Uses of Class
ProGAL.geom3d.Point

Packages that use Point

ProGAL.geom3d	This package contains classes that are all related to three-dimensional geometric concepts.
ProGAL.geom3d.complex	A simplicial complex is a topological space of a particular kind, constructed by "gluing together" points, line segments, triangles, and their n-dimensional counterparts.
ProGAL.geom3d.complex.alphaComplex	An alpha complex for a set of d-dimensional points and a real number alpha is a subset of the Delaunay complex where all simplices that can be enclosed by an alpha-probe (a hypersphere of radius alpha), without the probe enclosing any points, are removed.
ProGAL.geom3d.complex.delaunayComplex	A Delaunay complex for a set of d-dimensional points is a tesselation of the points such that no point is inside the circumscribing hypersphere of the d-simplices (for the 3D case: Tetrahedra).
ProGAL.geom3d.complex.tessellation
ProGAL.geom3d.predicates
ProGAL.geom3d.superposition
ProGAL.geom3d.surface
ProGAL.geom3d.viewer	All classes required for the 3D scene viewer J3DScene.
ProGAL.geom3d.volumes
ProGAL.math	This package contains math-classes that are not necessarily related to geometrical concepts.
ProGAL.proteins
ProGAL.proteins.beltaStructure
ProGAL.proteins.beltaStructure.sheet
ProGAL.proteins.chainTree
ProGAL.proteins.structure
ProGAL.proteins.viewer

