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. If the structure part of biojava becomes more powerful it could be moved out of the core - biojava and the dependency on java3d could be introduced.

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 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	rotate(Structure structure, double[][] m) rotate a structure
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

Throws:

StructureException

add

public static Atom add(Atom a,
                       Atom b)

add two atoms ( a + b)

substract

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

substract two atoms ( a - b)

Throws:

StructureException

vectorProduct

public static Atom vectorProduct(Atom a,
                                 Atom b)

Vector product

skalarProduct

public static double skalarProduct(Atom a,
                                   Atom b)

skalar product

amount

public static double amount(Atom a)

amount

angle

public static double angle(Atom a,
                           Atom b)

angle

unitVector

public static Atom unitVector(Atom a)

return the unit vector of vector a

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

Throws:

StructureException

getPhi

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

phi angle

Throws:

StructureException

getPsi

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

psi angle

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

Throws:

StructureException

rotate

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

rotate a structure

Throws:

StructureException

shift

public static void shift(Structure structure,
                         Atom a)

shift a structure with a vector