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protocols::fldsgn::potentials::sspot Namespace Reference

Classes

class  HSPairPotential
 secondary structure scoring cut from classic rosetta structure.h/structure.cc More...
 
class  NatbiasHelicesSheetPotential
 
class  NatbiasHelixPairPotential
 
class  NatbiasSecondaryStructureEnergy
 NatbiasSecondaryStructureEnergy. More...
 
class  NatbiasSecondaryStructureEnergyCreator
 
class  NatbiasStrandPairPotential
 secondary structure scoring cut from classic rosetta structure.h/structure.cc More...
 
class  SSPairPotential
 secondary structure scoring cut from classic rosetta structure.h/structure.cc More...
 

Typedefs

typedef
utility::pointer::shared_ptr
< HSPairPotential
HSPairPotentialOP
 
typedef
utility::pointer::shared_ptr
< NatbiasHelicesSheetPotential
NatbiasHelicesSheetPotentialOP
 
typedef
utility::pointer::shared_ptr
< NatbiasHelixPairPotential
NatbiasHelixPairPotentialOP
 
typedef
utility::pointer::shared_ptr
< NatbiasStrandPairPotential
NatbiasStrandPairPotentialOP
 
typedef
utility::pointer::shared_ptr
< SSPairPotential
SSPairPotentialOP
 
using Real = core::Real
 
using Vector = core::Vector
 
using Pose = core::pose::Pose
 
typedef core::Size Size
 

Functions

void spherical (Vector const &a2, Vector const &a4, Real &phi, Real &theta, Vector const &cen1, Vector const &cen2, Vector const &v21)
 
Size get_foldtree_seqsep (Pose const &pose, core::Size pos1, core::Size pos2, core::Size gap_size)
 identifies the sequence separation along the fold tree lin the old way to calculate the sequence separation takes an asumption of no-break chain lin when there is chain break between pos1 and pos2, we add a gap to make a correct calculation in ss energy More...
 

Typedef Documentation

Function Documentation

Size protocols::fldsgn::potentials::sspot::get_foldtree_seqsep ( Pose const &  pose,
core::Size  pos1,
core::Size  pos2,
core::Size  gap_size 
)

identifies the sequence separation along the fold tree lin the old way to calculate the sequence separation takes an asumption of no-break chain lin when there is chain break between pos1 and pos2, we add a gap to make a correct calculation in ss energy

identifies the sequence separation along the fold tree add the gap_size (default 10 ) into seqsep when there is chain break between pos1 and pos2

References core::sequence::end, core::pose::Pose::fold_tree(), core::kinematics::FoldTree::is_simple_tree(), core::chemical::ResidueType::is_terminus(), protocols::mean_field::max(), protocols::mean_field::min(), and core::pose::Pose::residue_type().

Referenced by protocols::fldsgn::potentials::sspot::HSPairPotential::score(), protocols::fldsgn::potentials::sspot::SSPairPotential::score(), and protocols::fldsgn::potentials::sspot::NatbiasStrandPairPotential::score().

void protocols::fldsgn::potentials::sspot::spherical ( Vector const &  a2,
Vector const &  a4,
Real &  phi,
Real &  theta,
Vector const &  cen1,
Vector const &  cen2,
Vector const &  v21 
)

define a coordinate system with Z axis along cen1->a2 (v1), xz plane defined by cen1->a2 and v21. and origin at cen1. Find the spherical coordinates phi,and theta of point a4 if vector cen2->a4 was moved such that cen2=cen1

Parameters
[out]v21vector connecting midpoints

References protocols::hybridization::r1.

Referenced by core::chemical::fill_ideal_xyz_from_icoor(), protocols::fldsgn::potentials::sspot::HSPairPotential::score(), protocols::fldsgn::potentials::sspot::NatbiasStrandPairPotential::score(), and protocols::fldsgn::potentials::sspot::SSPairPotential::score().