Examples of name.mjw.jamber.util.Torsion

name.mjw.jamber.util.Torsion
rtations.ub.rug.nl/FILES/faculties/science/1996/h.bekker/thesis.pdf}
This is the dot product definition of theta
An alternative form (cross product form) can be found starting from equation 2.39 in {@link ftp://ftp.dl.ac.uk/ccp5/DL_POLY/DL_POLY_CLASSIC/DOCUMENTS/USRMAN2.17.pdf}

    Point3d i = new Point3d(0.0, 0.0, 0.0);
    Point3d j = new Point3d(1.0, 1.0, 0.0);
    Point3d k = new Point3d(2.0, 1.0, 0.0);
    Point3d l = new Point3d(3.0, 2.0, 0.0);


    Torsion torsion = new Torsion();
    
    assertEquals(180.0, torsion.getAngle(i,j,k,l), delta);    
  }

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    Point3d i = new Point3d(60.614941, 67.371346, 12.713049);
    Point3d j = new Point3d(59.104156, 67.044731, 12.827555);
    Point3d k = new Point3d(58.827194, 65.911911, 13.835642);
    Point3d l = new Point3d(59.367950, 66.384277, 15.233553);


    Torsion torsion = new Torsion();
    
    assertEquals(59.66383665358091, torsion.getAngle(i,j,k,l), delta);
  }

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    Point3d i = new Point3d(30.958572, 73.709137, 38.031029);
    Point3d j = new Point3d(31.924915, 72.577698, 37.985279);
    Point3d k = new Point3d(31.643818, 71.563255, 36.873047);
    Point3d l = new Point3d(31.253489, 70.131218, 37.371773);


    Torsion torsion = new Torsion();
        
    assertEquals(-115.17206338216852, torsion.getAngle(i,j,k,l), delta);
    
    TorsionGradients gradients;
    
    gradients = torsion.getGradients(i,j,k,l);
    
    LOG.debug(gradients.getI());
    LOG.debug(gradients.getJ());
    LOG.debug(gradients.getK());
    LOG.debug(gradients.getL());

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    Point3d j = new Point3d(59.104156, 67.044731, 12.827555);
    Point3d k = new Point3d(58.827194, 65.911911, 13.835642);
    Point3d l = new Point3d(59.367950, 66.384277, 15.233553);


      
    Torsion torsion = new Torsion();
    
    TorsionGradients gradients;
    
    gradients = torsion.getGradients(i,j,k,l);
    
    // Correct Gradients
    Vector3d a = new Vector3d( 0.062885,  -0.469977,  -0.510851 );
    Vector3d b = new Vector3d(-0.267922,   0.730722,   0.747527 );
    Vector3d c = new Vector3d( 0.799196,  -0.529675,  -0.375642 );

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  /**
   * Gets the dihedral angle (phi) in degrees
   */
  public double getCurrentDihedralAngle() {
    Torsion torsion = new Torsion();
  
    return torsion.getAngle(i.getPosition(), j.getPosition(),
        k.getPosition(), l.getPosition());


  }

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    temp3d.sub(j.getPosition(), k.getPosition());


    double unitForce = getAnalyticalGradient() / temp3d.length();


    Torsion gt = new Torsion();


    TorsionGradients grad = gt.getGradients(i.getPosition(), j.getPosition(),
        k.getPosition(), l.getPosition());


    Vector3d tempI = grad.getI();
    tempI.scale(unitForce);

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Related Classes of name.mjw.jamber.util.Torsion

name.mjw.jamber.Dihedral

name.mjw.jamber.TorsionTest

javax.vecmath.Vector3d

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