Uses of Point in ProGAL.geom3d

Subclasses of Point in ProGAL.geom3d

class

PointWeighted

Fields in ProGAL.geom3d declared as Point

Point	Rectangle.center
Point	ParametricPlane.p

Methods in ProGAL.geom3d that return Point

Point	Point.add(Vector p) Returns p added to this (without changing this object).
Point	Point.addThis(Point p)
Point	Point.addThis(Vector p) Returns p added to this (changing this object).
Point	Triangle.circumcenter() Return the circumcenter of the triangle.
Point	Point.clone() Return a new object that equals this object.
static Point	Rectangle.closestSegmentPoint(Point p11, Point p12, Point p2)
static Point[]	Rectangle.closestSegmentPoint(Point p1, Point p2, Point q1, Point q2) 28HOps at most.
Point	LineSegment.getA() Get the first point spanning the segment.
Point	LineSegment.getB() Get the second point spanning the segment.
Point	Triangle.getCenter() Return the center of the triangle.
Point	Shape.getCenter() Get the geometric center of the shape.
Point	Point.getCenter() Returns a clone of this point.
Point	Plane.getCenter() Returns the defining point for this plane.
Point	LineSegment.getCenter() Returns the mid-point of this line-segment.
Point	Circle.getCenter() Get the center of the circle.
Point	PointList.getCentroid() Get the centroid of the points.
static Point	Point.getCircumCenter(Point a, Point b, Point c)
Point	LineSegment.getClosestPoint(Point q) Get the point on the segment closest to a given point q.
Point	Triangle.getCorner(int c) Get the specified corner of this triangle
Point[]	Rectangle.getCorners() Return corners of rectangle in counter-clockwise order.
static Point	Point.getEquilateralPoint(Point a, Point b, Point c)
Point	PointList.getExtreme(Vector direction) Get the most extreme point in the direction specified by the vector.
Point	PointList.getExtremeBack() Get the deepest point (in case of ties the left topmost point is returned).
Point	PointList.getExtremeBottom() Get the lowest point (in case of ties the bottom rightmost point is returned).
Point	PointList.getExtremeFront() Get the frontmost point (in case of ties the front rightmost point is returned).
Point	PointList.getExtremeLeft() Get the leftmost point (in case of ties the bottom lefttmost point is returned).
Point	PointList.getExtremeRight() Get the rightmost point (in case of ties the top rightmost point is returned).
Point	PointList.getExtremeTop() Get the highest point (in case of ties the left topmost point is returned).
Point[]	Plane.getIntersection(Circle circle) Get intersection of a circle with the plane.
Point[]	Circle.getIntersection(Circle c) Intersection of 2 circles in the same plane
Point[]	Plane.getIntersection(Circle circle, Vector u)
Point	Plane.getIntersection(Line line) Get the intersection of a line with the plane.
Point	Line.getIntersection(Line l) Gets the intersection-point of this line with l.
Point	Plane.getIntersection(LineSegment sgm) Get the intersection of a segment with the plane.
Point	Triangle.getIntersection(Point p, Vector dir)
Point	LineSegment.getMidPoint() Gets the midpoint of the segment.
static Point	Point.getMidpoint(Point p, Point q) Creates the midpoint of two points.
Point	ParametricPlane.getP()
Point	Line.getP() Returns the point defining this line.
Point	ParametricPlane.getP(double[] pars)
Point	Triangle.getP1() Get the first corner
Point	Triangle.getP2() Get the second corner
Point	Triangle.getP3() Get the third corner
Point	Plane.getPoint() Get the point defining this plane.
Point	Line.getPoint(double t) Gets the point on the line defined by the specified parameter.
Point	Triangle.getPoint(int c) Get the specified corner-point of this triangle
Point	Simplex.getPoint(int i) TODO: Comment
Point	Point.getPoint(int i)
Point	LineSegment.getPoint(int i) TODO: Comment and test
static Point	Point.getSteinerPoint(Point a, Point b, Point c)
Point	Triangle.incenter()
Point	Line.orthogonalProjection(Point q) Returns the othogonal projection of the point q onto this line.
Point	Plane.projectPoint(Point p) Get the projection of p onto this plane.
Point	Point.reflectThroughOrigoThis() Reflects this point through origo.
Point	Line.rotate(Point p, double angle) Return a rotation of p around this line.
Point	Line.rotateIn(Point point, double angle) Rotate point around this line, store the result in point and return the results.
Point	Point.subtract(Vector p) Returns p subtracted from this (without changing this object).
Point	Point.subtractThis(Point p)
Point	Point.subtractThis(Vector p) Returns p subtracted from this (changing this object).
Point	Vector.toPoint() Convert this vector to a point.

