def design(self, antibody=True, antigen=False, pack_only=False):
self.pose = self.native_pose.clone()
info = self.pose.pdb_info()
tf = TaskFactory()
tf.push_back(operation.InitializeFromCommandline())
epi_res = ''
for res in self.epitopes_pose:
epi_res += '{0},'.format(res)
epi_selector = ResidueIndexSelector(epi_res)
antibody_selector = ChainSelector()
vec = vector1_std_string()
for chain in self.antibody:
vec.append(chain)
vec.append(chain)
antibody_selector.set_chain_strings(vec)
interface_res_selector = InterGroupInterfaceByVectorSelector(
epi_selector, antibody_selector)
interface_antibody_selector = AndResidueSelector(
interface_res_selector, antibody_selector)
if pack_only: tf.push_back(operation.RestrictToRepacking())
else:
if antigen: design_selector = epi_selector
elif antibody: design_selector = interface_antibody_selector
# FIRST select designable residues and prevent everything else from design and packing
no_design_selector = NotResidueSelector(design_selector)
prevent_repacking_rlt = operation.PreventRepackingRLT()
#restrict_topack = operation.RestrictToRepackingRLT()
prevent_design = operation.OperateOnResidueSubset(
prevent_repacking_rlt, no_design_selector, False)
tf.push_back(prevent_design)
print(tf.create_task_and_apply_taskoperations(self.pose))
packer = pack_min.PackRotamersMover('ref2015')
packer.task_factory(tf)
packer.apply(self.pose)
def clash_based_taskfactory(pdbpath, pose):
insertion = get_insertion(pdbpath)
# How much to add to insertion['stop'] to get the residue number to
# design
lucs_relative_resfile = [4, 5, 6, 8, 12, 16, 20, 23, 24, 26, 27, 30]
# subtract 1 because LUCS loop definitions stop on the residue after the
# insertion, whereas normal loop definition stops at the end of the
# loop.
lucs_relative_resfile = [
i + insertion['stop'] - 1 for i in lucs_relative_resfile
]
# This should give us all designed positions
loop_list = [j for j in range(insertion['start'], insertion['stop'])]
lucs_relative_resfile += loop_list
design_mask = size_list_to_res_selector(lucs_relative_resfile, pose)
design_selector = select.residue_selector.ResidueIndexSelector(
numeric.intlist_to_vector1_size(lucs_relative_resfile))
# Takes a resfile and returns a task factory with a clash-based
# repack shell.
tf = TaskFactory()
cl = operation.InitializeFromCommandline()
notaa = operation.ProhibitSpecifiedBaseResidueTypes(
strlist_to_vector1_str(['C', 'H']), design_selector)
# read = operation.ReadResfile(resfile)
tf.push_back(cl)
tf.push_back(notaa)
# tf.push_back(read)
# Select repackable residues from designed residues
repack_only = operation.RestrictToRepackingRLT()
repack = operation.OperateOnResidueSubset(repack_only, design_selector,
False)
repack.flip_subset(True)
tf.push_back(repack)
all_selector = residue_selector.ClashBasedShellSelector(design_mask)
all_selector.set_num_shells(2)
all_selector.set_include_focus(True)
all_selector.invert(True)
no_packing = operation.PreventRepackingRLT()
static = operation.OperateOnResidueSubset(no_packing, all_selector, False)
packertask = tf.create_task_and_apply_taskoperations(pose)
ld = rosetta_scripts.XmlObjects.static_get_task_operation(
'''<LayerDesign name="layer_all" layer="core_boundary_surface_Nterm_Cterm" use_sidechain_neighbors="True">
<Nterm>
<all append="DEGHKNQRST" />
<all exclude="CAFILMPVWY" />
</Nterm>
<Cterm>
<all append="DEGHKNQRST" />
<all exclude="CAFILMPVWY" />
</Cterm>
</LayerDesign>''')
tf.push_back(static)
tf.push_back(ld)
