def main():
args = docopt.docopt(__doc__)
prefix = args['--prefix'] or ''
workspaces = find_validation_workspaces(args['<workspace>'],
args['<round>'])
designs = find_reasonable_designs(workspaces, args['--threshold'],
args['--verbose'])
metrics = [
DesignNameMetric(),
ResfileSequenceMetric(),
SequenceClusterMetric(args['--subs-matrix']),
StructureClusterMetric(args['--structure-threshold']),
RestraintDistMetric(),
ScoreGapMetric(),
PercentSubangstromMetric(),
BuriedUnsatHbondMetric(),
DunbrackScoreMetric(),
]
discover_filter_metrics(metrics, workspaces)
#discover_custom_metrics(metrics, workspaces)
calculate_quality_metrics(metrics, designs, args['--verbose'])
designs = find_pareto_optimal_designs(designs, metrics, args['--verbose'])
report_quality_metrics(designs, metrics, prefix + 'quality_metrics.xlsx')
#report_score_vs_rmsd_funnels(designs, prefix + 'score_vs_rmsd.pdf')
#report_pymol_sessions(designs, prefix + 'pymol_sessions')
annotate_designs(designs)
def main():
args = docopt.docopt(__doc__)
cluster.require_qsub()
# Setup the workspace.
workspace = pipeline.FixbbDesigns(args['<workspace>'], args['<round>'])
workspace.check_paths()
workspace.check_rosetta()
workspace.make_dirs()
if args['--clear'] or args['--test-run']:
workspace.clear_outputs()
# Decide which inputs to use.
inputs = workspace.unclaimed_inputs
nstruct = len(inputs) * int(args['--nstruct'])
if not inputs:
print """\
All the input structures have already been (or are already being) designed. If
you want to rerun all the inputs from scratch, use the --clear flag."""
raise SystemExit
# Submit the design job.
big_jobs.submit('pip_design.py',
workspace,
inputs=inputs,
nstruct=nstruct,
max_runtime=args['--max-runtime'],
max_memory=args['--max-memory'],
test_run=args['--test-run'])
def main():
args = docopt.docopt(__doc__)
cluster.require_qsub()
workspace = pipeline.workspace_from_path(args['<workspace>'])
workspace.check_paths()
workspace.make_dirs()
workspace.clear_fragments()
# Run the fragment generation script.
generate_fragments = [
'klab_generate_fragments',
workspace.input_pdb_path,
'--outdir',
workspace.fragments_dir,
'--memfree',
args['--mem_free'],
]
if not args['--ignore-loop-file']:
generate_fragments += [
'--loops_file',
workspace.loops_path,
]
if args['--dry-run']:
print(' '.join(generate_fragments))
else:
subprocess.call(generate_fragments)
def main():
args = docopt.docopt(__doc__)
root = args['<workspace>']
round = args['<round>']
output_path = args['<pdf_output>']
# Right now I'm looking at validated designs by default, but the user may
# be interested in fixbb designs or restrained models as well.
workspace = pipeline.ValidatedDesigns(root, round)
workspace.check_paths()
designs = [structures.Design(x) for x in workspace.output_subdirs]
sequences = corebio.seq.SeqList(
[corebio.seq.Seq(x.resfile_sequence) for x in designs],
alphabet=corebio.seq.unambiguous_protein_alphabet,
)
logo_data = weblogo.LogoData.from_seqs(sequences)
logo_options = weblogo.LogoOptions()
logo_options.title = workspace.focus_dir
logo_format = weblogo.LogoFormat(logo_data, logo_options)
with open(output_path, 'wb') as logo_file:
document = weblogo.pdf_formatter(logo_data, logo_format)
logo_file.write(document)
def main():
args = docopt.docopt(__doc__)
cluster.require_qsub()
workspace = pipeline.ValidatedDesigns(args['<workspace>'], args['<round>'])
workspace.check_paths()
workspace.check_rosetta()
workspace.make_dirs()
workspace.clear_fragments()
# Run the fragment generation script.
generate_fragments = [
'klab_generate_fragments',
'--loops_file',
workspace.loops_path,
'--outdir',
workspace.fragments_dir,
'--memfree',
args['--mem-free'],
workspace.input_dir,
]
if args['--dry-run']:
print ' '.join(generate_fragments)
else:
subprocess.call(generate_fragments)
def main():
args = docopt.docopt(__doc__)
pipeline.fetch_data(
args['<directory>'],
args['--remote'],
args['--include-logs'],
args['--dry-run'],
)
def discover_filter_metrics(metrics, workspaces):
for workspace in workspaces:
filter_list = pipeline.workspace_from_dir(
docopt.docopt(__doc__)['<workspace>']).filters_list
filters = []
with open(filter_list, "r") as file:
filters = yaml.load(file)
if filters:
for record in filters:
filterclass = ExtraFilterHandler(record)
metrics.append(filterclass)
def main():
args = docopt.docopt(__doc__)
num_models = 0
for directory in args['<directories>']:
records = structures.\
load(directory, args['--restraints'], not args['--recalc'])
if args['--query']:
records = records.query(args['--query'])
num_models += len(records)
print num_models
def main():
args = docopt.docopt(__doc__)
