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