Class CrystalCell

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