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 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 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 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 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 gradients_calculator(self):
if(not self.real_space):
if(self.fmodel is not None):
grad_calc = cartesian_dynamics.gradients_calculator_reciprocal_space(
restraints_manager = self.restraints_manager, # XXX WHY?
fmodel = self.fmodel,
sites_cart = self.fmodel.xray_structure.sites_cart(),
wx = self.wx,
wc = self.wc,
update_gradient_threshold = self.params.update_grads_shift)
else:
grad_calc = cartesian_dynamics.gradients_calculator_geometry_restraints(
restraints_manager = self.restraints_manager)
else:
grad_calc = cartesian_dynamics.gradients_calculator_real_space_simple(
restraints_manager = self.restraints_manager.geometry, # XXX WHY?
target_map = self.target_map,
unit_cell = self.xray_structure.unit_cell(),
sites_cart = self.xray_structure.sites_cart(),
wx = self.wx,
wc = self.wc,
update_gradient_threshold = 0)
return grad_calc
def gradients_calculator(self):
if (not self.real_space):
if (self.fmodel is not None):
grad_calc = cartesian_dynamics.gradients_calculator_reciprocal_space(
restraints_manager=self.restraints_manager, # XXX WHY?
fmodel=self.fmodel,
sites_cart=self.fmodel.xray_structure.sites_cart(),
wx=self.wx,
wc=self.wc,
update_gradient_threshold=self.params.update_grads_shift)
else:
grad_calc = cartesian_dynamics.gradients_calculator_geometry_restraints(
restraints_manager=self.restraints_manager)
else:
grad_calc = cartesian_dynamics.gradients_calculator_real_space_simple(
restraints_manager=self.restraints_manager.
geometry, # XXX WHY?
target_map=self.target_map,
unit_cell=self.xray_structure.unit_cell(),
sites_cart=self.xray_structure.sites_cart(),
wx=self.wx,
wc=self.wc,
update_gradient_threshold=0)
return grad_calc
