def benchmark_structure(pdb_in, mon_lib_srv, ener_lib, verbose=False, w=1.0):
log = StringIO()
params = mmtbx.model.manager.get_default_pdb_interpretation_params()
params.pdb_interpretation.peptide_link.ramachandran_restraints = True
params.pdb_interpretation.ramachandran_plot_restraints.inject_emsley8k_into_oldfield_favored = False
model = mmtbx.model.manager(model_input=pdb_in,
pdb_interpretation_params=params,
log=null_out(),
build_grm=True)
grm = model.get_restraints_manager().geometry
pdb_hierarchy = model.get_hierarchy()
r0 = ramalyze(pdb_hierarchy=pdb_hierarchy, outliers_only=False)
atoms = pdb_hierarchy.atoms()
sites_cart_1 = atoms.extract_xyz().deep_copy()
sites_cart_2 = sites_cart_1.deep_copy()
assert (grm is not None)
e = grm.energies_sites(sites_cart=sites_cart_1)
b0 = e.bond_deviations()[-1]
a0 = e.angle_deviations()[-1]
flags = cctbx.geometry_restraints.flags.flags(default=True)
lbfgs = geometry_minimization.lbfgs(
sites_cart=sites_cart_1,
correct_special_position_tolerance=1.0,
geometry_restraints_manager=grm,
geometry_restraints_flags=flags,
lbfgs_termination_params=scitbx.lbfgs.termination_parameters(
max_iterations=500))
a1 = lbfgs.rmsd_angles
b1 = lbfgs.rmsd_bonds
atoms.set_xyz(sites_cart_1)
r1 = ramalyze(pdb_hierarchy=pdb_hierarchy, outliers_only=False)
rama_params = ramachandran.master_phil.fetch().extract(
).ramachandran_plot_restraints
rama_manager = ramachandran.ramachandran_manager(pdb_hierarchy,
rama_params, log)
grm.set_ramachandran_restraints(rama_manager)
lbfgs = geometry_minimization.lbfgs(
sites_cart=sites_cart_2,
correct_special_position_tolerance=1.0,
geometry_restraints_manager=grm,
geometry_restraints_flags=flags,
lbfgs_termination_params=scitbx.lbfgs.termination_parameters(
max_iterations=500))
a2 = lbfgs.rmsd_angles
b2 = lbfgs.rmsd_bonds
atoms.set_xyz(sites_cart_2)
r2 = ramalyze(pdb_hierarchy=pdb_hierarchy, outliers_only=False)
return group_args(a0=a0,
a1=a1,
a2=a2,
b0=b0,
b1=b1,
b2=b2,
r0=r0,
r1=r1,
r2=r2)
def benchmark_structure (pdb_in, mon_lib_srv, ener_lib, verbose=False, w=1.0) :
params = pdb_interpretation.master_params.extract()
processed_pdb_file = pdb_interpretation.process(
mon_lib_srv=mon_lib_srv,
ener_lib=ener_lib,
params=params,
pdb_inp=pdb_in,
log=StringIO())
log = StringIO()
pdb_hierarchy = processed_pdb_file.all_chain_proxies.pdb_hierarchy
r0 = ramalyze(pdb_hierarchy=pdb_hierarchy, outliers_only=False)
atoms = pdb_hierarchy.atoms()
sites_cart_1 = atoms.extract_xyz().deep_copy()
sites_cart_2 = sites_cart_1.deep_copy()
grm = processed_pdb_file.geometry_restraints_manager()
assert (grm is not None)
e = grm.energies_sites(sites_cart=sites_cart_1)
b0 = e.bond_deviations()[-1]
a0 = e.angle_deviations()[-1]
flags = cctbx.geometry_restraints.flags.flags(default=True)
lbfgs = geometry_minimization.lbfgs(
sites_cart=sites_cart_1,
correct_special_position_tolerance=1.0,
geometry_restraints_manager=grm,
geometry_restraints_flags=flags,
lbfgs_termination_params=scitbx.lbfgs.termination_parameters(
max_iterations=500))
a1 = lbfgs.rmsd_angles
b1 = lbfgs.rmsd_bonds
