Classes
class	BasePartner
	silly vector1 wrapper class so we can derive from PoseCachedData More...

class	DirectReadoutPotential
	1st pass implementation of Kono + Sarai's protein-DNA interaction potential More...

class	DNA_BasePotential

class	DNA_DihedralPotential

class	DNA_EnvPairPotential

class	TorsionFourierComponent

class	DNABFormPotential

class	DNATorsionPotential

Typedefs
using	Matrix = numeric::xyzMatrix< Real >

using	Params = utility::vector1< Real >

typedef utility::pointer::shared_ptr< BasePartner >	BasePartnerOP

typedef utility::pointer::shared_ptr< DirectReadoutPotential >	DirectReadoutPotentialOP

typedef utility::pointer::shared_ptr< DirectReadoutPotential const >	DirectReadoutPotentialCOP

using	FArray1D_Real = ObjexxFCL::FArray1D< Real >

typedef utility::pointer::shared_ptr< DNA_BasePotential >	DNA_BasePotentialOP

typedef utility::pointer::shared_ptr< DNA_BasePotential const >	DNA_BasePotentialCOP

typedef utility::pointer::shared_ptr< DNA_DihedralPotential >	DNA_DihedralPotentialOP

typedef utility::pointer::shared_ptr< DNA_DihedralPotential const >	DNA_DihedralPotentialCOP

typedef utility::pointer::shared_ptr< DNA_EnvPairPotential >	DNA_EnvPairPotentialOP

typedef utility::pointer::shared_ptr< DNA_EnvPairPotential const >	DNA_EnvPairPotentialCOP

typedef utility::pointer::shared_ptr< DNABFormPotential >	DNABFormPotentialOP

typedef utility::pointer::shared_ptr< DNABFormPotential const >	DNABFormPotentialCOP

typedef utility::pointer::shared_ptr< TorsionFourierComponent >	TorsionFourierComponentOP

typedef utility::pointer::shared_ptr< TorsionFourierComponent const >	TorsionFourierComponentCOP

typedef utility::pointer::shared_ptr< DNATorsionPotential >	DNATorsionPotentialOP

typedef utility::pointer::shared_ptr< DNATorsionPotential const >	DNATorsionPotentialCOP

Enumerations
enum	{ WHATEVER , ALPHA , BETA , GAMMA , DELTA , EPSILON , ZETA , CHI , NU0 , NU1 , NU2 , NU3 , NU4 }

Functions
static basic::Tracer	TR ("core.scoring.dna.base_geometry")

Vector	lsf_normal (utility::vector1< Vector > const &atoms_in)
	FWD. More...

void	get_sugar_pucker (conformation::Residue const &rsd, std::pair< std::string, int > &pucker)
	this could be made faster... More...

void	get_sugar_pucker_distr (conformation::Residue const &rsd, utility::vector1< core::Real > &puckerProb)

utility::vector1< utility::vector1< std::string > >	sugar_torsion_atom_names ()

void	get_sugar_torsions (conformation::Residue const &rsd, utility::vector1< Real > &torsions)

std::string	dihedral_bin (Real phi)

std::string	get_DNA_backbone_bin (conformation::Residue const &rsd)

void	get_y_axis_atoms (chemical::ResidueType const &rsd_type, int const strand, std::string &a1, std::string &a2)

Vector	get_y_axis (conformation::Residue const &rsd, int const strand)

Vector	get_base_pair_y_axis_atom_xyz (conformation::Residue const &rsd)

Vector	get_z_axis (conformation::Residue const &rsd, Vector const &y_axis)

Vector	strand_orientation_vector (conformation::Residue const &rsd, int const strand)

Vector	get_z_axis (conformation::Residue const &rsd, Vector const &y_axis, int const strand, bool &flipped)

Vector	get_z_axis (conformation::Residue const &rsd, Vector const &y_axis, int const strand)

bool	is_orthonormal (numeric::xyzMatrix< Real > const &M, Real const tol)
	helper fxn More...

