def exercise_02(inputs, verbose=0):
#
# run at n_step = 0
#
if (inputs.xray_structure is None):
print("Skipping exercise_02(): input file not available")
return
structure_ = inputs.xray_structure.deep_copy_scatterers()
if (verbose): log = sys.stdout
else: log = StringIO()
gradients_calculator=cartesian_dynamics.gradients_calculator_reciprocal_space(
restraints_manager = inputs.restraints_manager,
sites_cart = structure_.sites_cart(),
wc = 1)
cartesian_dynamics.run(
xray_structure = structure_,
gradients_calculator = gradients_calculator,
temperature = 300,
n_steps = 0,
time_step = 0.0005,
log = log,
verbose = 1)
assert inputs.xray_structure.rms_difference(structure_) \
== structure_.rms_difference(inputs.xray_structure)
assert approx_equal(
structure_.rms_difference(inputs.xray_structure), 0.0, 1e-6)
def run_cartesian_dynamics (
xray_structure,
states_collector,
restraints_manager,
params,
stop_at_diff,
log) :
from mmtbx.dynamics import cartesian_dynamics
make_header("Simple cartesian dynamics", out=log)
sites_cart_start = xray_structure.sites_cart().deep_copy()
gradients_calculator = \
cartesian_dynamics.gradients_calculator_reciprocal_space(
restraints_manager = restraints_manager,
sites_cart = xray_structure.sites_cart(),
wc = 1)
cartesian_dynamics.run(
xray_structure=xray_structure,
gradients_calculator=gradients_calculator,
temperature=params.temperature,
states_collector=states_collector,
n_steps=params.number_of_steps,
time_step=params.time_step,
initial_velocities_zero_fraction=params.initial_velocities_zero_fraction,
n_print=params.n_print,
stop_cm_motion=params.stop_cm_motion,
stop_at_diff=stop_at_diff,
log=log,
verbose=1)
sites_cart_end = xray_structure.sites_cart()
rmsd = sites_cart_end.rms_difference(sites_cart_start)
print >> log, ""
print >> log, "RMSD from starting structure: %.3f" % rmsd
def exercise_02(inputs, verbose=0):
#
# run at n_step = 0
#
if inputs.xray_structure is None:
print "Skipping exercise_02(): input file not available"
return
structure_ = inputs.xray_structure.deep_copy_scatterers()
if verbose:
log = sys.stdout
else:
log = StringIO()
gradients_calculator = cartesian_dynamics.gradients_calculator_reciprocal_space(
restraints_manager=inputs.restraints_manager, sites_cart=structure_.sites_cart(), wc=1
)
cartesian_dynamics.run(
xray_structure=structure_,
gradients_calculator=gradients_calculator,
temperature=300,
n_steps=0,
time_step=0.0005,
log=log,
verbose=1,
)
assert inputs.xray_structure.rms_difference(structure_) == structure_.rms_difference(inputs.xray_structure)
assert approx_equal(structure_.rms_difference(inputs.xray_structure), 0.0, 1e-6)
def run_cartesian_dynamics(xray_structure, states_collector,
restraints_manager, params, stop_at_diff, log):
from mmtbx.dynamics import cartesian_dynamics
make_header("Simple cartesian dynamics", out=log)
sites_cart_start = xray_structure.sites_cart().deep_copy()
gradients_calculator = \
cartesian_dynamics.gradients_calculator_reciprocal_space(
restraints_manager = restraints_manager,
sites_cart = xray_structure.sites_cart(),
wc = 1)
cartesian_dynamics.run(xray_structure=xray_structure,
gradients_calculator=gradients_calculator,
temperature=params.temperature,
states_collector=states_collector,
n_steps=params.number_of_steps,
time_step=params.time_step,
initial_velocities_zero_fraction=params.
