CrystalCell (biojava 5.0.0 API)

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

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

All Methods Instance Methods Concrete Methods
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

Class CrystalCell

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

MIN_VALID_CELL_SIZE

Constructor Detail

CrystalCell

CrystalCell

Method Detail

getA

setA

getB

setB

getC

setC

getAlpha

setAlpha

getBeta

setBeta

getGamma

setGamma

getVolume

getCellIndices

transfToOriginCell

transfToOriginCell

transfToOriginCellOrthonormal

transfToOriginCellCrystal

transfToOrthonormal

transfToOrthonormal

transfToCrystal

transfToCrystal

getMTranspose

getMaxDimension

checkScaleMatrixConsistency

checkScaleMatrix

isCellReasonable

toString