org.biojava.bio.structure

Class Calc

java.lang.Object

org.biojava.bio.structure.Calc

public class Calc
extends java.lang.Object

utility operations on Atoms, AminoAcids, etc.

Currently the coordinates of an Atom are stored as an array of size 3 (double[3]). It would be more powerful to use Point3D from javax.vecmath. but unfortunately this is not a part of standard java installations, since it comes with java3d . So to keep things simple at the moment biojava does not depend on java3d.

Since:

1.4

Version:

%I% %G%

Author:

Andreas Prlic

Field Summary

Fields

Modifier and Type	Field and Description
static float	degreesPerRadian Degrees per radian.
static float	radiansPerDegree Radians per degree.

Constructor Summary

Constructors

Constructor and Description
Calc()

Method Summary

Methods

Modifier and Type	Method and Description
static Atom	add(Atom a, Atom b) add two atoms ( a + b).
static double	amount(Atom a) Gets the length of the vector (2-norm)
static double	angle(Atom a, Atom b) Get the angle between two vectors
static double	calcRotationAngleInDegrees(Atom centerPt, Atom targetPt) Calculates the angle from centerPt to targetPt in degrees.
static Atom[]	centerAtoms(Atom[] atomSet) Center the atoms at the Centroid.
static Atom[]	centerAtoms(Atom[] atomSet, Atom centroid) Center the atoms at the Centroid, if the centroid is already know.
static Atom	centerOfMass(Atom[] points)
static Atom	createVirtualCBAtom(AminoAcid amino) creates a virtual C-beta atom.
static Atom	getCenterVector(Atom[] atomSet) Returns the Vector that needs to be applied to shift a set of atoms to the Centroid.
static Atom	getCenterVector(Atom[] atomSet, Atom centroid) Returns the Vector that needs to be applied to shift a set of atoms to the Centroid, if the centroid is already known
static Atom	getCentroid(Atom[] atomSet) Returns the center of mass of the set of atoms.
static double	getDistance(Atom a, Atom b) calculate distance between two atoms.
static double	getDistanceFast(Atom a, Atom b) Will calculate the *square* of distances between two atoms.
static double	getPhi(AminoAcid a, AminoAcid b) phi angle.
static double	getPsi(AminoAcid a, AminoAcid b) psi angle.
static double[]	getXYZEuler(Matrix m) Convert a rotation Matrix to Euler angles.
static double[]	getZYZEuler(Matrix m) Gget euler angles for a matrix given in ZYZ convention.
static Atom	invert(Atom a)
static boolean	isConnected(AminoAcid a, AminoAcid b) test if two amino acids are connected, i.e.
static void	main(java.lang.String[] args)
static Matrix	matrixFromEuler(double heading, double attitude, double bank) This conversion uses NASA standard aeroplane conventions as described on page: http://www.euclideanspace.com/maths/geometry/rotations/euler/index.htm Coordinate System: right hand Positive angle: right hand Order of euler angles: heading first, then attitude, then bank.
static void	plus(Structure s, Matrix matrix) calculate structure + Matrix coodinates ...
static void	rotate(Atom[] ca, Matrix matrix)
static void	rotate(Atom atom, double[][] m) rotate a single atom aroud a rotation matrix.
static void	rotate(Atom atom, Matrix m) Rotate an atom around a Matrix object.
static void	rotate(Group group, double[][] rotationmatrix) rotate a structure .
static void	rotate(Group group, Matrix m) Rotate a group object.
static void	rotate(Structure structure, double[][] rotationmatrix) Rotate a structure.
static void	rotate(Structure structure, Matrix m) Rotate a structure object.
static double	scalarProduct(Atom a, Atom b) Scalar product (dot product).
static Atom	scale(Atom a, double s) Multiply elements of a by s
static Atom	scaleAdd(double s, Atom x, Atom b) Perform linear transformation s*X+B, and store the result in b
static Atom	scaleEquals(Atom a, double s) Multiply elements of a by s (in place)
static void	shift(Atom a, Atom b) Shift a vector.
static void	shift(Group group, Atom a) Shift a Group with a vector.
static void	shift(Structure structure, Atom a) shift a structure with a vector.
static double	skalarProduct(Atom a, Atom b) Deprecated. use scalarProduct(Atom, Atom) instead.
static Atom	substract(Atom a, Atom b) Deprecated. use subtract instead.
static Atom	subtract(Atom a, Atom b) subtract two atoms ( a - b).
static double	torsionAngle(Atom a, Atom b, Atom c, Atom d) torsion angle = angle between the normal vectors of the two plains a-b-c and b-c-d.
static Atom	unitVector(Atom a) return the unit vector of vector a .
static Atom	vectorProduct(Atom a, Atom b) Vector product (cross product).

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

radiansPerDegree

public static final float radiansPerDegree

Radians per degree.

See Also:

Constant Field Values

degreesPerRadian

public static final float degreesPerRadian

Degrees per radian.

See Also:

Constant Field Values

Constructor Detail

Calc

public Calc()

Method Detail

getDistance

public static final double getDistance(Atom a,
                 Atom b)
                                throws StructureException

calculate distance between two atoms.

