I am new to python. I have to make a program for a project that takes a PDB format file as input and returns a list of all the intra-chain and inter-chain charge pairs and their energies (using coulomb’s law assuming a dielectric constant of (?) of 40.0). For simplicity, the charged residues for this program are just Arg (CZ), Lys (NZ), Asp (CG) and Glu (CD) with the charge bearing atoms for each indicated in parentheses. The program should report any attractive or repulsive interactions within 8.0 Å.

Here is some additional information needed for the program.

Eij = energy of interaction between atoms i and j in kilocalories/mole (kcals/mol)
qi = charge for atom i (+1 for Lys or Arg, -1 for Glu or Asp)
rij = distance between atoms i and j in angstroms using the distance formula

The output should adhere to the following format:

First residue : Second residue  Distance           Energy
Lys 10 Chain A: ASP 46 Chain A D= 4.76 ang    E= -2.32 kcals/mol

(For some reason I can't organize the top two rows, but the first row should be lables and below it the corresponding values.)

I really have no idea how to tackle this problem, any and all help is greatly appreciated. I hope this is the right place to ask. Thank you in advance.

Using python 2.5