Class AlignTools
- java.lang.Object
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- org.biojava.bio.structure.align.helper.AlignTools
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public class AlignTools extends java.lang.Object
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Constructor Summary
Constructors Constructor Description AlignTools()
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Method Summary
All Methods Static Methods Concrete Methods Modifier and Type Method Description static Atom
getCenter(Atom[] ca, int pos, int fragmentLength)
get the centroid for the set of atoms starting fromposition pos, length fragmentLenghtstatic double[]
getDiagonalAtK(Atom[] atoms, int k)
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 lengthstatic Atom[]
getFragmentFromIdxList(Atom[] caall, int[] idx)
get a subset of Atoms based by their positionsstatic 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.
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Method Detail
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getFragmentFromIdxList
public static Atom[] getFragmentFromIdxList(Atom[] caall, int[] idx)
get a subset of Atoms based by their positions- Parameters:
caall
-idx
- an array where each element is a position of all the Atoms to return- Returns:
- at Atom[] array
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getFragment
public static Atom[] getFragment(Atom[] caall, int pos, int fragmentLength)
get a continue subset of Atoms based by the starting position and the length- Parameters:
caall
-pos
- ... the start positionfragmentLength
- .. the length of the subset to extract.- Returns:
- an Atom[] array
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getFragmentNoClone
public 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.- Parameters:
caall
-pos
- ... the start positionfragmentLength
- .. the length of the subset to extract.- Returns:
- an Atom[] array
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getCenter
public static Atom getCenter(Atom[] ca, int pos, int fragmentLength)
get the centroid for the set of atoms starting fromposition pos, length fragmentLenght- Parameters:
ca
-pos
-fragmentLength
-- Returns:
- an Atom
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getDiagonalAtK
public static double[] getDiagonalAtK(Atom[] atoms, int k)
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rms_dk_diag
public 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. i,j is the fpair start in mol1 and mol2, l is the length of the fragment- Parameters:
dk1
- distances of structure 1dk2
- distance of structure 2i
- position in structure 1j
- position in structure 2l
- length of the fragmentsk
- diagonal used- Returns:
- a double
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