# write to Trevor King, Drudge's University, Physics Dept., 3141 Chestnut St.,
# Philadelphia PA 19104, USA.
-from __future__ import with_statement
-
-import hashlib
-import os.path
-import shutil
-
import numpy
-from . import __version__, log
from .histogram import Histogram
-from .manager import InvokeJob, MANAGERS, get_manager
-from .sawsim import parse
-
-
-SAWSIM = 'sawsim' # os.path.expand(os.path.join('~', 'bin', 'sawsim'))
-CACHE_DIR = os.path.expanduser(os.path.join('~', '.sawsim_histogram'))
-DEFAULT_PARAM_STRING = (
- '-s cantilever,hooke,0.05 -N1 '
- '-s folded,null -N8 '
- "-s 'unfolded,wlc,{0.39e-9,28e-9}' "
- "-k 'folded,unfolded,bell,{3.3e-4,0.25e-9}' "
- '-q folded -v 1e-6')
-
-
-class SawsimHistogram (object):
- def __init__(self, use_cache=False, clean_cache=False):
- self._use_cache = use_cache
- self._clean_cache = clean_cache
-
- def _cache_dir(self, param_string):
- """
- >>> s = SawsimHistogram()
- >>> s._cache_dir(DEFAULT_PARAM_STRING) # doctest: +ELLIPSIS
- '/.../.sawsim_histogram/...'
- """
- return os.path.join(
- CACHE_DIR, hashlib.sha256(param_string).hexdigest())
+from .manager import MANAGERS, get_manager
+from .sawsim import SawsimRunner
- def _make_cache(self, param_string):
- cache_dir = self._cache_dir(param_string)
- os.makedirs(cache_dir)
- with open(os.path.join(cache_dir, 'param_string'), 'w') as f:
- f.write('# version: %s\n%s\n' % (__version__, param_string))
- def _load_cached_data(self, cache_dir, N):
- data = {}
- for i in range(N):
- simulation_path = os.path.join(cache_dir, '%d.dat' % i)
- if os.path.exists(simulation_path):
- with open(simulation_path, 'r') as f:
- data[i] = parse(f.read())
- else:
- break
- return data
+_multiprocess_can_split_ = True
+"""Allow nosetests to split tests between processes.
+"""
- def _cache_run(self, cache_dir, i, stdout):
- simulation_path = os.path.join(cache_dir, '%d.dat' % i)
- with open(simulation_path, 'w') as f:
- f.write(stdout)
- def __call__(self, param_string=None, N=400, bin_edges=None, manager=None):
+def sawsim_histogram(sawsim_runner, param_string, N=400, bin_edges=None):
"""Run `N` simulations and return a histogram with `bin_edges`.
If `bin_edges == None`, return a numpy array of all unfolding
forces.
-
- Use the `JobManager` instance `manager` for asynchronous job
- execution.
-
- If `_use_cache` is `True`, store an array of unfolding forces
- in `CACHE_DIR` for each simulated pull. If the cached forces
- are already present for `param_string`, do not redo the
- simulation unless `_clean_cache` is `True`.
"""
- data = {}
- if self._use_cache == True:
- d = self._cache_dir(param_string)
- if os.path.exists(d):
- if self._clean_cache == True:
- shutil.rmtree(d)
- self._make_cache(param_string)
- else:
- data = self._load_cached_data(d, N)
- log().debug('using %d cached runs for %s'
- % (len(data), param_string))
- else:
- self._make_cache(param_string)
-
- jobs = {}
- for i in range(N):
- if i in data:
- continue
- jobs[i] = manager.async_invoke(InvokeJob(
- target='%s %s' % (SAWSIM, param_string)))
- complete_jobs = manager.wait([job.id for job in jobs.itervalues()])
- for i,job in jobs.iteritems():
- j = complete_jobs[job.id]
- assert j.status == 0, j.data
- if self._use_cache == True:
- self._cache_run(d, i, j.data['stdout'])
- data[i] = parse(j.data['stdout'])
- del(jobs)
- del(complete_jobs)
-
- # generate histogram
events = []
- for d_i in data.values():
- events.extend([e.force for e in d_i
- if e.initial_state == 'folded'])
+ for run in sawsim_runner(param_string=param_string, N=N):
+ events.extend([event.force for event in run
+ if (event.initial_state == 'folded'
+ and event.final_state == 'unfolded')])
events = numpy.array(events)
if bin_edges == None:
return events
return h
-def main():
- import optparse
+def main(argv=None):
+ """
+ >>> main(['-N', '2'])
+ ... # doctest: +ELLIPSIS, +NORMALIZE_WHITESPACE
+ #Force (N) Unfolding events
+ ...
+ """
+ from optparse import OptionParser
import sys
- global SAWSIM, CACHE_DIR
-
- usage = "%prog [options] velocity_file"
+ if argv == None:
+ argv = sys.argv[1:]
- parser = optparse.OptionParser(usage)
- parser.add_option("-s","--sawsim", dest="sawsim",
- metavar="PATH",
- help="Set sawsim binary (%default).",
- default=SAWSIM)
- parser.add_option("-p","--params", dest="params",
- metavar="PARAMS",
- help="Initial params for fitting (%default).",
- default=DEFAULT_PARAM_STRING)
- parser.add_option("-N", "--number-of-runs", dest="N",
- metavar="INT", type='int',
- help="Number of sawsim runs at each point in parameter space (%default).",
- default=400)
- parser.add_option("-w", "--bin-width", dest="bin_width",
- metavar="FLOAT", type='float',
- help="Histogram bin width in newtons (%default).",
- default=None)
- parser.add_option("-m", "--manager", dest="manager",
- metavar="STRING",
- help="Job manager name (one of %s) (%%default)."
- % (', '.join(MANAGERS)),
- default=MANAGERS[0])
- parser.add_option("-C","--use-cache", dest="use_cache",
- help="Use cached simulations if they exist (vs. running new simulations) (%default)",
- default=False, action="store_true")
- parser.add_option("--clean-cache", dest="clean_cache",
- help="Remove previously cached simulations if they exist (%default)",
- default=False, action="store_true")
- parser.add_option("-d","--cache-dir", dest="cache_dir",
- metavar="STRING",
- help="Cache directory for sawsim unfolding forces (%default).",
- default=CACHE_DIR)
- options,args = parser.parse_args()
+ sr = SawsimRunner()
- SAWSIM = options.sawsim
- CACHE_DIR = options.cache_dir
+ usage = '%prog [options]'
+ epilog = '\n'.join([
+ 'Generate an unfolding force histogram from a series of `sawsim`',
+ 'runs.',
+ ])
+ parser = OptionParser(usage, epilog=epilog)
+ for option in sr.optparse_options:
+ parser.add_option(option)
+ parser.add_option('-w', '--bin-width', dest='bin_width',
+ metavar='FLOAT', type='float',
+ help='Histogram bin width in newtons (%default).',
+ default=10e-12)
- sh = SawsimHistogram(use_cache=options.use_cache,
- clean_cache=options.clean_cache)
+ options,args = parser.parse_args(argv)
- manager = get_manager(options.manager)()
+ sr_call_params = sr.initialize_from_options(options)
try:
- events = sh(param_string=options.params, N=options.N, manager=manager)
+ events = sawsim_histogram(
+ sawsim_runner=sr, bin_edges=None, **sr_call_params)
finally:
- manager.teardown()
+ sr.teardown()
if options.bin_width == None:
sys.stdout.write('# Unfolding force (N)\n')
projects / sawsim.git / blobdiff