#include <SymmOnTheFlyInteractionGraph.hh>

Inheritance diagram for core::pack::interaction_graph::SymmOnTheFlyNode:

Collaboration diagram for core::pack::interaction_graph::SymmOnTheFlyNode:

Public Types
typedef std::pair< Vector, Real >	BoundingSphere

Public Member Functions
	SymmOnTheFlyNode (InteractionGraphBase *owner, int node_id, int num_states)
	main constructor, no default or copy constructors More...

virtual	~SymmOnTheFlyNode ()

void	set_rotamers (rotamer_set::RotamerSetCOP rotamers)

virtual void	zero_one_body_energies ()

virtual void	add_to_one_body_energies (ObjexxFCL::FArray1< core::PackerEnergy > &energy1b)

virtual void	update_one_body_energy (int state, core::PackerEnergy energy)

virtual void	set_one_body_energy (int state, core::PackerEnergy energy)

virtual void	add_to_one_body_energy (int state, core::PackerEnergy energy)

virtual void	zero_one_body_energy (int state)

int	get_num_res_types () const
	the number of distinct ResidueType objects pointed to by all of the rotamrs for this node. More...

int	get_num_restype_groups () const
	the number of ResidueType groups, as defined by the RotamerSet's logic for grouping different ResidueType objects which have the same "name3" and the same neighbor radius. More...

utility::vector1< int > &	get_num_states_for_restype_group ()

utility::vector1< int > const &	get_num_states_for_restype_group () const

int	get_num_states_for_restype_group (int restype_group)

int	get_state_offset_for_restype_group (int restype_group) const

core::PackerEnergy	get_one_body_energy (int state) const

bool	distinguish_backbone_and_sidechain () const

void	distinguish_backbone_and_sidechain (bool setting)

virtual unsigned int	count_static_memory () const =0

virtual unsigned int	count_dynamic_memory () const

core::PackerEnergy	compute_rotamer_pair_energy (int edge_making_energy_request, int state_this, int state_other) const

conformation::Residue const &	get_rotamer (int state, int subunit) const
	Returns a reference to the rotamer object in the requested subunit. This reference is valid only until the next call to get_rotamer, and which point, the coordinates inside the requested rotamer may change. More...

BoundingSphere	sc_bounding_sphere (int state, int subunit) const
	Returns a bounding sphere for the sidechain of a given state on a particular subunit. More...

BoundingSphere	bb_bounding_sphere (int subunit) const
	Returns a bounding sphere for the backbone on a particular subunit. More...

SymmOnTheFlyEdge *	get_incident_otf_edge (int edge)

SymmOnTheFlyEdge const *	get_incident_otf_edge (int edge) const

SymmOnTheFlyNode *	get_adjacent_otf_node (int index)

SymmOnTheFlyNode const *	get_adjacent_otf_node (int index) const

SymmOnTheFlyInteractionGraph *	get_on_the_fly_owner ()

SymmOnTheFlyInteractionGraph const *	get_on_the_fly_owner () const

Public Member Functions inherited from core::pack::interaction_graph::FixedBBNode
virtual	~FixedBBNode ()

	FixedBBNode (InteractionGraphBase *owner, int node_id, int num_states)

Public Member Functions inherited from core::pack::interaction_graph::NodeBase
virtual	~NodeBase ()
	virtual destructor More...

	NodeBase (InteractionGraphBase *, int node_id, int num_states)
	Main constructor, no default constructor nor copy constructor. More...

int	get_num_states () const
	returns the number of states for this node More...

std::list< EdgeBase * >::iterator	add_edge (EdgeBase *edge_ptr)
	adds edge pointer to edge list; returns an iterator to the new list element More...

void	drop_edge (std::list< EdgeBase * >::iterator edge_iterator)
	removes an edge iterator from the node's edge list More...

void	drop_all_edges ()
	deletes all edges incident upon this node More...

EdgeBase *	find_edge (int other_node_index) const
	a slow (linear) search for an edge. The edge is identified by the index of the node to which the edge connects this node. Returns NULL when there is no such connecting edge. More...

virtual void	assign_zero_state ()=0

virtual void	prepare_for_simulated_annealing ()=0

virtual void	print () const =0

virtual bool	state_unassigned () const =0

void	depth_first_connected_component_counting ()
	performs a depth first traversal of the graph. Each node informs the graph that the traversal resulted in arriving at the node. More...

std::list< EdgeBase * > ::const_iterator	edge_list_begin ()

std::list< EdgeBase * > ::const_iterator	edge_list_end ()

int	get_node_index () const

int	get_num_incident_edges () const

int	get_num_edges_to_smaller_indexed_nodes () const

int	get_num_edges_to_larger_indexed_nodes () const

EdgeBase const *	get_incident_edge (int index) const
	These functions are public for the sake of writing good unit tests. More...

