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	NatbiasSheetPotential
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::owning_ptr < HSPairPotential >	HSPairPotentialOP
typedef utility::pointer::owning_ptr < NatbiasHelicesSheetPotential >	NatbiasHelicesSheetPotentialOP
typedef utility::pointer::owning_ptr < NatbiasHelixPairPotential >	NatbiasHelixPairPotentialOP
typedef utility::pointer::owning_ptr < NatbiasSheetPotential >	NatbiasSheetPotentialOP
typedef utility::pointer::owning_ptr < NatbiasStrandPairPotential >	NatbiasStrandPairPotentialOP
typedef utility::pointer::owning_ptr < SSPairPotential >	SSPairPotentialOP
typedef core::Size	Size
typedef core::Real	Real
typedef core::Vector	Vector
typedef core::pose::Pose	Pose

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, Size pos1, Size pos2, 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::owning_ptr< HSPairPotential > protocols::fldsgn::potentials::sspot::HSPairPotentialOP

Definition at line 26 of file HSPairPotential.fwd.hh.

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

Definition at line 26 of file NatbiasHelicesSheetPotential.fwd.hh.

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

Definition at line 28 of file NatbiasHelixPairPotential.fwd.hh.

typedef utility::pointer::owning_ptr< NatbiasSheetPotential > protocols::fldsgn::potentials::sspot::NatbiasSheetPotentialOP

Definition at line 28 of file NatbiasSheetPotential.fwd.hh.

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

Definition at line 26 of file NatbiasStrandPairPotential.fwd.hh.

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

Definition at line 40 of file util.cc.

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

Definition at line 38 of file util.cc.

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

Definition at line 37 of file util.cc.

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

Definition at line 28 of file SSPairPotential.fwd.hh.

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

Definition at line 39 of file util.cc.

Function Documentation

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

Definition at line 102 of file util.cc.

References core::sequence::end, core::pose::Pose::fold_tree(), core::kinematics::FoldTree::is_simple_tree(), core::chemical::ResidueType::is_terminus(), 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

Definition at line 48 of file util.cc.

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