protocols::dna Namespace Reference

Classes
class	DesignProteinBackboneAroundDNA
class	DesignProteinBackboneAroundDNACreator
class	DnaPosition
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	DnaNeighbor
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	Reversion
class	ResTypeSequence_lt
class	DnaInterfacePacker
class	DnaInterfacePackerCreator
class	DNABase
class	DNABasepair
class	DNABasestep
class	DNAParameters
class	PDBOutput
class	RestrictDesignToProteinDNAInterface
class	RestrictDesignToProteinDNAInterfaceCreator
class	RotamerDNAHBondFilter
class	SeparateDnaFromNonDna
class	SeparateDnaFromNonDnaCreator
class	PositionType
	basic struct for remembering position/type information before/during/after design More...
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
using	Reversions = vector1< Reversion >
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
using	Strings = utility::vector1< std::string >
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 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 basic::Tracer	TR ("protocols.dna.DnaInterfaceMinMover", t_info)
static basic::Tracer	TR ("protocols.dna.DnaInterfaceMultiStateDesign", t_info)
int const	PRECISION (3)
static basic::Tracer	TR ("protocols.dna.DnaInterfacePacker")
static basic::Tracer	TR_spec ("protocols.dna.Specificity")
static basic::Tracer	TR ("protocols.dna.PDBOutput", t_info)
std::string	string_join (PDBOutput::Strings const &list, std::string const &sep=", ")
void	make_subdirs (std::string const &name)
static basic::Tracer	TR ("protocols.dna.RestrictDesignToProteinDNAInterface", t_info)
static basic::Tracer	TR ("protocols.dna.SeparateDnaFromNonDna", basic::t_info)
static 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, core::Size presid, Residue const &, 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< core::Size >::const_iterator seqset_iter, utility::vector1< core::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, core::Size index, ResidueType const &new_type)
void	write_checkpoint (pose::Pose &pose, core::Size iter)
void	load_checkpoint (pose::Pose &pose, core::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 const &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, core::Size const num_jumps, char const this_chain, char const other_chain, ObjexxFCL::FArray2D< core::Size > &jump_pairs)
void	set_base_segment_chainbreak_constraints (pose::Pose &pose, core::Size const start_base, core::Size const end_base)
void	show_dna_geometry (core::pose::Pose const &pose, std::ostream &out)
void	show_dna_geometry_extra_details (pose::Pose const &pose, std::string tag, std::ostream &out)
core::Real	contact_distance2 (core::conformation::Atoms::const_iterator a_begin, core::conformation::Atoms::const_iterator a_end, core::conformation::Atoms::const_iterator b_begin, core::conformation::Atoms::const_iterator b_end, core::Real threshold=0.0)
void	restrict_to_single_sequence (core::pack::rotamer_set::RotamerSetsCOP rotamer_sets, utility::vector1< core::chemical::ResidueTypeCOP > const &single_sequence, utility::vector0< int > &rot_to_pack)
static basic::Tracer	TR ("protocols.dna.WatsonCrickRotamerCouplings", t_info)

Typedef Documentation

DnaChainsCOP

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

DnaChainsOP

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

DnaDesignDefCOP

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

DnaDesignDefOP

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

DnaDesignDefOPs

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

DnaDesignDefs

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

DnaInterfaceFinderCOP

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

DnaInterfaceFinderOP

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

DnaInterfaceMinMoverCOP

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

DnaInterfaceMinMoverOP

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

DnaInterfaceMultiStateDesignCOP

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

DnaInterfaceMultiStateDesignOP

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

DnaInterfacePackerCOP

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

DnaInterfacePackerOP

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

DnaNeighbors

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

DNAParametersCOP

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

DNAParametersOP

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

DnaPositions

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

PDBOutputCOP

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

PDBOutputOP

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

Positions

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

PositionTypes

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

ProteinInterfaceMultiStateDesignMoverCOP

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

ProteinInterfaceMultiStateDesignMoverOP

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

RestrictDesignToProteinDNAInterfaceOP

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

ResTypeSequence

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

ResTypeSequences

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

Reversions

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

RotamerDNAHBondFilterOP

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

SeparateDnaFromNonDnaCOP

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

SeparateDnaFromNonDnaOP

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

SequenceScores

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

Strings

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

TypesMap

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

WatsonCrickRotamerCouplingsOP

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

Function Documentation

add_constraints_from_file()

void protocols::dna::add_constraints_from_file

(

pose::Pose &

pose

)

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

argrot_dna_dis2()

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

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

Author

ashworth

References core::chemical::aa_arg, core::conformation::Residue::atom_begin(), contact_distance2(), core::pack::task::TaskFactory::create_packer_task(), core::pack::rotamer_set::RotamerSetFactory::create_rotamer_set(), core::scoring::ScoreFunctionFactory::create_score_function(), core::conformation::Residue::heavyAtoms_end(), core::chemical::num_canonical_aas, core::pack::task::ResidueLevelTask::or_ex1(), core::pack::task::ResidueLevelTask::restrict_absent_canonical_aas(), core::conformation::Residue::sidechainAtoms_begin(), core::pose::Pose::size(), and TR().