EdgeBase *	get_incident_edge (int index)

int	get_index_of_adjacent_node (int index) const

NodeBase const *	get_adjacent_node (int index) const

NodeBase *	get_adjacent_node (int index)

Private Attributes
rotamer_set::RotamerSetCOP	rotamer_set_

utility::vector1 < conformation::ResidueCOP >	rotamers_
	Pointers to the rotamers held in the rotamer set. More...

utility::vector1 < utility::vector1 < conformation::ResidueOP > >	rotamer_representatives_

utility::vector1< BoundingSphere >	sc_bounding_spheres_
	Bounding spheres for each of the rotamers in the asymmetric unit. More...

BoundingSphere	bb_bounding_sphere_

int	num_res_types_

int	num_restype_groups_

utility::vector1< int >	num_states_for_restype_group_

utility::vector1< int >	state_offset_for_restype_group_

utility::vector1 < core::PackerEnergy >	one_body_energies_

bool	distinguish_backbone_and_sidechain_

Additional Inherited Members
Protected Member Functions inherited from core::pack::interaction_graph::NodeBase
void	update_edge_vector ()
	converts edge-list to edge-vector representation More...

bool	get_edge_vector_up_to_date () const

InteractionGraphBase const *	get_owner () const

InteractionGraphBase *	get_owner ()

Detailed Description

Definition at line 65 of file SymmOnTheFlyInteractionGraph.hh.

Member Typedef Documentation

typedef std::pair< Vector, Real > core::pack::interaction_graph::SymmOnTheFlyNode::BoundingSphere

Definition at line 68 of file SymmOnTheFlyInteractionGraph.hh.

Constructor & Destructor Documentation

core::pack::interaction_graph::SymmOnTheFlyNode::SymmOnTheFlyNode	(	InteractionGraphBase *	owner,
		int	node_id,
		int	num_states
	)

main constructor, no default or copy constructors

Detailed:

Definition at line 48 of file SymmOnTheFlyInteractionGraph.cc.

core::pack::interaction_graph::SymmOnTheFlyNode::~SymmOnTheFlyNode ( )

virtual

Definition at line 68 of file SymmOnTheFlyInteractionGraph.cc.

Member Function Documentation

void core::pack::interaction_graph::SymmOnTheFlyNode::add_to_one_body_energies ( ObjexxFCL::FArray1< core::PackerEnergy > & energy1b)

virtual

Implements core::pack::interaction_graph::NodeBase.

Definition at line 146 of file SymmOnTheFlyInteractionGraph.cc.

References one_body_energies_.

void core::pack::interaction_graph::SymmOnTheFlyNode::add_to_one_body_energy	(	int	state,
		core::PackerEnergy	energy
	)

virtual

increments one body energies for a given state

Implements core::pack::interaction_graph::NodeBase.

Definition at line 169 of file SymmOnTheFlyInteractionGraph.cc.

References one_body_energies_.

Referenced by core::pack::interaction_graph::SymmOnTheFlyInteractionGraph::add_to_one_body_energy_for_node_state().

SymmOnTheFlyNode::BoundingSphere core::pack::interaction_graph::SymmOnTheFlyNode::bb_bounding_sphere ( int subunit) const

Returns a bounding sphere for the backbone on a particular subunit.

Definition at line 474 of file SymmOnTheFlyInteractionGraph.cc.

References bb_bounding_sphere_, get_on_the_fly_owner(), and core::pack::interaction_graph::SymmOnTheFlyInteractionGraph::symmetric_transform().

