def compute_functional_and_gradients(self):
sites_cart = flex.vec3_double(self.x)
f = 0
g = flex.vec3_double(sites_cart.size(), (0, 0, 0))
for sorted_asu_proxies in [self.conservative_pair_proxies.bond, self.conservative_pair_proxies.angle]:
if sorted_asu_proxies is None:
continue
f += geometry_restraints.bond_residual_sum(
sites_cart=sites_cart, sorted_asu_proxies=sorted_asu_proxies, gradient_array=g
)
return f, g.as_double()
def compute_functional_and_gradients(O):
cs = O.grm.crystal_symmetry
sst = O.grm.site_symmetry_table
sites_frac = sst.unpack_coordinates(packed_coordinates=O.x)
sites_cart = cs.unit_cell().orthogonalize(sites_frac)
g_cart = flex.vec3_double(sites_cart.size(), (0,0,0))
f = geometry_restraints.bond_residual_sum(
unit_cell=cs.unit_cell(),
sites_cart=sites_cart,
proxies=O.proxies,
gradient_array=g_cart)
g_frac = g_cart * cs.unit_cell().orthogonalization_matrix()
g = sst.pack_gradients(g_frac=g_frac)
return f, g
def compute_functional_and_gradients(self):
sites_cart = flex.vec3_double(self.x)
f = 0
g = flex.vec3_double(sites_cart.size(), (0, 0, 0))
for sorted_asu_proxies in [
self.conservative_pair_proxies.bond,
self.conservative_pair_proxies.angle
]:
if (sorted_asu_proxies is None): continue
f += geometry_restraints.bond_residual_sum(
sites_cart=sites_cart,
sorted_asu_proxies=sorted_asu_proxies,
gradient_array=g)
return f, g.as_double()
def __init__(self, sites_cart,
unit_cell=None,
bond_proxies=None,
nonbonded_proxies=None,
nonbonded_function=None,
angle_proxies=None,
dihedral_proxies=None,
reference_coordinate_proxies=None,
reference_dihedral_manager=None,
ncs_dihedral_manager=None,
den_manager=None,
chirality_proxies=None,
planarity_proxies=None,
parallelity_proxies=None,
bond_similarity_proxies=None,
ramachandran_manager=None,
external_energy_function=None,
compute_gradients=True,
gradients=None,
disable_asu_cache=False,
normalization=False,
extension_objects=[]):
# runsnaked away...
#adopt_init_args(self, locals())
#for local in sorted(locals()):
# print " self.%(local)s=%(local)s" % locals()
#assert 0
#
self.angle_proxies=angle_proxies
self.bond_proxies=bond_proxies
self.bond_similarity_proxies=bond_similarity_proxies
self.chirality_proxies=chirality_proxies
self.compute_gradients=compute_gradients
self.den_manager=den_manager
self.dihedral_proxies=dihedral_proxies
self.disable_asu_cache=disable_asu_cache
self.extension_objects=extension_objects
self.external_energy_function=external_energy_function
self.gradients=gradients
self.ncs_dihedral_manager=ncs_dihedral_manager
self.nonbonded_function=nonbonded_function
self.nonbonded_proxies=nonbonded_proxies
self.normalization=normalization
self.parallelity_proxies=parallelity_proxies
self.planarity_proxies=planarity_proxies
self.ramachandran_manager=ramachandran_manager
self.reference_coordinate_proxies=reference_coordinate_proxies
self.reference_dihedral_manager=reference_dihedral_manager
self.sites_cart=sites_cart
self.unit_cell=unit_cell
#
scitbx.restraints.energies.__init__(self,
compute_gradients=compute_gradients,
gradients=gradients,
gradients_size=sites_cart.size(),
gradients_factory=flex.vec3_double,
normalization=normalization)
self.n_dihedral_restraints = None
self.dihedral_restraints_residual_sum = 0
if (nonbonded_proxies is not None): assert nonbonded_function is not None
if (compute_gradients):
if (self.gradients is None):
self.gradients = flex.vec3_double(sites_cart.size(), [0,0,0])
else:
assert self.gradients.size() == sites_cart.size()
if (bond_proxies is None):
self.n_bond_proxies = None
self.bond_residual_sum = 0
else:
self.n_bond_proxies = bond_proxies.n_total()
