#include <ResiduePairJump.hh>

Public Member Functions
	ResiduePairJump ()

virtual	~ResiduePairJump ()

	ResiduePairJump (core::chemical::ResidueType const &residue1, core::chemical::ResidueType const &residue2)

void	add_residue_pair (core::chemical::ResidueType const &residue1, core::chemical::ResidueType const &residue2)

void	add_residue_single (core::chemical::ResidueType const &residue)

bool	jumpAtoms_defined () const

bool	cstAtoms_defined () const

bool	cstInfoMap_defined () const

void	set_cstAtoms (core::Size rsd, core::Size atom, std::string name)

utility::vector1< std::string > const &	cstAtoms (core::Size i) const

void	set_jumpAtoms (core::Size rsd, core::Size atom, std::string name)

utility::vector1< std::string > const &	jumpAtoms (core::Size i) const

void	set_cstInfo (cstType type, core::Real value)

void	set_cstInfo (cstType type, utility::vector1< core::Real > const &values)

core::fragment::FrameOP	generate_frame ()

void	init_mini_pose ()

void	diversify_dof_conformers (dofType type, core::Size max_index)

void	diversify_dof_conformers ()

core::pose::PoseOP	apply_dof_conformer (std::map< dofType, core::Size > const &conformer_map)

void	build_sidechain_rotamers ()

void	build_cst_conformer_jumps ()

void	diversify_cst_conformers (cstType type, core::Size max_index)

void	diversify_cst_conformers ()

Private Types
typedef std::map< cstType, utility::vector1< core::Real > >	cstInfoMap

typedef std::map< cstType, utility::vector1< core::Real > >::iterator	cstInfoMapIterator

Private Attributes
utility::vector1 < ResiduePairJumpSingleOP >	residues_

std::map< cstType, utility::vector1< core::Real > >	cstInfoMap_

utility::vector1< std::map < cstType, core::Size > >	cst_conformers_

utility::vector1 < core::kinematics::Jump >	cst_jumps_

utility::vector1 < core::pack::rotamer_set::RotamerSetOP >	rotsets_

utility::vector1< std::map < dofType, core::Size > >	dof_conformers_

core::pose::PoseOP	miniPose_

Member Typedef Documentation

typedef std::map< cstType, utility::vector1< core::Real > > protocols::jumping::ResiduePairJump::cstInfoMap

private

typedef std::map< cstType, utility::vector1< core::Real > >::iterator protocols::jumping::ResiduePairJump::cstInfoMapIterator

private

Constructor & Destructor Documentation

protocols::jumping::ResiduePairJump::ResiduePairJump ( )

protocols::jumping::ResiduePairJump::~ResiduePairJump ( )

virtual

protocols::jumping::ResiduePairJump::ResiduePairJump	(	core::chemical::ResidueType const &	residue1,
		core::chemical::ResidueType const &	residue2
	)

References residues_.

Member Function Documentation

void protocols::jumping::ResiduePairJump::add_residue_pair	(	core::chemical::ResidueType const &	residue1,
		core::chemical::ResidueType const &	residue2
	)

References cstInfoMap_, and residues_.

void protocols::jumping::ResiduePairJump::add_residue_single ( core::chemical::ResidueType const & residue )

References cstInfoMap_, residues_, and utility_exit_with_message.

core::pose::PoseOP protocols::jumping::ResiduePairJump::apply_dof_conformer ( std::map< dofType, core::Size > const & conformer_map )

References cst_jumps_, miniPose_, residues_, protocols::jumping::rot1, protocols::jumping::rot2, rotsets_, core::pose::Pose::set_chi(), core::pose::Pose::set_jump(), and type.

Referenced by generate_frame().

void protocols::jumping::ResiduePairJump::build_cst_conformer_jumps ( )

References cst_conformers_, cst_jumps_, cstInfoMap_, protocols::jumping::disAB, diversify_cst_conformers(), core::kinematics::Jump::from_bond_cst(), j, jumpAtoms(), miniPose_, numeric::conversions::radians(), type, and core::pose::Pose::xyz().

Referenced by init_mini_pose().

void protocols::jumping::ResiduePairJump::build_sidechain_rotamers ( )

References core::pack::create_packer_graph(), core::pack::task::TaskFactory::create_packer_task(), core::pack::rotamer_set::RotamerSetFactory::create_rotamer_set(), getScoreFunction(), miniPose_, core::pose::Pose::residue(), residues_, rotsets_, runtime_assert, core::pose::Pose::set_phi(), core::pose::Pose::set_psi(), and core::pose::Pose::total_residue().

Referenced by init_mini_pose().

utility::vector1< std::string > const& protocols::jumping::ResiduePairJump::cstAtoms ( core::Size i ) const

inline

References residues_.

