GameObjected "sucked" into another GameObject effect while dragging - unity3d

Question

I am building a chemistry game where the user can drag around different atoms and connect them together to build molecules. I am able to get the atoms to "stick" to one another when they collide. However, the spheres are stuck just on the outside of each other. I want to get them to overlap slightly like the picture below.
Basically, I want the user to click and drag the mouse to drag atom spheres within the radius of other atom spheres. When that collision happens, I want the atom to be "sucked" into the other atom. However, the problem I am facing is that because the user is holding on to the atom with the mouse, any sort of movement is negated. I've tried each of the three lines of code below but none of them work in getting that atom to suck into the other one while the user is holding the mouse.
atom_entering.transform.position = Vector3.MoveTowards(atom_entering.transform.position, this_atom.transform.position, 5*Time.deltaTime);
atom_entering.GetComponent<Rigidbody>().MovePosition(this_atom.transform.position + (atom_entering.transform.position - this_atom.transform.position));
atom_entering.GetComponent<Rigidbody>().AddForce(this_atom.transform.position, ForceMode.Acceleration);
If I try to decrease the radius of each atom, it can work but then the atom starts clipping any other collisions like the table itself.
Edit: Asked to post complete code:
void OnCollisionEnter(Collision collision)
{
GameObject atom_entering = collision.gameObject;
GameObject this_atom = this.gameObject;
if(atom_entering.name == "HydrogenPrefab(Clone)" && num_hydrogens < max_hydrogens && !hydrogen_connected)
{
// Code to make the "suction" effect here
// One of the three lines above went here but none of them worked.
// First, make the hydrogen a child of this oxygen atom.
// Next, create a Fixed Joint component on the hydrogen and stick it to the oxygen
atom_entering.transform.parent = this_atom.transform;
atom_entering.AddComponent<FixedJoint>();
atom_entering.GetComponent<FixedJoint>().connectedBody = this_atom.GetComponent<Rigidbody>();
atom_entering.GetComponent<HydrogenCollider>().setConnectedStatus(true);
// Increment the number of hydrogens connected to the oxygen
num_hydrogens += 1;
}
}
In a separate C# script:
void OnMouseDrag()
{
this.GetComponent<Rigidbody>().isKinematic = true;
Ray ray = Camera.main.ScreenPointToRay(Input.mousePosition);
RaycastHit hit;
if(Physics.Raycast(ray, out hit, Camera.main.farClipPlane))
{
float oldY = this.transform.position.y;
this.transform.position = new Vector3(hit.point.x, oldY, hit.point.z);
}
this.GetComponent<Rigidbody>().isKinematic = false;
}
Edit: Here is a video of how it is currently behaving. https://vimeo.com/185896832
I want that same behavior expect I just want to get it "sucked into" the parent atom. If I do anything with the radius, the atoms sink into the floor a bit which is not what I want. It doesn't make sense to have an object with a normal radius when it interacts with the floor and a different radius when it interacts with an atom.

Answer 1

Well here's how I would do it :
I would create prefabs of my atoms with empty GameObjects as children serving as references (example : OxygenAtom => HydrogenPos1, HydrogenPos2, HydrogenPos3 and HydrogenPos4)
On atoms I would have a script managing the available position and occupied ones
When the atom you're carrying (let's say Atom2) collides with another atom (Atom1), you check the available positions for one that fits the Atom2 type.
If it fits, you tag the available position as occupied and parent Atom2 as child of Atom1 and finally place him at the position you just checked as occupied.
EDIT : here's a sample of code to bind atoms together :
protected void OnCollisionEnter(Collision collision)
{
if(gameObject.name.Equals("Oxygen") && collision.gameObject.name.Equals("Hydrogen"))
{
Debug.Log("Binding...");
StartCoroutine(BindAtomAfterFixedUpdate(collision.gameObject));
}
}
private IEnumerator BindAtomAfterFixedUpdate(GameObject atomToBind)
{
GetComponent<SphereCollider>().isTrigger = true;
// or GetComponent<SphereCollider>().enabled = false;
yield return new WaitForFixedUpdate();
atomToBind.transform.position = transform.FindChild("HydrogenSpot").position;
gameObject.AddComponent<FixedJoint>().connectedBody = atomToBind.GetComponent<Rigidbody>();
GetComponent<SphereCollider>().isTrigger = false;
// or GetComponent<SphereCollider>().enabled = true;
}