self.bond_residual_sum = geometry_restraints.bond_residual_sum(
sites_cart=sites_cart,
sorted_asu_proxies=bond_proxies,
gradient_array=self.gradients,
disable_cache=disable_asu_cache)
self.number_of_restraints += self.n_bond_proxies
self.residual_sum += self.bond_residual_sum
if (nonbonded_proxies is None):
self.n_nonbonded_proxies = None
self.nonbonded_residual_sum = 0
else:
self.n_nonbonded_proxies = nonbonded_proxies.n_total()
self.nonbonded_residual_sum = geometry_restraints.nonbonded_residual_sum(
sites_cart=sites_cart,
sorted_asu_proxies=nonbonded_proxies,
gradient_array=self.gradients,
function=nonbonded_function,
disable_cache=False)
self.number_of_restraints += self.n_nonbonded_proxies
self.residual_sum += self.nonbonded_residual_sum
# ====================================================================
# Unit cell dependent
# ====================================================================
# name, parameter, function to call
for name, proxies, residual_sum_function in [
("angle", angle_proxies, geometry_restraints.angle_residual_sum),
("dihedral",dihedral_proxies, geometry_restraints.dihedral_residual_sum),
("planarity", planarity_proxies, geometry_restraints.planarity_residual_sum),
("parallelity", parallelity_proxies, geometry_restraints.parallelity_residual_sum),
("bond_similarity", bond_similarity_proxies, geometry_restraints.bond_similarity_residual_sum)]:
setattr(self, "n_%s_proxies" % name, None)
setattr(self, "%s_residual_sum" % name, 0)
if proxies is not None:
n_proxies = proxies.size()
# setattr(self, "n_%s_proxies" % name, proxies.size())
if unit_cell is None:
res_sum = residual_sum_function(
sites_cart=sites_cart,
proxies=proxies,
gradient_array=self.gradients)
else:
res_sum = residual_sum_function(
unit_cell=unit_cell,
sites_cart=sites_cart,
proxies=proxies,
gradient_array=self.gradients)
self.number_of_restraints += n_proxies
self.residual_sum += res_sum
setattr(self, "n_%s_proxies" % name, n_proxies)
setattr(self, "%s_residual_sum" % name, res_sum)
# ====================================================================
# Managers
# ====================================================================
for name, manager in [
("reference_dihedral", reference_dihedral_manager),
("ncs_dihedral", ncs_dihedral_manager),
("den", den_manager),
("ramachandran", ramachandran_manager)]:
setattr(self, "n_%s_proxies" % name, None)
setattr(self, "%s_residual_sum" % name, 0)
if manager is not None:
n_proxies = manager.get_n_proxies()
res_sum = manager.target_and_gradients(
unit_cell=unit_cell,
sites_cart=sites_cart,
gradient_array=self.gradients)
self.number_of_restraints += n_proxies
self.residual_sum += res_sum
setattr(self, "n_%s_proxies" % name, n_proxies)
setattr(self, "%s_residual_sum" % name, res_sum)
# ====================================================================
# The rest (not yet unified)
# ====================================================================
if reference_coordinate_proxies is None:
self.n_reference_coordinate_proxies = None
self.reference_coordinate_residual_sum = 0
else:
import boost.python
ext = boost.python.import_ext("mmtbx_reference_coordinate_ext")
self.n_reference_coordinate_proxies = reference_coordinate_proxies.size()
self.reference_coordinate_residual_sum = \
ext.reference_coordinate_residual_sum(
sites_cart=sites_cart,
proxies=reference_coordinate_proxies,
gradient_array=self.gradients)
self.number_of_restraints += self.n_reference_coordinate_proxies
self.residual_sum += self.reference_coordinate_residual_sum
if (chirality_proxies is None):
self.n_chirality_proxies = None
self.chirality_residual_sum = 0
