Package org.biojava.nbio.structure

Class Calc

java.lang.Object
org.biojava.nbio.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

    Constructors
    Constructor
    Description
    Calc()
     

  • Method Summary

    Modifier and Type
    Method
    Description
    static final Atom
    add(Atom a, Atom b)
    add two atoms ( a + b).
    static final double
    amount(Atom a)
    Gets the length of the vector (2-norm)
    static final double
    angle(Atom a, Atom b)
    Gets the angle between two vectors
    static javax.vecmath.Point3d[]
    atomsToPoints(Atom[] atoms)
    Convert an array of atoms into an array of vecmath points
    static double
    calcRotationAngleInDegrees(Atom centerPt, Atom targetPt)
    Calculates the angle from centerPt to targetPt in degrees.
    static final Atom[]
    centerAtoms(Atom[] atomSet)
    Center the atoms at the Centroid.
    static final Atom[]
    centerAtoms(Atom[] atomSet, Atom centroid)
    Center the atoms at the Centroid, if the centroid is already know.
    static Atom
    centerOfMass(Atom[] points)
     
    static final Atom
    createVirtualCBAtom(AminoAcid amino)
    creates a virtual C-beta atom.
    static final Atom
    getCenterVector(Atom[] atomSet)
    Returns the Vector that needs to be applied to shift a set of atoms to the Centroid.
    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
    static final Atom
    getCentroid(Atom[] atomSet)
    Returns the center of mass of the set of atoms.
    static final 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 final double
    getPhi(AminoAcid a, AminoAcid b)
    Calculate the phi angle.
    static final double
    getPsi(AminoAcid a, AminoAcid b)
    Calculate the psi angle.
    static Matrix
    getRotationMatrix(javax.vecmath.Matrix4d transform)
    Convert Vecmath transformation into a JAMA rotation matrix.
    static javax.vecmath.Matrix4d
    getTransformation(Matrix rot, Atom trans)
    Convert JAMA rotation and translation to a Vecmath transformation matrix.
    static javax.vecmath.Matrix4d
    getTransformation(Matrix rot, Matrix trans)
    Convert JAMA rotation and translation to a Vecmath transformation matrix.
    static Atom
    getTranslationVector(javax.vecmath.Matrix4d transform)
    Extract the translational vector of a Vecmath transformation.
    static final double[]
    getXYZEuler(Matrix m)
    Convert a rotation Matrix to Euler angles.
    static final double[]
    getZYZEuler(Matrix m)
    Gets euler angles for a matrix given in ZYZ convention.
    static final Atom
    invert(Atom a)
     
    static final boolean
    isConnected(AminoAcid a, AminoAcid b)
    Test if two amino acids are connected, i.e.
    static void
    main(String[] args)
     
    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.
    static final void
    plus(Structure s, Matrix matrix)
    calculate structure + Matrix coodinates ...
    static void
    rotate(Atom[] ca, Matrix matrix)
     
    static final void
    rotate(Atom atom, double[][] m)
    Rotate a single Atom aroud a rotation matrix.
    static final void
    rotate(Atom atom, Matrix m)
    Rotate an Atom around a Matrix object.
    static final void
    rotate(Group group, double[][] rotationmatrix)
    Rotate a Group.
    static final void
    rotate(Group group, Matrix m)
    Rotate a group object.
    static final void
    rotate(Structure structure, double[][] rotationmatrix)
    Rotate a structure.
    static final void
    rotate(Structure structure, Matrix m)
    Rotate a structure object.
    static final 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[] ca, Atom b)
    Shift an array of atoms at once.
    static final void
    shift(Atom a, Atom b)
    Shift a vector.
    static final void
    shift(Group group, Atom a)
    Shift a Group with a vector.
    static final void
    shift(Structure structure, Atom a)
    shift a structure with a vector.
    static final Atom
    subtract(Atom a, Atom b)
    subtract two atoms ( a - b).
    static final double
    torsionAngle(Atom a, Atom b, Atom c, Atom d)
    Calculate the torsion angle, i.e.
    static void
    transform(Atom[] ca, javax.vecmath.Matrix4d t)
    Transform an array of atoms at once.
    static final void
    transform(Atom atom, javax.vecmath.Matrix4d m)
    Transforms an atom object, given a Matrix4d (i.e.
    static final void
    transform(Chain chain, javax.vecmath.Matrix4d m)
    Transforms a chain object, given a Matrix4d (i.e.
    static final void
    transform(Group group, javax.vecmath.Matrix4d m)
    Transforms a group object, given a Matrix4d (i.e.
    static final void
    transform(Structure structure, javax.vecmath.Matrix4d m)
    Transforms a structure object, given a Matrix4d (i.e.
    static final void
    translate(Atom atom, javax.vecmath.Vector3d v)
    Translates an atom object, given a Vector3d (i.e.
    static final void
    translate(Chain chain, javax.vecmath.Vector3d v)
    Translates a chain object, given a Vector3d (i.e.
    static final void
    translate(Group group, javax.vecmath.Vector3d v)
    Translates a group object, given a Vector3d (i.e.
    static final void
    translate(Structure structure, javax.vecmath.Vector3d v)
    Translates a Structure object, given a Vector3d (i.e.
    static final Atom
    unitVector(Atom a)
    Returns the unit vector of vector a .
    static final 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