initial_velocities_zero_fraction,
n_print=params.n_print,
stop_cm_motion=params.stop_cm_motion,
stop_at_diff=stop_at_diff,
log=log,
verbose=1)
sites_cart_end = xray_structure.sites_cart()
rmsd = sites_cart_end.rms_difference(sites_cart_start)
print("", file=log)
print("RMSD from starting structure: %.3f" % rmsd, file=log)
def exercise_03(mon_lib_srv, ener_lib, verbose=0):
#
# normal run with real model
#
pdb_file = libtbx.env.find_in_repositories(
relative_path="phenix_regression/pdb/2ERL_noH.pdb", test=os.path.isfile)
if (pdb_file is None):
print("Skipping exercise_03: input file not available")
return
if (verbose): log = sys.stdout
else: log = StringIO()
params = mmtbx.monomer_library.pdb_interpretation.master_params.extract()
params.nonbonded_weight = 16
processed_pdb = mmtbx.monomer_library.pdb_interpretation.process(
mon_lib_srv = mon_lib_srv,
params=params,
ener_lib = ener_lib,
file_name = pdb_file,
log = log)
xray_structure = processed_pdb.xray_structure()
restraints_manager = mmtbx.restraints.manager(
geometry=processed_pdb.geometry_restraints_manager())
structure_ = xray_structure.deep_copy_scatterers()
gradients_calculator=cartesian_dynamics.gradients_calculator_reciprocal_space(
restraints_manager = restraints_manager,
sites_cart = xray_structure.sites_cart(),
wc = 1)
cartesian_dynamics.run(
xray_structure = xray_structure,
gradients_calculator = gradients_calculator,
temperature = 300,
n_steps = 200,
time_step = 0.0005,
log = log,
verbose = 1)
rms1 = xray_structure.rms_difference(structure_)
rms2 = structure_.rms_difference(xray_structure)
assert rms1 == rms2
rms = rms1
if(verbose):
print("rms between structures before and after dynamics = ", rms)
array_of_distances_between_each_atom = \
flex.sqrt(structure_.difference_vectors_cart(xray_structure).dot())
if(verbose):
flex.histogram(
data=array_of_distances_between_each_atom,
n_slots=12).show(
format_cutoffs="%6.4f")
n_rms = 5.3
selected_by_rms = (array_of_distances_between_each_atom > n_rms * rms)
outlier_sc = xray_structure.scatterers().select(selected_by_rms)
if (outlier_sc.size() != 0):
print("number of rms outliers:", outlier_sc.size())
outlier_d = array_of_distances_between_each_atom.select(selected_by_rms)
for sc,d in zip(outlier_sc, outlier_d):
print(sc.label, d)
raise RuntimeError("rms outliers.")
def shake_sites(xrs, random, shift, grm=None):
if (random):
xrs.shake_sites_in_place(mean_distance=shift)
else:
grad_calc = cartesian_dynamics.gradients_calculator_geometry_restraints(
restraints_manager=grm)
cartesian_dynamics.run(xray_structure=xrs,
gradients_calculator=grad_calc,
temperature=1000,
n_steps=100000,
time_step=0.0005,
stop_cm_motion=True,
stop_at_diff=shift)
return xrs
def exercise_03(mon_lib_srv, ener_lib, verbose=0):
#
# normal run with real model
#
pdb_file = libtbx.env.find_in_repositories(relative_path="phenix_regression/pdb/2ERL_noH.pdb", test=os.path.isfile)
if pdb_file is None:
print "Skipping exercise_03: input file not available"
return
if verbose:
log = sys.stdout
else:
log = StringIO()
params = mmtbx.monomer_library.pdb_interpretation.master_params.extract()
params.nonbonded_weight = 16
processed_pdb = mmtbx.monomer_library.pdb_interpretation.process(
mon_lib_srv=mon_lib_srv, params=params, ener_lib=ener_lib, file_name=pdb_file, log=log
)
xray_structure = processed_pdb.xray_structure()
restraints_manager = mmtbx.restraints.manager(geometry=processed_pdb.geometry_restraints_manager())
structure_ = xray_structure.deep_copy_scatterers()
gradients_calculator = cartesian_dynamics.gradients_calculator_reciprocal_space(
restraints_manager=restraints_manager, sites_cart=xray_structure.sites_cart(), wc=1
)
cartesian_dynamics.run(
xray_structure=xray_structure,
gradients_calculator=gradients_calculator,
temperature=300,
n_steps=200,
time_step=0.0005,
log=log,
verbose=1,
)
rms1 = xray_structure.rms_difference(structure_)
rms2 = structure_.rms_difference(xray_structure)
assert rms1 == rms2
rms = rms1
if verbose:
print "rms between structures before and after dynamics = ", rms
array_of_distances_between_each_atom = flex.sqrt(structure_.difference_vectors_cart(xray_structure).dot())
if verbose:
flex.histogram(data=array_of_distances_between_each_atom, n_slots=12).show(format_cutoffs="%6.4f")
n_rms = 5.3
selected_by_rms = array_of_distances_between_each_atom > n_rms * rms
outlier_sc = xray_structure.scatterers().select(selected_by_rms)
if outlier_sc.size() != 0:
print "number of rms outliers:", outlier_sc.size()
outlier_d = array_of_distances_between_each_atom.select(selected_by_rms)
for sc, d in zip(outlier_sc, outlier_d):
print sc.label, d
raise RuntimeError("rms outliers.")
