Class SuperPosition
- java.lang.Object
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- org.biojava.nbio.structure.symmetry.geometry.SuperPosition
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public final class SuperPosition extends java.lang.Object
- Author:
- Peter
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Constructor Summary
Constructors Constructor Description SuperPosition()
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Method Summary
All Methods Static Methods Concrete Methods Modifier and Type Method Description static void
center(javax.vecmath.Point3d[] x)
static javax.vecmath.Point3d
centroid(javax.vecmath.Point3d[] x)
static javax.vecmath.Point3d[]
clonePoint3dArray(javax.vecmath.Point3d[] x)
static int
contacts(javax.vecmath.Point3d[] x, javax.vecmath.Point3d[] y, double maxDistance)
static double
GTSlikeScore(javax.vecmath.Point3d[] x, javax.vecmath.Point3d[] y)
static double
rmsd(javax.vecmath.Point3d[] x, javax.vecmath.Point3d[] y)
static double
rmsdMin(javax.vecmath.Point3d[] x, javax.vecmath.Point3d[] y)
static javax.vecmath.Matrix4d
superpose(javax.vecmath.Point3d[] x, javax.vecmath.Point3d[] y)
static javax.vecmath.Matrix4d
superposeAtOrigin(javax.vecmath.Point3d[] x, javax.vecmath.Point3d[] y)
static javax.vecmath.Matrix4d
superposeAtOrigin(javax.vecmath.Point3d[] x, javax.vecmath.Point3d[] y, javax.vecmath.AxisAngle4d axisAngle)
static javax.vecmath.Matrix4d
superposeWithTranslation(javax.vecmath.Point3d[] x, javax.vecmath.Point3d[] y)
static double
TMScore(javax.vecmath.Point3d[] x, javax.vecmath.Point3d[] y, int lengthNative)
Returns the TM-Score for two superimposed sets of coordinates Yang Zhang and Jeffrey Skolnick, PROTEINS: Structure, Function, and Bioinformatics 57:702–710 (2004)static void
transform(javax.vecmath.Matrix4d rotTrans, javax.vecmath.Point3d[] x)
static void
translate(javax.vecmath.Point3d trans, javax.vecmath.Point3d[] x)
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Method Detail
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superpose
public static javax.vecmath.Matrix4d superpose(javax.vecmath.Point3d[] x, javax.vecmath.Point3d[] y)
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superposeWithTranslation
public static javax.vecmath.Matrix4d superposeWithTranslation(javax.vecmath.Point3d[] x, javax.vecmath.Point3d[] y)
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superposeAtOrigin
public static javax.vecmath.Matrix4d superposeAtOrigin(javax.vecmath.Point3d[] x, javax.vecmath.Point3d[] y)
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superposeAtOrigin
public static javax.vecmath.Matrix4d superposeAtOrigin(javax.vecmath.Point3d[] x, javax.vecmath.Point3d[] y, javax.vecmath.AxisAngle4d axisAngle)
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rmsd
public static double rmsd(javax.vecmath.Point3d[] x, javax.vecmath.Point3d[] y)
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rmsdMin
public static double rmsdMin(javax.vecmath.Point3d[] x, javax.vecmath.Point3d[] y)
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TMScore
public static double TMScore(javax.vecmath.Point3d[] x, javax.vecmath.Point3d[] y, int lengthNative)
Returns the TM-Score for two superimposed sets of coordinates Yang Zhang and Jeffrey Skolnick, PROTEINS: Structure, Function, and Bioinformatics 57:702–710 (2004)- Parameters:
x
- coordinate set 1y
- coordinate set 2lengthNative
- total length of native sequence- Returns:
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GTSlikeScore
public static double GTSlikeScore(javax.vecmath.Point3d[] x, javax.vecmath.Point3d[] y)
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contacts
public static int contacts(javax.vecmath.Point3d[] x, javax.vecmath.Point3d[] y, double maxDistance)
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transform
public static void transform(javax.vecmath.Matrix4d rotTrans, javax.vecmath.Point3d[] x)
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translate
public static void translate(javax.vecmath.Point3d trans, javax.vecmath.Point3d[] x)
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center
public static void center(javax.vecmath.Point3d[] x)
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centroid
public static javax.vecmath.Point3d centroid(javax.vecmath.Point3d[] x)
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clonePoint3dArray
public static javax.vecmath.Point3d[] clonePoint3dArray(javax.vecmath.Point3d[] x)
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