def main():
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)
folder = workspace.output_prefix(job_info)
test_run = job_info.get('test_run', False)
combiner = '/wynton/home/kortemme/krivacic/rosetta/source/bin/combine_silent.linuxgccrelease'
# for folder in workspace.output_subdirs:
cmd = [
combiner, '-database',
'/wynton/home/kortemme/krivacic/rosetta/database', '-out:file:silent',
os.path.join(folder, 'silent.out')
]
for f in glob.glob(folder + '/*.out'):
cmd.extend([
'-in:file:silent',
f,
])
print('Running ROSETTA command:')
print(' '.join(cmd))
subprocess.call(cmd)
def main():
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
abinitio = '/wynton/home/kortemme/krivacic/rosetta/source/bin/AbinitioRelax.linuxgccrelease'
# find necessary files
print('fdir :', workspace.fragments_dir)
print('pdb :', pdbpath)
print(
os.path.join(workspace.fragments_dir,
workspace.fragments_tag(pdbpath.lower()) + '?',
'*3mers.gz'))
tmers = glob.glob(
os.path.join(workspace.fragments_dir,
workspace.fragments_tag(pdbpath.lower()) + '?',
'*3mers.gz'))[0]
nmers = glob.glob(
os.path.join(workspace.fragments_dir,
workspace.fragments_tag(pdbpath.lower()) + '?',
'*9mers.gz'))[0]
ss2 = glob.glob(
os.path.join(workspace.fragments_dir,
workspace.fragments_tag(pdbpath.lower()) + '?',
'*psipred_ss2'))[0]
fasta = glob.glob(
os.path.join(workspace.fragments_dir,
workspace.fragments_tag(pdbpath.lower()) + '?',
'*fasta'))[0]
# Set up tempdir
if 'TMPDIR' in os.environ:
os_tmp = os.environ['TMPDIR']
elif args['--task']:
os_tmp = os.path.join(os.environ['HOME'], 'temp')
else:
os_tmp = os.path.join('/scratch', os.environ['USER'])
outdir_temp = os.path.join(os_tmp, str(task_num))
if not os.path.exists(outdir_temp):
os.makedirs(outdir_temp, exist_ok=True)
# Run the ab initio relax script.
outfile = os.path.join(
outdir_temp, 'silent{}.out'.format(workspace.output_suffix(job_info)))
relax_abinitio = [
abinitio,
'-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',
fasta,
'-in:file:frag3',
tmers,
'-in:file:frag9',
nmers,
'-in:file:psipred_ss2',
ss2,
'-nstruct',
'10',
# '-out:pdb_gz',
# '-out:sf', workspace.output_prefix(job_info) + 'score{}.sc'.format(workspace.output_suffix(job_info)),
# '-out:file:silent', workspace.output_prefix(job_info) + 'silent{}.out'.format(workspace.output_suffix(job_info)),
'-out:file:silent',
outfile,
# '-out:prefix', workspace.output_prefix(job_info),
# '-out:suffix', workspace.output_suffix(job_info),
'-out:no_nstruct_label'
# '--outdir', workspace.fragments_dir,
# '--memfree', args['--mem-free']
]
print('Running ROSETTA command:')
print(' '.join(relax_abinitio))
subprocess.call(relax_abinitio)
from shutil import copyfile
if not os.path.exists(workspace.output_prefix(job_info)):
os.makedirs(workspace.output_prefix(job_info), exist_ok=True)
final = os.path.join(
workspace.output_prefix(job_info),
'silent{}.out'.format(workspace.output_suffix(job_info)))
copyfile(outfile, final)
from roseasy import big_jobs
from pyrosetta.rosetta.core.pack.task import TaskFactory
from pyrosetta.rosetta.core.pack.task.operation import ReadResfile
from pyrosetta import create_score_function
from roseasy.movers import fastdesign
#from roseasy.standard_params.filters import FilterContainer
import time
def get_workspace(root_dir, step):
return pipeline.DesignWorkspace(root_dir, step)
if __name__ == '__main__':
start_time = time.time()
workspace, job_info = big_jobs.initiate()
test_run = job_info.get('test_run', False)
init('-out:levels protocols.fixbb.LayerDesignOperation:warning')
# Figure out input pdb and create a pose
pdbpath = workspace.input_path(job_info)
pose = pose_from_file(pdbpath)
# Create FastDesign object
fd = fastdesign.FastDesign()
fd.pose = pose
fd.add_init_arg('-ex1 -ex2 -use_input_sc -ex1aro')
# Create task factory (tells Rosetta which positions to design and
# which to move) and read the resfile
taskfactory = TaskFactory()
def main():
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
abinitio = '/wynton/home/kortemme/krivacic/rosetta/source/bin/AbinitioRelax.linuxgccrelease'
# find necessary files
print('fdir :', workspace.fragments_dir)
print('pdb :', pdbpath)
print(
os.path.join(workspace.fragments_dir,
workspace.fragments_tag(pdbpath.lower()) + '?',
'*3mers.gz'))
tmers = glob.glob(
os.path.join(workspace.fragments_dir,
workspace.fragments_tag(pdbpath.lower()) + '?',
'*3mers.gz'))[0]
nmers = glob.glob(
os.path.join(workspace.fragments_dir,
workspace.fragments_tag(pdbpath.lower()) + '?',
'*9mers.gz'))[0]
ss2 = glob.glob(
os.path.join(workspace.fragments_dir,
workspace.fragments_tag(pdbpath.lower()) + '?',
'*psipred_ss2'))[0]
fasta = glob.glob(
os.path.join(workspace.fragments_dir,
workspace.fragments_tag(pdbpath.lower()) + '?',
'*fasta'))[0]
# Run the ab initio relax script.
relax_abinitio = [
abinitio,
'-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',
fasta,
'-in:file:frag3',
tmers,
'-in:file:frag9',
nmers,
'-in:file:psipred_ss2',
ss2,
'-nstruct',
'10',
# '-out:pdb_gz',
'-out:file:silent',
workspace.output_prefix(job_info) +
'silent_{}.out'.format(workspace.output_suffix(job_info)),
# '-out:prefix', workspace.output_prefix(job_info),
# '-out:suffix', workspace.output_suffix(job_info),
'-out:no_nstruct_label'
# '--outdir', workspace.fragments_dir,
# '--memfree', args['--mem-free']
]
print('Running ROSETTA command:')
print(' '.join(relax_abinitio))
subprocess.call(relax_abinitio)
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))
