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

typedef utility::pointer::shared_ptr< HSPairPotential > protocols::fldsgn::potentials::sspot::HSPairPotentialOP

typedef utility::pointer::shared_ptr< NatbiasHelicesSheetPotential > protocols::fldsgn::potentials::sspot::NatbiasHelicesSheetPotentialOP

typedef utility::pointer::shared_ptr< NatbiasHelixPairPotential > protocols::fldsgn::potentials::sspot::NatbiasHelixPairPotentialOP

typedef utility::pointer::shared_ptr< NatbiasStrandPairPotential > protocols::fldsgn::potentials::sspot::NatbiasStrandPairPotentialOP

typedef core::pose::Pose protocols::fldsgn::potentials::sspot::Pose

typedef core::Real protocols::fldsgn::potentials::sspot::Real

typedef core::Size protocols::fldsgn::potentials::sspot::Size

typedef utility::pointer::shared_ptr< SSPairPotential > protocols::fldsgn::potentials::sspot::SSPairPotentialOP

typedef core::Vector protocols::fldsgn::potentials::sspot::Vector

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]

v21

vector 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().