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:

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Collaboration diagram for core::pack::scmin::ResidueAtomTreeCollection:

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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...

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.

Definition at line 86 of file AtomTreeCollection.hh.

Constructor & Destructor Documentation

core::pack::scmin::ResidueAtomTreeCollection::ResidueAtomTreeCollection	(	task::ResidueLevelTask const &	rltask,
		conformation::Conformation const &	conformation,
		conformation::Residue const &	orig_res
	)

Definition at line 90 of file AtomTreeCollection.cc.

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.

Definition at line 126 of file AtomTreeCollection.cc.

References atom_tree_representatives_, core::conformation::build_residue_tree(), core::io::serialization::clone(), 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

Definition at line 152 of file AtomTreeCollection.cc.

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.

Definition at line 131 of file AtomTreeCollection.hh.

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.

Definition at line 121 of file AtomTreeCollection.hh.

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

Definition at line 172 of file AtomTreeCollection.cc.

References active_residue_.

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

Definition at line 166 of file AtomTreeCollection.cc.

References active_residue_.

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

inline

Definition at line 103 of file AtomTreeCollection.hh.

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

Definition at line 226 of file AtomTreeCollection.cc.

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

Definition at line 314 of file AtomTreeCollection.cc.

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)

Definition at line 156 of file AtomTreeCollection.cc.

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()

Definition at line 233 of file AtomTreeCollection.cc.

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

Definition at line 242 of file AtomTreeCollection.cc.

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().

Definition at line 268 of file AtomTreeCollection.cc.

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)

Definition at line 284 of file AtomTreeCollection.cc.

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
	)

Definition at line 298 of file AtomTreeCollection.cc.

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

Definition at line 254 of file AtomTreeCollection.cc.

References active_restype_, atom_tree_representatives_, 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.

Definition at line 210 of file AtomTreeCollection.cc.

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)

Definition at line 321 of file AtomTreeCollection.cc.

References active_residue_, active_restype_, atom_tree_representatives_, core::pack::scmin::ResidueAtomTreeCollectionMomento::coord(), core::id::PHI, core::pack::scmin::ResidueAtomTreeCollectionMomento::restype_index(), set_active_restype_index(), and update_atom_tree().

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.

Definition at line 181 of file AtomTreeCollection.cc.

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::id::PHI, residue_representatives_, residue_uptodate_, and core::conformation::Residue::set_xyz().