def add_missing_residues(root_output_directory):
'''Add the removed loop residue backbone atoms back into the Rosetta preminimized structures but in a clearly non-native manner.'''
# Set up the run
input_directories = [
['..', 'structures', '12_res', 'rosetta', 'pruned'],
['..', 'structures', '14_17_res', 'rosetta', 'pruned'],
]
cases = []
for input_directory in input_directories:
output_directory = os.path.join(root_output_directory, input_directory[2], input_directory[3], input_directory[4])
try:
os.makedirs(output_directory)
except: pass
if not(os.path.exists(output_directory)):
raise Exception('The output directory {0} could not be created.')
cases.append((os.path.join(*input_directory), output_directory))
# Determine path to RosettaScripts
rosetta_scripts_binary = None
release_binaries = []
other_binaries = []
from libraries import settings
try:
settings.load(arguments, allow_failure = True)
except Exception, e:
raise colortext.Exception('An exception occurred reading the settings.conf file: {0}.'.format(str(e)))
#$ -S /usr/bin/python
#$ -l mem_free=1G
#$ -l arch=linux-x64
#$ -l netapp=1G
#$ -cwd
import os
import sys; sys.path.append(os.getcwd())
import optparse
import subprocess
import re
import json
from libraries import utilities
from libraries import settings; settings.load(interactive=False)
from libraries import database
# Parse arguments.
if len(sys.argv) != 2 or 'SGE_TASK_ID' not in os.environ:
print 'Usage: SGE_TASK_ID=<id> loop_benchmark.py <benchmark_id>'
sys.exit(1)
task_id = int(os.environ['SGE_TASK_ID']) - 1
benchmark_id = int(sys.argv[1])
# Figure out which loop to benchmark.
with database.connect() as session:
benchmark = session.query(database.Benchmarks).get(benchmark_id)
s.append('{0}: {1}'.format(k, progress_fn(v)))
s.append('')
return '\n'.join(s)
def report_progress(database_name, benchmark_name, only_show_summary):
print(
get_progress_for_terminal(database_name, benchmark_name,
only_show_summary))
if __name__ == '__main__':
try:
from libraries import docopt
arguments = docopt.docopt(__doc__)
settings.load()
benchmark_name = arguments['<benchmark_name>']
summary = arguments['--summary']
database_name = arguments['--database'] or settings.db_name
if arguments['--list']:
name_list = get_benchmark_list_by_name(database_name)
if name_list:
colortext.pgreen(
'\nList of available benchmarks in the {0} database:\n'.
format(database_name))
for n in name_list:
colortext.pcyan(' - {0}'.format(n))
print('')
else:
colortext.pred(
'\nNo benchmarks defined in the {0} database.\n'.format(
#$ -l netapp=1G
#$ -cwd
import os
import sys
sys.path.append(os.getcwd())
import optparse
import subprocess
import re
import json
from libraries import utilities
from libraries import settings
settings.load(interactive=False)
from libraries import database
# Parse arguments.
if len(sys.argv) != 2 or 'SGE_TASK_ID' not in os.environ:
print 'Usage: SGE_TASK_ID=<id> loop_benchmark.py <benchmark_id>'
sys.exit(1)
task_id = int(os.environ['SGE_TASK_ID']) - 1
benchmark_id = int(sys.argv[1])
# Figure out which loop to benchmark.
with database.connect() as session:
benchmark = session.query(database.Benchmarks).get(benchmark_id)
"""
# Add options to pick a particular structure.
# Add options to pick given structure (i.e 1-500 index) or lowest scoring.
# Add options to show logs for jobs that died.
# Default: only benchmark id required. Default structure is the lowest energy
# model for the first PDB tag sorted alphabetically.
from libraries import settings
from libraries import database
from libraries import docopt
arguments = docopt.docopt(__doc__.format(**locals()))
benchmark_id = arguments['<benchmark_id>']
settings.load(arguments)
with database.connect() as session:
query = session.query(database.TracerLogs).\
filter_by(benchmark_id=benchmark_id)
if arguments['--pdb']:
print "This filter is not yet supported."
raise SystemExit
if arguments['--broken']:
query = query.filter_by(protocol_id=0)
tracer_log = query.first()
if tracer_log is None:
"""
import os, re, glob, subprocess
from libraries import settings, docopt
arguments = docopt.docopt(__doc__.format(**locals()))
script_path = os.path.abspath(arguments['<script>'])
pdb_path = os.path.abspath(arguments['<pdb>'] or 'input/structures/1srp.pdb')
pdb_tag = os.path.splitext(os.path.basename(pdb_path))[0]
loop_path = re.sub('\.pdb(\.gz)?$', '.loop', pdb_path)
flags_path = arguments['--flags']
fragments_path = arguments['--fragments']
output_dir = arguments['--output'] or 'sandbox'
settings.load(arguments)
rosetta_path = settings.rosetta
if os.path.isabs(rosetta_path): pass
elif os.path.isabs(os.path.expanduser(rosetta_path)): # e.g. ~/some/path
rosetta_path = os.path.expanduser(rosetta_path)
else:
rosetta_path = os.path.abspath(rosetta_path)
rosetta_path = os.path.normpath(rosetta_path)
rosetta_scripts = os.path.join(rosetta_path, 'source', 'bin', 'rosetta_scripts')
rosetta_database = os.path.join(rosetta_path, 'database')
if not os.path.exists(rosetta_scripts):
raise Exception('The RosettaScripts binary %(rosetta_scripts)s does not exist. By default, Rosetta executables are named after the operating system and build type e.g. rosetta_scripts.linuxgccrelease. Either: i) rename an appropriate binary to %(rosetta_scripts)s; or ii) use a symbolic link.' % locals())
# Copyright (c) 2015 Kale Kundert
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included in
# all copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
# THE SOFTWARE.
"""\
Pull the latest changes to the rosetta checkout being benchmarked.
"""
import os, subprocess
from libraries import settings
settings.load()
os.chdir(settings.rosetta)
subprocess.check_call(('git', 'pull'))