def shake_sites(xrs, random, shift, grm=None):
if(random):
xrs.shake_sites_in_place(mean_distance = shift)
else:
grad_calc = cartesian_dynamics.gradients_calculator_geometry_restraints(
restraints_manager = grm)
cartesian_dynamics.run(
xray_structure = xrs,
gradients_calculator = grad_calc,
temperature = 1000,
n_steps = 100000,
time_step = 0.0005,
stop_cm_motion = True,
stop_at_diff = shift)
return xrs
def cd(xray_structure, restraints_manager, params):
gradients_calculator = cartesian_dynamics.gradients_calculator_reciprocal_space(
restraints_manager=restraints_manager,
sites_cart=xray_structure.sites_cart(),
wc=1)
cartesian_dynamics.run(gradients_calculator=gradients_calculator,
xray_structure=xray_structure,
temperature=3000,
n_steps=500000,
time_step=0.0005,
initial_velocities_zero_fraction=0,
n_print=100,
stop_cm_motion=True,
log=None,
stop_at_diff=params.stop_cartesian_dynamics_at_diff,
verbose=-1)
def exercise_00(inputs, verbose=0):
#
# normal run
#
if (inputs.xray_structure is None):
print("Skipping exercise_00(): input file not available")
return
structure_ = inputs.xray_structure.deep_copy_scatterers()
if (verbose): log = sys.stdout
else: log = StringIO()
gradients_calculator=cartesian_dynamics.gradients_calculator_reciprocal_space(
restraints_manager = inputs.restraints_manager,
sites_cart = structure_.sites_cart(),
wc = 1)
cartesian_dynamics.run(
gradients_calculator=gradients_calculator,
xray_structure = structure_,
temperature = 300,
n_steps = 200,
time_step = 0.0005,
log = log,
verbose = 1)
rms1 = inputs.xray_structure.rms_difference(structure_)
rms2 = structure_.rms_difference(inputs.xray_structure)
assert rms1 == rms2
rms = rms1
if(verbose):
print("rms between structures before and after dynamics = ", rms)
array_of_distances_between_each_atom = \
flex.sqrt(structure_.difference_vectors_cart(
inputs.xray_structure).dot())
if(verbose):
print()
for d in array_of_distances_between_each_atom:
print(d)
n_rms = 4.0
selected_by_rms = (array_of_distances_between_each_atom > n_rms * rms)
if(n_rms > 1.0):
assert selected_by_rms.count(True) == 0
if(verbose):
print("number of outliers = ", selected_by_rms.count(True))
selected = array_of_distances_between_each_atom.select(selected_by_rms)
if(verbose):
print("list of outliers : ")
for s in selected:
print(s)
def cd(xray_structure, restraints_manager, params):
gradients_calculator=cartesian_dynamics.gradients_calculator_reciprocal_space(
restraints_manager = restraints_manager,
sites_cart = xray_structure.sites_cart(),
wc = 1)
cartesian_dynamics.run(
gradients_calculator = gradients_calculator,
xray_structure = xray_structure,
temperature = 3000,
n_steps = 500000,
time_step = 0.0005,
initial_velocities_zero_fraction = 0,
n_print = 100,
stop_cm_motion = True,
log = None,
stop_at_diff = params.stop_cartesian_dynamics_at_diff,
verbose = -1)
def exercise_00(inputs, verbose=0):
#
# normal run
#
if inputs.xray_structure is None:
print "Skipping exercise_00(): input file not available"
return
structure_ = inputs.xray_structure.deep_copy_scatterers()
if verbose:
log = sys.stdout
else:
log = StringIO()
gradients_calculator = cartesian_dynamics.gradients_calculator_reciprocal_space(
restraints_manager=inputs.restraints_manager, sites_cart=structure_.sites_cart(), wc=1
)
cartesian_dynamics.run(
gradients_calculator=gradients_calculator,
xray_structure=structure_,
temperature=300,
n_steps=200,
time_step=0.0005,
log=log,
verbose=1,
)
rms1 = inputs.xray_structure.rms_difference(structure_)
rms2 = structure_.rms_difference(inputs.xray_structure)
assert rms1 == rms2
rms = rms1
if verbose:
print "rms between structures before and after dynamics = ", rms
array_of_distances_between_each_atom = flex.sqrt(structure_.difference_vectors_cart(inputs.xray_structure).dot())
if verbose:
print
for d in array_of_distances_between_each_atom:
print d
n_rms = 4.0
selected_by_rms = array_of_distances_between_each_atom > n_rms * rms
if n_rms > 1.0:
assert selected_by_rms.count(True) == 0
if verbose:
print "number of outliers = ", selected_by_rms.count(True)
selected = array_of_distances_between_each_atom.select(selected_by_rms)
if verbose:
print "list of outliers : "
for s in selected:
print s
def __init__(self,
params,
restraints_manager,
xray_structure = None,
wx = None,
wc = None,
fmodel = None,
target_map = None,
