showOccupancies should support atoms kwarg or extract them from ensemble

[jamesmkrieger]

At the moment, it just uses plt.plot and gives this error if we try to use them:

---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)
<ipython-input-214-67a022bd432d> in <module>
----> 1 showOccupancies(dali_ens, normed=True, atoms=dali_ens.getAtoms())
      2 plt.ylim([0, 1.1])

/mnt/c/Users/james/code/ProDy/prody/ensemble/functions.py in showOccupancies(pdbensemble, *args, **kwargs)
    333     if weights is None:
    334         return None
--> 335     show = plt.plot(weights, *args, **kwargs)
    336     axis = list(plt.axis())
    337     axis[2] = 0

~/anaconda3/lib/python3.8/site-packages/matplotlib/pyplot.py in plot(scalex, scaley, data, *args, **kwargs)
   2838 @_copy_docstring_and_deprecators(Axes.plot)
   2839 def plot(*args, scalex=True, scaley=True, data=None, **kwargs):
-> 2840     return gca().plot(
   2841         *args, scalex=scalex, scaley=scaley,
   2842         **({"data": data} if data is not None else {}), **kwargs)

~/anaconda3/lib/python3.8/site-packages/matplotlib/axes/_axes.py in plot(self, scalex, scaley, data, *args, **kwargs)
   1741         """
   1742         kwargs = cbook.normalize_kwargs(kwargs, mlines.Line2D)
-> 1743         lines = [*self._get_lines(*args, data=data, **kwargs)]
   1744         for line in lines:
   1745             self.add_line(line)

~/anaconda3/lib/python3.8/site-packages/matplotlib/axes/_base.py in __call__(self, data, *args, **kwargs)
    271                 this += args[0],
    272                 args = args[1:]
--> 273             yield from self._plot_args(this, kwargs)
    274 
    275     def get_next_color(self):

~/anaconda3/lib/python3.8/site-packages/matplotlib/axes/_base.py in _plot_args(self, tup, kwargs)
    416         if ncx > 1 and ncy > 1 and ncx != ncy:
    417             raise ValueError(f"x has {ncx} columns but y has {ncy} columns")
--> 418         return [func(x[:, j % ncx], y[:, j % ncy], kw, kwargs)
    419                 for j in range(max(ncx, ncy))]
    420 

~/anaconda3/lib/python3.8/site-packages/matplotlib/axes/_base.py in <listcomp>(.0)
    416         if ncx > 1 and ncy > 1 and ncx != ncy:
    417             raise ValueError(f"x has {ncx} columns but y has {ncy} columns")
--> 418         return [func(x[:, j % ncx], y[:, j % ncy], kw, kwargs)
    419                 for j in range(max(ncx, ncy))]
    420 

~/anaconda3/lib/python3.8/site-packages/matplotlib/axes/_base.py in _makeline(self, x, y, kw, kwargs)
    310         default_dict = self._getdefaults(set(), kw)
    311         self._setdefaults(default_dict, kw)
--> 312         seg = mlines.Line2D(x, y, **kw)
    313         return seg
    314 

~/anaconda3/lib/python3.8/site-packages/matplotlib/lines.py in __init__(self, xdata, ydata, linewidth, linestyle, color, marker, markersize, markeredgewidth, markeredgecolor, markerfacecolor, markerfacecoloralt, fillstyle, antialiased, dash_capstyle, solid_capstyle, dash_joinstyle, solid_joinstyle, pickradius, drawstyle, markevery, **kwargs)
    388         # update kwargs before updating data to give the caller a
    389         # chance to init axes (and hence unit support)
--> 390         self.update(kwargs)
    391         self.pickradius = pickradius
    392         self.ind_offset = 0

~/anaconda3/lib/python3.8/site-packages/matplotlib/artist.py in update(self, props)
    994                     func = getattr(self, f"set_{k}", None)
    995                     if not callable(func):
--> 996                         raise AttributeError(f"{type(self).__name__!r} object "
    997                                              f"has no property {k!r}")
    998                     ret.append(func(v))

AttributeError: 'Line2D' object has no property 'atoms'

[jamesmkrieger]

using showAtomicLines from dynamics.plotting is not an option because of circular imports related to ClustENM