Problems with loading more than two trajectories

[orthonalmatrix]

fdir = '../testdata/' feat = pyemma.coordinates.featurizer(fdir+'/step3_pbcsetup.psf') feat.add_backbone_torsions(selstr='residue 38 to 155 and protein' ,cossin=True,deg = False,periodic = False) feats = pyemma.coordinates.source([fdir+'step5.3_200ps_production.dcd',fdir+'step5.5_200ps_production.dcd'] ,features=feat, stride = 100)

The above works fine, but when I use the command (with 3 dcds)

feats = pyemma.coordinates.source([fdir+'step5.3_200ps_production.dcd',fdir+'step5.5_200ps_production.dcd',fdir+'step5.6_200ps_production.dcd'] ,features=feat, stride = 100)

I get the following error. I get this error no matter what dcd's I use so i do not think there is something wrong with them. Any ideas?

HBox(children=(HBox(children=(Label(value='Obtaining file info'),), layout=Layout(max_width='35%', min_width='…

<function pyemma._base.progress.reporter.notebook.my_tqdm_notebook.status_printer..print_status(s='', close=False, bar_style=None, desc=None)>

---

AttributeError Traceback (most recent call last)
in ()
15 fdir+'step5.6_200ps_production.dcd',
16 fdir+'step5.7_200ps_production.dcd']
---> 17 feats = pyemma.coordinates.source([fdir+'step5.3_200ps_production.dcd',fdir+'step5.4_200ps_production.dcd',fdir+'step5.5_200ps_production.dcd'] ,features=feat, stride = 100)
18 #feats = pyemma.coordinates.source([fdir+'step5.3_200ps_production.dcd',fdir+'step5.5_200ps_production.dcd'] ,features=feat, stride = 100)

~/anaconda3/envs/ms/lib/python3.5/site-packages/pyemma/coordinates/api.py in source(inp, features, top, chunksize, **kw)
384 isinstance(inp, (list, tuple))
385 and (any(isinstance(item, (list, tuple, _string_types)) for item in inp) or len(inp) is 0)):
--> 386 reader = create_file_reader(inp, top, features, chunksize=cs, **kw)
387
388 elif isinstance(inp, _np.ndarray) or (isinstance(inp, (list, tuple))

~/anaconda3/envs/ms/lib/python3.5/site-packages/pyemma/coordinates/data/util/reader_utils.py in create_file_reader(input_files, topology, featurizer, chunksize, **kw)
111
112 reader = FeatureReader(input_list, featurizer=featurizer, topologyfile=topology,
--> 113 chunksize=chunksize)
114 else:
115 if suffix in ['.npy', '.npz']:

~/anaconda3/envs/ms/lib/python3.5/site-packages/pyemma/coordinates/data/feature_reader.py in init(self, trajectories, topologyfile, chunksize, featurizer)
93 self._is_reader = True
94 self.topfile = topologyfile
---> 95 self.filenames = trajectories
96 self._return_traj_obj = False
97

~/anaconda3/envs/ms/lib/python3.5/site-packages/pyemma/coordinates/data/_base/datasource.py in filenames(self, filename_list)
117 from pyemma._base.progress import ProgressReporter
118 pg = ProgressReporter()
--> 119 pg.register(len(filename_list), 'Obtaining file info')
120 with pg.context():
121 for filename in filename_list:

~/anaconda3/envs/ms/lib/python3.5/site-packages/pyemma/_base/progress/reporter/init.py in register(self, amount_of_work, description, stage, tqdm_args)
218
219 def register(self, amount_of_work, description='', stage=0, tqdm_args=None):
--> 220 self._progress_register(amount_of_work=amount_of_work, description=description, stage=stage, tqdm_args=tqdm_args)
221
222 def update(self, increment, stage=0):

~/anaconda3/envs/ms/lib/python3.5/site-packages/pyemma/_base/progress/reporter/init.py in _progress_register(self, amount_of_work, description, stage, tqdm_args)
143 if _attached_to_ipy_notebook_with_widgets():
144 from .notebook import my_tqdm_notebook
--> 145 pg = my_tqdm_notebook(leave=False, **args)
146 else:
147 import tqdm

~/anaconda3/envs/ms/lib/python3.5/site-packages/tqdm/notebook.py in init(self, *args, **kwargs)
247 self.displayed = True
248 self.disp = self.display
--> 249 self.colour = colour
250
251 # Print initial bar state

~/anaconda3/envs/ms/lib/python3.5/site-packages/tqdm/notebook.py in colour(self, bar_color)
206 def colour(self, bar_color):
207 if hasattr(self, 'container'):
--> 208 self.container.children[-2].style.bar_color = bar_color
209
210 def init(self, *args, **kwargs):

AttributeError: 'function' object has no attribute 'children'

[clonker]

This seems to be a problem with progress bars. As quick workaround please try the following at the top of your notebook:

from pyemma import config 
config.show_progress_bars = False 

[orthonalmatrix]

That worked! Thank you!