From 50b7213101469e86f8e543e10ff5c6f5d5d4f760 Mon Sep 17 00:00:00 2001 From: gph82 Date: Tue, 14 Mar 2017 12:12:31 +0100 Subject: [PATCH] [visualize] moved some methods to unused_untested.py --- molpx/unused_untested.py | 101 ++++++++++++++++++++++++++++++++++++++- molpx/visualize.py | 98 ------------------------------------- 2 files changed, 100 insertions(+), 99 deletions(-) diff --git a/molpx/unused_untested.py b/molpx/unused_untested.py index bb74239..b4c2756 100644 --- a/molpx/unused_untested.py +++ b/molpx/unused_untested.py @@ -523,4 +523,103 @@ def _onclick(event): axes_widget = _AxesWidget(ax) axes_widget.connect_event('button_release_event', onclick) - return vmdpipe \ No newline at end of file + return vmdpipe + +# Do I really need this? Don't think so +def _fnamez(fname, + path_type='min_rmsd', + proj_type='TIC', + only_selection=True, + selection_label='within 1 sigma', + figsize=(10,10) + ): + + proj_name = _basename(fname)[:_basename(fname).find(proj_type)].strip('.') + + data, selection, x, y, h, v_crd_1, v_crd_2 = _extract_visual_fnamez(fname, path_type) + data = data[:,[v_crd_1,v_crd_2]] + + # Load geometry + geom = _md.load(fname.replace('.npz','.%s.pdb'%path_type)) + + # Create contourplot + _plt.figure(figsize=figsize) + _plt.contourf(x[:-1],y[:-1], h.T, alpha=.50) + #_plt.contourf(project_dict["h"].T, alpha=.50) + # This can be take care of in "visualize sample" + _plt.plot(data[:, v_crd_1], + data[:, v_crd_2], + alpha=.25, label=path_type) + + if only_selection: + geom = geom[selection] + data = data[selection] + _plt.plot(data[:,0],data[:,1],'o', label=path_type+' '+selection_label) + + _plt.legend(loc='best') + _plt.xlabel('%s %u'%(proj_type, v_crd_1)) + _plt.ylabel('%s %u'%(proj_type, v_crd_2)) + _plt.xlim(x[[0,-1]]) + _plt.ylim(y[[0,-1]]) + _plt.title('%s\n-np.log(counts)'%proj_name) + + iwd = sample(data, geom, _plt.gca(), plot_path=False, clear_lines=False) + + project_dict = {} + for key, value in _np.load(fname).items(): + project_dict[key] = value + + return iwd, project_dict + +# Do I really need this? Don't think so +def _project_dict(project_dict, + path_type='min_rmsd', + proj_type='TIC', + only_compact_path=True, + selection_label='within 1 sigma', + figsize=(10,10), + project_name = None + ): + + + + # From dict to variables + if path_type == 'min_rmsd': + path = project_dict["Y_path_smpl"] + compact_path = project_dict["compact_path_sample"] + elif path_type == 'min_disp': + path = project_dict["Y_path"] + compact_path = project_dict["compact_path"] + v_crd_1 = project_dict["v_crd_1"] + v_crd_2 = project_dict["v_crd_2"] + path = path[:, [v_crd_1, v_crd_2]] + geom = project_dict["geom_"+path_type] + x = project_dict["x"] + y = project_dict["y"] + h = project_dict["h"] + + # Create contourplot + _plt.figure(figsize=figsize) + _plt.contourf(x[:-1],y[:-1], h.T, alpha=.50) #ATTN h is already log(PDF) + + # This can be taken care of in "visualize sample", but i'm doing it here + _plt.plot(path[:, 0], + path[:, 1], + alpha=.25, label=path_type) + + if only_compact_path: + geom = geom[compact_path] + path = path[compact_path] + _plt.plot(path[:,0],path[:,1],'o', label=path_type+' '+selection_label) + + _plt.legend(loc='best') + _plt.xlabel('%s %u'%(proj_type, v_crd_1)) + _plt.ylabel('%s %u'%(proj_type, v_crd_2)) + _plt.xlim(x[[0,-1]]) + _plt.ylim(y[[0,-1]]) + if project_name is not None: + _plt.title('-np.log(counts)\n%s'%project_name) + + iwd = sample(path, geom, _plt.gca(), plot_path=False, clear_lines=False) + + return iwd diff --git a/molpx/visualize.py b/molpx/visualize.py index c7f21f6..fee0add 100644 --- a/molpx/visualize.py +++ b/molpx/visualize.py @@ -340,101 +340,3 @@ def sample(positions, geom, ax, return iwd -# Do I really need this? Don't think so -def _fnamez(fname, - path_type='min_rmsd', - proj_type='TIC', - only_selection=True, - selection_label='within 1 sigma', - figsize=(10,10) - ): - - proj_name = _basename(fname)[:_basename(fname).find(proj_type)].strip('.') - - data, selection, x, y, h, v_crd_1, v_crd_2 = _extract_visual_fnamez(fname, path_type) - data = data[:,[v_crd_1,v_crd_2]] - - # Load geometry - geom = _md.load(fname.replace('.npz','.%s.pdb'%path_type)) - - # Create contourplot - _plt.figure(figsize=figsize) - _plt.contourf(x[:-1],y[:-1], h.T, alpha=.50) - #_plt.contourf(project_dict["h"].T, alpha=.50) - # This can be take care of in "visualize sample" - _plt.plot(data[:, v_crd_1], - data[:, v_crd_2], - alpha=.25, label=path_type) - - if only_selection: - geom = geom[selection] - data = data[selection] - _plt.plot(data[:,0],data[:,1],'o', label=path_type+' '+selection_label) - - _plt.legend(loc='best') - _plt.xlabel('%s %u'%(proj_type, v_crd_1)) - _plt.ylabel('%s %u'%(proj_type, v_crd_2)) - _plt.xlim(x[[0,-1]]) - _plt.ylim(y[[0,-1]]) - _plt.title('%s\n-np.log(counts)'%proj_name) - - iwd = sample(data, geom, _plt.gca(), plot_path=False, clear_lines=False) - - project_dict = {} - for key, value in _np.load(fname).items(): - project_dict[key] = value - - return iwd, project_dict - -# Do I really need this? Don't think so -def _project_dict(project_dict, - path_type='min_rmsd', - proj_type='TIC', - only_compact_path=True, - selection_label='within 1 sigma', - figsize=(10,10), - project_name = None - ): - - - - # From dict to variables - if path_type == 'min_rmsd': - path = project_dict["Y_path_smpl"] - compact_path = project_dict["compact_path_sample"] - elif path_type == 'min_disp': - path = project_dict["Y_path"] - compact_path = project_dict["compact_path"] - v_crd_1 = project_dict["v_crd_1"] - v_crd_2 = project_dict["v_crd_2"] - path = path[:, [v_crd_1, v_crd_2]] - geom = project_dict["geom_"+path_type] - x = project_dict["x"] - y = project_dict["y"] - h = project_dict["h"] - - # Create contourplot - _plt.figure(figsize=figsize) - _plt.contourf(x[:-1],y[:-1], h.T, alpha=.50) #ATTN h is already log(PDF) - - # This can be taken care of in "visualize sample", but i'm doing it here - _plt.plot(path[:, 0], - path[:, 1], - alpha=.25, label=path_type) - - if only_compact_path: - geom = geom[compact_path] - path = path[compact_path] - _plt.plot(path[:,0],path[:,1],'o', label=path_type+' '+selection_label) - - _plt.legend(loc='best') - _plt.xlabel('%s %u'%(proj_type, v_crd_1)) - _plt.ylabel('%s %u'%(proj_type, v_crd_2)) - _plt.xlim(x[[0,-1]]) - _plt.ylim(y[[0,-1]]) - if project_name is not None: - _plt.title('-np.log(counts)\n%s'%project_name) - - iwd = sample(path, geom, _plt.gca(), plot_path=False, clear_lines=False) - - return iwd