#include <AminoAcidNeighborSparseMatrix.hh>

Public Types
typedef T	value_type

Public Member Functions
	AminoAcidNeighborSparseMatrix (utility::vector1< int > const &first_node_num_states_per_aa, utility::vector1< int > const &second_node_num_states_per_aa)
	Constructor. The amino acid neighbor sparse matrix stores the rotamer pair energies for a pair of residues - or more generally - for a pair of nodes in an interaction graph. Template type T must support: operator < operator = operator +=. More...

void	set_sparse_aa_info (ObjexxFCL::FArray2_bool const &sparse_conn_info)
	Method for telling the sparse matrix which amino acid pairs to allocate space for. The input is a 2D FArray where the first dimension indexes over the amino-acids of the second node, and the second dimension indexes over the amino-acids of the first node. This is somewhat iverted, but it is the natural consequence of a column-major 2D array. More...

bool	get_sparse_aa_info (int node1aa, int node2aa) const
	returns true if node1aa and node2aa neighbor More...

int	get_table_size () const
	returns the number of entries in the sparse matrix More...

unsigned int	get_offset_table_size_in_bytes () const
	returns the number of bytes spent on the offset table More...

value_type	get (SparseMatrixIndex const &ind1, SparseMatrixIndex const &ind2) const
	retrieves the value held for a pair of states. State pairs without entries in the sparse matrix interact with zero energy. More...

int	size () const
	how many values are stored in this sparse matrix? Valid indices are 1 to size() for the operator [] method More...

value_type	operator[] (int index) const
	accessor that does not use sparse matrix data – ignorant of aa type for both dimensions. useful for when traversing all of the values stored in the sparse matrix. More...

value_type &	operator[] (int index)
	non-const accessor for sparse matrix data – ignorant of hte aa type for both dimensions. useful for when traversing all of the values stored in the sparse matrix. More...

void	set (SparseMatrixIndex const &ind1, SparseMatrixIndex const &ind2, value_type const val)
	stores a value for a pair of states. Does not store anything for state pairs without entries in the sparse matrix. Does not give a warning if you try to store a value where you cannot. Maybe it should. More...

void	blanket_set (value_type val)

void	add (SparseMatrixIndex const &ind1, SparseMatrixIndex const &ind2, value_type const val)
	adds to a value for a pair of states. Does not add anything for state pairs without entries in the sparse matrix. Does not give a warning if you try to add to a value where you cannot. Maybe it should. More...

void	scale (SparseMatrixIndex const &ind1, SparseMatrixIndex const &ind2, value_type const scaler)
	scale a particular energy by a constant. Danger: There's no undoing a scale-by-zero operation. More...

void	scale (value_type const scaler)
	scale all energies by a constant. Danger: There's no undoing a scale-by-zero operation. More...

value_type &	getMatrixPointer ()
	returns a reference to the first position in the sparse matrix to be used in a proxy array constructor. More...

ObjexxFCL::FArray2D_int const &	getAANeighborOffsets ()
	returns a reference to the first position in the amion acid pair offset matrix to be used in a proxy array constructor. More...

ObjexxFCL::FArray2D< value_type >	get_aa_submatrix_energies (int node1aa, int node2aa) const

void	force_all_aa_neighbors ()
	set this sparse-matrix to a completely-non-sparse state. All entries are potentially non-zero. Preserves the already-stored energies. More...

void	force_aa_neighbors (int node1aa, int node2aa)
	Sets a pair of amino acids as neighboring. Preserves energies already stored in the table. More...

void	drop_zero_submatrices_where_possible ()
	Deallocates amino-acid pair submatrices from the table that contain only zero-valued entries. More...

void	drop_small_submatrices_where_possible (value_type const epsilon)
	Deallocates amino-acid pair submatrices from the table where the largest magnitude entry in the submatrix fails to exceed the threshold, epsilon. More...

void	drop_all_submatrices ()
	delcare every submatrix to be not worth keeping More...

