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:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
static double	MIN_VALID_CELL_SIZE

Constructor Summary

Constructors

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

Method Summary

Modifier and Type	Method and 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 Detail

MIN_VALID_CELL_SIZE

public static final double MIN_VALID_CELL_SIZE

See Also:

Constant Field Values

Constructor Detail

CrystalCell

public CrystalCell()

CrystalCell

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

Method Detail

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