_options().

void protocols::dna::load_dna_design_defs_from_options	(	DnaDesignDefOPs &	defs,
		std::string	pdb_prefix
	)

References load_dna_design_defs_from_file(), load_dna_design_defs_from_strings(), option, and user.

Referenced by protocols::motifs::get_target_position_map_make_dna_mutations(), protocols::motifs::get_target_positions_make_dna_mutations(), protocols::motifs::MotifDnaPacker::init_standard(), protocols::motifs::make_dna_mutations(), and protocols::dna::RestrictDesignToProteinDNAInterface::parse_tag().

void protocols::dna::load_dna_design_defs_from_strings	(	DnaDesignDefOPs &	defs,
		utility::vector1< std::string > const &	str_defs
	)

loads command-line dna design definitions (shorthand alternative to using resfile) option value is string vector i.e. -dna_defs C.-6 C.-5 or -dna_defs C.-6.GUA C.-5.CYT

Author

ashworth

void protocols::dna::load_dna_design_defs_from_strings	(	DnaDesignDefOPs &	defs,
		Strings const &	str_defs
	)

loads command-line dna design definitions (shorthand alternative to using resfile) option value is string vector i.e. -dna_defs C.-6 C.-5 or -dna_defs C.-6.GUA C.-5.CYT

load_dna_design_defs

Author

ashworth

References end.

Referenced by protocols::motifs::get_motif_build_position_defs_user(), protocols::motifs::get_motif_build_positions_user(), protocols::motifs::get_target_position_map_make_dna_mutations(), protocols::motifs::get_target_positions_make_dna_mutations(), protocols::motifs::MotifDnaPacker::init_standard(), load_dna_design_defs_from_file(), load_dna_design_defs_from_options(), protocols::motifs::make_dna_mutations(), and protocols::dna::RestrictDesignToProteinDNAInterface::parse_tag().

core::kinematics::FoldTree protocols::dna::make_base_pair_aware_fold_tree

(

pose::Pose const &

pose

)

References numeric::xyzVector< class >::distance_squared(), core::conformation::Residue::is_DNA(), core::conformation::Residue::is_protein(), not_already_connected(), core::pose::Pose::pdb_info(), core::pose::Pose::residue(), core::pose::Pose::total_residue(), core::kinematics::FoldTree::tree_from_jumps_and_cuts(), utility_exit_with_message, and core::conformation::Residue::xyz().

void protocols::dna::make_sequence_combinations	(	utility::vector1< Size >::const_iterator	seqset_iter,
		utility::vector1< Size > const &	seq_indices,
		task::PackerTaskCOP	ptask,
		ResTypeSequence &	sequence,
		ResTypeSequences &	sequences
	)

make_sequence_combinations

populates a set of all possible sequence combinations over a given range of positions. recursive.

Authors

ashworth

Referenced by protocols::dna::DnaInterfacePacker::make_dna_sequence_combinations().

void protocols::dna::make_single_mutants	(	ResTypeSequence const &	sequence,
		task::PackerTaskCOP	ptask,
		ResTypeSequences &	sequences
	)

make a list of all single mutants from a base sequence

make_single_mutants

Authors

ashworth

ashworth

Referenced by protocols::dna::DnaInterfacePacker::measure_specificity().

void protocols::dna::make_subdirs

(

std::string const &

name

)

References utility::file::create_directory(), utility::file::file_exists(), and string_split().

Referenced by protocols::dna::PDBOutput::operator()().

bool protocols::dna::not_already_connected	(	pose::Pose const &	pose,
		Size const	num_jumps,
		char const	this_chain,
		char const	other_chain,
		ObjexxFCL::FArray2D_int &	jump_pairs
	)

References core::pose::Pose::pdb_info().

