|
|||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | ||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |
java.lang.Objectbelka.geom.Kabscher
public class Kabscher
The implementation of the Kabsch algorith for least-square fitting of two
sets of points as describe in:
W. Kabsch, A solution for the best rotation to relate two sets of vectors.
Acta Cryst. (1976). A32, 922-923.
W. Kabsch, A discussion of the solution for the best rotation to relate two
sets of vectors.
Acta Cryst. (1978). A34, 827-828.
The code is adapted from the protein geometry library
http://geometry.molmovdb.org/
Constructor Summary | |
---|---|
Kabscher()
|
Method Summary | |
---|---|
double |
fit(Atom[] atoms1,
Atom[] atoms2)
The function performs least-square fit of given atoms. |
double |
fitCA(Chain[] chains1,
Chain[] chains2)
The function performs least-square fit of C-alpha protein or P-phosphate nucleotide atoms and returns RMSD of the fit. |
double |
fitCA(Chain[] chains1,
Chain[] chains2,
boolean selected)
The function performs least-square fit of C-alpha protein or P-phosphate nucleotide atoms and returns RMSD of the fit. |
double |
fitCA(Chain c1,
Chain c2)
The function performs least-square fit of C-alpha protein or P-phosphate nucleotide atoms and returns RMSD of the fit. |
double |
fitCA(Chain chain1,
Chain chain2,
boolean selected)
The function performs least-square fit of C-alpha protein or P-phosphate nucleotide atoms and returns RMSD of the fit. |
int |
getNFitted()
Returns number of fitted atoms. |
double |
getRMSD()
Returns RMSD of fit. |
double[][] |
getRotation()
Returns rotation matrix. |
double[][] |
getRotationCopy()
Returns copy of rotation matrix. |
double[] |
getTranslation()
Returns translation vector. |
double[] |
getTranslationCopy()
Returns copy translation vector. |
Methods inherited from class java.lang.Object |
---|
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
---|
public Kabscher()
Method Detail |
---|
public double[][] getRotation()
public double[][] getRotationCopy()
public double[] getTranslation()
public double[] getTranslationCopy()
public int getNFitted()
public double getRMSD()
public double fitCA(Chain c1, Chain c2)
c1
- first chain.c2
- second chain.
public double fitCA(Chain[] chains1, Chain[] chains2)
chains1
- first set of chains.chains2
- second set of chains.
public double fitCA(Chain chain1, Chain chain2, boolean selected)
chain1
- first chain.chain2
- second chain.selected
- flag to indicate that only selected atoms must be used.
public double fitCA(Chain[] chains1, Chain[] chains2, boolean selected)
chains1
- first set of chains.chains2
- second set of chains.selected
- flag to indicate that only selected atoms must be used.
public double fit(Atom[] atoms1, Atom[] atoms2)
atoms1
- first array with atoms.atoms2
- second array with atoms.
|
|||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | ||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |