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protocols::sic_dock::scores Namespace Reference

Classes

class  MotifHashRigidScore
 
class  TrisBpyScore
 

Typedefs

using Real = core::Real
 
using Pose = core::pose::Pose
 
using Xform = Xform
 
using Vec = numeric::xyzVector< Real >
 
using Mat = numeric::xyzMatrix< Real >
 
using Vecs = utility::vector1< Vec >
 
using Reals = utility::vector1< Real >
 
using Sizes = utility::vector1< core::Size >
 
using Xforms = numeric::Xforms
 
using Scores = utility::vector1< RigidScoreCOP >
 
typedef
utility::pointer::shared_ptr
< MotifHashRigidScore > 		MotifHashRigidScoreOP
 
typedef
utility::pointer::shared_ptr
< MotifHashRigidScore const > 		MotifHashRigidScoreCOP
 
typedef
utility::pointer::shared_ptr
< TrisBpyScore > 		TrisBpyScoreOP
 
typedef
utility::pointer::shared_ptr
< TrisBpyScore const > 		TrisBpyScoreCOP
 

Functions

static basic::Tracer TR ("protocols.sic_dock.scores.MotifHashRigidScore")
 
core::scoring::motif::Real6 get_rt6 (Xform const &x)
 
static basic::Tracer TR ("protocols.sic_dock.scores.TrisBpyScore")
 
static Vec const N (2.649,-1.227, 1.777)
 
static Vec const CA (3.946,-0.851, 1.187)
 
static Vec const C (4.775, 0.037, 2.144)
 
static Vec const O (4.410, 0.106, 3.359)
 
static Vec const CB (3.569,-0.000, 0.000)
 
static Vec const CG (3.018,-0.767,-1.287)
 
static Vec const CD (1.984,-0.166,-1.966)
 
static Vec const C28 (3.529,-1.952,-1.749)
 
static Vec const N5 (0.291,-1.619,-5.187)
 
static Vec const N6 (1.455,-0.715,-3.073)
 
static Vec const C21 (-0.325,-1.956,-6.336)
 
static Vec const C22 (0.087,-3.028,-7.100)
 
static Vec const C23 (1.133,-3.793,-6.665)
 
static Vec const C24 (1.768,-3.468,-5.482)
 
static Vec const C25 (1.336,-2.377,-4.760)
 
static Vec const C29 (3.015,-2.510,-2.888)
 
static Vec const C30 (1.975,-1.875,-3.536)
 
static Vec const FE (0.000, 0.000,-4.157)
 
static Xform const bpybb (CA, N, CA, C)
 
static Vec const CBlocal (~bpybb *CB)
 
static Mat const R3z1 (numeric::z_rotation_matrix_degrees(0.0))
 
static Mat const R3z2 (numeric::z_rotation_matrix_degrees(120.0))
 
static Mat const R3z3 (numeric::z_rotation_matrix_degrees(240.0))
 
static Mat const chiral1 (Mat::cols(1, 0, 0, 0, 1, 0, 0, 0, 1))
 
static Mat const chiral2 (Mat::cols(1, 0, 0, 0, 1, 0, 0, 0,-1))
 
static Mat const chiral3 (Mat::cols(1, 0, 0, 0,-1, 0, 0, 0, 1))
 
static Mat const chiral4 (Mat::cols(1, 0, 0, 0,-1, 0, 0, 0,-1))
 
static Vec const nbr2 (C29)
 
static Vec const nbr1 (C22)
 
void printbpy (std::ostream &out, Xform const &x, int resi=1000)
 

Variables

static Vec const clash_coords [12] = {CB,CD,C28,N5,N6,C21,C22,C23,C24,C25,C29,C30 }
 
static Mat const R3z [3] = { R3z1, R3z2, R3z3 }
 
static Mat const chiral [4] = { chiral1, chiral2, chiral3, chiral4 }
 
static Vec const nbr [6] = { nbr1, nbr2, R3z2*nbr1, R3z2*nbr2, R3z3*nbr1, R3z3*nbr2 }
 

Typedef Documentation

typedef numeric::xyzMatrix< Real > protocols::sic_dock::scores::Mat
typedef utility::pointer::shared_ptr< MotifHashRigidScore const > protocols::sic_dock::scores::MotifHashRigidScoreCOP
typedef utility::pointer::shared_ptr< MotifHashRigidScore > protocols::sic_dock::scores::MotifHashRigidScoreOP
typedef core::pose::Pose protocols::sic_dock::scores::Pose
typedef core::Real protocols::sic_dock::scores::Real
typedef utility::vector1< Real > protocols::sic_dock::scores::Reals
typedef utility::vector1< RigidScoreCOP > protocols::sic_dock::scores::Scores
typedef utility::vector1< core::Size > protocols::sic_dock::scores::Sizes
typedef utility::pointer::shared_ptr< TrisBpyScore const > protocols::sic_dock::scores::TrisBpyScoreCOP
typedef utility::pointer::shared_ptr< TrisBpyScore > protocols::sic_dock::scores::TrisBpyScoreOP
typedef numeric::xyzVector< Real > protocols::sic_dock::scores::Vec
typedef utility::vector1< Vec > protocols::sic_dock::scores::Vecs
typedef Xform protocols::sic_dock::scores::Xform
typedef numeric::Xforms protocols::sic_dock::scores::Xforms