Referenced by make_base_pair_aware_fold_tree().

std::ostream & protocols::dna::operator<<	(	std::ostream &	os,
		DnaDesignDef const &	def
	)

References protocols::dna::DnaDesignDef::chain, protocols::dna::DnaDesignDef::name3, and protocols::dna::DnaDesignDef::pdbpos.

std::ostream & protocols::dna::operator<<	(	std::ostream &	os,
		DnaDesignDefs const &	defs
	)

References end.

std::ostream & protocols::dna::operator<<	(	std::ostream &	os,
		DnaDesignDefOPs const &	defs
	)

References end.

std::ostream & protocols::dna::operator<<	(	std::ostream &	os,
		ResTypeSequence const &	seq
	)

std::ostream & protocols::dna::operator<<	(	std::ostream &	os,
		ResTypeSequences const &	seqs
	)

void protocols::dna::print_sequence_pdb_nums	(	ResTypeSequence const &	seq,
		pose::Pose const &	pose,
		std::ostream &	os
	)

References seq_pdb_str().

Referenced by print_sequences_pdb_nums(), and protocols::dna::DnaInterfacePacker::standard_packing().

void protocols::dna::print_sequences_pdb_nums	(	ResTypeSequences const &	seqs,
		pose::Pose const &	pose,
		std::ostream &	os
	)

References print_sequence_pdb_nums().

Referenced by protocols::dna::DnaInterfacePacker::init_standard().

void protocols::dna::restrict_dna_rotamers	(	RotamerSetsCOP	rotamer_sets,
		ResTypeSequence const &	seq,
		utility::vector0< int > &	rot_to_pack
	)

restrict_dna_rotamers

for packing a single DNA sequence out of a multi-DNA-sequence RotamerSet

Authors

ashworth

for packing a single DNA sequence out of a multi-DNA-sequence RotamerSet

Authors

ashworth

Referenced by protocols::dna::DnaInterfacePacker::standard_packing().

void protocols::dna::restrict_to_single_sequence	(	rotamer_set::RotamerSetsCOP	rotamer_sets,
		vector1< ResidueTypeCOP > const &	single_sequence,
		utility::vector0< int > &	rot_to_pack
	)

restrict_to_single_sequence

for packing a single sequence out of a RotamerSets that (potentially) represents sequence variability

Authors

ashworth

for packing a single sequence out of a RotamerSets that (potentially) represents sequence variability

Authors

ashworth

Referenced by protocols::dna::DnaInterfacePacker::measure_specificities(), protocols::dna::DnaInterfacePacker::protein_scan(), and protocols::dna::DnaInterfacePacker::reversion_scan().

std::string protocols::dna::seq_pdb_str	(	ResTypeSequence const &	seq,
		pose::Pose const &	pose
	)

References core::pose::Pose::chain(), dna_full_name3(), core::pose::Pose::pdb_info(), and core::pose::Pose::total_residue().

Referenced by protocols::dna::DnaInterfacePacker::measure_bp_specificities(), protocols::dna::DnaInterfacePacker::post_packing(), and print_sequence_pdb_nums().

std::string protocols::dna::seq_to_str

(

ResTypeSequence const &

seq

)

References protocols::kinmatch::str().

void protocols::dna::set_base_segment_chainbreak_constraints	(	pose::Pose &	pose,
		core::Size const	start_base,
		core::Size const	end_base
	)

References core::pose::Pose::add_constraint(), core::chemical::ResidueType::is_lower_terminus(), core::chemical::ResidueType::is_upper_terminus(), core::pose::Pose::pdb_info(), numeric::conversions::radians(), radians(), core::pose::Pose::residue(), and core::pose::Pose::residue_type().

std::string protocols::dna::string_join	(	PDBOutput::Strings const &	list,
		std::string	sep = ", "
	)

References end.

Referenced by protocols::dna::PDBOutput::output_design_tags().

void protocols::dna::substitute_residue	(	pose::Pose &	pose,
		Size	index,
		ResidueType const &	new_type
	)

substitute_residue

Authors

ashworth

References core::pose::Pose::conformation(), core::conformation::ResidueFactory::create_residue(), core::pose::Pose::replace_residue(), and core::pose::Pose::residue().

