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::owning_ptr < DnaChains >	DnaChainsOP
typedef utility::pointer::owning_ptr < DnaChains const >	DnaChainsCOP
typedef std::map< core::Size, DnaPosition >	DnaPositions
typedef utility::pointer::owning_ptr < DnaDesignDef >	DnaDesignDefOP
typedef utility::pointer::owning_ptr < DnaDesignDef const >	DnaDesignDefCOP
typedef utility::vector1 < DnaDesignDef >	DnaDesignDefs
typedef utility::vector1 < DnaDesignDefOP >	DnaDesignDefOPs
typedef utility::pointer::owning_ptr < DnaInterfaceFinder >	DnaInterfaceFinderOP
typedef utility::pointer::owning_ptr < DnaInterfaceFinder const >	DnaInterfaceFinderCOP
typedef std::map< core::Size, DnaNeighbor >	DnaNeighbors
typedef utility::pointer::owning_ptr < DnaInterfaceMinMover >	DnaInterfaceMinMoverOP
typedef utility::pointer::owning_ptr < DnaInterfaceMinMover const >	DnaInterfaceMinMoverCOP
typedef utility::pointer::owning_ptr < DnaInterfaceMultiStateDesign >	DnaInterfaceMultiStateDesignOP
typedef utility::pointer::owning_ptr < DnaInterfaceMultiStateDesign const >	DnaInterfaceMultiStateDesignCOP
typedef vector1< Reversion >	Reversions
typedef utility::pointer::owning_ptr < DnaInterfacePacker >	DnaInterfacePackerOP
typedef utility::pointer::owning_ptr < DnaInterfacePacker const >	DnaInterfacePackerCOP
typedef std::map < ResTypeSequence, core::Real, ResTypeSequence_lt >	SequenceScores
typedef utility::pointer::owning_ptr < DNAParameters >	DNAParametersOP
typedef utility::pointer::owning_ptr < DNAParameters const >	DNAParametersCOP
typedef utility::pointer::owning_ptr < PDBOutput >	PDBOutputOP
typedef utility::pointer::owning_ptr < PDBOutput const >	PDBOutputCOP
typedef utility::pointer::owning_ptr < RestrictDesignToProteinDNAInterface >	RestrictDesignToProteinDNAInterfaceOP
typedef utility::pointer::owning_ptr < RotamerDNAHBondFilter >	RotamerDNAHBondFilterOP
typedef utility::pointer::owning_ptr < SeparateDnaFromNonDna >	SeparateDnaFromNonDnaOP
typedef utility::pointer::owning_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::owning_ptr < WatsonCrickRotamerCouplings >	WatsonCrickRotamerCouplingsOP
typedef utility::pointer::owning_ptr < ProteinInterfaceMultiStateDesignMover >	ProteinInterfaceMultiStateDesignMoverOP
typedef utility::pointer::owning_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 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, 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)
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	make_single_mutants (ResTypeSequence const &sequence, core::pack::task::PackerTaskCOP ptask, ResTypeSequences &sequences)
void	design_residues_list (std::list< PositionType > &design_residues, core::pose::Pose const &pose, core::pack::task::PackerTask const &ptask)
void	make_sequence_combinations (utility::vector1< core::Size >::const_iterator seqset_iter, utility::vector1< core::Size > const &seq_indices, core::pack::task::PackerTaskCOP ptask, ResTypeSequence &sequence, ResTypeSequences &sequences)
void	restrict_dna_rotamers (core::pack::rotamer_set::RotamerSetsCOP rotsets, ResTypeSequence const &seq, utility::vector0< int > &rot_to_pack)
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)
void	load_dna_design_defs_from_strings (DnaDesignDefOPs &defs, utility::vector1< std::string > const &str_defs)
static basic::Tracer	TR ("protocols.dna.WatsonCrickRotamerCouplings", t_info)

Typedef Documentation

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

Definition at line 25 of file DnaChains.fwd.hh.

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

Definition at line 23 of file DnaChains.fwd.hh.

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

Definition at line 25 of file DnaDesignDef.fwd.hh.

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

Definition at line 23 of file DnaDesignDef.fwd.hh.

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

Definition at line 27 of file DnaDesignDef.fwd.hh.

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

Definition at line 26 of file DnaDesignDef.fwd.hh.

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

Definition at line 25 of file DnaInterfaceFinder.fwd.hh.

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

Definition at line 22 of file DnaInterfaceFinder.fwd.hh.

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

Definition at line 24 of file DnaInterfaceMinMover.fwd.hh.

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

Definition at line 22 of file DnaInterfaceMinMover.fwd.hh.

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

Definition at line 24 of file DnaInterfaceMultiStateDesign.fwd.hh.

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

Definition at line 22 of file DnaInterfaceMultiStateDesign.fwd.hh.

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

Definition at line 22 of file DnaInterfacePacker.fwd.hh.

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

Definition at line 20 of file DnaInterfacePacker.fwd.hh.

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

Definition at line 43 of file DnaInterfaceFinder.hh.

