core::pack::interaction_graph::InvRotamerDots Class Reference

Used to determine whether the overlap between two atoms is buried or exposed. More...

#include <RotamerDots.hh>

Inheritance diagram for core::pack::interaction_graph::InvRotamerDots:

Public Member Functions
	InvRotamerDots ()
	InvRotamerDots (InvRotamerDots const &src)
	~InvRotamerDots () override
InvRotamerDots &	operator= (InvRotamerDots const &rhs)
void	setup_from_rotamer_dots (RotamerDots const &rdots)
void	setup_from_rotamer_dots (RotamerDots const &rdots, utility::vector1< Size > const &ats_to_update)
core::conformation::ResidueCOP	rotamer () const
bool	atom_overlap_is_exposed (Size at1, Size at2) const
	Is the intersection between two atoms on this inv-rotamer-dots object exposed? More...
bool	atom_overlap_is_exposed (Size at_this, InvRotamerDots const &other, Size at_other) const
	Is the intersection between one atom on this inv-rotamer-dots object, and one atom on another inv-rotamer-dots object exposed? More...
bool	dot_exposed (Size atomid, Size dot_index) const
void	write_exposed_dots_to_kinemage (std::ostream &ostr, bool group=false) const
void	write_circle_intersection_mask_to_kinemage (std::ostream &ostr, Size const atom_this, InvRotamerDots const &invdots_other, Size const atom_other, bool group=false) const

Private Member Functions
bool	overlap_exposed (core::conformation::Atom const &at1, utility::vector1< ObjexxFCL::ubyte > const &at1exposed_dots, core::conformation::Atom const &at2, utility::vector1< ObjexxFCL::ubyte > const &at2exposed_dots) const
void	print_dot_bit_string (utility::vector1< ObjexxFCL::ubyte > &values) const
	Helper method I am using to confirm that the dots are being overlapped and bits are being set correctly. More...

Private Attributes
core::conformation::ResidueCOP	rotamer_
utility::vector1 < utility::vector1 < ObjexxFCL::ubyte > >	inv_dots_
utility::vector1< Real > const *	radii_

Static Private Attributes
static Real const	max_dist_from_dot_to_intersection = 0.8

Detailed Description

Used to determine whether the overlap between two atoms is buried or exposed.

Constructor & Destructor Documentation

core::pack::interaction_graph::InvRotamerDots::InvRotamerDots

(

)

core::pack::interaction_graph::InvRotamerDots::InvRotamerDots

(

InvRotamerDots const &

src

)

core::pack::interaction_graph::InvRotamerDots::~InvRotamerDots ( )

overridedefault

Member Function Documentation

bool core::pack::interaction_graph::InvRotamerDots::atom_overlap_is_exposed	(	Size	at1,
		Size	at2
	)		const

Is the intersection between two atoms on this inv-rotamer-dots object exposed?

References inv_dots_, overlap_exposed(), and rotamer_.

Referenced by core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >::update_disjoint_sets_using_cache().

bool core::pack::interaction_graph::InvRotamerDots::atom_overlap_is_exposed	(	Size	at_this,
		InvRotamerDots const &	other,
		Size	at_other
	)		const

Is the intersection between one atom on this inv-rotamer-dots object, and one atom on another inv-rotamer-dots object exposed?

References inv_dots_, overlap_exposed(), and rotamer_.

bool core::pack::interaction_graph::InvRotamerDots::dot_exposed	(	Size	atomid,
		Size	dot_index
	)		const

References inv_dots_, and core::pack::interaction_graph::unpack_ubyte().

InvRotamerDots & core::pack::interaction_graph::InvRotamerDots::operator=

(

InvRotamerDots const &

rhs

)

References inv_dots_, radii_, and rotamer_.

bool core::pack::interaction_graph::InvRotamerDots::overlap_exposed ( core::conformation::Atom const &  at1, utility::vector1< ObjexxFCL::ubyte > const &  at1exposed_dots, core::conformation::Atom const &  at2, utility::vector1< ObjexxFCL::ubyte > const &  at2exposed_dots  ) const

private

References core::kinematics::distance(), core::scoring::sasa::get_legrand_2way_orientation(), core::scoring::sasa::get_legrand_atomic_overlap(), core::pack::interaction_graph::RotamerDots::lg_masks_, max_dist_from_dot_to_intersection, core::pack::interaction_graph::RotamerDots::num_bytes_, core::pack::interaction_graph::RotamerDots::probe_radius_, core::conformation::Atom::type(), and core::conformation::Atom::xyz().

