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Class pmr.euclid.Point3Vector

java.lang.Object
   |
   +----java.util.Vector
           |
           +----pmr.euclid.EuclidVector
                   |
                   +----pmr.euclid.Point3Vector

public class Point3Vector

extends EuclidVector

There are a large number of routines for manipulating 3-D coordinates. Examples are distance, torsion, angle, planes, fitting, etc. The routines have NOT been optimised. In the previous incarnation (C++) all coordinates were handled by Point3s, etc because pointers are fragile. In Java, however, a lot more intermediate information could be passed through double[] arrays and this will be gradually converted.

All the routines compile and give answers. The answers were right in the C++ version. Most seem to be right here, but the FITTING ROUTINES ARE CURRENTLY NOT WORKING PROPERLY. This will be fixed...

Default is an empty (Java) Vector;

Author:

(C) P. Murray-Rust, 1996

Point3Vector()

Point3Vector(double[])

Formed by feeding in an existing array to a 3xn matrix.

Point3Vector(int)

create a Vector with given number of points

Point3Vector(int, double[], double[], double[])

from three parallel arrays of x, y and z - by REFERENCE

Point3Vector(Point3Vector)

copy constructor from Point3Vector COPIES pv

Point3Vector(RealArray)

constructor from RealArray - by REFERENCE

addElement(Point3)

angle(int, int, int)

get angle between 3 points

angle(IntSet)

get angle between 3 points

bestPlane()

get best plane

deviationsFromPlane(Plane3)

get deviations of coordinates from plane

distance(int, int)

get distance between 2 points

distance(IntSet)

get distance between 2 points

fitTo(Point3Vector)

fit two coordinates of same length and alignment CURRENTLY NOT VALIDATED

getCentroid()

get centroid of all points

getCoordinate(int, Choice3)

get a single coordinate value

getDistanceMatrix()

distance matrix

getLine(int, int)

get the line between two points

getPoint3(int)

get a single point by REFERENCE

getRange(Choice3)

get range of one coordinate

getRange3()

get range of all 3 coordinates

getXYZ()

get the coordinate coordinate array as doubles x,y,z,x,y,z, ...

getXYZ(Choice3)

get a single coordinate array - e.g.

inertialAxes(RealArray, RealSquareMatrix, IllConditionedMatrixException)

get Inertial axes; do not throw exception for pathological cases, but return it.

inertialTensor()

get inertial tensor (second moments)

moveToCentroid()

centre molecule on origin - translate to centroid MODIFIES PV

plus(Point3Vector)

form the point+point sum for two vectors of points

plus(Vector3)

translate by a vector - do NOT modify this

rms(Point3Vector)

rms between two molecules - per atom

roughAlign(Point3Vector)

fit two coordinates of same length and alignment - rough private method fit this to ref (i.e.

setElementAt(Vector3, int)

sets a given coordinate (i) to v.

subArray(IntSet)

create a NEW subset of the points; points are COPIED

subtract(Point3Vector)

form the point+point difference for two vectors of points

subtract(Vector3)

translate negatively

torsion(int, int, int, int)

get torsion angle between 4 points

torsion(IntSet)

get torsion angle between 4 points

transform(Transform3)

transform all coordinates MODIFIES Vector

transform(Transform3, IntSet)

transform subset of coordinates - MODIFIES Vector

  public Point3Vector()

  public Point3Vector(int size)

create a Vector with given number of points

  public Point3Vector(double flarray[]) throws InvalidArgumentException

Formed by feeding in an existing array to a 3xn matrix. flarray is in form (x, y, z, x, y, z ...)

Throws: InvalidArgumentException

size of flarray must be multiple of 3

  public Point3Vector(int n,
                      double x[],
                      double y[],
                      double z[])

from three parallel arrays of x, y and z - by REFERENCE

  public Point3Vector(RealArray m) throws InvalidArgumentException

constructor from RealArray - by REFERENCE

Throws: InvalidArgumentException

size of flarray must be multiple of 3

  public Point3Vector(Point3Vector pv)

copy constructor from Point3Vector COPIES pv

  public void addElement(Point3 p)

  public void setElementAt(Vector3 v,
                           int i) throws ArrayIndexOutOfBoundsException

sets a given coordinate (i) to v.

