Distance between Atoms

In this assignment, you will write code to calculate distances between atoms in a molecular structure and produce a connectivity matrix M.

The matrix M is square, with dimensions NxN (rows, columns), where N is the number of atoms in the molecule. Each cell of the matrix represents the connectivity between two atoms, i and j, which can either be 1 (connected) or 0 (not connected).

Your code should take as an input a URL to a molecular structure in PDB format.

In terms of organization, write your code in three separate modules:

• js/parser.js should have a function to read the molecular data.
• js/distance.js should have code to calculate distances between atoms.
• js/connectivity.js should define the matrix M from the coordinates.