def set_relative_movers(self, max_translation, max_rotation):
"""
Generate the relative models form the transfors. The transforms
is a list with triplets [id1, id2, transform_file]
@param max_translation Maximum translation distance allowed for
the moves
@param nax_rotation Maximum rotation angle allowed for the moves
"""
log.info("Setting relative movers")
self.movers = []
relative_movers = []
relative_names = []
for d in self.dock_transforms:
rb_id = representation.get_rb_name(d[1])
if rb_id not in relative_names:
log.debug("Checking for %s", rb_id)
rb_lig = representation.get_rigid_body(self.rbs, rb_id)
mv = em2d.RelativePositionMover(rb_lig, max_translation,
max_rotation)
relative_movers.append(mv)
relative_names.append(rb_id)
log.debug("added a RelativePositionMover for %s",rb_id)
i = relative_names.index(rb_id)
relative_movers[i].set_random_move_probability(
self.non_relative_move_prob)
rb_rec = representation.get_rigid_body(self.rbs,
representation.get_rb_name(d[0]))
log.debug("Reference added for %s: %s. ref. frame %s ",
rb_id, rb_rec.get_name(), rb_rec)
Tis = io.read_transforms(d[2])
relative_movers[i].add_internal_transformations(rb_rec, Tis)
# add regular movers for the rigid bodies that are neither moved
# anchored nor moved relative to others
regular_movers = []
for is_anchored, rb in zip(self.anchored, self.rbs):
if(not is_anchored):
name =rb.get_name()
if(not name in relative_names):
log.debug("adding a RigidBodyMover for %s",name)
mv = core.RigidBodyMover(rb, max_translation, max_rotation)
regular_movers.append(mv)
self.movers = regular_movers
self.movers += relative_movers
sel = atom.ATOMPDBSelector()
m = IMP.Model()
h_receptor = atom.read_pdb(args.fn_receptor, m, sel)
rb_receptor = atom.create_rigid_body(h_receptor)
h_ligand = atom.read_pdb(args.fn_ligand, m, sel)
rb_ligand = atom.create_rigid_body(h_ligand)
if args.dock:
check_for_hexdock()
if not args.fn_transforms or not args.fn_internal_transforms:
raise IOError("Docking requires the --int and --hex arguments")
hex_docking = HexDocking()
hex_docking.dock(args.fn_receptor, args.fn_ligand, args.fn_transforms)
# read the HEX file of solutions and get the internal transformations
# giving the relative orientation of the ligand respect to the receptor
Ts = read_hex_transforms(args.fn_transforms)
rb_receptor = atom.create_rigid_body(h_receptor)
Tis = [get_internal_transform(T, rb_receptor, rb_ligand) for T in Ts]
io.write_transforms(Tis, args.fn_internal_transforms)
elif args.write:
# To write the positions correctly, the script requires that the
# ligand file is the same that was used for the docking
Tinternal = io.read_transforms(args.fn_internal_transforms)
max_number = min(args.write, len(Tinternal))
Trec = rb_receptor.get_reference_frame().get_transformation_to()
for i in range(max_number):
Tdock = alg.compose(Trec, Tinternal[i])
ref = alg.ReferenceFrame3D(Tdock)
rb_ligand.set_reference_frame(ref)
atom.write_pdb(h_ligand,"docked-%03d.pdb" % i)
logging.root.setLevel(logging.DEBUG)
sel = atom.ATOMPDBSelector()
m = IMP.Model()
h_receptor = atom.read_pdb(fn_receptor, m, sel)
rb_receptor = atom.create_rigid_body(h_receptor)
h_ligand = atom.read_pdb(fn_ligand, m, sel)
rb_ligand = atom.create_rigid_body(h_ligand)
if opts.dock:
check_for_hexdock()
if not opts.fn_transforms or not opts.fn_internal_transforms:
raise IOError("Docking requires the --int and --hex arguments")
hex_docking = HexDocking()
hex_docking.dock(fn_receptor, fn_ligand, opts.fn_transforms)
# read the HEX file of solutions and get the internal transformations
# giving the relative orientation of the ligand respect to the receptor
Ts = read_hex_transforms(opts.fn_transforms)
Tis = [get_internal_transform(T, rb_receptor, rb_ligand) for T in Ts]
io.write_transforms(Tis, opts.fn_internal_transforms)
elif opts.write:
# To write the positions correctly, the script requires that the
# ligand file is the same that was used for the docking
Tinternal = io.read_transforms(opts.fn_internal_transforms)
max_number = min(opts.write, len(Tinternal))
Trec = rb_receptor.get_reference_frame().get_transformation_to()
for i in range(max_number):
Tdock = alg.compose(Trec, Tinternal[i])
ref = alg.ReferenceFrame3D(Tdock)
rb_ligand.set_reference_frame(ref)
atom.write_pdb(h_ligand,"docked-%03d.pdb" % i)
