Handles sphere-sphere overlap calculations for the HPatchInteractionGraph. More...

#include <RotamerDots.hh>

Inheritance diagram for core::pack::interaction_graph::RotamerDots:

Public Member Functions
	RotamerDots ()

	RotamerDots (conformation::ResidueCOP rotamer, bool exclude_hydrogen_atoms=false, bool use_expanded_polar_atom_radii=false)
	Custom constructor for a RotamerDots object. More...

	~RotamerDots () override

	RotamerDots (RotamerDots const &rhs)
	copy constructor More...

void	copy (RotamerDots const &rhs)
	Copy method for the RotamerDots class. Also used by the assignment operator. More...

RotamerDots &	operator= (RotamerDots const &rhs)

bool	operator!= (RotamerDots const &rhs)
	Used during debugging of the HPatchIG. Some extra information is printed if current state dots is NOT EQUAL to alternate state dots at a Node/BGNode. More...

void	zero ()
	Zeros out all of the contained data except the rotamer pointer and the radii array. More...

bool	overlaps (RotamerDots const &other) const
	Returns true if this RotamerDots object has any sphere overlap with the passed in RotamerDots object. More...

core::conformation::ResidueCOP	rotamer () const

bool	state_unassigned () const
	Is the state of this RotamerDots object unassigned? More...

core::Size	get_num_atoms () const
	Returns the number of atoms this RotamerDots object is keeping SASA for. More...

numeric::xyzVector< Real >	get_atom_coords_xyz (Size atom_index) const
	Return the xyz coordinates of an atom in this RotamerDots instance. More...

core::Real	get_atom_radius (Size atom_index) const
	Returns the SASA radius for the passed in atom type. The DB file should have been read in at construct time. More...

core::Real	radius_for_attype (Size const attype_index)
	Same as the above, but skips the conversion from atom index to atom type index. More...

core::Real	max_atom_radius ()
	Returns the maximum atom radius. Used only by the SurfacePotential class. More...

utility::vector1< Real > const *	get_radii () const
	Returns a pointer to the radii vector. Used only by the InvRotamerDots class. More...

void	increment_self_overlap ()
	computes and stores self-induced dot coverage. uses a vector1 of vector1 of ubytes to store the calculated overlap information. More...

void	increment_this_and_cache (RotamerDots const &other, RotamerDotsCache &this_overlap_on_other, utility::vector1< utility::vector1< bool > > &atom_atom_overlaps_cache)
	Add rotamer coverage counts for dots on this object only, leaving rhs unaltered. More...

void	get_res_res_overlap (RotamerDots const &other_res, utility::vector1< utility::vector1< ObjexxFCL::ubyte > > &res1_covered_by_res2, utility::vector1< utility::vector1< ObjexxFCL::ubyte > > &res2_covered_by_res1, utility::vector1< utility::vector1< bool > > &atom_atom_overlaps_cache) const
	Calls get_atom_atom_coverage for all atom pairs between res1 and res2. This method gets called by RotamerDots::get_overlap_cache(). More...

bool	get_atom_atom_coverage (Vector const &at1_xyz, Real at1_base_radius, Vector const &at2_xyz, Real at2_base_radius, utility::vector1< ObjexxFCL::ubyte > &at1_sphere_covered, utility::vector1< ObjexxFCL::ubyte > &at2_sphere_covered, Real dist_sq) const
	returns false if the two spheres do not overlap at all. otherwise, saves the overlap masks to the input vectors. More...

void	increment_from_cached (RotamerDotsCache const &cached_dot_overlap)
	Increments the dot coverage count for this rotamer from a coverage cache. More...

void	decrement_from_cached (RotamerDotsCache const &cached_dot_overlap)
	decrements the dot coverage count for this by the coverage stored in the input RotamerDotsCache object More...

void	increment_both (RotamerDots &other)
	Add rotamer coverage counts for dots on both this and other. sets sasa_is_current_ to false on both this and rhs. More...

void	increment_both_and_cache (RotamerDots &other_rotamer, RotamerDotsCache &others_dots_covered_by_this, RotamerDotsCache &this_dots_covered_by_other, utility::vector1< utility::vector1< bool > > &atom_atom_overlaps_cache)

core::Real	get_sasa () const
	Given the current dot coverage counts, returns the total SASA of this residue. More...

