def mini(total_step=100, gradient=0.001, interval=100, obj='rt'):
global state
if not state:
print(" realtime.mini: please run setup first.")
else:
state.echo = 0
model = state.model
print(" realtime.mini: %d atoms total\n" % model.nAtom)
xtra_kw = []
xtra_kw.extend(keyword.get_inactive(model, 3))
xtra_kw.extend(keyword.get_restrain_positions(model, 2, 0, 10))
xtra_kw.extend(keyword.get_restrain_positions(model, 5, 0.5, 1))
xtra_kw.extend(keyword.get_inactive(model, 6))
state.keywords['chg-cutoff'] = 10.0
state.keywords['vdw-cutoff'] = 7.00
state.keywords['lights'] = ''
state.keywords['restrainterm'] = ''
iter = total_step / interval
for x in range(0, iter):
state.minimize(gradient=gradient, max_iter=interval, kw=xtra_kw)
cmd.delete(obj)
cmd.load_model(model, obj, 1)
cmd.refresh()
if not len(state.summary):
break
for a in state.summary:
print(a)
if state.summary[-1][7] == 'SmallGrad':
break
io.pkl.toFile(model, "realtime.pkl")
print(" realtime.mini: terminated after %d steps." % state.counter)
def mini(total_step=100, gradient=0.001, interval=100, obj="rt"):
global state
if not state:
print " realtime.mini: please run setup first."
else:
state.echo = 0
model = state.model
print " realtime.mini: %d atoms total\n" % model.nAtom
xtra_kw = []
xtra_kw.extend(keyword.get_inactive(model, 3))
xtra_kw.extend(keyword.get_restrain_positions(model, 2, 0, 10))
xtra_kw.extend(keyword.get_restrain_positions(model, 5, 0.5, 1))
xtra_kw.extend(keyword.get_inactive(model, 6))
state.keywords["chg-cutoff"] = 10.0
state.keywords["vdw-cutoff"] = 7.00
state.keywords["lights"] = ""
state.keywords["restrainterm"] = ""
iter = total_step / interval
for x in range(0, iter):
state.minimize(gradient=gradient, max_iter=interval, kw=xtra_kw)
cmd.delete(obj)
cmd.load_model(model, obj, 1)
cmd.refresh()
if not len(state.summary):
break
for a in state.summary:
print a
if state.summary[-1][7] == "SmallGrad":
break
io.pkl.toFile(model, "realtime.pkl")
print " realtime.mini: terminated after %d steps." % state.counter
def dyna(steps, iter=1):
global state
if not state:
print(" realtime.dyna: please run setup first.")
else:
state.echo = 0
model = state.model
print(" realtime.dyna: %d atoms total\n" % model.nAtom)
xtra_kw = []
xtra_kw.extend(keyword.get_inactive(model, 3))
xtra_kw.extend(keyword.get_restrain_positions(model, 2, 0, 10))
xtra_kw.extend(keyword.get_restrain_positions(model, 5, 0.5, 1))
xtra_kw.extend(keyword.get_inactive(model, 6))
state.keywords['chg-cutoff'] = 10.0
state.keywords['vdw-cutoff'] = 7.00
state.keywords['lights'] = ''
state.keywords['restrainterm'] = ''
for x in range(0, iter):
state.dynamics(steps=steps, timestep=1, kw=xtra_kw)
if not len(state.summary):
break
for a in state.summary:
print(a)
cmd.load_model(model, 'dyna')
cmd.ending()
cmd.refresh()
io.pkl.toFile("realtime.pkl")
print(" realtime.dyna: terminated after %d steps." % state.counter)
def dyna(steps, iter=1):
global state
if not state:
print " realtime.dyna: please run setup first."
else:
state.echo = 0
model = state.model
print " realtime.dyna: %d atoms total\n" % model.nAtom
xtra_kw = []
xtra_kw.extend(keyword.get_inactive(model, 3))
xtra_kw.extend(keyword.get_restrain_positions(model, 2, 0, 10))
xtra_kw.extend(keyword.get_restrain_positions(model, 5, 0.5, 1))
xtra_kw.extend(keyword.get_inactive(model, 6))
state.keywords["chg-cutoff"] = 10.0
state.keywords["vdw-cutoff"] = 7.00
state.keywords["lights"] = ""
state.keywords["restrainterm"] = ""
for x in range(0, iter):
state.dynamics(steps=steps, timestep=1, kw=xtra_kw)
if not len(state.summary):
break
for a in state.summary:
print a
cmd.load_model(model, "dyna")
cmd.ending()
cmd.refresh()
io.pkl.toFile("realtime.pkl")
print " realtime.dyna: terminated after %d steps." % state.counter
