Package ffx.crystal

Class NCSCrystal

java.lang.Object

ffx.crystal.Crystal

ffx.crystal.NCSCrystal

public class NCSCrystal
extends Crystal

The NCSCrystal class extends Crystal to support non-crystallographic symmetry (NCS). The NCS operators can be obtained from the BIOMT records of a PDB file, and are permuted with the space group symmetry operators.

Since:

1.0

Author:

Aaron J. Nessler, Michael J. Schnieders

Field Summary

Fields inherited from class ffx.crystal.Crystal

a, A, A00, A01, A02, A10, A11, A12, A20, A21, A22, Ai, Ai00, Ai01, Ai02, Ai10, Ai11, Ai12, Ai20, Ai21, Ai22, alpha, b, beta, c, dVdA, dVdAlpha, dVdB, dVdBeta, dVdC, dVdGamma, G, gamma, interfacialRadiusA, interfacialRadiusB, interfacialRadiusC, scaleB, scaleN, spaceGroup, volume

Method Summary

Modifier and Type	Method	Description
boolean	changeUnitCellParameters(double a, double b, double c, double alpha, double beta, double gamma)	Change the cell parameters for the base unit cell, which is followed by an update of the ReplicateCrystal parameters and possibly the number of replicated cells.
boolean	equals(Object o)	Two crystals are equal only if all unit cell parameters are exactly the same.
Crystal	getUnitCell()	The ReplicatesCrystal over-rides this method to return the unit cell rather than the ReplicateCell.
static Crystal	NCSCrystalFactory(Crystal unitCell, List<SymOp> symOps)	Returns an NCSCrystal by expanding the orignal unit cell with the symmetry operators provided by the BIOMT records in the PDB files.
String	toString()

Methods inherited from class ffx.crystal.Crystal

aperiodic, applySymOp, applySymOp, applySymRot, applyTransSymRot, averageTensor, averageTensor, changeUnitCellParametersAndVolume, checkProperties, getCellParametersFromVectors, getCheckRestrictions, getDensity, getNumSymOps, getRandomCartTranslation, getSpecialPositionCutoff, getSpecialPositionCutoff2, getTransformationOperator, hashCode, image, image, image, invressq, minDistOverSymOps, perturbCellVectors, randomParameters, res, setAperiodic, setCellVectors, setCellVectorsAndVolume, setCheckRestrictions, setDensity, setSpecialPositionCutoff, toCartesianCoordinates, toCartesianCoordinates, toCartesianCoordinates, toCRYST1, toFractionalCoordinates, toFractionalCoordinates, toFractionalCoordinates, toPrimaryCell, toShortString, updateCrystal

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Method Details

NCSCrystalFactory

public static Crystal NCSCrystalFactory(Crystal unitCell,
 List<SymOp> symOps)

Returns an NCSCrystal by expanding the orignal unit cell with the symmetry operators provided by the BIOMT records in the PDB files. See REMARK 350.

Parameters:

unitCell - The unit cell of the crystal.

symOps - Symmetry operators for non-crystallographic symmetry

Returns:

A Crystal or NCSCrystal

changeUnitCellParameters

public boolean changeUnitCellParameters(double a,
 double b,
 double c,
 double alpha,
 double beta,
 double gamma)

Change the cell parameters for the base unit cell, which is followed by an update of the ReplicateCrystal parameters and possibly the number of replicated cells.

Overrides:

changeUnitCellParameters in class Crystal

Parameters:

a - The length of the a-axis for the base unit cell (in Angstroms).

b - The length of the b-axis for the base unit cell (in Angstroms).

c - The length of the c-axis for the base unit cell (in Angstroms).

alpha - The angle between the b-axis and c-axis (in Degrees).

beta - The angle between the a-axis and c-axis (in Degrees).

gamma - The angle between the a-axis and b-axis (in Degrees).

Returns:

True is returned if the unit cell and replicates cell are updated successfully.

equals

public boolean equals(Object o)

Two crystals are equal only if all unit cell parameters are exactly the same.

Overrides:

equals in class Crystal

Parameters:

o - the Crystal to compare to.

Returns:

true if all unit cell parameters are exactly the same.

getUnitCell

public Crystal getUnitCell()

The ReplicatesCrystal over-rides this method to return the unit cell rather than the ReplicateCell.

Returns the unit cell for this NCSCrystal. This is useful for the reciprocal space portion of PME that operates on the unit cell.

Overrides:

getUnitCell in class Crystal

Returns:

The unit cell Crystal instance.

toString

public String toString()

Include information about the base unit cell and NCS cell.

Overrides:

toString in class Crystal