Constructor Detail

• Helix

  public Helix​()

Method Detail

• getScores

  public QuatSymmetryScores getScores​()

  Returns:

  the scores

• setScores

  public void setScores​(QuatSymmetryScores scores)

  Parameters:

  scores - the scores to set

• getPermutation

  public java.util.List<java.lang.Integer> getPermutation​()

  Returns:

  the permutation

• setPermutation

  public void setPermutation​(java.util.List<java.lang.Integer> permutation)

  Parameters:

  permutation - the permutation to set

• getRepeatUnits

  public java.util.List<java.util.List<java.lang.Integer>> getRepeatUnits​()

• setRepeatUnits

  public void setRepeatUnits​(java.util.List<java.util.List<java.lang.Integer>> repeatUnits)

• getTransformation

  public javax.vecmath.Matrix4d getTransformation​()

  Returns:

  the transformation

• setTransformation

  public void setTransformation​(javax.vecmath.Matrix4d transformation)

  Parameters:

  transformation - the transformation to set

• getRise

  public double getRise​()

• setRise

  public void setRise​(double rise)

• getAngle

  public double getAngle​()

  Returns the pitch angle of the helix

  Parameters:

  transformation - helix transformation

  Returns:

• getAxisAngle

  public javax.vecmath.AxisAngle4d getAxisAngle​()

  Returns the AxisAngle of the helix transformation

  Parameters:

  transformation - helix transformation

  Returns:

• getnStart

  public int getnStart​()

• setnStart

  public void setnStart​(int nStart)

• getFold

  public int getFold​()

  Returns:

  the fold

• setFold

  public void setFold​(int fold)

  Parameters:

  fold - the fold to set

• getContacts

  public int getContacts​()

• setContacts

  public void setContacts​(int contacts)

• toString

  public java.lang.String toString​()

  Overrides:

  toString in class java.lang.Object

• getLayerLines

  public java.util.List<java.util.List<java.lang.Integer>> getLayerLines​()