Static Public Member Functions
static value_type	get (SparseMatrixIndex const &ind1, SparseMatrixIndex const &ind2, int ind2num_states_per_aatype, int aa_offset, ObjexxFCL::FArray1< value_type > const &sparse_matrix)
	cache efficient version of the energy lookup function. All private data for a particular sparse matrix has been held at a node, and now the node provides that data back to this static method. Saves a considerable amount of time in simulated annealing - enough that this OO version of Chris's energy2b table is as fast as his was. More...

static value_type	get (SparseMatrixIndex ind2, int ind1_node_state_offset_minus_1, int ind2_num_states_per_aatype, int aa_offset, ObjexxFCL::FArray1< value_type > const &sparse_matrix)
	cache efficient version of the energy lookup function. All private data for a particular sparse matrix has been held at a node, and now the node provides that data back to this static method. Saves a considerable amount of time in simulated annealing - enough that this OO version of Chris's energy2b table is as fast as his was. More...

static void	set (SparseMatrixIndex const &ind1, SparseMatrixIndex const &ind2, int ind2num_states_per_aatype, int aa_offset, ObjexxFCL::FArray1< value_type > &sparse_matrix, value_type val)
	cache efficient version of the energy lookup function. All private data for a particular sparse matrix has been held at a node, and now the node provides that data back to this static method. Saves a considerable amount of time in simulated annealing - enough that this OO version of Chris's energy2b table is as fast as his was. More...

static void	set (SparseMatrixIndex ind2, int ind1_node_state_offset_minus_1, int ind2_num_states_per_aatype, int aa_offset, ObjexxFCL::FArray1< value_type > &sparse_matrix, value_type val)
	cache efficient version of the energy lookup function. All private data for a particular sparse matrix has been held at a node, and now the node provides that data back to this static method. Saves a considerable amount of time in simulated annealing - enough that this OO version of Chris's energy2b table is as fast as his was. More...

Protected Member Functions
int	get_offset (SparseMatrixIndex const &ind1, SparseMatrixIndex const &ind2) const
	Lookup for offset into sparse table. Prevents index-out-of-bounds error if either amino-acid types of the SparseMatrixIndices are 0. More...

int	get_submatrix_index (SparseMatrixIndex const &ind1, SparseMatrixIndex const &ind2) const
	submatrix indexing function More...

void	copy_old_data_into_new_table (ObjexxFCL::FArray2D_int const &old_aa_offsets, ObjexxFCL::FArray1D< value_type > const &old_sparse_matrix)
	Assigns to the (freshly allocated) sparse_matrix_ member variable the values held in the input sparse matrix . Used in both shrinking and growing the sparse matrix. More...

Protected Attributes
int const	num_aa_

ObjexxFCL::FArray2D_int	aa_offsets_

utility::vector1< int > const &	first_node_num_states_per_aatype_

utility::vector1< int > const &	second_node_num_states_per_aatype_

ObjexxFCL::FArray1D< value_type >	sparse_matrix_

int	table_size_

Member Typedef Documentation

template<class T>

typedef T core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T >::value_type

Constructor & Destructor Documentation

template<class T>

core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T >::AminoAcidNeighborSparseMatrix	(	utility::vector1< int > const &	first_node_num_states_per_aa,
		utility::vector1< int > const &	second_node_num_states_per_aa
	)

inline

Constructor. The amino acid neighbor sparse matrix stores the rotamer pair energies for a pair of residues - or more generally - for a pair of nodes in an interaction graph. Template type T must support: operator < operator = operator +=.

The constructor requires references to the arrays holding state counts for each amino acid type. Multiple sparse-matrices may refer to the same state-count-per-amino acid arrays. By using proxy arrays instead of copying the state-counts, the sparse-matrix saves memory.

Parameters

first_node_num_states_per_aa	- [in] - reference to array with the number of states for the first dimension for each amino acid.
second_node_num_states_per_aa	- [in] - reference to array with the number of states for the second dimension for each amino acid.

