|
||||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | |||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |
java.lang.Object ProGAL.proteins.chainTree.ChainTree
public class ChainTree
A chain tree representation of the structure of a protein sub-chain.
Constructor Summary | |
---|---|
ChainTree(PrimaryStructure ps)
Construct a chain tree representing the structure of the specified sequence. |
|
ChainTree(PrimaryStructure ps,
int firstRes,
int lastRes)
Construct a chain tree representing the structure of the residues in the specified interval. |
Method Summary | |
---|---|
double |
closeCCD(Point[] target,
int iterations)
Perform cyclic coordinate descent on this chain so the positions of the end-atoms overlap with those specified in the target -array. |
Point[] |
getAllBackboneAtoms()
Collect all backbone atoms using the leaves only. |
Point |
getBackboneAtom(int res,
int atom)
Return the position of a specific backbone atom. |
double |
getTorsionAngle(int res,
int bond)
Return the torsion angle of the specified residue and bond. |
boolean |
isLocked(int res,
int bond)
|
static void |
main(java.lang.String[] args)
|
void |
setFirstTransformation(Matrix m)
Change the orientation and translation of the entire chain. |
void |
setLocked(int res,
int bond)
|
void |
setTorsionAngle(int res,
int bond,
double value)
Changes the torsion angle of the specified residue and bond. |
Methods inherited from class java.lang.Object |
---|
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
---|
public ChainTree(PrimaryStructure ps)
ps
- Primary structure specifying the sequencepublic ChainTree(PrimaryStructure ps, int firstRes, int lastRes)
ps
- Primary structure specifying the sequencefirstRes
- The residue-index of the first residue in the loop.lastRes
- The residue-index of the last residue in the loop.Method Detail |
---|
public double getTorsionAngle(int res, int bond)
res
- The residue-index in this chain-tree (0 is the first residue)bond
- Indication of which bond in the residue (0=phi, 1=psi and 2=omega).
public void setTorsionAngle(int res, int bond, double value)
res
- The residue-index in this chain-tree (0 is the first residue)bond
- Indication of which bond in the residue (0=phi, 1=psi and 2=omega).value
- The new value of the torsion anglepublic void setLocked(int res, int bond)
public boolean isLocked(int res, int bond)
public void setFirstTransformation(Matrix m)
m
- The new first-transformationpublic Point getBackboneAtom(int res, int atom)
res
- The residue index in this chain tree (0 is the first residue).atom
- The atom index in the residue (0=N, 1=CA and 2=C).
public Point[] getAllBackboneAtoms()
public double closeCCD(Point[] target, int iterations)
target
-array.
target
- The desired position of the target.length
last atoms in the chain.iterations
- The number of iterations of CCD to perform
public static void main(java.lang.String[] args)
|
||||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | |||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |