model.reorder_atoms() -- standardize order of MODEL atoms

Requirements:

topology library

Description:

This routine reorders atoms within the residues of MODEL so that they follow the order in the current residue topology library.

Example: examples/commands/reorder_atoms.py

# Example for: model.reorder_atoms()

# This will standardize the order of atoms in the model.

env = environ()

# Order the atoms according to a topology library:
env.libs.topology.read(file='$(LIB)/top_heav.lib')

mdl = model(env, file='1fas')
mdl.reorder_atoms()
mdl.write(file='1fas.ini1')