atoms.set_xyz(sites_cart_1)
r1 = ramalyze(pdb_hierarchy=pdb_hierarchy, outliers_only=False)
rama_params = ramachandran.master_phil.fetch().extract()
rama_manager = ramachandran.ramachandran_manager(
pdb_hierarchy, None, rama_params, log)
grm.set_ramachandran_restraints(rama_manager)
lbfgs = geometry_minimization.lbfgs(
sites_cart=sites_cart_2,
correct_special_position_tolerance=1.0,
geometry_restraints_manager=grm,
geometry_restraints_flags=flags,
lbfgs_termination_params=scitbx.lbfgs.termination_parameters(
max_iterations=500))
a2 = lbfgs.rmsd_angles
b2 = lbfgs.rmsd_bonds
atoms.set_xyz(sites_cart_2)
r2 = ramalyze(pdb_hierarchy=pdb_hierarchy, outliers_only=False)
return group_args(
a0=a0,
a1=a1,
a2=a2,
b0=b0,
b1=b1,
b2=b2,
r0=r0,
r1=r1,
r2=r2)
def benchmark_structure(pdb_in, mon_lib_srv, ener_lib, verbose=False, w=1.0):
params = pdb_interpretation.master_params.extract()
processed_pdb_file = pdb_interpretation.process(mon_lib_srv=mon_lib_srv,
ener_lib=ener_lib,
params=params,
pdb_inp=pdb_in,
log=StringIO())
log = StringIO()
pdb_hierarchy = processed_pdb_file.all_chain_proxies.pdb_hierarchy
r0 = ramalyze(pdb_hierarchy=pdb_hierarchy, outliers_only=False)
atoms = pdb_hierarchy.atoms()
sites_cart_1 = atoms.extract_xyz().deep_copy()
sites_cart_2 = sites_cart_1.deep_copy()
grm = processed_pdb_file.geometry_restraints_manager()
assert (grm is not None)
e = grm.energies_sites(sites_cart=sites_cart_1)
b0 = e.bond_deviations()[-1]
a0 = e.angle_deviations()[-1]
flags = cctbx.geometry_restraints.flags.flags(default=True)
lbfgs = geometry_minimization.lbfgs(
sites_cart=sites_cart_1,
correct_special_position_tolerance=1.0,
geometry_restraints_manager=grm,
geometry_restraints_flags=flags,
lbfgs_termination_params=scitbx.lbfgs.termination_parameters(
max_iterations=500))
a1 = lbfgs.rmsd_angles
b1 = lbfgs.rmsd_bonds
atoms.set_xyz(sites_cart_1)
r1 = ramalyze(pdb_hierarchy=pdb_hierarchy, outliers_only=False)
rama_params = ramachandran.master_phil.fetch().extract()
rama_manager = ramachandran.ramachandran_manager(pdb_hierarchy, None,
rama_params, log)
grm.set_ramachandran_restraints(rama_manager)
lbfgs = geometry_minimization.lbfgs(
sites_cart=sites_cart_2,
correct_special_position_tolerance=1.0,
geometry_restraints_manager=grm,
geometry_restraints_flags=flags,
lbfgs_termination_params=scitbx.lbfgs.termination_parameters(
max_iterations=500))
a2 = lbfgs.rmsd_angles
b2 = lbfgs.rmsd_bonds
atoms.set_xyz(sites_cart_2)
r2 = ramalyze(pdb_hierarchy=pdb_hierarchy, outliers_only=False)
return group_args(a0=a0,
a1=a1,
a2=a2,
b0=b0,
b1=b1,
b2=b2,
r0=r0,
r1=r1,
r2=r2)
def run(self, random_seed):
tmp = self.xray_structure.deep_copy_scatterers()
# Shake and minimize to get variable starting points
tmp.shake_sites_in_place(rms_difference=None, mean_distance=5)
sites_cart_ = tmp.sites_cart()
minimized = geometry_minimization.lbfgs(
sites_cart=sites_cart_,
correct_special_position_tolerance=1.0,
geometry_restraints_manager=self.restraints_manager.geometry,
geometry_restraints_flags=self.grf,
lbfgs_exception_handling_params=self.