real_space = False,
log = None,
states_collector = None,
callback = None,
verbose=True):
adopt_init_args(self, locals())
assert (callback is None) or hasattr(callback, "__call__")
if(self.params is None): self.params = master_params().extract()
if(log is None): self.log = sys.stdout
if(self.fmodel is not None):
self.xray_structure = self.fmodel.xray_structure
self.sites_cart_start = self.xray_structure.sites_cart()
self.curr_temp = params.start_temperature
verbose = params.verbose
reset_velocities = True
vxyz = None
den_manager = restraints_manager.geometry.den_manager
cartesian_den_restraints = False
if(den_manager is not None):
if("cartesian" in den_manager.params.annealing_type):
# restraints_manager.geometry.generic_restraints_manager.flags.den = True
cartesian_den_restraints = True
verbose = False
while params.final_temperature <= self.curr_temp:
#if(self.curr_temp == params.start_temperature):
# cmremove=True
#else: cmremove=False
cmremove=True
cd_manager = cartesian_dynamics.run(
xray_structure = self.xray_structure,
gradients_calculator = self.gradients_calculator(),
temperature = self.curr_temp,
interleaved_minimization = self.params.interleave_minimization,
vxyz = vxyz,
n_steps = self.params.number_of_steps,
time_step = self.params.time_step,
n_print = self.params.n_print,
random_seed = self.params.random_seed,
stop_cm_motion = cmremove,
reset_velocities = reset_velocities,
log = self.log,
verbose = verbose)
reset_velocities = False
vxyz = cd_manager.vxyz
self.xray_structure = cd_manager.xray_structure
if(self.fmodel is not None):
self.fmodel.update_xray_structure(
xray_structure = self.xray_structure,
update_f_calc = True,
update_f_mask = True)
if(states_collector is not None):
self.states_collector.add(sites_cart = cd_manager.xray_structure.sites_cart())
if (callback is not None) :
callback(fmodel=self.fmodel)
self.show(curr_temp = self.curr_temp)
self.curr_temp -= params.cool_rate
if(cartesian_den_restraints):
print >> self.log, "update DEN eq distances at temp=%.1f" % self.curr_temp
den_manager.update_eq_distances(
sites_cart=fmodel.xray_structure.sites_cart())
def __init__(self,
params,
restraints_manager,
xray_structure=None,
wx=None,
wc=None,
fmodel=None,
target_map=None,
real_space=False,
log=None,
states_collector=None,
callback=None,
verbose=True):
adopt_init_args(self, locals())
assert (callback is None) or hasattr(callback, "__call__")
if (self.params is None): self.params = master_params().extract()
if (log is None): self.log = sys.stdout
if (self.fmodel is not None):
self.xray_structure = self.fmodel.xray_structure
self.sites_cart_start = self.xray_structure.sites_cart()
self.curr_temp = params.start_temperature
verbose = params.verbose
reset_velocities = True
vxyz = None
den_manager = restraints_manager.geometry.den_manager
cartesian_den_restraints = False
if (den_manager is not None):
if ("cartesian" in den_manager.params.annealing_type):
# restraints_manager.geometry.generic_restraints_manager.flags.den = True
cartesian_den_restraints = True
verbose = False
while params.final_temperature <= self.curr_temp:
#if(self.curr_temp == params.start_temperature):
# cmremove=True
#else: cmremove=False
cmremove = True
cd_manager = cartesian_dynamics.run(
xray_structure=self.xray_structure,
gradients_calculator=self.gradients_calculator(),
temperature=self.curr_temp,
interleaved_minimization=self.params.interleave_minimization,
vxyz=vxyz,
n_steps=self.params.number_of_steps,
time_step=self.params.time_step,
n_print=self.params.n_print,
random_seed=self.params.random_seed,
stop_cm_motion=cmremove,
reset_velocities=reset_velocities,
log=self.log,
verbose=verbose)
reset_velocities = False
vxyz = cd_manager.vxyz
self.xray_structure = cd_manager.xray_structure
if (self.fmodel is not None):
self.fmodel.update_xray_structure(
xray_structure=self.xray_structure,
update_f_calc=True,
update_f_mask=True)
if (states_collector is not None):
self.states_collector.add(
sites_cart=cd_manager.xray_structure.sites_cart())
if (callback is not None):
callback(fmodel=self.fmodel)
self.show(curr_temp=self.curr_temp)
self.curr_temp -= params.cool_rate
if (cartesian_den_restraints):
print >> self.log, "update DEN eq distances at temp=%.1f" % self.curr_temp
den_manager.update_eq_distances(
sites_cart=fmodel.xray_structure.sites_cart())