Referenced by compute_rotamer_pair_energy().

core::PackerEnergy core::pack::interaction_graph::SymmOnTheFlyNode::compute_rotamer_pair_energy	(	int	edge_making_energy_request,
		int	state_this,
		int	state_other
	)		const

Compute all the energies that are appropriately two body energies for this edge. In the outter loop, pick one of the two nodes on this edge and consider its rotamer as having originated from the asymmetric unit. In the inner loop, iterate across all subunits, considering each subunit as the origination of the rotamer for the other node (that is, if ii == 1, then "this" node is treated as if its rotamer is originating from the asymmetric unit, and the "other" node takes its rotamer from subunit jj – which may very well be the asymmetric unit. If however, ii == 2, then the "other" node is treated as if its rotamer is originating from the asymmetric unit and the "this" node's rotamer is taken from jj). Now, inside this inner loop, with ii and jj known, first, ask the edge whether given ii, jj, and the amino acid types of the two rotamers, the two rotamers implied by ii and jj should have their interaction energies calculated. If not, continue. If so, then ask each edge for a representative rotamer, telling each node which subunit that rotamer should come from. This may likely require rotating and translating the rotamers from the asymmetric unit into the appropriate symmetric clone

Definition at line 215 of file SymmOnTheFlyInteractionGraph.cc.

Referenced by core::pack::interaction_graph::SymmMinimalistNode::compute_pair_energy_for_alternate_state(), core::pack::interaction_graph::SymmLinearMemNode::compute_pair_energy_for_alternate_state(), core::pack::interaction_graph::SymmMinimalistNode::compute_pair_energy_for_current_state(), and core::pack::interaction_graph::SymmLinearMemNode::compute_pair_energy_for_current_state().

unsigned int core::pack::interaction_graph::SymmOnTheFlyNode::count_dynamic_memory ( ) const

virtual

reports the amount of dynamic memory this node allocates recursing to its base class

Reimplemented from core::pack::interaction_graph::NodeBase.

Reimplemented in core::pack::interaction_graph::SymmLinearMemNode, and core::pack::interaction_graph::SymmMinimalistNode.

Definition at line 185 of file SymmOnTheFlyInteractionGraph.cc.

References core::pack::interaction_graph::NodeBase::count_dynamic_memory(), one_body_energies_, and rotamers_.

Referenced by core::pack::interaction_graph::SymmMinimalistNode::count_dynamic_memory(), and core::pack::interaction_graph::SymmLinearMemNode::count_dynamic_memory().

virtual unsigned int core::pack::interaction_graph::SymmOnTheFlyNode::count_static_memory ( ) const

pure virtual

Implements core::pack::interaction_graph::NodeBase.

Implemented in core::pack::interaction_graph::SymmLinearMemNode, and core::pack::interaction_graph::SymmMinimalistNode.

bool core::pack::interaction_graph::SymmOnTheFlyNode::distinguish_backbone_and_sidechain ( ) const

inline

Definition at line 151 of file SymmOnTheFlyInteractionGraph.hh.

Referenced by core::pack::interaction_graph::SymmOnTheFlyInteractionGraph::distinguish_backbone_and_sidechain_for_node(), and core::pack::interaction_graph::SymmOnTheFlyEdge::SymmOnTheFlyEdge().

void core::pack::interaction_graph::SymmOnTheFlyNode::distinguish_backbone_and_sidechain ( bool setting)

Definition at line 130 of file SymmOnTheFlyInteractionGraph.cc.

References distinguish_backbone_and_sidechain_, and core::pack::interaction_graph::NodeBase::get_num_incident_edges().

SymmOnTheFlyNode * core::pack::interaction_graph::SymmOnTheFlyNode::get_adjacent_otf_node ( int index)

inline

Definition at line 576 of file SymmOnTheFlyInteractionGraph.hh.

Referenced by compute_rotamer_pair_energy().

SymmOnTheFlyNode const * core::pack::interaction_graph::SymmOnTheFlyNode::get_adjacent_otf_node ( int index) const

inline

Definition at line 584 of file SymmOnTheFlyInteractionGraph.hh.

SymmOnTheFlyEdge * core::pack::interaction_graph::SymmOnTheFlyNode::get_incident_otf_edge ( int edge)

inline

Definition at line 560 of file SymmOnTheFlyInteractionGraph.hh.

Referenced by compute_rotamer_pair_energy().

SymmOnTheFlyEdge const * core::pack::interaction_graph::SymmOnTheFlyNode::get_incident_otf_edge ( int edge) const

inline

Definition at line 568 of file SymmOnTheFlyInteractionGraph.hh.

int core::pack::interaction_graph::SymmOnTheFlyNode::get_num_res_types ( ) const

inline

the number of distinct ResidueType objects pointed to by all of the rotamrs for this node.

Definition at line 93 of file SymmOnTheFlyInteractionGraph.hh.

int core::pack::interaction_graph::SymmOnTheFlyNode::get_num_restype_groups ( ) const

inline

the number of ResidueType groups, as defined by the RotamerSet's logic for grouping different ResidueType objects which have the same "name3" and the same neighbor radius.