Member Function Documentation

template<class T>

void core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T >::add	(	SparseMatrixIndex const &	ind1,
		SparseMatrixIndex const &	ind2,
		value_type const	val
	)

inline

adds to a value for a pair of states. Does not add anything for state pairs without entries in the sparse matrix. Does not give a warning if you try to add to a value where you cannot. Maybe it should.

Parameters

ind1	- [in] - the SparseMatrixIndex for node1's state.
ind2	- [in] - the SparseMatrixIndex for node2's state.
val	- [in] - the value to add for this state pair

template<class T>

void core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T >::blanket_set ( value_type val )

inline

Referenced by core::pack::interaction_graph::LazyEdge::force_aa_neighbors(), core::pack::interaction_graph::LazyEdge::force_all_aa_neighbors(), and core::pack::interaction_graph::LazyEdge::set_sparse_aa_info().

template<class T>

void core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T >::copy_old_data_into_new_table	(	ObjexxFCL::FArray2D_int const &	old_aa_offsets,
		ObjexxFCL::FArray1D< value_type > const &	old_sparse_matrix
	)

inlineprotected

Assigns to the (freshly allocated) sparse_matrix_ member variable the values held in the input sparse matrix . Used in both shrinking and growing the sparse matrix.

Parameters

old_aa_offsets	- [in] - aa offset data for the original table
old_sparse_matrix	- [in] - original table

Referenced by core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< core::PackerEnergy >::drop_all_submatrices(), core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< core::PackerEnergy >::drop_small_submatrices_where_possible(), core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< core::PackerEnergy >::force_aa_neighbors(), and core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< core::PackerEnergy >::force_all_aa_neighbors().

template<class T>

void core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T >::drop_all_submatrices ( )

inline

delcare every submatrix to be not worth keeping

Author: Jack Maguire, jackm.nosp@m.agui.nosp@m.re144.nosp@m.4@gm.nosp@m.ail.c.nosp@m.om

Referenced by core::pack::hbonds::BareMinimumPDEdge::BareMinimumPDEdge().

template<class T>

void core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T >::drop_small_submatrices_where_possible ( value_type const epsilon )

inline

Deallocates amino-acid pair submatrices from the table where the largest magnitude entry in the submatrix fails to exceed the threshold, epsilon.

Parameters

epsilon - [in] - threshold for submatrix preservation

Referenced by core::pack::interaction_graph::PDEdge::drop_small_submatrices_where_possible(), and core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< core::PackerEnergy >::drop_zero_submatrices_where_possible().

template<class T>

void core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T >::drop_zero_submatrices_where_possible ( )

inline

Deallocates amino-acid pair submatrices from the table that contain only zero-valued entries.

Referenced by core::pack::interaction_graph::PDEdge::prepare_for_simulated_annealing_no_deletion().

template<class T>

void core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T >::force_aa_neighbors	(	int	node1aa,
		int	node2aa
	)

inline

Sets a pair of amino acids as neighboring. Preserves energies already stored in the table.

Referenced by core::pack::interaction_graph::LazyEdge::force_aa_neighbors(), and core::pack::interaction_graph::PDEdge::force_aa_neighbors().

template<class T>

void core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T >::force_all_aa_neighbors ( )

inline

set this sparse-matrix to a completely-non-sparse state. All entries are potentially non-zero. Preserves the already-stored energies.

In some places, its easier to set the matrix to completely-non-sparse first and then to deallocate the zero-entry submatrices after computing all pair energies.

Global Read:

Global Write:

Remarks

References:

Author: apl

Referenced by core::pack::interaction_graph::LazyEdge::force_all_aa_neighbors(), and core::pack::interaction_graph::PDEdge::force_all_aa_neighbors().

template<class T>

value_type core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T >::get	(	SparseMatrixIndex const &	ind1,
		SparseMatrixIndex const &	ind2
	)		const

inline

retrieves the value held for a pair of states. State pairs without entries in the sparse matrix interact with zero energy.

