#include <devel/init.hh>
#include <core/conformation/Conformation.hh>
#include <core/pose/Pose.hh>
#include <core/types.hh>
#include <core/import_pose/import_pose.hh>
#include <numeric/xyzVector.hh>
#include <numeric/xyz.functions.hh>
#include <numeric/conversions.hh>
#include <utility/vector1.hh>
#include <basic/Tracer.hh>
#include <numeric/numeric.functions.hh>
#include <numeric/util.hh>

Functions
AtomID_Map< bool >	concave_shell (core::pose::Pose &pose, core::Real min_z, core::Real max_z, core::Real incr_z, core::Real shell_radius)
	compute the concave shell from the pose, computes along a slice and takes the atoms within a shell, not just the outermost ones More...

utility::vector1< utility::vector1< core::Size > >	convex_hull (std::map< core::Size, core::Vector > coords, core::Real min_z, core::Real max_z)
	computes 2D convex hull: points in a slice on z-dimension are flattened into xy plane; the output is three lists of points for inside, outside and boundary More...

utility::vector1< utility::vector1< core::Size > >	concave_hull (std::map< core::Size, core::Vector > coords, utility::vector1< utility::vector1< core::Size > > point_lists, core::Real dist_cutoff=4.0)
	computes 2D concave hull from three lists of points for inside, outside and boundary More...

utility::vector1< utility::vector1< core::Size > >	add_shell (std::map< core::Size, core::Vector > coords, utility::vector1< utility::vector1< core::Size > > point_lists, core::Real shell_radius)
	adds a shell to boundary points which are taken from the inside point list More...

utility::vector1< core::Real >	get_distances (std::map< core::Size, core::Vector > coords, core::Size p1, core::Size p2, utility::vector1< core::Size > points, bool clock=false)
	compute distances in point list from line p1p2 which points: i,o,b for inside, outside or boundary More...

utility::vector1< core::Real >	get_angles (std::map< core::Size, core::Vector > coords, core::Size p1, core::Size p2, utility::vector1< core::Size > points, bool clock=false)
	compute enclosing angles in point list from line p1p2 which points: i,o,b for inside, outside or boundary More...

core::Size	find_closest (std::map< core::Size, core::Vector > coords, core::Size p1, core::Size p2, utility::vector1< core::Size > inside_points, bool clock=false)
	find point id that is closest to line connecting p1p2 which points: i,o,b for inside, outside or boundary More...

core::Size	find_farthest (std::map< core::Size, core::Vector > coords, core::Size p1, core::Size p2, utility::vector1< core::Size > outside_points, bool clock=false)
	find point id that is farthest from line connecting p1p2 which points: i,o,b for inside, outside or boundary More...

std::string	inside_polygon (std::map< core::Size, core::Vector > coords, utility::vector1< core::Size > polygon, core::Vector q)
	checks whether the point q is inside the polygon or not i.e. compute the number of crossing points with polygon 0 outside 1 inside 2 on boundary More...

utility::vector1< core::Size >	points_in_triangle (std::map< core::Size, core::Vector > coords, core::Size p1, core::Size p2, core::Size q, utility::vector1< core::Size > points)
	returns the points that are within the triangle between points p1, p2, q More...

core::Real	distance_from_line2D (core::Vector p1, core::Vector p2, core::Vector q)
	distance of point q from line between points p1 and p2 More...

bool	on_segment (core::Vector p1, core::Vector p2, core::Vector q)
	is point q on line segment between points p1 and p2? More...

bool	clockwise (core::Vector p1, core::Vector p2, core::Vector q)
	is q clockwise from p1p2? More...

bool	to_left (core::Vector p1, core::Vector p2, core::Vector q)
	check whether q is to the left of p1p2 More...

bool	intersect (core::Vector p1, core::Vector p2, core::Vector q)
	check whether line p1p2 intersects with (q to infinity); q is the test point More...

core::Real	enclosing_angles (core::Vector p1, core::Vector p2, core::Vector q)
	find the sum of angles p1q and p2q; p1, p2, q are points, not vectors More...

int	main (int argc, char *argv[])
	Main method. More...

