jumbo.euclid
Class Point3Vector

java.lang.Object
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  +--java.util.AbstractCollection
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        +--java.util.AbstractList
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              +--java.util.Vector
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                    +--jumbo.euclid.EuclidVector
                          |
                          +--jumbo.euclid.Point3Vector

public class Point3Vector

extends EuclidVector

Point3Vector - a (Java) Vector of Point3s. (Note that 'Vector' is used by Java to describe an array of objects - there is no relationship to geometrical vectors in this package.)

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;

See Also:

Serialized Form

Fields inherited from class java.util.Vector

capacityIncrement, elementCount, elementData

Fields inherited from class java.util.AbstractList

modCount

Constructor Summary

Point3Vector()

Point3Vector(double[] flarray)
Formed by feeding in an existing array to a 3xn matrix.

Point3Vector(int size)
create a Vector with given number of points

Point3Vector(int n, double[] x, double[] y, double[] z)
from three parallel arrays of x, y and z - by REFERENCE

Point3Vector(Point3Vector pv)
copy constructor from Point3Vector COPIES pv

Point3Vector(RealArray m)
constructor from RealArray - by REFERENCE

Method Summary

void	addElement(Point3 p)
Angle	angle(int i1, int i2, int i3) get angle between 3 points
Angle	angle(IntSet is) get angle between 3 points
Plane3	bestPlane() get best plane
RealArray	deviationsFromPlane(Plane3 p) get deviations of coordinates from plane
double	distance(int i1, int i2) get distance between 2 points
double	distance(IntSet is) get distance between 2 points
Transform3	fitTo(Point3Vector ref) fit two coordinates of same length and alignment CURRENTLY NOT VALIDATED
Point3	getCentroid() get centroid of all points
double	getCoordinate(int i, Choice3 j) get a single coordinate value
RealSquareMatrix	getDistanceMatrix() distance matrix
Line3	getLine(int i1, int i2) get the line between two points
Point3	getPoint3(int i) get a single point by REFERENCE
RealRange	getRange(Choice3 ax) get range of one coordinate
Real3Range	getRange3() get range of all 3 coordinates
RealArray	getXYZ() get the coordinate coordinate array as doubles x,y,z,x,y,z, ...
RealArray	getXYZ(Choice3 axis) get a single coordinate array - e.g.
void	inertialAxes(RealArray eigval, RealSquareMatrix eigvect, IllCondMatrixException illCond) get Inertial axes; do not throw exception for pathological cases, but return it.
RealSquareMatrix	inertialTensor() get inertial tensor (second moments)
void	moveToCentroid() centre molecule on origin - translate to centroid MODIFIES PV
Point3Vector	plus(Point3Vector pv2) form the point+point sum for two vectors of points
Point3Vector	plus(Vector3 v) translate by a vector - do NOT modify this
double	rms(Point3Vector c) rms between two molecules - per atom
Transform3	roughAlign(Point3Vector ref) fit two coordinates of same length and alignment - rough private method fit this to ref (i.e.
void	setElementAt(Vector3 v, int i) sets a given coordinate (i) to v.
Point3Vector	subArray(IntSet is) create a NEW subset of the points; points are COPIED
Point3Vector	subtract(Point3Vector pv2) form the point+point difference for two vectors of points
Point3Vector	subtract(Vector3 v) translate negatively
Angle	torsion(int i1, int i2, int i3, int i4) get torsion angle between 4 points
Angle	torsion(IntSet is) get torsion angle between 4 points
void	transform(Transform3 t) transform all coordinates MODIFIES Vector
void	transform(Transform3 t, IntSet is) transform subset of coordinates - MODIFIES Vector

Methods inherited from class jumbo.euclid.EuclidVector

concatenate

Methods inherited from class java.util.Vector

add, add, addAll, addAll, addElement, capacity, clear, clone, contains, containsAll, copyInto, elementAt, elements, ensureCapacity, equals, firstElement, get, hashCode, indexOf, indexOf, insertElementAt, isEmpty, lastElement, lastIndexOf, lastIndexOf, remove, remove, removeAll, removeAllElements, removeElement, removeElementAt, removeRange, retainAll, set, setElementAt, setSize, size, subList, toArray, toArray, toString, trimToSize

Methods inherited from class java.util.AbstractList

iterator, listIterator, listIterator

Methods inherited from class java.lang.Object

finalize, getClass, notify, notifyAll, wait, wait, wait

Constructor Detail

Point3Vector

public Point3Vector()