Parameters:

a - an Atom object

b - an Atom object

Returns:

a double

Throws:

StructureException - ...

getDistanceFast

public static double getDistanceFast(Atom a,
                     Atom b)
                              throws StructureException

Will calculate the *square* of distances between two atoms. This will be faster as it will not perform the final square root to get the actual distance. Use this if doing large numbers of distance comparisons - it is marginally faster than getDistance().

Parameters:

a - an Atom object

b - an Atom object

Returns:

a double

Throws:

StructureException - ...

invert

public static final Atom invert(Atom a)
                         throws StructureException

Throws:

StructureException

add

public static final Atom add(Atom a,
       Atom b)

add two atoms ( a + b).

Parameters:

a - an Atom object

b - an Atom object

Returns:

an Atom object

substract

public static final Atom substract(Atom a,
             Atom b)
                            throws StructureException

Deprecated. use subtract instead.

subtract two atoms ( a - b).

Parameters:

a - an Atom object

b - an Atom object

Returns:

an Atom object

Throws:

StructureException - ...

subtract

public static final Atom subtract(Atom a,
            Atom b)

subtract two atoms ( a - b).

Parameters:

a - an Atom object

b - an Atom object

Returns:

n new Atom object representing the difference

Throws:

StructureException - ...

vectorProduct

public static final Atom vectorProduct(Atom a,
                 Atom b)

Vector product (cross product).

Parameters:

a - an Atom object

b - an Atom object

Returns:

an Atom object

skalarProduct

public static final double skalarProduct(Atom a,
                   Atom b)

Deprecated. use scalarProduct(Atom, Atom) instead.

Scalar product (dot product).

Parameters:

a - an Atom object

b - an Atom object

Returns:

a double

scalarProduct

public static final double scalarProduct(Atom a,
                   Atom b)

Scalar product (dot product).

Parameters:

a - an Atom object

b - an Atom object

Returns:

a double

amount

public static final double amount(Atom a)

Gets the length of the vector (2-norm)

Parameters:

a - an Atom object

Returns:

Square root of the sum of the squared elements

angle

public static final double angle(Atom a,
           Atom b)

Get the angle between two vectors

Parameters:

a - an Atom object

b - an Atom object

Returns:

Angle between a and b, in degrees

unitVector

public static final Atom unitVector(Atom a)

return the unit vector of vector a .

Parameters:

a - an Atom object

Returns:

an Atom object

torsionAngle

public static final double torsionAngle(Atom a,
                  Atom b,
                  Atom c,
                  Atom d)
                                 throws StructureException

torsion angle = angle between the normal vectors of the two plains a-b-c and b-c-d.

Parameters:

a - an Atom object

b - an Atom object

c - an Atom object

d - an Atom object

Returns:

a double

Throws:

StructureException - ...

getPhi

public static final double getPhi(AminoAcid a,
            AminoAcid b)
                           throws StructureException

phi angle.

Parameters:

a - an AminoAcid object

b - an AminoAcid object

Returns:

a double

Throws:

StructureException - ...

getPsi

public static final double getPsi(AminoAcid a,
            AminoAcid b)
                           throws StructureException

psi angle.

Parameters:

a - an AminoAcid object

b - an AminoAcid object

Returns:

a double

Throws:

StructureException - ...

isConnected

public static final boolean isConnected(AminoAcid a,
                  AminoAcid b)
                                 throws StructureException

test if two amino acids are connected, i.e. if the distance from C to N < 2,5 Angstrom.

Parameters:

a - an AminoAcid object

b - an AminoAcid object

Returns:

true if ...

Throws:

StructureException - ...

rotate

public static final void rotate(Atom atom,
          double[][] m)

rotate a single atom aroud a rotation matrix. matrix must be a 3x3 matrix. If the matrix is indexed m[row][col], then the matrix will be pre-multiplied (y=atom*M)

Parameters:

atom - atom to be rotated

m - a rotation matrix represented as a double[3][3] array

rotate

public static final void rotate(Structure structure,
          double[][] rotationmatrix)
                         throws StructureException

Rotate a structure.

Parameters:

structure - a Structure object

rotationmatrix - an array (3x3) of double representing the rotation matrix.

Throws:

StructureException - ...

rotate

public static final void rotate(Group group,
          double[][] rotationmatrix)
                         throws StructureException

rotate a structure .

Parameters:

group - a group object

rotationmatrix - an array (3x3) of double representing the rotation matrix.

Throws:

StructureException - ...

rotate

public static final void rotate(Atom atom,
          Matrix m)

Rotate an atom around a Matrix object.

Parameters:

atom - atom to be rotated

m - rotation matrix to be applied to the atom

rotate

public static final void rotate(Group group,
          Matrix m)

Rotate a group object.

Parameters:

group - a group to be rotated

m - a Matrix object representing the rotation matrix

rotate

public static final void rotate(Structure structure,
          Matrix m)

Rotate a structure object.

