Question

I want to store molecules in memory. These can be simple molecules:

Methane (CH4)
C-H bond-length: 108.7 pm
H-H angle: 109 degrees

But also more complex molecules, like paracetamol (C8H9NO2):

How can I store molecules in memory, including all bond-lengths and angles?

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A good idea to store atom-structs in an array? Or is there a better way?

Answer 1

It looks like some kind of graph data structure:

• A molecule has a set of atoms
• Atoms are linked by bonds:
  • A bond can be double, single or tripple
  • A bond has a length
  • A bond has an angle
• It’s a cyclic graph (for instance, the example in the question has a ring of alternating single and double bonds)
• It’s not a directed graph (if two atoms are bonded, it doesn’t matter from which end you approach the bond)

Typically you’d store a graph as an array of nodes (atoms) and an array of edges (bonds). Nodes and edges would both be pointers to structs.

A node (atom) would store the element.

An edge (bond) would store the following fields:

• A pair of pointers to nodes
• The type of bond (double/single)
• The bond length and angle

Since it’s not a directed graph, your data structure would consider an edge between A and B to be equivalent to an edge between B and A. That is, for a given pair of atoms, you’d expect your edge array to contain an edge from A to B and never from B to A.