Rosetta 3.4
Public Member Functions
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>

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List of all members.

Public Member Functions

 ResidueAtomTreeCollection (task::ResidueLevelTask const &rltask, conformation::Conformation const &conformation, conformation::Residue const &orig_res)
virtual ~ResidueAtomTreeCollection ()
Size ative_restype_index () const
void set_active_restype_index (Size restype_index)
void update_residue ()
 void idealize_active_restype(); // set all atom tree sidechain coordinates to their ideal values
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.
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.
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.
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()
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().
void set_rescoords (utility::vector1< Vector > const &coords)
void save_momento (ResidueAtomTreeCollectionMomento &momento) const
void update_from_momento (ResidueAtomTreeCollectionMomento const &momento)

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 ( ) [virtual]

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.

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.

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
chemical::ResidueType const & core::pack::scmin::ResidueAtomTreeCollection::active_restype ( ) const
Size core::pack::scmin::ResidueAtomTreeCollection::ative_restype_index ( ) const [inline]
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 core::id::PHI.

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

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::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.

References core::kinematics::AtomTree::dof(), core::conformation::Residue::natoms(), core::id::RB1, core::kinematics::AtomTree::set_xyz(), and core::conformation::Residue::xyz().

Referenced by core::pack::minimize_alt_rotamer(), set_rescoords(), and update_from_momento().

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

void idealize_active_restype(); // set all atom tree sidechain coordinates to their ideal values

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 core::conformation::Residue::chi(), core::conformation::Residue::chi_atoms(), core::conformation::Residue::natoms(), core::conformation::Residue::nchi(), core::id::PHI, and core::conformation::Residue::set_xyz().

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


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