lbfgs_exception_handling_params,
lbfgs_termination_params=scitbx.lbfgs.termination_parameters(
max_iterations=50))
tmp = tmp.replace_sites_cart(new_sites=sites_cart_)
#
random.seed(random_seed)
flex.set_random_seed(random_seed)
sa.run(params=self.params,
xray_structure=tmp,
real_space=True,
target_map=self.map_data,
restraints_manager=self.restraints_manager,
wx=self.weight,
wc=1.,
verbose=False)
return tmp
def run(self, random_seed):
tmp = self.xray_structure.deep_copy_scatterers()
# Shake and minimize to get variable starting points
tmp.shake_sites_in_place(
rms_difference = None,
mean_distance = 5)
sites_cart_ = tmp.sites_cart()
minimized = geometry_minimization.lbfgs(
sites_cart = sites_cart_,
correct_special_position_tolerance= 1.0,
geometry_restraints_manager = self.restraints_manager.geometry,
geometry_restraints_flags = self.grf,
lbfgs_exception_handling_params = self.lbfgs_exception_handling_params,
lbfgs_termination_params = scitbx.lbfgs.termination_parameters(
max_iterations=50))
tmp = tmp.replace_sites_cart(new_sites = sites_cart_)
#
random.seed(random_seed)
flex.set_random_seed(random_seed)
sa.run(
params = self.params,
xray_structure = tmp,
real_space = True,
target_map = self.map_data,
restraints_manager = self.restraints_manager,
wx = self.weight,
wc = 1.,
verbose = False)
return tmp
def geometry_minimization(self,
selection=None,
bond=True,
nonbonded=True,
angle=True,
dihedral=True,
chirality=True,
planarity=True,
max_number_of_iterations=500,
number_of_macro_cycles=5,
rmsd_bonds_termination_cutoff=0,
rmsd_angles_termination_cutoff=0):
"""
Perform geometry minimization on a selection of boxed atoms.
"""
from mmtbx.refinement import geometry_minimization
from cctbx import geometry_restraints
from scitbx.array_family import flex
import scitbx.lbfgs
if (selection is None):
selection = self.selection_in_box
if (type(selection).__name__ == 'size_t'):
selection = flex.bool(self.n_sites_box,
False).set_selected(selection, True)
lbfgs_termination_params = scitbx.lbfgs.termination_parameters(
max_iterations=max_number_of_iterations)
geometry_restraints_flags = geometry_restraints.flags.flags(
bond=bond,
nonbonded=nonbonded,
angle=angle,
dihedral=dihedral,
chirality=chirality,
planarity=planarity)
site_labels = self.box.xray_structure_box.scatterers().extract_labels()
for i in range(number_of_macro_cycles):
sites_cart = self.box.xray_structure_box.sites_cart()
exception_handling_params = scitbx.lbfgs.exception_handling_parameters(
ignore_line_search_failed_step_at_lower_bound=True)
minimized = geometry_minimization.lbfgs(
sites_cart=sites_cart,
correct_special_position_tolerance=1.0,
geometry_restraints_manager=self.geo_box,
geometry_restraints_flags=geometry_restraints_flags,
lbfgs_termination_params=lbfgs_termination_params,
lbfgs_exception_handling_params=exception_handling_params,
sites_cart_selection=selection,
rmsd_bonds_termination_cutoff=rmsd_bonds_termination_cutoff,
rmsd_angles_termination_cutoff=rmsd_angles_termination_cutoff,
site_labels=site_labels)
self.update_coordinates(sites_cart)
def geometry_minimization (self,
selection=None,
bond=True,
nonbonded=True,
angle=True,
dihedral=True,
chirality=True,
planarity=True,
max_number_of_iterations=500,
number_of_macro_cycles=5,
rmsd_bonds_termination_cutoff = 0,
rmsd_angles_termination_cutoff = 0) :
"""
Perform geometry minimization on a selection of boxed atoms.
"""
from mmtbx.refinement import geometry_minimization
from cctbx import geometry_restraints
from scitbx.array_family import flex
import scitbx.lbfgs
if (selection is None) :
selection = self.selection_in_box
if (type(selection).__name__ == 'size_t') :
selection = flex.bool(self.n_sites_box, False).set_selected(selection, True)
lbfgs_termination_params = scitbx.lbfgs.termination_parameters(
max_iterations = max_number_of_iterations)
geometry_restraints_flags = geometry_restraints.flags.flags(
bond = bond,
nonbonded = nonbonded,
angle = angle,
dihedral = dihedral,
chirality = chirality,
planarity = planarity)
site_labels = self.box.xray_structure_box.scatterers().extract_labels()
for i in xrange(number_of_macro_cycles):
sites_cart = self.box.xray_structure_box.sites_cart()
exception_handling_params = scitbx.lbfgs.exception_handling_parameters(
ignore_line_search_failed_step_at_lower_bound = True)
minimized = geometry_minimization.lbfgs(
sites_cart = sites_cart,
correct_special_position_tolerance = 1.0,
