java.lang.Object
- com.actelion.research.chem.Coordinates

All Implemented Interfaces:

java.io.Serializable, java.lang.Comparable<Coordinates>
```
public final class Coordinates
extends java.lang.Object
implements java.io.Serializable, java.lang.Comparable<Coordinates>
```
Class to encapsulate 3D coordinates

See Also:

Serialized Form

Field Summary

Fields
Modifier and Type Field Description

double x

double y

double z

Constructor Summary

Constructors
Constructor Description

Coordinates()

Coordinates(double x, double y, double z)

Coordinates(Coordinates c)

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`void`	`add(double dx, double dy, double dz)`
`Coordinates`	`add(Coordinates c)`
`Coordinates`	`addC(Coordinates c)`
`Coordinates`	`between(Coordinates c1, Coordinates c2, double f)`	Updates this to contain a point on the straight line through c1 and c2.
`Coordinates`	`center(Coordinates c)`	Calculates the center point between this and c and sets this to the center point.
`void`	`center(Coordinates c1, Coordinates c2)`	Updates this to contains the center between c1 and c2.
`int`	`compareTo(Coordinates o)`
`double`	`cosAngle(Coordinates c)`
`static Coordinates`	`createBarycenter(Coordinates... coords)`
`Coordinates`	`cross(Coordinates c)`
`double`	`dist()`
`double`	`distance(Coordinates c)`
`double`	`distanceSquared(Coordinates c)`
`double`	`distSq()`
`double`	`distSquareTo(Coordinates c)`
`double`	`dot(Coordinates c)`
`boolean`	`equals(java.lang.Object o)`
`double`	`getAngle(Coordinates c)`	Gets the angle formed between the 2 vectors ([0,PI])
`double`	`getAngleXY(Coordinates c)`	Calculates the angle of the line from this location to c projected into the x/y plane.
`double`	`getDihedral(Coordinates c2, Coordinates c3, Coordinates c4)`
`static double`	`getDihedral(Coordinates c1, Coordinates c2, Coordinates c3, Coordinates c4)`	Calculates a signed torsion as an exterior spherical angle from a valid sequence of 4 points in space.
`double`	`getLength()`
`static Coordinates`	`getMirror(Coordinates p, Coordinates c1, Coordinates c2, Coordinates c3)`	Get the mirror image of p through the plane defined by c1, c2, c3
`static double`	`getRmsd(Coordinates[] c1, Coordinates[] c2)`
`static double`	`getRmsd(Coordinates[] c1, Coordinates[] c2, int l)`
`boolean`	`insideBounds(Coordinates[] bounds)`
`boolean`	`isNaN()`
`Coordinates`	`max(Coordinates c)`
`static Coordinates`	`max(Coordinates[] c)`
`Coordinates`	`min(Coordinates c)`
`static Coordinates`	`min(Coordinates[] c)`
`void`	`negate()`
`static Coordinates`	`random()`
`Coordinates`	`rotate(double[][] m)`
`Coordinates`	`rotate(Coordinates normal, double theta)`
`Coordinates`	`rotateC(double[][] m)`
`Coordinates`	`scale(double scale)`
`Coordinates`	`scaleC(double scale)`
`void`	`set(double x, double y, double z)`
`Coordinates`	`set(Coordinates c)`	Copies x,y,z from c to this
`Coordinates`	`sub(Coordinates c)`
`Coordinates`	`subC(Coordinates c)`
`java.lang.String`	`toString()`
`java.lang.String`	`toStringSpaceDelimited()`
`Coordinates`	`unit()`
`Coordinates`	`unitC()`

Methods inherited from class java.lang.Object
clone, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

x
```
public double x
```

y
```
public double y
```

z
```
public double z
```

Constructor Detail

Coordinates
```
public Coordinates()
```

Coordinates
```
public Coordinates(Coordinates c)
```

Coordinates

public Coordinates(double x,
                   double y,
                   double z)

Method Detail

set
```
public Coordinates set(Coordinates c)
```
Copies x,y,z from c to this

Parameters:

c -

Returns:

this after copying c

set

public void set(double x,
                double y,
                double z)

getLength
```
public double getLength()
```

dist
```
public final double dist()
```

distSq
```
public final double distSq()
```

distanceSquared

public final double distanceSquared(Coordinates c)

distSquareTo

public final double distSquareTo(Coordinates c)

distance

public final double distance(Coordinates c)

dot

public final double dot(Coordinates c)

cross

public final Coordinates cross(Coordinates c)

getAngle
```
public final double getAngle(Coordinates c)
```
Gets the angle formed between the 2 vectors ([0,PI])

Parameters:

c -

Returns:

angle in radian

getAngleXY
```
public double getAngleXY(Coordinates c)
```
Calculates the angle of the line from this location to c projected into the x/y plane. With Y facing upwards and X right, if the line points in Y direction, ten angle is 0.0 increasing in clockwise direction.