Methods in ProGAL.geom3d with parameters of type Point

int	Plane.above(Point p) Returns 1/0/-1 if point p is above/on/below this plane.
Vector	Vector.add(Point p) Add p to this vector and return the result (without changing this object).
Vector	Vector.addThis(Point p) Add p to this vector and return the result (changing this object).
Point	Point.addThis(Point p)
int	Plane.below(Point p) Returns 1/0/-1 if point p is below/on/above this plane
static Point	Rectangle.closestSegmentPoint(Point p11, Point p12, Point p2)
static Point[]	Rectangle.closestSegmentPoint(Point p1, Point p2, Point q1, Point q2) 28HOps at most.
static boolean	Point.collinear(Point p0, Point p1, Point p2) Returns true if three points are on the same line.
boolean	Triangle.contains(Point p)
static boolean	Point.coplanar(Point p0, Point p1, Point p2, Point p3) Returns true if four specified points are in the same plane
double	Point.distance(Point q) Get the distance from this point to point q
double	Point.distanceSquared(Point q) Get the squared distance from this point to point q.
boolean	Point.dominates(Point q) Returns true if this point dominates point q.
boolean	Point.dominates(Point q, int i, int j, int k) Returns true if this point dominates point q (i=0,1,2 is the most important coordinate, j=0,1,2 is the second most important coordinate and k=0,1,2 is the least important coordinate).
double	Point.dot(Point p)
boolean	Point.equals(Point p) Returns true iff this point and point p are overlapping.
static double	Point.getAngle(Point p1, Point p2, Point p3) Get the angle between the line segments p2->p1 and p2->p3.
static Plane	Point.getBisector(Point p, Point q) Creates a bisector between points p and q
static Point	Point.getCircumCenter(Point a, Point b, Point c)
Point	LineSegment.getClosestPoint(Point q) Get the point on the segment closest to a given point q.
static double	Point.getCosDihedralAngle(Point p1, Point p2, Point p3, Point p4)
static double	Point.getDihedralAngle(Point p1, Point p2, Point p3, Point p4) Get the dihedral angle defined by the 4 non-collinear points p1, p2, p3, p4.
double	Plane.getDistance(Point p) Gets perpendicular distance of point to this plane
double	LineSegment.getDistance(Point q) Gets the distance from q to the nearest point on this segment.
double	Line.getDistance(Point q) Gets the orthogonal distance to a point.
double	Line.getDistanceSquared(Point q) Gets the squared orthogonal distance to a point.
static Circle	Circle.getEquilateralCircle(Point a, Point b) Create the equilateral circle of two points.
static Point	Point.getEquilateralPoint(Point a, Point b, Point c)
java.lang.Double	Circle.getFirstIntersection(Circle c, Point p, Vector dir) returns the smallest rotation angle (direction determined by vector dir) needed to bring point p on this circle to be on the circle c as well.
java.lang.Double	Circle.getFirstIntersection(Line line, Point p, Vector dir, J3DScene scene) returns the smallest rotation angle (direction determined by vector dir) needed to bring point p on this circle to be on the line l as well.
Point	Triangle.getIntersection(Point p, Vector dir)
java.lang.Double	Plane.getIntersectionAngle(Circle circle, Point p, Vector dir, J3DScene scene)
static Point	Point.getMidpoint(Point p, Point q) Creates the midpoint of two points.
double	LineSegment.getSquaredDistance(Point q) Gets the squared distance from q to the nearest point on this segment.
static Point	Point.getSteinerPoint(Point a, Point b, Point c)
static double	Point.inSphere(Point p, Point q, Point r, Point s, Point t) Returns a positive double if point t is inside the sphere through points p, q, r, s.
double	Line.optimalRotation(Point[] moving, Point[] target) Return the optimal right-hand rotation around the line that brings the m-points as close to the f-points as possible.
double	Line.optimalRotation(Point[] moving, Point[] target) Return the optimal right-hand rotation around the line that brings the m-points as close to the f-points as possible.
static double	Point.orientation(Point p, Point q, Point r, Point s)
static double	Point.orientation(Point p, Point q, Point r, Point s, Point t)
Point	Line.orthogonalProjection(Point q) Returns the othogonal projection of the point q onto this line.
double	Line.orthogonalProjectionParameter(Point q) Returns the line-parameter of the othogonal projection of the point q onto this line.
Point	Plane.projectPoint(Point p) Get the projection of p onto this plane.
double[]	ParametricPlane.projectPoint(Point v) Projects the point v onto this plane and returns the parameters of the projected point (scaling of v1, of v2 and finally the distance or scaling along n).
Point	Line.rotate(Point p, double angle) Return a rotation of p around this line.
Point	Line.rotateIn(Point point, double angle) Rotate point around this line, store the result in point and return the results.
void	Point.rotation(Vector v, double alpha, Point p) rotates (clockwise) the point around the line through the point p with the direction unit vector v.
void	LineSegment.setA(Point a) Change the first point spanning the segment.
void	LineSegment.setB(Point b) Change the second point spanning the segment.
static Sphere	ApolloniusSolver.solveApollonius(Point[] centers, double[] radii, int[] s)
Point	Point.subtractThis(Point p)
Vector	Point.vectorTo(Point p) Get the vector that points from this point to p

Constructors in ProGAL.geom3d with parameters of type Point

Circle(Point center, double radius, Vector normal)

Circle(Point p0, Point p1, Point p2)
Circle in the plane through p0, p1, p2

Circle(Point center, Point through, Vector normal)
A circle with given center through a given point and with specified normal vector

Line(Point p1, Point p2)
Constructs a line through the two specified points.

