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 __init__(
self,
# pdb_hierarchy,
# standard_geometry_restraints_manager,
params,
energy_components=None,
# gradients=None,
# number_of_restraints=0,
gradients_factory=flex.vec3_double,
# amber_structs=None,
log=StringIO()):
self.gradients_factory = gradients_factory
# self.number_of_restraints = number_of_restraints
# self.amber_structs = amber_structs
adopt_init_args(self, locals(), exclude=["log"])
self.initialisation(params, log)
from amber_adaptbx import interface
self.amber_structs, self.sander = interface.get_amber_struct_object(
params)
# self.sander = sander # used for cleanup
# self.sites_cart = self.pdb_hierarchy.atoms().extract_xyz()
compute_gradients = False
# amber_geometry_manager = amber_adaptbx.geometry_manager(
# sites_cart=sites_cart,
# gradients_factory=flex.vec3_double,
# amber_structs=self.amber_structs)
# order_converter is a Python dict that map amber atom order to phenix order
# assign later
if manager.COUNT == 0:
# compute order_converter from original sites_cart or load from file
initialize_order_converter(self)
self.print_amber_energies = params.amber.print_amber_energies
# self.qmmask = params.amber.qmmask
# sites_cart = self.pdb_hierarchy.atoms().extract_xyz()
# print('sites_cart',len(sites_cart))
# geometry = self.energies_sites(
# sites_cart = self.pdb_hierarchy.atoms().extract_xyz(),
# compute_gradients = compute_gradients,
# log=log,
# print_amber_energies=self.print_amber_energies,
# #qmmask=self.qmmask,
# )
# increase COUNT to avoid recompute order_converter
manager.COUNT += 1
if self.energy_components is None:
self.energy_components = flex.double(
[0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0])