protocols::vardist_solaccess::VarSolDRotamerDots Class Reference

Handles sphere-sphere overlap calculations. More...

#include <VarSolDRotamerDots.hh>

Inheritance diagram for protocols::vardist_solaccess::VarSolDRotamerDots:

Public Member Functions
	VarSolDRotamerDots (core::conformation::ResidueCOP rotamer, VarSolDistSasaCalculatorCOP vsasa_calc)
	~VarSolDRotamerDots () override
	VarSolDRotamerDots (const VarSolDRotamerDots &rhs)
	copy constructor More...
void	copy (VarSolDRotamerDots const &rhs)
	Copy method for the RotamerDots class. Also used by the assignment operator. More...
VarSolDRotamerDots &	operator= (VarSolDRotamerDots const &rhs)
bool	overlaps (VarSolDRotamerDots 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
core::Size	get_num_atoms () const
	Is the state of this RotamerDots object unassigned? More...
core::Vector	get_atom_coords_xyz (core::Size atom_index) const
	Return the xyz coordinates of an atom in this RotamerDots instance. More...
core::Real	get_atom_collision_radius (core::Size atom_index) const
	Returns the collision radius for the passed in atom type. More...
core::Real	get_atom_interaction_radius (core::Size atom_index) const
core::Size	nshells_for_atom (core::Size atom_index) const
core::Real	shell_radius_for_atom (core::Size atom_index, core::Size shell_index) const
core::Size	ndots () const
bool	get_dot_covered (core::Size atom_index, core::Size shell_index, core::Size dot_index) const
void	increment_self_overlap ()
	computes and stores self-induced dot coverage. uses a vector1 of vector1s of vector1s of ubytes to store the calculated overlap information. More...
void	intersect_residues (VarSolDRotamerDots &other_res)
void	write_dot_kinemage (std::ostream &kinfile) const
bool	any_exposed_dots (core::Size atom) const
core::Real	msas_for_atom (core::Size atom_index) const

Private Member Functions
bool	get_atom_overlap_masks (VarSolDRotamerDots const &other, core::Size at_this, core::Size at_other, core::Real &distance, core::Size &closest_dot1, core::Size &closest_dot2) const
bool	overlap_atoms (VarSolDRotamerDots const &other, core::Size at_this, core::Size at_other, utility::vector1< utility::vector1< ObjexxFCL::ubyte > > &at_this_coverage, utility::vector1< utility::vector1< ObjexxFCL::ubyte > > &at_other_coverage) const
void	initialize_sasa_arrays ()
core::Real	interaction_radii_squared (core::Size attype1, core::Size attype2) const
void	write_dot (std::ostream &kinfile, core::Size atom, core::Size dot, core::Real radius) const
void	write_dot (std::ostream &kinfile, core::Vector const &coord, std::string const &atname) const
void	write_dotlist_header (std::ostream &kinfile, std::string const &master_name, std::string const &color) const

Private Attributes
VarSolDistSasaCalculatorCAP	owner_
core::conformation::ResidueCOP	rotamer_
const utility::vector1 < utility::vector1< core::Real > > &	radii_
const utility::vector1 < core::Real > &	msas_radii_
const utility::vector1 < core::Real > &	coll_radii_
const utility::vector1 < core::Real > &	int_radii_
const utility::vector1 < utility::vector1< core::Real > > &	int_radii_sum_
const utility::vector1 < utility::vector1< core::Real > > &	int_radii_sum2_
const ObjexxFCL::FArray2D_int *	lg_angles_
const ObjexxFCL::FArray2D_ubyte *	lg_masks_
const core::Size &	num_bytes_
const core::Real &	polar_expansion_radius_
core::Size	num_atoms_
utility::vector1 < utility::vector1 < core::pack::interaction_graph::DotSphere > >	atom_coverage_
utility::vector1< core::Vector >	dot_coords_

Detailed Description

Handles sphere-sphere overlap calculations.

