core::pack::interaction_graph::RotamerDotsCache Class Reference

A lightweight version of the RotamerDots class. Used to cache overlap between interaction graph Nodes and BGNodes. More...

#include <RotamerDots.hh>

Public Member Functions
	RotamerDotsCache ()
	RotamerDotsCache (core::Size num_atoms)
	RotamerDotsCache (RotamerDotsCache const &rhs)
	copy constructor More...
RotamerDotsCache &	operator= (RotamerDotsCache const &rhs)
	assignment operator More...
	~RotamerDotsCache ()
void	resize (core::Size num_atoms)
void	zero ()
	sets the dot counts to zero for all atoms More...
void	increment_count (utility::vector1< utility::vector1< ObjexxFCL::ubyte > > &covered)
	increments the dot coverage counts for all atoms in the cache More...
void	write_to_compact_array (utility::vector1< utility::vector1< ObjexxFCL::ubyte > > &compact) const
void	print_bit_string (utility::vector1< ObjexxFCL::ubyte > &values) const
void	print (std::ostream &os) const
utility::vector1< DotSphere > const &	get_atom_counts () const

Private Attributes
utility::vector1< DotSphere >	atom_counts_

Friends
class	RotamerDots

Detailed Description

A lightweight version of the RotamerDots class. Used to cache overlap between interaction graph Nodes and BGNodes.

During packing, when a first class node has to respond to another Node changing state, it's faster to decrement the coverage the previous state produced and increment the coverage the new state produces than to completely recalculate how the new state overlaps the node. But instead of holding that coverage information in a RotamerDots object (which does alot of other things), hold it in this cache class instead.

Constructor & Destructor Documentation

RotamerDotsCache() [1/3]

core::pack::interaction_graph::RotamerDotsCache::RotamerDotsCache ( )

default

RotamerDotsCache() [2/3]

core::pack::interaction_graph::RotamerDotsCache::RotamerDotsCache

(

core::Size

num_atoms

)

References core::pack::interaction_graph::RotamerDots::atom_counts_, and core::pose::num_atoms().

RotamerDotsCache() [3/3]

core::pack::interaction_graph::RotamerDotsCache::RotamerDotsCache ( RotamerDotsCache const &  rhs )

default

copy constructor

~RotamerDotsCache()

core::pack::interaction_graph::RotamerDotsCache::~RotamerDotsCache ( )

default

Member Function Documentation

get_atom_counts()

utility::vector1< DotSphere > const& core::pack::interaction_graph::RotamerDotsCache::get_atom_counts ( ) const

inline

References atom_counts_.

increment_count()

void core::pack::interaction_graph::RotamerDotsCache::increment_count

(

utility::vector1< utility::vector1< ObjexxFCL::ubyte > > &

covered

)

increments the dot coverage counts for all atoms in the cache

Parameters

covered

- [in] - compact ubyte array of dots; '1' for any covered dot for the vdw + 1.4 A sphere

References core::pack::interaction_graph::RotamerDots::atom_counts_.

Referenced by core::pack::interaction_graph::RotamerDots::get_overlap_cache().

operator=()

RotamerDotsCache & core::pack::interaction_graph::RotamerDotsCache::operator= ( RotamerDotsCache const &  rhs )

default

assignment operator

print()

void core::pack::interaction_graph::RotamerDotsCache::print

(

std::ostream &

os

)

const

References core::pack::interaction_graph::RotamerDots::atom_counts_, and core::chemical::element::I.

print_bit_string()

void core::pack::interaction_graph::RotamerDotsCache::print_bit_string

(

utility::vector1< ObjexxFCL::ubyte > &

values

)

const

resize()

void core::pack::interaction_graph::RotamerDotsCache::resize

(

core::Size

num_atoms

)

References core::pack::interaction_graph::RotamerDots::atom_counts_, and core::pose::num_atoms().

write_to_compact_array()

void core::pack::interaction_graph::RotamerDotsCache::write_to_compact_array

(

utility::vector1< utility::vector1< ObjexxFCL::ubyte > > &

compact

)

const

Called by BGEdges with a reference to a vector1 of vector1 of ubytes representing where to put the compact (count) based representation of all the atom overlap masks.

Note: This method only writes the standard SASA dot counts to the passed in array. No version of this function exists for expanded polar atom SASA dot counts.

References core::pack::interaction_graph::RotamerDots::atom_counts_.

zero()

void core::pack::interaction_graph::RotamerDotsCache::zero

(

)

sets the dot counts to zero for all atoms

if the cache already knows the atom's counts are uniformly 0, it skips it

References core::pack::interaction_graph::RotamerDots::atom_counts_.

Referenced by core::pack::interaction_graph::RotamerDots::get_overlap_cache(), and core::pack::interaction_graph::RotamerDots::increment_both().

Friends And Related Function Documentation

RotamerDots

friend class RotamerDots

friend

Member Data Documentation

atom_counts_

utility::vector1< DotSphere > core::pack::interaction_graph::RotamerDotsCache::atom_counts_

private

Referenced by core::pack::interaction_graph::RotamerDots::decrement_from_cached(), get_atom_counts(), and core::pack::interaction_graph::RotamerDots::increment_from_cached().

---

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

• src/core/pack/interaction_graph/RotamerDots.hh
• src/core/pack/interaction_graph/RotamerDots.cc