Line(Point p, Vector d)
Constructs a line through p with direction d.

LineSegment(Point a, Point b)
Constructs a segment between points a and b.

LineSegment(Point a, Vector v)
Constructs a segment from a to a+v.

ParametricPlane(Point p, Vector normal)
Construct a parametric plane with the specified point and normal.

ParametricPlane(Point p, Vector v1, Vector v2)
8 + 31 = 39HOps

Plane(Point p, Point q, Point r)
Constructs a plane through three points using the first point as defining point.

Plane(Point p, Vector n)
Constructs a plane with the normal vector n containing point p.

Point(Point p)
Construct a point that is a clone of p.

PointList(Point[] elements)
Construc a point-list from an array of points.

Rectangle(Point center, Vector[] bases)

Triangle(Point[] p)

Triangle(Point p1, Point p2, Point p3)
Construct a triangle using the three specified points as corners

Vector(Point p)
Construct a vector pointing from origo to p.

Vector(Point p1, Point p2)
Constructs a vector between two points p1 and p2 - added by pawel 12-11-2011

Constructor parameters in ProGAL.geom3d with type arguments of type Point

PointList(java.util.Collection<Point> points)

Uses of Point in ProGAL.geom3d.complex

Subclasses of Point in ProGAL.geom3d.complex

class

CVertex

Methods in ProGAL.geom3d.complex with parameters of type Point

boolean

CEdge.containsPoint(Point p)

Constructors in ProGAL.geom3d.complex with parameters of type Point

CVertex(Point p)

CVertex(Point p, boolean bigpoint)

Uses of Point in ProGAL.geom3d.complex.alphaComplex

Constructor parameters in ProGAL.geom3d.complex.alphaComplex with type arguments of type Point

AlphaComplex(java.util.List<Point> pl, double alpha)
Build the alpha-complex of the specified point-list.

AlphaFiltration(java.util.List<Point> pl)
Build the alpha-filtration of the specified point-list.

VoidTree(java.util.List<Point> points, double interval)

Uses of Point in ProGAL.geom3d.complex.delaunayComplex

Constructor parameters in ProGAL.geom3d.complex.delaunayComplex with type arguments of type Point

DelaunayComplex(java.util.List<Point> points)
Builds the Delaunay complex of the specified point-set

DelaunayComplexRotation(java.util.List<Point> points)

RegularComplex(java.util.List<Point> points)

Uses of Point in ProGAL.geom3d.complex.tessellation

Constructor parameters in ProGAL.geom3d.complex.tessellation with type arguments of type Point

DelaunayTessellation(java.util.List<Point> points)
Builds the Delaunay complex of the specified point-set