Variables
static basic::Tracer	TR ("apps.pilot.jkleman.mpframework_test2")

Function Documentation

◆ add_shell()

utility::vector1< utility::vector1< core::Size > > add_shell	(	std::map< core::Size, core::Vector >	coords,
		utility::vector1< utility::vector1< core::Size > >	point_lists,
		core::Real	shell_radius
	)

adds a shell to boundary points which are taken from the inside point list

References dist(), utility::vector1< T, A >::has_value(), create_a3b_hbs::i, create_a3b_hbs::j, erraser_util::remove(), and basic::options::OptionKeys::mp::lipid_acc::shell_radius.

Referenced by concave_shell().

◆ clockwise()

bool clockwise	(	core::Vector	p1,
		core::Vector	p2,
		core::Vector	q
	)

is q clockwise from p1p2?

References p2, and enumerate_junctions::q.

Referenced by get_angles(), get_distances(), points_in_triangle(), and to_left().

◆ concave_hull()

utility::vector1< utility::vector1< core::Size > > concave_hull	(	std::map< core::Size, core::Vector >	coords,
		utility::vector1< utility::vector1< core::Size > >	point_lists,
		core::Real	dist_cutoff = `4.0`
	)

computes 2D concave hull from three lists of points for inside, outside and boundary

References dist(), dist_cutoff, find_closest(), utility::vector1< T, A >::has_value(), create_a3b_hbs::i, create_a3b_hbs::j, p2, points_in_triangle(), and erraser_util::remove().

Referenced by concave_shell().

◆ concave_shell()

AtomID_Map< bool > concave_shell	(	core::pose::Pose &	pose,
		core::Real	min_z,
		core::Real	max_z,
		core::Real	incr_z,
		core::Real	shell_radius
	)

compute the concave shell from the pose, computes along a slice and takes the atoms within a shell, not just the outermost ones

compute the concave shell from the pose, computes along a slice and takes the atoms within a shell, not just the outermost ones from the concave hull

References a, add_shell(), concave_hull(), convex_hull(), create_a3b_hbs::i, natoms(), beta_nonlocal::pose, create_a3b_hbs::r, kic_runner::shell, and basic::options::OptionKeys::mp::lipid_acc::shell_radius.

Referenced by main().

◆ convex_hull()

utility::vector1< utility::vector1< core::Size > > convex_hull	(	std::map< core::Size, core::Vector >	coords,
		core::Real	min_z,
		core::Real	max_z
	)

computes 2D convex hull: points in a slice on z-dimension are flattened into xy plane; the output is three lists of points for inside, outside and boundary

References find_farthest(), utility::vector1< T, A >::has_value(), create_a3b_hbs::i, utility::vector1< T, A >::index(), inside_polygon(), create_a3b_hbs::j, numeric::max(), numeric::min(), p2, points_in_triangle(), erraser_util::remove(), x, predPRE::y, and predPRE::z.

Referenced by concave_shell().

◆ distance_from_line2D()

core::Real distance_from_line2D	(	core::Vector	p1,
		core::Vector	p2,
		core::Vector	q
	)

distance of point q from line between points p1 and p2

References ObjexxFCL::abs(), build_jacobian::distance, p2, ObjexxFCL::pow(), and enumerate_junctions::q.

Referenced by get_distances().

◆ enclosing_angles()

core::Real enclosing_angles	(	core::Vector	p1,
		core::Vector	p2,
		core::Vector	q
	)

find the sum of angles p1q and p2q; p1, p2, q are points, not vectors

References a, numeric::angle_of(), compute_difference::b, kmeans_adaptive_kernel_density_bb_dependent_rotlib::c, numeric::conversions::degrees(), p2, and enumerate_junctions::q.

Referenced by get_angles().

◆ find_closest()

core::Size find_closest	(	std::map< core::Size, core::Vector >	coords,
		core::Size	p1,
		core::Size	p2,
		utility::vector1< core::Size >	inside_points,
		bool	clock = `false`
	)

find point id that is closest to line connecting p1p2 which points: i,o,b for inside, outside or boundary

find point in AtomIDMap that is closest to line connecting p1p2

References oop_conformations::angles, get_angles(), numeric::min(), and p2.

Referenced by concave_hull().

