def init_amber(self, params, pdb_hierarchy, log):
if hasattr(params, "amber"):
self.use_amber = params.amber.use_amber
print_amber_energies = params.amber.print_amber_energies
if (self.use_amber):
sites_cart = pdb_hierarchy.atoms().extract_xyz()
compute_gradients = False
make_header("Initializing AMBER", out=log)
print >> log, " topology : %s" % params.amber.topology_file_name
print >> log, " atom order : %s" % params.amber.order_file_name
if params.amber.coordinate_file_name:
print >> log, " coordinates : %s" % params.amber.coordinate_file_name
from amber_adaptbx import interface
self.amber_structs, sander = interface.get_amber_struct_object(
params)
self.sander = sander # used for cleanup
import amber_adaptbx
amber_geometry_manager = amber_adaptbx.geometry_manager(
sites_cart=sites_cart,
#number_of_restraints=geometry_energy.number_of_restraints,
gradients_factory=flex.vec3_double,
amber_structs=self.amber_structs)
geometry = amber_geometry_manager.energies_sites(
crystal_symmetry=self.geometry.crystal_symmetry,
compute_gradients=compute_gradients)
def show(self, amber_structs, log=None):
import amber_adaptbx as amber
amber_geometry_manager=amber.geometry_manager(
sites_cart=self.pdb_hierarchy.atoms().extract_xyz(),
amber_structs=amber_structs)
amber_geometry=amber_geometry_manager.energies_sites(
self.restraints_manager.geometry.crystal_symmetry,
log=log,
)
amber_geometry.show()
def energies_sites(
self,
sites_cart,
geometry_flags=None,
external_energy_function=None,
custom_nonbonded_function=None,
compute_gradients=False,
gradients=None,
force_restraints_model=False,
disable_asu_cache=False,
hd_selection=None,
):
"""
Compute energies for coordinates. Originally this just used the standard
geometry restraints from the monomer library, but it has since been
extended to optionally incorporate a variety of external energy functions.
:returns: scitbx.restraints.energies object
"""
result = scitbx.restraints.energies(
compute_gradients=compute_gradients,
gradients=gradients,
gradients_size=sites_cart.size(),
gradients_factory=flex.vec3_double,
normalization=self.normalization)
if (self.geometry is None):
result.geometry = None
else:
if (self.use_amber and not force_restraints_model):
geometry_energy = self.geometry.energies_sites(
sites_cart=sites_cart,
flags=geometry_flags,
external_energy_function=external_energy_function,
custom_nonbonded_function=custom_nonbonded_function,
compute_gradients=False,
gradients=None,
disable_asu_cache=disable_asu_cache,
normalization=False)
##################################################################
# #
# AMBER CALL - Amber force field gradients and target #
# #
##################################################################
import amber_adaptbx
amber_geometry_manager = amber_adaptbx.geometry_manager(
sites_cart=sites_cart,
number_of_restraints=geometry_energy.number_of_restraints,
gradients_factory=flex.vec3_double,
amber_structs=self.amber_structs)
result.geometry = amber_geometry_manager.energies_sites(
crystal_symmetry=self.geometry.crystal_symmetry,
compute_gradients=compute_gradients)
elif (self.use_afitt
and len(sites_cart) == self.afitt_object.total_model_atoms):
##################################################################
# #
# AFITT CALL - OpenEye AFITT gradients and target #
# #
##################################################################
from mmtbx.geometry_restraints import afitt
result.geometry = self.geometry.energies_sites(
sites_cart=sites_cart,
flags=geometry_flags,
external_energy_function=external_energy_function,
custom_nonbonded_function=custom_nonbonded_function,
compute_gradients=compute_gradients,
gradients=result.gradients,
disable_asu_cache=disable_asu_cache,
normalization=False,
)
result = afitt.apply(result, self.afitt_object, sites_cart)
result = afitt.adjust_energy_and_gradients(
result,
self,
sites_cart,
hd_selection,
self.afitt_object,
)
result.target = result.residual_sum
result.afitt_energy = result.residual_sum