Uses of Point in ProGAL.geom3d.predicates

Methods in ProGAL.geom3d.predicates with parameters of type Point

abstract double	Predicates.circumradius(Point p0, Point p1, Point p2)
double	InexactRegularJavaPredicates.circumradius(Point p0, Point p1, Point p2)
double	InexactJavaPredicates.circumradius(Point p0, Point p1, Point p2)
double	ExactNativePredicates.circumradius(Point p0, Point p1, Point p2)
double	ExactJavaPredicates.circumradius(Point p0, Point p1, Point p2)
abstract double	Predicates.circumradius(Point p0, Point p1, Point p2, Point p3)
double	InexactRegularJavaPredicates.circumradius(Point p0, Point p1, Point p2, Point p3)
double	InexactJavaPredicates.circumradius(Point p0, Point p1, Point p2, Point p3)
double	ExactNativePredicates.circumradius(Point p0, Point p1, Point p2, Point p3)
double	ExactJavaPredicates.circumradius(Point p0, Point p1, Point p2, Point p3)
abstract Predicates.PlaneConfig	Predicates.diffsides(Point p0, Point p1, Point p2, Point q0, Point q1)
Predicates.PlaneConfig	InexactRegularJavaPredicates.diffsides(Point p0, Point p1, Point p2, Point q0, Point q1)
Predicates.PlaneConfig	InexactJavaPredicates.diffsides(Point p0, Point p1, Point p2, Point q0, Point q1)
Predicates.PlaneConfig	ExactNativePredicates.diffsides(Point p0, Point p1, Point p2, Point q0, Point q1)
Predicates.PlaneConfig	ExactJavaPredicates.diffsides(Point p0, Point p1, Point p2, Point q0, Point q1)
abstract Predicates.SphereConfig	Predicates.edgeinsphere(LineSegment e, Point q)
Predicates.SphereConfig	InexactRegularJavaPredicates.edgeinsphere(LineSegment e, Point q)
Predicates.SphereConfig	InexactJavaPredicates.edgeinsphere(LineSegment e, Point q)
Predicates.SphereConfig	ExactNativePredicates.edgeinsphere(LineSegment ls, Point q) TODO: This isnt exact
Predicates.SphereConfig	ExactJavaPredicates.edgeinsphere(LineSegment ls, Point q) TODO: This isnt exact
abstract boolean	Predicates.inplane(Point p0, Point p1, Point p2, Point p3)
boolean	InexactRegularJavaPredicates.inplane(Point p0, Point p1, Point p2, Point p3)
boolean	InexactJavaPredicates.inplane(Point p0, Point p1, Point p2, Point p3)
boolean	ExactNativePredicates.inplane(Point p0, Point p1, Point p2, Point p3)
boolean	ExactJavaPredicates.inplane(Point p0, Point p1, Point p2, Point p3)
abstract Predicates.SphereConfig	Predicates.insphere(Point p0, Point p1, Point p2, Point q)
Predicates.SphereConfig	InexactRegularJavaPredicates.insphere(Point p0, Point p1, Point p2, Point q)
Predicates.SphereConfig	InexactJavaPredicates.insphere(Point p0, Point p1, Point p2, Point q)
Predicates.SphereConfig	ExactNativePredicates.insphere(Point p0, Point p1, Point p2, Point q)
Predicates.SphereConfig	ExactJavaPredicates.insphere(Point p0, Point p1, Point p2, Point q)
abstract Predicates.SphereConfig	Predicates.insphere(Point p0, Point p1, Point p2, Point p3, Point q)
Predicates.SphereConfig	InexactRegularJavaPredicates.insphere(Point p0, Point p1, Point p2, Point p3, Point q)
Predicates.SphereConfig	InexactJavaPredicates.insphere(Point p0, Point p1, Point p2, Point p3, Point q)
Predicates.SphereConfig	ExactNativePredicates.insphere(Point p0, Point p1, Point p2, Point p3, Point q)
Predicates.SphereConfig	ExactJavaPredicates.insphere(Point p0, Point p1, Point p2, Point p3, Point q)
abstract Predicates.SphereConfig	Predicates.insphere(Tetrahedron t, Point q)
Predicates.SphereConfig	InexactRegularJavaPredicates.insphere(Tetrahedron t, Point q)
Predicates.SphereConfig	InexactJavaPredicates.insphere(Tetrahedron t, Point q)
Predicates.SphereConfig	ExactNativePredicates.insphere(Tetrahedron t, Point q)
Predicates.SphereConfig	ExactJavaPredicates.insphere(Tetrahedron t, Point q)
abstract Predicates.SphereConfig	Predicates.insphere(Triangle tri, Point q)
Predicates.SphereConfig	InexactRegularJavaPredicates.insphere(Triangle tri, Point q)
Predicates.SphereConfig	InexactJavaPredicates.insphere(Triangle tri, Point q)
Predicates.SphereConfig	ExactNativePredicates.insphere(Triangle tri, Point q)
Predicates.SphereConfig	ExactJavaPredicates.insphere(Triangle tri, Point q)
abstract double	Predicates.orient(Point p0, Point p1, Point p2, Point q)
double	InexactRegularJavaPredicates.orient(Point p0, Point p1, Point p2, Point q)
double	InexactJavaPredicates.orient(Point p0, Point p1, Point p2, Point q)
double	ExactNativePredicates.orient(Point p0, Point p1, Point p2, Point q)
double	ExactJavaPredicates.orient(Point p0, Point p1, Point p2, Point q)

