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!