Overview

A program to calculate the total formal charge of a model.

Running the program

qr.charges can be executed on a PDB model file but the primary use if from the clustering code. The two main functions are

• cap the cluster with hydrogens to provide a neutral buffer layer and better SCF convergence
• to determine the charge for each cluster

List of all available keywords

• model_file_name = None Model file name
• ligand_cif_file_name = None This restraints file will be used to get the formal charge of the ligand.
• list_charges = False Print a list of all the atoms with non-zero charge.
• electrons = True debug option - do not change.
• assert_correct_chain_terminii = True Tests for hydrogens on the N terminii.
• verbose = False