Package org.biojava.nbio.structure.xtal

Class CrystalCell

java.lang.Object
org.biojava.nbio.structure.xtal.CrystalCell
All Implemented Interfaces:
Serializable
public class CrystalCell extends Object implements Serializable
A crystal cell's parameters.
Author:
duarte_j
See Also:

  • Field Summary

    Fields
    Modifier and Type
    Field
    Description
    static final double
    MIN_VALID_CELL_SIZE
     

  • Constructor Summary

    Constructors
    Constructor
    Description
    CrystalCell()
     
    CrystalCell(double a, double b, double c, double alpha, double beta, double gamma)
     

  • Method Summary

    Modifier and Type
    Method
    Description
    boolean
    checkScaleMatrix(javax.vecmath.Matrix4d scaleMatrix)
    Given a scale matrix parsed from a PDB entry (SCALE1,2,3 records), compares it to our calculated Mtranspose matrix to see if they coincide and returns true if they do.
    boolean
    checkScaleMatrixConsistency(javax.vecmath.Matrix4d scaleMatrix)
    Given a scale matrix parsed from the PDB entry (SCALE1,2,3 records), checks that the matrix is a consistent scale matrix by comparing the cell volume to the inverse of the scale matrix determinant (tolerance of 1/100).
    double
    getA()
     
    double
    getAlpha()
     
    double
    getB()
     
    double
    getBeta()
     
    double
    getC()
     
    javax.vecmath.Point3i
    getCellIndices(javax.vecmath.Tuple3d pt)
    Get the index of a unit cell to which the query point belongs.
    double
    getGamma()
     
    double
    getMaxDimension()
    Gets the maximum dimension of the unit cell.
    javax.vecmath.Matrix3d
    getMTranspose()
     
    double
    getVolume()
    Returns the volume of this unit cell.
    boolean
    isCellReasonable()
    Checks whether the dimensions of this crystal cell are reasonable for protein crystallography: if all 3 dimensions are below 10.0 the cell is considered unrealistic and false returned
    void
    setA(double a)
     
    void
    setAlpha(double alpha)
     
    void
    setB(double b)
     
    void
    setBeta(double beta)
     
    void
    setC(double c)
     
    void
    setGamma(double gamma)
     
    String
    toString()
     
    javax.vecmath.Matrix4d
    transfToCrystal(javax.vecmath.Matrix4d m)
    Transform given Matrix4d in orthonormal basis to the crystal basis using the PDB axes convention (NCODE=1)
    void
    transfToCrystal(javax.vecmath.Tuple3d v)
    Transforms the given orthonormal basis coordinates into crystal coordinates.
    void
    transfToOriginCell(javax.vecmath.Tuple3d pt)
    Converts the coordinates in pt so that they occur within the (0,0,0) unit cell
    void
    transfToOriginCell(javax.vecmath.Tuple3d[] points, javax.vecmath.Tuple3d reference)
    Converts a set of points so that the reference point falls in the unit cell.
    javax.vecmath.Matrix4d[]
    transfToOriginCellCrystal(javax.vecmath.Matrix4d[] ops, javax.vecmath.Tuple3d reference)
     
    javax.vecmath.Matrix4d[]
    transfToOriginCellOrthonormal(javax.vecmath.Matrix4d[] ops, javax.vecmath.Tuple3d reference)
     
    javax.vecmath.Matrix4d
    transfToOrthonormal(javax.vecmath.Matrix4d m)
    Transform given Matrix4d in crystal basis to the orthonormal basis using the PDB axes convention (NCODE=1)
    void
    transfToOrthonormal(javax.vecmath.Tuple3d v)
    Transforms the given crystal basis coordinates into orthonormal coordinates.

    Methods inherited from class java.lang.Object

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

  • Field Details

  • Constructor Details

    • CrystalCell

      public CrystalCell()

    • CrystalCell

      public CrystalCell(double a, double b, double c, double alpha, double beta, double gamma)

  • Method Details

    • getA

      public double getA()

    • setA

      public void setA(double a)

    • getB

      public double getB()

    • setB

      public void setB(double b)

    • getC

      public double getC()

    • setC

      public void setC(double c)

    • getAlpha

      public double getAlpha()

    • setAlpha

      public void setAlpha(double alpha)

    • getBeta

      public double getBeta()

    • setBeta

      public void setBeta(double beta)

    • getGamma

      public double getGamma()

    • setGamma

      public void setGamma(double gamma)

    • getVolume

      public double getVolume()
      Returns the volume of this unit cell. See http://en.wikipedia.org/wiki/Parallelepiped
      Returns:

    • getCellIndices

      public javax.vecmath.Point3i getCellIndices(javax.vecmath.Tuple3d pt)
      Get the index of a unit cell to which the query point belongs.

      For instance, all points in the unit cell at the origin will return (0,0,0); Points in the unit cell one unit further along the `a` axis will return (1,0,0), etc.

