Rosetta  2020.37
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Macros Pages
Classes | Typedefs | Enumerations | Functions
core::scoring::dna Namespace Reference

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  DNABFormPotential
 
class  DNAChiEnergy
 
class  DNAChiEnergyCreator
 
class  DNATorsionEnergy
 
class  DNATorsionEnergyCreator
 
class  DNATorsionPotential
 
class  TorsionFourierComponent
 

Typedefs

typedef
utility::pointer::shared_ptr
< DNATorsionEnergy
DNATorsionEnergyOP
 
typedef
utility::pointer::shared_ptr
< DNATorsionEnergy const > 
DNATorsionEnergyCOP
 
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_base_pucker (conformation::Residue const &rsd, std::pair< std::string, int > &pucker)
 
void get_sugar_pucker (conformation::Residue const &rsd, std::pair< std::string, int > &pucker)
 this could be made faster... More...
 
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 show_dna_geometry (pose::Pose const &pose, std::ostream &out)
 
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)
 
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

typedef utility::pointer::shared_ptr< BasePartner > core::scoring::dna::BasePartnerOP
typedef utility::pointer::shared_ptr< DirectReadoutPotential const > core::scoring::dna::DirectReadoutPotentialCOP
typedef utility::pointer::shared_ptr< DNA_BasePotential const > core::scoring::dna::DNA_BasePotentialCOP
typedef utility::pointer::shared_ptr< DNA_BasePotential > core::scoring::dna::DNA_BasePotentialOP
typedef utility::pointer::shared_ptr< DNA_DihedralPotential const > core::scoring::dna::DNA_DihedralPotentialCOP
typedef utility::pointer::shared_ptr< DNA_DihedralPotential > core::scoring::dna::DNA_DihedralPotentialOP
typedef utility::pointer::shared_ptr< DNA_EnvPairPotential const > core::scoring::dna::DNA_EnvPairPotentialCOP
typedef utility::pointer::shared_ptr< DNA_EnvPairPotential > core::scoring::dna::DNA_EnvPairPotentialOP
typedef utility::pointer::shared_ptr< DNABFormPotential const > core::scoring::dna::DNABFormPotentialCOP
typedef utility::pointer::shared_ptr< DNABFormPotential > core::scoring::dna::DNABFormPotentialOP
typedef utility::pointer::shared_ptr< DNATorsionEnergy const > core::scoring::dna::DNATorsionEnergyCOP
typedef utility::pointer::shared_ptr< DNATorsionEnergy > core::scoring::dna::DNATorsionEnergyOP
typedef utility::pointer::shared_ptr< DNATorsionPotential const > core::scoring::dna::DNATorsionPotentialCOP
typedef utility::pointer::shared_ptr< DNATorsionPotential > core::scoring::dna::DNATorsionPotentialOP
using core::scoring::dna::FArray1D_Real = typedef ObjexxFCL::FArray1D<Real>
using core::scoring::dna::Matrix = typedef numeric::xyzMatrix<Real>
using core::scoring::dna::Params = typedef utility::vector1<Real>
typedef utility::pointer::shared_ptr< TorsionFourierComponent const > core::scoring::dna::TorsionFourierComponentCOP

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)

Referenced by get_DNA_backbone_bin().