Throws: ArrayIndexOutOfBoundsException

i is >= number of current points (cann use this to increase size of Point3Vector)

  public RealRange getRange(Choice3 ax)

get range of one coordinate

  public Real3Range getRange3()

get range of all 3 coordinates

  public Point3Vector subArray(IntSet is) throws BadSubscriptException

create a NEW subset of the points; points are COPIED

Throws: BadSubscriptException

an element of is is outside range of this

  public Point3Vector plus(Point3Vector pv2) throws UnequalLengthArraysException

form the point+point sum for two vectors of points

Throws: UnequalLengthArraysException

pv2 is different size from this

  public Point3Vector subtract(Point3Vector pv2) throws UnequalLengthArraysException

form the point+point difference for two vectors of points

Throws: UnequalLengthArraysException

pv2 is different size from this

  public Line3 getLine(int i1,
                       int i2)

get the line between two points

  public Point3 getCentroid()

get centroid of all points

  public Point3Vector plus(Vector3 v)

translate by a vector - do NOT modify this

  public Point3Vector subtract(Vector3 v)

translate negatively

  public void moveToCentroid()

centre molecule on origin - translate to centroid MODIFIES PV

  public RealSquareMatrix inertialTensor()

get inertial tensor (second moments)

  public void transform(Transform3 t)

transform all coordinates MODIFIES Vector

  public void transform(Transform3 t,
                        IntSet is)

transform subset of coordinates - MODIFIES Vector

  public double distance(int i1,
                         int i2)

get distance between 2 points

  public double distance(IntSet is) throws InvalidArgumentException

get distance between 2 points

Throws: InvalidArgumentException

is must have exactly 2 points

  public Angle angle(int i1,
                     int i2,
                     int i3) throws ZeroLengthVectorException

get angle between 3 points

Throws: ZeroLengthVectorException

two points are coincident or identical

  public Angle angle(IntSet is) throws InvalidArgumentException, ZeroLengthVectorException

get angle between 3 points

Throws: InvalidArgumentException

is must have exactly 3 points

Throws: ZeroLengthVectorException

two points are coincident or identical

  public Angle torsion(int i1,
                       int i2,
                       int i3,
                       int i4) throws ZeroLengthVectorException

get torsion angle between 4 points

Throws: ZeroLengthVectorException

either 2 points are identical or coincident or 3 successive points are colinear

  public Angle torsion(IntSet is) throws InvalidArgumentException, ZeroLengthVectorException

get torsion angle between 4 points

Throws: InvalidArgumentException

is must have exactly 4 points

Throws: ZeroLengthVectorException

either 2 points are identical or coincident or 3 successive points are colinear

  public RealSquareMatrix getDistanceMatrix()

distance matrix

  public void inertialAxes(RealArray eigval,
                           RealSquareMatrix eigvect,
                           IllConditionedMatrixException illCond) throws ArrayTooSmallException

get Inertial axes; do not throw exception for pathological cases, but return it. Axes (lengths and unit vectors) are returned through the arguments eigval and eigvect.

Throws: ArrayTooSmallException

must have at least 3 points

  public Plane3 bestPlane() throws ArrayTooSmallException

get best plane

Throws: ArrayTooSmallException

must have at least 3 points

  public RealArray deviationsFromPlane(Plane3 p)

get deviations of coordinates from plane

  public Point3 getPoint3(int i)

get a single point by REFERENCE

  public RealArray getXYZ()

get the coordinate coordinate array as doubles x,y,z,x,y,z, ...

  public double getCoordinate(int i,
                              Choice3 j)

get a single coordinate value

  public RealArray getXYZ(Choice3 axis)

get a single coordinate array - e.g. all x-coordinates

  public double rms(Point3Vector c)

rms between two molecules - per atom

  public Transform3 roughAlign(Point3Vector ref) throws IllConditionedMatrixException, ArrayTooSmallException

fit two coordinates of same length and alignment - rough private method fit this to ref (i.e. 1 is moving molecule, 2 is fixed) pick three points in molecule 2 which are well separated (use best plane projection). Find the plane of these three and use the normal, together with one of the points, to define two coordinate axes. Do the same for the other molecule and fit the two sets of axes. This is rough, but will be a good starting point for most molecules.

CURRENTLY NOT VALIDATED (i.e. broken)

Throws: IllConditionedMatrixException

some unusual geometry (e.g. one coordinate set is linear, has coincident points, etc.)

Throws: ArrayTooSmallException

must have at least 3 points

  public Transform3 fitTo(Point3Vector ref) throws ArrayTooSmallException, IllConditionedMatrixException

fit two coordinates of same length and alignment CURRENTLY NOT VALIDATED

Throws: IllConditionedMatrixException

some unusual geometry (e.g. one coordinate set is linear, has coincident points, etc.)

Throws: ArrayTooSmallException

must have at least 3 points

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