protocols::jumping::ResiduePairJump Class Reference

#include <ResiduePairJump.hh>

Inheritance diagram for protocols::jumping::ResiduePairJump:

Collaboration diagram for protocols::jumping::ResiduePairJump:

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_

Detailed Description

Definition at line 151 of file ResiduePairJump.hh.

Member Typedef Documentation

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

private

Definition at line 153 of file ResiduePairJump.hh.

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

private

Definition at line 154 of file ResiduePairJump.hh.

Constructor & Destructor Documentation

protocols::jumping::ResiduePairJump::ResiduePairJump

(

)

Definition at line 129 of file ResiduePairJump.cc.

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

virtual

Definition at line 130 of file ResiduePairJump.cc.

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

Definition at line 133 of file ResiduePairJump.cc.

References residues_.

Member Function Documentation

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

Definition at line 143 of file ResiduePairJump.cc.

References cstInfoMap_, and residues_.

void protocols::jumping::ResiduePairJump::add_residue_single

(

core::chemical::ResidueType const &

residue)

Definition at line 155 of file ResiduePairJump.cc.

References cstInfoMap_, and residues_.

core::pose::PoseOP protocols::jumping::ResiduePairJump::apply_dof_conformer

(

std::map< dofType, core::Size > const &

conformer_map)

Definition at line 388 of file ResiduePairJump.cc.

References cst_jumps_, miniPose_, residues_, protocols::jumping::rot1, protocols::jumping::rot2, and rotsets_.

Referenced by generate_frame().

void protocols::jumping::ResiduePairJump::build_cst_conformer_jumps

(

)

Definition at line 450 of file ResiduePairJump.cc.

References cst_conformers_, cst_jumps_, cstInfoMap_, protocols::jumping::disAB, diversify_cst_conformers(), core::kinematics::Jump::from_bond_cst(), jumpAtoms(), and miniPose_.

Referenced by init_mini_pose().

void protocols::jumping::ResiduePairJump::build_sidechain_rotamers

(

)

Definition at line 412 of file ResiduePairJump.cc.

References core::pack::create_packer_graph(), core::pack::task::TaskFactory::create_packer_task(), core::pack::rotamer_set::RotamerSetFactory::create_rotamer_set(), core::scoring::ScoreFunctionFactory::create_score_function(), miniPose_, residues_, rotsets_, core::scoring::SCORE12_PATCH, and core::scoring::STANDARD_WTS.

Referenced by init_mini_pose().

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

inline

Definition at line 207 of file ResiduePairJump.hh.

References residues_.

Referenced by init_mini_pose().

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

inline

Definition at line 187 of file ResiduePairJump.hh.

References residues_.

Referenced by init_mini_pose().

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

inline

Definition at line 192 of file ResiduePairJump.hh.

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

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

Definition at line 483 of file ResiduePairJump.cc.

References cst_conformers_.

void protocols::jumping::ResiduePairJump::diversify_cst_conformers

(

)

Definition at line 513 of file ResiduePairJump.cc.

References cstInfoMap_.

Referenced by build_cst_conformer_jumps().

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

Definition at line 344 of file ResiduePairJump.cc.

References dof_conformers_.

void protocols::jumping::ResiduePairJump::diversify_dof_conformers

(

)

Definition at line 376 of file ResiduePairJump.cc.

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

(

)

Definition at line 208 of file ResiduePairJump.cc.

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

void protocols::jumping::ResiduePairJump::init_mini_pose

(

)

Definition at line 237 of file ResiduePairJump.cc.

References build_cst_conformer_jumps(), build_sidechain_rotamers(), cstAtoms(), cstAtoms_defined(), miniPose_, and residues_.

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

inline

Definition at line 222 of file ResiduePairJump.hh.

References residues_.

Referenced by build_cst_conformer_jumps(), and generate_frame().

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

inline

Definition at line 182 of file ResiduePairJump.hh.

References residues_.

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

inline

Definition at line 197 of file ResiduePairJump.hh.

References residues_.

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

add a value to cst type

Definition at line 171 of file ResiduePairJump.cc.

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

Definition at line 197 of file ResiduePairJump.cc.

References set_cstInfo().

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

inline

Definition at line 212 of file ResiduePairJump.hh.

References residues_.

Member Data Documentation

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

private

Definition at line 256 of file ResiduePairJump.hh.

Referenced by build_cst_conformer_jumps(), and diversify_cst_conformers().

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

private

Definition at line 258 of file ResiduePairJump.hh.

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

Definition at line 254 of file ResiduePairJump.hh.

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

Definition at line 262 of file ResiduePairJump.hh.

Referenced by diversify_dof_conformers(), and generate_frame().

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

private

Definition at line 264 of file ResiduePairJump.hh.

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

Definition at line 252 of file ResiduePairJump.hh.

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

Definition at line 260 of file ResiduePairJump.hh.

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

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

• src/protocols/jumping/ResiduePairJump.hh
• src/protocols/jumping/ResiduePairJump.cc