else:
self.n_chirality_proxies = len(chirality_proxies)
self.chirality_residual_sum = geometry_restraints.chirality_residual_sum(
sites_cart=sites_cart,
proxies=chirality_proxies,
gradient_array=self.gradients)
self.number_of_restraints += self.n_chirality_proxies
self.residual_sum += self.chirality_residual_sum
if (external_energy_function is not None) :
self.external_energy = external_energy_function(
sites_cart=sites_cart,
gradient_array=self.gradients)
self.residual_sum += self.external_energy
else :
self.external_energy = 0
for extension_obj in self.extension_objects:
extension_obj.energies_add(energies_obj=self)
self.finalize_target_and_gradients()
def __init__(self,
sites_cart,
unit_cell=None,
bond_proxies=None,
nonbonded_proxies=None,
nonbonded_function=None,
angle_proxies=None,
dihedral_proxies=None,
reference_coordinate_proxies=None,
reference_dihedral_manager=None,
ncs_dihedral_manager=None,
den_manager=None,
chirality_proxies=None,
planarity_proxies=None,
parallelity_proxies=None,
bond_similarity_proxies=None,
ramachandran_manager=None,
external_energy_function=None,
compute_gradients=True,
gradients=None,
disable_asu_cache=False,
normalization=False,
extension_objects=[]):
# runsnaked away...
#adopt_init_args(self, locals())
#for local in sorted(locals()):
# print " self.%(local)s=%(local)s" % locals()
#assert 0
#
self.angle_proxies = angle_proxies
self.bond_proxies = bond_proxies
self.bond_similarity_proxies = bond_similarity_proxies
self.chirality_proxies = chirality_proxies
self.compute_gradients = compute_gradients
self.den_manager = den_manager
self.dihedral_proxies = dihedral_proxies
self.disable_asu_cache = disable_asu_cache
self.extension_objects = extension_objects
self.external_energy_function = external_energy_function
self.gradients = gradients
self.ncs_dihedral_manager = ncs_dihedral_manager
self.nonbonded_function = nonbonded_function
self.nonbonded_proxies = nonbonded_proxies
self.normalization = normalization
self.parallelity_proxies = parallelity_proxies
self.planarity_proxies = planarity_proxies
self.ramachandran_manager = ramachandran_manager
self.reference_coordinate_proxies = reference_coordinate_proxies
self.reference_dihedral_manager = reference_dihedral_manager
self.sites_cart = sites_cart
self.unit_cell = unit_cell
#
scitbx.restraints.energies.__init__(
self,
compute_gradients=compute_gradients,
gradients=gradients,
gradients_size=sites_cart.size(),
gradients_factory=flex.vec3_double,
normalization=normalization)
self.n_dihedral_restraints = None
self.dihedral_restraints_residual_sum = 0
if (nonbonded_proxies is not None):
assert nonbonded_function is not None
if (compute_gradients):
if (self.gradients is None):
self.gradients = flex.vec3_double(sites_cart.size(), [0, 0, 0])
else:
assert self.gradients.size() == sites_cart.size()
if (bond_proxies is None):
self.n_bond_proxies = None
self.bond_residual_sum = 0
else:
self.n_bond_proxies = bond_proxies.n_total()
self.bond_residual_sum = geometry_restraints.bond_residual_sum(
sites_cart=sites_cart,
sorted_asu_proxies=bond_proxies,
gradient_array=self.gradients,
disable_cache=disable_asu_cache)
self.number_of_restraints += self.n_bond_proxies
self.residual_sum += self.bond_residual_sum
if (nonbonded_proxies is None):
self.n_nonbonded_proxies = None
self.nonbonded_residual_sum = 0
else:
self.n_nonbonded_proxies = nonbonded_proxies.n_total()
self.nonbonded_residual_sum = geometry_restraints.nonbonded_residual_sum(
sites_cart=sites_cart,
sorted_asu_proxies=nonbonded_proxies,
gradient_array=self.gradients,
function=nonbonded_function,
disable_cache=False)