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

checkpoint_cleanup()

void protocols::dna::checkpoint_cleanup

(

)

References protocols::abinitio::filename().

close_to_dna()

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

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

Author

ashworth

References core::conformation::Residue::atom_begin(), core::sequence::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::enzdes::DetectProteinLigandInterface::find_design_interface_arg_sweep(), and protocols::dna::RotamerDNAHBondFilter::operator()().

contact_distance2() [1/2]

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
	)

distance check for contact between two sets of atoms

Author

ashworth

Referenced by argrot_dna_dis2().

contact_distance2() [2/2]

core::Real protocols::dna::contact_distance2	(	core::conformation::Atoms::const_iterator	a_begin,
		core::conformation::Atoms::const_iterator	a_end,
		core::conformation::Atoms::const_iterator	b_begin,
		core::conformation::Atoms::const_iterator	b_end,
		core::Real	threshold = 0.0
	)

distance check for contact between two sets of atoms

Author

ashworth

design_residues_list()

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

References core::pack::task::ResidueLevelTask::being_designed(), core::pack::task::PackerTask::design_residue(), core::pack::task::ResidueLevelTask::has_behavior(), core::chemical::ResidueTypeBase::is_DNA(), core::pack::task::PackerTask::pack_residue(), core::pack::task::PackerTask::residue_task(), core::pose::Pose::residue_type(), core::pose::Pose::residue_type_ptr(), and core::pose::Pose::size().

dna_base_partner()

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

(

chemical::AA const &

na

)

helper function

References core::chemical::aa_unk, core::chemical::na_ade, core::chemical::na_cyt, core::chemical::na_gua, core::chemical::na_thy, and core::chemical::name_from_aa().

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

dna_comp_name_str()

std::string protocols::dna::dna_comp_name_str

(

std::string const &

dna

)

also consider using the dna_base_partner function below

Author

ashworth

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

dna_full_name3()

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)

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

find_basepairs()

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

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

Author

ashworth

References core::conformation::Residue::aa(), protocols::dna::DnaChains::clear(), protocols::dna::DnaChains::contains(), protocols::dna::DnaChains::empty(), core::scoring::dna::get_y_axis(), core::scoring::dna::get_z_axis(), core::conformation::Residue::is_DNA(), core::chemical::na_ade, core::chemical::na_cyt, core::chemical::na_gua, core::chemical::na_rad, core::chemical::na_rcy, core::chemical::na_rgu, core::chemical::na_thy, core::chemical::na_ura, core::conformation::Residue::name3(), core::pose::Pose::pdb_info(), protocols::dna::DnaChains::print(), core::pose::Pose::residue(), core::pose::Pose::size(), TR(), and core::conformation::Residue::xyz().

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

load_checkpoint()

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

References protocols::abinitio::filename(), core::import_pose::PDB_file, core::import_pose::pose_from_file(), and TR().

load_dna_design_defs_from_file()

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

References protocols::abinitio::filename(), load_dna_design_defs_from_strings(), and TR().

Referenced by load_dna_design_defs_from_options().

load_dna_design_defs_from_options()

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

References load_dna_design_defs_from_file(), load_dna_design_defs_from_strings(), and TR().

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().

load_dna_design_defs_from_strings()

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

Author

ashworth

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().

make_base_pair_aware_fold_tree()

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

(

pose::Pose const &

pose

)

References protocols::dna::DNAParameters::find_partner(), 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::size(), TR(), core::kinematics::FoldTree::tree_from_jumps_and_cuts(), and core::conformation::Residue::xyz().

make_sequence_combinations()

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

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

Author

ashworth

References core::chemical::ADDUCT_VARIANT, core::pack::task::ResidueLevelTask::allowed_residue_types_begin(), and core::pack::task::ResidueLevelTask::allowed_residue_types_end().

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

make_single_mutants()

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

Author

ashworth

References core::chemical::ADDUCT_VARIANT, core::pack::task::ResidueLevelTask::allowed_residue_types_begin(), and core::pack::task::ResidueLevelTask::allowed_residue_types_end().

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

make_subdirs()

void protocols::dna::make_subdirs

(

std::string const &

name

)

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

not_already_connected()

bool protocols::dna::not_already_connected	(	pose::Pose const &	pose,
		core::Size const	num_jumps,
		char const	this_chain,
		char const	other_chain,
		ObjexxFCL::FArray2D< core::Size > &	jump_pairs
	)

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

Referenced by make_base_pair_aware_fold_tree().

operator<<() [1/5]

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.

operator<<() [2/5]

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

References core::sequence::end.

operator<<() [3/5]

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

References core::sequence::end.

operator<<() [4/5]

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

operator<<() [5/5]

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

PRECISION()

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().

print_sequence_pdb_nums()

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().

print_sequences_pdb_nums()

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().

restrict_dna_rotamers()

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

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

Author

ashworth

References core::chemical::ResidueTypeBase::name3(), and TR().