# Setup the workspace.
workspace = pipeline.ValidatedDesigns(args['<workspace>'], args['<round>'])
workspace.check_paths()
workspace.make_dirs()
if args['--clear']:
workspace.clear_inputs()
# Copy the manual designs into the input directory.
for source_path in args['<pdbs>']:
dest_path = os.path.join(workspace.input_dir, os.path.basename(source_path))
shutil.copy(source_path, dest_path)
def main():
args = docopt.docopt(__doc__)
cluster.require_qsub()
# Setup the workspace.
workspace = pipeline.ValidatedDesigns(args['<workspace>'], args['<round>'])
workspace.check_paths()
workspace.make_dirs()
if args['--clear'] or args['--test-run']:
workspace.clear_outputs()
# Setup an output directory for each input.
inputs = workspace.unclaimed_inputs
nstruct = len(inputs) * int(args['--nstruct'])
if nstruct == 0:
scripting.print_error_and_die("""\
No unclaimed input files.
If you previously started a round of simulations and then stopped them for some
reason, the problem is probably that all the inputs are still claimed by those
simulations. Use the '--clear' flag to remove the claims and try again.""")
for input in inputs:
subdir = workspace.output_subdir(input)
scripting.clear_directory(subdir)
# Launch the validation job.
big_jobs.submit(
'pip_validate.py',
workspace,
inputs=inputs,
nstruct=nstruct,
max_runtime=args['--max-runtime'],
max_memory=args['--max-memory'],
test_run=args['--test-run'],
)
def main():
args = docopt.docopt(__doc__)
wait_time = 60 * eval(args['--wait-time'])
if args['--keep-going']:
while True:
pipeline.fetch_and_cache_data(
args['<directory>'],
args['--remote'],
args['--include-logs'],
)
print "Waiting {} min...".format(wait_time // 60)
time.sleep(wait_time)
else:
pipeline.fetch_and_cache_data(
args['<directory>'],
args['--remote'],
args['--include-logs'],
)
def main():
arguments = docopt.docopt(__doc__)
cluster.require_qsub()
# Setup the workspace.
workspace = pipeline.RestrainedModels(arguments['<workspace>'])
workspace.check_paths()
workspace.check_rosetta()
workspace.make_dirs()
if arguments['--clear'] or arguments['--test-run']:
workspace.clear_outputs()
# Submit the model building job.
big_jobs.submit('pip_build.py',
workspace,
nstruct=arguments['--nstruct'],
max_runtime=arguments['--max-runtime'],
max_memory=arguments['--max-memory'],
test_run=arguments['--test-run'])
def main():
args = docopt.docopt(__doc__)
print structures.load(args['<directory>'], args['--restraints'],
not args['--recalc']).head()
def main():
args = docopt.docopt(__doc__)
pipeline.push_data(args['<directory>'], args['--remote'],
args['--dry-run'])
def main():
arguments = docopt.docopt(__doc__)
workspace = pipeline.Workspace(arguments['<workspace>'])
# Make a new workspace directory.
if workspace.incompatible_with_fragments_script:
scripting.print_error_and_die("""\
Illegal character(s) found in workspace path:
{}
The full path to a workspace must contain only characters that are alphanumeric
or '.' or '_'. The reason for this ridiculous rule is the fragment generation
script, which will silently fail if the full path to its input file contains
any characters but those.""", workspace.abs_root_dir)
if workspace.exists():
if arguments['--overwrite']:
shutil.rmtree(workspace.root_dir)
else:
scripting.print_error_and_die("""\
Design '{0}' already exists. Use '-o' to overwrite.""", workspace.root_dir)
workspace.make_dirs()
# Decide which settings to ask for.
if arguments['--remote']:
installers = (
RosettaDir,
RsyncUrl,
)
else:
installers = (
RosettaDir,
InputPdb,
LoopsFile,
Resfile,
RestraintsFile,
ScoreFunction,
BuildScript,
DesignScript,
ValidateScript,
FilterScript,
SharedDefs,
FlagsFile,
)
# Get the necessary settings from the user and use them to fill in the
# workspace.
print "Please provide the following pieces of information:"
print
scripting.use_path_completion()
for installer in installers:
# If the installer doesn't have a prompt, just install it without
# asking any questions.
if installer.prompt is None:
installer.install(workspace)
continue
# Otherwise, print a description of the setting being installed and
# prompt the user for a value.
print installer.description
print
while True:
try:
setting = raw_input(installer.prompt)
installer.install(workspace, setting)
except (ValueError, IOError) as problem:
print problem
continue
except (KeyboardInterrupt, EOFError):
shutil.rmtree(workspace.root_dir)
scripting.print_error_and_die("\nReceived exit command, no workspace created.")