kinematics::Stub	get_base_stub (conformation::Residue const &rsd, int const strand)

kinematics::Stub	get_base_pair_stub (conformation::Residue const &rsd1, conformation::Residue const &rsd2)

kinematics::Stub	get_base_pair_stub_slow (conformation::Residue const &rsd1, conformation::Residue const &rsd2)

void	show_base_pair_params_with_z_scores (conformation::Residue const &rsd1, conformation::Residue const &rsd2, std::ostream &out)

void	show_base_pair_params (conformation::Residue const &rsd1, conformation::Residue const &rsd2, std::ostream &out)

void	show_base_pair_params (conformation::Residue const &rsd1, conformation::Residue const &rsd2)

void	get_stub_stub_params (kinematics::Stub const &stub1, kinematics::Stub const &stub2, Params &params)

void	get_base_pair_params (conformation::Residue const &rsd1, conformation::Residue const &rsd2, Params &params)

void	get_base_step_params (conformation::Residue const &rsd11, conformation::Residue const &rsd12, conformation::Residue const &rsd21, conformation::Residue const &rsd22, Params &params)

bool	seqpos_is_base_step_anchor (Size const seqpos, pose::Pose const &pose)

void	show_base_step_params (Size const seqpos, pose::Pose const &pose, std::ostream &out)

void	show_new_base_step_params (conformation::Residue const &rsd1, conformation::Residue const &rsd2)

void	show_base_step_params (pose::Pose const &pose, std::ostream &out)

void	show_base_pair_params (pose::Pose const &pose, std::ostream &out)

void	get_groove_widths (Size const i, pose::Pose const &pose, Real &major_width, Real &minor_width, Real &major_length)

void	get_base_step_params (conformation::Residue const &rsd1, conformation::Residue const &rsd2, Params &params)

void	get_base_pair_params (conformation::Residue const &rsd1, conformation::Residue const &rsd2, utility::vector1< Real > &params)

void	get_base_step_params (conformation::Residue const &rsd1, conformation::Residue const &rsd2, utility::vector1< Real > &params)

void	get_base_step_params (conformation::Residue const &rsd11, conformation::Residue const &rsd12, conformation::Residue const &rsd21, conformation::Residue const &rsd22, utility::vector1< Real > &params)

BasePartner const &	retrieve_base_partner_from_pose (pose::Pose const &pose)
	helper routine More...

static basic::Tracer	TR ("core.scoring.dna.DNA_DihedralPotential")

Size	get_iname1_from_name1 (char const name1)
	iname1 goes from 1-4 : acgt More...

void	put_angle_in_0to360 (Real &angle)

Real	get_triple_bin (Real angle)

Real	get_b1b2_bin (Real epsilon, Real zeta)

Real	get_b1b2_weight (Real epsilon, Real zeta)

Real	get_db1b2_weight_deps (Real epsilon, Real zeta)

void	get_mean_median_and_sdev (vector1< Real > vals, Real &mean, Real &median, Real &sdev)

void	filter_torsions_by_iname (Size const iname, vector1< Size > const &torsion_inames, vector1< Real > &torsions)

chemical::AA	dna_aa_from_oneletter_code (char const c)

static basic::Tracer	TR ("core.scoring.dna.setup")

void	set_base_partner (pose::Pose &pose)

void	find_basepairs (pose::Pose const &pose, utility::vector1< Size > &partner)

Typedef Documentation

◆ BasePartnerOP

typedef utility::pointer::shared_ptr< BasePartner > core::scoring::dna::BasePartnerOP

◆ DirectReadoutPotentialCOP

typedef utility::pointer::shared_ptr< DirectReadoutPotential const > core::scoring::dna::DirectReadoutPotentialCOP

◆ DirectReadoutPotentialOP

typedef utility::pointer::shared_ptr< DirectReadoutPotential > core::scoring::dna::DirectReadoutPotentialOP

◆ DNA_BasePotentialCOP

typedef utility::pointer::shared_ptr< DNA_BasePotential const > core::scoring::dna::DNA_BasePotentialCOP

◆ DNA_BasePotentialOP

typedef utility::pointer::shared_ptr< DNA_BasePotential > core::scoring::dna::DNA_BasePotentialOP

◆ DNA_DihedralPotentialCOP

typedef utility::pointer::shared_ptr< DNA_DihedralPotential const > core::scoring::dna::DNA_DihedralPotentialCOP

◆ DNA_DihedralPotentialOP

typedef utility::pointer::shared_ptr< DNA_DihedralPotential > core::scoring::dna::DNA_DihedralPotentialOP

◆ DNA_EnvPairPotentialCOP

typedef utility::pointer::shared_ptr< DNA_EnvPairPotential const > core::scoring::dna::DNA_EnvPairPotentialCOP