chemical::AA core::scoring::dna::dna_aa_from_oneletter_code ( char const  c)
void core::scoring::dna::filter_torsions_by_iname ( Size const  iname,
vector1< Size > const &  torsion_inames,
vector1< Real > &  torsions 
)
void core::scoring::dna::find_basepairs ( pose::Pose const &  pose,
utility::vector1< Size > &  partner 
)
Real core::scoring::dna::get_b1b2_bin ( Real  epsilon,
Real  zeta 
)
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 
)
kinematics::Stub core::scoring::dna::get_base_pair_stub ( conformation::Residue const &  rsd1,
conformation::Residue const &  rsd2 
)
kinematics::Stub core::scoring::dna::get_base_pair_stub_slow ( conformation::Residue const &  rsd1,
conformation::Residue const &  rsd2 
)
Vector core::scoring::dna::get_base_pair_y_axis_atom_xyz ( conformation::Residue const &  rsd)
void core::scoring::dna::get_base_pucker ( conformation::Residue const &  rsd,
std::pair< std::string, int > &  pucker 
)
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 
)
void core::scoring::dna::get_base_step_params ( conformation::Residue const &  rsd1,
conformation::Residue const &  rsd2,
Params &  params 
)
kinematics::Stub core::scoring::dna::get_base_stub ( conformation::Residue const &  rsd,
int const  strand 
)
std::string core::scoring::dna::get_DNA_backbone_bin ( conformation::Residue const &  rsd)
Size core::scoring::dna::get_iname1_from_name1 ( char const  name1)
inline
void core::scoring::dna::get_mean_median_and_sdev ( vector1< Real >  vals,
Real &  mean,
Real &  median,
Real &  sdev 
)
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().

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::methods::DNA_DihedralEnergy::eval_dof_derivative(), core::scoring::methods::DNA_DihedralEnergy::eval_residue_derivatives(), core::scoring::dna::DNA_DihedralPotential::get_mean_sugar_pucker_dependent_chi(), and core::scoring::methods::DNA_DihedralEnergy::residue_energy().

void core::scoring::dna::get_sugar_torsions ( conformation::Residue const &  rsd,
utility::vector1< Real > &  torsions 
)
Real core::scoring::dna::get_triple_bin ( Real  angle)
Vector core::scoring::dna::get_y_axis ( conformation::Residue const &  rsd,
int const  strand 
)
void core::scoring::dna::get_y_axis_atoms ( chemical::ResidueType const &  rsd_type,
int const  strand,
std::string &  a1,
std::string &  a2 
)
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 
)
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 
)
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 protocols::comparative_modeling::features::A, core::pose::motif::a(), protocols::match::upstream::b, and protocols::antibody::lambda.

Referenced by get_base_pair_stub_slow().

void core::scoring::dna::put_angle_in_0to360 ( Real &  angle)
BasePartner const & core::scoring::dna::retrieve_base_partner_from_pose ( pose::Pose const &  pose)
bool core::scoring::dna::seqpos_is_base_step_anchor ( Size const  seqpos,
pose::Pose const &  pose 
)
void core::scoring::dna::set_base_partner ( pose::Pose pose)
void core::scoring::dna::show_base_pair_params ( conformation::Residue const &  rsd1,
conformation::Residue const &  rsd2,
std::ostream &  out 
)
void core::scoring::dna::show_base_pair_params ( conformation::Residue const &  rsd1,
conformation::Residue const &  rsd2 
)
void core::scoring::dna::show_base_pair_params ( pose::Pose const &  pose,
std::ostream &  out 
)
void core::scoring::dna::show_base_pair_params_with_z_scores ( conformation::Residue const &  rsd1,
conformation::Residue const &  rsd2,
std::ostream &  out 
)
void core::scoring::dna::show_base_step_params ( Size const  seqpos,
pose::Pose const &  pose,
std::ostream &  out 
)
void core::scoring::dna::show_base_step_params ( pose::Pose const &  pose,
std::ostream &  out 
)
void core::scoring::dna::show_dna_geometry ( pose::Pose const &  pose,
std::ostream &  out 
)
void core::scoring::dna::show_new_base_step_params ( conformation::Residue const &  rsd1,
conformation::Residue const &  rsd2 
)
Vector core::scoring::dna::strand_orientation_vector ( conformation::Residue const &  rsd,
int const  strand 
)
static basic::Tracer core::scoring::dna::TR ( "core.scoring.dna.setup"  )
static
static basic::Tracer core::scoring::dna::TR ( "core.scoring.dna.base_geometry"  )
static
static basic::Tracer core::scoring::dna::TR ( "core.scoring.dna.DNA_DihedralPotential"  )
static