Parameters

ind1	- [in] - the SparseMatrixIndex for node1's state.
ind2	- [in] - the SparseMatrixIndex for node2's state.

Referenced by core::pack::interaction_graph::LazyEdge::get_alternate_state_energy_first_node(), core::pack::interaction_graph::PDEdge::get_alternate_state_energy_first_node(), core::pack::interaction_graph::LazyEdge::get_alternate_state_energy_second_node(), core::pack::interaction_graph::PDEdge::get_alternate_state_energy_second_node(), core::pack::interaction_graph::LazyEdge::get_energy_for_state_pair(), core::pack::interaction_graph::LazyEdge::get_two_body_energy(), and core::pack::interaction_graph::PDEdge::get_two_body_energy().

template<class T>

static value_type core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T >::get	(	SparseMatrixIndex const &	ind1,
		SparseMatrixIndex const &	ind2,
		int	ind2num_states_per_aatype,
		int	aa_offset,
		ObjexxFCL::FArray1< value_type > const &	sparse_matrix
	)

inlinestatic

cache efficient version of the energy lookup function. All private data for a particular sparse matrix has been held at a node, and now the node provides that data back to this static method. Saves a considerable amount of time in simulated annealing - enough that this OO version of Chris's energy2b table is as fast as his was.

called when node2 is entertaining an alternate state during sim annealing

Parameters

ind1	- [in] - the SparseMatrixIndex for node1's state.
ind2	- [in] - the SparseMatrixIndex for node2's state.
ind2num_states_per_aatype	- [in] - for node2's state, how many other states does node2 have of the same amino acid type.
aa_offset	- [in] - offset into sparse matrix. Node2 does not need to know what this offset represents; it only needs to know that it must provide this data to this method.
sparse_matrix	- [in] - the sparse matrix that this method reads from

template<class T>

static value_type core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T >::get	(	SparseMatrixIndex	ind2,
		int	ind1_node_state_offset_minus_1,
		int	ind2_num_states_per_aatype,
		int	aa_offset,
		ObjexxFCL::FArray1< value_type > const &	sparse_matrix
	)

inlinestatic

cache efficient version of the energy lookup function. All private data for a particular sparse matrix has been held at a node, and now the node provides that data back to this static method. Saves a considerable amount of time in simulated annealing - enough that this OO version of Chris's energy2b table is as fast as his was.

called when node1 is entertaining an alternate state during sim annealing

Parameters

ind2	- [in] - the SparseMatrixIndex for node2's state.
ind1_node_state_offset_minus_1	- [in] -
ind2_num_states_per_aatype	[in] -
aa_offset	- [in] - offset into sparse matrix. Node1 does not need to know what this offset represents; it only needs to know that it must provide this data to this method.
sparse_matrix	- [in] - the sparse matrix that this method reads from

template<class T>

ObjexxFCL::FArray2D< value_type > core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T >::get_aa_submatrix_energies	(	int	node1aa,
		int	node2aa
	)		const

inline

Referenced by core::pack::interaction_graph::LazyEdge::get_aa_submatrix_energies(), and core::pack::interaction_graph::PDEdge::get_aa_submatrix_energies().

template<class T>

int core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T >::get_offset	(	SparseMatrixIndex const &	ind1,
		SparseMatrixIndex const &	ind2
	)		const

inlineprotected

Lookup for offset into sparse table. Prevents index-out-of-bounds error if either amino-acid types of the SparseMatrixIndices are 0.