◆ DNA_EnvPairPotentialOP

typedef utility::pointer::shared_ptr< DNA_EnvPairPotential > core::scoring::dna::DNA_EnvPairPotentialOP

◆ DNABFormPotentialCOP

typedef utility::pointer::shared_ptr< DNABFormPotential const > core::scoring::dna::DNABFormPotentialCOP

◆ DNABFormPotentialOP

typedef utility::pointer::shared_ptr< DNABFormPotential > core::scoring::dna::DNABFormPotentialOP

◆ DNATorsionPotentialCOP

typedef utility::pointer::shared_ptr< DNATorsionPotential const > core::scoring::dna::DNATorsionPotentialCOP

◆ DNATorsionPotentialOP

typedef utility::pointer::shared_ptr< DNATorsionPotential > core::scoring::dna::DNATorsionPotentialOP

◆ FArray1D_Real

using core::scoring::dna::FArray1D_Real = typedef ObjexxFCL::FArray1D<Real>

◆ Matrix

using core::scoring::dna::Matrix = typedef numeric::xyzMatrix<Real>

◆ Params

using core::scoring::dna::Params = typedef utility::vector1<Real>

◆ TorsionFourierComponentCOP

typedef utility::pointer::shared_ptr< TorsionFourierComponent const > core::scoring::dna::TorsionFourierComponentCOP

◆ TorsionFourierComponentOP

typedef utility::pointer::shared_ptr< TorsionFourierComponent > core::scoring::dna::TorsionFourierComponentOP

Enumeration Type Documentation

◆ anonymous enum

anonymous enum

Enumerator
WHATEVER
ALPHA
BETA
GAMMA
DELTA
EPSILON
ZETA
CHI
NU0
NU1
NU2
NU3
NU4

Function Documentation

◆ dihedral_bin()

std::string core::scoring::dna::dihedral_bin ( Real phi )

Referenced by get_DNA_backbone_bin().

◆ dna_aa_from_oneletter_code()

chemical::AA core::scoring::dna::dna_aa_from_oneletter_code ( char const c )

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

Referenced by core::scoring::dna::DNA_EnvPairPotential::load_score_tables().

◆ filter_torsions_by_iname()

void core::scoring::dna::filter_torsions_by_iname	(	Size const	iname,
		vector1< Size > const &	torsion_inames,
		vector1< Real > &	torsions
	)

Referenced by core::scoring::dna::DNA_DihedralPotential::parse_dna_geometry_log().

◆ find_basepairs()

void core::scoring::dna::find_basepairs	(	pose::Pose const &	pose,
		utility::vector1< Size > &	partner
	)

References get_y_axis(), core::chemical::na_ade, core::chemical::na_cyt, core::chemical::na_gua, core::chemical::na_thy, core::pose::Pose::residue(), core::pose::Pose::size(), TR(), and protocols::hybridization::u.

Referenced by protocols::motifs::MotifDnaPacker::apply(), protocols::dna::DNAParameters::calculate(), and set_base_partner().

◆ get_b1b2_bin()

Real core::scoring::dna::get_b1b2_bin	(	Real	epsilon,
		Real	zeta
	)

Referenced by core::scoring::dna::DNA_DihedralPotential::parse_dna_geometry_log().

◆ get_b1b2_weight()

Real core::scoring::dna::get_b1b2_weight	(	Real	epsilon,
		Real	zeta
	)

Referenced by core::scoring::dna::DNA_DihedralPotential::eval_harmonic_backbone_torsion_score_and_deriv().

◆ get_base_pair_params() [1/2]

void core::scoring::dna::get_base_pair_params	(	conformation::Residue const &	rsd1,
		conformation::Residue const &	rsd2,
		Params &	params
	)

References get_base_stub(), and get_stub_stub_params().

Referenced by core::scoring::dna::DNA_BasePotential::base_pair_score(), protocols::dna::DNABasepair::DNABasepair(), core::scoring::dna::DNA_BasePotential::eval_base_pair_derivative(), core::scoring::dna::DNA_BasePotential::eval_base_pair_Z_scores(), show_base_pair_params(), and show_base_pair_params_with_z_scores().