Uses of Point in ProGAL.geom3d.superposition

Methods in ProGAL.geom3d.superposition that return Point

Point	Transform.transform(Point p)
Point	Transform.transformIn(Point p)

Methods in ProGAL.geom3d.superposition that return types with arguments of type Point

java.util.List<Point>	Transform.transform(java.util.List<Point> pl)
java.util.List<Point>	Transform.transformIn(java.util.List<Point> pl)

Methods in ProGAL.geom3d.superposition with parameters of type Point

Point	Transform.transform(Point p)
Point	Transform.transformIn(Point p)

Method parameters in ProGAL.geom3d.superposition with type arguments of type Point

static double	GDT.getGDT(java.util.List<Point> points1, java.util.List<Point> points2, double cutoff)
static double	GDT.getGDT(java.util.List<Point> points1, java.util.List<Point> points2, double cutoff)
static double	GDT.getGDT(java.util.List<Point> points1, java.util.List<Point> points2, double cutoff, int method)
static double	GDT.getGDT(java.util.List<Point> points1, java.util.List<Point> points2, double cutoff, int method)
static double	Superposition.getRMSD(java.util.List<Point> x, java.util.List<Point> y)
static double	Superposition.getRMSD(java.util.List<Point> x, java.util.List<Point> y)
static double	RMSD.getRMSD(java.util.List<Point> points1, java.util.List<Point> points2)
static double	RMSD.getRMSD(java.util.List<Point> points1, java.util.List<Point> points2)
static double	FastRMSD.getRMSD(java.util.List<Point> points1, java.util.List<Point> points2)
static double	FastRMSD.getRMSD(java.util.List<Point> points1, java.util.List<Point> points2)
static Transform	RMSD.optimalSuperposition(java.util.List<Point> points, java.util.List<Point> superposeTo)
static Transform	RMSD.optimalSuperposition(java.util.List<Point> points, java.util.List<Point> superposeTo)
static Transform	RMSD.optimalSuperposition(java.util.List<Point> points, java.util.List<Point> superposeTo, java.util.List<java.lang.Integer> indices)
static Transform	RMSD.optimalSuperposition(java.util.List<Point> points, java.util.List<Point> superposeTo, java.util.List<java.lang.Integer> indices)
java.util.List<Point>	Transform.transform(java.util.List<Point> pl)
java.util.List<Point>	Transform.transformIn(java.util.List<Point> pl)

Uses of Point in ProGAL.geom3d.surface

Methods in ProGAL.geom3d.surface that return Point

Point	ParametricSurface.getCenter()
abstract Point	ParametricSurface.getPoint(double u, double v)
Point	ParametricPlane.getPoint(double u, double v)
Point	ParametricParaboloid.getPoint(double u, double v)
Point	ParametricSurface.getPoint(Point p)
Point	ParametricParaboloid.getPoint(Point par)

Constructors in ProGAL.geom3d.surface with parameters of type Point

ParametricPlane(Point p, Vector[] bases)

Uses of Point in ProGAL.geom3d.viewer

Fields in ProGAL.geom3d.viewer declared as Point

Point

TextShape.pos

Methods in ProGAL.geom3d.viewer that return Point

Point	TextShape.getCenter()
Point	Camera.getLocation()
Point	Camera.getLookingAt()