Parameters:

c -

Returns:

-PI < angle < PI

getDihedral

public final double getDihedral(Coordinates c2,
                                Coordinates c3,
                                Coordinates c4)

subC

public final Coordinates subC(Coordinates c)

addC

public final Coordinates addC(Coordinates c)

scaleC

public final Coordinates scaleC(double scale)

sub

public final Coordinates sub(Coordinates c)

Parameters:: c -
Returns:: this after subtracting c

add

public final Coordinates add(Coordinates c)

Parameters:: c -
Returns:: this after subtracting c

add

public void add(double dx,
                double dy,
                double dz)

scale

public final Coordinates scale(double scale)

Parameters:: scale -
Returns:: this after scaling this

negate
```
public final void negate()
```

rotate
```
public Coordinates rotate(double[][] m)
```
Parameters:

m -

Returns:

this after rotating it with rotation matrix m

rotateC
```
public Coordinates rotateC(double[][] m)
```
Parameters:

m -

Returns:

new Coordinates created from this point rotated by rotation matrix m

rotate

public final Coordinates rotate(Coordinates normal,
                                double theta)

unitC
```
public final Coordinates unitC()
```
Returns:

new Coordinates with a copy of this scaled to length=1.0

unit
```
public final Coordinates unit()
```
Returns:

this after scaling it to length=1.0

center
```
public Coordinates center(Coordinates c)
```
Calculates the center point between this and c and sets this to the center point.

Parameters:

c -

Returns:

this after updating it to the center position

center

public void center(Coordinates c1,
                   Coordinates c2)

Updates this to contains the center between c1 and c2.

Parameters:: c1 -; c2 -

between
```
public Coordinates between(Coordinates c1,
                           Coordinates c2,
                           double f)
```
Updates this to contain a point on the straight line through c1 and c2.

Parameters:

c1 -

c2 -

f - location on line 0.0 -> c1, 1.0 -> c2

Returns:

this after updating to be a point on the line

insideBounds

public final boolean insideBounds(Coordinates[] bounds)

toString
```
public final java.lang.String toString()
```
Overrides:

toString in class java.lang.Object

toStringSpaceDelimited

public final java.lang.String toStringSpaceDelimited()

equals

public final boolean equals(java.lang.Object o)

Overrides:: equals in class java.lang.Object

isNaN
```
public final boolean isNaN()
```

min

public final Coordinates min(Coordinates c)

max

public final Coordinates max(Coordinates c)

cosAngle

public double cosAngle(Coordinates c)

min

public static final Coordinates min(Coordinates[] c)

max

public static final Coordinates max(Coordinates[] c)

createBarycenter

public static final Coordinates createBarycenter(Coordinates... coords)

getMirror

public static final Coordinates getMirror(Coordinates p,
                                          Coordinates c1,
                                          Coordinates c2,
                                          Coordinates c3)

Get the mirror image of p through the plane defined by c1, c2, c3

Parameters:: p -; c1 -; c2 -; c3 -
Returns:

getDihedral
```
public static final double getDihedral(Coordinates c1,
                                       Coordinates c2,
                                       Coordinates c3,
                                       Coordinates c4)
```
Calculates a signed torsion as an exterior spherical angle from a valid sequence of 4 points in space. Looking along the line from c2 to c3, the torsion angle is 0.0, if the projection of c2->c1 and c3->c4 point in the same direction. If the projection of vector c2-c1 is rotated in clockwise direction, the angle increases, i.e. has a positive value. http://en.wikipedia.org/wiki/Dihedral_angle

Parameters:

c1 -

c2 -

c3 -

c4 -

Returns:

torsion in the range: -pi <= torsion <= pi

compareTo
```
public int compareTo(Coordinates o)
```
Specified by:

compareTo in interface java.lang.Comparable<Coordinates>

random

public static final Coordinates random()

getRmsd

public static double getRmsd(Coordinates[] c1,
                             Coordinates[] c2)

getRmsd

public static double getRmsd(Coordinates[] c1,
                             Coordinates[] c2,
                             int l)

Constructor	Description
`Coordinates()`
`Coordinates(double x, double y, double z)`
`Coordinates(Coordinates c)`

Class Coordinates

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

x

y

z

Constructor Detail

Coordinates

Coordinates

Coordinates

Method Detail

set

set

getLength

dist

distSq

distanceSquared

distSquareTo

distance

dot

cross

getAngle

getAngleXY

getDihedral

subC

addC

scaleC

sub

add

add

scale

negate

rotate

rotateC

rotate

unitC

unit

center

center

between

insideBounds

toString

toStringSpaceDelimited

equals

isNaN

min

max

cosAngle

min

max

createBarycenter

getMirror

getDihedral

compareTo

random

getRmsd

getRmsd