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java.lang.Objectorg.biojava.bio.structure.align.helper.AlignTools
public class AlignTools
Constructor Summary | |
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AlignTools()
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Method Summary | |
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static Atom |
getCenter(Atom[] ca,
int pos,
int fragmentLength)
get the centroid for the set of atoms starting fromposition pos, length fragmentLenght |
static double[] |
getDiagonalAtK(Atom[] atoms,
int k)
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static Matrix |
getDistanceMatrix(Atom[] ca1,
Atom[] ca2)
matrix of all distances between two sets of 3d coords" |
static Atom[] |
getFragment(Atom[] caall,
int pos,
int fragmentLength)
get a continue subset of Atoms based by the starting position and the length |
static Atom[] |
getFragmentFromIdxList(Atom[] caall,
int[] idx)
get a subset of Atoms based by their positions |
static Atom[] |
getFragmentNoClone(Atom[] caall,
int pos,
int fragmentLength)
get a continue subset of Atoms based by the starting position and the length does not clone the original atoms. |
static double |
rms_dk_diag(double[] dk1,
double[] dk2,
int i,
int j,
int l,
int k)
Given distance matrix diagonals dk1, dk2, get the rmsd of a fpair. |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
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public AlignTools()
Method Detail |
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public static Atom[] getFragmentFromIdxList(Atom[] caall, int[] idx)
caall
- idx
- an array where each element is a position of all the Atoms to return
public static Atom[] getFragment(Atom[] caall, int pos, int fragmentLength)
caall
- pos
- ... the start positionfragmentLength
- .. the length of the subset to extract.
public static Atom[] getFragmentNoClone(Atom[] caall, int pos, int fragmentLength)
caall
- pos
- ... the start positionfragmentLength
- .. the length of the subset to extract.
public static Atom getCenter(Atom[] ca, int pos, int fragmentLength)
ca
- pos
- fragmentLength
-
public static double[] getDiagonalAtK(Atom[] atoms, int k)
public static double rms_dk_diag(double[] dk1, double[] dk2, int i, int j, int l, int k)
dk1
- distances of structure 1dk2
- distance of structure 2i
- position in structure 1j
- position in structure 2l
- length of the fragmentsk
- diagonal used
public static Matrix getDistanceMatrix(Atom[] ca1, Atom[] ca2)
ca1
- ca2
-
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