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

restrict_to_single_sequence() [1/2]

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

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

Author

ashworth

restrict_to_single_sequence() [2/2]

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

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

Author

ashworth

References core::chemical::ResidueTypeBase::name3(), and TR().

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

seq_pdb_str()

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(), core::pose::Pose::size(), and TR().

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

seq_to_str()

std::string protocols::dna::seq_to_str

(

ResTypeSequence const &

seq

)

References protocols::kinmatch::str().

set_base_segment_chainbreak_constraints()

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::conformation::Residue::atom_index(), core::chemical::ResidueType::is_lower_terminus(), core::chemical::ResidueType::is_upper_terminus(), core::pose::Pose::pdb_info(), core::pose::Pose::residue(), and core::pose::Pose::residue_type().

show_dna_geometry()

void protocols::dna::show_dna_geometry	(	core::pose::Pose const &	pose,
		std::ostream &	out
	)

References core::conformation::Residue::chi(), core::chemical::element::F, core::scoring::dna::get_DNA_backbone_bin(), core::scoring::dna::get_sugar_pucker(), core::chemical::element::I, core::conformation::Residue::is_DNA(), core::conformation::Residue::is_RNA(), core::conformation::Residue::mainchain_torsion(), core::conformation::Residue::name1(), core::conformation::membrane::out, core::pose::Pose::residue(), core::scoring::dna::show_base_pair_params(), core::scoring::dna::show_base_step_params(), and core::pose::Pose::size().

show_dna_geometry_extra_details()

void protocols::dna::show_dna_geometry_extra_details	(	pose::Pose const &	pose,
		std::string	tag,
		std::ostream &	out
	)

References core::conformation::Residue::chi(), core::scoring::dna_dihedral_bb, core::scoring::dna_dihedral_chi, core::scoring::dna_dihedral_sugar, core::energy_methods::DNA_DihedralEnergy::eval_intrares_energy(), core::chemical::element::F, core::scoring::dna::get_DNA_backbone_bin(), core::scoring::dna::get_groove_widths(), core::scoring::dna::get_sugar_pucker(), core::scoring::dna::get_sugar_torsions(), core::conformation::Residue::has(), core::chemical::element::I, core::conformation::Residue::is_DNA(), core::conformation::Residue::is_lower_terminus(), core::conformation::Residue::is_upper_terminus(), core::conformation::Residue::mainchain_torsion(), core::conformation::Residue::name1(), core::conformation::membrane::out, core::pose::Pose::residue(), core::scoring::dna::retrieve_base_partner_from_pose(), core::scoring::dna::show_base_pair_params(), core::scoring::dna::show_base_step_params(), core::pose::Pose::total_residue(), and core::conformation::Residue::xyz().

string_join()

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

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

substitute_residue()

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

Author

ashworth

References core::conformation::Residue::chi(), 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().

TR() [1/9]

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

static

Referenced by protocols::dna::DnaInterfaceMultiStateDesign::add_dna_states(), protocols::dna::SeparateDnaFromNonDna::apply(), protocols::dna::DesignProteinBackboneAroundDNA::apply(), protocols::dna::RestrictDesignToProteinDNAInterface::apply(), protocols::dna::WatsonCrickRotamerCouplings::apply(), argrot_dna_dis2(), find_basepairs(), protocols::dna::DnaInterfacePacker::init_standard(), protocols::dna::DnaInterfaceMultiStateDesign::initialize(), load_checkpoint(), load_dna_design_defs_from_file(), load_dna_design_defs_from_options(), make_base_pair_aware_fold_tree(), 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::RestrictDesignToProteinDNAInterface::parse_tag(), protocols::dna::DnaInterfacePacker::post_packing(), protocols::dna::DnaInterfacePacker::protein_scan(), protocols::dna::RotamerDNAHBondFilter::report(), restrict_dna_rotamers(), restrict_to_single_sequence(), protocols::dna::DnaInterfacePacker::reversion_scan(), protocols::dna::DnaInterfaceMultiStateDesign::run(), seq_pdb_str(), protocols::dna::DnaInterfacePacker::standard_packing(), and write_checkpoint().

TR() [2/9]

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

static

TR() [3/9]

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

static

TR() [4/9]

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

static

TR() [5/9]

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

static

TR() [6/9]

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

static

TR() [7/9]

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

static

TR() [8/9]

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

static

TR() [9/9]

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

static

TR_spec()

static 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().

write_checkpoint()

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

References core::pose::Pose::dump_pdb(), core::conformation::membrane::out, and TR().

z_axis_dist()

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

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').

Author

ashworth

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

Referenced by protocols::dna::DnaInterfaceFinder::determine_dna_interface().