@TestClass(value="org.openscience.cdk.geometry.CrystalGeometryToolsTest") public class CrystalGeometryTools extends Object
Constructor and Description |
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CrystalGeometryTools() |
Modifier and Type | Method and Description |
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static javax.vecmath.Vector3d[] |
calcInvertedAxes(javax.vecmath.Vector3d aAxis,
javax.vecmath.Vector3d bAxis,
javax.vecmath.Vector3d cAxis)
Inverts three cell axes.
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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.
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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.
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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.
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@TestMethod(value="testCalcInvertedAxes_Vector3d_Vector3d_Vector3d") public static javax.vecmath.Vector3d[] calcInvertedAxes(javax.vecmath.Vector3d aAxis, javax.vecmath.Vector3d bAxis, javax.vecmath.Vector3d cAxis)
@TestMethod(value="testCartesianToFractional_Vector3d_Vector3d_Vector3d_Point3d") public static javax.vecmath.Point3d cartesianToFractional(javax.vecmath.Vector3d aAxis, javax.vecmath.Vector3d bAxis, javax.vecmath.Vector3d cAxis, javax.vecmath.Point3d cartPoint)
@TestMethod(value="testFractionalToCartesian_Vector3d_Vector3d_Vector3d_Point3d") public static javax.vecmath.Point3d fractionalToCartesian(javax.vecmath.Vector3d aAxis, javax.vecmath.Vector3d bAxis, javax.vecmath.Vector3d cAxis, javax.vecmath.Point3d frac)
@TestMethod(value="testNotionalToCartesian_double_double_double_double_double_double") public static javax.vecmath.Vector3d[] notionalToCartesian(double alength, double blength, double clength, double alpha, double beta, double gamma)
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 fullfil the remaining constraints. (See also the CCL archive.)
alength
- length of the a axisblength
- length of the b axisclength
- length of the c axisalpha
- angle between b and c axes in degreesbeta
- angle between a and c axes in degreesgamma
- angle between a and b axes in degrees@TestMethod(value="testCartesianToNotional_Vector3d_Vector3d_Vector3d") public static double[] cartesianToNotional(javax.vecmath.Vector3d aAxis, javax.vecmath.Vector3d bAxis, javax.vecmath.Vector3d cAxis)
public static boolean hasCrystalCoordinates(IAtomContainer container)
public static void fractionalToCartesian(ICrystal crystal)