  • Constructor Details

    • Calc

      public Calc()

  • Method Details

    • getDistance

      public static final double getDistance(Atom a, Atom b)
      calculate distance between two atoms.
      Parameters:
      a - an Atom object
      b - an Atom object
      Returns:
      a double

    • getDistanceFast

      public static double getDistanceFast(Atom a, Atom b)
      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

    • invert

      public static final Atom invert(Atom a)

    • 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

    • 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

    • 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

    • 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)
      Gets the angle between two vectors
      Parameters:
      a - an Atom object
      b - an Atom object
      Returns:
      Angle between a and b in degrees, in range [0,180]. If either vector has length 0 then angle is not defined and NaN is returned

    • unitVector

      public static final Atom unitVector(Atom a)
      Returns 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)
      Calculate the torsion angle, i.e. the angle between the normal vectors of the two plains a-b-c and b-c-d. See http://en.wikipedia.org/wiki/Dihedral_angle
      Parameters:
      a - an Atom object
      b - an Atom object
      c - an Atom object
      d - an Atom object
      Returns:
      the torsion angle in degrees, in range +-[0,180]. If either first 3 or last 3 atoms are colinear then torsion angle is not defined and NaN is returned

    • getPhi

      public static final double getPhi(AminoAcid a, AminoAcid b) throws StructureException
      Calculate the phi angle.
      Parameters:
      a - an AminoAcid object
      b - an AminoAcid object
      Returns:
      a double
      Throws:
      StructureException - if aminoacids not connected or if any of the 4 needed atoms missing

    • getPsi

      public static final double getPsi(AminoAcid a, AminoAcid b) throws StructureException
      Calculate the psi angle.
      Parameters:
      a - an AminoAcid object
      b - an AminoAcid object
      Returns:
      a double
      Throws:
      StructureException - if aminoacids not connected or if any of the 4 needed atoms missing

    • isConnected

      public static final boolean isConnected(AminoAcid a, AminoAcid b)
      Test if two amino acids are connected, i.e. if the distance from C to N < 2.5 Angstrom. If one of the AminoAcids has an atom missing, returns false.
      Parameters:
      a - an AminoAcid object
      b - an AminoAcid object
      Returns:
      true if ...

    • rotate

      public static final void rotate(Atom atom, double[][] m)
      Rotate a single Atom aroud a rotation matrix. The rotation Matrix must be a pre-multiplication 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. The rotation Matrix must be a pre-multiplication Matrix.
      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 Group. The rotation Matrix must be a pre-multiplication Matrix.
      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. The rotation Matrix must be a pre-multiplication Matrix.
      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. The rotation Matrix must be a pre-multiplication Matrix.
      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. The rotation Matrix must be a pre-multiplication Matrix.
      Parameters:
      structure - the structure to be rotated
      m - rotation matrix to be applied

    • transform

      public static void transform(Atom[] ca, javax.vecmath.Matrix4d t)
      Transform an array of atoms at once. The transformation Matrix must be a post-multiplication Matrix.
      Parameters:
      ca - array of Atoms to shift
      t - transformation Matrix4d