packertask = tf.create_task_and_apply_taskoperations(pose)
print('PRINTING PACKERTASK')
print(packertask)
repack_mask = packertask.repacking_residues()
design_mask = packertask.designing_residues()
movemap = setup_movemap_from_resselectors(design_mask, repack_mask)
return tf, movemap
# score WT and N501Y mutant
WT_score = scorefxn(pose_relaxed)
N501Y_score = scorefxn(pose_N501Y)
print('\nWT score: ' + str(WT_score))
print('\nN501Y score: ' + str(N501Y_score))
# to run FastRelax, make a task factory, a movemap factory, and add them to a FastRelax protocol object
# Make task factory
tf = TaskFactory()
tf.push_back(operation.InitializeFromCommandline())
tf.push_back(operation.IncludeCurrent())
tf.push_back(operation.NoRepackDisulfides())
tf.push_back(operation.OperateOnResidueSubset(
operation.RestrictToRepackingRLT(),
residue_selector.TrueResidueSelector()))
# make movemap factory
mmf = pyrosetta.rosetta.core.select.movemap.MoveMapFactory()
mmf.all_bb(setting=True)
mmf.all_bondangles(setting=True)
mmf.all_bondlengths(setting=True)
mmf.all_chi(setting=True)
mmf.all_jumps(setting=True)
mmf.set_cartesian(setting=True)
# make fastrelax protocol
fr = pyrosetta.rosetta.protocols.relax.FastRelax(standard_repeats=5)
fr.set_scorefxn(scorefxn)
fr.set_task_factory(tf)
def clash_based_taskfactory(pdbpath, pose, workspace):
insertion = lucs.get_insertion(pdbpath, workspace)
# How much to add to insertion['stop'] to get the residue number to
# design
input_pose = pose_from_file(workspace.input_pdb_path)
designable, repackable = lucs.relative_resfile_from_reference(
workspace, insertion, pose, input_pose)
# Ignoring repackable residues in resfile.
# This should give us all designed positions
design_mask = size_list_to_res_selector(designable, pose)
design_selector = select.residue_selector.ResidueIndexSelector(
numeric.intlist_to_vector1_size(designable))
# Takes a resfile and returns a task factory with a clash-based
# repack shell.
tf = TaskFactory()
cl = operation.InitializeFromCommandline()
notaa = operation.ProhibitSpecifiedBaseResidueTypes(
strlist_to_vector1_str(['C', 'H']), design_selector)
# read = operation.ReadResfile(resfile)
tf.push_back(cl)
tf.push_back(notaa)
# tf.push_back(read)
# Select repackable residues from designed residues
repack_only = operation.RestrictToRepackingRLT()
repack = operation.OperateOnResidueSubset(repack_only, design_selector,
False)
repack.flip_subset(True)
tf.push_back(repack)
all_selector = residue_selector.ClashBasedShellSelector(design_mask)
all_selector.set_num_shells(2)
all_selector.set_include_focus(True)
all_selector.invert(True)
no_packing = operation.PreventRepackingRLT()
static = operation.OperateOnResidueSubset(no_packing, all_selector, False)
packertask = tf.create_task_and_apply_taskoperations(pose)
ld = rosetta_scripts.XmlObjects.static_get_task_operation(
'''<LayerDesign name="layer_all" layer="core_boundary_surface_Nterm_Cterm" use_sidechain_neighbors="True">
<core>
<all exclude="CW" />
</core>
<boundary>
<all exclude="CW" />
</boundary>
<Nterm>
<all append="DEGHKNQRST" />
<all exclude="CAFILMPVWY" />
</Nterm>
<Cterm>
<all append="DEGHKNQRST" />
<all exclude="CAFILMPVWY" />
</Cterm>
</LayerDesign>''')
tf.push_back(static)
tf.push_back(ld)
packertask = tf.create_task_and_apply_taskoperations(pose)
print('PRINTING PACKERTASK')
print(packertask)
repack_mask = packertask.repacking_residues()
design_mask = packertask.designing_residues()
movemap = setup_movemap_from_resselectors(design_mask, repack_mask)
return tf, movemap