Definition at line 103 of file SymmOnTheFlyInteractionGraph.hh.

Referenced by core::pack::interaction_graph::SymmOnTheFlyEdge::set_residues_adjacent_for_subunit_pair().

utility::vector1< int >& core::pack::interaction_graph::SymmOnTheFlyNode::get_num_states_for_restype_group ( )

inline

Definition at line 110 of file SymmOnTheFlyInteractionGraph.hh.

utility::vector1< int > const& core::pack::interaction_graph::SymmOnTheFlyNode::get_num_states_for_restype_group ( ) const

inline

Definition at line 117 of file SymmOnTheFlyInteractionGraph.hh.

int core::pack::interaction_graph::SymmOnTheFlyNode::get_num_states_for_restype_group ( int restype_group)

inline

Definition at line 124 of file SymmOnTheFlyInteractionGraph.hh.

SymmOnTheFlyInteractionGraph * core::pack::interaction_graph::SymmOnTheFlyNode::get_on_the_fly_owner ( )

inline

Definition at line 593 of file SymmOnTheFlyInteractionGraph.hh.

Referenced by bb_bounding_sphere(), compute_rotamer_pair_energy(), get_rotamer(), sc_bounding_sphere(), and set_rotamers().

SymmOnTheFlyInteractionGraph const * core::pack::interaction_graph::SymmOnTheFlyNode::get_on_the_fly_owner ( ) const

inline

Definition at line 601 of file SymmOnTheFlyInteractionGraph.hh.

core::PackerEnergy core::pack::interaction_graph::SymmOnTheFlyNode::get_one_body_energy ( int state) const

inline

Definition at line 145 of file SymmOnTheFlyInteractionGraph.hh.

Referenced by core::pack::interaction_graph::SymmMinimalistNode::assign_state(), core::pack::interaction_graph::SymmLinearMemNode::assign_state(), core::pack::interaction_graph::SymmMinimalistNode::complete_state_assignment(), core::pack::interaction_graph::SymmLinearMemNode::complete_state_assignment(), and core::pack::interaction_graph::SymmOnTheFlyInteractionGraph::get_one_body_energy_for_node_state().

conformation::Residue const & core::pack::interaction_graph::SymmOnTheFlyNode::get_rotamer	(	int	state,
		int	subunit
	)		const

Returns a reference to the rotamer object in the requested subunit. This reference is valid only until the next call to get_rotamer, and which point, the coordinates inside the requested rotamer may change.

Definition at line 428 of file SymmOnTheFlyInteractionGraph.cc.

References core::conformation::Residue::actcoord(), core::conformation::Residue::chi(), get_on_the_fly_owner(), core::conformation::Residue::mainchain_torsions(), core::conformation::Residue::natoms(), rotamer_representatives_, rotamer_set_, rotamers_, core::conformation::Residue::set_xyz(), core::pack::interaction_graph::SymmOnTheFlyInteractionGraph::symmetric_transform(), core::conformation::Residue::type(), and core::conformation::Residue::xyz().

Referenced by compute_rotamer_pair_energy(), and core::pack::interaction_graph::SymmOnTheFlyEdge::set_residues_adjacent_for_subunit_pair().

int core::pack::interaction_graph::SymmOnTheFlyNode::get_state_offset_for_restype_group ( int restype_group) const

inline

Definition at line 139 of file SymmOnTheFlyInteractionGraph.hh.

Referenced by core::pack::interaction_graph::SymmOnTheFlyEdge::set_residues_adjacent_for_subunit_pair().

SymmOnTheFlyNode::BoundingSphere core::pack::interaction_graph::SymmOnTheFlyNode::sc_bounding_sphere	(	int	state,
		int	subunit
	)		const

Returns a bounding sphere for the sidechain of a given state on a particular subunit.

Definition at line 465 of file SymmOnTheFlyInteractionGraph.cc.

References get_on_the_fly_owner(), sc_bounding_spheres_, and core::pack::interaction_graph::SymmOnTheFlyInteractionGraph::symmetric_transform().

Referenced by compute_rotamer_pair_energy().

void core::pack::interaction_graph::SymmOnTheFlyNode::set_one_body_energy	(	int	state,
		core::PackerEnergy	energy
	)

virtual

sets one body energies for a given state

Definition at line 162 of file SymmOnTheFlyInteractionGraph.cc.

References one_body_energies_.