Referenced by init_mini_pose().

bool protocols::jumping::ResiduePairJump::cstAtoms_defined ( ) const

inline

References residues_.

Referenced by init_mini_pose().

bool protocols::jumping::ResiduePairJump::cstInfoMap_defined ( ) const

inline

References cstInfoMap_, and protocols::jumping::dihedralB.

void protocols::jumping::ResiduePairJump::diversify_cst_conformers	(	cstType	type,
		core::Size	max_index
	)

References cst_conformers_, and j.

void protocols::jumping::ResiduePairJump::diversify_cst_conformers ( )

References cstInfoMap_.

Referenced by build_cst_conformer_jumps().

void protocols::jumping::ResiduePairJump::diversify_dof_conformers	(	dofType	type,
		core::Size	max_index
	)

References dof_conformers_, and j.

void protocols::jumping::ResiduePairJump::diversify_dof_conformers ( )

References cst_jumps_, protocols::jumping::cstJump, dof_conformers_, protocols::jumping::rot1, protocols::jumping::rot2, and rotsets_.

Referenced by generate_frame().

core::fragment::FrameOP protocols::jumping::ResiduePairJump::generate_frame ( )

References apply_dof_conformer(), diversify_dof_conformers(), dof_conformers_, jumpAtoms(), miniPose_, and residues_.

void protocols::jumping::ResiduePairJump::init_mini_pose ( )

References core::pose::Pose::append_residue_by_jump(), build_cst_conformer_jumps(), build_sidechain_rotamers(), cstAtoms(), cstAtoms_defined(), miniPose_, residues_, and runtime_assert.

utility::vector1< std::string > const& protocols::jumping::ResiduePairJump::jumpAtoms ( core::Size i ) const

inline

References residues_.

Referenced by build_cst_conformer_jumps(), and generate_frame().

bool protocols::jumping::ResiduePairJump::jumpAtoms_defined ( ) const

inline

References residues_.

void protocols::jumping::ResiduePairJump::set_cstAtoms	(	core::Size	rsd,
		core::Size	atom,
		std::string	name
	)

inline

References residues_.

void protocols::jumping::ResiduePairJump::set_cstInfo	(	cstType	type,
		core::Real	value
	)

add a value to cst type

References cstInfoMap_.

Referenced by set_cstInfo().

void protocols::jumping::ResiduePairJump::set_cstInfo	(	cstType	type,
		utility::vector1< core::Real > const &	values
	)

add a vector of values to cstInfo type

References set_cstInfo().

void protocols::jumping::ResiduePairJump::set_jumpAtoms	(	core::Size	rsd,
		core::Size	atom,
		std::string	name
	)

inline

References residues_.

Member Data Documentation

utility::vector1< std::map< cstType, core::Size > > protocols::jumping::ResiduePairJump::cst_conformers_

private

Referenced by build_cst_conformer_jumps(), and diversify_cst_conformers().

utility::vector1< core::kinematics::Jump > protocols::jumping::ResiduePairJump::cst_jumps_

private

Referenced by apply_dof_conformer(), build_cst_conformer_jumps(), and diversify_dof_conformers().

std::map< cstType, utility::vector1< core::Real > > protocols::jumping::ResiduePairJump::cstInfoMap_

private

Referenced by add_residue_pair(), add_residue_single(), build_cst_conformer_jumps(), cstInfoMap_defined(), diversify_cst_conformers(), and set_cstInfo().

utility::vector1< std::map< dofType, core::Size > > protocols::jumping::ResiduePairJump::dof_conformers_

private

Referenced by diversify_dof_conformers(), and generate_frame().

core::pose::PoseOP protocols::jumping::ResiduePairJump::miniPose_

private

Referenced by apply_dof_conformer(), build_cst_conformer_jumps(), build_sidechain_rotamers(), generate_frame(), and init_mini_pose().

utility::vector1< ResiduePairJumpSingleOP > protocols::jumping::ResiduePairJump::residues_

private

Referenced by add_residue_pair(), add_residue_single(), apply_dof_conformer(), build_sidechain_rotamers(), cstAtoms(), cstAtoms_defined(), generate_frame(), init_mini_pose(), jumpAtoms(), jumpAtoms_defined(), ResiduePairJump(), set_cstAtoms(), and set_jumpAtoms().

utility::vector1< core::pack::rotamer_set::RotamerSetOP > protocols::jumping::ResiduePairJump::rotsets_

private

Referenced by apply_dof_conformer(), build_sidechain_rotamers(), and diversify_dof_conformers().

The documentation for this class was generated from the following files:

symlinks/rosetta/src/protocols/jumping/ResiduePairJump.hh
symlinks/rosetta/src/protocols/jumping/ResiduePairJump.cc

Public Member Functions

Private Types

Private Attributes

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation