/// <summary> Translates the geometric 2DCenter of the given
/// AtomContainer container to the specified Point2d p.
///
/// </summary>
/// <param name="container"> AtomContainer which should be translated.
/// </param>
/// <param name="p"> New Location of the geometric 2D Center.
/// </param>
/// <seealso cref="get2DCenter">
/// </seealso>
/// <seealso cref="translate2DCentreOfMassTo">
/// </seealso>
public static void translate2DCenterTo(IAtomContainer container, Point2d p)
{
Point2d com = get2DCenter(container);
Vector2d translation = new Vector2d(p.x - com.x, p.y - com.y);
IAtom[] atoms = container.Atoms;
for (int i = 0; i < atoms.Length; i++)
{
if (atoms[i].getPoint2d() != null)
{
atoms[i].getPoint2d().add(translation);
}
}
}
/// <summary> Translates a molecule from the origin to a new point denoted by a vector.
/// See comment for center(IAtomContainer atomCon, Dimension areaDim, HashMap renderingCoordinates) for details on coordinate sets
///
/// </summary>
/// <param name="atomCon"> molecule to be translated
/// </param>
/// <param name="vector"> dimension that represents the translation vector
/// </param>
public static void translate2D(IAtomContainer atomCon, Vector2d vector)
{
IAtom[] atoms = atomCon.Atoms;
for (int i = 0; i < atoms.Length; i++)
{
if (atoms[i].getPoint2d() != null)
{
atoms[i].getPoint2d().add(vector);
}
else
{
//logger.warn("Could not translate atom in 2D space");
}
}
}
/// <summary> Translates a molecule from the origin to a new point denoted by a vector, using an external set of coordinates.
/// See comment for center(IAtomContainer atomCon, Dimension areaDim, HashMap renderingCoordinates) for details on coordinate sets
///
/// </summary>
/// <param name="atomCon"> molecule to be translated
/// </param>
/// <param name="vector"> dimension that represents the translation vector
/// </param>
/// <param name="renderingCoordinates"> The set of coordinates to use coming from RendererModel2D
/// </param>
//UPGRADE_TODO: Class 'java.util.HashMap' was converted to 'System.Collections.Hashtable' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073_javautilHashMap'"
public static void translate2D(IAtomContainer atomCon, Vector2d vector, System.Collections.Hashtable renderingCoordinates)
{
IAtom[] atoms = atomCon.Atoms;
for (int i = 0; i < atoms.Length; i++)
{
//UPGRADE_TODO: Method 'java.util.HashMap.get' was converted to 'System.Collections.Hashtable.Item' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073_javautilHashMapget_javalangObject'"
if (renderingCoordinates[atoms[i]] == null && atoms[i].getPoint2d() != null)
{
renderingCoordinates[atoms[i]] = new Point2d(atoms[i].getPoint2d().x, atoms[i].getPoint2d().y);
}
//UPGRADE_TODO: Method 'java.util.HashMap.get' was converted to 'System.Collections.Hashtable.Item' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073_javautilHashMapget_javalangObject'"
if (((Point2d)renderingCoordinates[atoms[i]]) != null)
{
//UPGRADE_TODO: Method 'java.util.HashMap.get' was converted to 'System.Collections.Hashtable.Item' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073_javautilHashMapget_javalangObject'"
((Point2d)renderingCoordinates[atoms[i]]).add(vector);
}
else
{
//logger.warn("Could not translate atom in 2D space");
}
}
}
/// <summary> Determines the normalized vector orthogonal on the vector p1->p2.
///
/// </summary>
/// <param name="p1"> Description of the Parameter
/// </param>
/// <param name="p2"> Description of the Parameter
/// </param>
/// <returns> Description of the Return Value
/// </returns>
public static Vector2d calculatePerpendicularUnitVector(Point2d p1, Point2d p2)
{
Vector2d v = new Vector2d();
v.sub(p2, p1);
v.normalize();
// Return the perpendicular vector
return new Vector2d((-1.0) * v.y, v.x);
}
/// <summary> Constructs and initializes a Vector2f from the specified Vector2d.</summary>
/// <param name="v1">the Vector2f containing the initialization x y data
/// </param>
public Vector2f(Vector2d v1):base(v1)
{
}
/// <summary> Returns the angle in radians between this vector and
/// the vector parameter; the return value is constrained to the
/// range [0,PI].
/// </summary>
/// <param name="v1"> the other vector
/// </param>
/// <returns> the angle in radians in the range [0,PI]
/// </returns>
public double angle(Vector2d v1)
{
// stabler than acos
return System.Math.Abs(System.Math.Atan2(x * v1.y - y * v1.x, dot(v1)));
}
/// <summary> Sets the value of this vector to the normalization of vector v1.</summary>
/// <param name="v1">the un-normalized vector
/// </param>
public void normalize(Vector2d v1)
{
set_Renamed(v1);
normalize();
}
/// <summary> Computes the dot product of the this vector and vector v1.</summary>
/// <param name="v1">the other vector
/// </param>
public double dot(Vector2d v1)
{
return x * v1.x + y * v1.y;
}