else:
result.geometry = self.geometry.energies_sites(
sites_cart=sites_cart,
flags=geometry_flags,
external_energy_function=external_energy_function,
custom_nonbonded_function=custom_nonbonded_function,
compute_gradients=compute_gradients,
gradients=result.gradients,
disable_asu_cache=disable_asu_cache,
normalization=False)
result += result.geometry
if (self.cartesian_ncs_manager is None):
result.cartesian_ncs_manager = None
else:
result.cartesian_ncs_manager = self.cartesian_ncs_manager.energies_sites(
sites_cart=sites_cart,
compute_gradients=compute_gradients,
gradients=result.gradients,
normalization=False)
result += result.cartesian_ncs_manager
result.finalize_target_and_gradients()
return result
def energies_sites(self,
sites_cart,
geometry_flags=None,
external_energy_function=None,
custom_nonbonded_function=None,
compute_gradients=False,
gradients=None,
force_restraints_model=False,
disable_asu_cache=False,
hd_selection=None,
):
"""
Compute energies for coordinates. Originally this just used the standard
geometry restraints from the monomer library, but it has since been
extended to optionally incorporate a variety of external energy functions.
:returns: scitbx.restraints.energies object
"""
result = scitbx.restraints.energies(
compute_gradients=compute_gradients,
gradients=gradients,
gradients_size=sites_cart.size(),
gradients_factory=flex.vec3_double,
normalization=self.normalization)
if (self.geometry is None):
result.geometry = None
else:
if (self.use_amber and not force_restraints_model) :
geometry_energy = self.geometry.energies_sites(
sites_cart=sites_cart,
flags=geometry_flags,
external_energy_function=external_energy_function,
custom_nonbonded_function=custom_nonbonded_function,
compute_gradients=False,
gradients=None,
disable_asu_cache=disable_asu_cache,
normalization=False)
##################################################################
# #
# AMBER CALL - Amber force field gradients and target #
# #
##################################################################
import amber_adaptbx
amber_geometry_manager = amber_adaptbx.geometry_manager(
sites_cart=sites_cart,
number_of_restraints=geometry_energy.number_of_restraints,
gradients_factory=flex.vec3_double,
amber_structs=self.amber_structs)
result.geometry = amber_geometry_manager.energies_sites(
crystal_symmetry = self.geometry.crystal_symmetry,
compute_gradients = compute_gradients)
elif (self.use_afitt and
len(sites_cart)==self.afitt_object.total_model_atoms
):
##################################################################
# #
# AFITT CALL - OpenEye AFITT gradients and target #
# #
##################################################################
from mmtbx.geometry_restraints import afitt
result.geometry = self.geometry.energies_sites(
sites_cart=sites_cart,
flags=geometry_flags,
external_energy_function=external_energy_function,
custom_nonbonded_function=custom_nonbonded_function,
compute_gradients=compute_gradients,
gradients=result.gradients,
disable_asu_cache=disable_asu_cache,
normalization=False,
)
result = afitt.apply(result, self.afitt_object, sites_cart)
result = afitt.adjust_energy_and_gradients(
result,
self,
sites_cart,
hd_selection,
self.afitt_object,
)
result.target = result.residual_sum
result.afitt_energy=result.residual_sum
else :
result.geometry = self.geometry.energies_sites(
sites_cart=sites_cart,
flags=geometry_flags,
external_energy_function=external_energy_function,
custom_nonbonded_function=custom_nonbonded_function,
compute_gradients=compute_gradients,
gradients=result.gradients,
disable_asu_cache=disable_asu_cache,
normalization=False)
result += result.geometry
if (self.ncs_groups is None):
result.ncs_groups = None
else:
result.ncs_groups = self.ncs_groups.energies_sites(
sites_cart=sites_cart,
compute_gradients=compute_gradients,
gradients=result.gradients,
normalization=False)
result += result.ncs_groups
result.finalize_target_and_gradients()
return result