Rosetta 3.4
Classes | Typedefs | 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

Typedefs

typedef numeric::xyzMatrix< RealMatrix
typedef utility::vector1< RealParams
typedef
utility::pointer::owning_ptr
< BasePartner
BasePartnerOP
typedef ObjexxFCL::FArray1D< RealFArray1D_Real

Functions

Vector lsf_normal (utility::vector1< Vector > const &atoms_in)
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
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_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)
BasePartner const & retrieve_base_partner_from_pose (pose::Pose const &pose)
 helper routine
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 ObjexxFCL::FArray1D< Real > core::scoring::dna::FArray1D_Real

Function Documentation

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

Referenced by get_DNA_backbone_bin().

void core::scoring::dna::find_basepairs ( pose::Pose const &  pose,
utility::vector1< Size > &  partner 
)
void core::scoring::dna::get_base_pair_params ( conformation::Residue const &  rsd1,
conformation::Residue const &  rsd2,
Params &  params 
)
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_old ( 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 &  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 
)
void core::scoring::dna::get_base_step_params ( conformation::Residue const &  rsd1,
conformation::Residue const &  rsd2,
utility::vector1< Real > &  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)
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 make_table_of_pilot_apps::f, is_orthonormal(), core::kinematics::Stub::M, core::scoring::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 
)
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, 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)
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 
)
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 ( 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]

Referenced by find_basepairs().

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