util

Functions used by other modules.

util.align_homologues(Areduced, Breduced, aln)

util.all_post_hist(results, save=False, show=False, wlims=None, rlims=None)

util.check_results(residues, times, ts)

util.collect_n_plot(resids, comps)

util.confidence_interval(data, percentage=95)

util.expand_times(contacts)

util.extract_data(gibbs)

util.get_bars(tau)

util.get_bins(x, ts)

util.get_code(resname)

util.get_color(i)

util.get_dec(ts)

util.get_delta_tau(aln, protA, protB, tausA, tausB)

util.get_diffcode(sel, index)

util.get_fa_sel(aln, protA, protB)

util.get_fa_sel_match(aln, protA, protB)

util.get_indices(resnames, sequence)

util.get_remaining_residue_inds(residues, invert=True)

util.get_s(x, ts)

util.get_start_stop_frames(simtime, timelen, ts)

util.get_write_frames(u, time, trajtime, lipind, comp)

util.make_residue_plots(results, comps=None, show=False)

util.make_surv(ahist)

util.mixture_and_plot(gibbs, scale=2, sparse=1, remove_noise=False, wlim=None, rlim=None, show=True, **kwargs)

util.plot_delta_tau(A, B, dtau, protA, protB, factor=2)

util.plot_hists(timelens, indicators, residues)

util.plot_post(results, attr, comp=None, save=False, show=False)

util.plot_protein(residues, t_slow, bars, prot=None, label_cutoff=3, ylim=None, major_tick=None, minor_tick=None, scale=1)

util.plot_r_vs_w(r, rrange=None, wrange=None)

util.plot_results(results, cond='ml', save=False, show=False)

util.plot_trace(results, attr, comp=None, xrange=None, yrange=None, save=False, show=False)

util.siground(x, dec)

util.simulate_hn(n, weights, rates)

util.slice_trajectory(u, nslices)

util.tm(Prot, i)

util.unique_rates(ncomp, mcrates)

util.write_trajs(u, time, trajtime, indicator, residue, lipind, step)