def _execute(self, directory, available_resources):
from paprika.evaluator import Setup
# Construct the restraints to keep the host in place and
# with an open cavity.
static_restraints = Setup.build_static_restraints(
self.complex_coordinate_path,
len(self.attach_lambdas),
None,
None,
self.restraint_schemas.get("static", []),
)
conformational_restraints = Setup.build_conformational_restraints(
self.complex_coordinate_path,
self.attach_lambdas,
None,
None,
self.restraint_schemas.get("conformational", []),
)
# Construct the restraints to keep the guest at the correct
# distance and orientation relative to the host.
symmetry_restraints = Setup.build_symmetry_restraints(
self.complex_coordinate_path,
len(self.attach_lambdas),
self.restraint_schemas.get("symmetry", []),
)
wall_restraints = Setup.build_wall_restraints(
self.complex_coordinate_path,
len(self.attach_lambdas),
self.restraint_schemas.get("wall", []),
)
guest_restraints = Setup.build_guest_restraints(
self.complex_coordinate_path,
self.attach_lambdas,
None,
self.restraint_schemas.get("guest", []),
)
self._save_restraints(
directory,
static_restraints,
conformational_restraints,
symmetry_restraints,
wall_restraints,
guest_restraints,
)
def _execute(self, directory, available_resources):
from paprika.evaluator import Setup
# Construct the restraints to keep the host in place and
# with an open cavity.
static_restraints = Setup.build_static_restraints(
self.complex_coordinate_path,
len(self.attach_lambdas),
self.n_pull_windows,
None,
self.restraint_schemas.get("static", []),
)
conformational_restraints = Setup.build_conformational_restraints(
self.complex_coordinate_path,
self.attach_lambdas,
self.n_pull_windows,
None,
self.restraint_schemas.get("conformational", []),
)
# Construct the restraints to keep the guest at the correct
# distance to the host.
guest_restraints = Setup.build_guest_restraints(
self.complex_coordinate_path,
self.attach_lambdas,
self.n_pull_windows,
self.restraint_schemas.get("guest", []),
)
# Remove the attach phases from the restraints as these restraints are
# only being used for the pull phase.
for restraint in (
static_restraints + conformational_restraints + guest_restraints
):
for key in restraint.phase["attach"]:
restraint.phase["attach"][key] = None
self._save_restraints(
directory,
static_restraints,
conformational_restraints,
None,
None,
guest_restraints,
)