Referenced by protocols::dna::DnaInterfaceMultiStateDesign::add_dna_states().

static thread_local basic::Tracer protocols::dna::TR ( "protocols.dna.SeparateDnaFromNonDna"  , basic::t_info    )

static

static thread_local basic::Tracer protocols::dna::TR ( "protocols.dna.WatsonCrickRotamerCouplings"  , t_info    )

static

static thread_local basic::Tracer protocols::dna::TR ( "protocols.dna.DnaInterfaceMinMover"  , t_info    )

static

static thread_local basic::Tracer protocols::dna::TR ( "protocols.dna.RestrictDesignToProteinDNAInterface"  , t_info    )

static

static thread_local basic::Tracer protocols::dna::TR ( "protocols.dna.PDBOutput"  , t_info    )

static

static thread_local basic::Tracer protocols::dna::TR ( "protocols.dna.DesignProteinBackboneAroundDNA"  , t_info    )

static

Referenced by protocols::dna::DnaInterfaceMultiStateDesign::add_dna_states(), protocols::dna::WatsonCrickRotamerCouplings::apply(), protocols::dna::SeparateDnaFromNonDna::apply(), protocols::dna::DesignProteinBackboneAroundDNA::apply(), protocols::dna::RestrictDesignToProteinDNAInterface::apply(), protocols::dna::DnaInterfacePacker::init_standard(), protocols::dna::DnaInterfaceMultiStateDesign::initialize(), protocols::dna::DnaInterfacePacker::measure_bp_specificities(), protocols::dna::DnaInterfacePacker::measure_specificity(), protocols::dna::PDBOutput::output_buried_unsatisfied_hbonds(), protocols::dna::DnaInterfaceMultiStateDesign::output_results(), protocols::dna::DnaInterfaceMinMover::parse_my_tag(), protocols::dna::RestrictDesignToProteinDNAInterface::parse_tag(), protocols::dna::DnaInterfacePacker::post_packing(), protocols::dna::DnaInterfacePacker::protein_scan(), protocols::dna::RotamerDNAHBondFilter::report(), protocols::dna::DnaInterfacePacker::reversion_scan(), protocols::dna::DnaInterfaceMultiStateDesign::run(), and protocols::dna::DnaInterfacePacker::standard_packing().

static thread_local basic::Tracer protocols::dna::TR ( "protocols.dna.DnaInterfaceMultiStateDesign"  , t_info    )

static

static thread_local basic::Tracer protocols::dna::TR ( "protocols.dna.util"  , basic::t_info    )

static

static thread_local basic::Tracer protocols::dna::TR ( "protocols.dna.DnaInterfacePacker"  )

static

static thread_local basic::Tracer protocols::dna::TR_spec ( "protocols.dna.Specificity"  )

static

Referenced by protocols::dna::DnaInterfacePacker::calculate_specificity(), protocols::dna::DnaInterfacePacker::measure_bp_specificities(), and protocols::dna::DnaInterfacePacker::measure_specificity().

void protocols::dna::write_checkpoint	(	pose::Pose &	pose,
		Size	iter
	)

References core::pose::Pose::dump_pdb(), option, runtime_assert, and user.

core::Real protocols::dna::z_axis_dist	(	Residue const &	pres,
		Residue const &	dres
	)

z_axis_dist

A sanity check for the arginine rotamer screen. Can prevent the design of positions that are best left alone because they are too far away along the helical axis ('laterally').

Authors

ashworth

A sanity check for the arginine rotamer screen. Can prevent the design of positions that are best left alone because they are too far away along the helical axis ('laterally').

Authors

ashworth

References dot(), core::conformation::Residue::first_sidechain_atom(), get_y_axis(), get_z_axis(), core::conformation::Residue::nbr_atom_xyz(), and core::conformation::Residue::xyz().

Referenced by protocols::dna::DnaInterfaceFinder::determine_dna_interface(), and protocols::dna::DnaInterfaceFinder::determine_protein_interface().

Variable Documentation

int const protocols::dna::PRECISION(3)

Referenced by protocols::dna::DnaInterfacePacker::calculate_specificity(), protocols::dna::DnaInterfacePacker::init_standard(), protocols::dna::DnaInterfacePacker::measure_bp_specificities(), protocols::dna::DnaInterfacePacker::post_packing(), and protocols::dna::DnaInterfacePacker::protein_scan().