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

Definition at line 24 of file DNAParameters.fwd.hh.

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

Definition at line 21 of file DNAParameters.fwd.hh.

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

Definition at line 56 of file DnaChains.hh.

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

Definition at line 22 of file PDBOutput.fwd.hh.

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

Definition at line 20 of file PDBOutput.fwd.hh.

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

Definition at line 30 of file typedefs.hh.

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

Definition at line 57 of file util.hh.

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

Definition at line 24 of file ProteinInterfaceMultiStateDesignMover.fwd.hh.

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

Definition at line 22 of file ProteinInterfaceMultiStateDesignMover.fwd.hh.

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

Definition at line 22 of file RestrictDesignToProteinDNAInterface.fwd.hh.

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

Definition at line 27 of file typedefs.hh.

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

Definition at line 28 of file typedefs.hh.

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

Definition at line 894 of file DnaInterfacePacker.cc.

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

Definition at line 22 of file RotamerDNAHBondFilter.fwd.hh.

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

Definition at line 22 of file SeparateDnaFromNonDna.fwd.hh.

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

Definition at line 20 of file SeparateDnaFromNonDna.fwd.hh.

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

Definition at line 49 of file DnaInterfacePacker.hh.

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

Definition at line 87 of file util.cc.

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

Definition at line 29 of file typedefs.hh.

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

Definition at line 18 of file WatsonCrickRotamerCouplings.fwd.hh.

Function Documentation

void protocols::dna::add_constraints_from_file

(

pose::Pose &

pose)

Definition at line 795 of file util.cc.

References core::pose::Pose::constraint_set(), core::scoring::constraints::ConstraintIO::get_instance(), and core::scoring::constraints::ConstraintIO::read_constraints_new().

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

Definition at line 113 of file util.cc.

References core::chemical::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(), core::chemical::num_canonical_aas, core::pack::task::ResidueLevelTask::or_ex1(), core::conformation::Residue::sidechainAtoms_begin(), and core::pose::Pose::total_residue().

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

(

)

Definition at line 708 of file util.cc.

References protocols::swa::rna::file_exists(), and protocols::abinitio::filename().

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

Definition at line 93 of file util.cc.

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

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
	)

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

Definition at line 185 of file util.cc.

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
	)

Definition at line 470 of file util.cc.

References 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

Definition at line 259 of file util.cc.

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().

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

Definition at line 229 of file util.cc.

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

Definition at line 244 of file util.cc.

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

Definition at line 283 of file util.cc.

References 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::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::pose::Pose::pdb_info(), protocols::dna::DnaChains::print(), core::pose::Pose::residue(), 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
	)

Definition at line 673 of file util.cc.

References protocols::abinitio::filename(), and core::import_pose::pose_from_pdb().

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

Definition at line 745 of file util.cc.

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

Referenced by load_dna_design_defs_from_options().

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

Definition at line 774 of file util.cc.

References load_dna_design_defs_from_file(), and load_dna_design_defs_from_strings().

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
	)

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

Definition at line 733 of file util.cc.

References core::sequence::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)

Definition at line 814 of file util.cc.

References 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(), and core::conformation::Residue::xyz().

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

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

Definition at line 419 of file util.cc.

References core::chemical::ADDUCT.

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

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

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

Definition at line 447 of file util.cc.

References core::chemical::ADDUCT.

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

void protocols::dna::make_subdirs

(

std::string const &

name)

Definition at line 592 of file PDBOutput.cc.

References protocols::swa::rna::file_exists().

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
	)

Definition at line 1056 of file util.cc.

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
	)

Definition at line 46 of file DnaDesignDef.cc.

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
	)

Definition at line 52 of file DnaDesignDef.cc.

References core::sequence::end.

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

Definition at line 62 of file DnaDesignDef.cc.

References core::sequence::end.

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

Definition at line 490 of file util.cc.

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

Definition at line 507 of file util.cc.

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().

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

Definition at line 538 of file util.cc.

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
	)

Definition at line 547 of file util.cc.

References print_sequence_pdb_nums().

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

void protocols::dna::restrict_dna_rotamers	(	core::pack::rotamer_set::RotamerSetsCOP	rotsets,
		ResTypeSequence const &	seq,
		utility::vector0< int > &	rot_to_pack
	)

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

Definition at line 562 of file util.cc.

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

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
	)

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

Definition at line 593 of file util.cc.

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
	)

Definition at line 515 of file util.cc.

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)

Definition at line 499 of file util.cc.

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
	)

Definition at line 1084 of file util.cc.

References core::pose::Pose::add_constraint(), 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().

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

Definition at line 290 of file PDBOutput.cc.

References core::sequence::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

Definition at line 621 of file util.cc.

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

static

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

static

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

static

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

static

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

static

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

static

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

static

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

static

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().

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

Definition at line 637 of file util.cc.

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

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

Definition at line 209 of file util.cc.

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(), and protocols::dna::DnaInterfaceFinder::determine_protein_interface().