geometry_restraints_manager = self.geo_box,
geometry_restraints_flags = geometry_restraints_flags,
lbfgs_termination_params = lbfgs_termination_params,
lbfgs_exception_handling_params = exception_handling_params,
sites_cart_selection = selection,
rmsd_bonds_termination_cutoff = rmsd_bonds_termination_cutoff,
rmsd_angles_termination_cutoff = rmsd_angles_termination_cutoff,
site_labels=site_labels)
self.update_coordinates(sites_cart)
def regularize_geometry(xray_structure, restraints_manager, params):
from mmtbx.refinement import geometry_minimization as gm
import scitbx.lbfgs
sites_cart = xray_structure.sites_cart()
minimized = gm.lbfgs(
sites_cart = sites_cart,
correct_special_position_tolerance = 1.0,
geometry_restraints_manager = restraints_manager.geometry,
geometry_restraints_flags = gm.geometry_restraints.flags.flags(default=True),
rmsd_bonds_termination_cutoff=params.rmsd_bonds_target,
rmsd_angles_termination_cutoff=params.rmsd_angles_target,
lbfgs_termination_params=scitbx.lbfgs.termination_parameters(
max_iterations=500))
xray_structure = xray_structure.replace_sites_cart(new_sites = sites_cart)
return xray_structure
def regularize_geometry(xray_structure, restraints_manager, params):
from mmtbx.refinement import geometry_minimization as gm
import scitbx.lbfgs
sites_cart = xray_structure.sites_cart()
minimized = gm.lbfgs(
sites_cart = sites_cart,
correct_special_position_tolerance = 1.0,
geometry_restraints_manager = restraints_manager.geometry,
geometry_restraints_flags = gm.geometry_restraints.flags.flags(default=True),
rmsd_bonds_termination_cutoff=params.rmsd_bonds_target,
rmsd_angles_termination_cutoff=params.rmsd_angles_target,
lbfgs_termination_params=scitbx.lbfgs.termination_parameters(
max_iterations=500))
xray_structure = xray_structure.replace_sites_cart(new_sites = sites_cart)
return xray_structure
def adiabatic_mapping (pdb_hierarchy,
restraints_manager,
start_coords,
end_coords,
params,
nsteps=10,
verbose=False,
out=None) :
"""
Linear interpolation with energy minimization. The number of minimizer
cycles should be kept low to prevent each "frame" from snapping back to the
starting coordinates. Interpolating the dihedral restraint target angles
may help remediate this problem.
"""
from mmtbx.refinement import geometry_minimization
from cctbx import geometry_restraints
import scitbx.lbfgs
if (start_coords.size() != end_coords.size()) :
raise RuntimeError("Coordinate size mismatch: %d versus %d" %
(start_coords.size(), end_coords.size()))
grm = restraints_manager
include_dihedrals = (params.interpolate_dihedrals or
(not params.exclude_dihedrals))
grm_flags = geometry_restraints.flags.flags(
default=True,
dihedral=include_dihedrals)
term_params = scitbx.lbfgs.termination_parameters(
max_iterations=params.n_min_steps)
dihedral_steps = []
n = nsteps - 1
if (params.interpolate_dihedrals) :
# FIXME this needs work - should find the optimal path instead of the
# simplistic assumption currently made
for proxy in grm.dihedral_proxies :
sites1 = []
sites2 = []
for k in range(4) :
sites1.append(start_coords[proxy.i_seqs[k]])
sites2.append(end_coords[proxy.i_seqs[k]])
dihe_start = geometry_restraints.dihedral(
sites=sites1,
angle_ideal=0,
weight=1).angle_model
dihe_end = geometry_restraints.dihedral(
sites=sites2,
angle_ideal=0,
weight=1).angle_model
delta = (dihe_end - dihe_start) / n
dihedral_steps.append(delta)
proxy.weight = 0.1
m = morph(pdb_hierarchy)
m.add_frame(start_coords)
current_xyz = start_coords
final_xyz = end_coords
while n > 0 :
print >> out, "Interpolation step %d" % (nsteps - n)
if (verbose) :
print >> out, ""
new_xyz = current_xyz.deep_copy()
dxyz = (final_xyz - new_xyz) * (1. / n)
new_xyz += dxyz
if (params.minimize) :
if (params.interpolate_dihedrals) :
for k, proxy in enumerate(grm.dihedral_proxies) :
proxy.angle_ideal += dihedral_steps[k]
minimized = geometry_minimization.lbfgs(
sites_cart=new_xyz,
geometry_restraints_manager=grm,
geometry_restraints_flags=grm_flags,
lbfgs_termination_params=term_params)
if (verbose) :
n_iter = minimized.minimizer.iter()
print >> out, ""
print >> out, "Number of minimization iterations:", n_iter
print >> out, ""
print >> out, "Energies at end of minimization:"
minimized.final_target_result.show(f=out)
print >> out, "RMS coordinate change: %.3f" % current_xyz.rms_difference(new_xyz)
m.add_frame(new_xyz)
n -= 1
current_xyz = new_xyz
m.add_frame(final_xyz)
return m
