molecule | cross platform web/native react apps | Frontend Framework library

Let RDKit compute 2D coordinates and use the CoordGen library.

Your copy constructors are just doing shallow copies of each field. That's fine for strings because they're immutable, and it's fine for ints because they're primitive (which means they lack identity and are immutable). In those cases, there is no important difference between shallow and deep copies. But it doesn't work in general for lists because lists can be mutable and so can their elements. So instead of just pointing at the same list, you need to make a new list and deep copy each element of the original list into the new one.

Use this helper method to make deep copies of any lists:

Something like this.

Are you asking for a general approach recommendation, or for support with the particular solution you have?

If it's for the first, then I think your best bet for communicating between the server and the client is through websockets, perhaps with something like Socket.io. A long lived connection will serve you well here, since it will take a long time to transmit all your data across.

Then you can send data from the server to the client any time you like. At that point you can read your data on the server as a node.js stream and emit the data one at a time.

The problem with using Oboe and writing to the response on every node is that it requires a long running response, and there's a high likelihood the connection could get interrupted before you've sent all the data across.

In computer science terms, what you have here is what is known as a graph. Your molecules are what known as "nodes" or "vertices" and your connections between them is known as "edges". You need to find the distance between the oxygen and all other nodes. This can be done with what is called a Breadth first search (there are other methods, but i think this is the easiest one to start with)

I strongly suggest you read the wikipedia page on this, but here is a python version adapted to your data structure:

You can add renderables and anchors when you detect a tape event, or when the user presses a button.

So long as you know the relative positions that you want to add them, you can set the position for each node you add individually by setting a Pose translation.

See below an example of adding a node 1M in front of the centre point of the preview screen:

I don't know why the original code sample doesn't work. But this did the trick for me:

You can do something like below, i have used dummy data. I have iterated over all items of the array, you can use loop if required. So basically we are testing cell() with mock data pass to return required string.