[visualize] moved some methods to unused_untested.py

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
+    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

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