◆ get_base_pair_params() [2/2]

void core::scoring::dna::get_base_pair_params	(	conformation::Residue const &	rsd1,
		conformation::Residue const &	rsd2,
		utility::vector1< Real > &	params
	)

◆ get_base_pair_stub()

kinematics::Stub core::scoring::dna::get_base_pair_stub	(	conformation::Residue const &	rsd1,
		conformation::Residue const &	rsd2
	)

References get_base_pair_y_axis_atom_xyz(), get_z_axis(), and TR().

◆ get_base_pair_stub_slow()

kinematics::Stub core::scoring::dna::get_base_pair_stub_slow	(	conformation::Residue const &	rsd1,
		conformation::Residue const &	rsd2
	)

References core::conformation::Residue::atom_is_backbone(), core::conformation::Residue::chi_atoms(), core::conformation::Residue::first_sidechain_atom(), get_base_pair_y_axis_atom_xyz(), core::conformation::Residue::is_RNA(), lsf_normal(), core::conformation::Residue::nheavyatoms(), strand_orientation_vector(), and core::conformation::Residue::xyz().

Referenced by get_base_step_params().

◆ get_base_pair_y_axis_atom_xyz()

Vector core::scoring::dna::get_base_pair_y_axis_atom_xyz ( conformation::Residue const & rsd )

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

Referenced by get_base_pair_stub(), and get_base_pair_stub_slow().

◆ get_base_step_params() [1/4]

void core::scoring::dna::get_base_step_params	(	conformation::Residue const &	rsd1,
		conformation::Residue const &	rsd2,
		Params &	params
	)

References get_base_stub(), is_orthonormal(), core::kinematics::Stub::M, TR(), and core::kinematics::Stub::v.

◆ get_base_step_params() [2/4]

void core::scoring::dna::get_base_step_params	(	conformation::Residue const &	rsd1,
		conformation::Residue const &	rsd2,
		utility::vector1< Real > &	params
	)

◆ get_base_step_params() [3/4]

void core::scoring::dna::get_base_step_params	(	conformation::Residue const &	rsd11,
		conformation::Residue const &	rsd12,
		conformation::Residue const &	rsd21,
		conformation::Residue const &	rsd22,
		Params &	params
	)

References get_base_pair_stub_slow(), get_stub_stub_params(), and core::conformation::Residue::seqpos().

Referenced by core::scoring::dna::DNA_BasePotential::base_step_score(), protocols::dna::DNABasestep::DNABasestep(), core::scoring::dna::DNA_BasePotential::eval_base_step_derivative(), core::scoring::dna::DNA_BasePotential::eval_base_step_Z_scores(), show_base_step_params(), and show_new_base_step_params().

◆ get_base_step_params() [4/4]

void core::scoring::dna::get_base_step_params	(	conformation::Residue const &	rsd11,
		conformation::Residue const &	rsd12,
		conformation::Residue const &	rsd21,
		conformation::Residue const &	rsd22,
		utility::vector1< Real > &	params
	)

◆ get_base_stub()

kinematics::Stub core::scoring::dna::get_base_stub	(	conformation::Residue const &	rsd,
		int const	strand
	)

References get_y_axis_atoms(), get_z_axis(), protocols::loops::loop_closure::ccd::strand, TR(), core::conformation::Residue::type(), and core::conformation::Residue::xyz().

Referenced by core::scoring::dna::DNA_BasePotential::eval_base_pair_derivative(), core::scoring::dna::DNA_BasePotential::eval_base_step_derivative(), get_base_pair_params(), and get_base_step_params().

◆ get_db1b2_weight_deps()

Real core::scoring::dna::get_db1b2_weight_deps	(	Real	epsilon,
		Real	zeta
	)

Referenced by core::scoring::dna::DNA_DihedralPotential::eval_harmonic_backbone_torsion_score_and_deriv().

◆ get_DNA_backbone_bin()

std::string core::scoring::dna::get_DNA_backbone_bin ( conformation::Residue const & rsd )

References dihedral_bin(), core::conformation::Residue::is_lower_terminus(), core::conformation::Residue::is_upper_terminus(), and core::conformation::Residue::mainchain_torsion().

Referenced by protocols::dna::show_dna_geometry(), and protocols::dna::show_dna_geometry_extra_details().

