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>

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...

virtual	~ResidueAtomTreeCollection ()

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...

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 &)

ResidueAtomTreeCollection const &	operator= (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
	)

References core::pack::task::ResidueLevelTask::allowed_residue_types_begin(), core::pack::task::ResidueLevelTask::allowed_residue_types_end(), atom_tree_representatives_, core::conformation::build_residue_tree(), core::pack::task::ResidueLevelTask::preserve_c_beta(), residue_representatives_, core::id::AtomID_Map< T >::resize(), and core::conformation::Residue::seqpos().

core::pack::scmin::ResidueAtomTreeCollection::ResidueAtomTreeCollection	(	rotamer_set::RotamerSet const &	rset,
		core::Size	resid
	)

Constructor for a RotamerSet that has already been built.

References atom_tree_representatives_, core::conformation::build_residue_tree(), core::pack::rotamer_set::RotamerSet::get_n_residue_types(), core::pack::rotamer_set::RotamerSet::get_residue_type_begin(), residue_representatives_, core::id::AtomID_Map< T >::resize(), and core::pack::rotamer_set::RotamerSet::rotamer().

core::pack::scmin::ResidueAtomTreeCollection::~ResidueAtomTreeCollection ( )

virtual

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_.

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 const& core::pack::scmin::ResidueAtomTreeCollection::operator= ( ResidueAtomTreeCollection const & )

private

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

References active_restype_, atom_tree_uptodate_, core::pack::scmin::ResidueAtomTreeCollectionMomento::copy_coords(), residue_representatives_, residue_uptodate_, and core::pack::scmin::ResidueAtomTreeCollectionMomento::set_restype_index().

void core::pack::scmin::ResidueAtomTreeCollection::set_active_restype_index ( Size restype_index )

References active_atom_tree_, active_residue_, active_restype_, atom_tree_representatives_, and residue_representatives_.

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

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_, numeric::constants::d::degrees_to_radians, 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 )

Assigns the coordinates for a residue. Must be followed by a call to update_atom_tree() before the next cal to active_atom_tree().

References active_restype_, atom_tree_uptodate_, core::conformation::Residue::chi(), core::conformation::Residue::natoms(), core::conformation::Residue::nchi(), residue_representatives_, core::conformation::Residue::type(), and core::conformation::Residue::xyz().

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

void core::pack::scmin::ResidueAtomTreeCollection::set_rescoords ( utility::vector1< Vector > const & coords )

References active_restype_, residue_representatives_, update_atom_tree(), and update_residue().

void core::pack::scmin::ResidueAtomTreeCollection::set_rescoords	(	utility::vector1< id::AtomID > const &	atms,
		utility::vector1< Vector > const &	coords
	)

References active_restype_, residue_representatives_, update_atom_tree(), and update_residue().

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_, numeric::constants::d::degrees_to_radians, residue_representatives_, residue_uptodate_, and core::id::THETA.

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 active_restype_, atom_tree_representatives_, atom_tree_uptodate_, core::kinematics::AtomTree::dof(), core::conformation::Residue::natoms(), core::id::RB1, residue_representatives_, 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 )

References active_residue_, active_restype_, atom_tree_representatives_, core::conformation::Residue::chi(), core::conformation::Residue::chi_atoms(), core::pack::scmin::ResidueAtomTreeCollectionMomento::coord(), numeric::xyzVector< class >::distance_squared(), core::conformation::Residue::natoms(), core::conformation::Residue::nchi(), core::chemical::PHI, numeric::constants::d::radians_to_degrees, core::pack::scmin::ResidueAtomTreeCollectionMomento::restype_index(), set_active_restype_index(), core::conformation::Residue::set_xyz(), update_atom_tree(), and core::conformation::Residue::xyz().

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

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::chemical::PHI, numeric::constants::d::radians_to_degrees, residue_representatives_, residue_uptodate_, and core::conformation::Residue::update_actcoord().

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