Point3Vector

public Point3Vector(int size)

create a Vector with given number of points

Point3Vector

public Point3Vector(double[] flarray)
             throws BadArgumentException

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

Throws:

BadArgumentException - size of flarray must be multiple of 3

Point3Vector

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

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

Point3Vector

public Point3Vector(RealArray m)
             throws BadArgumentException

constructor from RealArray - by REFERENCE

Throws:

BadArgumentException - size of flarray must be multiple of 3

Point3Vector

public Point3Vector(Point3Vector pv)

copy constructor from Point3Vector COPIES pv

Method Detail

addElement

public void addElement(Point3 p)

setElementAt

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

sets a given coordinate (i) to v.

Throws:

java.lang.ArrayIndexOutOfBoundsException - i is >= number of current points (cann use this to increase size of Point3Vector)

getRange

public RealRange getRange(Choice3 ax)

get range of one coordinate

getRange3

public Real3Range getRange3()

get range of all 3 coordinates

subArray

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

plus

public Point3Vector plus(Point3Vector pv2)
                  throws UnequalArraysException

form the point+point sum for two vectors of points

Throws:

UnequalArraysException - pv2 is different size from this

subtract

public Point3Vector subtract(Point3Vector pv2)
                      throws UnequalArraysException

form the point+point difference for two vectors of points

Throws:

UnequalArraysException - pv2 is different size from this

getLine

public Line3 getLine(int i1,
                     int i2)

get the line between two points

getCentroid

public Point3 getCentroid()

get centroid of all points

plus

public Point3Vector plus(Vector3 v)

translate by a vector - do NOT modify this

subtract

public Point3Vector subtract(Vector3 v)

translate negatively

moveToCentroid

public void moveToCentroid()

centre molecule on origin - translate to centroid MODIFIES PV

inertialTensor

public RealSquareMatrix inertialTensor()

get inertial tensor (second moments)

transform

public void transform(Transform3 t)

transform all coordinates MODIFIES Vector

transform

public void transform(Transform3 t,
                      IntSet is)

transform subset of coordinates - MODIFIES Vector

distance

public double distance(int i1,
                       int i2)

get distance between 2 points

distance

public double distance(IntSet is)
                throws BadArgumentException

get distance between 2 points

Throws:

BadArgumentException - is must have exactly 2 points

angle

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

get angle between 3 points

Throws:

ZeroVectorException - two points are coincident or identical

angle

public Angle angle(IntSet is)
            throws BadArgumentException,
                   ZeroVectorException

get angle between 3 points

Throws:

BadArgumentException - is must have exactly 3 points

ZeroVectorException - two points are coincident or identical

torsion

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

get torsion angle between 4 points

Throws:

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

torsion

public Angle torsion(IntSet is)
              throws BadArgumentException,
                     ZeroVectorException

get torsion angle between 4 points

Throws:

BadArgumentException - is must have exactly 4 points

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

getDistanceMatrix

public RealSquareMatrix getDistanceMatrix()

distance matrix

inertialAxes

public void inertialAxes(RealArray eigval,
                         RealSquareMatrix eigvect,
                         IllCondMatrixException 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

bestPlane

public Plane3 bestPlane()
                 throws ArrayTooSmallException

get best plane

Throws:

ArrayTooSmallException - must have at least 3 points

deviationsFromPlane

public RealArray deviationsFromPlane(Plane3 p)

get deviations of coordinates from plane

getPoint3

public Point3 getPoint3(int i)

get a single point by REFERENCE

getXYZ

public RealArray getXYZ()

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

getCoordinate

public double getCoordinate(int i,
                            Choice3 j)

get a single coordinate value

getXYZ

public RealArray getXYZ(Choice3 axis)

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

rms

public double rms(Point3Vector c)

rms between two molecules - per atom

roughAlign

public Transform3 roughAlign(Point3Vector ref)
                      throws IllCondMatrixException,
                             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:

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

ArrayTooSmallException - must have at least 3 points

fitTo

public Transform3 fitTo(Point3Vector ref)
                 throws ArrayTooSmallException,
                        IllCondMatrixException

fit two coordinates of same length and alignment CURRENTLY NOT VALIDATED

Throws:

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

ArrayTooSmallException - must have at least 3 points