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core::pack::scmin::ResidueAtomTreeCollection Class Reference

The conformation::Residues and kinematics::AtomTrees for a single collection of rotamers (e.g. a RotamerSet). Each chemical::ResidueType gets its own residue/atomtree pair. A particular AtomTree/Residue pair can be set as "active" and manipulated by setter and getters for either the coordinates of the Residues or the chi dihedrals of the AtomTree. More...

#include <AtomTreeCollection.hh>

Inheritance diagram for core::pack::scmin::ResidueAtomTreeCollection:
Inheritance graph
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Public Member Functions

 ResidueAtomTreeCollection (task::ResidueLevelTask const &rltask, conformation::Conformation const &conformation, conformation::Residue const &orig_res)
 
 ResidueAtomTreeCollection (rotamer_set::RotamerSet const &rset, Size resid)
 Constructor for a RotamerSet that has already been built. More...
 
 ~ResidueAtomTreeCollection () override
 
Size active_restype_index () const
 
void set_active_restype_index (Size restype_index)
 
void update_residue ()
 The responsibility for making sure that the active residue and the active atomtree are in synch is offloaded to an external class so that the calls to "active_residue()" and "active_atom_tree()" are as fast as possible (and bitwise const for future multithreaded use). After a round of set_chi() calls, the user for this class must update the residue coordinates. More...
 
void update_atom_tree ()
 See comments for update_residue(). After a call to "set_rescoords", the user must call update_atomtree() to make sure the atomtree and the residue are in synch. More...
 
chemical::ResidueType const & active_restype () const
 
conformation::Residue const & active_residue () const
 Inline accessor for the active residue. asserts residue_uptodate_ – make sure that update_residue is called first. More...
 
basic::datacache::BasicDataCache & active_residue_data ()
 Accessor for the active residue's data cache asserts residue_uptodate_ – make sure that update_residue is called first. More...
 
conformation::ResidueCOP active_residue_cop () const
 
kinematics::AtomTree const & active_atom_tree () const
 Inline accessor for the active atom tree. asserts atom_tree_uptodate_ – make sure that update_atom_tree is called first. More...
 
core::Real dof (core::id::DOF_ID const &dofid)
 
void set_chi (Size chi_index, Real value)
 Assigns the chi dihedral for the active restype. Must be followed by a call to update_residue() before the next call to active_residue() More...
 
void set_d (Size chi_index, Real value)
 
void set_theta (Size chi_index, Real value)
 
void set_rescoords (conformation::Residue const &res)
 Assigns the coordinates for a residue. Must be followed by a call to update_atom_tree() before the next cal to active_atom_tree(). More...
 
void set_rescoords (utility::vector1< Vector > const &coords)
 
void set_rescoords (utility::vector1< id::AtomID > const &atms, utility::vector1< Vector > const &coords)
 
void save_momento (ResidueAtomTreeCollectionMomento &momento) const
 
void update_from_momento (ResidueAtomTreeCollectionMomento const &momento)
 

Private Member Functions

 ResidueAtomTreeCollection (ResidueAtomTreeCollection const &)
 
ResidueAtomTreeCollectionoperator= (ResidueAtomTreeCollection const &)
 

Private Attributes

Size active_restype_
 
kinematics::AtomTreeOP active_atom_tree_
 
conformation::ResidueOP active_residue_
 
bool residue_uptodate_
 
bool atom_tree_uptodate_
 
utility::vector1
< kinematics::AtomTreeOP
atom_tree_representatives_
 
utility::vector1
< conformation::ResidueOP
residue_representatives_
 

Detailed Description

The conformation::Residues and kinematics::AtomTrees for a single collection of rotamers (e.g. a RotamerSet). Each chemical::ResidueType gets its own residue/atomtree pair. A particular AtomTree/Residue pair can be set as "active" and manipulated by setter and getters for either the coordinates of the Residues or the chi dihedrals of the AtomTree.

Constructor & Destructor Documentation

core::pack::scmin::ResidueAtomTreeCollection::ResidueAtomTreeCollection ( task::ResidueLevelTask const &  rltask,
conformation::Conformation const &  conformation,
conformation::Residue const &  orig_res 
)
core::pack::scmin::ResidueAtomTreeCollection::ResidueAtomTreeCollection ( rotamer_set::RotamerSet const &  rset,
core::Size  resid 
)
core::pack::scmin::ResidueAtomTreeCollection::~ResidueAtomTreeCollection ( )
overridedefault
core::pack::scmin::ResidueAtomTreeCollection::ResidueAtomTreeCollection ( ResidueAtomTreeCollection const &  )
private

Member Function Documentation

kinematics::AtomTree const& core::pack::scmin::ResidueAtomTreeCollection::active_atom_tree ( ) const
inline

Inline accessor for the active atom tree. asserts atom_tree_uptodate_ – make sure that update_atom_tree is called first.

References active_atom_tree_, and atom_tree_uptodate_.

conformation::Residue const& core::pack::scmin::ResidueAtomTreeCollection::active_residue ( ) const
inline

Inline accessor for the active residue. asserts residue_uptodate_ – make sure that update_residue is called first.