Function Documentation

static Xform const protocols::sic_dock::scores::bpybb ( CA  ,
N  ,
CA  ,
C   
)
static
static Vec const protocols::sic_dock::scores::C ( 4.  775,
0.  037,
2.  144 
)
static

Referenced by protocols::sic_dock::scores::MotifHashRigidScore::MotifHashRigidScore(), and protocols::sic_dock::scores::TrisBpyScore::TrisBpyScore().

static Vec const protocols::sic_dock::scores::C21 ( -0.  325,
-1.  956,
-6.  336 
)
static

Referenced by printbpy().

static Vec const protocols::sic_dock::scores::C22 ( 0.  087,
-3.  028,
-7.  100 
)
static

Referenced by printbpy().

static Vec const protocols::sic_dock::scores::C23 ( 1.  133,
-3.  793,
-6.  665 
)
static

Referenced by printbpy().

static Vec const protocols::sic_dock::scores::C24 ( 1.  768,
-3.  468,
-5.  482 
)
static

Referenced by printbpy().

static Vec const protocols::sic_dock::scores::C25 ( 1.  336,
-2.  377,
-4.  760 
)
static

Referenced by printbpy().

static Vec const protocols::sic_dock::scores::C28 ( 3.  529,
-1.  952,
-1.  749 
)
static

Referenced by printbpy().

static Vec const protocols::sic_dock::scores::C29 ( 3.  015,
-2.  510,
-2.  888 
)
static

Referenced by printbpy().

static Vec const protocols::sic_dock::scores::C30 ( 1.  975,
-1.  875,
-3.  536 
)
static

Referenced by printbpy().

static Vec const protocols::sic_dock::scores::CA ( 3.  946,
-0.  851,
1.  187 
)
static

Referenced by protocols::sic_dock::scores::MotifHashRigidScore::MotifHashRigidScore(), and protocols::sic_dock::scores::TrisBpyScore::TrisBpyScore().

static Vec const protocols::sic_dock::scores::CB ( 3.  569,
-0.  000,
0.  000 
)
static

Referenced by printbpy().

static Vec const protocols::sic_dock::scores::CBlocal ( ~bpybb *  CB)
static

Referenced by protocols::sic_dock::scores::TrisBpyScore::score_extra().

static Vec const protocols::sic_dock::scores::CD ( 1.  984,
-0.  166,
-1.  966 
)
static

Referenced by printbpy().

static Vec const protocols::sic_dock::scores::CG ( 3.  018,
-0.  767,
-1.  287 
)
static

Referenced by printbpy(), and protocols::sic_dock::scores::TrisBpyScore::score_extra().

static Mat const protocols::sic_dock::scores::chiral1 ( Mat::  cols1, 0, 0, 0, 1, 0, 0, 0, 1)
static
static Mat const protocols::sic_dock::scores::chiral2 ( Mat::  cols1, 0, 0, 0, 1, 0, 0, 0,-1)
static
static Mat const protocols::sic_dock::scores::chiral3 ( Mat::  cols1, 0, 0, 0,-1, 0, 0, 0, 1)
static
static Mat const protocols::sic_dock::scores::chiral4 ( Mat::  cols1, 0, 0, 0,-1, 0, 0, 0,-1)
static
static Vec const protocols::sic_dock::scores::FE ( 0.  000,
0.  000,
-4.  157 
)
static

Referenced by printbpy().

core::scoring::motif::Real6 protocols::sic_dock::scores::get_rt6 ( Xform const &  x)

Referenced by protocols::sic_dock::scores::MotifHashRigidScore::score_meta().

static Vec const protocols::sic_dock::scores::N ( 2.  649,
-1.  227,
1.  777 
)
static

Referenced by protocols::sic_dock::scores::MotifHashRigidScore::MotifHashRigidScore(), and protocols::sic_dock::scores::TrisBpyScore::TrisBpyScore().

static Vec const protocols::sic_dock::scores::N5 ( 0.  291,
-1.  619,
-5.  187 
)
static

Referenced by printbpy().

static Vec const protocols::sic_dock::scores::N6 ( 1.  455,
-0.  715,
-3.  073 
)
static

Referenced by printbpy().

static Vec const protocols::sic_dock::scores::nbr1 ( C22  )
static

Referenced by protocols::enzdes::ModifyStoredRBConfs::closest_orient_atoms_msd(), core::conformation::get_stub_from_residue(), core::conformation::Residue::orient_onto_location(), core::conformation::Residue::orient_onto_residue(), protocols::match::MatcherMover::process_pose(), and core::chemical::ResidueType::select_orient_atoms().

