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# 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])
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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