    • transform

      public static final void transform(Atom atom, javax.vecmath.Matrix4d m)
      Transforms an atom object, given a Matrix4d (i.e. the vecmath library double-precision 4x4 rotation+translation matrix). The transformation Matrix must be a post-multiplication Matrix.
      Parameters:
      atom -
      m -

    • transform

      public static final void transform(Group group, javax.vecmath.Matrix4d m)
      Transforms a group object, given a Matrix4d (i.e. the vecmath library double-precision 4x4 rotation+translation matrix). The transformation Matrix must be a post-multiplication Matrix.
      Parameters:
      group -
      m -

    • transform

      public static final void transform(Structure structure, javax.vecmath.Matrix4d m)
      Transforms a structure object, given a Matrix4d (i.e. the vecmath library double-precision 4x4 rotation+translation matrix). The transformation Matrix must be a post-multiplication Matrix.
      Parameters:
      structure -
      m -

    • transform

      public static final void transform(Chain chain, javax.vecmath.Matrix4d m)
      Transforms a chain object, given a Matrix4d (i.e. the vecmath library double-precision 4x4 rotation+translation matrix). The transformation Matrix must be a post-multiplication Matrix.
      Parameters:
      chain -
      m -

    • translate

      public static final void translate(Atom atom, javax.vecmath.Vector3d v)
      Translates an atom object, given a Vector3d (i.e. the vecmath library double-precision 3-d vector)
      Parameters:
      atom -
      v -

    • translate

      public static final void translate(Group group, javax.vecmath.Vector3d v)
      Translates a group object, given a Vector3d (i.e. the vecmath library double-precision 3-d vector)
      Parameters:
      group -
      v -

    • translate

      public static final void translate(Chain chain, javax.vecmath.Vector3d v)
      Translates a chain object, given a Vector3d (i.e. the vecmath library double-precision 3-d vector)
      Parameters:
      chain -
      v -

    • translate

      public static final void translate(Structure structure, javax.vecmath.Vector3d v)
      Translates a Structure object, given a Vector3d (i.e. the vecmath library double-precision 3-d vector)
      Parameters:
      structure -
      v -

    • 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)
      Gets 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(String[] args)

    • rotate

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

    • shift

      public static void shift(Atom[] ca, Atom b)
      Shift an array of atoms at once.
      Parameters:
      ca - array of Atoms to shift
      b - reference Atom vector

    • getTransformation

      public static javax.vecmath.Matrix4d getTransformation(Matrix rot, Matrix trans)
      Convert JAMA rotation and translation to a Vecmath transformation matrix. Because the JAMA matrix is a pre-multiplication matrix and the Vecmath matrix is a post-multiplication one, the rotation matrix is transposed to ensure that the transformation they produce is the same.
      Parameters:
      rot - 3x3 Rotation matrix
      trans - 3x1 Translation matrix
      Returns:
      4x4 transformation matrix

    • getTransformation

      public static javax.vecmath.Matrix4d getTransformation(Matrix rot, Atom trans)
      Convert JAMA rotation and translation to a Vecmath transformation matrix. Because the JAMA matrix is a pre-multiplication matrix and the Vecmath matrix is a post-multiplication one, the rotation matrix is transposed to ensure that the transformation they produce is the same.
      Parameters:
      rot - 3x3 Rotation matrix
      trans - 3x1 translation vector in Atom coordinates
      Returns:
      4x4 transformation matrix

    • getRotationMatrix

      public static Matrix getRotationMatrix(javax.vecmath.Matrix4d transform)
      Convert Vecmath transformation into a JAMA rotation matrix. Because the JAMA matrix is a pre-multiplication matrix and the Vecmath matrix is a post-multiplication one, the rotation matrix is transposed to ensure that the transformation they produce is the same.
      Parameters:
      transform - Matrix4d with transposed rotation matrix
      Returns:

    • getTranslationVector

      public static Atom getTranslationVector(javax.vecmath.Matrix4d transform)
      Extract the translational vector of a Vecmath transformation.
      Parameters:
      transform - Matrix4d
      Returns:
      Atom shift vector

    • atomsToPoints

      public static javax.vecmath.Point3d[] atomsToPoints(Atom[] atoms)
      Convert an array of atoms into an array of vecmath points
      Parameters:
      atoms - list of atoms
      Returns:
      list of Point3ds storing the x,y,z coordinates of each atom