Parameters

ind1	- [in] - the sparse matrix index of node1
ind2	- [in] - the sparse matrix index of node2

Referenced by core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< core::PackerEnergy >::add(), core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< core::PackerEnergy >::get(), core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< core::PackerEnergy >::scale(), and core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< core::PackerEnergy >::set().

template<class T>

unsigned int core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T >::get_offset_table_size_in_bytes ( ) const

inline

returns the number of bytes spent on the offset table

Referenced by core::pack::interaction_graph::LazyEdge::count_dynamic_memory(), and core::pack::interaction_graph::PDEdge::count_dynamic_memory().

template<class T>

bool core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T >::get_sparse_aa_info	(	int	node1aa,
		int	node2aa
	)		const

inline

returns true if node1aa and node2aa neighbor

Parameters

node1aa	- [in] - amino acid on node 1
node2aa	- [in] - amino acid on node 2

Referenced by core::pack::interaction_graph::LazyEdge::get_sparse_aa_info(), and core::pack::interaction_graph::PDEdge::get_sparse_aa_info().

template<class T>

int core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T >::get_submatrix_index	(	SparseMatrixIndex const &	ind1,
		SparseMatrixIndex const &	ind2
	)		const

inlineprotected

submatrix indexing function

Parameters

ind1	- [in] - the sparse matrix index of node1
ind2	- [in] - the sparse matrix index of node2

Referenced by core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< core::PackerEnergy >::add(), core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< core::PackerEnergy >::get(), core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< core::PackerEnergy >::scale(), and core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< core::PackerEnergy >::set().

template<class T>

int core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T >::get_table_size ( ) const

inline

returns the number of entries in the sparse matrix

Referenced by core::pack::interaction_graph::LazyEdge::count_dynamic_memory(), core::pack::interaction_graph::PDEdge::count_dynamic_memory(), core::pack::interaction_graph::LazyEdge::get_two_body_table_size(), core::pack::interaction_graph::PDEdge::get_two_body_table_size(), core::pack::interaction_graph::PDEdge::pd_edge_table_all_zeros(), and core::pack::interaction_graph::PDEdge::prepare_for_simulated_annealing().

template<class T>

ObjexxFCL::FArray2D_int const& core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T >::getAANeighborOffsets ( )

inline

returns a reference to the first position in the amion acid pair offset matrix to be used in a proxy array constructor.

used to offload the private data in this class onto a node for cache efficiency during simulated annealing.

Referenced by core::pack::interaction_graph::LazyEdge::get_offsets_for_aatypes(), and core::pack::interaction_graph::PDEdge::get_offsets_for_aatypes().

template<class T>

value_type& core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T >::getMatrixPointer ( )

inline

returns a reference to the first position in the sparse matrix to be used in a proxy array constructor.

used to offload the private data in this class onto a node for cache efficiency during simulated annealing.

Referenced by core::pack::interaction_graph::LazyEdge::get_edge_table_ptr(), and core::pack::interaction_graph::PDEdge::get_edge_table_ptr().

template<class T>

value_type core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T >::operator[] ( int index ) const

inline

accessor that does not use sparse matrix data – ignorant of aa type for both dimensions. useful for when traversing all of the values stored in the sparse matrix.

template<class T>

value_type& core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T >::operator[] ( int index )

inline

non-const accessor for sparse matrix data – ignorant of hte aa type for both dimensions. useful for when traversing all of the values stored in the sparse matrix.

template<class T>

void core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T >::scale	(	SparseMatrixIndex const &	ind1,
		SparseMatrixIndex const &	ind2,
		value_type const	scaler
	)

inline

scale a particular energy by a constant. Danger: There's no undoing a scale-by-zero operation.

Referenced by core::pack::interaction_graph::PDEdge::set_edge_weight().

template<class T>

void core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T >::scale ( value_type const scaler )

inline

scale all energies by a constant. Danger: There's no undoing a scale-by-zero operation.

template<class T>

void core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T >::set	(	SparseMatrixIndex const &	ind1,
		SparseMatrixIndex const &	ind2,
		value_type const	val
	)

inline

stores a value for a pair of states. Does not store anything for state pairs without entries in the sparse matrix. Does not give a warning if you try to store a value where you cannot. Maybe it should.