◆ get_groove_widths()

void core::scoring::dna::get_groove_widths	(	Size const	i,
		pose::Pose const &	pose,
		Real &	major_width,
		Real &	minor_width,
		Real &	major_length
	)

References core::pose::Pose::chain(), core::conformation::Residue::is_DNA(), core::conformation::Residue::is_lower_terminus(), core::conformation::Residue::is_upper_terminus(), core::pose::Pose::residue(), retrieve_base_partner_from_pose(), seqpos_is_base_step_anchor(), core::pose::Pose::total_residue(), and core::conformation::Residue::xyz().

Referenced by protocols::dna::show_dna_geometry_extra_details().

◆ get_iname1_from_name1()

Size core::scoring::dna::get_iname1_from_name1 ( char const name1 )

inline

iname1 goes from 1-4 : acgt

Referenced by core::scoring::dna::DNA_DihedralPotential::eval_harmonic_sugar_pucker_dependent_chi_torsion_score_and_deriv(), core::scoring::dna::DNA_DihedralPotential::eval_sugar_torsion_score_and_deriv(), core::scoring::dna::DNA_DihedralPotential::get_mean_sugar_pucker_dependent_chi(), core::scoring::dna::DNA_DihedralPotential::get_sugar_torsion_mean_and_sdev(), and core::scoring::dna::DNA_DihedralPotential::parse_dna_geometry_log().

◆ get_mean_median_and_sdev()

void core::scoring::dna::get_mean_median_and_sdev	(	vector1< Real >	vals,
		Real &	mean,
		Real &	median,
		Real &	sdev
	)

References core::simple_metrics::metrics::mean, and protocols::hybridization::val.

Referenced by core::scoring::dna::DNA_DihedralPotential::parse_dna_geometry_log().

◆ get_stub_stub_params()

void core::scoring::dna::get_stub_stub_params	(	kinematics::Stub const &	stub1,
		kinematics::Stub const &	stub2,
		Params &	params
	)

works as-is for base pair with stub1 ~ strand I, stub2 ~ strand II for base-step we use the mapping:

step pair

z -> y y -> x

x -> z

i+1 -> I (stub1)

i -> II (stub2)

mid-stub coordsys generated by aligning the y-axes.

params[1] = oriented angle from the stub2 z-axis to the stub1 z-axis after aligning y-axes = ( same as oriented angle from the stub2 x-axis to the stub1 x-axis after aligning y-axes ) = atan2( dot( stub1-z, stub2-x ), dot( stub1-z, stub2-z ) ) = atan2( y-coord( stub1-z ), x-coord( stub1-z ) ) in z-x coordinate system. = propeller (twist)

params[2] = x-component of the rotation axis from stub2-y to stub1-y, weighted by rotation angle = buckle (roll)

params[3] = z-component of the rotation axis from stub2-y to stub1-y, weighted by rotation angle = opening (tilt)

params[4] = x-coordinate of the vector from stub2-origin to stub1-origin = shear (slide)

params[5] = y-coordinate of the vector from stub2-origin to stub1-origin = stretch (rise)

params[6] = z-coordinate of the vector from stub2-origin to stub1-origin = stagger (shift)

NAMES pair step

params[1] = propeller twist params[2] = buckle roll params[3] = opening tilt params[4] = shear slide params[5] = stretch rise params[6] = stagger shift

References is_orthonormal(), core::kinematics::Stub::M, TR(), and core::kinematics::Stub::v.

Referenced by get_base_pair_params(), and get_base_step_params().

◆ get_sugar_pucker()

void core::scoring::dna::get_sugar_pucker	(	conformation::Residue const &	rsd,
		std::pair< std::string, int > &	pucker
	)

this could be made faster...

Get the sugar pucker. additional int parameter as follows:

0 - C1' endo 1 - C2' exxo 2 - C3' endo 3 - C4' exxo 4 - O4' endo 5 - C1' exxo 6 - C2' endo 7 - C3' exxo 8 - C4' endo 9 - O4' exxo

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

Referenced by core::scoring::dna::DNA_DihedralPotential::get_mean_sugar_pucker_dependent_chi(), protocols::dna::show_dna_geometry(), and protocols::dna::show_dna_geometry_extra_details().

◆ get_sugar_pucker_distr()

void core::scoring::dna::get_sugar_pucker_distr	(	conformation::Residue const &	rsd,
		utility::vector1< core::Real > &	puckerProb
	)

A "soft" version of the function above, that assigns a probability distribution over the 10 puckers This is necessary to smoothly minimize between puckers

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

Referenced by core::energy_methods::DNA_DihedralEnergy::eval_intrares_derivatives(), core::energy_methods::DNA_DihedralEnergy::eval_intrares_energy(), and core::energy_methods::DNA_DihedralEnergy::eval_intraresidue_dof_derivative().

