|
||||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | |||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |
java.lang.ObjectRdcPanda.sp3Carbon
public class sp3Carbon
represeting the tetrahedral of the sp3 Carbon configuration IN order to compute the coordinates we need only to know the coordinates of the top atom then using the information provided by the sp3Carbon object we should be able to compute all the coordinates of other atoms. atomOfChi | | Top | | center / | \ / | \ / | \ vertex1 vertex2 vertex3 The angles are defined as shown in the above figure. Written by Lincong Wang (2001-2005).
Constructor Summary | |
---|---|
sp3Carbon()
Instantiates a new sp3 carbon. |
|
sp3Carbon(double[] anglesAndLen,
boolean ter)
The Constructor. |
|
sp3Carbon(double[] atomOfChi,
double[] top,
double[] center,
double[] vertex1,
double[] vertex2,
double[] vertex3,
boolean ter)
Instantiates a new sp3 carbon. |
|
sp3Carbon(double theta1a,
double theta2a,
double theta3a,
double chia,
double theta2da,
double theta3da,
double d1a,
double d2a,
double d3a,
boolean ter)
Instantiates a new sp3 carbon. |
Method Summary | |
---|---|
double[] |
addCoords(double[] n1,
double[] n2)
Add two coordinates. |
double[] |
anglesAndLenOfSp3(double[] atomOfChi,
double[] top,
double[] center,
double[] vertex1,
double[] vertex2,
double[] vertex3)
Compute the side-chain angles as represented by SP3 object from the coordinates of 4 atoms. |
double[] |
getAll()
Gets the all. |
boolean |
isTerminal()
Checks if is terminal. |
void |
printArray(double[] n1)
Prints the array. |
Matrix[] |
tetrahedral(double[] center,
Matrix mat,
sp3Carbon atomC)
Compute the coordinates of sp3 atoms from a sp3Carbon object. |
java.lang.String |
toString()
|
Methods inherited from class java.lang.Object |
---|
equals, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Constructor Detail |
---|
public sp3Carbon()
public sp3Carbon(double theta1a, double theta2a, double theta3a, double chia, double theta2da, double theta3da, double d1a, double d2a, double d3a, boolean ter)
theta1a
- the theta1atheta2a
- the theta2atheta3a
- the theta3achia
- the chiatheta2da
- the theta2datheta3da
- the theta3dad1a
- the d1ad2a
- the d2ad3a
- the d3ater
- the terpublic sp3Carbon(double[] anglesAndLen, boolean ter)
anglesAndLen
- has all the data for specifying a sp3Carbon object except whether
it is a termial oneter
- the terpublic sp3Carbon(double[] atomOfChi, double[] top, double[] center, double[] vertex1, double[] vertex2, double[] vertex3, boolean ter)
atomOfChi
- the atom of chitop
- the topcenter
- the centervertex1
- the vertex1vertex2
- the vertex2vertex3
- the vertex3ter
- the terMethod Detail |
---|
public java.lang.String toString()
toString
in class java.lang.Object
public boolean isTerminal()
public double[] getAll()
public double[] addCoords(double[] n1, double[] n2)
n1
- the coordinate for the nucleus of the atom 1n2
- the coordinate for the nucleus of the atom 2
public void printArray(double[] n1)
n1
- the n1public Matrix[] tetrahedral(double[] center, Matrix mat, sp3Carbon atomC)
mat
- the Matrix to the center ("top") of the tetrahedral, that is: a matrix
specifying the plane defined by the three atoms (atomOfChi, top, center) with
the top-->center vector on the +y axis and z-axis also in the plane,
This is also the first plane defining the Chi anglecenter
- coordinate of the center, really the top atom (vertice) of tetrahedral.atomC
- the carbon atom of SP3 class with all the informs about bond angles
public double[] anglesAndLenOfSp3(double[] atomOfChi, double[] top, double[] center, double[] vertex1, double[] vertex2, double[] vertex3)
atomOfChi
- the coord for the atom leading to the top, needed for computing Chi di-angletop
- the coord for top atomcenter
- the coord for center of the tetrahedral, really its "top" atomvertex1
- the coord for 1st bottom atom of the tetrahedralvertex2
- the coord for 2nd bottom atom of the tetrahedralvertex3
- the coord for 3rd bottom atom of the tetrahedral
|
||||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | |||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |