1 # Copyright (C) 2009-2010 W. Trevor King <wking@drexel.edu>
3 # This program is free software: you can redistribute it and/or modify
4 # it under the terms of the GNU General Public License as published by
5 # the Free Software Foundation, either version 3 of the License, or
6 # (at your option) any later version.
8 # This program is distributed in the hope that it will be useful,
9 # but WITHOUT ANY WARRANTY; without even the implied warranty of
10 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
11 # GNU General Public License for more details.
13 # You should have received a copy of the GNU General Public License
14 # along with this program. If not, see <http://www.gnu.org/licenses/>.
16 # The author may be contacted at <wking@drexel.edu> on the Internet, or
17 # write to Trevor King, Drudge's University, Physics Dept., 3141 Chestnut St.,
18 # Philadelphia PA 19104, USA.
22 from .histogram import Histogram
23 from .manager import MANAGERS, get_manager
24 from .sawsim import SawsimRunner
27 _multiprocess_can_split_ = True
28 """Allow nosetests to split tests between processes.
32 def sawsim_histogram(sawsim_runner, param_string, N=400, bin_edges=None):
33 """Run `N` simulations and return a histogram with `bin_edges`.
35 If `bin_edges == None`, return a numpy array of all unfolding
39 for run in sawsim_runner(param_string=param_string, N=N):
40 events.extend([event.force for event in run
41 if (event.initial_state == 'folded'
42 and event.final_state == 'unfolded')])
43 events = numpy.array(events)
47 h.from_data(events, bin_edges)
54 ... # doctest: +ELLIPSIS, +NORMALIZE_WHITESPACE
55 #Force (N) Unfolding events
58 from optparse import OptionParser
66 usage = '%prog [options]'
68 'Generate an unfolding force histogram from a series of `sawsim`',
71 parser = OptionParser(usage, epilog=epilog)
72 for option in sr.optparse_options:
73 parser.add_option(option)
74 parser.add_option('-w', '--bin-width', dest='bin_width',
75 metavar='FLOAT', type='float',
76 help='Histogram bin width in newtons (%default).',
79 options,args = parser.parse_args(argv)
81 sr_call_params = sr.initialize_from_options(options)
83 events = sawsim_histogram(
84 sawsim_runner=sr, bin_edges=None, **sr_call_params)
88 if options.bin_width == None:
89 sys.stdout.write('# Unfolding force (N)\n')
90 events.tofile(sys.stdout, sep='\n')
91 sys.stdout.write('\n')
94 h.from_data(events, bin_edges=h.calculate_bin_edges(
95 events, options.bin_width))
96 h.headings = ['Force (N)', 'Unfolding events']
97 h.to_stream(sys.stdout)