◆ get_sugar_torsions()

void core::scoring::dna::get_sugar_torsions	(	conformation::Residue const &	rsd,
		utility::vector1< Real > &	torsions
	)

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

Referenced by core::energy_methods::DNA_DihedralEnergy::eval_intrares_derivatives(), core::energy_methods::DNA_DihedralEnergy::eval_intrares_energy(), core::energy_methods::DNA_DihedralEnergy::eval_intraresidue_dof_derivative(), and protocols::dna::show_dna_geometry_extra_details().

◆ get_triple_bin()

Real core::scoring::dna::get_triple_bin ( Real angle )

References put_angle_in_0to360().

Referenced by core::scoring::dna::DNA_DihedralPotential::eval_harmonic_backbone_torsion_score_and_deriv(), and core::scoring::dna::DNA_DihedralPotential::parse_dna_geometry_log().

◆ get_y_axis()

Vector core::scoring::dna::get_y_axis	(	conformation::Residue const &	rsd,
		int const	strand
	)

References get_y_axis_atoms(), protocols::loops::loop_closure::ccd::strand, core::conformation::Residue::type(), and core::conformation::Residue::xyz().

Referenced by protocols::dna::find_basepairs(), find_basepairs(), protocols::motifs::parallel_base_test(), and protocols::dna::z_axis_dist().

◆ get_y_axis_atoms()

void core::scoring::dna::get_y_axis_atoms	(	chemical::ResidueType const &	rsd_type,
		int const	strand,
		std::string &	a1,
		std::string &	a2
	)

References core::chemical::ResidueTypeBase::aa(), 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, and protocols::loops::loop_closure::ccd::strand.

Referenced by get_base_stub(), and get_y_axis().

◆ get_z_axis() [1/3]

Vector core::scoring::dna::get_z_axis	(	conformation::Residue const &	rsd,
		Vector const &	y_axis
	)

References core::conformation::Residue::aa(), core::conformation::Residue::is_DNA(), core::conformation::Residue::is_RNA(), 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, and core::conformation::Residue::xyz().

Referenced by protocols::dna::find_basepairs(), get_base_pair_stub(), get_base_stub(), get_z_axis(), protocols::motifs::parallel_base_test(), core::scoring::dna::DirectReadoutPotential::rsd_rsd_energy(), and protocols::dna::z_axis_dist().

◆ get_z_axis() [2/3]

Vector core::scoring::dna::get_z_axis	(	conformation::Residue const &	rsd,
		Vector const &	y_axis,
		int const	strand
	)

References get_z_axis(), and protocols::loops::loop_closure::ccd::strand.

◆ get_z_axis() [3/3]

Vector core::scoring::dna::get_z_axis	(	conformation::Residue const &	rsd,
		Vector const &	y_axis,
		int const	strand,
		bool &	flipped
	)

References get_z_axis(), protocols::loops::loop_closure::ccd::strand, and strand_orientation_vector().

◆ is_orthonormal()

bool core::scoring::dna::is_orthonormal	(	numeric::xyzMatrix< Real > const &	M,
		Real const	tol
	)

helper fxn

References protocols::comparative_modeling::features::X.

Referenced by core::scoring::dna::DNA_BasePotential::eval_base_pair_derivative(), core::scoring::dna::DNA_BasePotential::eval_base_step_derivative(), get_base_step_params(), and get_stub_stub_params().

◆ lsf_normal()

Vector core::scoring::dna::lsf_normal ( utility::vector1< Vector > const & atoms_in )

FWD.

if you really want the least-squares plane: Thanks to Alex Morozov for implementing this:

V.Schomaker et al. Acta Cryst. (1959) 12, 600-604 D.M.Blow Acta Cryst. (1960) 13, 168

Note: no guarantee about the orientation of the returned vector...

References core::pose::motif::a(), protocols::comparative_modeling::features::A, protocols::match::upstream::b, and protocols::antibody::lambda.

Referenced by get_base_pair_stub_slow().

◆ put_angle_in_0to360()

void core::scoring::dna::put_angle_in_0to360 ( Real & angle )

Referenced by core::scoring::dna::DNA_DihedralPotential::eval_harmonic_sugar_pucker_dependent_chi_torsion_score_and_deriv(), and get_triple_bin().