core::Real	get_atom_sasa (Size atom_index) const
	Given the current dot coverage counts, returns the total SASA for a particular atom index. Assumes that get_atom_sasa() will never be called when the object is in the unassigned state. More...

core::Size	get_num_uncovered (core::Size atom) const
	Returns the number of uncovered dots on the given atom, when using standard SASA radii. Note: no expanded polars version of this method. More...

core::Size	get_num_covered_total () const
	Note: no expanded polars version of this method. More...

void	print (std::ostream &os) const

std::string	name3 () const

core::Size	seqpos () const

utility::vector1< DotSphere > const &	get_atom_counts ()

void	invert_to_boolmasks (utility::vector1< utility::vector1< ObjexxFCL::ubyte > > &inv_dots) const
	Inverts the current dot counts and saves them to the passed in vector. More...

void	invert_to_boolmasks (utility::vector1< utility::vector1< ObjexxFCL::ubyte > > &inv_dots, utility::vector1< Size > const &ats_to_update) const
	invert the current dot counts for a subset of the atoms in this rotamer. More...

Static Public Member Functions
static core::Vector	dot_coord (Size index)

Static Public Attributes
static core::Size const	num_bytes_ = 21

static core::Real	probe_radius_ = 1.4

static ObjexxFCL::FArray2D_int const *	lg_angles_
	TEMP! More...

static ObjexxFCL::FArray2D_ubyte const *	lg_masks_

Private Member Functions
void	get_overlap_cache (RotamerDots const &other, RotamerDotsCache &others_dots_covered_by_this, RotamerDotsCache &this_dots_covered_by_other, utility::vector1< utility::vector1< bool > > &atom_atom_overlaps_cache) const
	computes the overlap each rotamer (this & other) induce on each other and stores that information in the RotamerDotsCache objects More...

Static Private Member Functions
static void	initialize_sasa_arrays ()
	Initializes the pointers to the angles and masks FArrays used by sasa.cc and inits the dot sphere coordinates. More...

static void	initialize_dot_coords (utility::vector1< core::Vector > &dot_coords)

Private Attributes
core::conformation::ResidueCOP	rotamer_

Size	num_atoms_

utility::vector1< DotSphere >	atom_counts_

core::Real	sasa_

bool	sasa_is_current_

utility::vector1< core::Real >	atom_sasa_

utility::vector1< Real > const *	radii_

Static Private Attributes
static bool	sasa_arrays_initialized_ = false

static utility::vector1 < core::Vector >	dot_coords_

Detailed Description

Handles sphere-sphere overlap calculations for the HPatchInteractionGraph.

One big change from the r++ version of this class is that this class now includes all of the information that was previously stored in the RotamerCoords class. Since I'm not storing atoms in trie ordering (perhaps I'll add this later), there is no need to have a separate class for the rotamer coordinates.

RotamerDots hold DotSphere objects for the atoms of a given Residue (or really, of the current state on some interaction graph Node). Default use of the class will result in RotamerDots objects keeping DotSpheres for every atom of a residue. For the hpatch interaction graph, though, we only care about the SASA of the heavy atoms. No need to include the hydrogens when looking for hydrophobic patches. By not keeping track of the hydrogens, we save a huge amount of time on computing updates to the SASA score because hydrogen atoms generally make up half of a protein. So I'm adding a boolean flag to the non-default constructor which toggles whether we're tracking SASA of all atoms, or just the heavy atoms.

Two other big changes being made to this class are that 1) the class will now keep track of two kinds of SASA and 2) it will no longer keep score or score_is_current variables. The two kinds of SASA the class will keep track of are the standard SASA, and a SASA with polar atom radii extended. The expanded polar SASA will only be kept if a boolean flag is set at construct time. If not, it will just calculate standard SASA and that's it. The second change is that this class is now only keeping track of SASA. RotamerDots objects will not be responsible for calculating a score.

Constructor & Destructor Documentation

core::pack::interaction_graph::RotamerDots::RotamerDots ( )

core::pack::interaction_graph::RotamerDots::RotamerDots	(	conformation::ResidueCOP	rotamer,
		bool	exclude_hydrogen_atoms = `false`,
		bool	use_expanded_polar_atom_radii = `false`
	)

Custom constructor for a RotamerDots object.