else:
break
print
# If we made a link to a remote workspace, immediately try to synchronize
# with it. Rsync will say whether or not it succeeded. Otherwise just
# print a success message.
if arguments['--remote']:
pipeline.fetch_data(workspace.root_dir)
else:
print "Setup successful for design '{0}'.".format(workspace.root_dir)
reversion_seq[aa_num - first_res] = wt_aa
name = original_design + "_reversion"
num_reversion_designs = 1
while name in reverted_sequences:
num_reversion_designs += 1
name = name + str(num_reversion_designs)
reverted_sequences[name] = "".join(reversion_seq)
for design in reverted_sequences:
protein_sequences[design] = reverted_sequences[design]
return protein_sequences
arguments = docopt.docopt(__doc__)
inputs = arguments['<input_fasta_or_folder>']
template_dna = arguments['--template-dna']
wt_sequence_file = arguments['--combine-chains']
wt_sequence_str = ''
reversion_mutations = arguments['--reversion-mutations']
if wt_sequence_file:
wt_sequence_str = import_wt_protein_sequence(wt_sequence_file)
from_files = arguments['--from-pdb-folder']
if from_files:
def main():
args = docopt.docopt(__doc__)
root = args['<workspace>']
round = args['<round>']
query = ' and '.join(args['<queries>'])
temp = float(args['--temp'])
# Import ``pylab`` after handling the help message, because otherwise
# ``matplotlib`` sometimes issues warnings that then show up in the docs.
import pylab
workspace = pipeline.ValidatedDesigns(root, round)
workspace.check_paths()
workspace.make_dirs()
if args['--clear']:
workspace.clear_inputs()
predecessor = workspace.predecessor
# Get sequences and scores for each design.
seqs_scores = structures.load(
predecessor.output_dir,
use_cache=not args['--recalc'],
)
seqs_scores.dropna(inplace=True)
print 'Total number of designs: ', len(seqs_scores)
# If a query was given on the command line, find models that satisfy it.
if query:
seqs_scores = seqs_scores.query(query)
print ' minus given query: ', len(seqs_scores)
# Keep only the lowest scoring model for each set of identical sequences.
groups = seqs_scores.groupby('sequence', group_keys=False)
seqs_scores = groups.\
apply(lambda df: df.ix[df.total_score.idxmin()]).\
reset_index(drop=True)
print ' minus duplicate sequences:', len(seqs_scores)
# Remove designs that have already been picked.
existing_inputs = set(
os.path.basename(os.path.realpath(x)) for x in workspace.input_paths)
seqs_scores = seqs_scores.query('path not in @existing_inputs')
print ' minus current inputs: ', len(seqs_scores)
print
# Use a Boltzmann weighting scheme to pick designs.
seq_scores = seqs_scores.sort_values(by='total_score')
scores = seqs_scores.total_score.values
scores -= median(scores)
weights = exp(-scores / temp)
indices = arange(len(scores))
pdf = array(weights)
cdf = cumsum(pdf) / sum(pdf)
num_to_pick = min(int(args['--num']), len(scores))
picked_indices = set()
while len(picked_indices) < num_to_pick:
choice = random.random()
picked_index = indices[cdf > choice][0]
picked_indices.add(picked_index)
picked_indices = sorted(picked_indices)
# Show the user the probability distributions used to pick designs.
raw_input("""\
Press [enter] to view the designs that were picked and the distributions that
were used to pick them. Pay particular attention to the CDF. If it is too
flat, the temperature (T={0}) is too high and designs are essentially being
picked randomly. If it is too sharp, the temperature is too low and only the
highest scoring designs are being picked.
""".format(temp))
color = '#204a87' # Tango dark blue
base_format = dict(color=color)
picked_format = dict(marker='o', ls='none', mfc=color, mec='none')
pylab.figure(num=1, figsize=(8, 3))
pylab.subplot(1, 3, 1)
pylab.title('Rosetta Scores')
pylab.plot(indices, scores, **base_format)
pylab.plot(picked_indices, scores[picked_indices], **picked_format)
pylab.subplot(1, 3, 2)
pylab.title('Boltzmann PDF')
pylab.plot(indices, pdf, **base_format)
pylab.plot(picked_indices, pdf[picked_indices], **picked_format)
pylab.yscale('log')
pylab.subplot(1, 3, 3)
pylab.title('Boltzmann CDF')
pylab.plot(indices, cdf, **base_format)
pylab.plot(picked_indices, cdf[picked_indices], **picked_format)
pylab.tight_layout()
pylab.show()
if raw_input("Accept these picks? [Y/n] ") == 'n':
print "Aborting."
sys.exit()
# Make symlinks to the picked designs.
if not args['--dry-run']:
existing_ids = set(
int(x[0:-len('.pdb.gz')]) for x in os.listdir(workspace.input_dir))
next_id = max(existing_ids) + 1 if existing_ids else 0
for id, picked_index in enumerate(picked_indices, next_id):
basename = seqs_scores.iloc[picked_index]['path']
target = os.path.join(predecessor.output_dir, basename)
link_name = os.path.join(workspace.input_dir, '{0:04}.pdb.gz')
scripting.relative_symlink(target, link_name.format(id))
print "Picked {} designs.".format(len(picked_indices))
if args['--dry-run']:
print "(Dry run: no symlinks created.)"