◆ retrieve_base_partner_from_pose()

BasePartner const & core::scoring::dna::retrieve_base_partner_from_pose ( pose::Pose const & pose )

helper routine

helper fcn

References core::pose::datacache::CacheableDataType::BASE_PARTNER, and core::pose::Pose::data().

Referenced by protocols::motifs::MotifDnaPacker::apply(), get_groove_widths(), protocols::motifs::make_base_pair_mutation(), seqpos_is_base_step_anchor(), show_base_pair_params(), show_base_step_params(), and protocols::dna::show_dna_geometry_extra_details().

◆ seqpos_is_base_step_anchor()

bool core::scoring::dna::seqpos_is_base_step_anchor	(	Size const	seqpos,
		pose::Pose const &	pose
	)

References core::conformation::Residue::is_DNA(), core::conformation::Residue::is_RNA(), core::pose::Pose::residue(), retrieve_base_partner_from_pose(), core::pose::Pose::size(), and core::pose::Pose::total_residue().

Referenced by get_groove_widths(), and show_base_step_params().

◆ set_base_partner()

void core::scoring::dna::set_base_partner ( pose::Pose & pose )

References core::pose::datacache::CacheableDataType::BASE_PARTNER, core::pose::Pose::data(), and find_basepairs().

Referenced by protocols::motifs::make_dna_mutations(), core::energy_methods::DNA_BaseEnergy::setup_for_derivatives(), core::energy_methods::DNA_BaseEnergy::setup_for_packing(), and core::energy_methods::DNA_BaseEnergy::setup_for_scoring().

◆ show_base_pair_params() [1/3]

void core::scoring::dna::show_base_pair_params	(	conformation::Residue const &	rsd1,
		conformation::Residue const &	rsd2
	)

References show_base_pair_params().

◆ show_base_pair_params() [2/3]

void core::scoring::dna::show_base_pair_params	(	conformation::Residue const &	rsd1,
		conformation::Residue const &	rsd2,
		std::ostream &	out
	)

References core::chemical::element::F, get_base_pair_params(), core::chemical::element::I, core::conformation::Residue::name1(), core::conformation::membrane::out, and core::conformation::Residue::seqpos().

Referenced by show_base_pair_params(), protocols::dna::show_dna_geometry(), and protocols::dna::show_dna_geometry_extra_details().

◆ show_base_pair_params() [3/3]

void core::scoring::dna::show_base_pair_params	(	pose::Pose const &	pose,
		std::ostream &	out
	)

References core::conformation::membrane::out, core::pose::Pose::residue(), retrieve_base_partner_from_pose(), show_base_pair_params(), and core::pose::Pose::size().

◆ show_base_pair_params_with_z_scores()

void core::scoring::dna::show_base_pair_params_with_z_scores	(	conformation::Residue const &	rsd1,
		conformation::Residue const &	rsd2,
		std::ostream &	out
	)

References core::scoring::dna::DNA_BasePotential::base_pair_score(), core::scoring::dna::DNA_BasePotential::eval_base_pair_Z_scores(), core::chemical::element::F, get_base_pair_params(), core::chemical::element::I, core::conformation::Residue::name1(), core::conformation::membrane::out, and core::conformation::Residue::seqpos().

◆ show_base_step_params() [1/2]

void core::scoring::dna::show_base_step_params	(	pose::Pose const &	pose,
		std::ostream &	out
	)

References core::conformation::membrane::out, seqpos_is_base_step_anchor(), show_base_step_params(), and core::pose::Pose::size().

◆ show_base_step_params() [2/2]

void core::scoring::dna::show_base_step_params	(	Size const	seqpos,
		pose::Pose const &	pose,
		std::ostream &	out
	)

References core::chemical::element::F, get_base_step_params(), core::chemical::element::I, core::conformation::Residue::name1(), core::conformation::membrane::out, core::pose::Pose::residue(), retrieve_base_partner_from_pose(), and seqpos_is_base_step_anchor().

Referenced by show_base_step_params(), protocols::dna::show_dna_geometry(), and protocols::dna::show_dna_geometry_extra_details().