◆ find_farthest()

core::Size find_farthest	(	std::map< core::Size, core::Vector >	coords,
		core::Size	p1,
		core::Size	p2,
		utility::vector1< core::Size >	outside_points,
		bool	clock = `false`
	)

find point id that is farthest from line connecting p1p2 which points: i,o,b for inside, outside or boundary

find point in AtomIDMap that is closest to line connecting p1p2

References get_distances(), utility::vector1< T, A >::index(), numeric::max(), and p2.

Referenced by convex_hull().

◆ get_angles()

utility::vector1< core::Real > get_angles	(	std::map< core::Size, core::Vector >	coords,
		core::Size	p1,
		core::Size	p2,
		utility::vector1< core::Size >	points,
		bool	clock = `false`
	)

compute enclosing angles in point list from line p1p2 which points: i,o,b for inside, outside or boundary

compute enclosing angles in point list from line p1p2

References oop_conformations::angles, clockwise(), enclosing_angles(), create_a3b_hbs::i, p2, and enumerate_junctions::q.

Referenced by find_closest().

◆ get_distances()

utility::vector1< core::Real > get_distances	(	std::map< core::Size, core::Vector >	coords,
		core::Size	p1,
		core::Size	p2,
		utility::vector1< core::Size >	points,
		bool	clock = `false`
	)

compute distances in point list from line p1p2 which points: i,o,b for inside, outside or boundary

compute distances in point list from line p1p2

References clockwise(), distance_from_line2D(), create_a3b_hbs::i, p2, and enumerate_junctions::q.

Referenced by find_farthest().

◆ inside_polygon()

std::string inside_polygon	(	std::map< core::Size, core::Vector >	coords,
		utility::vector1< core::Size >	polygon,
		core::Vector	q
	)

checks whether the point q is inside the polygon or not i.e. compute the number of crossing points with polygon 0 outside 1 inside 2 on boundary

References create_a3b_hbs::i, intersect(), on_segment(), p2, subloop_histogram::polygon, and enumerate_junctions::q.

Referenced by convex_hull(), and points_in_triangle().

◆ intersect()

bool intersect	(	core::Vector	p1,
		core::Vector	p2,
		core::Vector	q
	)

check whether line p1p2 intersects with (q to infinity); q is the test point

References max(), min(), p2, enumerate_junctions::q, and to_left().

Referenced by inside_polygon().

◆ main()

int main	(	int	argc,
		char *	argv[]
	)

Main method.

References argv, concave_shell(), test.T009_Exceptions::e, basic::init(), beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, kic_runner::shell, and basic::options::OptionKeys::mp::lipid_acc::shell_radius.

◆ on_segment()

bool on_segment	(	core::Vector	p1,
		core::Vector	p2,
		core::Vector	q
	)

is point q on line segment between points p1 and p2?

References max(), min(), p2, and enumerate_junctions::q.

Referenced by inside_polygon().

◆ points_in_triangle()

utility::vector1< core::Size > points_in_triangle	(	std::map< core::Size, core::Vector >	coords,
		core::Size	p1,
		core::Size	p2,
		core::Size	q,
		utility::vector1< core::Size >	points
	)

returns the points that are within the triangle between points p1, p2, q

References clockwise(), create_a3b_hbs::i, inside_polygon(), p2, enumerate_junctions::q, and numeric::kinematic_closure::triangle().

Referenced by concave_hull(), and convex_hull().

◆ to_left()

bool to_left	(	core::Vector	p1,
		core::Vector	p2,
		core::Vector	q
	)

check whether q is to the left of p1p2

References clockwise(), p2, and enumerate_junctions::q.

Referenced by intersect().

Variable Documentation

◆ TR

basic::Tracer TR("apps.pilot.jkleman.mpframework_test2") ( "apps.pilot.jkleman.mpframework_test2" )

static

Functions

Variables

Function Documentation

◆ add_shell()

◆ clockwise()

◆ concave_hull()

◆ concave_shell()

◆ convex_hull()

◆ distance_from_line2D()

◆ enclosing_angles()

◆ find_closest()

◆ find_farthest()

◆ get_angles()

◆ get_distances()

◆ inside_polygon()

◆ intersect()

◆ main()

◆ on_segment()

◆ points_in_triangle()

◆ to_left()

Variable Documentation

◆ TR