RdcPanda
Class ppGlobal

java.lang.Object
  extended by RdcPanda.ppGlobal
All Implemented Interfaces:
java.lang.Cloneable

public class ppGlobal
extends java.lang.Object
implements java.lang.Cloneable

A class for computing the first peptide plane from an NCA and NH vector. Several common methods used by other classes are implemented here. Written by Lincong Wang (2001-2005).


Constructor Summary
ppGlobal()
          Instantiates a new pp global.
 
Method Summary
 double[] dirCos(double[] vec)
          cal the directioal cosines of the vector vec.
 double interAngle(double[] v1, double[] v2)
          calculate the angles between two vectors v1 and v2 The returned angle is in the [0,Pi] range.
 double length(double[] v1)
          calculate the length between two vectors v1 and v2 The returned angle is the [0,Pi] region.
 Matrix RgCal(double[] nToh, double gamma)
          compute global rotation (Rg) with two no colinear vectors Rg is the same as the last method Here the input are the NH vector and one Euler angle gamma for the N(i)->CA(i) vector accounting the rotation of the peptide plane along the NH vector.
 Matrix RgCal(double[] nToh, double[] nToca)
          compute global rotation (Rg) with two noncolinear vectors, Rg is the rotation matrix for rotating the PDB coordinate system into the following system: +z-axis along the bond NH(i)->N(i), "->" means from atom N(i) to atom NH(i).
 Matrix RgCal(double[] nToh, double[] nToca, boolean rightHand)
          Rg cal.
 
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

ppGlobal

public ppGlobal()
Instantiates a new pp global.

Method Detail

length

public double length(double[] v1)
calculate the length between two vectors v1 and v2 The returned angle is the [0,Pi] region.

Parameters:
v1 - the v1
Returns:
the double

interAngle

public double interAngle(double[] v1,
                         double[] v2)
calculate the angles between two vectors v1 and v2 The returned angle is in the [0,Pi] range.

Parameters:
v1 - the v1
v2 - the v2
Returns:
the double

dirCos

public double[] dirCos(double[] vec)
cal the directioal cosines of the vector vec.

Parameters:
vec - the vec
Returns:
the double[]

RgCal

public Matrix RgCal(double[] nToh,
                    double[] nToca)
compute global rotation (Rg) with two noncolinear vectors, Rg is the rotation matrix for rotating the PDB coordinate system into the following system: +z-axis along the bond NH(i)->N(i), "->" means from atom N(i) to atom NH(i). +y-axis in the peptide plane i,and the angle between +y and the N(i)->CA(i) < 90 degree. +x-axis is defined based on the right-handedness.

Parameters:
nToh - the directional cosine of N->NH vector
nToca - the directional cosine of N->CA vector
Returns:
All the rotational Matrix, not just one

RgCal

public Matrix RgCal(double[] nToh,
                    double[] nToca,
                    boolean rightHand)
Rg cal.

Parameters:
nToh - the n toh
nToca - the n toca
rightHand - the right hand
Returns:
the matrix

RgCal

public Matrix RgCal(double[] nToh,
                    double gamma)
compute global rotation (Rg) with two no colinear vectors Rg is the same as the last method Here the input are the NH vector and one Euler angle gamma for the N(i)->CA(i) vector accounting the rotation of the peptide plane along the NH vector.

Parameters:
nToh - the n toh
gamma - the gamma
Returns:
the matrix