One RotamerDots object get allocated for every state of a first class IG Node, for all first class IG Nodes of a protein being designed. That's potentially a very large number of states. This class should only hold the information it needs to hold to do its job.

References atom_counts_, atom_sasa_, initialize_sasa_arrays(), num_atoms_, radii_, and sasa_arrays_initialized_.

core::pack::interaction_graph::RotamerDots::~RotamerDots ( )

override

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

copy constructor

Member Function Documentation

void core::pack::interaction_graph::RotamerDots::copy ( RotamerDots const & rhs )

Copy method for the RotamerDots class. Also used by the assignment operator.

References atom_counts_, atom_sasa_, num_atoms_, radii_, rotamer_, sasa_, and sasa_is_current_.

Referenced by operator=().

void core::pack::interaction_graph::RotamerDots::decrement_from_cached ( RotamerDotsCache const & cached_dot_overlap )

decrements the dot coverage count for this by the coverage stored in the input RotamerDotsCache object

References atom_counts_, core::pack::interaction_graph::RotamerDotsCache::atom_counts_, num_atoms_, and sasa_is_current_.

core::Vector core::pack::interaction_graph::RotamerDots::dot_coord ( Size index )

static

References dot_coords_, initialize_sasa_arrays(), and sasa_arrays_initialized_.

Referenced by protocols::vardist_solaccess::VarSolDRotamerDots::write_dot().

bool core::pack::interaction_graph::RotamerDots::get_atom_atom_coverage	(	Vector const &	at1_xyz,
		Real	at1_base_radius,
		Vector const &	at2_xyz,
		Real	at2_base_radius,
		utility::vector1< ObjexxFCL::ubyte > &	at1_sphere_covered,
		utility::vector1< ObjexxFCL::ubyte > &	at2_sphere_covered,
		Real	dist_sq
	)		const

returns false if the two spheres do not overlap at all. otherwise, saves the overlap masks to the input vectors.

References core::kinematics::distance(), core::scoring::sasa::get_legrand_2way_orientation(), core::scoring::sasa::get_legrand_atomic_overlap(), num_bytes_, and probe_radius_.

Referenced by get_res_res_overlap(), and increment_self_overlap().

numeric::xyzVector< Real > core::pack::interaction_graph::RotamerDots::get_atom_coords_xyz ( Size atom_index ) const

Return the xyz coordinates of an atom in this RotamerDots instance.

References rotamer_.

Referenced by get_res_res_overlap(), increment_self_overlap(), and overlaps().

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

inline

References atom_counts_.

Real core::pack::interaction_graph::RotamerDots::get_atom_radius ( Size atom_index ) const

Returns the SASA radius for the passed in atom type. The DB file should have been read in at construct time.

Many of the functions in this class iterate over 1 .. num_atoms_. That's not the same thing as an atom type index which is what the radii vector is indexed with. So before we can return the radius, we have to convert the passed in atom_index into the right atom in the residue and then use that to get the right type.

References radii_, and rotamer_.

Referenced by get_res_res_overlap(), get_sasa(), increment_self_overlap(), core::pack::interaction_graph::HPatchNode< V, E, G >::initialize_atom_atom_overlap_cache(), overlaps(), and print().

Real core::pack::interaction_graph::RotamerDots::get_atom_sasa ( Size atom_index ) const

Given the current dot coverage counts, returns the total SASA for a particular atom index. Assumes that get_atom_sasa() will never be called when the object is in the unassigned state.

References atom_sasa_, get_sasa(), and sasa_is_current_.

Size core::pack::interaction_graph::RotamerDots::get_num_atoms ( ) const

Returns the number of atoms this RotamerDots object is keeping SASA for.

References num_atoms_.

Referenced by core::pack::interaction_graph::HPatchNode< V, E, G >::get_alt_state_num_atoms(), core::pack::interaction_graph::HPatchNode< V, E, G >::get_current_state_num_atoms(), get_overlap_cache(), get_res_res_overlap(), increment_both(), core::pack::interaction_graph::HPatchBackgroundEdge< V, E, G >::initialize_overlap_cache(), core::pack::interaction_graph::HPatchNode< V, E, G >::initialize_overlap_with_background(), overlaps(), core::pack::interaction_graph::InvRotamerDots::setup_from_rotamer_dots(), and core::pack::interaction_graph::HPatchEdge< V, E, G >::update_state_at_neighbor().

Size core::pack::interaction_graph::RotamerDots::get_num_covered_total ( ) const

Note: no expanded polars version of this method.

References atom_counts_.

Referenced by print().

Size core::pack::interaction_graph::RotamerDots::get_num_uncovered ( core::Size atom ) const

Returns the number of uncovered dots on the given atom, when using standard SASA radii. Note: no expanded polars version of this method.

References atom_counts_.

Referenced by get_sasa().

void core::pack::interaction_graph::RotamerDots::get_overlap_cache	(	RotamerDots const &	other,
		RotamerDotsCache &	others_dots_covered_by_this,
		RotamerDotsCache &	this_dots_covered_by_other,
		utility::vector1< utility::vector1< bool > > &	atom_atom_overlaps_cache
	)		const

private

computes the overlap each rotamer (this & other) induce on each other and stores that information in the RotamerDotsCache objects

Parameters

other - [in] - the other RotamerDots object other_dots_covered_by_this - [out] - the Cache for the dots on the surface of other that are covered by the atoms on this rotamer this_dots_covered_by_other - [out] - the Cache for the dots on the surface of this that are covered by the atoms on the other rotamer atom_atom_overlaps_cache - [out] - holds a boolean indicating whether two atoms have overlapping, solvent-exposed surface area

References get_num_atoms(), get_res_res_overlap(), core::pack::interaction_graph::RotamerDotsCache::increment_count(), num_atoms_, num_bytes_, and core::pack::interaction_graph::RotamerDotsCache::zero().

Referenced by increment_both_and_cache(), and increment_this_and_cache().

utility::vector1< Real > const * core::pack::interaction_graph::RotamerDots::get_radii ( ) const

Returns a pointer to the radii vector. Used only by the InvRotamerDots class.

References radii_.

Referenced by core::pack::interaction_graph::InvRotamerDots::setup_from_rotamer_dots().

void core::pack::interaction_graph::RotamerDots::get_res_res_overlap	(	RotamerDots const &	other_res,
		utility::vector1< utility::vector1< ObjexxFCL::ubyte > > &	res1_covered_by_res2,
		utility::vector1< utility::vector1< ObjexxFCL::ubyte > > &	res2_covered_by_res1,
		utility::vector1< utility::vector1< bool > > &	atom_atom_overlaps_cache
	)		const

Calls get_atom_atom_coverage for all atom pairs between res1 and res2. This method gets called by RotamerDots::get_overlap_cache().

References get_atom_atom_coverage(), get_atom_coords_xyz(), get_atom_radius(), get_num_atoms(), num_atoms_, and core::scoring::packstat::overlap().

Referenced by get_overlap_cache().

Real core::pack::interaction_graph::RotamerDots::get_sasa ( ) const

Given the current dot coverage counts, returns the total SASA of this residue.

This method does not do any work figuring out who is overlapping with this rotamer. It assumes that work has been done. Instead, it returns the SASA of the dot counts currently held. If the dot counts have not changed since the last time get_sasa() got called then sasa_is_current_ will be true. In that case, the method will just return the the variable sasa_. If the counts have changed, it iterates over all the atoms and recalculates the total SASA. That value is stored in sasa_ and sasa_is_current_ is set to true.

The reason both sasa_ and sasa_is_current_ are "mutable" is so that they can be modified inside this const function.

References atom_counts_, atom_sasa_, get_atom_radius(), get_num_uncovered(), probe_radius_, sasa_, sasa_is_current_, and state_unassigned().

Referenced by get_atom_sasa(), core::pack::interaction_graph::operator<<(), and print().

void core::pack::interaction_graph::RotamerDots::increment_both ( RotamerDots & other )

Add rotamer coverage counts for dots on both this and other. sets sasa_is_current_ to false on both this and rhs.

One use case involves BGNodes initializing overlap with other BGNodes. This is a brute force all BGNode v all BGNode pairwise increment on the RotamerDots objects each Node holds. That's why we call increment both. We don't care about the cache values in this case, but to use increment_both_and_cache, we have to create Cache variables to use as references.

References get_num_atoms(), increment_both_and_cache(), num_atoms_, and core::pack::interaction_graph::RotamerDotsCache::zero().

void core::pack::interaction_graph::RotamerDots::increment_both_and_cache	(	RotamerDots &	other_rotamer,
		RotamerDotsCache &	others_dots_covered_by_this,
		RotamerDotsCache &	this_dots_covered_by_other,
		utility::vector1< utility::vector1< bool > > &	atom_atom_overlaps_cache
	)

Add rotamer coverage counts for dots on both this and other. Cache's the overlap this and other have with each other for greater efficiency. The second parameter are the dots on the surface of other_rotamer that this overlaps. The third parameter are the dots on the surface of this that other_rotamer overlaps. The fourth parameter lives on the Edges of the IG and stores a boolean indicating whether two atoms have overlapping, solvent-exposed surface area. Instead of recalculating this for all residue pairs every substitution, keep it in this cache. The vectors are already sized. The outer vector has the "other_rotamer"'s atoms and the inner vector is for the atoms in this class's residue. The structure just gets passed down to get_overlap_cache() and it eventually gets filled in get_atom_atom_coverage().

If the class is keeping the expanded polar atom SASA also, then this function makes an extra call to get_overlap_cache() to get the extra overlap that happens when polar atom radii are expanded.

References get_overlap_cache(), and increment_from_cached().

Referenced by increment_both().

void core::pack::interaction_graph::RotamerDots::increment_from_cached ( RotamerDotsCache const & cached_dot_overlap )

Increments the dot coverage count for this rotamer from a coverage cache.

References atom_counts_, core::pack::interaction_graph::RotamerDotsCache::atom_counts_, num_atoms_, sasa_is_current_, and TR_RD().

Referenced by increment_both_and_cache(), and increment_this_and_cache().

void core::pack::interaction_graph::RotamerDots::increment_self_overlap ( )

computes and stores self-induced dot coverage. uses a vector1 of vector1 of ubytes to store the calculated overlap information.

uses get_atom_atom_coverage() which in turn uses get_overlap() and get_orientation() method calls in sasa.cc to get the right overlap "masks". when all atom pairs are complete, converts the masks into coverage "counts" which are stored in the DotSphere class (member variable atom_counts_).

to handle the possibility of keeping expanded_polar SASA, we have to run the nested loop over atoms a second time through using the expanded_polar version of get_atom_radius().

References atom_counts_, get_atom_atom_coverage(), get_atom_coords_xyz(), get_atom_radius(), num_atoms_, num_bytes_, and sasa_is_current_.

void core::pack::interaction_graph::RotamerDots::increment_this_and_cache	(	RotamerDots const &	other,
		RotamerDotsCache &	this_overlap_on_other,
		utility::vector1< utility::vector1< bool > > &	atom_atom_overlaps_cache
	)

Add rotamer coverage counts for dots on this object only, leaving rhs unaltered.

In the context of the HPatchIG, this method is called by all FCNodes to increment the overlap a BG residue has on the FCNode. It is called by all BG Edges, to make sure that all FCNodes that are connected to a BG residue get this method called by them. 'other' in this case is a BG residue, and 'this_overlap_on_other' is the overlap that is caused by all-states-possible-at-this-node on the BG node. Yes, that's keeping the same information in two places, but it makes updating hpatch score calculations later faster. (ronj)

References get_overlap_cache(), increment_from_cached(), and num_atoms_.

void core::pack::interaction_graph::RotamerDots::initialize_dot_coords ( utility::vector1< core::Vector > & dot_coords )

staticprivate

The contents of "sphere.txt", now hard coded. The coordinates in the original file are all on the opposite size of the unit sphere from where they genuinely appear to be.

Referenced by initialize_sasa_arrays().

void core::pack::interaction_graph::RotamerDots::initialize_sasa_arrays ( )

staticprivate

Initializes the pointers to the angles and masks FArrays used by sasa.cc and inits the dot sphere coordinates.

This call should only occur once (when the first RotamerDots object get constructed) and never again.