static Vec const protocols::sic_dock::scores::nbr2 ( C29  )
static

Referenced by protocols::enzdes::ModifyStoredRBConfs::closest_orient_atoms_msd(), core::conformation::get_stub_from_residue(), core::conformation::Residue::orient_onto_location(), core::conformation::Residue::orient_onto_residue(), protocols::match::MatcherMover::process_pose(), and core::chemical::ResidueType::select_orient_atoms().

static Vec const protocols::sic_dock::scores::O ( 4.  410,
0.  106,
3.  359 
)
static
void protocols::sic_dock::scores::printbpy ( std::ostream &  out,
Xform const &  x,
int  resi = 1000 
)

References C21(), C22(), C23(), C24(), C25(), C28(), C29(), C30(), CB(), CD(), CG(), core::chemical::element::F, FE(), core::chemical::element::I, N5(), N6(), and R3z.

Referenced by protocols::sic_dock::scores::TrisBpyScore::dump_trisbpy().

static Mat const protocols::sic_dock::scores::R3z1 ( numeric::  z_rotation_matrix_degrees0.0)
static
static Mat const protocols::sic_dock::scores::R3z2 ( numeric::  z_rotation_matrix_degrees120.0)
static
static Mat const protocols::sic_dock::scores::R3z3 ( numeric::  z_rotation_matrix_degrees240.0)
static
static basic::Tracer protocols::sic_dock::scores::TR ( "protocols.sic_dock.scores.MotifHashRigidScore"  )
static
static basic::Tracer protocols::sic_dock::scores::TR ( "protocols.sic_dock.scores.TrisBpyScore"  )
static

Variable Documentation

Mat const protocols::sic_dock::scores::chiral[4] = { chiral1, chiral2, chiral3, chiral4 }
static

Referenced by protocols::sic_dock::scores::TrisBpyScore::score_extra().

Vec const protocols::sic_dock::scores::clash_coords[12] = {CB,CD,C28,N5,N6,C21,C22,C23,C24,C25,C29,C30 }
static

Referenced by protocols::sic_dock::scores::TrisBpyScore::score_extra().

Vec const protocols::sic_dock::scores::nbr[6] = { nbr1, nbr2, R3z2*nbr1, R3z2*nbr2, R3z3*nbr1, R3z3*nbr2 }
static

Referenced by core::kinematics::add_atom(), core::chemical::annotate_backbone(), core::conformation::Residue::apply_transform_downstream(), core::pack::interaction_graph::NPDHBSimpleNode::commit_change_no_res_pointer_update(), core::pack::interaction_graph::NPDHBSimpleNode::commit_change_npd(), core::scoring::packstat::Slice::compute_events(), core::chemical::sdf::MolFileIOMolecule::convert_to_ResidueType(), core::chemical::ResidueType::define_mainchain_atoms(), core::energy_methods::StackElecEnergy::eval_atom_derivative(), core::scoring::methods::MMLJEnergyInter::eval_atom_derivative(), core::energy_methods::LK_PolarNonPolarEnergy::eval_atom_derivative(), core::energy_methods::RNA_FA_ElecEnergy::eval_atom_derivative(), core::scoring::elec::FA_ElecEnergy::eval_atom_derivative(), core::scoring::etable::BaseEtableEnergy< Derived >::eval_atom_derivative(), core::energy_methods::RNA_FA_ElecEnergy::finalize_total_energy(), core::energy_methods::RNA_CoarseDistEnergy::finalize_total_energy(), core::energy_methods::StackElecEnergy::finalize_total_energy(), core::scoring::elec::FA_ElecEnergy::finalize_total_energy(), core::scoring::etable::BaseEtableEnergy< Derived >::finalize_total_energy(), core::pack::interaction_graph::NPDHBSimpleNode::find_curr_hbonds_to_upper_neighbors(), core::pack::interaction_graph::NPDHBSimpleNode::get_npdhb_deltaE_for_substitution(), core::chemical::ResidueDatabaseIO::report_residue_type_bond(), core::scoring::etable::BaseEtableEnergy< Derived >::residue_pair_energy_ext(), protocols::sic_dock::scores::TrisBpyScore::score_extra(), core::chemical::ResidueType::select_orient_atoms(), core::chemical::ResidueType::select_orient_atoms_standard_logic(), core::chemical::sdf::MolFileIOMolecule::set_from_extra_data(), core::chemical::rdkit::RDMolToRestype::set_nbr(), core::conformation::setup_atom_links(), and core::chemical::ResidueTypeKinWriter::write_restype().

Mat const protocols::sic_dock::scores::R3z[3] = { R3z1, R3z2, R3z3 }
static

Referenced by printbpy(), and protocols::sic_dock::scores::TrisBpyScore::score_extra().

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