Parameters

ind1	- [in] - the SparseMatrixIndex for node1's state.
ind2	- [in] - the SparseMatrixIndex for node2's state.
val	- [in] - the value to store for this state pair

Referenced by core::pack::interaction_graph::LazyEdge::get_aa_submatrix_energies(), core::pack::interaction_graph::LazyEdge::get_energy_for_state_pair(), core::pack::interaction_graph::LazyEdge::get_two_body_energy(), core::pack::interaction_graph::LazyEdge::store_interaction_energy_first_node(), core::pack::interaction_graph::LazyEdge::store_interaction_energy_second_node(), and core::pack::interaction_graph::LazyEdge::wipe_two_body_energies_for_node_state().

template<class T>

static void core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T >::set	(	SparseMatrixIndex const &	ind1,
		SparseMatrixIndex const &	ind2,
		int	ind2num_states_per_aatype,
		int	aa_offset,
		ObjexxFCL::FArray1< value_type > &	sparse_matrix,
		value_type	val
	)

inlinestatic

cache efficient version of the energy lookup function. All private data for a particular sparse matrix has been held at a node, and now the node provides that data back to this static method. Saves a considerable amount of time in simulated annealing - enough that this OO version of Chris's energy2b table is as fast as his was.

called when node2 is entertaining an alternate state during sim annealing

Parameters

ind1	- [in] - the SparseMatrixIndex for node1's state.
ind2	- [in] - the SparseMatrixIndex for node2's state.
ind2num_states_per_aatype	- [in] - for node2's state, how many other states does node2 have of the same amino acid type.
aa_offset	- [in] - offset into sparse matrix. Node2 does not need to know what this offset represents; it only needs to know that it must provide this data to this method.
sparse_matrix	- [in] - the sparse matrix that this method reads from
val	- [in] - the value to store for this state pair

template<class T>

static void core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T >::set	(	SparseMatrixIndex	ind2,
		int	ind1_node_state_offset_minus_1,
		int	ind2_num_states_per_aatype,
		int	aa_offset,
		ObjexxFCL::FArray1< value_type > &	sparse_matrix,
		value_type	val
	)

inlinestatic

cache efficient version of the energy lookup function. All private data for a particular sparse matrix has been held at a node, and now the node provides that data back to this static method. Saves a considerable amount of time in simulated annealing - enough that this OO version of Chris's energy2b table is as fast as his was.

called when node1 is entertaining an alternate state during sim annealing

Parameters

ind2	- [in] - the SparseMatrixIndex for node2's state.
ind1_node_state_offset_minus_1	- [in] -
ind2_num_states_per_aatype	[in] -
aa_offset	- [in] - offset into sparse matrix. Node1 does not need to know what this offset represents; it only needs to know that it must provide this data to this method.
sparse_matrix	- [in] - the sparse matrix that this method reads from
val	- [in] - the value to store for this state pair

template<class T>

void core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T >::set_sparse_aa_info ( ObjexxFCL::FArray2_bool const & sparse_conn_info )

inline

Method for telling the sparse matrix which amino acid pairs to allocate space for. The input is a 2D FArray where the first dimension indexes over the amino-acids of the second node, and the second dimension indexes over the amino-acids of the first node. This is somewhat iverted, but it is the natural consequence of a column-major 2D array.

Parameters

sparse_conn_info - [in] - table of boolean values representing which amino acid pairs that neighbor.

Referenced by core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< core::PackerEnergy >::drop_all_submatrices(), core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< core::PackerEnergy >::drop_small_submatrices_where_possible(), core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< core::PackerEnergy >::force_aa_neighbors(), core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< core::PackerEnergy >::force_all_aa_neighbors(), core::pack::interaction_graph::LazyEdge::set_sparse_aa_info(), and core::pack::interaction_graph::PDEdge::set_sparse_aa_info().

template<class T>

int core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T >::size ( ) const

inline

how many values are stored in this sparse matrix? Valid indices are 1 to size() for the operator [] method

Referenced by core::pack::interaction_graph::LazyEdge::prepare_for_simulated_annealing(), and core::pack::interaction_graph::LazyEdge::set_edge_weight().