Methods in ProGAL.geom3d.viewer with parameters of type Point

void	J3DScene.addText(java.lang.String t, Point pos) Add a text-object at the specified position.
void	J3DScene.addText(java.lang.String t, Point pos, double height)
void	J3DScene.addText(java.lang.String t, Point pos, double height, java.awt.Color c)
void	J3DScene.centerCamera(Point newCenter)
void	Camera.setLocation(Point p)
void	Camera.setLookingAt(Point p)

Constructors in ProGAL.geom3d.viewer with parameters of type Point

TextShape(java.lang.String t, Point p)

TextShape(java.lang.String t, Point p, double height)

Uses of Point in ProGAL.geom3d.volumes

Fields in ProGAL.geom3d.volumes declared as Point

Point	Cone.p1
Point	Cone.p2

Methods in ProGAL.geom3d.volumes that return Point

Point	Tetrahedron.circumCenter() Find the center of the circumscribing sphere.
Point	OBB.getAnchor()
Point	Tetrahedron.getCenter()
Point	Sphere.getCenter() Get the center
Point	RSS.getCenter()
Point	OBB.getCenter()
Point	LSS.getCenter()
Point	Lens.getCenter()
Point	Cylinder.getCenter()
Point	Cone.getCenter()
Point	Tetrahedron.getCorner(int c) Return the specified corner.
Point[]	Tetrahedron.getCorners() Return all four corners
Point[]	Sphere.getIntersections(Circle c)
static Point[]	Sphere.getIntersections(Sphere s1, Sphere s2, Sphere s3) Find the two, one or zero points that is at the intersection of the three sphere shells.
Point	Tetrahedron.getPoint(int c) Return the specified corner-point.
Point	Lens.getSphereCenter(int i)
Point[]	OBB.getVertices()
Point	Tetrahedron.incenter() Find the center of the inscribed sphere.

Methods in ProGAL.geom3d.volumes with parameters of type Point

boolean	Sphere.contains(Point p) Returns true if the given point is in the sphere.
boolean	LSS.contains(Point p)
double	Lens.distance(Point p)
double	LSS.distanceToPoint(Point point)
java.lang.Double	Sphere.getIntersectionAngle(Circle c, Point p, Vector dir)
static Sphere	Sphere.getMinSphere(Point p1, Point p2) Get the smallest sphere through two given points.
static Sphere	Sphere.getMinSphere(Point p0, Point p1, Point p2) Get the smallest sphere through three points.
static Sphere	Sphere.getMinSphere(Point p0, Point p1, Point p2, Point p3) Constructs the sphere through four points.
boolean	Cylinder.inCylinder(Point p)
boolean	Sphere.isEmpty(Point[] points, double eps)
boolean	Tetrahedron.isInside(Point p) Returns true if the point p is inside this tetrahedron.
boolean	Sphere.isInside(Point p) Returns true if the point is inside this sphere
boolean	Sphere.isInside(Point p, double eps)
double	Sphere.powerDistance(Point p) Gets the squared distance of a point from a sphere surface (negative if the point is inside the sphere).
void	OBB.setAnchor(Point pos)
void	Sphere.setCenter(Point center)
void	Sphere.setCenter(Point p0, Point p1, Point p2, Point p3)
void	Tetrahedron.setPoint(int c, Point point) TODO: Comment
void	Tetrahedron.translate(Point q)

Method parameters in ProGAL.geom3d.volumes with type arguments of type Point

boolean	Sphere.containsNone(java.util.List<Point> points) Returns true if none of the given points is in the sphere.
static OBB	OBB.createBoxFromBases(Vector[] bases, java.util.List<Point> points) Creates a bounding box enclosing the points in points using the supplied bases.

Constructors in ProGAL.geom3d.volumes with parameters of type Point

Cone(Point p1, Point p2, double r)

Cylinder(Point p1, Point p2, double r)

LSS(Point p1, Point p2, double r)
Construct a capsule using two endpoints (center of hemispheres) and a radius (used both for hemispheres and cylinder shape).