Parameters:

structure - the structure to be rotated

m - rotation matrix to be applied

plus

public static final void plus(Structure s,
        Matrix matrix)

calculate structure + Matrix coodinates ...

Parameters:

s - the structure to operate on

matrix - a Matrix object

shift

public static final void shift(Structure structure,
         Atom a)

shift a structure with a vector.

Parameters:

structure - a Structure object

a - an Atom object representing a shift vector

shift

public static final void shift(Atom a,
         Atom b)

Shift a vector.

Parameters:

a - vector a

b - vector b

shift

public static final void shift(Group group,
         Atom a)

Shift a Group with a vector.

Parameters:

group - a group object

a - an Atom object representing a shift vector

getCentroid

public static final Atom getCentroid(Atom[] atomSet)

Returns the center of mass of the set of atoms.

Parameters:

atomSet - a set of Atoms

Returns:

an Atom representing the Centroid of the set of atoms

centerOfMass

public static Atom centerOfMass(Atom[] points)

scaleEquals

public static Atom scaleEquals(Atom a,
               double s)

Multiply elements of a by s (in place)

Parameters:

a -

s -

Returns:

the modified a

scale

public static Atom scale(Atom a,
         double s)

Multiply elements of a by s

Parameters:

a -

s -

Returns:

A new Atom with s*a

scaleAdd

public static Atom scaleAdd(double s,
            Atom x,
            Atom b)

Perform linear transformation s*X+B, and store the result in b

Parameters:

s - Amount to scale x

x - Input coordinate

b - Vector to translate (will be modified)

Returns:

b, after modification

getCenterVector

public static final Atom getCenterVector(Atom[] atomSet)

Returns the Vector that needs to be applied to shift a set of atoms to the Centroid.

Parameters:

atomSet - array of Atoms

Returns:

the vector needed to shift the set of atoms to its geometric center

getCenterVector

public static final Atom getCenterVector(Atom[] atomSet,
                   Atom centroid)

Returns the Vector that needs to be applied to shift a set of atoms to the Centroid, if the centroid is already known

Parameters:

atomSet - array of Atoms

Returns:

the vector needed to shift the set of atoms to its geometric center

centerAtoms

public static final Atom[] centerAtoms(Atom[] atomSet)
                                throws StructureException

Center the atoms at the Centroid.

Parameters:

atomSet - a set of Atoms

Returns:

an Atom representing the Centroid of the set of atoms

Throws:

StructureException

centerAtoms

public static final Atom[] centerAtoms(Atom[] atomSet,
                 Atom centroid)
                                throws StructureException

Center the atoms at the Centroid, if the centroid is already know.

Parameters:

atomSet - a set of Atoms

Returns:

an Atom representing the Centroid of the set of atoms

Throws:

StructureException

createVirtualCBAtom

public static final Atom createVirtualCBAtom(AminoAcid amino)
                                      throws StructureException

creates a virtual C-beta atom. this might be needed when working with GLY thanks to Peter Lackner for a python template of this method.

Parameters:

amino - the amino acid for which a "virtual" CB atom should be calculated

Returns:

a "virtual" CB atom

Throws:

StructureException

getZYZEuler

public static final double[] getZYZEuler(Matrix m)

Gget euler angles for a matrix given in ZYZ convention. (as e.g. used by Jmol)

Parameters:

m - the rotation matrix

Returns:

the euler values for a rotation around Z, Y, Z in degrees...

getXYZEuler

public static final double[] getXYZEuler(Matrix m)

Convert a rotation Matrix to Euler angles. This conversion uses conventions as described on page: http://www.euclideanspace.com/maths/geometry/rotations/euler/index.htm Coordinate System: right hand Positive angle: right hand Order of euler angles: heading first, then attitude, then bank

Parameters:

m - the rotation matrix

Returns:

a array of three doubles containing the three euler angles in radians

matrixFromEuler

public static final Matrix matrixFromEuler(double heading,
                     double attitude,
                     double bank)

This conversion uses NASA standard aeroplane conventions as described on page: http://www.euclideanspace.com/maths/geometry/rotations/euler/index.htm Coordinate System: right hand Positive angle: right hand Order of euler angles: heading first, then attitude, then bank. matrix row column ordering: [m00 m01 m02] [m10 m11 m12] [m20 m21 m22]

Parameters:

heading - in radians

attitude - in radians

bank - in radians

Returns:

the rotation matrix

calcRotationAngleInDegrees

public static double calcRotationAngleInDegrees(Atom centerPt,
                                Atom targetPt)

Calculates the angle from centerPt to targetPt in degrees. The return should range from [0,360), rotating CLOCKWISE, 0 and 360 degrees represents NORTH, 90 degrees represents EAST, etc... Assumes all points are in the same coordinate space. If they are not, you will need to call SwingUtilities.convertPointToScreen or equivalent on all arguments before passing them to this function.

Parameters:

centerPt - Point we are rotating around.

targetPt - Point we want to calculate the angle to.

Returns:

angle in degrees. This is the angle from centerPt to targetPt.

main

public static void main(java.lang.String[] args)

rotate

public static void rotate(Atom[] ca,
          Matrix matrix)