def relative_resfile_from_reference(workspace, insertion, pose,
reference_pose):
'''
Convert a resfile to relative resfiles given a LUCS insertion.
Note: Resfile/original PDB must have Rosetta numbering, i.e. start
with the first residue having the number 1. Otherwise, the function
will require the original pose and the LUCS pose.
'''
resfile_parser = input_files.Resfile(input_resfile=workspace.resfile_path)
start = insertion['start']
chain = 'A'
designable = []
for res in resfile_parser.design[chain]:
if int(res) < insertion['start']:
designable.append(int(res))
else:
designable.append(int(res) + (pose.size() -
reference_pose.size()))
designable.extend([j for j in range(insertion['start'],
insertion['stop'])])
repackable = []
if chain in resfile_parser.repack:
for res in resfile_parser.repack[chain]:
if int(res) < insertion['start']:
repackable.append(int(res))
else:
repackable.append(int(res) + (pose.size() -
reference_pose.size()))
return designable, repackable
def fold_tree_from_resfile(workspace, pose):
from klab.rosetta import input_files
resfile_parser = input_files.Resfile(input_resfile=workspace.resfile_path)
ft_dict = {}
for chain in resfile_parser.design:
designable = [int(key) for key in resfile_parser.design[chain]]
if chain in resfile_parser.repack:
repackable = [int(key) for key in resfile_parser.repack[chain]]
print(repackable)
else:
repackable = []
designable.extend(repackable)
if designable:
start = pose.pdb_info().pdb2pose(chain, min(designable))
end = pose.pdb_info().pdb2pose(chain, max(designable))
mid = int((start + end) / 2)
ft_dict[chain] = (start, mid, end)
print(ft_dict)
ft = FoldTree()
# go through each chain
jumpno = 1
for chain in range(1, pose.num_chains() + 1):
chainstart = pose.chain_begin(chain)
chainstop = pose.chain_end(chain)
pdbchain = pose.pdb_info().pose2pdb(chainstart).split(' ')[1]
print(pdbchain)
if pdbchain in ft_dict:
# Edge to start of design region
ft.add_edge(chainstart, ft_dict[pdbchain][0], -1)
# Edge from start of design region to middle of design region
ft.add_edge(ft_dict[pdbchain][0], ft_dict[pdbchain][1], -1)
# Edge from end of design region to end of chain
ft.add_edge(ft_dict[pdbchain][2], chainstop, -1)
# Edge from end of design region to middle of chain
ft.add_edge(ft_dict[pdbchain][2], ft_dict[pdbchain][1], -1)
# Jump from start of design region to end of design region
ft.add_edge(ft_dict[pdbchain][0], ft_dict[pdbchain][2], jumpno)
jumpno += 1
else:
ft.add_edge(chainstart, chainstop, -1)
# Add jump between chain and next chain
if chain < pose.num_chains():
ft.add_edge(chainstop, chainstop + 1, jumpno)
jumpno += 1
return ft
<Nterm>
<all append="DEGHKNQRST" />
<all exclude="CAFILMPVWY" />
</Nterm>
<Cterm>
<all append="DEGHKNQRST" />
<all exclude="CAFILMPVWY" />
</Cterm>
</LayerDesign>''')
taskfactory.push_back(ld)
packertask = taskfactory.create_task_and_apply_taskoperations(pose)
fd.task_factory = taskfactory
# Parse resfile & create movemap
resfile_parser = input_files.Resfile(input_resfile=workspace.resfile_path)
designable = []
repackable = []
for chain in resfile_parser.design:
designable.extend([int(key) for key in resfile_parser.design[chain]])
for chain in resfile_parser.repack:
repackable.extend([int(key) for key in resfile_parser.repack[chain]])
fd.setup_default_movemap(bb=designable.extend(repackable),
chi=designable.extend(repackable))
if test_run:
fd.rounds = 1
print(fd.movemap)
print(fd.task_factory)
fd.apply()