◆ show_new_base_step_params()

void core::scoring::dna::show_new_base_step_params	(	conformation::Residue const &	rsd1,
		conformation::Residue const &	rsd2
	)

References core::scoring::dna::DNA_BasePotential::base_step_score(), core::scoring::dna::DNA_BasePotential::eval_base_step_Z_scores(), core::chemical::element::F, get_base_step_params(), core::chemical::element::I, core::conformation::Residue::name1(), and core::conformation::Residue::seqpos().

◆ strand_orientation_vector()

Vector core::scoring::dna::strand_orientation_vector	(	conformation::Residue const &	rsd,
		int const	strand
	)

References protocols::loops::loop_closure::ccd::strand, and core::conformation::Residue::xyz().

Referenced by get_base_pair_stub_slow(), and get_z_axis().

◆ sugar_torsion_atom_names()

utility::vector1< utility::vector1< std::string > > core::scoring::dna::sugar_torsion_atom_names ( )

Referenced by core::energy_methods::DNA_DihedralEnergy::atoms_with_dof_derivatives(), and get_sugar_torsions().

◆ TR() [1/3]

static basic::Tracer core::scoring::dna::TR ( "core.scoring.dna.base_geometry" )

static

Referenced by find_basepairs(), get_base_pair_stub(), get_base_step_params(), get_base_stub(), get_stub_stub_params(), and core::scoring::dna::DNA_DihedralPotential::parse_dna_geometry_log().

◆ TR() [2/3]

static basic::Tracer core::scoring::dna::TR ( "core.scoring.dna.DNA_DihedralPotential" )

static

◆ TR() [3/3]

static basic::Tracer core::scoring::dna::TR ( "core.scoring.dna.setup" )

static

Classes

Typedefs

Enumerations

Functions

Typedef Documentation

◆ BasePartnerOP

◆ DirectReadoutPotentialCOP

◆ DirectReadoutPotentialOP

◆ DNA_BasePotentialCOP

◆ DNA_BasePotentialOP

◆ DNA_DihedralPotentialCOP

◆ DNA_DihedralPotentialOP

◆ DNA_EnvPairPotentialCOP

◆ DNA_EnvPairPotentialOP

◆ DNABFormPotentialCOP

◆ DNABFormPotentialOP

◆ DNATorsionPotentialCOP

◆ DNATorsionPotentialOP

◆ FArray1D_Real

◆ Matrix

◆ Params

◆ TorsionFourierComponentCOP

◆ TorsionFourierComponentOP

Enumeration Type Documentation

◆ anonymous enum

Function Documentation

◆ dihedral_bin()

◆ dna_aa_from_oneletter_code()

◆ filter_torsions_by_iname()

◆ find_basepairs()

◆ get_b1b2_bin()

◆ get_b1b2_weight()

◆ get_base_pair_params() [1/2]

◆ get_base_pair_params() [2/2]

◆ get_base_pair_stub()

◆ get_base_pair_stub_slow()

◆ get_base_pair_y_axis_atom_xyz()

◆ get_base_step_params() [1/4]

◆ get_base_step_params() [2/4]

◆ get_base_step_params() [3/4]

◆ get_base_step_params() [4/4]

◆ get_base_stub()

◆ get_db1b2_weight_deps()

◆ get_DNA_backbone_bin()

◆ get_groove_widths()

◆ get_iname1_from_name1()

◆ get_mean_median_and_sdev()

◆ get_stub_stub_params()

step pair

x -> z

i -> II (stub2)

NAMES pair step

◆ get_sugar_pucker()

◆ get_sugar_pucker_distr()

◆ get_sugar_torsions()

◆ get_triple_bin()

◆ get_y_axis()

◆ get_y_axis_atoms()

◆ get_z_axis() [1/3]

◆ get_z_axis() [2/3]

◆ get_z_axis() [3/3]

◆ is_orthonormal()

◆ lsf_normal()

◆ put_angle_in_0to360()

◆ retrieve_base_partner_from_pose()

◆ seqpos_is_base_step_anchor()

◆ set_base_partner()

◆ show_base_pair_params() [1/3]

◆ show_base_pair_params() [2/3]

◆ show_base_pair_params() [3/3]

◆ show_base_pair_params_with_z_scores()

◆ show_base_step_params() [1/2]

◆ show_base_step_params() [2/2]

◆ show_new_base_step_params()

◆ strand_orientation_vector()

◆ sugar_torsion_atom_names()

◆ TR() [1/3]

◆ TR() [2/3]

◆ TR() [3/3]