OBB(Point anchor, Vector[] bases, double[] extents)

OBB(Point anchor, Vector xdir, Vector ydir, Vector zdir)

RSS(Point center, Vector[] bases, double radius)

Sphere(Point[] points)

Sphere(Point center, double radius)
Constructs a sphere with the specified center and the specified radius.

Sphere(Point p0, Point p1, Point p2, Point p3)

Tetrahedron(Point[] corners)

Tetrahedron(Point p1, Point p2, Point p3, Point p4)

Uses of Point in ProGAL.math

Methods in ProGAL.math that return Point

Point

Matrix.multiply(Point p)

Methods in ProGAL.math with parameters of type Point

Point

Matrix.multiply(Point p)

Uses of Point in ProGAL.proteins

Fields in ProGAL.proteins declared as Point

Point

PDBFile.AtomRecord.coords

Fields in ProGAL.proteins with type parameters of type Point

java.util.LinkedList<Point>

PDBFile.AtomRecord.alternativeCoords

Methods in ProGAL.proteins that return types with arguments of type Point

java.util.List<Point>	PDBFile.getAtomCoords() Returns all atom-coordinates in the first chain in the first model.
java.util.List<Point>	PDBFile.getAtomCoords(int modelNum, int chainNum) Returns all atom-coordinates of the specified model and chain.
java.util.List<Point>	PDBFile.getAtomCoords(java.lang.String atomTypes) Returns the coordinates of the specified atom types.
java.util.List<Point>	PDBFile.getCACoords() Returns the CA-coordinates of atoms in the first chain in the first model.
java.util.List<Point>	PDBFile.getCACoords(int modelNum, int chainNum) Returns the CA-coordinates of the specified model and chain.

Methods in ProGAL.proteins with parameters of type Point

PDBFile.AtomRecord	ProteinComplex.getAtom(Point p)
char	ProteinComplex.getAtomType(Point p)
CVertex	ProteinComplex.getVertex(Point p)

Uses of Point in ProGAL.proteins.beltaStructure

Methods in ProGAL.proteins.beltaStructure that return Point

Point

CanonicalSheet.strandCenter(int strand)

Uses of Point in ProGAL.proteins.beltaStructure.sheet

Methods in ProGAL.proteins.beltaStructure.sheet that return Point

Point	SurfaceSheetStructure.getAtomPosition(int res, int atom) Return the specified atom-position.
abstract Point	ParametricSurface.getPoint(double u, double v)
Point	ParametricSurface.getPoint(Point p)

Uses of Point in ProGAL.proteins.chainTree

Methods in ProGAL.proteins.chainTree that return Point

Point[]	ChainTree.getAllBackboneAtoms() Collect all backbone atoms using the leaves only.
Point	ChainTree.getBackboneAtom(int res, int atom) Return the position of a specific backbone atom.

Methods in ProGAL.proteins.chainTree with parameters of type Point

double

ChainTree.closeCCD(Point[] target, int iterations) Perform cyclic coordinate descent on this chain so the positions of the end-atoms overlap with those specified in the target-array.

Uses of Point in ProGAL.proteins.structure

Subclasses of Point in ProGAL.proteins.structure

class

Atom A class to represent the following properties of an atom: Position Van der waals radius covalent bonds name an id unique to this atom among all the atoms within the same amino acid a pointer to the residue that the atom belongs to The position is maintained in the super-class Point.

Uses of Point in ProGAL.proteins.viewer

Methods in ProGAL.proteins.viewer that return Point

Point	StrandSurface.getCenter()
Point	HelixSurface.getCenter()
Point	CoilSurface.getCenter()
Point	StrandSurface.getPoint(double u, double v)
Point	HelixSurface.getPoint(double u, double v)
Point	CoilSurface.getPoint(double u, double v)