Translates an atom object, given a Vector3d (i.e. the vecmath library
double-precision 3-d vector)

@param atom
@param v
545327
public static final void translate (Atom atom, Vector3d v) {

		atom.setX(atom.getX()+v.x);
		atom.setY(atom.getY()+v.y);
		atom.setZ(atom.getZ()+v.z);
	}
629879
public void set(Vector3D v, double width, double height) {
        this.x = v.getX();
        this.y = v.getY();
        this.width = width;
        this.height = height;
    }
1098185
public void addTranslation(double[] v) {
    if(trans == null) {
      trans = new AffineTransformation(dim);
    }
    trans.addTranslation(v);
  }
1365662
public static Point3d[] atomsToPoints(Atom[] atoms) {
		Point3d[] points = new Point3d[atoms.length];
		for(int i = 0; i< atoms.length;i++) {
			points[i] = atoms[i].getCoordsAsPoint3d();
		}
		return points;
	}
254072
public float dot(Vector3fc v) {
        return dot(v.x(), v.y(), v.z());
    }
1085543
public void vertex(Vector3D v) {
        MODE = LINES_3D;
        this.cornerX.add(v.getX());
        this.cornerY.add(v.getY());
        this.cornerZ.add(v.getZ());
        setNumberOfCorner(this.cornerX.size());
        calcG();
    }
218755
public void setImport(StylesheetComposed v)
  {

    if (null == m_imports)
      m_imports = new Vector();

    // I'm going to insert the elements in backwards order,
    // so I can walk them 0 to n.
    m_imports.addElement(v);
  }
1339638
function (v) {
/*Line 23 - 'AtomYesNoCustom.js' */                this._value = v;
/*Line 24 - 'AtomYesNoCustom.js' */                AtomBinder.setValue(this, "hasValue", v ? true : false);
/*Line 25 - 'AtomYesNoCustom.js' */                if (!this._onUIChanged) {
/*Line 26 - 'AtomYesNoCustom.js' */                    $(this._input).val(v);
/*Line 27 - 'AtomYesNoCustom.js' */                }
/*Line 28 - 'AtomYesNoCustom.js' */            }
1366423
@Override
    public void setAtom(IAtom atom, int position) {
        if (atoms[position] == null && atom != null) atomCount++;
        if (atoms[position] != null && atom == null) atomCount--;
        atoms[position] = atom;
    }
81255
public static final Atom getCenterVector(Atom[] atomSet, Atom centroid){

		double[] coords = new double[3];
		coords[0] = 0 - centroid.getX();
		coords[1] = 0 - centroid.getY();
		coords[2] = 0 - centroid.getZ();

		Atom shiftVec = new AtomImpl();
		shiftVec.setCoords(coords);
		return shiftVec;

	}
987272
private void reflect(int v, IBond bond) {
        visited[v] = true;
        IAtom atom = container.getAtom(v);
        atom.setPoint2d(reflect(atom.getPoint2d(), bond));
        for (int w : graph[v]) {
            if (!visited[w]) reflect(w, bond);
        }
    }
1081755
public Vector3d set(Vector2dc v, double z) {
        return set(v.x(), v.y(), z);
    }
1094104
public Vector3d transform(Vector3d vec){
        return transform(vec.x, vec.y, vec.z, vec);
    }
757256
function Vector3D( x , y , z ) {
	this.x = + x ;
	this.y = + y ;
	this.z = + z ;
}
24928
public void set(Vector3D v1, Vector3D v2) {
        this.MODE = LINES;
        this.x1 = v1.getX();
        this.y1 = v1.getY();
        this.z1 = v1.getZ();
        this.x2 = v2.getX();
        this.y2 = v2.getY();
        this.z2 = v2.getZ();
        calcG();
        dx[0] = x1 - this.x;
        dx[1] = x2 - this.x;
        dy[0] = y1 - this.y;
        dy[1] = y2 - this.y;
        dz[0] = z1 - this.z;
        dz[1] = z2 - this.z;
        if (dashed) calcDashedLine();
    }
22073
function (v) {
/*Line 477 - 'Atom.js' */        if (!v)
/*Line 478 - 'Atom.js' */            return "";
/*Line 479 - 'Atom.js' */        v = AtomDate.parse(v);
/*Line 480 - 'Atom.js' */        var d = new Date(v.getTime() + AtomDate.zoneOffset);
/*Line 481 - 'Atom.js' */        return d;
/*Line 482 - 'Atom.js' */    }
384000
public Vector3f set(Vector2ic v, float z) {
        return set(v.x(), v.y(), z);
    }