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commands.py

# commands extensions to PyMOL for batchmin

from pymol import cmd
from chempy.bmin import realtime
import threading

def amin(*arg,**kwarg):
   realtime.assign(arg[0])
   apply(bmin,arg,kwarg)

def bmin(object,iter=500,grad=0.1,interval=100,
         solvation=None):
   realtime.setup(object)
   t = threading.Thread(target=realtime.mini,
                        args=(int(iter),float(grad),int(interval),str(object)),
                        kwargs={
      'solvation':solvation, # turn on GB/SA (cdie)
      'rest_flag':2, # atoms with flag 2 set are restrained
      'fix_flag':3, # atoms with flag 3 set are fixed
      }
                        )
   t.setDaemon(1)
   t.start()

def bmin_sync(object,iter=500,grad=0.1,interval=100,
         solvation=None):
   realtime.setup(object)
   realtime.mini(int(iter),float(grad),int(interval),str(object),
                 solvation=solvation,
                 rest_flag=2,
                 fix_flag=3)
   
def pmin():
   cmd.delete('min')
   realtime.assign('lig')
   cmd.create('min','(lig|prot)')
   bmin('min')
   
cmd.extend('bmin',bmin)
cmd.extend('bmin_sync',bmin_sync)
cmd.extend('amin',amin)
cmd.extend('pmin',pmin)


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