Constructor & Destructor Documentation

protocols::vardist_solaccess::VarSolDRotamerDots::VarSolDRotamerDots	(	core::conformation::ResidueCOP	rotamer,
		VarSolDistSasaCalculatorCOP	vsasa_calc
	)

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_coverage_, num_atoms_, radii_, and rotamer_.

protocols::vardist_solaccess::VarSolDRotamerDots::~VarSolDRotamerDots ( )

override

protocols::vardist_solaccess::VarSolDRotamerDots::VarSolDRotamerDots

(

const VarSolDRotamerDots &

rhs

)

copy constructor

Member Function Documentation

bool protocols::vardist_solaccess::VarSolDRotamerDots::any_exposed_dots

(

core::Size

atom

)

const

void protocols::vardist_solaccess::VarSolDRotamerDots::copy

(

VarSolDRotamerDots const &

rhs

)

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

References atom_coverage_, num_atoms_, and rotamer_.

Referenced by operator=().

core::Real protocols::vardist_solaccess::VarSolDRotamerDots::get_atom_collision_radius

(

core::Size

atom_index

)

const

Returns the collision radius for the passed in atom type.

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_.

core::Vector protocols::vardist_solaccess::VarSolDRotamerDots::get_atom_coords_xyz

(

core::Size

atom_index

)

const

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

References rotamer_.

Referenced by overlaps().

core::Real protocols::vardist_solaccess::VarSolDRotamerDots::get_atom_interaction_radius

(

core::Size

atom_index

)

const

References radii_, and rotamer_.

bool protocols::vardist_solaccess::VarSolDRotamerDots::get_atom_overlap_masks ( VarSolDRotamerDots const &  other, core::Size  at_this, core::Size  at_other, core::Real &  distance, core::Size &  closest_dot1, core::Size &  closest_dot2  ) const

private

References core::scoring::sasa::get_legrand_2way_orientation(), protocols::vardist_solaccess::VarSolDistSasaCalculator::interaction_radii_squared(), and rotamer_.

bool protocols::vardist_solaccess::VarSolDRotamerDots::get_dot_covered	(	core::Size	atom_index,
		core::Size	shell_index,
		core::Size	dot_index
	)		const

References atom_coverage_.

Size protocols::vardist_solaccess::VarSolDRotamerDots::get_num_atoms

(

)

const

Is the state of this RotamerDots object unassigned?

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

References num_atoms_.

Referenced by overlaps().

void protocols::vardist_solaccess::VarSolDRotamerDots::increment_self_overlap

(

)

computes and stores self-induced dot coverage. uses a vector1 of vector1s of vector1s of ubytes to store the calculated overlap information.

uses overlap_atoms() which in turn uses get_atom_overlap_masks()

References protocols::vardist_solaccess::VarSolDistSasaCalculator::num_bytes_.

void protocols::vardist_solaccess::VarSolDRotamerDots::initialize_sasa_arrays ( )

private

core::Real protocols::vardist_solaccess::VarSolDRotamerDots::interaction_radii_squared ( core::Size  attype1, core::Size  attype2  ) const

private

References protocols::vardist_solaccess::VarSolDistSasaCalculator::int_radii_sum2_.

Referenced by overlaps().

void protocols::vardist_solaccess::VarSolDRotamerDots::intersect_residues

(

VarSolDRotamerDots &

other_res

)

References atom_coverage_, num_atoms_, and protocols::vardist_solaccess::VarSolDistSasaCalculator::num_bytes_.

Real protocols::vardist_solaccess::VarSolDRotamerDots::msas_for_atom

(

core::Size

atom_index

)

const

References protocols::vardist_solaccess::VarSolDistSasaCalculator::msas_radii_.

core::Size protocols::vardist_solaccess::VarSolDRotamerDots::ndots

(

)

const

References atom_coverage_, and num_atoms_.

core::Size protocols::vardist_solaccess::VarSolDRotamerDots::nshells_for_atom

(

core::Size

atom_index

)

const

References radii_, and rotamer_.

VarSolDRotamerDots & protocols::vardist_solaccess::VarSolDRotamerDots::operator=

(

VarSolDRotamerDots const &

rhs

)

References copy().

bool protocols::vardist_solaccess::VarSolDRotamerDots::overlap_atoms ( VarSolDRotamerDots const &  other, core::Size  at_this, core::Size  at_other, utility::vector1< utility::vector1< ObjexxFCL::ubyte > > &  at_this_coverage, utility::vector1< utility::vector1< ObjexxFCL::ubyte > > &  at_other_coverage  ) const

private

References atom_coverage_, core::kinematics::distance(), core::scoring::sasa::get_legrand_atomic_overlap(), protocols::vardist_solaccess::VarSolDistSasaCalculator::num_bytes_, protocols::vardist_solaccess::VarSolDistSasaCalculator::radii_, and rotamer_.

