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()
# Create new pose from input file for comparison
input_pose = pose_from_file(pdbpath)
#input_pose = pose_from_file(workspace.input_pdb_path)
# Calculate several different types of RMSD
ca_rmsd = CA_rmsd(fd.pose, input_pose)
all_atom_rmsd = all_atom_rmsd(fd.pose, input_pose)
filters = workspace.get_filters(fd.pose,
task_id=job_info['task_id'],
score_fragments=False,
test_run=test_run)
filters.run_filters()
# Add RMSDs as extra metrics, which will be printed at the end of
# the PDB file.
setPoseExtraScore(fd.pose, 'EXTRA_METRIC_CA_RMSD', ca_rmsd)
setPoseExtraScore(fd.pose, 'EXTRA_METRIC_AllAtom_RMSD', all_atom_rmsd)
total_time = time.time() - start_time
setPoseExtraScore(fd.pose, 'EXTRA_METRIC_Run time', total_time)
if test_run:
# What happens when --test-run is supplied?
lm.mark_as_test_run()
# Add pose and apply
lm.pose = pose
lm.apply()
# Get and run default filters
filters = workspace.get_filters(lm.pose,
task_id=job_info['task_id'], score_fragments=True,
test_run=test_run)
filters.run_filters()
# Calculate RMSD from input
input_pose = pose_from_file(workspace.input_path(job_info))
ca_rmsd = CA_rmsd(lm.pose, input_pose)
all_atom_rmsd = all_atom_rmsd(lm.pose, input_pose)
loop = workspace.largest_loop
rmsd = CA_rmsd(input_pose, lm.pose, loop.start,
loop.end)
# Add RMSDs to pose for parsing
setPoseExtraScore(lm.pose, 'EXTRA_METRIC_CA_RMSD', ca_rmsd)
setPoseExtraScore(lm.pose, 'EXTRA_METRIC_AllAtom_RMSD', all_atom_rmsd)
setPoseExtraScore(lm.pose, 'EXTRA_METRIC_Loop_RMSD', rmsd)
if not os.path.exists(workspace.output_prefix(job_info)):
os.mkdir(workspace.output_prefix(job_info))
pose.dump_pdb(workspace.output_path(job_info))
# print(fd.movemap)
# print(fd.task_factory)
# fd.mover.add_constraint_generator(csts)
# fd.mover.constrain_relax_to_start_coords(True)
# fd.mover.ramp_down_constraints(False)
# Before we apply FastDesign, also setup and run RotamerTrials
# fd.apply()
protocol.apply(pose)
# This will compare it to the input to the step
input_pose = pose_from_file(pdbpath)
# But you can uncomment this to compare it to the input to the
# project
#input_pose = pose_from_file(workspace.input_pdb_path)
ca_rmsd = CA_rmsd(pose, input_pose)
all_atom_rmsd = all_atom_rmsd(pose, input_pose)
# score_fragments = os.path.exists(workspace.loops_path)
score_fragments = False
filters = workspace.get_filters(pose,
task_id=job_info['task_id'],
score_fragments=score_fragments,
test_run=test_run)
filters.run_filters()
input_name = os.path.basename(pdbpath).split(".")[0]
out = workspace.output_prefix(
job_info) + input_name + workspace.output_suffix(job_info) + '.pdb.gz'
setPoseExtraScore(pose, 'EXTRA_METRIC_CA_RMSD', ca_rmsd)
setPoseExtraScore(pose, 'EXTRA_METRIC_AllAtom_RMSD', all_atom_rmsd)
relax.add_init_arg('-total_threads 1')
if test_run:
relax.rounds = 1
relax.pose = pose
# Warning: This is an all-atom movemap. Constrain to input coords if
# you don't want things to move around a lot.
relax.setup_default_movemap()
relax.apply()
# This will compare it to the input to this step
input_pose = pose_from_file(pdbpath)
# But you can uncomment this to compare to the input to the
# workspace
#input_pose = pose_from_file(workspace.input_pdb_path)
ca_rmsd = CA_rmsd(relax.pose, input_pose)
all_atom_rmsd = all_atom_rmsd(relax.pose, input_pose)
score_fragments = os.path.exists(workspace.loops_path)
filters = workspace.get_filters(relax.pose,
task_id=job_info['task_id'],
score_fragments=score_fragments,
test_run=test_run)
filters.run_filters()
input_name = os.path.basename(pdbpath).split(".")[0]
out = workspace.output_prefix(
job_info) + input_name + workspace.output_suffix(job_info) + '.pdb.gz'
setPoseExtraScore(relax.pose, 'EXTRA_METRIC_CA_RMSD', ca_rmsd)
setPoseExtraScore(relax.pose, 'EXTRA_METRIC_AllAtom_RMSD', all_atom_rmsd)
def main():
args = docopt.docopt(__doc__)
print(args)
cluster.require_qsub()
start_time = time.time()
workspace, job_info = big_jobs.initiate()
pdbpath = workspace.input_path(job_info)
if not os.path.exists(workspace.output_prefix(job_info)):
os.mkdir(workspace.output_prefix(job_info))
outpath = workspace.output_path(job_info)
test_run = job_info.get('test_run', False)
# append location of Rosetta binaries to path
sys.path.append('/wynton/home/kortemme/krivacic/source/bin')
# find necessary files
tmers = glob.glob(
os.path.join(workspace.fragments_dir,
workspace.fragments_tag(pdbpath) + '?', '*3mers.gz'))
nmers = glob.glob(
os.path.join(workspace.fragments_dir,
workspace.fragments_tag(pdbpath) + '?', '*9mers.gz'))
ss2 = glob.glob(
os.path.join(workspace.fragments_dir,
workspace.fragments_tag(pdbpath) + '?', '*psipred_ss2'))
# Run the ab initio relaxation script.
relax_abinitio = [
'AbinitioRelax.linuxgccrelease',
'-abinitio:relax',
'-use_filters',
'true',
'-abinitio::increase_cycles',
'10',
'-abinitio::rg_reweight',
'0.5',
'-abinitio::rsd_wt_helix',
'0.5',
'-abinitio::rsd_wt_loop',
'0.5',
'-relax::fast',
'-in:file:fasta',
workspace.fasta_path,
'-in:file:frag3',
tmers,
'-in:file:frag9',
nmers,
'-in:file:psipred_ss2',
ss2,
'-nstruct',
args.nstruct,
'-out:pdb_gz',
'-out:prefix',
workspace.output_prefix(job_info),
'-out:suffix',
workspace.output_suffix(job_info),
# '--outdir', workspace.fragments_dir,
# '--memfree', args['--mem-free']
]
if args['--dry-run']:
print(' '.join(relax_abinitio))
else:
subprocess.call(relax_abinitio)
init()
pose = pose_from_file(outpath)
input_pose = pose_from_file(pdbpath)
ca_rmsd = CA_rmsd(pose, input_pose)
all_atom_rmsd = all_atom_rmsd(pose, input_pose)
setPoseExtraScore(pose, 'EXTRA_METRIC_CA_RMSD [[-]]', ca_rmsd)
setPoseExtraScore(pose, 'EXTRA_METRIC_AllAtom_RMSD [[-]]', all_atom_rmsd)
filters = workspace.get_filters(pose,
task_id=job_info['task_id'],
score_fragments=not test_run,
test_run=test_run)
filters.run_filters()
total_time = time.time() - start_time
setPoseExtraScore(pose, 'EXTRA_METRIC_Run time', total_time)
outname = os.path.basename(outpath)
outfolder = os.path.join(workspace.output_prefix(job_info), 'filtered')
pose.dump_pdb(os.path.join(outfolder, outpath))