      Parameters:
      pt - Input point (in orthonormal coordinates)
      Returns:
      A new point with the three indices of the cell containing pt

    • transfToOriginCell

      public void transfToOriginCell(javax.vecmath.Tuple3d pt)
      Converts the coordinates in pt so that they occur within the (0,0,0) unit cell
      Parameters:
      pt -

    • transfToOriginCell

      public void transfToOriginCell(javax.vecmath.Tuple3d[] points, javax.vecmath.Tuple3d reference)
      Converts a set of points so that the reference point falls in the unit cell. This is useful to transform a whole chain at once, allowing some of the atoms to be outside the unit cell, but forcing the centroid to be within it.
      Parameters:
      points - A set of points to transform (in orthonormal coordinates)
      reference - The reference point, which is unmodified but which would be in the unit cell were it to have been transformed. It is safe to use a member of the points array here.

    • transfToOriginCellOrthonormal

      public javax.vecmath.Matrix4d[] transfToOriginCellOrthonormal(javax.vecmath.Matrix4d[] ops, javax.vecmath.Tuple3d reference)
      Parameters:
      ops - Set of operations in orthonormal coordinates
      reference - Reference point, which should be in the unit cell after each operation (also in orthonormal coordinates)
      Returns:
      A set of orthonormal operators with equivalent rotation to the inputs, but with translation such that the reference point would fall within the unit cell

    • transfToOriginCellCrystal

      public javax.vecmath.Matrix4d[] transfToOriginCellCrystal(javax.vecmath.Matrix4d[] ops, javax.vecmath.Tuple3d reference)
      Parameters:
      ops - Set of operations in crystal coordinates
      reference - Reference point, which should be in the unit cell after each operation (also in crystal coordinates)
      Returns:
      A set of crystal operators with equivalent rotation to the inputs, but with translation such that the reference point would fall within the unit cell

    • transfToOrthonormal

      public javax.vecmath.Matrix4d transfToOrthonormal(javax.vecmath.Matrix4d m)
      Transform given Matrix4d in crystal basis to the orthonormal basis using the PDB axes convention (NCODE=1)
      Parameters:
      m -
      Returns:

    • transfToOrthonormal

      public void transfToOrthonormal(javax.vecmath.Tuple3d v)
      Transforms the given crystal basis coordinates into orthonormal coordinates. e.g. transfToOrthonormal(new Point3d(1,1,1)) returns the orthonormal coordinates of the vertex of the unit cell. See Giacovazzo section 2.E, eq. 2.E.1 (or any linear algebra manual)
      Parameters:
      v -

    • transfToCrystal

      public javax.vecmath.Matrix4d transfToCrystal(javax.vecmath.Matrix4d m)
      Transform given Matrix4d in orthonormal basis to the crystal basis using the PDB axes convention (NCODE=1)
      Parameters:
      m -
      Returns:

    • transfToCrystal

      public void transfToCrystal(javax.vecmath.Tuple3d v)
      Transforms the given orthonormal basis coordinates into crystal coordinates. See Giacovazzo eq 2.20 (or any linear algebra manual)
      Parameters:
      v -

    • getMTranspose

      public javax.vecmath.Matrix3d getMTranspose()

    • getMaxDimension

      public double getMaxDimension()
      Gets the maximum dimension of the unit cell.
      Returns:

    • checkScaleMatrixConsistency

      public boolean checkScaleMatrixConsistency(javax.vecmath.Matrix4d scaleMatrix)
      Given a scale matrix parsed from the PDB entry (SCALE1,2,3 records), checks that the matrix is a consistent scale matrix by comparing the cell volume to the inverse of the scale matrix determinant (tolerance of 1/100). If they don't match false is returned. See the PDB documentation for the SCALE record. See also last equation of section 2.5 of "Fundamentals of Crystallography" C. Giacovazzo
      Parameters:
      scaleMatrix -
      Returns:

    • checkScaleMatrix

      public boolean checkScaleMatrix(javax.vecmath.Matrix4d scaleMatrix)
      Given a scale matrix parsed from a PDB entry (SCALE1,2,3 records), compares it to our calculated Mtranspose matrix to see if they coincide and returns true if they do. If they don't that means that the PDB entry is not in the standard orthogonalisation (NCODE=1 in ccp4). In 2011's remediation only 148 PDB entries were found not to be in a non-standard orthogonalisation. See: http://www.wwpdb.org/documentation/2011remediation_overview-061711.pdf For normal cases the scale matrix is diagonal without a translation component. Additionally the translation component of the SCALE matrix is also checked to make sure it is (0,0,0), if not false is return
      Parameters:
      scaleMatrix -
      Returns:

    • isCellReasonable

      public boolean isCellReasonable()
      Checks whether the dimensions of this crystal cell are reasonable for protein crystallography: if all 3 dimensions are below 10.0 the cell is considered unrealistic and false returned
      Returns:

    • toString

      public String toString()
      Overrides:
      toString in class Object