References active_residue_, and residue_uptodate_.

Referenced by core::pack::get_residue_current_energy(), core::pack::get_total_energy_for_state(), and core::pack::minimize_alt_rotamer().

conformation::ResidueCOP core::pack::scmin::ResidueAtomTreeCollection::active_residue_cop ( ) const

References active_residue_.

basic::datacache::BasicDataCache & core::pack::scmin::ResidueAtomTreeCollection::active_residue_data ( )

Accessor for the active residue's data cache asserts residue_uptodate_ – make sure that update_residue is called first.

References active_residue_, and residue_uptodate_.

Referenced by core::pack::get_residue_current_energy(), core::pack::get_total_energy_for_state(), and core::pack::minimize_alt_rotamer().

chemical::ResidueType const & core::pack::scmin::ResidueAtomTreeCollection::active_restype ( ) const

References active_residue_.

Size core::pack::scmin::ResidueAtomTreeCollection::active_restype_index ( ) const
inline

References active_restype_.

core::Real core::pack::scmin::ResidueAtomTreeCollection::dof ( core::id::DOF_ID const &  dofid)

fpd get dof value by DOF_ID NOTE input resid must be 1

References active_restype_, and atom_tree_representatives_.

ResidueAtomTreeCollection& core::pack::scmin::ResidueAtomTreeCollection::operator= ( ResidueAtomTreeCollection const &  )
private
void core::pack::scmin::ResidueAtomTreeCollection::save_momento ( ResidueAtomTreeCollectionMomento momento) const
void core::pack::scmin::ResidueAtomTreeCollection::set_active_restype_index ( Size  restype_index)
void core::pack::scmin::ResidueAtomTreeCollection::set_chi ( Size  chi_index,
Real  value 
)

Assigns the chi dihedral for the active restype. Must be followed by a call to update_residue() before the next call to active_residue()

References active_restype_, atom_tree_representatives_, core::id::PHI, residue_representatives_, and residue_uptodate_.

Referenced by core::pack::assign_random_continuous_rotamer().

void core::pack::scmin::ResidueAtomTreeCollection::set_d ( Size  chi_index,
Real  value 
)

fpd bondlength analog to set_chi like set_chi, assumes changes propagate to atomtree keyed off of chi#, so we only allow distances corresponding to chi angles to refine distance corresponds to the distance between atoms 3 and 4 defining the chi chino==0 ==> CA-CB distance, which allows us to refine ALA CB position for example

References active_restype_, atom_tree_representatives_, core::id::D, residue_representatives_, and residue_uptodate_.

void core::pack::scmin::ResidueAtomTreeCollection::set_rescoords ( conformation::Residue const &  res)
void core::pack::scmin::ResidueAtomTreeCollection::set_rescoords ( utility::vector1< Vector > const &  coords)
void core::pack::scmin::ResidueAtomTreeCollection::set_rescoords ( utility::vector1< id::AtomID > const &  atms,
utility::vector1< Vector > const &  coords 
)
void core::pack::scmin::ResidueAtomTreeCollection::set_theta ( Size  chi_index,
Real  value 
)

fpd bondangle analog to set_chi same idea as set_d

References active_restype_, atom_tree_representatives_, residue_representatives_, residue_uptodate_, and core::id::THETA.

void core::pack::scmin::ResidueAtomTreeCollection::update_atom_tree ( )
void core::pack::scmin::ResidueAtomTreeCollection::update_from_momento ( ResidueAtomTreeCollectionMomento const &  momento)
void core::pack::scmin::ResidueAtomTreeCollection::update_residue ( )

The responsibility for making sure that the active residue and the active atomtree are in synch is offloaded to an external class so that the calls to "active_residue()" and "active_atom_tree()" are as fast as possible (and bitwise const for future multithreaded use). After a round of set_chi() calls, the user for this class must update the residue coordinates.

References active_residue_, active_restype_, atom_tree_representatives_, core::conformation::Residue::chi(), core::conformation::Residue::chi_atoms(), core::conformation::Residue::natoms(), core::conformation::Residue::nchi(), core::chemical::rings::PHI, residue_representatives_, residue_uptodate_, and core::conformation::Residue::set_xyz().

Referenced by core::pack::assign_random_continuous_rotamer(), and set_rescoords().

Member Data Documentation

kinematics::AtomTreeOP core::pack::scmin::ResidueAtomTreeCollection::active_atom_tree_
private
conformation::ResidueOP core::pack::scmin::ResidueAtomTreeCollection::active_residue_
private
Size core::pack::scmin::ResidueAtomTreeCollection::active_restype_
private
utility::vector1< kinematics::AtomTreeOP > core::pack::scmin::ResidueAtomTreeCollection::atom_tree_representatives_
private
bool core::pack::scmin::ResidueAtomTreeCollection::atom_tree_uptodate_
private
utility::vector1< conformation::ResidueOP > core::pack::scmin::ResidueAtomTreeCollection::residue_representatives_
private
bool core::pack::scmin::ResidueAtomTreeCollection::residue_uptodate_
private

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