#!/usr/bin/env python

from pymol import cmd

import sys

mobile = sys.argv[1]

target = sys.argv[2]

out_pdb = sys.argv[3]

#mobile = 'altered_cwza.pdb'

#target = 'final_opt_cwza_L.pdb'

#target = 'with_seq_final_opt_cwza_L.pdb'

#target = 'bb_cwza_opt.pdb'

cmd.load(mobile, 'MyProtein')

cmd.load(target, 'MyModelBB')

Chains = cmd.get_chains('MyProtein')

for chain in Chains:

cmd.create('MyChain'+chain, '/MyProtein//'+chain)

mobile_bb = 'MyChain'+chain

target_bb = '/MyModelBB//'+chain

cmd.align(mobile_bb, target_bb)

cmd.delete('MyProtein')

cmd.delete('MyModelBB')

cmd.orient()

cmd.create('MyModel', 'all')

cmd.select('sidechains', 'MyModel')

## Protect rest of the protein from modifications by sculpting

cmd.protect('(not sidechains)')

## Carry out Sculpting for 5000 cycles

cmd.sculpt_activate('MyModel')

cmd.sculpt_iterate('MyModel', cycles=500)

cmd.sculpt_deactivate('MyModel')

cmd.deprotect()

cmd.save(out_pdb, "MyModel")