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java.lang.ObjectRdcPanda.ppGlobal
public class ppGlobal
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 | |
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ppGlobal()
Instantiates a new pp global. |
Method Summary | |
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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 |
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equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
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public ppGlobal()
Method Detail |
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public double length(double[] v1)
v1
- the v1
public double interAngle(double[] v1, double[] v2)
v1
- the v1v2
- the v2
public double[] dirCos(double[] vec)
vec
- the vec
public Matrix RgCal(double[] nToh, double[] nToca)
nToh
- the directional cosine of N->NH vectornToca
- the directional cosine of N->CA vector
public Matrix RgCal(double[] nToh, double[] nToca, boolean rightHand)
nToh
- the n tohnToca
- the n tocarightHand
- the right hand
public Matrix RgCal(double[] nToh, double gamma)
nToh
- the n tohgamma
- the gamma
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