bool protocols::vardist_solaccess::VarSolDRotamerDots::overlaps

(

VarSolDRotamerDots 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_num_atoms(), interaction_radii_squared(), num_atoms_, and rotamer_.

core::conformation::ResidueCOP protocols::vardist_solaccess::VarSolDRotamerDots::rotamer

(

)

const

References rotamer_.

core::Real protocols::vardist_solaccess::VarSolDRotamerDots::shell_radius_for_atom	(	core::Size	atom_index,
		core::Size	shell_index
	)		const

References radii_, and rotamer_.

void protocols::vardist_solaccess::VarSolDRotamerDots::write_dot ( std::ostream &  kinfile, core::Size  atom, core::Size  dot, core::Real  radius  ) const

private

References core::pack::interaction_graph::RotamerDots::dot_coord(), and core::pack::interaction_graph::write_dot().

void protocols::vardist_solaccess::VarSolDRotamerDots::write_dot ( std::ostream &  kinfile, core::Vector const &  coord, std::string const &  atname  ) const

private

void protocols::vardist_solaccess::VarSolDRotamerDots::write_dot_kinemage

(

std::ostream &

kinfile

)

const

References protocols::vardist_solaccess::VarSolDistSasaCalculator::radii_, and core::pack::interaction_graph::write_dot().

void protocols::vardist_solaccess::VarSolDRotamerDots::write_dotlist_header ( std::ostream &  kinfile, std::string const &  master_name, std::string const &  color  ) const

private

Member Data Documentation

utility::vector1< utility::vector1< core::pack::interaction_graph::DotSphere > > protocols::vardist_solaccess::VarSolDRotamerDots::atom_coverage_

private

Referenced by copy(), get_dot_covered(), intersect_residues(), ndots(), overlap_atoms(), and VarSolDRotamerDots().

const utility::vector1< core::Real >& protocols::vardist_solaccess::VarSolDRotamerDots::coll_radii_

private

utility::vector1< core::Vector > protocols::vardist_solaccess::VarSolDRotamerDots::dot_coords_

private

const utility::vector1< core::Real >& protocols::vardist_solaccess::VarSolDRotamerDots::int_radii_

private

const utility::vector1< utility::vector1< core::Real > >& protocols::vardist_solaccess::VarSolDRotamerDots::int_radii_sum2_

private

const utility::vector1< utility::vector1< core::Real > >& protocols::vardist_solaccess::VarSolDRotamerDots::int_radii_sum_

private

const ObjexxFCL::FArray2D_int* protocols::vardist_solaccess::VarSolDRotamerDots::lg_angles_

private

const ObjexxFCL::FArray2D_ubyte* protocols::vardist_solaccess::VarSolDRotamerDots::lg_masks_

private

const utility::vector1< core::Real >& protocols::vardist_solaccess::VarSolDRotamerDots::msas_radii_

private

core::Size protocols::vardist_solaccess::VarSolDRotamerDots::num_atoms_

private

Referenced by copy(), get_num_atoms(), intersect_residues(), ndots(), overlaps(), and VarSolDRotamerDots().

const core::Size& protocols::vardist_solaccess::VarSolDRotamerDots::num_bytes_

private

VarSolDistSasaCalculatorCAP protocols::vardist_solaccess::VarSolDRotamerDots::owner_

private

const core::Real& protocols::vardist_solaccess::VarSolDRotamerDots::polar_expansion_radius_

private

const utility::vector1< utility::vector1< core::Real > >& protocols::vardist_solaccess::VarSolDRotamerDots::radii_

private

Referenced by get_atom_collision_radius(), get_atom_interaction_radius(), nshells_for_atom(), shell_radius_for_atom(), and VarSolDRotamerDots().

core::conformation::ResidueCOP protocols::vardist_solaccess::VarSolDRotamerDots::rotamer_

private

Referenced by copy(), get_atom_collision_radius(), get_atom_coords_xyz(), get_atom_interaction_radius(), get_atom_overlap_masks(), nshells_for_atom(), overlap_atoms(), overlaps(), rotamer(), shell_radius_for_atom(), and VarSolDRotamerDots().

---

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

• src/protocols/vardist_solaccess/VarSolDRotamerDots.hh
• src/protocols/vardist_solaccess/VarSolDRotamerDots.cc