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	TorsionFourierComponent

class	DNABFormPotential

class	DNAChiEnergy

class	DNAChiEnergyCreator

class	DNATorsionEnergy

class	DNATorsionEnergyCreator

class	DNATorsionPotential

Typedefs
typedef numeric::xyzMatrix< Real >	Matrix

typedef utility::vector1< Real >	Params

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

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

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

typedef ObjexxFCL::FArray1D< Real >	FArray1D_Real

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

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

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

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

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

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

typedef utility::pointer::owning_ptr < DNATorsionEnergy >	DNATorsionEnergyOP

typedef utility::pointer::owning_ptr < DNATorsionEnergy const >	DNATorsionEnergyCOP

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

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

void	get_base_pucker (conformation::Residue const &rsd, std::pair< std::string, int > &pucker)

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	show_dna_geometry (pose::Pose const &pose, std::ostream &out)

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

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

void	get_base_pucker (conformation::Residue const &rsd, std::pair< std::string, int > &pucker, Real &pseudorotation, Real &amplitude)

kinematics::Stub	get_midstep_stub (kinematics::Stub const &in_stub1, kinematics::Stub const &in_stub2)

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.setup")

void	set_base_partner (pose::Pose &pose)

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

Typedef Documentation

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

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

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

Definition at line 34 of file DirectReadoutPotential.fwd.hh.

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

Definition at line 31 of file DirectReadoutPotential.fwd.hh.

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

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

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

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

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

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

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

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

typedef utility::pointer::owning_ptr< DNATorsionEnergy const > core::scoring::dna::DNATorsionEnergyCOP

Definition at line 28 of file DNATorsionEnergy.fwd.hh.

typedef utility::pointer::owning_ptr< DNATorsionEnergy > core::scoring::dna::DNATorsionEnergyOP

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

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

Definition at line 48 of file DNA_BasePotential.cc.

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

Definition at line 49 of file base_geometry.cc.

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

Definition at line 51 of file base_geometry.cc.

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

Definition at line 29 of file DNABFormPotential.fwd.hh.

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

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

Enumeration Type Documentation

anonymous enum

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

Definition at line 60 of file DNATorsionPotential.cc.

Function Documentation

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

Definition at line 120 of file base_geometry.cc.

Referenced by get_DNA_backbone_bin().

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

Definition at line 48 of file setup.cc.

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::total_residue(), and TR().

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

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

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

Definition at line 697 of file base_geometry.cc.

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().

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

saved for comparison and debugging purposes

Definition at line 986 of file base_geometry.cc.

References get_base_stub(), is_orthonormal(), core::kinematics::Stub::M, core::pack::interaction_graph::T(), and core::kinematics::Stub::v.

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

Definition at line 357 of file base_geometry.cc.

References get_base_pair_y_axis_atom_xyz(), get_z_axis(), and core::pack::interaction_graph::T().

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

Definition at line 388 of file base_geometry.cc.

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().

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

Definition at line 204 of file base_geometry.cc.

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().

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

Definition at line 63 of file base_geometry.cc.

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

Referenced by show_dna_geometry().

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

Definition at line 1260 of file base_geometry.cc.

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

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

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
	)

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
	)

Definition at line 714 of file base_geometry.cc.

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().

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

Definition at line 1124 of file base_geometry.cc.

References get_base_stub(), is_orthonormal(), core::kinematics::Stub::M, core::pack::interaction_graph::T(), and core::kinematics::Stub::v.

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

Definition at line 321 of file base_geometry.cc.

References get_y_axis_atoms(), get_z_axis(), core::pack::interaction_graph::T(), 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(), get_base_pair_params_old(), and get_base_step_params().

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

Definition at line 130 of file base_geometry.cc.

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

Referenced by show_dna_geometry().

kinematics::Stub core::scoring::dna::get_midstep_stub	(	kinematics::Stub const &	in_stub1,
		kinematics::Stub const &	in_stub2
	)

Definition at line 1339 of file base_geometry.cc.

References is_orthonormal(), core::kinematics::Stub::M, core::pack::interaction_graph::T(), and core::kinematics::Stub::v.

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

Definition at line 545 of file base_geometry.cc.

References is_orthonormal(), core::kinematics::Stub::M, core::pack::interaction_graph::T(), and core::kinematics::Stub::v.

Referenced by get_base_pair_params(), and get_base_step_params().

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

Definition at line 190 of file base_geometry.cc.

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

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

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

Definition at line 159 of file base_geometry.cc.

References core::chemical::ResidueType::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, and core::chemical::na_ura.

Referenced by get_base_stub(), and get_y_axis().

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

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

Definition at line 258 of file base_geometry.cc.

References get_z_axis(), and strand_orientation_vector().

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

Definition at line 285 of file base_geometry.cc.

References get_z_axis().

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

helper fxn

Definition at line 299 of file base_geometry.cc.

References core::scoring::rna::X.

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

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...

Definition at line 911 of file base_geometry.cc.

References protocols::comparative_modeling::features::A, and protocols::match::upstream::b.

Referenced by get_base_pair_stub_slow().

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

helper routine

helper fcn

Definition at line 30 of file BasePartner.cc.

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

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

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

Definition at line 739 of file base_geometry.cc.

References core::pose::Pose::residue(), retrieve_base_partner_from_pose(), and core::pose::Pose::total_residue().

Referenced by show_base_step_params().

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

Definition at line 37 of file setup.cc.

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

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

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

Definition at line 463 of file base_geometry.cc.

References get_base_pair_params(), core::conformation::Residue::name1(), and core::conformation::Residue::seqpos().

Referenced by show_base_pair_params(), and show_dna_geometry().

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

Definition at line 485 of file base_geometry.cc.

References show_base_pair_params().

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

Definition at line 833 of file base_geometry.cc.

References core::pose::Pose::residue(), retrieve_base_partner_from_pose(), show_base_pair_params(), and core::pose::Pose::total_residue().

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