Referenced by core::pack::interaction_graph::SymmOnTheFlyInteractionGraph::set_one_body_energy_for_node_state().

void core::pack::interaction_graph::SymmOnTheFlyNode::set_rotamers ( rotamer_set::RotamerSetCOP rotamers)

avoid polymorphic lookup later by nabbing rotamers now.

Definition at line 73 of file SymmOnTheFlyInteractionGraph.cc.

References bb_bounding_sphere_, core::io::serialization::clone(), core::scoring::compute_bb_centroid(), core::scoring::compute_bb_radius(), core::scoring::compute_sc_centroid(), core::scoring::compute_sc_radius(), core::pack::interaction_graph::NodeBase::get_num_states(), get_on_the_fly_owner(), num_res_types_, num_restype_groups_, num_states_for_restype_group_, core::pack::interaction_graph::SymmOnTheFlyInteractionGraph::pose(), core::pose::Pose::residue(), rotamer_representatives_, rotamer_set_, rotamers_, sc_bounding_spheres_, state_offset_for_restype_group_, and core::pack::interaction_graph::SymmOnTheFlyInteractionGraph::symm_info().

Referenced by core::pack::interaction_graph::SymmOnTheFlyInteractionGraph::initialize().

void core::pack::interaction_graph::SymmOnTheFlyNode::update_one_body_energy	(	int	state,
		core::PackerEnergy	energy
	)

virtual

Implements core::pack::interaction_graph::NodeBase.

Definition at line 154 of file SymmOnTheFlyInteractionGraph.cc.

References one_body_energies_.

void core::pack::interaction_graph::SymmOnTheFlyNode::zero_one_body_energies ( )

virtual

Implements core::pack::interaction_graph::NodeBase.

Definition at line 140 of file SymmOnTheFlyInteractionGraph.cc.

References one_body_energies_.

void core::pack::interaction_graph::SymmOnTheFlyNode::zero_one_body_energy ( int state)

virtual

Definition at line 177 of file SymmOnTheFlyInteractionGraph.cc.

References one_body_energies_.

Referenced by core::pack::interaction_graph::SymmOnTheFlyInteractionGraph::zero_one_body_energy_for_node_state().

Member Data Documentation

BoundingSphere core::pack::interaction_graph::SymmOnTheFlyNode::bb_bounding_sphere_

private

Definition at line 222 of file SymmOnTheFlyInteractionGraph.hh.

Referenced by bb_bounding_sphere(), and set_rotamers().

bool core::pack::interaction_graph::SymmOnTheFlyNode::distinguish_backbone_and_sidechain_

private

Definition at line 230 of file SymmOnTheFlyInteractionGraph.hh.

Referenced by distinguish_backbone_and_sidechain().

int core::pack::interaction_graph::SymmOnTheFlyNode::num_res_types_

private

Definition at line 224 of file SymmOnTheFlyInteractionGraph.hh.

Referenced by set_rotamers().

int core::pack::interaction_graph::SymmOnTheFlyNode::num_restype_groups_

private

Definition at line 225 of file SymmOnTheFlyInteractionGraph.hh.

Referenced by set_rotamers().

utility::vector1< int > core::pack::interaction_graph::SymmOnTheFlyNode::num_states_for_restype_group_

private

Definition at line 226 of file SymmOnTheFlyInteractionGraph.hh.

Referenced by set_rotamers().

utility::vector1< core::PackerEnergy > core::pack::interaction_graph::SymmOnTheFlyNode::one_body_energies_

private

Definition at line 229 of file SymmOnTheFlyInteractionGraph.hh.

Referenced by add_to_one_body_energies(), add_to_one_body_energy(), count_dynamic_memory(), set_one_body_energy(), update_one_body_energy(), zero_one_body_energies(), and zero_one_body_energy().

utility::vector1< utility::vector1< conformation::ResidueOP > > core::pack::interaction_graph::SymmOnTheFlyNode::rotamer_representatives_

private

An array of arrays of rotamer_set_->get_n_residue_types() rotamer representatives who will be filled, just in time, with the transformed coordinates that map between the rotamers built for the asymmetric unit, and those on all of the symmetric clones.

Definition at line 218 of file SymmOnTheFlyInteractionGraph.hh.

Referenced by get_rotamer(), and set_rotamers().

rotamer_set::RotamerSetCOP core::pack::interaction_graph::SymmOnTheFlyNode::rotamer_set_

private

Definition at line 210 of file SymmOnTheFlyInteractionGraph.hh.

Referenced by compute_rotamer_pair_energy(), get_rotamer(), and set_rotamers().