References dot_coords_, core::scoring::sasa::get_legrand_sasa_angles(), core::scoring::sasa::get_legrand_sasa_masks(), initialize_dot_coords(), lg_angles_, lg_masks_, and sasa_arrays_initialized_.

Referenced by dot_coord(), and RotamerDots().

void core::pack::interaction_graph::RotamerDots::invert_to_boolmasks ( utility::vector1< utility::vector1< ObjexxFCL::ubyte > > & inv_dots ) const

Inverts the current dot counts and saves them to the passed in vector.

References atom_counts_, and num_atoms_.

Referenced by core::pack::interaction_graph::InvRotamerDots::setup_from_rotamer_dots().

void core::pack::interaction_graph::RotamerDots::invert_to_boolmasks	(	utility::vector1< utility::vector1< ObjexxFCL::ubyte > > &	inv_dots,
		utility::vector1< Size > const &	ats_to_update
	)		const

invert the current dot counts for a subset of the atoms in this rotamer.

References atom_counts_.

core::Real core::pack::interaction_graph::RotamerDots::max_atom_radius ( )

Returns the maximum atom radius. Used only by the SurfacePotential class.

References protocols::mean_field::max(), and radii_.

std::string core::pack::interaction_graph::RotamerDots::name3 ( ) const

References rotamer_.

Referenced by core::pack::interaction_graph::operator<<().

bool core::pack::interaction_graph::RotamerDots::operator!= ( RotamerDots const & rhs )

Used during debugging of the HPatchIG. Some extra information is printed if current state dots is NOT EQUAL to alternate state dots at a Node/BGNode.

References atom_counts_, atom_sasa_, num_atoms_, radii_, rotamer_, sasa_, sasa_is_current_, and state_unassigned().

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

References copy().

bool core::pack::interaction_graph::RotamerDots::overlaps ( RotamerDots const & other ) const

Returns true if this RotamerDots object has any sphere overlap with the passed in RotamerDots object.

This method only checks to see if two RotamerDots objects are within touching distance of each other. It is used to determine whether Edges or BGEdges should be created in the IG. Calculate this using the expanded polar atom radii. If we don't, there's a chance that a state substitution on a Node may cause SASA changes (when expanded polars are used) on a BGNode, but if we didn't assume expanded radii in this method, there would be no edge between the two nodes.

References core::kinematics::tree::distance_squared(), get_atom_coords_xyz(), get_atom_radius(), get_num_atoms(), num_atoms_, and probe_radius_.

void core::pack::interaction_graph::RotamerDots::print ( std::ostream & os ) const

References atom_counts_, get_atom_radius(), get_num_covered_total(), get_sasa(), core::chemical::element::I, num_atoms_, rotamer_, sasa_is_current_, and state_unassigned().

core::Real core::pack::interaction_graph::RotamerDots::radius_for_attype ( Size const attype_index )

Same as the above, but skips the conversion from atom index to atom type index.

References radii_.

core::conformation::ResidueCOP core::pack::interaction_graph::RotamerDots::rotamer ( ) const

References rotamer_.

Referenced by core::pack::interaction_graph::HPatchNode< V, E, G >::alt_state_inv_dots(), core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >::alt_state_inv_dots(), core::pack::interaction_graph::HPatchNode< V, E, G >::curr_state_inv_dots(), core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >::curr_state_inv_dots(), and core::pack::interaction_graph::InvRotamerDots::setup_from_rotamer_dots().

core::Size core::pack::interaction_graph::RotamerDots::seqpos ( ) const

References rotamer_.

Referenced by core::pack::interaction_graph::operator<<().

bool core::pack::interaction_graph::RotamerDots::state_unassigned ( ) const

Is the state of this RotamerDots object unassigned?

References rotamer_.

Referenced by get_sasa(), operator!=(), core::pack::interaction_graph::operator<<(), and print().

void core::pack::interaction_graph::RotamerDots::zero ( )

Zeros out all of the contained data except the rotamer pointer and the radii array.

So far, this function only gets called by the BGNode::prep_for_simA() call so that multiple runs through an interaction graph can be done. If the rotamer dots object on the BGNodes isn't "cleared" after a run, then the run immediately following will have the incorrect counts.

References atom_counts_, atom_sasa_, sasa_, and sasa_is_current_.