Rosetta
Public Member Functions | Private Types | Private Attributes | List of all members
protocols::jumping::ResiduePairJump Class Reference

#include <ResiduePairJump.hh>

Inheritance diagram for protocols::jumping::ResiduePairJump:
Inheritance graph
[legend]

Public Member Functions

 ResiduePairJump ()
 
 ~ResiduePairJump () override
 
 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

◆ cstInfoMap

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

◆ cstInfoMapIterator

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

Constructor & Destructor Documentation

◆ ResiduePairJump() [1/2]

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

◆ ~ResiduePairJump()

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

◆ ResiduePairJump() [2/2]

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

References residues_.

Member Function Documentation

◆ add_residue_pair()

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

References cstInfoMap_, and residues_.

◆ add_residue_single()

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

References cstInfoMap_, and residues_.

◆ apply_dof_conformer()

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, and rotsets_.

Referenced by generate_frame().

◆ build_cst_conformer_jumps()

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(), jumpAtoms(), and miniPose_.

Referenced by init_mini_pose().

◆ build_sidechain_rotamers()

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(), core::scoring::get_score_function(), miniPose_, residues_, and rotsets_.

Referenced by init_mini_pose().

◆ cstAtoms()

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

References residues_.

Referenced by init_mini_pose().

◆ cstAtoms_defined()

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

References residues_.

Referenced by init_mini_pose().

◆ cstInfoMap_defined()

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

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

◆ diversify_cst_conformers() [1/2]

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

References cstInfoMap_.

Referenced by build_cst_conformer_jumps().

◆ diversify_cst_conformers() [2/2]

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

References cst_conformers_.

◆ diversify_dof_conformers() [1/2]

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().

◆ diversify_dof_conformers() [2/2]

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

References dof_conformers_.

◆ generate_frame()

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

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

◆ init_mini_pose()

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

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

◆ jumpAtoms()

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().

◆ jumpAtoms_defined()

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

References residues_.

◆ set_cstAtoms()

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

References residues_.

◆ set_cstInfo() [1/2]

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

add a value to cst type

References cstInfoMap_.

Referenced by set_cstInfo().

◆ set_cstInfo() [2/2]

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().

◆ set_jumpAtoms()

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

References residues_.

Member Data Documentation

◆ cst_conformers_

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

Referenced by build_cst_conformer_jumps(), and diversify_cst_conformers().

◆ cst_jumps_

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

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

◆ cstInfoMap_

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().

◆ dof_conformers_

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

Referenced by diversify_dof_conformers(), and generate_frame().

◆ miniPose_

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().

◆ residues_

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().

◆ rotsets_

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:
Generated on Thu Sep 11 2025 21:32:47 for Rosetta by doxygen 1.9.1