self.number_of_restraints += self.n_nonbonded_proxies
self.residual_sum += self.nonbonded_residual_sum
# ====================================================================
# Unit cell dependent
# ====================================================================
# name, parameter, function to call
for name, proxies, residual_sum_function in [
("angle", angle_proxies, geometry_restraints.angle_residual_sum),
("dihedral", dihedral_proxies,
geometry_restraints.dihedral_residual_sum),
("planarity", planarity_proxies,
geometry_restraints.planarity_residual_sum),
("parallelity", parallelity_proxies,
geometry_restraints.parallelity_residual_sum),
("bond_similarity", bond_similarity_proxies,
geometry_restraints.bond_similarity_residual_sum)
]:
setattr(self, "n_%s_proxies" % name, None)
setattr(self, "%s_residual_sum" % name, 0)
if proxies is not None:
n_proxies = proxies.size()
# setattr(self, "n_%s_proxies" % name, proxies.size())
if unit_cell is None:
res_sum = residual_sum_function(
sites_cart=sites_cart,
proxies=proxies,
gradient_array=self.gradients)
else:
res_sum = residual_sum_function(
unit_cell=unit_cell,
sites_cart=sites_cart,
proxies=proxies,
gradient_array=self.gradients)
self.number_of_restraints += n_proxies
self.residual_sum += res_sum
setattr(self, "n_%s_proxies" % name, n_proxies)
setattr(self, "%s_residual_sum" % name, res_sum)
# ====================================================================
# Managers
# ====================================================================
for name, manager in [("reference_dihedral",
reference_dihedral_manager),
("ncs_dihedral", ncs_dihedral_manager),
("den", den_manager),
("ramachandran", ramachandran_manager)]:
setattr(self, "n_%s_proxies" % name, None)
setattr(self, "%s_residual_sum" % name, 0)
if manager is not None:
n_proxies = manager.get_n_proxies()
res_sum = manager.target_and_gradients(
unit_cell=unit_cell,
sites_cart=sites_cart,
gradient_array=self.gradients)
self.number_of_restraints += n_proxies
self.residual_sum += res_sum
setattr(self, "n_%s_proxies" % name, n_proxies)
setattr(self, "%s_residual_sum" % name, res_sum)
# ====================================================================
# The rest (not yet unified)
# ====================================================================
if reference_coordinate_proxies is None:
self.n_reference_coordinate_proxies = None
self.reference_coordinate_residual_sum = 0
else:
import boost.python
ext = boost.python.import_ext("mmtbx_reference_coordinate_ext")
self.n_reference_coordinate_proxies = reference_coordinate_proxies.size(
)
self.reference_coordinate_residual_sum = \
ext.reference_coordinate_residual_sum(
sites_cart=sites_cart,
proxies=reference_coordinate_proxies,
gradient_array=self.gradients)
self.number_of_restraints += self.n_reference_coordinate_proxies
self.residual_sum += self.reference_coordinate_residual_sum
if (chirality_proxies is None):
self.n_chirality_proxies = None
self.chirality_residual_sum = 0
else:
self.n_chirality_proxies = len(chirality_proxies)
self.chirality_residual_sum = geometry_restraints.chirality_residual_sum(
sites_cart=sites_cart,
proxies=chirality_proxies,
gradient_array=self.gradients)
self.number_of_restraints += self.n_chirality_proxies
self.residual_sum += self.chirality_residual_sum
if (external_energy_function is not None):
self.external_energy = external_energy_function(
sites_cart=sites_cart, gradient_array=self.gradients)
self.residual_sum += self.external_energy
else:
self.external_energy = 0
for extension_obj in self.extension_objects:
extension_obj.energies_add(energies_obj=self)
self.finalize_target_and_gradients()
