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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public static javax.vecmath.Vector3d[] calcInvertedAxes(javax.vecmath.Vector3d aAxis, javax.vecmath.Vector3d bAxis, javax.vecmath.Vector3d cAxis)
public static javax.vecmath.Point3d cartesianToFractional(javax.vecmath.Vector3d aAxis, javax.vecmath.Vector3d bAxis, javax.vecmath.Vector3d cAxis, javax.vecmath.Point3d cartPoint)
public static javax.vecmath.Point3d fractionalToCartesian(javax.vecmath.Vector3d aAxis, javax.vecmath.Vector3d bAxis, javax.vecmath.Vector3d cAxis, javax.vecmath.Point3d frac)
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 fulfill 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 degreespublic 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)
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