org.openscience.cdk.geometry

Class CrystalGeometryTools

java.lang.Object

org.openscience.cdk.geometry.CrystalGeometryTools

public class CrystalGeometryTools
extends Object

A set of static methods for working with crystal coordinates.

Author:

Egon Willighagen <egonw@sci.kun.nl>

Source code:

master

Belongs to CDK module:

standard

Keywords:

fractional coordinates, crystal

Constructor Summary

Constructors

Constructor and Description
CrystalGeometryTools()

Method Summary

Methods

Modifier and Type	Method and Description
static javax.vecmath.Vector3d[]	calcInvertedAxes(javax.vecmath.Vector3d aAxis, javax.vecmath.Vector3d bAxis, javax.vecmath.Vector3d cAxis) Inverts three cell axes.
static javax.vecmath.Point3d	cartesianToFractional(javax.vecmath.Vector3d aAxis, javax.vecmath.Vector3d bAxis, javax.vecmath.Vector3d cAxis, javax.vecmath.Point3d cartPoint)
static double[]	cartesianToNotional(javax.vecmath.Vector3d aAxis, javax.vecmath.Vector3d bAxis, javax.vecmath.Vector3d cAxis)
static void	fractionalToCartesian(ICrystal crystal) Creates Cartesian coordinates for all Atoms in the Crystal.
static javax.vecmath.Point3d	fractionalToCartesian(javax.vecmath.Vector3d aAxis, javax.vecmath.Vector3d bAxis, javax.vecmath.Vector3d cAxis, javax.vecmath.Point3d frac)
static boolean	hasCrystalCoordinates(IAtomContainer container) Determines if this model contains fractional (crystal) coordinates.
static javax.vecmath.Vector3d[]	notionalToCartesian(double alength, double blength, double clength, double alpha, double beta, double gamma) Calculates Cartesian vectors for unit cell axes from axes lengths and angles between axes.

Methods inherited from class java.lang.Object

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

Constructor Detail

CrystalGeometryTools

public CrystalGeometryTools()

Method Detail

calcInvertedAxes

public static javax.vecmath.Vector3d[] calcInvertedAxes(javax.vecmath.Vector3d aAxis,
                                        javax.vecmath.Vector3d bAxis,
                                        javax.vecmath.Vector3d cAxis)

Inverts three cell axes.

Returns:

a 3x3 matrix with the three Cartesian vectors representing the unit cell axes. The a axis is the first row.

cartesianToFractional

public static javax.vecmath.Point3d cartesianToFractional(javax.vecmath.Vector3d aAxis,
                                          javax.vecmath.Vector3d bAxis,
                                          javax.vecmath.Vector3d cAxis,
                                          javax.vecmath.Point3d cartPoint)

Dictionary pointer(s):

convertCartesianIntoFractionalCoordinates in the Blue Obelisk Chemoinformatics Dictionary [blue-obelisk:convertCartesianIntoFractionalCoordinates]

fractionalToCartesian

public static javax.vecmath.Point3d fractionalToCartesian(javax.vecmath.Vector3d aAxis,
                                          javax.vecmath.Vector3d bAxis,
                                          javax.vecmath.Vector3d cAxis,
                                          javax.vecmath.Point3d frac)

Dictionary pointer(s):

convertFractionIntoCartesianCoordinates in the Blue Obelisk Chemoinformatics Dictionary [blue-obelisk:convertFractionIntoCartesianCoordinates]

notionalToCartesian

public static javax.vecmath.Vector3d[] notionalToCartesian(double alength,
                                           double blength,
                                           double clength,
                                           double alpha,
                                           double beta,
                                           double gamma)

Calculates Cartesian vectors for unit cell axes from axes lengths and angles between axes.

To calculate Cartesian coordinates, it places the a axis on the x axes, the b axis in the xy plane, making an angle gamma with the a axis, and places the c axis to fulfill the remaining constraints. (See also the CCL archive.)

Parameters:

alength - length of the a axis

blength - length of the b axis

clength - length of the c axis

alpha - angle between b and c axes in degrees

beta - angle between a and c axes in degrees

gamma - angle between a and b axes in degrees

Returns:

an array of Vector3d objects with the three Cartesian vectors representing the unit cell axes.

Dictionary pointer(s):

convertNotionalIntoCartesianCoordinates in the Blue Obelisk Chemoinformatics Dictionary [blue-obelisk:convertNotionalIntoCartesianCoordinates]

Keywords:

notional coordinates

cartesianToNotional

public static double[] cartesianToNotional(javax.vecmath.Vector3d aAxis,
                           javax.vecmath.Vector3d bAxis,
                           javax.vecmath.Vector3d cAxis)

Dictionary pointer(s):

convertCartesianIntoNotionalCoordinates in the Blue Obelisk Chemoinformatics Dictionary [blue-obelisk:convertCartesianIntoNotionalCoordinates]

hasCrystalCoordinates

public static boolean hasCrystalCoordinates(IAtomContainer container)

Determines if this model contains fractional (crystal) coordinates.

Returns:

boolean indication that 3D coordinates are available

fractionalToCartesian

public static void fractionalToCartesian(ICrystal crystal)

Creates Cartesian coordinates for all Atoms in the Crystal.