org.biojava.bio.structure
Class Calc

java.lang.Object
  org.biojava.bio.structure.Calc

public class Calc
extends 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

Constructor Summary

Calc()

Method Summary

static Atom	add(Atom a, Atom b) add two atoms ( a + b).
static double	amount(Atom a) amount.
static double	angle(Atom a, Atom b) angle.
static Atom[]	centerAtoms(Atom[] atomSet) center the atoms at the Centroid
static Atom	createVirtualCBAtom(AminoAcid amino) creates a virtual C-beta atom.
static Atom	getCenterVector(Atom[] atomSet)
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	getPhi(AminoAcid a, AminoAcid b) phi angle.
static double	getPsi(AminoAcid a, AminoAcid b) psi angle.
static boolean	isConnected(AminoAcid a, AminoAcid b) test if two amino acids are connected, i.e.
static void	plus(Structure s, Matrix matrix) calculate structure + Matrix coodinates ...
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 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) skalar product.
static Atom	substract(Atom a, Atom b) substract 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 .

Methods inherited from class java.lang.Object

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

Constructor Detail

Calc

public Calc()

Method Detail

getDistance

public static 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 - ...

add

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

substract two atoms ( a - b).

Parameters:

a - an Atom object

b - an Atom object

Returns:

an Atom object

Throws:

StructureException - ...

vectorProduct

public static Atom vectorProduct(Atom a,
                                 Atom b)

Vector product .

Parameters:

a - an Atom object

b - an Atom object

Returns:

an Atom object

skalarProduct

public static double skalarProduct(Atom a,
                                   Atom b)

skalar product.

Parameters:

a - an Atom object

b - an Atom object

Returns:

a double

amount

public static double amount(Atom a)

amount.

Parameters:

a - an Atom object

Returns:

a double

angle

public static double angle(Atom a,
                           Atom b)

angle.

Parameters:

a - an Atom object

b - an Atom object

Returns:

a double

unitVector

public static Atom unitVector(Atom a)

return the unit vector of vector a .

Parameters:

a - an Atom object

Returns:

an Atom object

torsionAngle

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

rotate a single atom aroud a rotation matrix. matrix must be a 3x3 matrix.

Parameters:

atom -

m -

rotate

public static 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 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 void rotate(Atom atom,
                          Matrix m)

rotate an atom around a Matrix object

Parameters:

atom -

m -

rotate

public static void rotate(Group group,
                          Matrix m)

rotate a group object

Parameters:

group - a group to be rotated

m - a Matrix object representing the translation matrix

rotate

public static void rotate(Structure structure,
                          Matrix m)

rotate a structure object

Parameters:

structure -

m -

plus

public static void plus(Structure s,
                        Matrix matrix)

calculate structure + Matrix coodinates ...

Parameters:

s -

matrix -

shift

public static 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 void shift(Atom a,
                         Atom b)

shift a vector

Parameters:

a - vector a

b - vector b

shift

public static 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 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

getCenterVector

public static Atom getCenterVector(Atom[] atomSet)

centerAtoms

public static 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

createVirtualCBAtom

public static 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 -

Returns:

a "virtual" CB atom

Throws:

StructureException