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	DNABFormPotential

class	DNAChiEnergy

class	DNAChiEnergyCreator

class	DNATorsionEnergy

class	DNATorsionEnergyCreator

class	DNATorsionPotential

class	TorsionFourierComponent

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...

void	set_base_partner (pose::Pose &pose)

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

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

Typedef Documentation

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Enumeration Type Documentation

anonymous enum

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

Function Documentation

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

References basic::periodic_range().

Referenced by get_DNA_backbone_bin().

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

References chemical, dot(), get_y_axis(), core::chemical::na_ade, core::chemical::na_cyt, core::chemical::na_gua, core::chemical::na_thy, nres, core::pose::Pose::residue(), basic::t_debug, core::pose::Pose::total_residue(), and TR.

Referenced by 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
	)

References get_base_stub(), and get_stub_stub_params().

Referenced by core::scoring::dna::DNA_BasePotential::base_pair_score(), 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

References numeric::arccos(), arccos(), numeric::xyzMatrix< class >::col_y(), numeric::xyzMatrix< class >::col_z(), cross(), numeric::conversions::degrees(), degrees(), dot(), get_base_stub(), is_orthonormal(), length, core::kinematics::Stub::M, rotation_matrix(), basic::T(), numeric::xyzMatrix< class >::transposed(), and core::kinematics::Stub::v.

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

References numeric::xyzMatrix< Real >::cols(), cross(), numeric::conversions::degrees(), numeric::xyzVector< class >::dot(), get_base_pair_y_axis_atom_xyz(), get_z_axis(), numeric::xyzVector< class >::normalize(), basic::T(), and basic::t_warning.

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(), numeric::xyzMatrix< Real >::cols(), cross(), numeric::conversions::degrees(), numeric::xyzVector< class >::dot(), core::conformation::Residue::first_sidechain_atom(), get_base_pair_y_axis_atom_xyz(), numeric::xyzVector< class >::is_normalized(), core::conformation::Residue::is_RNA(), lsf_normal(), core::conformation::Residue::nheavyatoms(), numeric::xyzVector< class >::normalize(), 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 )

References core::conformation::Residue::aa(), chemical, 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, utility_exit_with_message, 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
	)

References cross(), numeric::xyzVector< class >::dot(), dot(), and 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
	)

References cross(), numeric::conversions::degrees(), degrees(), dihedral_radians(), numeric::xyzVector< class >::dot(), dot(), basic::periodic_range(), radians(), numeric::conversions::radians(), and 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
	)

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(), 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
	)

References numeric::arccos(), arccos(), numeric::xyzMatrix< class >::col_z(), cross(), numeric::cross(), numeric::conversions::degrees(), degrees(), dot(), get_base_stub(), is_orthonormal(), length, core::kinematics::Stub::M, rotation_matrix(), basic::T(), numeric::xyzMatrix< class >::transposed(), and core::kinematics::Stub::v.

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

References numeric::xyzMatrix< Real >::cols(), cross(), numeric::conversions::degrees(), dot(), get_y_axis_atoms(), get_z_axis(), numeric::xyzVector< class >::normalize(), basic::T(), basic::t_warning, 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 )

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

Referenced by show_dna_geometry().

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

References numeric::arccos(), arccos(), numeric::xyzMatrix< class >::col_x(), numeric::xyzMatrix< class >::col_y(), numeric::xyzMatrix< class >::col_z(), numeric::xyzMatrix< Real >::cols(), cross(), numeric::conversions::degrees(), dot(), is_orthonormal(), core::kinematics::Stub::M, rotation_matrix(), basic::T(), numeric::xyzMatrix< class >::transposed(), 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

References numeric::arccos(), arccos(), numeric::xyzMatrix< class >::col_x(), numeric::xyzMatrix< class >::col_y(), numeric::xyzMatrix< class >::col_z(), cross(), degrees(), numeric::conversions::degrees(), dot(), is_orthonormal(), length, core::kinematics::Stub::M, rotation_matrix(), basic::T(), numeric::xyzMatrix< class >::transposed(), 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
	)

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

Referenced by find_basepairs().

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::ResidueType::aa(), chemical, 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 utility_exit.

Referenced by get_base_stub(), and get_y_axis().

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

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

Referenced by get_base_pair_stub(), get_base_stub(), get_z_axis(), and core::scoring::dna::DirectReadoutPotential::rsd_rsd_energy().

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

References dot(), numeric::xyzVector< class >::dot(), 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
	)

References get_z_axis().

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

helper fxn

References numeric::xyzMatrix< class >::transposed().

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...

References cm, and numeric::xyzVector< class >::normalize().

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

References core::pose::datacache::CacheableDataType::BASE_PARTNER, core::pose::Pose::data(), basic::datacache::BasicDataCache::get(), and basic::datacache::BasicDataCache::has().

Referenced by 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
	)

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 )

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

Referenced by 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
	)

References core::chemical::element::F, get_base_pair_params(), core::chemical::element::I, core::conformation::Residue::name1(), params, 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
	)

References show_base_pair_params().

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

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
	)

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::scoring::ScoringManager::get_instance(), core::chemical::element::I, core::conformation::Residue::name1(), params, and core::conformation::Residue::seqpos().

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, params, core::pose::Pose::residue(), retrieve_base_partner_from_pose(), and seqpos_is_base_step_anchor().

Referenced by show_base_step_params(), and show_dna_geometry().

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

References seqpos_is_base_step_anchor(), show_base_step_params(), and core::pose::Pose::total_residue().

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

References core::chemical::element::F, get_base_pucker(), get_DNA_backbone_bin(), core::chemical::element::I, nres, core::pose::Pose::residue(), show_base_pair_params(), show_base_step_params(), and core::pose::Pose::total_residue().

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::scoring::ScoringManager::get_instance(), core::chemical::element::I, core::conformation::Residue::name1(), params, and core::conformation::Residue::seqpos().

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

References numeric::xyzVector< class >::normalize(), and core::conformation::Residue::xyz().

Referenced by get_base_pair_stub_slow(), and get_z_axis().

Variable Documentation

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

static

Referenced by find_basepairs().

Classes

Typedefs

Enumerations

Functions

Variables