Referenced by atom_overlap_is_exposed().

void core::pack::interaction_graph::InvRotamerDots::print_dot_bit_string ( utility::vector1< ObjexxFCL::ubyte > &  values ) const

private

Helper method I am using to confirm that the dots are being overlapped and bits are being set correctly.

References core::pack::interaction_graph::RotamerDots::num_bytes_.

Referenced by write_circle_intersection_mask_to_kinemage().

core::conformation::ResidueCOP core::pack::interaction_graph::InvRotamerDots::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(), and core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >::curr_state_inv_dots().

void core::pack::interaction_graph::InvRotamerDots::setup_from_rotamer_dots

(

RotamerDots const &

rdots

)

References core::pack::interaction_graph::RotamerDots::get_num_atoms(), core::pack::interaction_graph::RotamerDots::get_radii(), inv_dots_, core::pack::interaction_graph::RotamerDots::invert_to_boolmasks(), core::pack::interaction_graph::RotamerDots::num_bytes_, radii_, core::pack::interaction_graph::RotamerDots::rotamer(), and rotamer_.

void core::pack::interaction_graph::InvRotamerDots::setup_from_rotamer_dots	(	RotamerDots const &	rdots,
		utility::vector1< Size > const &	ats_to_update
	)

References core::pack::interaction_graph::RotamerDots::get_num_atoms(), core::pack::interaction_graph::RotamerDots::get_radii(), inv_dots_, core::pack::interaction_graph::RotamerDots::invert_to_boolmasks(), core::pack::interaction_graph::RotamerDots::num_bytes_, radii_, core::pack::interaction_graph::RotamerDots::rotamer(), and rotamer_.

void core::pack::interaction_graph::InvRotamerDots::write_circle_intersection_mask_to_kinemage	(	std::ostream &	ostr,
		Size const	atom_this,
		InvRotamerDots const &	invdots_other,
		Size const	atom_other,
		bool	group = false
	)		const

References core::kinematics::distance(), core::scoring::sasa::get_legrand_2way_orientation(), core::scoring::sasa::get_legrand_atomic_overlap(), inv_dots_, core::pack::interaction_graph::RotamerDots::lg_masks_, max_dist_from_dot_to_intersection, core::pack::interaction_graph::RotamerDots::num_bytes_, print_dot_bit_string(), core::pack::interaction_graph::RotamerDots::probe_radius_, rotamer_, and core::pack::interaction_graph::write_sphere_list_uv1().

void core::pack::interaction_graph::InvRotamerDots::write_exposed_dots_to_kinemage	(	std::ostream &	ostr,
		bool	group = false
	)		const

References inv_dots_, core::pack::interaction_graph::RotamerDots::probe_radius_, rotamer_, and core::pack::interaction_graph::write_sphere_list_uv1().

Member Data Documentation

utility::vector1< utility::vector1< ObjexxFCL::ubyte > > core::pack::interaction_graph::InvRotamerDots::inv_dots_

private

Referenced by atom_overlap_is_exposed(), dot_exposed(), operator=(), setup_from_rotamer_dots(), write_circle_intersection_mask_to_kinemage(), and write_exposed_dots_to_kinemage().

Real const core::pack::interaction_graph::InvRotamerDots::max_dist_from_dot_to_intersection = 0.8

staticprivate

Referenced by overlap_exposed(), and write_circle_intersection_mask_to_kinemage().

utility::vector1< Real > const* core::pack::interaction_graph::InvRotamerDots::radii_

private

Referenced by operator=(), and setup_from_rotamer_dots().

core::conformation::ResidueCOP core::pack::interaction_graph::InvRotamerDots::rotamer_

private

Referenced by atom_overlap_is_exposed(), operator=(), rotamer(), setup_from_rotamer_dots(), write_circle_intersection_mask_to_kinemage(), and write_exposed_dots_to_kinemage().

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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